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-
-
-
-This crate provides [rust](https://www.rust-lang.org/) bindings to [tskit](https://github.com/tskit-dev/tskit).
-
-This package provides the following:
-
-1. Low-level bindings to the C API of both `tskit` and `kastore`.
- We use [bindgen](https://docs.rs/bindgen) to automatically generate the bindings.
-2. Support for table collections, tree sequences, and tree iteration.
-3. An error handling system that maps `tskit` error
- codes to `rust` errors while preserving error messages.
-
-The overview is:
-
-1. `tskit` and `kastore` C code are include in `subprojects/`
-2. These two tools are compiled into the `rust` package.
-3. Then `bindgen` generates the bindings.
-4. Finally, the entire rust package is generated.
-
-The result is a `rust` library with all of these two C libraries statically compiled in.
-Further, `rust` types and functions exist in the module name `tskit::bindings`, allowing `unsafe` access to the low-level API.
-
-Help wanted!
-
-## Quick start guide
-
-### Cloning the repository and running the test suite
-
-```sh
-git clone https://github.com/tskit-dev/tskit-rust
-cd tskit-rust
-cargo test --all-features
-```
-
-### Viewing the documentation
-
-```
-cargo doc --all-features --open
-```
-
-API documentation for the latest release is [here](https://docs.rs/tskit).
-A manual is [here](https://tskit-dev.github.io/tskit-rust).
-
-### Calculating code coverage
-
-First, install `tarpaulin`:
-
-```sh
-cargo install cargo-tarpaulin
-```
-
-Then, we use all tests, doc tests, and example programs to calculate code coverage for all available features:
-
-```sh
-cargo tarpaulin --all-features --doc --tests --examples --exclude-files '*.c' --exclude-files '*.h' --ignore-tests -o html
-```
-
-Then, point your favorite browser to `tarpaulin-report.html`.
-
-The last few flags exclude the C code and any `rust` code that is test-only from being part of the denominator of the coverage calculation.
-The goal here is not to have high *test* coverage of the C API, as it is up to the [upstream project](https://github.com/tskit-dev/tskit) to provide that.
-
-**Note:** `tarpaulin` can be fickle, and changing the order of some of those flags can cause the coverage run to fail.
-
-## Change log
-
-See [here](https://github.com/tskit-dev/tskit-rust/blob/main/CHANGELOG.md).
-
-### Updating the change log.
-
-**under scrutinty**
-
-Example:
-
-```sh
-git cliff -u --tag v0.11.0 --date-order -p CHANGELOG.md
-```
diff --git a/ayu-highlight.css b/ayu-highlight.css
new file mode 100644
index 000000000..32c943222
--- /dev/null
+++ b/ayu-highlight.css
@@ -0,0 +1,78 @@
+/*
+Based off of the Ayu theme
+Original by Dempfi (https://github.com/dempfi/ayu)
+*/
+
+.hljs {
+ display: block;
+ overflow-x: auto;
+ background: #191f26;
+ color: #e6e1cf;
+}
+
+.hljs-comment,
+.hljs-quote {
+ color: #5c6773;
+ font-style: italic;
+}
+
+.hljs-variable,
+.hljs-template-variable,
+.hljs-attribute,
+.hljs-attr,
+.hljs-regexp,
+.hljs-link,
+.hljs-selector-id,
+.hljs-selector-class {
+ color: #ff7733;
+}
+
+.hljs-number,
+.hljs-meta,
+.hljs-builtin-name,
+.hljs-literal,
+.hljs-type,
+.hljs-params {
+ color: #ffee99;
+}
+
+.hljs-string,
+.hljs-bullet {
+ color: #b8cc52;
+}
+
+.hljs-title,
+.hljs-built_in,
+.hljs-section {
+ color: #ffb454;
+}
+
+.hljs-keyword,
+.hljs-selector-tag,
+.hljs-symbol {
+ color: #ff7733;
+}
+
+.hljs-name {
+ color: #36a3d9;
+}
+
+.hljs-tag {
+ color: #00568d;
+}
+
+.hljs-emphasis {
+ font-style: italic;
+}
+
+.hljs-strong {
+ font-weight: bold;
+}
+
+.hljs-addition {
+ color: #91b362;
+}
+
+.hljs-deletion {
+ color: #d96c75;
+}
diff --git a/book.js b/book.js
new file mode 100644
index 000000000..aa12e7ecc
--- /dev/null
+++ b/book.js
@@ -0,0 +1,697 @@
+"use strict";
+
+// Fix back button cache problem
+window.onunload = function () { };
+
+// Global variable, shared between modules
+function playground_text(playground, hidden = true) {
+ let code_block = playground.querySelector("code");
+
+ if (window.ace && code_block.classList.contains("editable")) {
+ let editor = window.ace.edit(code_block);
+ return editor.getValue();
+ } else if (hidden) {
+ return code_block.textContent;
+ } else {
+ return code_block.innerText;
+ }
+}
+
+(function codeSnippets() {
+ function fetch_with_timeout(url, options, timeout = 6000) {
+ return Promise.race([
+ fetch(url, options),
+ new Promise((_, reject) => setTimeout(() => reject(new Error('timeout')), timeout))
+ ]);
+ }
+
+ var playgrounds = Array.from(document.querySelectorAll(".playground"));
+ if (playgrounds.length > 0) {
+ fetch_with_timeout("https://play.rust-lang.org/meta/crates", {
+ headers: {
+ 'Content-Type': "application/json",
+ },
+ method: 'POST',
+ mode: 'cors',
+ })
+ .then(response => response.json())
+ .then(response => {
+ // get list of crates available in the rust playground
+ let playground_crates = response.crates.map(item => item["id"]);
+ playgrounds.forEach(block => handle_crate_list_update(block, playground_crates));
+ });
+ }
+
+ function handle_crate_list_update(playground_block, playground_crates) {
+ // update the play buttons after receiving the response
+ update_play_button(playground_block, playground_crates);
+
+ // and install on change listener to dynamically update ACE editors
+ if (window.ace) {
+ let code_block = playground_block.querySelector("code");
+ if (code_block.classList.contains("editable")) {
+ let editor = window.ace.edit(code_block);
+ editor.addEventListener("change", function (e) {
+ update_play_button(playground_block, playground_crates);
+ });
+ // add Ctrl-Enter command to execute rust code
+ editor.commands.addCommand({
+ name: "run",
+ bindKey: {
+ win: "Ctrl-Enter",
+ mac: "Ctrl-Enter"
+ },
+ exec: _editor => run_rust_code(playground_block)
+ });
+ }
+ }
+ }
+
+ // updates the visibility of play button based on `no_run` class and
+ // used crates vs ones available on https://play.rust-lang.org
+ function update_play_button(pre_block, playground_crates) {
+ var play_button = pre_block.querySelector(".play-button");
+
+ // skip if code is `no_run`
+ if (pre_block.querySelector('code').classList.contains("no_run")) {
+ play_button.classList.add("hidden");
+ return;
+ }
+
+ // get list of `extern crate`'s from snippet
+ var txt = playground_text(pre_block);
+ var re = /extern\s+crate\s+([a-zA-Z_0-9]+)\s*;/g;
+ var snippet_crates = [];
+ var item;
+ while (item = re.exec(txt)) {
+ snippet_crates.push(item[1]);
+ }
+
+ // check if all used crates are available on play.rust-lang.org
+ var all_available = snippet_crates.every(function (elem) {
+ return playground_crates.indexOf(elem) > -1;
+ });
+
+ if (all_available) {
+ play_button.classList.remove("hidden");
+ } else {
+ play_button.classList.add("hidden");
+ }
+ }
+
+ function run_rust_code(code_block) {
+ var result_block = code_block.querySelector(".result");
+ if (!result_block) {
+ result_block = document.createElement('code');
+ result_block.className = 'result hljs language-bash';
+
+ code_block.append(result_block);
+ }
+
+ let text = playground_text(code_block);
+ let classes = code_block.querySelector('code').classList;
+ let edition = "2015";
+ if(classes.contains("edition2018")) {
+ edition = "2018";
+ } else if(classes.contains("edition2021")) {
+ edition = "2021";
+ }
+ var params = {
+ version: "stable",
+ optimize: "0",
+ code: text,
+ edition: edition
+ };
+
+ if (text.indexOf("#![feature") !== -1) {
+ params.version = "nightly";
+ }
+
+ result_block.innerText = "Running...";
+
+ fetch_with_timeout("https://play.rust-lang.org/evaluate.json", {
+ headers: {
+ 'Content-Type': "application/json",
+ },
+ method: 'POST',
+ mode: 'cors',
+ body: JSON.stringify(params)
+ })
+ .then(response => response.json())
+ .then(response => {
+ if (response.result.trim() === '') {
+ result_block.innerText = "No output";
+ result_block.classList.add("result-no-output");
+ } else {
+ result_block.innerText = response.result;
+ result_block.classList.remove("result-no-output");
+ }
+ })
+ .catch(error => result_block.innerText = "Playground Communication: " + error.message);
+ }
+
+ // Syntax highlighting Configuration
+ hljs.configure({
+ tabReplace: ' ', // 4 spaces
+ languages: [], // Languages used for auto-detection
+ });
+
+ let code_nodes = Array
+ .from(document.querySelectorAll('code'))
+ // Don't highlight `inline code` blocks in headers.
+ .filter(function (node) {return !node.parentElement.classList.contains("header"); });
+
+ if (window.ace) {
+ // language-rust class needs to be removed for editable
+ // blocks or highlightjs will capture events
+ code_nodes
+ .filter(function (node) {return node.classList.contains("editable"); })
+ .forEach(function (block) { block.classList.remove('language-rust'); });
+
+ code_nodes
+ .filter(function (node) {return !node.classList.contains("editable"); })
+ .forEach(function (block) { hljs.highlightBlock(block); });
+ } else {
+ code_nodes.forEach(function (block) { hljs.highlightBlock(block); });
+ }
+
+ // Adding the hljs class gives code blocks the color css
+ // even if highlighting doesn't apply
+ code_nodes.forEach(function (block) { block.classList.add('hljs'); });
+
+ Array.from(document.querySelectorAll("code.hljs")).forEach(function (block) {
+
+ var lines = Array.from(block.querySelectorAll('.boring'));
+ // If no lines were hidden, return
+ if (!lines.length) { return; }
+ block.classList.add("hide-boring");
+
+ var buttons = document.createElement('div');
+ buttons.className = 'buttons';
+ buttons.innerHTML = "";
+
+ // add expand button
+ var pre_block = block.parentNode;
+ pre_block.insertBefore(buttons, pre_block.firstChild);
+
+ pre_block.querySelector('.buttons').addEventListener('click', function (e) {
+ if (e.target.classList.contains('fa-eye')) {
+ e.target.classList.remove('fa-eye');
+ e.target.classList.add('fa-eye-slash');
+ e.target.title = 'Hide lines';
+ e.target.setAttribute('aria-label', e.target.title);
+
+ block.classList.remove('hide-boring');
+ } else if (e.target.classList.contains('fa-eye-slash')) {
+ e.target.classList.remove('fa-eye-slash');
+ e.target.classList.add('fa-eye');
+ e.target.title = 'Show hidden lines';
+ e.target.setAttribute('aria-label', e.target.title);
+
+ block.classList.add('hide-boring');
+ }
+ });
+ });
+
+ if (window.playground_copyable) {
+ Array.from(document.querySelectorAll('pre code')).forEach(function (block) {
+ var pre_block = block.parentNode;
+ if (!pre_block.classList.contains('playground')) {
+ var buttons = pre_block.querySelector(".buttons");
+ if (!buttons) {
+ buttons = document.createElement('div');
+ buttons.className = 'buttons';
+ pre_block.insertBefore(buttons, pre_block.firstChild);
+ }
+
+ var clipButton = document.createElement('button');
+ clipButton.className = 'fa fa-copy clip-button';
+ clipButton.title = 'Copy to clipboard';
+ clipButton.setAttribute('aria-label', clipButton.title);
+ clipButton.innerHTML = '';
+
+ buttons.insertBefore(clipButton, buttons.firstChild);
+ }
+ });
+ }
+
+ // Process playground code blocks
+ Array.from(document.querySelectorAll(".playground")).forEach(function (pre_block) {
+ // Add play button
+ var buttons = pre_block.querySelector(".buttons");
+ if (!buttons) {
+ buttons = document.createElement('div');
+ buttons.className = 'buttons';
+ pre_block.insertBefore(buttons, pre_block.firstChild);
+ }
+
+ var runCodeButton = document.createElement('button');
+ runCodeButton.className = 'fa fa-play play-button';
+ runCodeButton.hidden = true;
+ runCodeButton.title = 'Run this code';
+ runCodeButton.setAttribute('aria-label', runCodeButton.title);
+
+ buttons.insertBefore(runCodeButton, buttons.firstChild);
+ runCodeButton.addEventListener('click', function (e) {
+ run_rust_code(pre_block);
+ });
+
+ if (window.playground_copyable) {
+ var copyCodeClipboardButton = document.createElement('button');
+ copyCodeClipboardButton.className = 'fa fa-copy clip-button';
+ copyCodeClipboardButton.innerHTML = '';
+ copyCodeClipboardButton.title = 'Copy to clipboard';
+ copyCodeClipboardButton.setAttribute('aria-label', copyCodeClipboardButton.title);
+
+ buttons.insertBefore(copyCodeClipboardButton, buttons.firstChild);
+ }
+
+ let code_block = pre_block.querySelector("code");
+ if (window.ace && code_block.classList.contains("editable")) {
+ var undoChangesButton = document.createElement('button');
+ undoChangesButton.className = 'fa fa-history reset-button';
+ undoChangesButton.title = 'Undo changes';
+ undoChangesButton.setAttribute('aria-label', undoChangesButton.title);
+
+ buttons.insertBefore(undoChangesButton, buttons.firstChild);
+
+ undoChangesButton.addEventListener('click', function () {
+ let editor = window.ace.edit(code_block);
+ editor.setValue(editor.originalCode);
+ editor.clearSelection();
+ });
+ }
+ });
+})();
+
+(function themes() {
+ var html = document.querySelector('html');
+ var themeToggleButton = document.getElementById('theme-toggle');
+ var themePopup = document.getElementById('theme-list');
+ var themeColorMetaTag = document.querySelector('meta[name="theme-color"]');
+ var stylesheets = {
+ ayuHighlight: document.querySelector("[href$='ayu-highlight.css']"),
+ tomorrowNight: document.querySelector("[href$='tomorrow-night.css']"),
+ highlight: document.querySelector("[href$='highlight.css']"),
+ };
+
+ function showThemes() {
+ themePopup.style.display = 'block';
+ themeToggleButton.setAttribute('aria-expanded', true);
+ themePopup.querySelector("button#" + get_theme()).focus();
+ }
+
+ function updateThemeSelected() {
+ themePopup.querySelectorAll('.theme-selected').forEach(function (el) {
+ el.classList.remove('theme-selected');
+ });
+ themePopup.querySelector("button#" + get_theme()).classList.add('theme-selected');
+ }
+
+ function hideThemes() {
+ themePopup.style.display = 'none';
+ themeToggleButton.setAttribute('aria-expanded', false);
+ themeToggleButton.focus();
+ }
+
+ function get_theme() {
+ var theme;
+ try { theme = localStorage.getItem('mdbook-theme'); } catch (e) { }
+ if (theme === null || theme === undefined) {
+ return default_theme;
+ } else {
+ return theme;
+ }
+ }
+
+ function set_theme(theme, store = true) {
+ let ace_theme;
+
+ if (theme == 'coal' || theme == 'navy') {
+ stylesheets.ayuHighlight.disabled = true;
+ stylesheets.tomorrowNight.disabled = false;
+ stylesheets.highlight.disabled = true;
+
+ ace_theme = "ace/theme/tomorrow_night";
+ } else if (theme == 'ayu') {
+ stylesheets.ayuHighlight.disabled = false;
+ stylesheets.tomorrowNight.disabled = true;
+ stylesheets.highlight.disabled = true;
+ ace_theme = "ace/theme/tomorrow_night";
+ } else {
+ stylesheets.ayuHighlight.disabled = true;
+ stylesheets.tomorrowNight.disabled = true;
+ stylesheets.highlight.disabled = false;
+ ace_theme = "ace/theme/dawn";
+ }
+
+ setTimeout(function () {
+ themeColorMetaTag.content = getComputedStyle(document.documentElement).backgroundColor;
+ }, 1);
+
+ if (window.ace && window.editors) {
+ window.editors.forEach(function (editor) {
+ editor.setTheme(ace_theme);
+ });
+ }
+
+ var previousTheme = get_theme();
+
+ if (store) {
+ try { localStorage.setItem('mdbook-theme', theme); } catch (e) { }
+ }
+
+ html.classList.remove(previousTheme);
+ html.classList.add(theme);
+ updateThemeSelected();
+ }
+
+ // Set theme
+ var theme = get_theme();
+
+ set_theme(theme, false);
+
+ themeToggleButton.addEventListener('click', function () {
+ if (themePopup.style.display === 'block') {
+ hideThemes();
+ } else {
+ showThemes();
+ }
+ });
+
+ themePopup.addEventListener('click', function (e) {
+ var theme;
+ if (e.target.className === "theme") {
+ theme = e.target.id;
+ } else if (e.target.parentElement.className === "theme") {
+ theme = e.target.parentElement.id;
+ } else {
+ return;
+ }
+ set_theme(theme);
+ });
+
+ themePopup.addEventListener('focusout', function(e) {
+ // e.relatedTarget is null in Safari and Firefox on macOS (see workaround below)
+ if (!!e.relatedTarget && !themeToggleButton.contains(e.relatedTarget) && !themePopup.contains(e.relatedTarget)) {
+ hideThemes();
+ }
+ });
+
+ // Should not be needed, but it works around an issue on macOS & iOS: https://github.com/rust-lang/mdBook/issues/628
+ document.addEventListener('click', function(e) {
+ if (themePopup.style.display === 'block' && !themeToggleButton.contains(e.target) && !themePopup.contains(e.target)) {
+ hideThemes();
+ }
+ });
+
+ document.addEventListener('keydown', function (e) {
+ if (e.altKey || e.ctrlKey || e.metaKey || e.shiftKey) { return; }
+ if (!themePopup.contains(e.target)) { return; }
+
+ switch (e.key) {
+ case 'Escape':
+ e.preventDefault();
+ hideThemes();
+ break;
+ case 'ArrowUp':
+ e.preventDefault();
+ var li = document.activeElement.parentElement;
+ if (li && li.previousElementSibling) {
+ li.previousElementSibling.querySelector('button').focus();
+ }
+ break;
+ case 'ArrowDown':
+ e.preventDefault();
+ var li = document.activeElement.parentElement;
+ if (li && li.nextElementSibling) {
+ li.nextElementSibling.querySelector('button').focus();
+ }
+ break;
+ case 'Home':
+ e.preventDefault();
+ themePopup.querySelector('li:first-child button').focus();
+ break;
+ case 'End':
+ e.preventDefault();
+ themePopup.querySelector('li:last-child button').focus();
+ break;
+ }
+ });
+})();
+
+(function sidebar() {
+ var body = document.querySelector("body");
+ var sidebar = document.getElementById("sidebar");
+ var sidebarLinks = document.querySelectorAll('#sidebar a');
+ var sidebarToggleButton = document.getElementById("sidebar-toggle");
+ var sidebarResizeHandle = document.getElementById("sidebar-resize-handle");
+ var firstContact = null;
+
+ function showSidebar() {
+ body.classList.remove('sidebar-hidden')
+ body.classList.add('sidebar-visible');
+ Array.from(sidebarLinks).forEach(function (link) {
+ link.setAttribute('tabIndex', 0);
+ });
+ sidebarToggleButton.setAttribute('aria-expanded', true);
+ sidebar.setAttribute('aria-hidden', false);
+ try { localStorage.setItem('mdbook-sidebar', 'visible'); } catch (e) { }
+ }
+
+
+ var sidebarAnchorToggles = document.querySelectorAll('#sidebar a.toggle');
+
+ function toggleSection(ev) {
+ ev.currentTarget.parentElement.classList.toggle('expanded');
+ }
+
+ Array.from(sidebarAnchorToggles).forEach(function (el) {
+ el.addEventListener('click', toggleSection);
+ });
+
+ function hideSidebar() {
+ body.classList.remove('sidebar-visible')
+ body.classList.add('sidebar-hidden');
+ Array.from(sidebarLinks).forEach(function (link) {
+ link.setAttribute('tabIndex', -1);
+ });
+ sidebarToggleButton.setAttribute('aria-expanded', false);
+ sidebar.setAttribute('aria-hidden', true);
+ try { localStorage.setItem('mdbook-sidebar', 'hidden'); } catch (e) { }
+ }
+
+ // Toggle sidebar
+ sidebarToggleButton.addEventListener('click', function sidebarToggle() {
+ if (body.classList.contains("sidebar-hidden")) {
+ var current_width = parseInt(
+ document.documentElement.style.getPropertyValue('--sidebar-width'), 10);
+ if (current_width < 150) {
+ document.documentElement.style.setProperty('--sidebar-width', '150px');
+ }
+ showSidebar();
+ } else if (body.classList.contains("sidebar-visible")) {
+ hideSidebar();
+ } else {
+ if (getComputedStyle(sidebar)['transform'] === 'none') {
+ hideSidebar();
+ } else {
+ showSidebar();
+ }
+ }
+ });
+
+ sidebarResizeHandle.addEventListener('mousedown', initResize, false);
+
+ function initResize(e) {
+ window.addEventListener('mousemove', resize, false);
+ window.addEventListener('mouseup', stopResize, false);
+ body.classList.add('sidebar-resizing');
+ }
+ function resize(e) {
+ var pos = (e.clientX - sidebar.offsetLeft);
+ if (pos < 20) {
+ hideSidebar();
+ } else {
+ if (body.classList.contains("sidebar-hidden")) {
+ showSidebar();
+ }
+ pos = Math.min(pos, window.innerWidth - 100);
+ document.documentElement.style.setProperty('--sidebar-width', pos + 'px');
+ }
+ }
+ //on mouseup remove windows functions mousemove & mouseup
+ function stopResize(e) {
+ body.classList.remove('sidebar-resizing');
+ window.removeEventListener('mousemove', resize, false);
+ window.removeEventListener('mouseup', stopResize, false);
+ }
+
+ document.addEventListener('touchstart', function (e) {
+ firstContact = {
+ x: e.touches[0].clientX,
+ time: Date.now()
+ };
+ }, { passive: true });
+
+ document.addEventListener('touchmove', function (e) {
+ if (!firstContact)
+ return;
+
+ var curX = e.touches[0].clientX;
+ var xDiff = curX - firstContact.x,
+ tDiff = Date.now() - firstContact.time;
+
+ if (tDiff < 250 && Math.abs(xDiff) >= 150) {
+ if (xDiff >= 0 && firstContact.x < Math.min(document.body.clientWidth * 0.25, 300))
+ showSidebar();
+ else if (xDiff < 0 && curX < 300)
+ hideSidebar();
+
+ firstContact = null;
+ }
+ }, { passive: true });
+})();
+
+(function chapterNavigation() {
+ document.addEventListener('keydown', function (e) {
+ if (e.altKey || e.ctrlKey || e.metaKey || e.shiftKey) { return; }
+ if (window.search && window.search.hasFocus()) { return; }
+ var html = document.querySelector('html');
+
+ function next() {
+ var nextButton = document.querySelector('.nav-chapters.next');
+ if (nextButton) {
+ window.location.href = nextButton.href;
+ }
+ }
+ function prev() {
+ var previousButton = document.querySelector('.nav-chapters.previous');
+ if (previousButton) {
+ window.location.href = previousButton.href;
+ }
+ }
+ switch (e.key) {
+ case 'ArrowRight':
+ e.preventDefault();
+ if (html.dir == 'rtl') {
+ prev();
+ } else {
+ next();
+ }
+ break;
+ case 'ArrowLeft':
+ e.preventDefault();
+ if (html.dir == 'rtl') {
+ next();
+ } else {
+ prev();
+ }
+ break;
+ }
+ });
+})();
+
+(function clipboard() {
+ var clipButtons = document.querySelectorAll('.clip-button');
+
+ function hideTooltip(elem) {
+ elem.firstChild.innerText = "";
+ elem.className = 'fa fa-copy clip-button';
+ }
+
+ function showTooltip(elem, msg) {
+ elem.firstChild.innerText = msg;
+ elem.className = 'fa fa-copy tooltipped';
+ }
+
+ var clipboardSnippets = new ClipboardJS('.clip-button', {
+ text: function (trigger) {
+ hideTooltip(trigger);
+ let playground = trigger.closest("pre");
+ return playground_text(playground, false);
+ }
+ });
+
+ Array.from(clipButtons).forEach(function (clipButton) {
+ clipButton.addEventListener('mouseout', function (e) {
+ hideTooltip(e.currentTarget);
+ });
+ });
+
+ clipboardSnippets.on('success', function (e) {
+ e.clearSelection();
+ showTooltip(e.trigger, "Copied!");
+ });
+
+ clipboardSnippets.on('error', function (e) {
+ showTooltip(e.trigger, "Clipboard error!");
+ });
+})();
+
+(function scrollToTop () {
+ var menuTitle = document.querySelector('.menu-title');
+
+ menuTitle.addEventListener('click', function () {
+ document.scrollingElement.scrollTo({ top: 0, behavior: 'smooth' });
+ });
+})();
+
+(function controllMenu() {
+ var menu = document.getElementById('menu-bar');
+
+ (function controllPosition() {
+ var scrollTop = document.scrollingElement.scrollTop;
+ var prevScrollTop = scrollTop;
+ var minMenuY = -menu.clientHeight - 50;
+ // When the script loads, the page can be at any scroll (e.g. if you reforesh it).
