Merge pull request #1 from A-Baji/horst-changelog

horsto · web-flow · commit d50fce22e4a9 · 2023-05-15T09:29:13.000-04:00
pull from upstream and update changelog
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,7 +3,10 @@
 ### Upcoming
 - Fixed - Fix altering a part table that uses the "master" keyword - PR [#991](https://github.com/datajoint/datajoint-python/pull/991)
 - Fixed - `.ipynb` output in tutorials is not visible in dark mode ([#1078](https://github.com/datajoint/datajoint-python/issues/1078)) PR [#1080](https://github.com/datajoint/datajoint-python/pull/1080)
- 
+- Changed - Readme to update links and include example pipeline image
+- Changed - Docs to add landing page and update navigation
+- Changed - `.data` method to `.stream` in the `get()` method for S3 (external) objects PR [#1085](https://github.com/datajoint/datajoint-python/pull/1085)
+
 ### 0.14.0 -- Feb 13, 2023
 - Added - `json` data type ([#245](https://github.com/datajoint/datajoint-python/issues/245)) PR [#1051](https://github.com/datajoint/datajoint-python/pull/1051)
 - Fixed - Activating a schema requires all tables to exist even if `create_tables=False` PR [#1058](https://github.com/datajoint/datajoint-python/pull/1058)
diff --git a/README.md b/README.md
@@ -1,8 +1,6 @@
 [![DOI](https://zenodo.org/badge/16774/datajoint/datajoint-python.svg)](https://zenodo.org/badge/latestdoi/16774/datajoint/datajoint-python)
-[![Build Status](https://travis-ci.org/datajoint/datajoint-python.svg?branch=master)](https://travis-ci.org/datajoint/datajoint-python)
 [![Coverage Status](https://coveralls.io/repos/datajoint/datajoint-python/badge.svg?branch=master&service=github)](https://coveralls.io/github/datajoint/datajoint-python?branch=master)
 [![PyPI version](https://badge.fury.io/py/datajoint.svg)](http://badge.fury.io/py/datajoint)
-[![Requirements Status](https://requires.io/github/datajoint/datajoint-python/requirements.svg?branch=master)](https://requires.io/github/datajoint/datajoint-python/requirements/?branch=master)
 [![Slack](https://img.shields.io/badge/slack-chat-green.svg)](https://datajoint.slack.com/)
 
 # Welcome to DataJoint for Python!
@@ -12,22 +10,32 @@ DataJoint for Python is a framework for scientific workflow management based on
 DataJoint was initially developed in 2009 by Dimitri Yatsenko in Andreas Tolias' Lab at Baylor College of Medicine for the distributed processing and management of large volumes of data streaming from regular experiments. Starting in 2011, DataJoint has been available as an open-source project adopted by other labs and improved through contributions from several developers.
 Presently, the primary developer of DataJoint open-source software is the company DataJoint (https://datajoint.com).
 
-- [Getting Started](https://datajoint.com/docs/core/datajoint-python/latest/getting-started/)
-- [DataJoint Elements](https://datajoint.com/docs/elements/) - Catalog of example pipelines
-- [DataJoint CodeBook](https://codebook.datajoint.io) - Interactive online tutorials
-- Contribute
+## Data Pipeline Example
+
+![pipeline](https://raw.githubusercontent.com/datajoint/datajoint-python/master/images/pipeline.png)
+
+[Yatsenko et al., bioRxiv 2021](https://doi.org/10.1101/2021.03.30.437358)
+
+## Getting Started
+
+- Install from PyPI
+
+     ```bash
+     pip install datajoint
+     ```
+
+- [Documentation & Tutorials](https://datajoint.com/docs/core/datajoint-python/)
+
+- [Interactive Tutorials](https://github.com/datajoint/datajoint-tutorials) on GitHub Codespaces
 
+- [DataJoint Elements](https://datajoint.com/docs/elements/) - Catalog of example pipelines for neuroscience experiments
+
+- Contribute
   - [Development Environment](https://datajoint.com/docs/core/datajoint-python/latest/develop/)
+
   - [Guidelines](https://datajoint.com/docs/community/contribute/)
 
 - Legacy Resources (To be replaced by above)
   - [Documentation](https://docs.datajoint.org)
-  - [Tutorials](https://tutorials.datajoint.org)
 