+ menu.style.top = scrollTop + 'px';
+ // Same as parseInt(menu.style.top.slice(0, -2), but faster
+ var topCache = menu.style.top.slice(0, -2);
+ menu.classList.remove('sticky');
+ var stickyCache = false; // Same as menu.classList.contains('sticky'), but faster
+ document.addEventListener('scroll', function () {
+ scrollTop = Math.max(document.scrollingElement.scrollTop, 0);
+ // `null` means that it doesn't need to be updated
+ var nextSticky = null;
+ var nextTop = null;
+ var scrollDown = scrollTop > prevScrollTop;
+ var menuPosAbsoluteY = topCache - scrollTop;
+ if (scrollDown) {
+ nextSticky = false;
+ if (menuPosAbsoluteY > 0) {
+ nextTop = prevScrollTop;
+ }
+ } else {
+ if (menuPosAbsoluteY > 0) {
+ nextSticky = true;
+ } else if (menuPosAbsoluteY < minMenuY) {
+ nextTop = prevScrollTop + minMenuY;
+ }
+ }
+ if (nextSticky === true && stickyCache === false) {
+ menu.classList.add('sticky');
+ stickyCache = true;
+ } else if (nextSticky === false && stickyCache === true) {
+ menu.classList.remove('sticky');
+ stickyCache = false;
+ }
+ if (nextTop !== null) {
+ menu.style.top = nextTop + 'px';
+ topCache = nextTop;
+ }
+ prevScrollTop = scrollTop;
+ }, { passive: true });
+ })();
+ (function controllBorder() {
+ function updateBorder() {
+ if (menu.offsetTop === 0) {
+ menu.classList.remove('bordered');
+ } else {
+ menu.classList.add('bordered');
+ }
+ }
+ updateBorder();
+ document.addEventListener('scroll', updateBorder, { passive: true });
+ })();
+})();
diff --git a/book/book.toml b/book/book.toml
deleted file mode 100644
index cc8de95c6..000000000
--- a/book/book.toml
+++ /dev/null
@@ -1,9 +0,0 @@
-[book]
-authors = ["Kevin R. Thornton"]
-language = "en"
-multilingual = false
-src = "src"
-title = "The tskit (rust) book"
-
-[output.html]
-preferred-dark-theme = "light"
diff --git a/book/src/SUMMARY.md b/book/src/SUMMARY.md
deleted file mode 100644
index d0fb8d27a..000000000
--- a/book/src/SUMMARY.md
+++ /dev/null
@@ -1,33 +0,0 @@
-# Summary
-
-[Introduction](./introduction.md)
-
-- [Working with table collections](./working_with_table_collections.md)
- - [Creation](./table_collection_creation.md)
- - [Adding rows](./table_collection_adding_rows.md)
- - [Accessing table columns](./table_collection_column_access.md)
- - [Accessing table rows](./table_collection_row_access.md)
- - [Validating table collection contents](./table_collection_validation.md)
-
-- [Working with tree sequences](./working_with_tree_sequences.md)
- - [Initialization from a table collection](./tree_sequence_from_table_collection.md)
- - [Iterating over trees](./tree_sequence_iterate_trees.md)
- - [Working with trees](./tree_sequence_tree.md)
- - [Edge differences](./tree_sequence_edge_diffs.md)
- - [Miscellaneous operations](./tree_sequence_miscellaneous.md)
-
-* [Metadata](./metadata.md)
- - [Defining metadata types in rust](./metadata_derive.md)
- - [Metadata and tables](./metadata_tables.md)
- - [Metadata processing with Python](./metadata_python.md)
- - [Advanced topics](./metadata_advanced.md)
-
-* [Error handling](./error_handling.md)
-
-* [Example programs](./examples.md)
- - [Haploid Wright-Fisher simulation](./examples_haploid_wright_fisher.md)
-
-
-[Crate prelude](./prelude.md)
-[Changelog](./changelog.md)
-[Migration Guide](./migration_guide.md)
diff --git a/book/src/changelog.md b/book/src/changelog.md
deleted file mode 100644
index c16cb03d3..000000000
--- a/book/src/changelog.md
+++ /dev/null
@@ -1 +0,0 @@
-{{#include ../../CHANGELOG.md}}
diff --git a/book/src/error_handling.md b/book/src/error_handling.md
deleted file mode 100644
index 4cf78bc17..000000000
--- a/book/src/error_handling.md
+++ /dev/null
@@ -1,17 +0,0 @@
-# Error handling
-
-The error type is [`tskit::error::TskitError`](https://docs.rs/tskit/latest/tskit/error/enum.TskitError.html#).
-
-This type implements `Display` and may thus be printed via:
-
-```rust, noplayground, ignore
-let x = match operation() {
- Ok(y) => y,
- Err(e) => panic("{}", e);
-};
-```
-
-The enum variant `TskitError::ErrorCode` represents integer return values from `tskit-c`.
-When printed via `Display`, the detailed error message is fetched.
-When printed via `Debug`, the numerical error code is shown.
-
diff --git a/book/src/examples.md b/book/src/examples.md
deleted file mode 100644
index 1cb44c5fc..000000000
--- a/book/src/examples.md
+++ /dev/null
@@ -1 +0,0 @@
-# Example programs
diff --git a/book/src/examples_haploid_wright_fisher.md b/book/src/examples_haploid_wright_fisher.md
deleted file mode 100644
index 3f30ea21c..000000000
--- a/book/src/examples_haploid_wright_fisher.md
+++ /dev/null
@@ -1,13 +0,0 @@
-# Haploid Wright-Fisher simulation
-
-The following code simulates a haploid Wright-Fisher model.
-The code is a reimplementation of an example program distributed with `tskit-c`.
-
-In addition to `tskit`, the example uses:
-
-* [rand](https://crates.io/crates/rand) for random number generation.
-* [anyhow](https://crates.io/crates/anyhow) for error propagation.
-
-```rust, noplayground, ignore
-{{#include ../../examples/haploid_wright_fisher.rs:haploid_wright_fisher}}
-```
diff --git a/book/src/introduction.md b/book/src/introduction.md
deleted file mode 100644
index fdcec8be3..000000000
--- a/book/src/introduction.md
+++ /dev/null
@@ -1,75 +0,0 @@
-# Introduction
-
-## Required background.
-
-* We assume familiarity with `tskit`. See [tskit.dev](https://tskit.dev).
-* Comfort with rust is required.
- * [The book](https://doc.rust-lang.org/book/) is a good place to start.
- * [The Rustonomicon](https://doc.rust-lang.org/nomicon/) is for those who wish to dig deeper into `unsafe` rust and FFI.
- The 'nomicon is helpful for understanding how things like the `tskit` rust API can be built in the first place.
-
-## Conventions used in this document
-
-Here, `tskit` means the rust API.
-`tskit-c` and `tskit-python` refer to the C and Python APIs, respectively.
-
-The phrase "data model" refers to [this](https://tskit.dev/tskit/docs/stable/data-model.html). This document will make little sense without an understanding of the data model.
-
-## Relation to the C API
-
-Where necessary, we will note differences from the behavior of `tskit-c`.
-
-Much of the rust API works by calling the C API.
-We do not change the semantics of the C API.
-However, we do make stricter statements about the ownership relationships between types.
-For example, the C API can result in the following situation:
-
-* A heap-allocated table collection is used to record data about the ancestry of a sample.
-* That table collection is used to initialize a tree sequence.
- The tree sequence is told to take ownership of the tables.
-
-This is a case where the C API requires that you respectfully no longer work with the heap-allocated table collection. To do so is undefined behavior.
-
-The rust API forbids such situations.
-The creation of a tree sequence from tables consumes the tables via a move operation.
-Thus, any further actions on the tables is a compiler error.
-
-This example is the kinds of differences between `tskit` and `tskit-c`.
-Undefined behavior is (close to) impossible with `tskit`.
-
-
-## Quick overview
-
-### Do you need `tskit-rust`?
-
-The use-cases for `tskit-rust` are the same as for `tskit-c`:
-
-1. Developing a new performance-oriented application.
-2. The input/output of this application will be a `.trees` file.
-
-### What does `tskit-rust` add?
-
-Briefly, you get the performance of `C` and the strong safety guarantees of `rust`.
-
-### What is `tskit-rust` missing?
-
-The crate does not cover the entire `C` API.
-However, client code can make direct calls to that API via the module `tskit::bindings`.
-
-### Adding `tskit` as a dependency to a rust project
-
-In your `Cargo.toml`:
-
-```{toml}
-[dependencies]
-tskit = "~X.Y.Z"
-```
-
-The latest version to fill in `X.Y.Z` can be found [here](https://crates.io/crates/tskit).
-See [here](https://doc.rust-lang.org/cargo/reference/specifying-dependencies.html) for how to specify version numbers.
-
-#### Feature flags.
-
-`tskit` defines several [cargo features](https://doc.rust-lang.org/cargo/reference/features.html).
-These are defined in the [API docs](https://docs.rs/tskit/latest/tskit/#optional-features).
-
diff --git a/book/src/metadata.md b/book/src/metadata.md
deleted file mode 100644
index 940aa50c3..000000000
--- a/book/src/metadata.md
+++ /dev/null
@@ -1,8 +0,0 @@
-# Metadata
-
-Tables may contain additional information about rows that is not part of the data model.
-This metadata is optional.
-Tables are not required to have metadata.
-Tables with metadata do not require that every row has metadata.
-
-The next sections showcase the metadata API.
diff --git a/book/src/metadata_advanced.md b/book/src/metadata_advanced.md
deleted file mode 100644
index 8ddb95e37..000000000
--- a/book/src/metadata_advanced.md
+++ /dev/null
@@ -1,25 +0,0 @@
-## Advanced topics
-
-### Bulk decoding of metadata
-
-To populate a `Vec` with decoded metadata and accounting
-for some rows not having metadata:
-
-* Realize that the decode methods of the `MetadataRoundtrip` trait are associated functions.
-* We can use a lending iterator over rows to avoid unnecessary copying.
-
-Therefore:
-
-```rust, noplayground, ignore
-{{#include ../../tests/book_metadata.rs:metadata_bulk_decode_lending_iter}}
-```
-
-To filter out rows without metadata:
-
-```rust, noplayground, ignore
-{{#include ../../tests/book_metadata.rs:metadata_bulk_decode_lending_iter_with_filter}}
-```
-
-The first method gives `Vec
-
-The next sections cover how to work with the `TableCollection`, which is one of `tskit`'s fundamental types.
diff --git a/book/src/working_with_tree_sequences.md b/book/src/working_with_tree_sequences.md
deleted file mode 100644
index 81b06aebe..000000000
--- a/book/src/working_with_tree_sequences.md
+++ /dev/null
@@ -1,25 +0,0 @@
-# Working with tree sequences
-
-The next several sections provide examples based on a tree sequence with two trees.
-
-The first tree is:
-
-```md
- 0
- +++
- | | 1
- | | +++
- 2 3 4 5
-```
-
-The second tree is:
-
-```md
- 0
- +-+-+
- 1 |
- +-+-+ |
- 2 4 5 3
-```
-
-
diff --git a/build.rs b/build.rs
deleted file mode 100644
index 288535924..000000000
--- a/build.rs
+++ /dev/null
@@ -1,58 +0,0 @@
-extern crate bindgen;
-use std::path::Path;
-
-fn main() {
- pkg_config::Config::new().atleast_version("1.2");
-
- let src = [
- "subprojects/tskit/tskit/convert.c",
- "subprojects/tskit/tskit/core.c",
- "subprojects/tskit/tskit/genotypes.c",
- "subprojects/tskit/tskit/haplotype_matching.c",
- "subprojects/tskit/tskit/stats.c",
- "subprojects/tskit/tskit/tables.c",
- "subprojects/tskit/tskit/trees.c",
- "subprojects/kastore/kastore.c",
- ];
-
- let tskit_path = Path::new("subprojects/tskit/");
- let kastore_path = Path::new("subprojects/kastore/");
- let mut builder = cc::Build::new();
- let build = builder
- .files(src.iter())
- .include(tskit_path)
- .include(kastore_path)
- .flag("-Wno-unused-parameter");
- build.compile("tskit");
-
- // The bindgen::Builder is the main entry point
- // to bindgen, and lets you build up options for
- // the resulting bindings.
- let bindings = bindgen::Builder::default()
- // The input header we would like to generate
- // bindings for.
- .header("wrapper.h")
- .clang_arg("-Isubprojects/tskit")
- .clang_arg("-Isubprojects/kastore")
- .allowlist_type("tsk.*")
- .allowlist_function("tsk.*")
- .allowlist_type("TSK_.*")
- .allowlist_var("TSK_.*")
- .allowlist_type("KAS_.*")
- .allowlist_var("KAS_.*")
- .allowlist_type("kastore.*")
- .allowlist_function("kastore.*")
- // Tell cargo to invalidate the built crate whenever any of the
- // included header files changed.
- .parse_callbacks(Box::new(bindgen::CargoCallbacks::new()))
- // Finish the builder and generate the bindings.
- .generate()
- // Unwrap the Result and panic on failure.
- .expect("Unable to generate bindings");
-
- // Write the bindings to the $OUT_DIR/bindings.rs file.
- let out_path = std::path::PathBuf::from(std::env::var("OUT_DIR").unwrap());
- bindings
- .write_to_file(out_path.join("auto_bindings.rs"))
- .expect("Couldn't write bindings!");
-}
diff --git a/changelog.html b/changelog.html
new file mode 100644
index 000000000..077fc1710
--- /dev/null
+++ b/changelog.html
@@ -0,0 +1,791 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/cliff.toml b/cliff.toml
deleted file mode 100644
index e6bdee4f3..000000000
--- a/cliff.toml
+++ /dev/null
@@ -1,64 +0,0 @@
-# configuration file for git-cliff (0.1.0)
-
-[changelog]
-# changelog header
-header = """
-# Changelog\n
-All notable changes to this project will be documented in this file.\n
-"""
-# template for the changelog body
-# https://tera.netlify.app/docs/#introduction
-body = """
-{% if version %}\
- ## [{{ version | trim_start_matches(pat="v") }}] - {{ timestamp | date(format="%Y-%m-%d") }}
-{% else %}\
- ## [unreleased]
-{% endif %}\
-{% for group, commits in commits | group_by(attribute="group") %}
- ### {{ group | upper_first }}
- {% for commit in commits %}
- - {% if commit.breaking %}[**breaking**] {% endif %}{{ commit.message | upper_first }}\
- {% endfor %}
-{% endfor %}\n
-"""
-# remove the leading and trailing whitespace from the template
-trim = true
-# changelog footer
-footer = """
-
-"""
-
-[git]
-# parse the commits based on https://www.conventionalcommits.org
-conventional_commits = true
-# filter out the commits that are not conventional
-filter_unconventional = true
-# regex for preprocessing the commit messages
-commit_preprocessors = [
- { pattern = '\((\w+\s)?#([0-9]+)\)', replace = "([#${2}](https://github.com/tskit-dev/tskit-rust/pull/${2}))"},
-]
-# regex for parsing and grouping commits
-commit_parsers = [
- { message = "^feat", group = "Features"},
- { message = "^fix", group = "Bug Fixes"},
- { message = "^doc", group = "Documentation"},
- { message = "^perf", group = "Performance"},
- { message = "^refactor", group = "Refactor"},
- { message = "^style", group = "Styling"},
- { message = "^test", group = "Testing"},
- { message = "^chore\\(release\\): prepare for", skip = true},
- { message = "^chore", group = "Miscellaneous Tasks"},
- { body = ".*security", group = "Security"},
-]
-# filter out the commits that are not matched by commit parsers
-filter_commits = true
-# glob pattern for matching git tags
-tag_pattern = "v[0-9]*"
-# regex for skipping tags
-skip_tags = "v0.1.0-beta.1"
-# regex for ignoring tags
-ignore_tags = ""
-# sort the tags chronologically
-date_order = false
-# sort the commits inside sections by oldest/newest order
-sort_commits = "oldest"
diff --git a/clipboard.min.js b/clipboard.min.js
new file mode 100644
index 000000000..02c549e35
--- /dev/null
+++ b/clipboard.min.js
@@ -0,0 +1,7 @@
+/*!
+ * clipboard.js v2.0.4
+ * https://zenorocha.github.io/clipboard.js
+ *
+ * Licensed MIT © Zeno Rocha
+ */
+!function(t,e){"object"==typeof exports&&"object"==typeof module?module.exports=e():"function"==typeof define&&define.amd?define([],e):"object"==typeof exports?exports.ClipboardJS=e():t.ClipboardJS=e()}(this,function(){return function(n){var o={};function r(t){if(o[t])return o[t].exports;var e=o[t]={i:t,l:!1,exports:{}};return n[t].call(e.exports,e,e.exports,r),e.l=!0,e.exports}return r.m=n,r.c=o,r.d=function(t,e,n){r.o(t,e)||Object.defineProperty(t,e,{enumerable:!0,get:n})},r.r=function(t){"undefined"!=typeof Symbol&&Symbol.toStringTag&&Object.defineProperty(t,Symbol.toStringTag,{value:"Module"}),Object.defineProperty(t,"__esModule",{value:!0})},r.t=function(e,t){if(1&t&&(e=r(e)),8&t)return e;if(4&t&&"object"==typeof e&&e&&e.__esModule)return e;var n=Object.create(null);if(r.r(n),Object.defineProperty(n,"default",{enumerable:!0,value:e}),2&t&&"string"!=typeof e)for(var o in e)r.d(n,o,function(t){return e[t]}.bind(null,o));return n},r.n=function(t){var e=t&&t.__esModule?function(){return t.default}:function(){return t};return r.d(e,"a",e),e},r.o=function(t,e){return Object.prototype.hasOwnProperty.call(t,e)},r.p="",r(r.s=0)}([function(t,e,n){"use strict";var r="function"==typeof Symbol&&"symbol"==typeof Symbol.iterator?function(t){return typeof t}:function(t){return t&&"function"==typeof Symbol&&t.constructor===Symbol&&t!==Symbol.prototype?"symbol":typeof t},i=function(){function o(t,e){for(var n=0;n
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ Changelog
+All notable changes to this project will be documented in this file.
+[0.14.1] - 2023-04-16
+Bug Fixes
+-
+
- Tree now tied to TreeSequence lifetime (#497) +
Miscellaneous Tasks
+-
+
- Update delegate requirement from 0.8.0 to 0.9.0 (#494) +
[0.14.0] - 2023-03-17
+Documentation
+-
+
- Book section on node defaults (#491) +
Features
+-
+
- Allow use of bookmark in examples/haploid_wright_fisher (#479) +
- Impl Default for row id types (#484) +
- Impl Default for Bookmark (#486) +
- Implement Builder pattern for flags (#487) +
- Support adding nodes with defaults (#488) +
Miscellaneous Tasks
+-
+
- [breaking] Bump MSRV to 1.60.0 (#478) +
Refactor
+-
+
- Remove internal impl Deref/DerefMut for edge diff iterator. (#482) +
- Mod table_view is no longer pub (#483) +
- [breaking] TableCollection::simplify now takes &[NodeId] (#485) +
- Replace macros with fn for adding node table rows (#489) +
- Manually impl Default for NodeDefaultsWithMetadata (#490) +
[0.12.0] - 2022-12-23
+Documentation
+-
+
- Book section on lending row iterators (#406) +
- Advanced metadata topics in book (#407) +
- Book chapter on edge differences (#417) +
Features
+-
+
- TreeSequence::edge_differences_iter (#410) +
- Add convience functions to get usize from row ids. (#413) +
- Tree::total_branch_length now works. (#429) +
- Add getters/setters for Bookmark. (#437) +
Miscellaneous Tasks
+-
+
- Update bindgen requirement from 0.61.0 to 0.63.0 (#415) +
Refactor
+-
+
- [breaking] Replace Deref with delegation of TableViews API (#409) +
- [breaking] Remove TskitTypeAccess trait (#411) +
- Allow TreeSequence::edge_differences_iter to Err. (#412) +
- [breaking] Usize to SizeType conversion is now fallible. (#419) +
- Macros only use newtype public API. (#420) +
- Move newtypes into module (#421) +
- The raw_metadata fn for tables now takes Into
. (#425)
+ - Add low-level table wrappers to sys (#426) +
- Generalize slice building in sys (#427) +
- Remove many unsafe calls from tree_interface.rs (#428) +
- Add sys::LLTreeSeq. (#430) +
- Sys module no longer depends on TskitError (#431) +
- Move Drop details for TreeSequence to sys. (#432) +
- Add low level owning tables to sys (#433) +
- Tidy up table definitions (#434) +
Styling
+-
+
- [breaking] Rename all OwnedX tables to OwningX. (#408) +
- Replace column access macro with generic fn (#422) +
- Generic fns for ragged column access (#423) +
- Use fn to get array slices from Trees. (#424) +
[0.12.0-alpha.1] - 2022-11-09
+Bug Fixes
+-
+
- [breaking] MetadataError::RoundtripError now requires Send + Sync (#396) +
Documentation
+-
+
- Add haploid WF example to book (#397) +
Features
+-
+
- Add examples/haploid_wright_fisher.rs (#394) +
- Add lending iterators over table row "views" (#398) +
- Impl PartialEq for table row views. (#400) +
- Add ProvenenceTableRowView (#401) +
- Add row_view() for tables (#402) +
- Add row_view() for tables (#402) +
- Column slice getters for tables (#404) +
Refactor
+-
+
- [breaking] Return &str from provenance table getters (#403) +
- Deprecate NodeTable::flags_array_mut and NodeTable::time_array_mut (#405) +
[0.12.0-alpha.0] - 2022-11-06
+Documentation
+-
+
- Add book sections on table data access (#379) +
- Remove chapter number from book intro (#380) +
- Start book sections on tree sequences (#381) +
- Book section on the tree API. (#382) +
- Add book section on misc. ops on treeseqs (#385) +
- Appendix material for book (#386) +
- Rewrite book intro (#389) +
- Show prelude contents as book appendix (#390) +
- Book sections on metadata (#391) +
- Book section on error handling (#393) +
Refactor
+-
+
- [breaking] Improve Tree iterator ergonomics (#384) +
- [breaking] Improve Tree interface ergonomics (#388) +
[0.11.1] - 2022-11-04
+Documentation
+-
+
- Add mdbook (#378) +
Refactor
+-
+
- Apply functional style for NodeTable fns (#377) +
[0.11.0] - 2022-11-04
+Bug Fixes
+-
+
- Derive Debug for all table row types (#361) +
- [breaking] Update generic bounds on metadata getters (#370) +
- Impl DerefMut for "owned" tables. (#371) +
Documentation
+-
+
- Add migration guide (#376) +
Features
+-
+
- [breaking] Add TskitError::LibraryError (#342) +
Refactor
+-
+
- Streamline code for generating table rows. (#340) +
- Replace unwrap with expect in _macros.rs (#341) +
- Replace unwrap with errors in table_collection.rs (#343) +
- Remove unwraps in trees source files. (#344) +
- Streamline building individual table rows (#345) +
- Remove unwraps from node_table.rs (#346) +
- Unwrap to expect in error.rs (#347) +
- Remove type info from Display for newtypes. (#349) +
- [breaking] Return None for out-of-range row indexes. (#350) +
- [breaking] Return None for out-of-range row indexes, part II. (#351) +
- [breaking] Return None for out-of-range row indexes, part III. (#355) +
- Improve safety of tsk array access (#362) +
- Tree now stores
tsk_tree_tinMBox. (#367)
+ - [breaking] Provenance table getters now return Option (#369) +
- [breaking] Remove lifetime annotation from table types (#373) +
Styling
+ +Testing
+ +[0.10.0] - 2022-10-28
+Documentation
+-
+
- Display feature flags in docs.rs (#338) +
Miscellaneous Tasks
+-
+
- Set msrv to 1.57.0 (result of cargo msrv) (#322) +
- Fix tag_pattern in cliff.toml (#330) +
- Update github actions (#332) +
- Add github actions to monthly dependabot (#333) +
- Update bindgen requirement from 0.60.1 to 0.61.0 (#336) +
- Bump styfle/cancel-workflow-action from 0.6.0 to 0.11.0 (#334) +
Performance
+-
+
- Use Bookmark in forward simulation example (#318) +
Refactor
+-
+
- Streamline internal macros for adding nodes (#309) +
- Remove internal ffi module (#310) +
- Panics compatible with earlier rustc (#311) +
- Remove type name from SizeType Display output. (#315) +
- [breaking] TableCollection::simplify returns Option<&[NodeId]> (#316) +
- [breaking] Conversion from row id to usize is now fallible. (#319) +
- Use clap::Parser in example program. (#320) +
- Remove pontential panic! when instantiating table rows. (#329) +
- Examples/tree_traversals.rs now uses clap derive (#337) +
Styling
+-
+
- Remove unneeded ( ) from match. (#323) +
- Use auto-deref for pointer deref. (#325) +
- Fix +nightly clippy lints for all targets/features. (#326) +
Testing
+-
+
- Improve test work flow (#331) +
[0.10.0-alpha.1] - 2022-07-31
+Bug Fixes
+-
+
- Replace crate with $crate in macros (#287) +
Features
+-
+
- Add tskit::OwnedMutationTable (#281) +
- Add tskit::OwnedSiteTable (#283) +
- Add tskit::OwnedIndividualTable (#284) +
- Add tskit::OwnedMigrationTable (#285) +
- Add tskit::provenance::OwnedProvenanceTable (#286) +
- Set tables in collection from owned tables. (#288) +
- [breaking] Impl Send/Sync for TreeSequence (#297) +
Miscellaneous Tasks
+-
+
- Update to C API 1.1.1 (#304) +
Performance
+-
+
- [breaking] Implement slice access to individual data (#292) +
- [breaking] Eliminate several copies from C to rust (#293) +
Refactor
+-
+
- Deduplicate code for adding node table rows. (#278) +
- Use macros to implement adding table rows. (#279) +
- Add new macro to build owned tables (#282) +
- Separate tree ownership from API. (#300) +
- Bring back generic syntax for adding node table rows. (#302) +
- [breaking] Display for new types now omits type name. (#305) +
- Remove MBox for tsk_treeseq_t storage (#306) +
[0.10.0-alpha.0] - 2022-07-19
+Bug Fixes
+-
+
- Fix memory leak in TreeSequence::simplify (#274) +
- Fix leak in TableCollection::deepcopy (#275) +
- Fix leak in TreeSequence::dump_tables (#276) +
Documentation
+-
+
- Fix warnings from "cargo doc" (#255) +
Features
+-
+
- Make load from file generic over AsRef
(#254)
+ - Add tskit::OwnedPopulationTable (#267) +
- Add tskit::OwnedEdgeTable (#268) +
- Add tskit::OwnedNodeTable (#273) +
Miscellaneous Tasks
+-
+
- Add cliff.toml (config file for git-cliff) (#257) +
- Prefix "chore: " to dependabot.yml (#258) +
- Use cargo-hack to streamline CI. (#259) +
- Add cargo-valgrind CI workflow (#277) +
Refactor
+ +Testing
+-
+
- Add another experimental trait idea for metadata. (#261) +
- Redo doctest: TableCollection::new_from_file (#272) +
2022-06-20, Version 0.9.0
+Commits
+-
+
- [
068fdccdea] Bump version to 0.9.0 (Kevin R. Thornton)
+ - [
d700af7294] doc sorting requirements (#243) (Kevin R. Thornton)
+ - [
6114d2bd65] Change ffi to private visibility. (#241) (Kevin R. Thornton)
+ - [
b53105112a] Add new_sample and is_sample to NodeFlags public API. (#238) (Kevin R. Thornton)
+
2022-05-26, Version 0.8.1
+Commits
+-
+
- [
bd72b689ac] Bump version to 0.8.1 (molpopgen)
+ - [
b0abdfad5c] impl TryFromfor TreeSequence (#236) (Kevin R. Thornton)
+ - [
71e927a9bb] TreeSequence::new now takes ownership of the TableCollection. (#235) (Kevin R. Thornton)
+
2022-05-24, Version 0.8.0
+Commits
+-
+
- [
e463302ced] Bump package version to 0.8.0 (molpopgen)
+ - [
deffc58127] Replace Fromfor usize with TryFrom. (#234) (Kevin R. Thornton)
+ - [
a7c04213a1] update to CAPI 1.0.0 (#229) (Kevin R. Thornton)
+ - [
7c0b6169a3] Add CI for 32 bit Linux builds (#232) (Kevin R. Thornton)
+ - [
7458d85163] Invoke rust dependency caching after setting up rustc (#233) (Kevin R. Thornton)
+ - [
203a43a0e8] Only run CI for rust/stable. (#231) (Kevin R. Thornton)
+ - [
fb2128c0a5] Add dependency caching for CI. (#230) (Kevin R. Thornton)
+ - [
aff053c786] Improvements to handling of tsk_flags_t: (#227) (Kevin R. Thornton)
+ - [
5f558cb051] Audit pedantic lints re: integer casts (#223) (Kevin R. Thornton)
+ - [
609546185c] Fix several "pedantic" lints from clippy: (#222) (Kevin R. Thornton)
+
2022-03-24, Version 0.7.0
+Commits
+-
+
- [
8427c2fea7] Change order of generics to match argument order for all "add" (#221) (Kevin R. Thornton)
+ - [
6ef0406731] Fix typo in docstring for TableCollection::full_sort. (#219) (Kevin R. Thornton)
+ - [
a1a7e12208] Add TableCollection::topological_sort_individuals. (#218) (Kevin R. Thornton)
+ - [
4c17ca62a2] Update clap requirement from ~3.0.0 to ~3.1.3 (#215) (dependabot[bot])
+ - [
f40562a56a] Fix lint found by clippy. (#216) (Kevin R. Thornton)
+ - [
4efddb6f5d] Update clap requirement from ~2.34.0 to ~3.0.0 (#214) (dependabot[bot])
+
2021-12-15, Version 0.7.0-alpha.1
+Fixes various minor issues with the first alpha.
+Commits
+-
+
- [
44965969c0] Bump version to 0.7.0.alpha.1 (molpopgen)
+ - [
5d6a289490] Fix issues with Time, Position, Location newtypes (#212) (Kevin R. Thornton)
+ - [
99930e8bb0] Add explicit tests of tree roots. (#211) (Kevin R. Thornton)
+
2021-12-15, Version 0.7.0-alpha.0
+Breaking changes:
+-
+
- Update to tskit C API 0.99.15. +
- Add newtypes for Time, Position, and Location. +
- Add newtype SizeType, which wraps tsk_size_t. +
- tsk_id_t and tsk_size_t removed from library prelude. +
- The Provenance trait is removed and all "provenance stuff" +is now a first-class table API supported by the TableAccess trait. +
New features:
+-
+
- Update to tskit C API 0.99.15. +
- tskit C structs are now managed by MBox. +
- Support for virtual tree roots. +
- Add postorder node iterator for Tree +
Commits
+-
+
- [
272d0736e2] bump package version to 0.7.0-alpha.0 (molpopgen)
+ - [
b5946a4cc4] Redesign provenance feature: (#207) (Kevin R. Thornton)
+ - [
5699aab37f] Change return time of Tree::num_tracked_samples. (#206) (Kevin R. Thornton)
+ - [
2391c9e587] Add support for virtual roots (#205) (Kevin R. Thornton)
+ - [
4cf3496d82] Fix metadata links in lib.rs (#204) (Kevin R. Thornton)
+ - [
d7f70a7cfd] Use MBoxto manage lifetimes of tskit C structs. (#203) (Kevin R. Thornton)
+ - [
034204ed88] Add newtypes for Time, Position, and for Location. (#199) (Kevin R. Thornton)
+ - [
4ba44ef0c5] Bump editions to 2021. (#198) (Kevin R. Thornton)
+ - [
c4cc6e875a] Add tskit::SizeType (#192) (Kevin R. Thornton)
+ - [
8429cc37d2] Use type erasure for all table row iteration functions. (#189) (Kevin R. Thornton)
+ - [
f4cb6350e0] Add TableCollection::check_integrity. (#188) (Kevin R. Thornton)
+ - [
562014b04f] Add preorder node traversal using latest tskit C API. (#186) (Kevin R. Thornton)
+ - [
db8550f6d7] Replace Box with malloc'd raw pointer for tskit types. (#184) (Kevin R. Thornton)
+ - [
90a2d84a9d] Update to C API 0.99.15 (breaking) (#183) (Kevin R. Thornton)
+ - [
58e7c5ed73] Update clap requirement from ~2.33.3 to ~2.34.0 (#176) (dependabot[bot])
+
2021-11-29, Version 0.6.1
+Commits
+-
+
- [
3eadcb161e] Replace chrono with humantime in provenance doc tests. (#175) (Kevin R. Thornton)
+ - [
4def777ddf] Add security audit work flow. (#172) (Kevin R. Thornton)
+
2021-11-23, Version 0.6.0
+Commits
+-
+
- [
b07c035077] bump version to 0.6.0 (molpopgen)
+ - [
8bb08be83d] Replace chrono dependency with humantime to avoid RUSTSEC-2020-0071 and RUSTSEC-2020-0159 (#171) (Momo Langenstein)
+ - [
896b5891e0] Implement Display for Id newtypes. (#168) (Kevin R. Thornton)
+ - [
d2c6383ae9] Update to C API 0.99.14 (#165) (Kevin R. Thornton)
+
2021-09-03, Version 0.5.0
+Commits
+Derive macros for table metadata.
+-
+
- [
41633b60ed] Add metadata type registration via derive macros. (#163) (Kevin R. Thornton)
+
2021-08-31, Version 0.4.0
+The theme of this release is "type safety". +This release breaks API due to use of newtypes for row IDs and new metadata marker traits.
+Commits
+-
+
- [
a7d78b16aa] Bump version to 0.4.0 (molpopogen)
+ - [
b5e2c265dd] Add newtype row IDs to prelude. (#161) (Kevin R. Thornton)
+ - [
3dbe8c4b5e] Fix implementation of tree preorder stacking. (#160) (Kevin R. Thornton)
+ - [
fafd457033] Refactor metadata encoding: (#158) (Kevin R. Thornton)
+ - [
258b4ee5f0] replace IdIsNull trait with associated fn (#156) (Kevin R. Thornton)
+ - [
9987fc0472] Release build optimizations: (#155) (Kevin R. Thornton)
+ - [
58ac4a92d7] Refine what "NULL"-ness means for an Id type: (#154) (Kevin R. Thornton)
+ - [
ad4975fc70] Update bindgen requirement from 0.58.1 to 0.59.1 (#152) (dependabot[bot])
+ - [
8a553eaa80] fix clippy warnings that showed up in rust 1.54 (#153) (Kevin R. Thornton)
+ - [
bef4bb6c7a] Allow empty provenance records. (#151) (Kevin R. Thornton)
+ - [
86df702040] Improve test coverage of "adding rows to table collections" (#143): (Kevin R. Thornton)
+ - [
036680050b] * Update trees API to use NodeId (#145) (Kevin R. Thornton)
+ - [
7a716bbe76] Add additional member functions to TableCollection to (#141) (Kevin R. Thornton)
+ - [
baf6f17430] Fix Into< > type for TableCollection::add_individual_* (#142) (Kevin R. Thornton)
+ - [
689938eee7] fix link from ProvenanceId to ProvenanceTable in docs (#140) (Kevin R. Thornton)
+ - [
1203a5d523] strong id type cleanup (#139) (Kevin R. Thornton)
+ - [
6bae100e61] Add EdgeId (#138) (Kevin R. Thornton)
+ - [
9baff077b5] Add MigrationId and ProvenanceId (#137) (Kevin R. Thornton)
+ - [
7713ef669e] Add SiteId and MutationId (#136) (Kevin R. Thornton)
+ - [
de006a1f0e] Add PopulationId (#135) (Kevin R. Thornton)
+ - [
630ccd5f5e] Add IndividualId. (#133) (Kevin R. Thornton)
+ - [
8bf7d4b954] NodeTable::metadata now uses Into. (#134) (Kevin R. Thornton)
+ - [
3ac3d50f7b] * Establish a pattern for stronger ID types (#129) (Kevin R. Thornton)
+ - [
e19095d9a9] clippy vs bindgen (#130) (Kevin R. Thornton)
+ - [
d9abda5bb6] Change links in Cargo.toml to tskit-dev (#127) (Kevin R. Thornton)
+
2021-05-19, Version 0.3.0
+This release has a few API changes, etc., that streamline the public interface.
+The C code is updated to 0.99.12.
+Commits
+-
+
- [
ec0adc36ae] streamline API for creating table row objects (#126) (Kevin R. Thornton)
+ - [
edd36fa886] Add mutable access to NodeTable flag and time arrays. (#125) (Kevin R. Thornton)
+ - [
634df568af] Fix docs for Tree::total_branch_length. Fixes #114. (#124) (Kevin R. Thornton)
+ - [
202bcded3f] Give access to TableCollection edge indexes. (#123) (Kevin R. Thornton)
+ - [
3888fe5f10] update C code to version 0.99.12 (#122) (Kevin R. Thornton)
+ - [
6fa2057af6] Add prelude.rs (#119) (Kevin R. Thornton)
+ - [
a592126594] replace crate with $crate for all macros (#113) (Kevin R. Thornton)
+ - [
b618d75e5b] Add macro to aid returning from MetadataRoundtrip functions. (#110) (Kevin R. Thornton)
+ - [
79adaa1a4a] Add macro to remove code duplication (#111) (Kevin R. Thornton)
+ - [
159bbfe926] Add convenience macro to use all public traits. (#106) (Kevin R. Thornton)
+ - [
e912f7b2c8] Bump bindgen version. (#109) (Kevin R. Thornton)
+ - [
15fae9327b] Update clap requirement from ~2.27.0 to ~2.33.3 (#107) (dependabot[bot])
+ - [
55f18a1a4f] Refactor MetadataError: (#105) (Kevin R. Thornton)
+ - [
fbce6ca894] API fixes. (#104) (Kevin R. Thornton)
+
2021-04-27, Version 0.2.2
+This release fixes issues with the lifetime relationships of Tree and the raw C arrays.
+Technically, this is an API change, but only with respect to return type and the integer type used to index that return type.
Commits
+-
+
- [
89d234f674] Replace WrappedTskArray with idiomatic slices. Closes #99 (#101) (Kevin R. Thornton)
+ - [
ed8329b89e] Completely hide NodeIterator from public name spaces. (#100) (Kevin R. Thornton)
+
2021-04-26, Version 0.2.1
+-
+
- [
ff1c7ced82] Add Provenance trait as optional feature (#98). (Kevin R. Thornton)
+ - [
0fdd30067e] Fix error in transmitting nodes. Closes #96 (#97) (Kevin R. Thornton)
+ - [
299c83ae35] Update repo/homepage name in Cargo.toml (molpopgen)
+ - [
35ecf29933] Remove re-exports that are part of existing bitflags types. (#95) (Kevin R. Thornton)
+
2021-04-21, Version 0.2.0
+Commits
+-
+
- [
daffeda43e] bump version to 0.2.0 (molpopgen)
+ - [
0dad5e39d2] Update docs (#93) (Kevin R. Thornton)
+ - [
f905b9c384] Add reverse tree iteration. (#92) (Kevin R. Thornton)
+ - [
a1a033f901] Add development documentation. (#91) (Kevin R. Thornton)
+ - [
ce3d8f4849] Refine forward sim example (#90) (Kevin R. Thornton)
+ - [
b1022e1f59] Refactor how tskit flags are handled. (#89) (Kevin R. Thornton)
+ - [
56e43cb0ff] Add forward simulation example. Closes #71. (#86) (Kevin R. Thornton)
+ - [
5530d7b234] Refactor all examples into examples/ (#85) (Kevin R. Thornton)
+ - [
651e4edcac] Collect public traits in traits.rs. Closes #81. (#84) (Kevin R. Thornton)
+ - [
11ad49f0e1] Remove mention of use NodeIterator. Closes #68. (#83) (Kevin R. Thornton)
+ - [
df28231d9a] Add test fixtures module. Closes #73 (#80) (Kevin R. Thornton)
+ - [
3a8a82637e] Rename Tree::nodes to Tree::traverse_nodes. (#79) (Kevin R. Thornton)
+ - [
4e7af98ac5] Update GitHub actions. (#78) (Kevin R. Thornton)
+ - [
43e14bb8a6] Add NodeListGenerator trait bound to TableAccess. Closes #67. (#75) (Kevin R. Thornton)
+ - [
ae203769f4] add id field to table row types. Closes #76 (#77) (Kevin R. Thornton)
+ - [
346c804be8] Make tree arrays public. Closes #70 (#74) (Kevin R. Thornton)
+ - [
a2dfcfe8f6] Add TableCollection and TreeSequence simplification (#64) (Kevin R. Thornton)
+ - [
c62ccd21aa] Add TableAccess trait and implement for TableCollection and TreeSequence. (#66) (Kevin R. Thornton)
+ - [
167209466a] Remove duplication of entire table collection when creating a tree sequence. (#65) (Kevin R. Thornton)
+ - [
df258ad8d1] Fix useless conversion in lib::c_api_version (#63) (Kevin R. Thornton)
+ - [
fcca8bb682] remove unnecessary function from util (#62) (Kevin R. Thornton)
+ - [
0ee9f86db4] Merge pull request #61 from molpopgen/add_individual_and_migration_tables (Kevin R. Thornton)
+ - [
8f072c47d1] Add migrations and individuals tables. (molpopogen)
+ - [
b2c891300b] Merge pull request #60 from molpopgen/tskit_C_version (Kevin R. Thornton)
+ - [
f48b2fed57] Add functions to return C API version info (molpopogen)
+ - [
87593d4bdc] Merge pull request #59 from molpopgen/add_test_metadata_some_columns_only (Kevin R. Thornton)
+ - [
5ab8e8c9d0] Add test of metadata decoding when not all rows have metadata. (molpopogen)
+ - [
adcc321cc8] Merge pull request #58 from molpopgen/table_row_access (Kevin R. Thornton)
+ - [
860a647bf3] * Add ::row for all tables (molpopgen)
+ - [
6b0a77e106] Add util.rs (molpopgen)
+ - [
6b9631e1f1] Merge pull request #57 from molpopgen/unify_table_iteration (Kevin R. Thornton)
+ - [
3d79f8bbfa] Add ability to iterate tables from a TableCollection: (molpopogen)
+ - [
392ce57e0a] Merge pull request #52 from molpopgen/table_iteration (Kevin R. Thornton)
+ - [
2fe5912c34] Add table iteration w/optional handling of metadata. (molpopgen)
+ - [
9a59a148f7] Merge pull request #55 from molpopgen/wrapped_tsk_array_iter_adapter (Kevin R. Thornton)
+ - [
84b0b496c1] Replace built-in iteration with iterator adapter for WrappedTskArray (molpopgen)
+ - [
18234998ea] Merge pull request #56 from molpopgen/metadata_macro_fixes (Kevin R. Thornton)
+ - [
49bbd0f2f4] metadata_to_vector macro is now a simple return (no ? operator). (molpopgen)
+ - [
6e293acf14] Remove unused paramter to metadata_to_vector. Fixes #54. (molpopgen)
+ - [
45347a576c] Change log for 0.1.2 (molpopgen)
+
2021-04-12, Version 0.1.2
+Commits
+-
+
- [
f475a5c624] Bump version to 0.1.2 (molpopgen)
+ - [
f1887d55e0] Merge pull request #46 from molpopgen/add_important_missing_functions (Kevin R. Thornton)
+ - [
f5598256dd] Merge pull request #47 from molpopgen/add_changelog (Kevin R. Thornton)
+ - [
fb85ba9606] Add Tree::num_tracked_samples and Tree::kc_distance. (molpopogen)
+ - [
08febd5062] Add change log (molpopogen)
+ - [
e6495a959a] Merge pull request #51 from molpopgen/test_beta_instead_of_nightly (Kevin R. Thornton)
+ - [
fa7cca91a5] Test beta instead of nightly. (molpopgen)
+ - [
bd7185eef2] Merge pull request #45 from molpopgen/documentation (Kevin R. Thornton)
+ - [
2400906762] Add documentation related to Tree/TreeSequence (molpopogen)
+ - [
550aa76597] Fix typo in function name. (molpopogen)
+ - [
56eaf875b6] Merge pull request #44 from molpopgen/fix_clippy_warnings (Kevin R. Thornton)
+ - [
20ffe557ca] Fix warnings from clippy (molpopogen)
+ - [
0bf1dada4d] Merge pull request #43 from molpopgen/kc_distance (Kevin R. Thornton)
+ - [
2e8b4c1cfc] Add TreeSequence::kc_distance (molpopogen)
+ - [
efe5ce2b0b] Merge pull request #42 from molpopgen/fix_tskit_array_access_macro (Kevin R. Thornton)
+ - [
82bb6ec6a1] Modify unsafe_tsk_column_access to support idiomatic fall-through. (molpopogen)
+ - [
40e898910d] Merge pull request #41 from molpopgen/sample_list_traversal (Kevin R. Thornton)
+ - [
cb0e9a4355] Add support for samples iteration: (molpopogen)
+ - [
f1acfb06f2] Merge pull request #40 from molpopgen/more_node_iteration (Kevin R. Thornton)
+ - [
22684248d1] * Rename NodeIteration to NodeIterator (molpopogen)
+ - [
faa105d577] Merge pull request #38 from molpopgen/Tree_API (Kevin R. Thornton)
+ - [
896f921e91] Several changes to Tree and TreeSequence: (molpopogen)
+ - [
683ba84b10] Merge pull request #39 from molpopgen/ffi_array_wrapper (Kevin R. Thornton)
+ - [
dd3df03ca3] Add non-owning wrappers to C arrays. (molpopogen)
+ - [
85cc4a591f] Merge pull request #37 from molpopgen/add_tree (Kevin R. Thornton)
+ - [
be97490641] Add minimial Tree interface. (molpopgen)
+ - [
4b6257ed2c] Merge pull request #36 from molpopgen/streamline_macros (Kevin R. Thornton)
+ - [
238f652d24] Remove macro redundancy. (molpopgen)
+ - [
85505887e1] Merge pull request #35 from molpopgen/refine_ffi (Kevin R. Thornton)
+ - [
2cb4993f07] Refactor the ffi module: (molpopgen)
+ - [
1b9a054ff0] Merge pull request #34 from molpopgen/improve_error_handling_macro (Kevin R. Thornton)
+ - [
20a5486132] Add overload of handle_tsk_return_value. (molpopgen)
+ - [
eae11b4c8a] Merge pull request #33 from molpopgen/add_tree_sequence (Kevin R. Thornton)
+ - [
a57b947352] Add TskitConsumingType, macro to build one, and convert TreeSequence (molpopgen)
+ - [
dcb5a02f3c] change dependabot to monthly (molpopgen)
+ - [
4eb407ac61] Merge pull request #31 from molpopgen/dependabot/add-v2-config-file (Kevin R. Thornton)
+ - [
a759e0441b] Merge pull request #32 from molpopgen/dependabot/cargo/bindgen-0.57.0 (dependabot-preview[bot])
+ - [
fb2a56c868] Update bindgen requirement from 0.56.0 to 0.57.0 (dependabot-preview[bot])
+ - [
a8a0b1aabf] Create Dependabot config file (dependabot-preview[bot])
+
2021-03-26, Version 0.1.1
+Commits
+-
+
- [
e9d73e4912] Fix crate name in README.md (molpopogen)
+ - [
28deef7d04] update README (molpopogen)
+ - [
ef79a446c1] Bump version to 0.1.1 (molpopogen)
+ - [
d3c31fa0fc] Merge pull request #30 from molpopgen/fix_warnings (Kevin R. Thornton)
+ - [
bedfa02f76] Merge pull request #29 from molpopgen/metadata_docs (Kevin R. Thornton)
+ - [
f6f3304d75] Remove Drop constraint on TskitType. (molpopogen)
+ - [
d8873a7941] Quick fix regarding documenting metadata. Closes #25 (molpopogen)
+ - [
4518db4946] Merge pull request #28 from molpopgen/update_to_tskit_0_3_5 (Kevin R. Thornton)
+ - [
80893566ed] Update C files to tskit 0.3.5 (molpopogen)
+ - [
e81aad0bf6] Merge pull request #27 from molpopgen/fix_example_file_names (Kevin R. Thornton)
+ - [
dbaf304b38] Fix swapped example file names. Fixes #26 (molpopogen)
+ - [
30c34c2023] Merge pull request #23 from molpopgen/rename_crate (Kevin R. Thornton)
+ - [
e01b3e530e] rename crate to tskit (molpopgen)
+ - [
a7a69ad31d] Merge pull request #20 from molpopgen/metadata (Kevin R. Thornton)
+ - [
54ac4312a1] clippy and fmt (molpopgen)
+ - [
a1aea5cd95] add examples of metadata round trips (molpopgen)
+ - [
7352ca95b5] Update table operations to metadata API. (molpopgen)
+ - [
275074da30] Add metadata trait and API. (molpopgen)
+ - [
d89dcd19dd] Merge pull request #18 from molpopgen/tskit_wrapper_trait (Kevin R. Thornton)
+ - [
3445af368d] TableCollection uses new trait. (molpopgen)
+ - [
93c43aa2c7] Add trait to define what it means to wrap a tskit type. (molpopgen)
+
+
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diff --git a/examples.html b/examples.html
new file mode 100644
index 000000000..d7b270c4c
--- /dev/null
+++ b/examples.html
@@ -0,0 +1,228 @@
+
+
+
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+
+ Error handling
+
+
+
+
+ Error handling
+The error type is tskit::error::TskitError.
This type implements Display and may thus be printed via:
let x = match operation() {
+ Ok(y) => y,
+ Err(e) => panic("{}", e);
+};The enum variant TskitError::ErrorCode represents integer return values from tskit-c.
+When printed via Display, the detailed error message is fetched.
+When printed via Debug, the numerical error code is shown.
+
+
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diff --git a/examples/bincode_metadata.rs b/examples/bincode_metadata.rs
deleted file mode 100644
index 470211ed0..000000000
--- a/examples/bincode_metadata.rs
+++ /dev/null
@@ -1,51 +0,0 @@
-#[derive(serde::Serialize, serde::Deserialize, tskit::metadata::MutationMetadata)]
-#[serializer("bincode")]
-struct MutationMetadata {
- effect_size: f64,
- dominance: f64,
-}
-
-#[derive(serde::Serialize, serde::Deserialize, tskit::metadata::IndividualMetadata)]
-#[serializer("bincode")]
-struct IndividualMetadata {
- name: String,
- phenotypes: Vec
+
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+
+ Example programs
+
+
+
+
+
+ Example programs
+
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diff --git a/favicon.png b/favicon.png
new file mode 100644
index 000000000..a5b1aa16c
Binary files /dev/null and b/favicon.png differ
diff --git a/favicon.svg b/favicon.svg
new file mode 100644
index 000000000..90e0ea58b
--- /dev/null
+++ b/favicon.svg
@@ -0,0 +1,22 @@
+
+
diff --git a/fonts/OPEN-SANS-LICENSE.txt b/fonts/OPEN-SANS-LICENSE.txt
new file mode 100644
index 000000000..d64569567
--- /dev/null
+++ b/fonts/OPEN-SANS-LICENSE.txt
@@ -0,0 +1,202 @@
+
+ Apache License
+ Version 2.0, January 2004
+ http://www.apache.org/licenses/
+
+ TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
+ 1. Definitions.
+
+ "License" shall mean the terms and conditions for use, reproduction,
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+ 5. Submission of Contributions. Unless You explicitly state otherwise,
+ any Contribution intentionally submitted for inclusion in the Work
+ by You to the Licensor shall be under the terms and conditions of
+ this License, without any additional terms or conditions.
+ Notwithstanding the above, nothing herein shall supersede or modify
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+ 7. Disclaimer of Warranty. Unless required by applicable law or
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+ Contributor provides its Contributions) on an "AS IS" BASIS,
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+ whether in tort (including negligence), contract, or otherwise,
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+ on Your own behalf and on Your sole responsibility, not on behalf
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+ boilerplate notice, with the fields enclosed by brackets "[]"
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+ Unless required by applicable law or agreed to in writing, software
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+ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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diff --git a/fonts/SOURCE-CODE-PRO-LICENSE.txt b/fonts/SOURCE-CODE-PRO-LICENSE.txt
new file mode 100644
index 000000000..366206f54
--- /dev/null
+++ b/fonts/SOURCE-CODE-PRO-LICENSE.txt
@@ -0,0 +1,93 @@
+Copyright 2010, 2012 Adobe Systems Incorporated (http://www.adobe.com/), with Reserved Font Name 'Source'. All Rights Reserved. Source is a trademark of Adobe Systems Incorporated in the United States and/or other countries.
+
+This Font Software is licensed under the SIL Open Font License, Version 1.1.
+This license is copied below, and is also available with a FAQ at:
+http://scripts.sil.org/OFL
+
+
+-----------------------------------------------------------
+SIL OPEN FONT LICENSE Version 1.1 - 26 February 2007
+-----------------------------------------------------------
+
+PREAMBLE
+The goals of the Open Font License (OFL) are to stimulate worldwide
+development of collaborative font projects, to support the font creation
+efforts of academic and linguistic communities, and to provide a free and
+open framework in which fonts may be shared and improved in partnership
+with others.
+
+The OFL allows the licensed fonts to be used, studied, modified and
+redistributed freely as long as they are not sold by themselves. The
+fonts, including any derivative works, can be bundled, embedded,
+redistributed and/or sold with any software provided that any reserved
+names are not used by derivative works. The fonts and derivatives,
+however, cannot be released under any other type of license. The
+requirement for fonts to remain under this license does not apply
+to any document created using the fonts or their derivatives.
+
+DEFINITIONS
+"Font Software" refers to the set of files released by the Copyright
+Holder(s) under this license and clearly marked as such. This may
+include source files, build scripts and documentation.
+
+"Reserved Font Name" refers to any names specified as such after the
+copyright statement(s).
+
+"Original Version" refers to the collection of Font Software components as
+distributed by the Copyright Holder(s).
+
+"Modified Version" refers to any derivative made by adding to, deleting,
+or substituting -- in part or in whole -- any of the components of the
+Original Version, by changing formats or by porting the Font Software to a
+new environment.
+
+"Author" refers to any designer, engineer, programmer, technical
+writer or other person who contributed to the Font Software.
+
+PERMISSION & CONDITIONS
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of the Font Software, to use, study, copy, merge, embed, modify,
+redistribute, and sell modified and unmodified copies of the Font
+Software, subject to the following conditions:
+
+1) Neither the Font Software nor any of its individual components,
+in Original or Modified Versions, may be sold by itself.
+
+2) Original or Modified Versions of the Font Software may be bundled,
+redistributed and/or sold with any software, provided that each copy
+contains the above copyright notice and this license. These can be
+included either as stand-alone text files, human-readable headers or
+in the appropriate machine-readable metadata fields within text or
+binary files as long as those fields can be easily viewed by the user.
+
+3) No Modified Version of the Font Software may use the Reserved Font
+Name(s) unless explicit written permission is granted by the corresponding
+Copyright Holder. This restriction only applies to the primary font name as
+presented to the users.
+
+4) The name(s) of the Copyright Holder(s) or the Author(s) of the Font
+Software shall not be used to promote, endorse or advertise any
+Modified Version, except to acknowledge the contribution(s) of the
+Copyright Holder(s) and the Author(s) or with their explicit written
+permission.
+
+5) The Font Software, modified or unmodified, in part or in whole,
+must be distributed entirely under this license, and must not be
+distributed under any other license. The requirement for fonts to
+remain under this license does not apply to any document created
+using the Font Software.
+
+TERMINATION
+This license becomes null and void if any of the above conditions are
+not met.
+
+DISCLAIMER
+THE FONT SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO ANY WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT
+OF COPYRIGHT, PATENT, TRADEMARK, OR OTHER RIGHT. IN NO EVENT SHALL THE
+COPYRIGHT HOLDER BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+INCLUDING ANY GENERAL, SPECIAL, INDIRECT, INCIDENTAL, OR CONSEQUENTIAL
+DAMAGES, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF THE USE OR INABILITY TO USE THE FONT SOFTWARE OR FROM
+OTHER DEALINGS IN THE FONT SOFTWARE.
diff --git a/fonts/fonts.css b/fonts/fonts.css
new file mode 100644
index 000000000..858efa598
--- /dev/null
+++ b/fonts/fonts.css
@@ -0,0 +1,100 @@
+/* Open Sans is licensed under the Apache License, Version 2.0. See http://www.apache.org/licenses/LICENSE-2.0 */
+/* Source Code Pro is under the Open Font License. See https://scripts.sil.org/cms/scripts/page.php?site_id=nrsi&id=OFL */
+
+/* open-sans-300 - latin_vietnamese_latin-ext_greek-ext_greek_cyrillic-ext_cyrillic */
+@font-face {
+ font-family: 'Open Sans';
+ font-style: normal;
+ font-weight: 300;
+ src: local('Open Sans Light'), local('OpenSans-Light'),
+ url('open-sans-v17-all-charsets-300.woff2') format('woff2');
+}
+
+/* open-sans-300italic - latin_vietnamese_latin-ext_greek-ext_greek_cyrillic-ext_cyrillic */
+@font-face {
+ font-family: 'Open Sans';
+ font-style: italic;
+ font-weight: 300;
+ src: local('Open Sans Light Italic'), local('OpenSans-LightItalic'),
+ url('open-sans-v17-all-charsets-300italic.woff2') format('woff2');
+}
+
+/* open-sans-regular - latin_vietnamese_latin-ext_greek-ext_greek_cyrillic-ext_cyrillic */
+@font-face {
+ font-family: 'Open Sans';
+ font-style: normal;
+ font-weight: 400;
+ src: local('Open Sans Regular'), local('OpenSans-Regular'),
+ url('open-sans-v17-all-charsets-regular.woff2') format('woff2');
+}
+
+/* open-sans-italic - latin_vietnamese_latin-ext_greek-ext_greek_cyrillic-ext_cyrillic */
+@font-face {
+ font-family: 'Open Sans';
+ font-style: italic;
+ font-weight: 400;
+ src: local('Open Sans Italic'), local('OpenSans-Italic'),
+ url('open-sans-v17-all-charsets-italic.woff2') format('woff2');
+}
+
+/* open-sans-600 - latin_vietnamese_latin-ext_greek-ext_greek_cyrillic-ext_cyrillic */
+@font-face {
+ font-family: 'Open Sans';
+ font-style: normal;
+ font-weight: 600;
+ src: local('Open Sans SemiBold'), local('OpenSans-SemiBold'),
+ url('open-sans-v17-all-charsets-600.woff2') format('woff2');
+}
+
+/* open-sans-600italic - latin_vietnamese_latin-ext_greek-ext_greek_cyrillic-ext_cyrillic */
+@font-face {
+ font-family: 'Open Sans';
+ font-style: italic;
+ font-weight: 600;
+ src: local('Open Sans SemiBold Italic'), local('OpenSans-SemiBoldItalic'),
+ url('open-sans-v17-all-charsets-600italic.woff2') format('woff2');
+}
+
+/* open-sans-700 - latin_vietnamese_latin-ext_greek-ext_greek_cyrillic-ext_cyrillic */
+@font-face {
+ font-family: 'Open Sans';
+ font-style: normal;
+ font-weight: 700;
+ src: local('Open Sans Bold'), local('OpenSans-Bold'),
+ url('open-sans-v17-all-charsets-700.woff2') format('woff2');
+}
+
+/* open-sans-700italic - latin_vietnamese_latin-ext_greek-ext_greek_cyrillic-ext_cyrillic */
+@font-face {
+ font-family: 'Open Sans';
+ font-style: italic;
+ font-weight: 700;
+ src: local('Open Sans Bold Italic'), local('OpenSans-BoldItalic'),
+ url('open-sans-v17-all-charsets-700italic.woff2') format('woff2');
+}
+
+/* open-sans-800 - latin_vietnamese_latin-ext_greek-ext_greek_cyrillic-ext_cyrillic */
+@font-face {
+ font-family: 'Open Sans';
+ font-style: normal;
+ font-weight: 800;
+ src: local('Open Sans ExtraBold'), local('OpenSans-ExtraBold'),
+ url('open-sans-v17-all-charsets-800.woff2') format('woff2');
+}
+
+/* open-sans-800italic - latin_vietnamese_latin-ext_greek-ext_greek_cyrillic-ext_cyrillic */
+@font-face {
+ font-family: 'Open Sans';
+ font-style: italic;
+ font-weight: 800;
+ src: local('Open Sans ExtraBold Italic'), local('OpenSans-ExtraBoldItalic'),
+ url('open-sans-v17-all-charsets-800italic.woff2') format('woff2');
+}
+
+/* source-code-pro-500 - latin_vietnamese_latin-ext_greek_cyrillic-ext_cyrillic */
+@font-face {
+ font-family: 'Source Code Pro';
+ font-style: normal;
+ font-weight: 500;
+ src: url('source-code-pro-v11-all-charsets-500.woff2') format('woff2');
+}
diff --git a/fonts/open-sans-v17-all-charsets-300.woff2 b/fonts/open-sans-v17-all-charsets-300.woff2
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diff --git a/fonts/open-sans-v17-all-charsets-800.woff2 b/fonts/open-sans-v17-all-charsets-800.woff2
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diff --git a/fonts/open-sans-v17-all-charsets-italic.woff2 b/fonts/open-sans-v17-all-charsets-italic.woff2
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diff --git a/fonts/open-sans-v17-all-charsets-regular.woff2 b/fonts/open-sans-v17-all-charsets-regular.woff2
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diff --git a/fonts/source-code-pro-v11-all-charsets-500.woff2 b/fonts/source-code-pro-v11-all-charsets-500.woff2
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diff --git a/highlight.css b/highlight.css
new file mode 100644
index 000000000..ba57b82b2
--- /dev/null
+++ b/highlight.css
@@ -0,0 +1,82 @@
+/*
+ * An increased contrast highlighting scheme loosely based on the
+ * "Base16 Atelier Dune Light" theme by Bram de Haan
+ * (http://atelierbram.github.io/syntax-highlighting/atelier-schemes/dune)
+ * Original Base16 color scheme by Chris Kempson
+ * (https://github.com/chriskempson/base16)
+ */
+
+/* Comment */
+.hljs-comment,
+.hljs-quote {
+ color: #575757;
+}
+
+/* Red */
+.hljs-variable,
+.hljs-template-variable,
+.hljs-attribute,
+.hljs-tag,
+.hljs-name,
+.hljs-regexp,
+.hljs-link,
+.hljs-name,
+.hljs-selector-id,
+.hljs-selector-class {
+ color: #d70025;
+}
+
+/* Orange */
+.hljs-number,
+.hljs-meta,
+.hljs-built_in,
+.hljs-builtin-name,
+.hljs-literal,
+.hljs-type,
+.hljs-params {
+ color: #b21e00;
+}
+
+/* Green */
+.hljs-string,
+.hljs-symbol,
+.hljs-bullet {
+ color: #008200;
+}
+
+/* Blue */
+.hljs-title,
+.hljs-section {
+ color: #0030f2;
+}
+
+/* Purple */
+.hljs-keyword,
+.hljs-selector-tag {
+ color: #9d00ec;
+}
+
+.hljs {
+ display: block;
+ overflow-x: auto;
+ background: #f6f7f6;
+ color: #000;
+}
+
+.hljs-emphasis {
+ font-style: italic;
+}
+
+.hljs-strong {
+ font-weight: bold;
+}
+
+.hljs-addition {
+ color: #22863a;
+ background-color: #f0fff4;
+}
+
+.hljs-deletion {
+ color: #b31d28;
+ background-color: #ffeef0;
+}
diff --git a/highlight.js b/highlight.js
new file mode 100644
index 000000000..3256c00ed
--- /dev/null
+++ b/highlight.js
@@ -0,0 +1,53 @@
+/*
+ Highlight.js 10.1.1 (93fd0d73)
+ License: BSD-3-Clause
+ Copyright (c) 2006-2020, Ivan Sagalaev
+*/
+var hljs=function(){"use strict";function e(n){Object.freeze(n);var t="function"==typeof n;return Object.getOwnPropertyNames(n).forEach((function(r){!Object.hasOwnProperty.call(n,r)||null===n[r]||"object"!=typeof n[r]&&"function"!=typeof n[r]||t&&("caller"===r||"callee"===r||"arguments"===r)||Object.isFrozen(n[r])||e(n[r])})),n}class n{constructor(e){void 0===e.data&&(e.data={}),this.data=e.data}ignoreMatch(){this.ignore=!0}}function t(e){return e.replace(/&/g,"&").replace(//g,">").replace(/"/g,""").replace(/'/g,"'")}function r(e,...n){var t={};for(const n in e)t[n]=e[n];return n.forEach((function(e){for(const n in e)t[n]=e[n]})),t}function a(e){return e.nodeName.toLowerCase()}var i=Object.freeze({__proto__:null,escapeHTML:t,inherit:r,nodeStream:function(e){var n=[];return function e(t,r){for(var i=t.firstChild;i;i=i.nextSibling)3===i.nodeType?r+=i.nodeValue.length:1===i.nodeType&&(n.push({event:"start",offset:r,node:i}),r=e(i,r),a(i).match(/br|hr|img|input/)||n.push({event:"stop",offset:r,node:i}));return r}(e,0),n},mergeStreams:function(e,n,r){var i=0,s="",o=[];function l(){return e.length&&n.length?e[0].offset!==n[0].offset?e[0].offset
+
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+
+
+ Haploid Wright-Fisher simulation
+The following code simulates a haploid Wright-Fisher model.
+The code is a reimplementation of an example program distributed with tskit-c.
In addition to tskit, the example uses:
fn simulate(
+ seed: u64,
+ popsize: usize,
+ num_generations: i32,
+ simplify_interval: i32,
+ update_bookmark: bool,
+) -> Result<tskit::TreeSequence> {
+ if popsize == 0 {
+ return Err(anyhow::Error::msg("popsize must be > 0"));
+ }
+ if num_generations == 0 {
+ return Err(anyhow::Error::msg("num_generations must be > 0"));
+ }
+ if simplify_interval == 0 {
+ return Err(anyhow::Error::msg("simplify_interval must be > 0"));
+ }
+ let mut tables = tskit::TableCollection::new(1.0)?;
+
+ // create parental nodes
+ let mut parents_and_children = {
+ let mut temp = vec![];
+ let parental_time = f64::from(num_generations);
+ for _ in 0..popsize {
+ let node = tables.add_node(0, parental_time, -1, -1)?;
+ temp.push(node);
+ }
+ temp
+ };
+
+ // allocate space for offspring nodes
+ parents_and_children.resize(2 * parents_and_children.len(), tskit::NodeId::NULL);
+
+ // Construct non-overlapping mutable slices into our vector.
+ let (mut parents, mut children) = parents_and_children.split_at_mut(popsize);
+
+ let parent_picker = rand::distributions::Uniform::new(0, popsize);
+ let breakpoint_generator = rand::distributions::Uniform::new(0.0, 1.0);
+ let mut rng = rand::rngs::StdRng::seed_from_u64(seed);
+ let mut bookmark = tskit::types::Bookmark::default();
+
+ for birth_time in (0..num_generations).rev() {
+ for c in children.iter_mut() {
+ let bt = f64::from(birth_time);
+ let child = tables.add_node(0, bt, -1, -1)?;
+ let left_parent = parents
+ .get(parent_picker.sample(&mut rng))
+ .ok_or_else(|| anyhow::Error::msg("invalid left_parent index"))?;
+ let right_parent = parents
+ .get(parent_picker.sample(&mut rng))
+ .ok_or_else(|| anyhow::Error::msg("invalid right_parent index"))?;
+ let breakpoint = breakpoint_generator.sample(&mut rng);
+ tables.add_edge(0., breakpoint, *left_parent, child)?;
+ tables.add_edge(breakpoint, 1.0, *right_parent, child)?;
+ *c = child;
+ }
+
+ if birth_time % simplify_interval == 0 {
+ tables.sort(&bookmark, tskit::TableSortOptions::default())?;
+ if update_bookmark {
+ rotate_edges(&bookmark, &mut tables);
+ }
+ if let Some(idmap) =
+ tables.simplify(children, tskit::SimplificationOptions::default(), true)?
+ {
+ // remap child nodes
+ for o in children.iter_mut() {
+ *o = idmap[usize::try_from(*o)?];
+ }
+ }
+ if update_bookmark {
+ bookmark.set_edges(tables.edges().num_rows());
+ }
+ }
+ std::mem::swap(&mut parents, &mut children);
+ }
+
+ tables.build_index()?;
+ let treeseq = tables.tree_sequence(tskit::TreeSequenceFlags::default())?;
+
+ Ok(treeseq)
+}":e:f.tabReplace?e.replace(/\t/g,f.tabReplace):e):e}function E(e){let n=null;const t=function(e){var n=e.className+" ";n+=e.parentNode?e.parentNode.className:"";const t=f.languageDetectRe.exec(n);if(t){var r=T(t[1]);return r||(console.warn(g.replace("{}",t[1])),console.warn("Falling back to no-highlight mode for this block.",e)),r?t[1]:"no-highlight"}return n.split(/\s+/).find(e=>p(e)||T(e))}(e);if(p(t))return;S("before:highlightBlock",{block:e,language:t}),f.useBR?(n=document.createElement("div")).innerHTML=e.innerHTML.replace(/\n/g,"").replace(/
+
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diff --git a/introduction.html b/introduction.html
new file mode 100644
index 000000000..446d90f0f
--- /dev/null
+++ b/introduction.html
@@ -0,0 +1,276 @@
+
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+
+
+
+
+ Introduction
+Do you need
+What does
+What is
+Adding
+
+
+
+
+ Introduction
+Required background.
+-
+
- We assume familiarity with
tskit. See tskit.dev.
+ - Comfort with rust is required.
+
-
+
- The book is a good place to start. +
- The Rustonomicon is for those who wish to dig deeper into
unsaferust and FFI. +The 'nomicon is helpful for understanding how things like thetskitrust API can be built in the first place.
+
+
Conventions used in this document
+Here, tskit means the rust API.
+tskit-c and tskit-python refer to the C and Python APIs, respectively.
The phrase "data model" refers to this. This document will make little sense without an understanding of the data model.
+Relation to the C API
+Where necessary, we will note differences from the behavior of tskit-c.
Much of the rust API works by calling the C API. +We do not change the semantics of the C API. +However, we do make stricter statements about the ownership relationships between types. +For example, the C API can result in the following situation:
+-
+
- A heap-allocated table collection is used to record data about the ancestry of a sample. +
- That table collection is used to initialize a tree sequence. +The tree sequence is told to take ownership of the tables. +
This is a case where the C API requires that you respectfully no longer work with the heap-allocated table collection. To do so is undefined behavior.
+The rust API forbids such situations. +The creation of a tree sequence from tables consumes the tables via a move operation. +Thus, any further actions on the tables is a compiler error.
+This example is the kinds of differences between tskit and tskit-c.
+Undefined behavior is (close to) impossible with tskit.
Quick overview
+Do you need tskit-rust?
+The use-cases for tskit-rust are the same as for tskit-c:
-
+
- Developing a new performance-oriented application. +
- The input/output of this application will be a
.treesfile.
+
What does tskit-rust add?
+Briefly, you get the performance of C and the strong safety guarantees of rust.
What is tskit-rust missing?
+The crate does not cover the entire C API.
+However, client code can make direct calls to that API via the module tskit::bindings.
Adding tskit as a dependency to a rust project
+In your Cargo.toml:
[dependencies]
+tskit = "~X.Y.Z"
+The latest version to fill in X.Y.Z can be found here.
+See here for how to specify version numbers.
Feature flags.
+tskit defines several cargo features.
+These are defined in the API docs.
+
+
+
+
+
+
+
+
+
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diff --git a/mark.min.js b/mark.min.js
new file mode 100644
index 000000000..163623188
--- /dev/null
+++ b/mark.min.js
@@ -0,0 +1,7 @@
+/*!***************************************************
+* mark.js v8.11.1
+* https://markjs.io/
+* Copyright (c) 2014–2018, Julian Kühnel
+* Released under the MIT license https://git.io/vwTVl
+*****************************************************/
+!function(e,t){"object"==typeof exports&&"undefined"!=typeof module?module.exports=t():"function"==typeof define&&define.amd?define(t):e.Mark=t()}(this,function(){"use strict";var e="function"==typeof Symbol&&"symbol"==typeof Symbol.iterator?function(e){return typeof e}:function(e){return e&&"function"==typeof Symbol&&e.constructor===Symbol&&e!==Symbol.prototype?"symbol":typeof e},t=function(e,t){if(!(e instanceof t))throw new TypeError("Cannot call a class as a function")},n=function(){function e(e,t){for(var n=0;n
+
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+
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+
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+
+
+
+
+
+
+
+
+
+
+
+ Introduction
+Do you need
+What does
+What is
+Adding
+
+
+
+
+ Introduction
+Required background.
+-
+
- We assume familiarity with
tskit. See tskit.dev.
+ - Comfort with rust is required.
+
-
+
- The book is a good place to start. +
- The Rustonomicon is for those who wish to dig deeper into
unsaferust and FFI. +The 'nomicon is helpful for understanding how things like thetskitrust API can be built in the first place.
+
+
Conventions used in this document
+Here, tskit means the rust API.
+tskit-c and tskit-python refer to the C and Python APIs, respectively.
The phrase "data model" refers to this. This document will make little sense without an understanding of the data model.
+Relation to the C API
+Where necessary, we will note differences from the behavior of tskit-c.
Much of the rust API works by calling the C API. +We do not change the semantics of the C API. +However, we do make stricter statements about the ownership relationships between types. +For example, the C API can result in the following situation:
+-
+
- A heap-allocated table collection is used to record data about the ancestry of a sample. +
- That table collection is used to initialize a tree sequence. +The tree sequence is told to take ownership of the tables. +
This is a case where the C API requires that you respectfully no longer work with the heap-allocated table collection. To do so is undefined behavior.
+The rust API forbids such situations. +The creation of a tree sequence from tables consumes the tables via a move operation. +Thus, any further actions on the tables is a compiler error.
+This example is the kinds of differences between tskit and tskit-c.
+Undefined behavior is (close to) impossible with tskit.
Quick overview
+Do you need tskit-rust?
+The use-cases for tskit-rust are the same as for tskit-c:
-
+
- Developing a new performance-oriented application. +
- The input/output of this application will be a
.treesfile.
+
What does tskit-rust add?
+Briefly, you get the performance of C and the strong safety guarantees of rust.
What is tskit-rust missing?
+The crate does not cover the entire C API.
+However, client code can make direct calls to that API via the module tskit::bindings.
Adding tskit as a dependency to a rust project
+In your Cargo.toml:
[dependencies]
+tskit = "~X.Y.Z"
+The latest version to fill in X.Y.Z can be found here.
+See here for how to specify version numbers.
Feature flags.
+tskit defines several cargo features.
+These are defined in the API docs.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
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diff --git a/metadata_advanced.html b/metadata_advanced.html
new file mode 100644
index 000000000..0ee227c3a
--- /dev/null
+++ b/metadata_advanced.html
@@ -0,0 +1,259 @@
+
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+ Metadata
+
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+
+ Metadata
+Tables may contain additional information about rows that is not part of the data model. +This metadata is optional. +Tables are not required to have metadata. +Tables with metadata do not require that every row has metadata.
+The next sections showcase the metadata API.
+ +
+
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diff --git a/metadata_derive.html b/metadata_derive.html
new file mode 100644
index 000000000..648018f00
--- /dev/null
+++ b/metadata_derive.html
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+
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+ Advanced topics
+Bulk decoding of metadata
+To populate a Vec with decoded metadata and accounting
+for some rows not having metadata:
-
+
- Realize that the decode methods of the
MetadataRoundtriptrait are associated functions.
+ - We can use a lending iterator over rows to avoid unnecessary copying. +
Therefore:
+ let mut mutation_row_lending_iterator = tables.mutations().lending_iter();
+ let mut decoded_md = vec![];
+ while let Some(row_view) = mutation_row_lending_iterator.next() {
+ match row_view.metadata {
+ Some(slice) => decoded_md.push(Some(MutationMetadata::decode(slice).unwrap())),
+ None => decoded_md.push(None),
+ }
+ }To filter out rows without metadata:
+ let mut mutation_row_lending_iterator = tables.mutations().lending_iter();
+ let mut decoded_md = vec![];
+ while let Some(row_view) = mutation_row_lending_iterator
+ .next()
+ .filter(|rv| rv.metadata.is_some())
+ {
+ decoded_md.push((
+ row_view.id,
+ // The unwrap will never panic because of our filter
+ MutationMetadata::decode(row_view.metadata.unwrap()).unwrap(),
+ ));
+ }The first method gives Vec<Option<MutationMetadata>>.
+The second gives Vec<(MutationId, MutationMetadata)>.
+
+
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diff --git a/metadata_schema.html b/metadata_schema.html
new file mode 100644
index 000000000..32d523d18
--- /dev/null
+++ b/metadata_schema.html
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+
+ Defining metadata types in rust
+A key feature of the API is that metadata is specified on a per-table basis.
+In other words, a type to be used as node metadata implements the tskit::metadata::NodeMetadata trait.
Using the tskit cargo feature derive, we can use procedural macros to define metadata types.
+Here, we define a metadata type for a mutation table:
#[derive(serde::Serialize, serde::Deserialize, tskit::metadata::MutationMetadata)]
+ #[serializer("serde_json")]
+ struct MutationMetadata {
+ effect_size: f64,
+ dominance: f64,
+ }We require that you also manually specify the serde derive macros because the metadata API
+itself does not depend on serde.
+Rather, it expects raw bytes and serde happens to be a good way to get them from your data types.
The derive macro also enforces some helpful behavior at compile time. +You will get a compile-time error if you try to derive two different metadata types for the same rust type. +The error is due to conflicting implementations for a supertrait.
+ +
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diff --git a/metadata_tables.html b/metadata_tables.html
new file mode 100644
index 000000000..d9d558e2b
--- /dev/null
+++ b/metadata_tables.html
@@ -0,0 +1,304 @@
+
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+
+
+ Metadata schema
+For useful data interchange with tskit-python, we need to define metadata schema.
There are currently several points slowing down a rust API for schema:
+-
+
- It is not clear which
serdeformats are compatible with metadata on the Python side.
+ - Experiments have shown that
serde_jsonworks withtskit-python. +-
+
- Ideally, we would also like a binary format compatible with the Python
struct+module.
+
+ - Ideally, we would also like a binary format compatible with the Python
- However, we have not found a solution eliminating the need to manually write the
+schema as a string and add it to the tables.
+Various crates to generate JSON schema from rust structs return schema that are over-specified
+and fail to validate in
tskit-python.
+ - We also have the problem that we will need to add some Python to our CI to prove to ourselves +that some reasonable tests can pass. +
+
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diff --git a/migration_guide.html b/migration_guide.html
new file mode 100644
index 000000000..737a6600d
--- /dev/null
+++ b/migration_guide.html
@@ -0,0 +1,291 @@
+
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+
+ Metadata and tables
+Let us create a table and add a row with our mutation metadata:
+ let mut tables = tskit::TableCollection::new(50.0).unwrap();
+
+ let md = MutationMetadata {
+ effect_size: 1e-3,
+ dominance: 1.0,
+ };
+
+ let mut_id_0 = tables
+ .add_mutation_with_metadata(
+ 0, // site id
+ 0, // node id
+ -1, // mutation parent id
+ 0.0, // time
+ None, // derived state is Option<&[u8]>
+ &md, // metadata for this row
+ )
+ .unwrap();Meta data is optional on a per-row basis:
+ let mut_id_1 = tables
+ .add_mutation(
+ 0, // site id
+ 0, // node id
+ -1, // mutation parent id
+ 0.0, // time
+ None, // derived state is Option<&[u8]>
+ )
+ .unwrap();We can confirm that we have one row with, and one without, metadata:
+ assert_eq!(
+ tables
+ .mutations_iter()
+ .filter(|m| m.metadata.is_some())
+ .count(),
+ 1
+ );
+ assert_eq!(
+ tables
+ .mutations_iter()
+ .filter(|m| m.metadata.is_none())
+ .count(),
+ 1
+ );Fetching our metadata from the table requires specifying the metadata type.
+The result of a metadata retrieval is Option<Result, TskitError>.
+The None variant occurs if a row does not have metadata or if a row id does not exist.
+The error state occurs if decoding raw bytes into the metadata type fails.
+The details of the error variant are here.
+The reason why the error type holds Box<dyn Error> is that the API is very general.
+We assume nothing about the API used to encode/decode metadata.
+Therefore, the error could be anything.
let fetched_md = match tables.mutations().metadata::<MutationMetadata>(mut_id_0) {
+ Some(Ok(m)) => m,
+ Some(Err(e)) => panic!("metadata decoding failed: {:?}", e),
+ None => panic!(
+ "hmmm...row {} should have been a valid row with metadata...",
+ mut_id_0
+ ),
+ };
+
+ assert_eq!(md.effect_size, fetched_md.effect_size);
+ assert_eq!(md.dominance, fetched_md.dominance); // There is no metadata at row 1, so
+ // you get None back
+ assert!(tables
+ .mutations()
+ .metadata::<MutationMetadata>(mut_id_1)
+ .is_none());
+
+ // There is also no metadata at row 2,
+ // because that row does not exist, so
+ // you get None back
+ assert!(tables
+ .mutations()
+ .metadata::<MutationMetadata>(2.into())
+ .is_none());
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/prelude.html b/prelude.html
new file mode 100644
index 000000000..469e21fcc
--- /dev/null
+++ b/prelude.html
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+
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+ Migration guide
+This document helps with migration to newer versions of tskit-rust.
+This document will not be exhaustive.
+Rather, it will focus on highlights or "must know" items.
Regarding breaking changes:
+-
+
- This document will discuss breaking changes requiring change in client code. +
- Other changes listed in the change log as breaking are considered "technically breaking +but unlikely to affect anyone in practice". Please file an issue if we are wrong! +
Acronyms used:
+-
+
- UB = undefined behavior. +
v0.12.0
+Breaking changes
+-
+
- Provenance table getters now return
Option<&str>rather thanOption<String>. +These two types are very close to identical in API. +Breakage is only possible if code relied on the return value owning its data.
+ - Several member functions of Tree previously accepted
NodeIdas arguments. +They now takeN: Into<NodeId> + Copy. +Thus, code passing in integers will have to drop the.into()calls.
+ - Tree functions returning iterators previously returned
Option<Iterator<...>>. +They now returnIterator<...>. +Data leading toNonebeing returned in previous versions now return an iterator +that will end immediately.
+ DereftoTableViewswas replaced with delegation because usingDeref+to model inheritance is an anti-pattern.
+usizetoSizeTypeconversions are now fallible (e.g.,TryFromreplacesFrom).
+- The
TskitTypeAccesstrait was removed because it was a bad idea. +(It makes no sense to be generic over returning pointers to low-level tskit types.) +The functionality is replaced withimpl fns.
+ - The names of all
Ownedtables are nowOwning.
+ MetadataError::RoundtripErrornow requiresSend + Sync.
+
v0.11.0
+Bug fixes
+-
+
- Issue 363, which was introduced in PR 300. +The bug resulted in UB when advancing trees for release builds. +
Breaking changes
+New error variant.
+The error enum now includes LibraryError.
+Any code previously matching on errors will now break because the match is no longer exhaustive.
Row getters
+This change occurred over several PR.
+All "getter" functions for table rows now return Option instead of Result when a row index is out of bounds.
+These functions now return None for the out of bounds case.
+This behavior change brings the API in line with other rust APIs.
To update:
+-
+
- If
Noneshould represent an error for your use case, useOption::ok_or_else. +In the case of a previousResult<Option<_>, _>that is now anOption<Result<_, _>>, usetranspose.
+
Lifetime annotations of table types
+PR #373.
+Previously, a non-owning view of an edge table had a type EdgeTable<'a>.
+Those lifetimes are no longer necessary, which is a big design win.
Two traits, TableAccess and NodeListRowGenerator, have been removed.
+The TableCollection and TreeSequence types now contain that functionality as
+Deref targets.
Removing these traits implies:
+-
+
- Their removal from the crate prelude. +
- They can no longer be used as trait bounds. +
Some views of a node table that required mutability broke due to these changes.
+A new function in the Deref target is nodes_mut(&mut self) addresses this breakage.
+
+
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diff --git a/print.html b/print.html
new file mode 100644
index 000000000..e8c581f58
--- /dev/null
+++ b/print.html
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+
+ The
+
+
+
+
+ The tskit prelude
+The contents of the crate prelude are:
+//! Export commonly-use types and traits
+
+pub use streaming_iterator::DoubleEndedStreamingIterator;
+pub use streaming_iterator::StreamingIterator;
+pub use {
+ crate::EdgeId, crate::IndividualId, crate::Location, crate::MigrationId, crate::MutationId,
+ crate::NodeId, crate::PopulationId, crate::Position, crate::RawFlags, crate::SiteId,
+ crate::SizeType, crate::Time,
+};
+
+
+
+
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diff --git a/python/requirements.txt b/python/requirements.txt
deleted file mode 100644
index 7e2b5fe14..000000000
--- a/python/requirements.txt
+++ /dev/null
@@ -1,3 +0,0 @@
-tskit>=0.6.3
-pytest
-maturin
diff --git a/python/requirements_locked_3_13.txt b/python/requirements_locked_3_13.txt
deleted file mode 100644
index a464c4786..000000000
--- a/python/requirements_locked_3_13.txt
+++ /dev/null
@@ -1,32 +0,0 @@
-# This file was autogenerated by uv via the following command:
-# uv pip compile -p 3.13 requirements.txt
-attrs==25.3.0
- # via
- # jsonschema
- # referencing
-iniconfig==2.1.0
- # via pytest
-jsonschema==4.23.0
- # via tskit
-jsonschema-specifications==2025.4.1
- # via jsonschema
-maturin==1.8.6
- # via -r requirements.txt
-numpy==2.2.5
- # via tskit
-packaging==25.0
- # via pytest
-pluggy==1.6.0
- # via pytest
-pytest==8.3.5
- # via -r requirements.txt
-referencing==0.36.2
- # via
- # jsonschema
- # jsonschema-specifications
-rpds-py==0.25.0
- # via
- # jsonschema
- # referencing
-tskit==0.6.3
- # via -r requirements.txt
diff --git a/python/test_bincode_metadata.py b/python/test_bincode_metadata.py
deleted file mode 100644
index 3e106124a..000000000
--- a/python/test_bincode_metadata.py
+++ /dev/null
@@ -1,28 +0,0 @@
-import tskit
-import tskit_glue
-import numpy as np
-
-
-def setup_ts_without_schema():
- ts = tskit.TreeSequence.load("with_bincode_metadata.trees")
- return ts
-
-
-def test_individual_metadata():
- # NOTE: the assertions here rely on knowing
- # what examples/json_metadata.rs put into the
- # metadata!
- ts = setup_ts_without_schema()
- md = tskit_glue.decode_bincode_individual_metadata(ts.individual(0).metadata)
- assert md.name() == "Jerome"
- assert md.phenotypes() == [0, 1, 2, 0]
-
-
-def test_mutation_metadata():
- # NOTE: the assertions here rely on knowing
- # what examples/json_metadata.rs put into the
- # metadata!
- ts = setup_ts_without_schema()
- md = tskit_glue.decode_bincode_mutation_metadata(ts.mutation(0).metadata)
- assert np.isclose(md.effect_size(), -1e-3)
- assert np.isclose(md.dominance(), 0.1)
diff --git a/python/test_json_metadata.py b/python/test_json_metadata.py
deleted file mode 100644
index 5c05fa53e..000000000
--- a/python/test_json_metadata.py
+++ /dev/null
@@ -1,71 +0,0 @@
-import tskit
-import numpy as np
-
-
-def setup_ts_without_schema():
- ts = tskit.TreeSequence.load("with_json_metadata.trees")
- return ts
-
-
-def setup_ts_with_schema():
- ts = setup_ts_without_schema()
- tables = ts.tables
- tables.individuals.metadata_schema = tskit.metadata.MetadataSchema(
- {
- "codec": "json",
- "type": "object",
- "name": "Individual metadata",
- "properties": {"name": {"type": "string"},
- "phenotypes": {"type": "array"}},
- "additionalProperties": False,
- })
- tables.mutations.metadata_schema = tskit.metadata.MetadataSchema(
- {
- "codec": "json",
- "type": "object",
- "name": "Individual metadata",
- "properties": {"effect_size": {"type": "number"},
- "dominance": {"type": "number"}},
- "additionalProperties": False,
- })
- return tables.tree_sequence()
-
-
-def test_individual_metadata():
- # NOTE: the assertions here rely on knowing
- # what examples/json_metadata.rs put into the
- # metadata!
- ts = setup_ts_with_schema()
- md = ts.individual(0).metadata
- assert md["name"] == "Jerome"
- assert md["phenotypes"] == [0, 1, 2, 0]
-
-
-def test_individual_metadata_without_schema():
- # NOTE: the assertions here rely on knowing
- # what examples/json_metadata.rs put into the
- # metadata!
- ts = setup_ts_without_schema()
- md = eval(ts.individual(0).metadata)
- assert md["name"] == "Jerome"
- assert md["phenotypes"] == [0, 1, 2, 0]
-
-
-def test_mutation_metadata():
- # NOTE: the assertions here rely on knowing
- # what examples/json_metadata.rs put into the
- # metadata!
- ts = setup_ts_with_schema()
- md = ts.mutation(0).metadata
- assert np.isclose(md["effect_size"], -1e-3)
- assert np.isclose(md["dominance"], 0.1)
-
-
-def test_mutation_metadata_without_schema():
- # NOTE: the assertions here rely on knowing
- # what examples/json_metadata.rs put into the
- # metadata!
- ts = setup_ts_without_schema()
- md = eval(ts.mutation(0).metadata)
- assert np.isclose(md["effect_size"], -1e-3)
- assert np.isclose(md["dominance"], 0.1)
diff --git a/python/tskit_glue/Cargo.lock b/python/tskit_glue/Cargo.lock
deleted file mode 100644
index 855545b27..000000000
--- a/python/tskit_glue/Cargo.lock
+++ /dev/null
@@ -1,202 +0,0 @@
-# This file is automatically @generated by Cargo.
-# It is not intended for manual editing.
-version = 4
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-
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-name = "tskit_glue"
-version = "0.1.0"
-dependencies = [
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- "pyo3",
- "serde",
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-
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-
-[[package]]
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diff --git a/python/tskit_glue/Cargo.toml b/python/tskit_glue/Cargo.toml
deleted file mode 100644
index 535019b98..000000000
--- a/python/tskit_glue/Cargo.toml
+++ /dev/null
@@ -1,14 +0,0 @@
-[package]
-name = "tskit_glue"
-version = "0.1.0"
-edition = "2021"
-
-# See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
-[lib]
-name = "tskit_glue"
-crate-type = ["cdylib"]
-
-[dependencies]
-pyo3 = "0.24.0"
-serde = {version = "1.0.203", features = ["derive"]}
-bincode = {version = "1.3.1"}
diff --git a/python/tskit_glue/pyproject.toml b/python/tskit_glue/pyproject.toml
deleted file mode 100644
index 8433781f8..000000000
--- a/python/tskit_glue/pyproject.toml
+++ /dev/null
@@ -1,15 +0,0 @@
-[build-system]
-requires = ["maturin>=1.8,<2.0"]
-build-backend = "maturin"
-
-[project]
-name = "tskit_glue"
-requires-python = ">=3.8"
-classifiers = [
- "Programming Language :: Rust",
- "Programming Language :: Python :: Implementation :: CPython",
- "Programming Language :: Python :: Implementation :: PyPy",
-]
-dynamic = ["version"]
-[tool.maturin]
-features = ["pyo3/extension-module"]
diff --git a/python/tskit_glue/src/lib.rs b/python/tskit_glue/src/lib.rs
deleted file mode 100644
index 0adbc1b7f..000000000
--- a/python/tskit_glue/src/lib.rs
+++ /dev/null
@@ -1,75 +0,0 @@
-// NOTES:
-// This code shows how to decode metadata generated in rust
-// using a format that tskit-python does NOT support.
-//
-// This example works by creating rust structs that exactly mimic
-// our metadata types and are exposed to Python.
-// For production code, it would be wiser to reuse the rust types
-// that first generated the metadata.
-// We cannot do that here, else we'd have to publish the crates
-// defining those types to crates.io/PyPi, which is just
-// ecosystem pollution.
-//
-// Importantly, deserialization does not require that our
-// input/output types be identical!
-// Rather, they simply have to have the same fields.
-// We exploit this fact here, which allows us to make
-// new types with the same fields as our metadata.
-
-use pyo3::prelude::*;
-
-#[derive(serde::Serialize, serde::Deserialize)]
-#[pyclass]
-struct MutationMetadata {
- effect_size: f64,
- dominance: f64,
-}
-
-#[pymethods]
-impl MutationMetadata {
- fn effect_size(&self) -> f64 {
- self.effect_size
- }
- fn dominance(&self) -> f64 {
- self.dominance
- }
-}
-
-#[derive(serde::Serialize, serde::Deserialize)]
-#[pyclass]
-struct IndividualMetadata {
- name: String,
- phenotypes: Vec
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ Introduction
+Do you need
+What does
+What is
+Adding
+Working with table collections
+Working with tree sequences
+Metadata
+Error handling
+Example programs
+The
+
+
+
+
+ Introduction
+Required background.
+-
+
- We assume familiarity with
tskit. See tskit.dev.
+ - Comfort with rust is required.
+
-
+
- The book is a good place to start. +
- The Rustonomicon is for those who wish to dig deeper into
unsaferust and FFI. +The 'nomicon is helpful for understanding how things like thetskitrust API can be built in the first place.
+
+
Conventions used in this document
+Here, tskit means the rust API.
+tskit-c and tskit-python refer to the C and Python APIs, respectively.
The phrase "data model" refers to this. This document will make little sense without an understanding of the data model.
+Relation to the C API
+Where necessary, we will note differences from the behavior of tskit-c.
Much of the rust API works by calling the C API. +We do not change the semantics of the C API. +However, we do make stricter statements about the ownership relationships between types. +For example, the C API can result in the following situation:
+-
+
- A heap-allocated table collection is used to record data about the ancestry of a sample. +
- That table collection is used to initialize a tree sequence. +The tree sequence is told to take ownership of the tables. +
This is a case where the C API requires that you respectfully no longer work with the heap-allocated table collection. To do so is undefined behavior.
+The rust API forbids such situations. +The creation of a tree sequence from tables consumes the tables via a move operation. +Thus, any further actions on the tables is a compiler error.
+This example is the kinds of differences between tskit and tskit-c.
+Undefined behavior is (close to) impossible with tskit.
Quick overview
+Do you need tskit-rust?
+The use-cases for tskit-rust are the same as for tskit-c:
-
+
- Developing a new performance-oriented application. +
- The input/output of this application will be a
.treesfile.
+
What does tskit-rust add?
+Briefly, you get the performance of C and the strong safety guarantees of rust.
What is tskit-rust missing?
+The crate does not cover the entire C API.
+However, client code can make direct calls to that API via the module tskit::bindings.
Adding tskit as a dependency to a rust project
+In your Cargo.toml:
[dependencies]
+tskit = "~X.Y.Z"
+The latest version to fill in X.Y.Z can be found here.
+See here for how to specify version numbers.
Feature flags.
+tskit defines several cargo features.
+These are defined in the API docs.
Working with table collections
+The next sections cover how to work with the TableCollection, which is one of tskit's fundamental types.
Creation
+We initialize a TableCollection with a sequence length.
+In tskit-c, the genome length is a C double.
+Here it is a newtype called tskit::Position:
let sequence_length = tskit::Position::from(100.0);
+ if let Ok(tables) = tskit::TableCollection::new(sequence_length) {
+ assert_eq!(tables.sequence_length(), sequence_length);
+ // In tskit, the various newtypes can be compared to
+ // the low-level types they wrap.
+ assert_eq!(tables.sequence_length(), 100.0);
+ } else {
+ panic!(
+ "TableCollection creation sequence length = {} failed",
+ sequence_length
+ );
+ }The newtype pattern gives type safety by disallowing you to send a position to a function where a time is required, etc..
+However, it can be inconvenient to type out the full type names every time.
+Thus, the API defines most functions taking arguments Into<T> where T is one of our newtypes.
+This design means that the following is equivalent to what we wrote above:
let tables = tskit::TableCollection::new(100.0).unwrap();Adding rows to tables
+-
+
- For each table type (node, edge., etc.), we have a function to add a row. +
- We can only add rows to tables in mutable
TableCollectioninstances.
+
For example, to add a node:
+ let mut tables = tskit::TableCollection::new(100.0).unwrap();
+ if let Ok(node_id) = tables.add_node(
+ 0, // Node flags
+ tskit::Time::from(0.0), // Birth time
+ tskit::PopulationId::NULL, // Population id
+ tskit::IndividualId::NULL, // Individual id
+ ) {
+ assert_eq!(node_id, 0);
+ }We see from the if let pattern that functions adding rows return
+Result.
+In general, errors only occur when the C back-end fails to allocate memory
+to expand the table columns.
+If we add a row with invalid data, no error is returned!
+To catch such errors, we must explicitly check table integrity (see below).
Again, we can take advantage of being able to pass in any type that is Into<_> the required newtype:
let node_id = tables.add_node(0, 0.0, -1, -1).unwrap();See the API docs for more details and examples.
+Adding nodes using default values
+This section is more advanced and may be skipped during a first read.
+For some tables it may be common to input the same values over and over for some fields when adding rows. +Let's take a look at how to use default values when adding rows to a node table.
+Default instances of NodeDefaults contain default values for the flags, individual, and population fields:
let defaults = tskit::NodeDefaults::default();Add a node with these values and a given birth time:
+ let node = tables.add_node_with_defaults(0.0, &defaults).unwrap();We can use struct update syntax to create a new node marked as a sample while re-using our other defaults:
+ let node = tables
+ .add_node_with_defaults(
+ 0.0,
+ // Create a new, temporary defaults instance
+ &tskit::NodeDefaults {
+ // Mark the new node as a sample
+ flags: tskit::NodeFlags::new_sample(),
+ // Use remaining values from our current defaults
+ ..defaults
+ },
+ )
+ .unwrap();See the NodeDefaults section of the API reference for more.
Metadata
+Metadata can complicate the picture a bit:
+-
+
- Metadata types are defined by the client and are thus a generic in the
tskitAPI.
+ - We do not want to impose too many trait bounds on the client-defined types. +
- Metadata is optional on a per-row basis for any given table. +
NodeDefaultsWithMetadata handles the case where rows may or may not have metadata.
+The metadata type is generic with trait bound tskit::NodeMetadata.
+Because metadata are optional per-row, any metadata defaults are stored as an Option.
For the following examples, this will be our metadata type:
+ pub struct NodeMetadata {
+ pub value: i32,
+ }Case 1: no default metadata
+A common use case is that the metadata differs for every row.
+For this case, it makes sense for the default value to be the None variant of the Option.
This case is straightforward:
+
+ // Create a type alias for brevity
+ type DefaultsWithMetadata = tskit::NodeDefaultsWithMetadata<NodeMetadata>;
+ // Default metadata is None
+ let defaults = DefaultsWithMetadata::default();
+
+ // A row with no metadata
+ let n0 = tables.add_node_with_defaults(0.0, &defaults).unwrap();
+
+ // A row with metadata
+ let n1 = tables
+ .add_node_with_defaults(
+ 0.0,
+ &DefaultsWithMetadata {
+ population: 3.into(),
+ metadata: Some(NodeMetadata { value: 42 }),
+ ..defaults
+ },
+ )
+ .unwrap();
+
+ // Another row with metadata, different from the last.
+ let n2 = tables
+ .add_node_with_defaults(
+ 0.0,
+ &DefaultsWithMetadata {
+ population: 1.into(),
+ metadata: Some(NodeMetadata { value: 1234 }),
+ ..defaults
+ },
+ )
+ .unwrap();Case 2: default metadata
+TL;DR:
+-
+
- If table row defaults include metadata, you can run into use-after-move issues. +Fortunately, the compiler will catch this as an error. +
- The solution is for your metadata type to implement
Clone.
+
Consider the following case:
+ // What if there is default metadata for all rows?
+ let defaults = DefaultsWithMetadata {
+ metadata: Some(NodeMetadata { value: 42 }),
+ ..Default::default()
+ };Imagine that the first row we add uses different metadata but all the other default values:
+ let n0 = tables
+ .add_node_with_defaults(
+ 0.0,
+ &DefaultsWithMetadata {
+ metadata: Some(NodeMetadata { value: 2 * 42 }),
+ ..defaults
+ },
+ )
+ .unwrap();Nothing interesting has happened.
+However, let's take a look at what we need to do if our next row uses a non-default population field and the default metadata:
let n1 = tables
+ .add_node_with_defaults(
+ 0.0,
+ &DefaultsWithMetadata {
+ population: 6.into(),
+ ..defaults.clone()
+ },
+ )
+ .unwrap();Note the call to ..defaults.clone().
+(For that call to compile, NodeMetadata must implement Clone!.)
+Without that, our defaults instance would have moved, leading to a move-after-use compiler error when we add a third row:
let n2 = tables
+ .add_node_with_defaults(
+ 0.0,
+ &DefaultsWithMetadata {
+ individual: 7.into(),
+ ..defaults
+ },
+ )
+ .unwrap();Accessing table columns
+We can access table rows using either the relevant newtype or i32 (which is identical to the tskit-c typedef tsk_id_t).
+The following snippet adds and edge and then validates the data for that row of the table:
if let Ok(edge_id) = tables.add_edge(left, right, parent, child) {
+ // Take a reference to an edge table (& tskit::EdgeTable)
+ let edges = tables.edges();
+ if let Some(p) = edges.parent(edge_id) {
+ assert_eq!(p, parent);
+ }
+ if let Some(c) = edges.child(edge_id) {
+ assert_eq!(c, child);
+ }
+ if let Some(l) = edges.left(edge_id) {
+ assert_eq!(l, left);
+ }
+ if let Some(r) = edges.right(edge_id) {
+ assert_eq!(r, right);
+ }
+ } else {
+ panic!("that should have worked...");
+ }The return type of the getters is the Option enum. The None variant is returned when row indexes are out of range:
assert!(tables.edges().parent(tskit::EdgeId::NULL).is_none());Accessing table rows
+The rows of a table contain two types of data:
+-
+
- Numerical data consisting of a single value. +
- Ragged data. Examples include metadata for all tables, +ancestral states for sites, derived states for mutations, +parent and location information for individuals, etc.. +
tskit provides two ways to access row data.
+The first is by a "view", which contains non-owning references
+to the ragged column data.
+The second is by row objects containing copies of the ragged column data.
The former will be more efficient when the ragged columns are populated. +The latter will be more convenient to work with because the API is a standard +rust iterator.
+By holding references, row views have the usual implications for borrowing. +The row objects, however, own their data and are thus independent of their parent +objects.
+Row views
+To generate a row view using a row id:
+ if let Some(row) = tables.edges().row(edge_id) {
+ assert_eq!(row.id, 0);
+ assert_eq!(row.left, left);
+ assert_eq!(row.right, right);
+ assert_eq!(row.parent, parent);
+ assert_eq!(row.child, child);
+ } else {
+ panic!("that should have worked...");
+ }To iterate over all views we use lending iterators:
+ let mut edge_table_lending_iter = tables.edges().lending_iter();
+ while let Some(row_view) = edge_table_lending_iter.next() {
+ // there is only one row!
+ assert_eq!(row_view.id, 0);
+ assert_eq!(row_view.left, left);
+ assert_eq!(row_view.right, right);
+ assert_eq!(row_view.parent, parent);
+ assert_eq!(row_view.child, child);
+ assert!(row_view.metadata.is_none()); // no metadata in our table
+ }Lending iterators
+The lending iterators are implemented using the streaming_iterator crate.
+(The community now prefers the term "lending" over "streaming" for this concept.)
+The tskit prelude includes the trait declarations that allow the code shown above to compile.
rust 1.65.0 stabilized Generic Associated Types, or GATs.
+GATs allows lending iterators to be implemented directly without the workarounds used in the streaming_iterator crate.
+We have decided not to implement our own lending iterator using GATs.
+Rather, we will see what the community settles on and will decide in the future whether or not to adopt it.
Row objects
+We may access entire table rows by a row id:
+ if let Some(row) = tables.edges().row(edge_id) {
+ assert_eq!(row.id, 0);
+ assert_eq!(row.left, left);
+ assert_eq!(row.right, right);
+ assert_eq!(row.parent, parent);
+ assert_eq!(row.child, child);
+ } else {
+ panic!("that should have worked...");
+ }The row types are rust structures. The table data are copied into these structures, making them relatively more expensive to work with. We are looking into removing the copies and returning slices, but doing so currently impacts the design of table row iterators such as:
+ for row in tables.edges_iter() {
+ // there is only one row!
+ assert_eq!(row.id, 0);
+ assert_eq!(row.left, left);
+ assert_eq!(row.right, right);
+ assert_eq!(row.parent, parent);
+ assert_eq!(row.child, child);
+ }These iterators are rust iterator types--they impl Iterator<Item=X>, where X is a table row type.
Checking table integrity
+The data model involves lazy checking of inputs. +In other words, we can add invalid row data that is not caught by the "add row" functions. +We inherit this behavior from the C API.
+We can check that the tables contain valid data by:
+ let mut tables = tskit::TableCollection::new(100.0).unwrap();
+ // Everything about this edge is wrong...
+ tables.add_edge(-1.0, 110.0, 0, 1).unwrap();
+ // ...and we can catch that here
+ match tables.check_integrity(tskit::TableIntegrityCheckFlags::default()) {
+ Ok(code) => panic!("expected Err(e) but got code: {}", code),
+ // tskit::TskitError can be formatted into the same
+ // error messages that tskit-c/tskit-python give.
+ Err(e) => println!("{}", e),
+ }Working with tree sequences
+The next several sections provide examples based on a tree sequence with two trees.
+The first tree is:
+ 0
+ +++
+ | | 1
+ | | +++
+ 2 3 4 5
+The second tree is:
+ 0
+ +-+-+
+ 1 |
+ +-+-+ |
+ 2 4 5 3
+Initialization from a table collection
+The steps are:
+-
+
- Add rows to a table +
- Sort the table +
- Index the table +
- Create the tree sequence +
For brevity, we skip careful pattern matching of return values +and instead just unwrap them.
+Adding rows
+ use tskit::prelude::*;
+ use tskit::TableCollection;
+ use tskit::TableSortOptions;
+ use tskit::TreeFlags;
+ use tskit::TreeSequenceFlags;
+
+ let mut tables = TableCollection::new(1000.).unwrap();
+ tables
+ .add_node(0, 2.0, PopulationId::NULL, IndividualId::NULL)
+ .unwrap();
+ tables
+ .add_node(0, 1.0, PopulationId::NULL, IndividualId::NULL)
+ .unwrap();
+ tables
+ .add_node(
+ tskit::NodeFlags::new_sample(),
+ 0.0,
+ PopulationId::NULL,
+ IndividualId::NULL,
+ )
+ .unwrap();
+ tables
+ .add_node(
+ tskit::NodeFlags::new_sample(),
+ 0.0,
+ PopulationId::NULL,
+ IndividualId::NULL,
+ )
+ .unwrap();
+ tables
+ .add_node(
+ tskit::NodeFlags::new_sample(),
+ 0.0,
+ PopulationId::NULL,
+ IndividualId::NULL,
+ )
+ .unwrap();
+ tables
+ .add_node(
+ tskit::NodeFlags::new_sample(),
+ 0.0,
+ PopulationId::NULL,
+ IndividualId::NULL,
+ )
+ .unwrap();
+ tables.add_edge(500., 1000., 0, 1).unwrap();
+ tables.add_edge(0., 500., 0, 2).unwrap();
+ tables.add_edge(0., 1000., 0, 3).unwrap();
+ tables.add_edge(500., 1000., 1, 2).unwrap();
+ tables.add_edge(0., 1000., 1, 4).unwrap();
+ tables.add_edge(0., 1000., 1, 5).unwrap();Sorting
+ tables.full_sort(TableSortOptions::default()).unwrap();See the API docs for the details of sorting. +The behavior of this function can be confusing at first. +Only tables with strict sorting requirements are affected.
+Indexing
+ tables.build_index().unwrap();Create the tree sequence
+ let treeseq = tables.tree_sequence(TreeSequenceFlags::default()).unwrap();Notes:
+-
+
- We could have skipped
tables.build_index()and passedTreeSquenceFlags::BUILD_INDEXESinstead of the default flags.
+ - Creating a tree sequence from a table collection takes ownership of the table data and consumes the table collection variable. +Any further attempts to manipulate the table collection variable will result in a compiler error. +
Iterating over trees
+To iterate over trees left-to-right:
+ let mut tree_iterator = treeseq.tree_iterator(TreeFlags::default()).unwrap();
+
+ while let Some(_tree) = tree_iterator.next() {
+ // _tree is a tskit::Tree
+ }This API depends on traits most easily brought into scope via the crate prelude:
+use tskit::prelude::*;A next_back() function allows iteration to the next tree left of the current tree.
+We currently do not have an API expressing "build me an iterator starting from the rightmost tree".
+Such an thing is certainly doable.
Working with trees
+Iterating over a tree sequence returns instances of tskit::Tree.
+This type is immutable.
+No access is provided to the underlying pointers.
The API provides a set of iterators over the data in a tree.
+For example, to collect the siblings of each node into a vector:
+ // This is an enum defining supported
+ // traversal orders through a Tree.
+ use tskit::NodeTraversalOrder;
+ while let Some(tree) = tree_iterator.next() {
+ for node in tree.traverse_nodes(NodeTraversalOrder::Preorder) {
+ if let Some(parent) = tree.parent(node) {
+ // Collect the siblings of node into a Vec
+ // The children function returns another iterator
+ let _siblings = tree
+ .children(parent)
+ .filter(|child| child != &node)
+ .collect::<Vec<_>>();
+ }
+ }
+ }We may do the same calculation using API elements giving &[NodeId]
+(slices of node ids).
+This method more closely matches the tskit-c API.
while let Some(tree) = tree_iterator.next() {
+ let parents = tree.parent_array();
+ let rsibs = tree.right_sib_array();
+ let lchildren = tree.left_child_array();
+ for node in tree.traverse_nodes(NodeTraversalOrder::Preorder) {
+ let mut siblings = vec![];
+ assert!(!node.is_null());
+ if let Some(parent) = parents.get(usize::try_from(node).unwrap()) {
+ if !parent.is_null() {
+ if let Some(child) = lchildren.get(usize::try_from(*parent).unwrap()) {
+ let mut u = *child;
+ while !u.is_null() {
+ if u != node {
+ siblings.push(u);
+ }
+ if let Some(sib) = rsibs.get(usize::try_from(u).unwrap()) {
+ u = *sib;
+ }
+ }
+ }
+ }
+ }
+ }
+ }This approach is more complex:
+-
+
- Slice element access is via
usize(size_tin C/C++).
+ - Row ids are
i32(tsk_id_tintskit-c) behind the newtypes.
+ tskitimplementsTryFromto help you out, forcing +you to reckon with the fact that conversion fromi32+tousizeis fallible.
+
These conversion semantics require us to manually handle all possible error +paths at each step.
+We can have an intermediate level of complexity using getters from the tree arrays:
+ while let Some(tree) = tree_iterator.next() {
+ for node in tree.traverse_nodes(NodeTraversalOrder::Preorder) {
+ let mut siblings = vec![];
+ if let Some(parent) = tree.parent(node) {
+ if let Some(child) = tree.left_child(parent) {
+ let mut u = child;
+ while !u.is_null() {
+ if u != node {
+ siblings.push(u);
+ }
+ if let Some(sib) = tree.right_sib(u) {
+ u = sib;
+ }
+ }
+ }
+ }
+ }
+ }Iterating over edge differences
+As with trees, the API provides a lending iterator over edge differences.
+Each step of the iterator advances to the next tree in the tree sequence.
+For each tree, a standard Iterator over removals and insertions is available:
if let Ok(mut edge_diff_iterator) = treeseq.edge_differences_iter() {
+ while let Some(diffs) = edge_diff_iterator.next() {
+ for edge_removal in diffs.edge_removals() {
+ println!("{}", edge_removal);
+ }
+ for edge_insertion in diffs.edge_insertions() {
+ println!("{}", edge_insertion);
+ }
+ }
+ } else {
+ panic!("creating edge diffs iterator failed");
+ }Edge differences are the basis of efficient algorithms based on the incremental updating of summaries of trees. +The following example co-iterates over edge differences and trees. +The edge differences are used to calculate the parent array for each tree:
+ let num_nodes = treeseq.nodes().num_rows().as_usize();
+ // num_nodes + 1 to reflect a "virtual root" present in
+ // the tree arrays
+ let mut parents = vec![NodeId::NULL; num_nodes + 1];
+ match treeseq.edge_differences_iter() {
+ Ok(mut ediff_iter) => match treeseq.tree_iterator(0) {
+ Ok(mut tree_iter) => {
+ while let Some(diffs) = ediff_iter.next() {
+ let tree = tree_iter.next().unwrap();
+ for edge_out in diffs.edge_removals() {
+ let c = edge_out.child();
+ parents[c.as_usize()] = NodeId::NULL;
+ }
+ for edge_in in diffs.edge_insertions() {
+ let c = edge_in.child();
+ parents[c.as_usize()] = edge_in.parent();
+ }
+ assert_eq!(tree.parent_array(), &parents);
+ }
+ }
+ Err(e) => panic!("error creating tree iter: {:?}", e),
+ },
+ Err(e) => panic!("error creating edge diff iter: {:?}", e),
+ }Miscellaneous operations
+Writing to a file
+treeseq.dump("file.trees", tskit::TableOutputOptions::default()).unwrap();Loading from a file
+let treeseq = tskit::TreeSequence::load("file.trees").unwrap();Get a deep copy of the tables
+Get a copy of the table collection in the tree sequence:
+let tables = treeseq.dump_tables.unwrap();This function can error because the tskit-c functions to copy ,may return an error code.
This function is not necessary to access the tables. +See below.
+Read-only table access
+A TreeSequence has access to the tables.
+For example:
for _edge in treeseq.edges_iter() {
+}Metadata
+Tables may contain additional information about rows that is not part of the data model. +This metadata is optional. +Tables are not required to have metadata. +Tables with metadata do not require that every row has metadata.
+The next sections showcase the metadata API.
+Defining metadata types in rust
+A key feature of the API is that metadata is specified on a per-table basis.
+In other words, a type to be used as node metadata implements the tskit::metadata::NodeMetadata trait.
Using the tskit cargo feature derive, we can use procedural macros to define metadata types.
+Here, we define a metadata type for a mutation table:
#[derive(serde::Serialize, serde::Deserialize, tskit::metadata::MutationMetadata)]
+ #[serializer("serde_json")]
+ struct MutationMetadata {
+ effect_size: f64,
+ dominance: f64,
+ }We require that you also manually specify the serde derive macros because the metadata API
+itself does not depend on serde.
+Rather, it expects raw bytes and serde happens to be a good way to get them from your data types.
The derive macro also enforces some helpful behavior at compile time. +You will get a compile-time error if you try to derive two different metadata types for the same rust type. +The error is due to conflicting implementations for a supertrait.
+Metadata and tables
+Let us create a table and add a row with our mutation metadata:
+ let mut tables = tskit::TableCollection::new(50.0).unwrap();
+
+ let md = MutationMetadata {
+ effect_size: 1e-3,
+ dominance: 1.0,
+ };
+
+ let mut_id_0 = tables
+ .add_mutation_with_metadata(
+ 0, // site id
+ 0, // node id
+ -1, // mutation parent id
+ 0.0, // time
+ None, // derived state is Option<&[u8]>
+ &md, // metadata for this row
+ )
+ .unwrap();Meta data is optional on a per-row basis:
+ let mut_id_1 = tables
+ .add_mutation(
+ 0, // site id
+ 0, // node id
+ -1, // mutation parent id
+ 0.0, // time
+ None, // derived state is Option<&[u8]>
+ )
+ .unwrap();We can confirm that we have one row with, and one without, metadata:
+ assert_eq!(
+ tables
+ .mutations_iter()
+ .filter(|m| m.metadata.is_some())
+ .count(),
+ 1
+ );
+ assert_eq!(
+ tables
+ .mutations_iter()
+ .filter(|m| m.metadata.is_none())
+ .count(),
+ 1
+ );Fetching our metadata from the table requires specifying the metadata type.
+The result of a metadata retrieval is Option<Result, TskitError>.
+The None variant occurs if a row does not have metadata or if a row id does not exist.
+The error state occurs if decoding raw bytes into the metadata type fails.
+The details of the error variant are here.
+The reason why the error type holds Box<dyn Error> is that the API is very general.
+We assume nothing about the API used to encode/decode metadata.
+Therefore, the error could be anything.
let fetched_md = match tables.mutations().metadata::<MutationMetadata>(mut_id_0) {
+ Some(Ok(m)) => m,
+ Some(Err(e)) => panic!("metadata decoding failed: {:?}", e),
+ None => panic!(
+ "hmmm...row {} should have been a valid row with metadata...",
+ mut_id_0
+ ),
+ };
+
+ assert_eq!(md.effect_size, fetched_md.effect_size);
+ assert_eq!(md.dominance, fetched_md.dominance); // There is no metadata at row 1, so
+ // you get None back
+ assert!(tables
+ .mutations()
+ .metadata::<MutationMetadata>(mut_id_1)
+ .is_none());
+
+ // There is also no metadata at row 2,
+ // because that row does not exist, so
+ // you get None back
+ assert!(tables
+ .mutations()
+ .metadata::<MutationMetadata>(2.into())
+ .is_none());Metadata schema
+For useful data interchange with tskit-python, we need to define metadata schema.
There are currently several points slowing down a rust API for schema:
+-
+
- It is not clear which
serdeformats are compatible with metadata on the Python side.
+ - Experiments have shown that
serde_jsonworks withtskit-python. +-
+
- Ideally, we would also like a binary format compatible with the Python
struct+module.
+
+ - Ideally, we would also like a binary format compatible with the Python
- However, we have not found a solution eliminating the need to manually write the
+schema as a string and add it to the tables.
+Various crates to generate JSON schema from rust structs return schema that are over-specified
+and fail to validate in
tskit-python.
+ - We also have the problem that we will need to add some Python to our CI to prove to ourselves +that some reasonable tests can pass. +
Advanced topics
+Bulk decoding of metadata
+To populate a Vec with decoded metadata and accounting
+for some rows not having metadata:
-
+
- Realize that the decode methods of the
MetadataRoundtriptrait are associated functions.
+ - We can use a lending iterator over rows to avoid unnecessary copying. +
Therefore:
+ let mut mutation_row_lending_iterator = tables.mutations().lending_iter();
+ let mut decoded_md = vec![];
+ while let Some(row_view) = mutation_row_lending_iterator.next() {
+ match row_view.metadata {
+ Some(slice) => decoded_md.push(Some(MutationMetadata::decode(slice).unwrap())),
+ None => decoded_md.push(None),
+ }
+ }To filter out rows without metadata:
+ let mut mutation_row_lending_iterator = tables.mutations().lending_iter();
+ let mut decoded_md = vec![];
+ while let Some(row_view) = mutation_row_lending_iterator
+ .next()
+ .filter(|rv| rv.metadata.is_some())
+ {
+ decoded_md.push((
+ row_view.id,
+ // The unwrap will never panic because of our filter
+ MutationMetadata::decode(row_view.metadata.unwrap()).unwrap(),
+ ));
+ }The first method gives Vec<Option<MutationMetadata>>.
+The second gives Vec<(MutationId, MutationMetadata)>.
Error handling
+The error type is tskit::error::TskitError.
This type implements Display and may thus be printed via:
let x = match operation() {
+ Ok(y) => y,
+ Err(e) => panic("{}", e);
+};The enum variant TskitError::ErrorCode represents integer return values from tskit-c.
+When printed via Display, the detailed error message is fetched.
+When printed via Debug, the numerical error code is shown.
Example programs
+Haploid Wright-Fisher simulation
+The following code simulates a haploid Wright-Fisher model.
+The code is a reimplementation of an example program distributed with tskit-c.
In addition to tskit, the example uses:
fn simulate(
+ seed: u64,
+ popsize: usize,
+ num_generations: i32,
+ simplify_interval: i32,
+ update_bookmark: bool,
+) -> Result<tskit::TreeSequence> {
+ if popsize == 0 {
+ return Err(anyhow::Error::msg("popsize must be > 0"));
+ }
+ if num_generations == 0 {
+ return Err(anyhow::Error::msg("num_generations must be > 0"));
+ }
+ if simplify_interval == 0 {
+ return Err(anyhow::Error::msg("simplify_interval must be > 0"));
+ }
+ let mut tables = tskit::TableCollection::new(1.0)?;
+
+ // create parental nodes
+ let mut parents_and_children = {
+ let mut temp = vec![];
+ let parental_time = f64::from(num_generations);
+ for _ in 0..popsize {
+ let node = tables.add_node(0, parental_time, -1, -1)?;
+ temp.push(node);
+ }
+ temp
+ };
+
+ // allocate space for offspring nodes
+ parents_and_children.resize(2 * parents_and_children.len(), tskit::NodeId::NULL);
+
+ // Construct non-overlapping mutable slices into our vector.
+ let (mut parents, mut children) = parents_and_children.split_at_mut(popsize);
+
+ let parent_picker = rand::distributions::Uniform::new(0, popsize);
+ let breakpoint_generator = rand::distributions::Uniform::new(0.0, 1.0);
+ let mut rng = rand::rngs::StdRng::seed_from_u64(seed);
+ let mut bookmark = tskit::types::Bookmark::default();
+
+ for birth_time in (0..num_generations).rev() {
+ for c in children.iter_mut() {
+ let bt = f64::from(birth_time);
+ let child = tables.add_node(0, bt, -1, -1)?;
+ let left_parent = parents
+ .get(parent_picker.sample(&mut rng))
+ .ok_or_else(|| anyhow::Error::msg("invalid left_parent index"))?;
+ let right_parent = parents
+ .get(parent_picker.sample(&mut rng))
+ .ok_or_else(|| anyhow::Error::msg("invalid right_parent index"))?;
+ let breakpoint = breakpoint_generator.sample(&mut rng);
+ tables.add_edge(0., breakpoint, *left_parent, child)?;
+ tables.add_edge(breakpoint, 1.0, *right_parent, child)?;
+ *c = child;
+ }
+
+ if birth_time % simplify_interval == 0 {
+ tables.sort(&bookmark, tskit::TableSortOptions::default())?;
+ if update_bookmark {
+ rotate_edges(&bookmark, &mut tables);
+ }
+ if let Some(idmap) =
+ tables.simplify(children, tskit::SimplificationOptions::default(), true)?
+ {
+ // remap child nodes
+ for o in children.iter_mut() {
+ *o = idmap[usize::try_from(*o)?];
+ }
+ }
+ if update_bookmark {
+ bookmark.set_edges(tables.edges().num_rows());
+ }
+ }
+ std::mem::swap(&mut parents, &mut children);
+ }
+
+ tables.build_index()?;
+ let treeseq = tables.tree_sequence(tskit::TreeSequenceFlags::default())?;
+
+ Ok(treeseq)
+}The tskit prelude
+The contents of the crate prelude are:
+//! Export commonly-use types and traits
+
+pub use streaming_iterator::DoubleEndedStreamingIterator;
+pub use streaming_iterator::StreamingIterator;
+pub use {
+ crate::EdgeId, crate::IndividualId, crate::Location, crate::MigrationId, crate::MutationId,
+ crate::NodeId, crate::PopulationId, crate::Position, crate::RawFlags, crate::SiteId,
+ crate::SizeType, crate::Time,
+};Changelog
+All notable changes to this project will be documented in this file.
+[0.14.1] - 2023-04-16
+Bug Fixes
+-
+
- Tree now tied to TreeSequence lifetime (#497) +
Miscellaneous Tasks
+-
+
- Update delegate requirement from 0.8.0 to 0.9.0 (#494) +
[0.14.0] - 2023-03-17
+Documentation
+-
+
- Book section on node defaults (#491) +
Features
+-
+
- Allow use of bookmark in examples/haploid_wright_fisher (#479) +
- Impl Default for row id types (#484) +
- Impl Default for Bookmark (#486) +
- Implement Builder pattern for flags (#487) +
- Support adding nodes with defaults (#488) +
Miscellaneous Tasks
+-
+
- [breaking] Bump MSRV to 1.60.0 (#478) +
Refactor
+-
+
- Remove internal impl Deref/DerefMut for edge diff iterator. (#482) +
- Mod table_view is no longer pub (#483) +
- [breaking] TableCollection::simplify now takes &[NodeId] (#485) +
- Replace macros with fn for adding node table rows (#489) +
- Manually impl Default for NodeDefaultsWithMetadata (#490) +
[0.12.0] - 2022-12-23
+Documentation
+-
+
- Book section on lending row iterators (#406) +
- Advanced metadata topics in book (#407) +
- Book chapter on edge differences (#417) +
Features
+-
+
- TreeSequence::edge_differences_iter (#410) +
- Add convience functions to get usize from row ids. (#413) +
- Tree::total_branch_length now works. (#429) +
- Add getters/setters for Bookmark. (#437) +
Miscellaneous Tasks
+-
+
- Update bindgen requirement from 0.61.0 to 0.63.0 (#415) +
Refactor
+-
+
- [breaking] Replace Deref with delegation of TableViews API (#409) +
- [breaking] Remove TskitTypeAccess trait (#411) +
- Allow TreeSequence::edge_differences_iter to Err. (#412) +
- [breaking] Usize to SizeType conversion is now fallible. (#419) +
- Macros only use newtype public API. (#420) +
- Move newtypes into module (#421) +
- The raw_metadata fn for tables now takes Into
. (#425)
+ - Add low-level table wrappers to sys (#426) +
- Generalize slice building in sys (#427) +
- Remove many unsafe calls from tree_interface.rs (#428) +
- Add sys::LLTreeSeq. (#430) +
- Sys module no longer depends on TskitError (#431) +
- Move Drop details for TreeSequence to sys. (#432) +
- Add low level owning tables to sys (#433) +
- Tidy up table definitions (#434) +
Styling
+-
+
- [breaking] Rename all OwnedX tables to OwningX. (#408) +
- Replace column access macro with generic fn (#422) +
- Generic fns for ragged column access (#423) +
- Use fn to get array slices from Trees. (#424) +
[0.12.0-alpha.1] - 2022-11-09
+Bug Fixes
+-
+
- [breaking] MetadataError::RoundtripError now requires Send + Sync (#396) +
Documentation
+-
+
- Add haploid WF example to book (#397) +
Features
+-
+
- Add examples/haploid_wright_fisher.rs (#394) +
- Add lending iterators over table row "views" (#398) +
- Impl PartialEq for table row views. (#400) +
- Add ProvenenceTableRowView (#401) +
- Add row_view() for tables (#402) +
- Add row_view() for tables (#402) +
- Column slice getters for tables (#404) +
Refactor
+-
+
- [breaking] Return &str from provenance table getters (#403) +
- Deprecate NodeTable::flags_array_mut and NodeTable::time_array_mut (#405) +
[0.12.0-alpha.0] - 2022-11-06
+Documentation
+-
+
- Add book sections on table data access (#379) +
- Remove chapter number from book intro (#380) +
- Start book sections on tree sequences (#381) +
- Book section on the tree API. (#382) +
- Add book section on misc. ops on treeseqs (#385) +
- Appendix material for book (#386) +
- Rewrite book intro (#389) +
- Show prelude contents as book appendix (#390) +
- Book sections on metadata (#391) +
- Book section on error handling (#393) +
Refactor
+-
+
- [breaking] Improve Tree iterator ergonomics (#384) +
- [breaking] Improve Tree interface ergonomics (#388) +
[0.11.1] - 2022-11-04
+Documentation
+-
+
- Add mdbook (#378) +
Refactor
+-
+
- Apply functional style for NodeTable fns (#377) +
[0.11.0] - 2022-11-04
+Bug Fixes
+-
+
- Derive Debug for all table row types (#361) +
- [breaking] Update generic bounds on metadata getters (#370) +
- Impl DerefMut for "owned" tables. (#371) +
Documentation
+-
+
- Add migration guide (#376) +
Features
+-
+
- [breaking] Add TskitError::LibraryError (#342) +
Refactor
+-
+
- Streamline code for generating table rows. (#340) +
- Replace unwrap with expect in _macros.rs (#341) +
- Replace unwrap with errors in table_collection.rs (#343) +
- Remove unwraps in trees source files. (#344) +
- Streamline building individual table rows (#345) +
- Remove unwraps from node_table.rs (#346) +
- Unwrap to expect in error.rs (#347) +
- Remove type info from Display for newtypes. (#349) +
- [breaking] Return None for out-of-range row indexes. (#350) +
- [breaking] Return None for out-of-range row indexes, part II. (#351) +
- [breaking] Return None for out-of-range row indexes, part III. (#355) +
- Improve safety of tsk array access (#362) +
- Tree now stores
tsk_tree_tinMBox. (#367)
+ - [breaking] Provenance table getters now return Option (#369) +
- [breaking] Remove lifetime annotation from table types (#373) +
Styling
+ +Testing
+ +[0.10.0] - 2022-10-28
+Documentation
+-
+
- Display feature flags in docs.rs (#338) +
Miscellaneous Tasks
+-
+
- Set msrv to 1.57.0 (result of cargo msrv) (#322) +
- Fix tag_pattern in cliff.toml (#330) +
- Update github actions (#332) +
- Add github actions to monthly dependabot (#333) +
- Update bindgen requirement from 0.60.1 to 0.61.0 (#336) +
- Bump styfle/cancel-workflow-action from 0.6.0 to 0.11.0 (#334) +
Performance
+-
+
- Use Bookmark in forward simulation example (#318) +
Refactor
+-
+
- Streamline internal macros for adding nodes (#309) +
- Remove internal ffi module (#310) +
- Panics compatible with earlier rustc (#311) +
- Remove type name from SizeType Display output. (#315) +
- [breaking] TableCollection::simplify returns Option<&[NodeId]> (#316) +
- [breaking] Conversion from row id to usize is now fallible. (#319) +
- Use clap::Parser in example program. (#320) +
- Remove pontential panic! when instantiating table rows. (#329) +
- Examples/tree_traversals.rs now uses clap derive (#337) +
Styling
+-
+
- Remove unneeded ( ) from match. (#323) +
- Use auto-deref for pointer deref. (#325) +
- Fix +nightly clippy lints for all targets/features. (#326) +
Testing
+-
+
- Improve test work flow (#331) +
[0.10.0-alpha.1] - 2022-07-31
+Bug Fixes
+-
+
- Replace crate with $crate in macros (#287) +
Features
+-
+
- Add tskit::OwnedMutationTable (#281) +
- Add tskit::OwnedSiteTable (#283) +
- Add tskit::OwnedIndividualTable (#284) +
- Add tskit::OwnedMigrationTable (#285) +
- Add tskit::provenance::OwnedProvenanceTable (#286) +
- Set tables in collection from owned tables. (#288) +
- [breaking] Impl Send/Sync for TreeSequence (#297) +
Miscellaneous Tasks
+-
+
- Update to C API 1.1.1 (#304) +
Performance
+-
+
- [breaking] Implement slice access to individual data (#292) +
- [breaking] Eliminate several copies from C to rust (#293) +
Refactor
+-
+
- Deduplicate code for adding node table rows. (#278) +
- Use macros to implement adding table rows. (#279) +
- Add new macro to build owned tables (#282) +
- Separate tree ownership from API. (#300) +
- Bring back generic syntax for adding node table rows. (#302) +
- [breaking] Display for new types now omits type name. (#305) +
- Remove MBox for tsk_treeseq_t storage (#306) +
[0.10.0-alpha.0] - 2022-07-19
+Bug Fixes
+-
+
- Fix memory leak in TreeSequence::simplify (#274) +
- Fix leak in TableCollection::deepcopy (#275) +
- Fix leak in TreeSequence::dump_tables (#276) +
Documentation
+-
+
- Fix warnings from "cargo doc" (#255) +
Features
+-
+
- Make load from file generic over AsRef
(#254)
+ - Add tskit::OwnedPopulationTable (#267) +
- Add tskit::OwnedEdgeTable (#268) +
- Add tskit::OwnedNodeTable (#273) +
Miscellaneous Tasks
+-
+
- Add cliff.toml (config file for git-cliff) (#257) +
- Prefix "chore: " to dependabot.yml (#258) +
- Use cargo-hack to streamline CI. (#259) +
- Add cargo-valgrind CI workflow (#277) +
Refactor
+ +Testing
+-
+
- Add another experimental trait idea for metadata. (#261) +
- Redo doctest: TableCollection::new_from_file (#272) +
2022-06-20, Version 0.9.0
+Commits
+-
+
- [
068fdccdea] Bump version to 0.9.0 (Kevin R. Thornton)
+ - [
d700af7294] doc sorting requirements (#243) (Kevin R. Thornton)
+ - [
6114d2bd65] Change ffi to private visibility. (#241) (Kevin R. Thornton)
+ - [
b53105112a] Add new_sample and is_sample to NodeFlags public API. (#238) (Kevin R. Thornton)
+
2022-05-26, Version 0.8.1
+Commits
+-
+
- [
bd72b689ac] Bump version to 0.8.1 (molpopgen)
+ - [
b0abdfad5c] impl TryFromfor TreeSequence (#236) (Kevin R. Thornton)
+ - [
71e927a9bb] TreeSequence::new now takes ownership of the TableCollection. (#235) (Kevin R. Thornton)
+
2022-05-24, Version 0.8.0
+Commits
+-
+
- [
e463302ced] Bump package version to 0.8.0 (molpopgen)
+ - [
deffc58127] Replace Fromfor usize with TryFrom. (#234) (Kevin R. Thornton)
+ - [
a7c04213a1] update to CAPI 1.0.0 (#229) (Kevin R. Thornton)
+ - [
7c0b6169a3] Add CI for 32 bit Linux builds (#232) (Kevin R. Thornton)
+ - [
7458d85163] Invoke rust dependency caching after setting up rustc (#233) (Kevin R. Thornton)
+ - [
203a43a0e8] Only run CI for rust/stable. (#231) (Kevin R. Thornton)
+ - [
fb2128c0a5] Add dependency caching for CI. (#230) (Kevin R. Thornton)
+ - [
aff053c786] Improvements to handling of tsk_flags_t: (#227) (Kevin R. Thornton)
+ - [
5f558cb051] Audit pedantic lints re: integer casts (#223) (Kevin R. Thornton)
+ - [
609546185c] Fix several "pedantic" lints from clippy: (#222) (Kevin R. Thornton)
+
2022-03-24, Version 0.7.0
+Commits
+-
+
- [
8427c2fea7] Change order of generics to match argument order for all "add" (#221) (Kevin R. Thornton)
+ - [
6ef0406731] Fix typo in docstring for TableCollection::full_sort. (#219) (Kevin R. Thornton)
+ - [
a1a7e12208] Add TableCollection::topological_sort_individuals. (#218) (Kevin R. Thornton)
+ - [
4c17ca62a2] Update clap requirement from ~3.0.0 to ~3.1.3 (#215) (dependabot[bot])
+ - [
f40562a56a] Fix lint found by clippy. (#216) (Kevin R. Thornton)
+ - [
4efddb6f5d] Update clap requirement from ~2.34.0 to ~3.0.0 (#214) (dependabot[bot])
+
2021-12-15, Version 0.7.0-alpha.1
+Fixes various minor issues with the first alpha.
+Commits
+-
+
- [
44965969c0] Bump version to 0.7.0.alpha.1 (molpopgen)
+ - [
5d6a289490] Fix issues with Time, Position, Location newtypes (#212) (Kevin R. Thornton)
+ - [
99930e8bb0] Add explicit tests of tree roots. (#211) (Kevin R. Thornton)
+
2021-12-15, Version 0.7.0-alpha.0
+Breaking changes:
+-
+
- Update to tskit C API 0.99.15. +
- Add newtypes for Time, Position, and Location. +
- Add newtype SizeType, which wraps tsk_size_t. +
- tsk_id_t and tsk_size_t removed from library prelude. +
- The Provenance trait is removed and all "provenance stuff" +is now a first-class table API supported by the TableAccess trait. +
New features:
+-
+
- Update to tskit C API 0.99.15. +
- tskit C structs are now managed by MBox. +
- Support for virtual tree roots. +
- Add postorder node iterator for Tree +
Commits
+-
+
- [
272d0736e2] bump package version to 0.7.0-alpha.0 (molpopgen)
+ - [
b5946a4cc4] Redesign provenance feature: (#207) (Kevin R. Thornton)
+ - [
5699aab37f] Change return time of Tree::num_tracked_samples. (#206) (Kevin R. Thornton)
+ - [
2391c9e587] Add support for virtual roots (#205) (Kevin R. Thornton)
+ - [
4cf3496d82] Fix metadata links in lib.rs (#204) (Kevin R. Thornton)
+ - [
d7f70a7cfd] Use MBoxto manage lifetimes of tskit C structs. (#203) (Kevin R. Thornton)
+ - [
034204ed88] Add newtypes for Time, Position, and for Location. (#199) (Kevin R. Thornton)
+ - [
4ba44ef0c5] Bump editions to 2021. (#198) (Kevin R. Thornton)
+ - [
c4cc6e875a] Add tskit::SizeType (#192) (Kevin R. Thornton)
+ - [
8429cc37d2] Use type erasure for all table row iteration functions. (#189) (Kevin R. Thornton)
+ - [
f4cb6350e0] Add TableCollection::check_integrity. (#188) (Kevin R. Thornton)
+ - [
562014b04f] Add preorder node traversal using latest tskit C API. (#186) (Kevin R. Thornton)
+ - [
db8550f6d7] Replace Box with malloc'd raw pointer for tskit types. (#184) (Kevin R. Thornton)
+ - [
90a2d84a9d] Update to C API 0.99.15 (breaking) (#183) (Kevin R. Thornton)
+ - [
58e7c5ed73] Update clap requirement from ~2.33.3 to ~2.34.0 (#176) (dependabot[bot])
+
2021-11-29, Version 0.6.1
+Commits
+-
+
- [
3eadcb161e] Replace chrono with humantime in provenance doc tests. (#175) (Kevin R. Thornton)
+ - [
4def777ddf] Add security audit work flow. (#172) (Kevin R. Thornton)
+
2021-11-23, Version 0.6.0
+Commits
+-
+
- [
b07c035077] bump version to 0.6.0 (molpopgen)
+ - [
8bb08be83d] Replace chrono dependency with humantime to avoid RUSTSEC-2020-0071 and RUSTSEC-2020-0159 (#171) (Momo Langenstein)
+ - [
896b5891e0] Implement Display for Id newtypes. (#168) (Kevin R. Thornton)
+ - [
d2c6383ae9] Update to C API 0.99.14 (#165) (Kevin R. Thornton)
+
2021-09-03, Version 0.5.0
+Commits
+Derive macros for table metadata.
+-
+
- [
41633b60ed] Add metadata type registration via derive macros. (#163) (Kevin R. Thornton)
+
2021-08-31, Version 0.4.0
+The theme of this release is "type safety". +This release breaks API due to use of newtypes for row IDs and new metadata marker traits.
+Commits
+-
+
- [
a7d78b16aa] Bump version to 0.4.0 (molpopogen)
+ - [
b5e2c265dd] Add newtype row IDs to prelude. (#161) (Kevin R. Thornton)
+ - [
3dbe8c4b5e] Fix implementation of tree preorder stacking. (#160) (Kevin R. Thornton)
+ - [
fafd457033] Refactor metadata encoding: (#158) (Kevin R. Thornton)
+ - [
258b4ee5f0] replace IdIsNull trait with associated fn (#156) (Kevin R. Thornton)
+ - [
9987fc0472] Release build optimizations: (#155) (Kevin R. Thornton)
+ - [
58ac4a92d7] Refine what "NULL"-ness means for an Id type: (#154) (Kevin R. Thornton)
+ - [
ad4975fc70] Update bindgen requirement from 0.58.1 to 0.59.1 (#152) (dependabot[bot])
+ - [
8a553eaa80] fix clippy warnings that showed up in rust 1.54 (#153) (Kevin R. Thornton)
+ - [
bef4bb6c7a] Allow empty provenance records. (#151) (Kevin R. Thornton)
+ - [
86df702040] Improve test coverage of "adding rows to table collections" (#143): (Kevin R. Thornton)
+ - [
036680050b] * Update trees API to use NodeId (#145) (Kevin R. Thornton)
+ - [
7a716bbe76] Add additional member functions to TableCollection to (#141) (Kevin R. Thornton)
+ - [
baf6f17430] Fix Into< > type for TableCollection::add_individual_* (#142) (Kevin R. Thornton)
+ - [
689938eee7] fix link from ProvenanceId to ProvenanceTable in docs (#140) (Kevin R. Thornton)
+ - [
1203a5d523] strong id type cleanup (#139) (Kevin R. Thornton)
+ - [
6bae100e61] Add EdgeId (#138) (Kevin R. Thornton)
+ - [
9baff077b5] Add MigrationId and ProvenanceId (#137) (Kevin R. Thornton)
+ - [
7713ef669e] Add SiteId and MutationId (#136) (Kevin R. Thornton)
+ - [
de006a1f0e] Add PopulationId (#135) (Kevin R. Thornton)
+ - [
630ccd5f5e] Add IndividualId. (#133) (Kevin R. Thornton)
+ - [
8bf7d4b954] NodeTable::metadata now uses Into. (#134) (Kevin R. Thornton)
+ - [
3ac3d50f7b] * Establish a pattern for stronger ID types (#129) (Kevin R. Thornton)
+ - [
e19095d9a9] clippy vs bindgen (#130) (Kevin R. Thornton)
+ - [
d9abda5bb6] Change links in Cargo.toml to tskit-dev (#127) (Kevin R. Thornton)
+
2021-05-19, Version 0.3.0
+This release has a few API changes, etc., that streamline the public interface.
+The C code is updated to 0.99.12.
+Commits
+-
+
- [
ec0adc36ae] streamline API for creating table row objects (#126) (Kevin R. Thornton)
+ - [
edd36fa886] Add mutable access to NodeTable flag and time arrays. (#125) (Kevin R. Thornton)
+ - [
634df568af] Fix docs for Tree::total_branch_length. Fixes #114. (#124) (Kevin R. Thornton)
+ - [
202bcded3f] Give access to TableCollection edge indexes. (#123) (Kevin R. Thornton)
+ - [
3888fe5f10] update C code to version 0.99.12 (#122) (Kevin R. Thornton)
+ - [
6fa2057af6] Add prelude.rs (#119) (Kevin R. Thornton)
+ - [
a592126594] replace crate with $crate for all macros (#113) (Kevin R. Thornton)
+ - [
b618d75e5b] Add macro to aid returning from MetadataRoundtrip functions. (#110) (Kevin R. Thornton)
+ - [
79adaa1a4a] Add macro to remove code duplication (#111) (Kevin R. Thornton)
+ - [
159bbfe926] Add convenience macro to use all public traits. (#106) (Kevin R. Thornton)
+ - [
e912f7b2c8] Bump bindgen version. (#109) (Kevin R. Thornton)
+ - [
15fae9327b] Update clap requirement from ~2.27.0 to ~2.33.3 (#107) (dependabot[bot])
+ - [
55f18a1a4f] Refactor MetadataError: (#105) (Kevin R. Thornton)
+ - [
fbce6ca894] API fixes. (#104) (Kevin R. Thornton)
+
2021-04-27, Version 0.2.2
+This release fixes issues with the lifetime relationships of Tree and the raw C arrays.
+Technically, this is an API change, but only with respect to return type and the integer type used to index that return type.
Commits
+-
+
- [
89d234f674] Replace WrappedTskArray with idiomatic slices. Closes #99 (#101) (Kevin R. Thornton)
+ - [
ed8329b89e] Completely hide NodeIterator from public name spaces. (#100) (Kevin R. Thornton)
+
2021-04-26, Version 0.2.1
+-
+
- [
ff1c7ced82] Add Provenance trait as optional feature (#98). (Kevin R. Thornton)
+ - [
0fdd30067e] Fix error in transmitting nodes. Closes #96 (#97) (Kevin R. Thornton)
+ - [
299c83ae35] Update repo/homepage name in Cargo.toml (molpopgen)
+ - [
35ecf29933] Remove re-exports that are part of existing bitflags types. (#95) (Kevin R. Thornton)
+
2021-04-21, Version 0.2.0
+Commits
+-
+
- [
daffeda43e] bump version to 0.2.0 (molpopgen)
+ - [
0dad5e39d2] Update docs (#93) (Kevin R. Thornton)
+ - [
f905b9c384] Add reverse tree iteration. (#92) (Kevin R. Thornton)
+ - [
a1a033f901] Add development documentation. (#91) (Kevin R. Thornton)
+ - [
ce3d8f4849] Refine forward sim example (#90) (Kevin R. Thornton)
+ - [
b1022e1f59] Refactor how tskit flags are handled. (#89) (Kevin R. Thornton)
+ - [
56e43cb0ff] Add forward simulation example. Closes #71. (#86) (Kevin R. Thornton)
+ - [
5530d7b234] Refactor all examples into examples/ (#85) (Kevin R. Thornton)
+ - [
651e4edcac] Collect public traits in traits.rs. Closes #81. (#84) (Kevin R. Thornton)
+ - [
11ad49f0e1] Remove mention of use NodeIterator. Closes #68. (#83) (Kevin R. Thornton)
+ - [
df28231d9a] Add test fixtures module. Closes #73 (#80) (Kevin R. Thornton)
+ - [
3a8a82637e] Rename Tree::nodes to Tree::traverse_nodes. (#79) (Kevin R. Thornton)
+ - [
4e7af98ac5] Update GitHub actions. (#78) (Kevin R. Thornton)
+ - [
43e14bb8a6] Add NodeListGenerator trait bound to TableAccess. Closes #67. (#75) (Kevin R. Thornton)
+ - [
ae203769f4] add id field to table row types. Closes #76 (#77) (Kevin R. Thornton)
+ - [
346c804be8] Make tree arrays public. Closes #70 (#74) (Kevin R. Thornton)
+ - [
a2dfcfe8f6] Add TableCollection and TreeSequence simplification (#64) (Kevin R. Thornton)
+ - [
c62ccd21aa] Add TableAccess trait and implement for TableCollection and TreeSequence. (#66) (Kevin R. Thornton)
+ - [
167209466a] Remove duplication of entire table collection when creating a tree sequence. (#65) (Kevin R. Thornton)
+ - [
df258ad8d1] Fix useless conversion in lib::c_api_version (#63) (Kevin R. Thornton)
+ - [
fcca8bb682] remove unnecessary function from util (#62) (Kevin R. Thornton)
+ - [
0ee9f86db4] Merge pull request #61 from molpopgen/add_individual_and_migration_tables (Kevin R. Thornton)
+ - [
8f072c47d1] Add migrations and individuals tables. (molpopogen)
+ - [
b2c891300b] Merge pull request #60 from molpopgen/tskit_C_version (Kevin R. Thornton)
+ - [
f48b2fed57] Add functions to return C API version info (molpopogen)
+ - [
87593d4bdc] Merge pull request #59 from molpopgen/add_test_metadata_some_columns_only (Kevin R. Thornton)
+ - [
5ab8e8c9d0] Add test of metadata decoding when not all rows have metadata. (molpopogen)
+ - [
adcc321cc8] Merge pull request #58 from molpopgen/table_row_access (Kevin R. Thornton)
+ - [
860a647bf3] * Add ::row for all tables (molpopgen)
+ - [
6b0a77e106] Add util.rs (molpopgen)
+ - [
6b9631e1f1] Merge pull request #57 from molpopgen/unify_table_iteration (Kevin R. Thornton)
+ - [
3d79f8bbfa] Add ability to iterate tables from a TableCollection: (molpopogen)
+ - [
392ce57e0a] Merge pull request #52 from molpopgen/table_iteration (Kevin R. Thornton)
+ - [
2fe5912c34] Add table iteration w/optional handling of metadata. (molpopgen)
+ - [
9a59a148f7] Merge pull request #55 from molpopgen/wrapped_tsk_array_iter_adapter (Kevin R. Thornton)
+ - [
84b0b496c1] Replace built-in iteration with iterator adapter for WrappedTskArray (molpopgen)
+ - [
18234998ea] Merge pull request #56 from molpopgen/metadata_macro_fixes (Kevin R. Thornton)
+ - [
49bbd0f2f4] metadata_to_vector macro is now a simple return (no ? operator). (molpopgen)
+ - [
6e293acf14] Remove unused paramter to metadata_to_vector. Fixes #54. (molpopgen)
+ - [
45347a576c] Change log for 0.1.2 (molpopgen)
+
2021-04-12, Version 0.1.2
+Commits
+-
+
- [
f475a5c624] Bump version to 0.1.2 (molpopgen)
+ - [
f1887d55e0] Merge pull request #46 from molpopgen/add_important_missing_functions (Kevin R. Thornton)
+ - [
f5598256dd] Merge pull request #47 from molpopgen/add_changelog (Kevin R. Thornton)
+ - [
fb85ba9606] Add Tree::num_tracked_samples and Tree::kc_distance. (molpopogen)
+ - [
08febd5062] Add change log (molpopogen)
+ - [
e6495a959a] Merge pull request #51 from molpopgen/test_beta_instead_of_nightly (Kevin R. Thornton)
+ - [
fa7cca91a5] Test beta instead of nightly. (molpopgen)
+ - [
bd7185eef2] Merge pull request #45 from molpopgen/documentation (Kevin R. Thornton)
+ - [
2400906762] Add documentation related to Tree/TreeSequence (molpopogen)
+ - [
550aa76597] Fix typo in function name. (molpopogen)
+ - [
56eaf875b6] Merge pull request #44 from molpopgen/fix_clippy_warnings (Kevin R. Thornton)
+ - [
20ffe557ca] Fix warnings from clippy (molpopogen)
+ - [
0bf1dada4d] Merge pull request #43 from molpopgen/kc_distance (Kevin R. Thornton)
+ - [
2e8b4c1cfc] Add TreeSequence::kc_distance (molpopogen)
+ - [
efe5ce2b0b] Merge pull request #42 from molpopgen/fix_tskit_array_access_macro (Kevin R. Thornton)
+ - [
82bb6ec6a1] Modify unsafe_tsk_column_access to support idiomatic fall-through. (molpopogen)
+ - [
40e898910d] Merge pull request #41 from molpopgen/sample_list_traversal (Kevin R. Thornton)
+ - [
cb0e9a4355] Add support for samples iteration: (molpopogen)
+ - [
f1acfb06f2] Merge pull request #40 from molpopgen/more_node_iteration (Kevin R. Thornton)
+ - [
22684248d1] * Rename NodeIteration to NodeIterator (molpopogen)
+ - [
faa105d577] Merge pull request #38 from molpopgen/Tree_API (Kevin R. Thornton)
+ - [
896f921e91] Several changes to Tree and TreeSequence: (molpopogen)
+ - [
683ba84b10] Merge pull request #39 from molpopgen/ffi_array_wrapper (Kevin R. Thornton)
+ - [
dd3df03ca3] Add non-owning wrappers to C arrays. (molpopogen)
+ - [
85cc4a591f] Merge pull request #37 from molpopgen/add_tree (Kevin R. Thornton)
+ - [
be97490641] Add minimial Tree interface. (molpopgen)
+ - [
4b6257ed2c] Merge pull request #36 from molpopgen/streamline_macros (Kevin R. Thornton)
+ - [
238f652d24] Remove macro redundancy. (molpopgen)
+ - [
85505887e1] Merge pull request #35 from molpopgen/refine_ffi (Kevin R. Thornton)
+ - [
2cb4993f07] Refactor the ffi module: (molpopgen)
+ - [
1b9a054ff0] Merge pull request #34 from molpopgen/improve_error_handling_macro (Kevin R. Thornton)
+ - [
20a5486132] Add overload of handle_tsk_return_value. (molpopgen)
+ - [
eae11b4c8a] Merge pull request #33 from molpopgen/add_tree_sequence (Kevin R. Thornton)
+ - [
a57b947352] Add TskitConsumingType, macro to build one, and convert TreeSequence (molpopgen)
+ - [
dcb5a02f3c] change dependabot to monthly (molpopgen)
+ - [
4eb407ac61] Merge pull request #31 from molpopgen/dependabot/add-v2-config-file (Kevin R. Thornton)
+ - [
a759e0441b] Merge pull request #32 from molpopgen/dependabot/cargo/bindgen-0.57.0 (dependabot-preview[bot])
+ - [
fb2a56c868] Update bindgen requirement from 0.56.0 to 0.57.0 (dependabot-preview[bot])
+ - [
a8a0b1aabf] Create Dependabot config file (dependabot-preview[bot])
+
2021-03-26, Version 0.1.1
+Commits
+-
+
- [
e9d73e4912] Fix crate name in README.md (molpopogen)
+ - [
28deef7d04] update README (molpopogen)
+ - [
ef79a446c1] Bump version to 0.1.1 (molpopogen)
+ - [
d3c31fa0fc] Merge pull request #30 from molpopgen/fix_warnings (Kevin R. Thornton)
+ - [
bedfa02f76] Merge pull request #29 from molpopgen/metadata_docs (Kevin R. Thornton)
+ - [
f6f3304d75] Remove Drop constraint on TskitType. (molpopogen)
+ - [
d8873a7941] Quick fix regarding documenting metadata. Closes #25 (molpopogen)
+ - [
4518db4946] Merge pull request #28 from molpopgen/update_to_tskit_0_3_5 (Kevin R. Thornton)
+ - [
80893566ed] Update C files to tskit 0.3.5 (molpopogen)
+ - [
e81aad0bf6] Merge pull request #27 from molpopgen/fix_example_file_names (Kevin R. Thornton)
+ - [
dbaf304b38] Fix swapped example file names. Fixes #26 (molpopogen)
+ - [
30c34c2023] Merge pull request #23 from molpopgen/rename_crate (Kevin R. Thornton)
+ - [
e01b3e530e] rename crate to tskit (molpopgen)
+ - [
a7a69ad31d] Merge pull request #20 from molpopgen/metadata (Kevin R. Thornton)
+ - [
54ac4312a1] clippy and fmt (molpopgen)
+ - [
a1aea5cd95] add examples of metadata round trips (molpopgen)
+ - [
7352ca95b5] Update table operations to metadata API. (molpopgen)
+ - [
275074da30] Add metadata trait and API. (molpopgen)
+ - [
d89dcd19dd] Merge pull request #18 from molpopgen/tskit_wrapper_trait (Kevin R. Thornton)
+ - [
3445af368d] TableCollection uses new trait. (molpopgen)
+ - [
93c43aa2c7] Add trait to define what it means to wrap a tskit type. (molpopgen)
+
Migration guide
+This document helps with migration to newer versions of tskit-rust.
+This document will not be exhaustive.
+Rather, it will focus on highlights or "must know" items.
Regarding breaking changes:
+-
+
- This document will discuss breaking changes requiring change in client code. +
- Other changes listed in the change log as breaking are considered "technically breaking +but unlikely to affect anyone in practice". Please file an issue if we are wrong! +
Acronyms used:
+-
+
- UB = undefined behavior. +
v0.12.0
+Breaking changes
+-
+
- Provenance table getters now return
Option<&str>rather thanOption<String>. +These two types are very close to identical in API. +Breakage is only possible if code relied on the return value owning its data.
+ - Several member functions of Tree previously accepted
NodeIdas arguments. +They now takeN: Into<NodeId> + Copy. +Thus, code passing in integers will have to drop the.into()calls.
+ - Tree functions returning iterators previously returned
Option<Iterator<...>>. +They now returnIterator<...>. +Data leading toNonebeing returned in previous versions now return an iterator +that will end immediately.
+ DereftoTableViewswas replaced with delegation because usingDeref+to model inheritance is an anti-pattern.
+usizetoSizeTypeconversions are now fallible (e.g.,TryFromreplacesFrom).
+- The
TskitTypeAccesstrait was removed because it was a bad idea. +(It makes no sense to be generic over returning pointers to low-level tskit types.) +The functionality is replaced withimpl fns.
+ - The names of all
Ownedtables are nowOwning.
+ MetadataError::RoundtripErrornow requiresSend + Sync.
+
v0.11.0
+Bug fixes
+-
+
- Issue 363, which was introduced in PR 300. +The bug resulted in UB when advancing trees for release builds. +
Breaking changes
+New error variant.
+The error enum now includes LibraryError.
+Any code previously matching on errors will now break because the match is no longer exhaustive.
Row getters
+This change occurred over several PR.
+All "getter" functions for table rows now return Option instead of Result when a row index is out of bounds.
+These functions now return None for the out of bounds case.
+This behavior change brings the API in line with other rust APIs.
To update:
+-
+
- If
Noneshould represent an error for your use case, useOption::ok_or_else. +In the case of a previousResult<Option<_>, _>that is now anOption<Result<_, _>>, usetranspose.
+
Lifetime annotations of table types
+PR #373.
+Previously, a non-owning view of an edge table had a type EdgeTable<'a>.
+Those lifetimes are no longer necessary, which is a big design win.
Two traits, TableAccess and NodeListRowGenerator, have been removed.
+The TableCollection and TreeSequence types now contain that functionality as
+Deref targets.
Removing these traits implies:
+-
+
- Their removal from the crate prelude. +
- They can no longer be used as trait bounds. +
Some views of a node table that required mutability broke due to these changes.
+A new function in the Deref target is nodes_mut(&mut self) addresses this breakage.