-## Citation
-
-- If your work uses DataJoint for Python, please cite the following Research Resource Identifier (RRID) and manuscript.
-
-- DataJoint ([RRID:SCR_014543](https://scicrunch.org/resolver/SCR_014543)) - DataJoint for Python (version `<Enter version number>`)
-
-- Yatsenko D, Reimer J, Ecker AS, Walker EY, Sinz F, Berens P, Hoenselaar A, Cotton RJ, Siapas AS, Tolias AS. DataJoint: managing big scientific data using MATLAB or Python. bioRxiv. 2015 Jan 1:031658. doi: https://doi.org/10.1101/031658
+  - [Tutorials](https://tutorials.datajoint.org)
diff --git a/docs/docker-compose.yaml b/docs/docker-compose.yaml
@@ -7,7 +7,7 @@ services:
       context: ../
       args:
         - PACKAGE
-    image: ${PACKAGE}-docs
+    image: ${PACKAGE}_python-docs
     environment:
       - PACKAGE
       - UPSTREAM_REPO
@@ -16,7 +16,7 @@ services:
       - ..:/main
     user: ${HOST_UID}:anaconda
     ports:
-      - 8080:80
+      - 80:80
     command:
       - sh
       - -c
diff --git a/docs/mkdocs.yaml b/docs/mkdocs.yaml
@@ -1,10 +1,10 @@
 # ---------------------- PROJECT SPECIFIC ---------------------------
 
-site_name: DataJoint Python
+site_name: DataJoint Documentation
 repo_url: https://github.com/datajoint/datajoint-python
 repo_name: datajoint/datajoint-python
 nav:
-  - DataJoint Python: getting-started/index.md
+  - DataJoint Python: index.md
   - Getting Started: getting-started/index.md
   - Existing Pipelines: concepts/existing-pipelines.md
   - Query Language:
@@ -18,6 +18,7 @@ nav:
   - Tutorials:
       - tutorials/json.ipynb
   - Develop: develop.md
+  - Citation: citation.md
   - Changelog: about/changelog.md
   - API: api/ # defer to gen-files + literate-nav
 
@@ -50,9 +51,6 @@ theme:
         name: Switch to light mode
 plugins:
   - search
-  - redirects:
-      redirect_maps:
-        "index.md": "getting-started/index.md"
   - mkdocstrings:
       default_handler: python
       handlers:
@@ -95,11 +93,11 @@ markdown_extensions:
         - name: mermaid
           class: mermaid
           format: !!python/name:pymdownx.superfences.fence_code_format
+  - pymdownx.magiclink # Displays bare URLs as links
+  - pymdownx.tasklist: # Renders check boxes in tasks lists
+      custom_checkbox: true
 extra:
   generator: false # Disable watermark
-  analytics:
-    provider: google
-    property: !ENV GOOGLE_ANALYTICS_KEY
   version:
     provider: mike
   social:
diff --git a/docs/src/.overrides/partials/nav.html b/docs/src/.overrides/partials/nav.html
@@ -14,7 +14,7 @@
         {#-
         Add DataJoint home link to navigation header, otherwise unchanged
         -#}
-        <a href="https://datajoint.com/docs/" title="DataJoint">
+        <a href="https://datajoint.com/docs/core/" title="DataJoint">
             ⬅ Home
         </a>
     </label>
diff --git a/docs/src/citation.md b/docs/src/citation.md
@@ -0,0 +1,7 @@
+# Citation
+
+If your work uses the DataJoint API for Python, please cite the following manuscript and Research Resource Identifier (RRID):
+
+- Yatsenko D, Reimer J, Ecker AS, Walker EY, Sinz F, Berens P, Hoenselaar A, Cotton RJ, Siapas AS, Tolias AS. DataJoint: managing big scientific data using MATLAB or Python. bioRxiv. 2015 Jan 1:031658. doi: https://doi.org/10.1101/031658
+
+- DataJoint API for Python - [RRID:SCR_014543](https://scicrunch.org/resolver/SCR_014543) - Version `Enter version here`
diff --git a/docs/src/index.md b/docs/src/index.md
@@ -0,0 +1,36 @@
+# Welcome to the DataJoint API for Python!
+
+The DataJoint API for Python is a framework for scientific workflow management based on relational principles. DataJoint is built on the foundation of the relational data model and prescribes a consistent method for organizing, populating, computing, and querying data.
+
+DataJoint was initially developed in 2009 by Dimitri Yatsenko in Andreas Tolias' Lab at Baylor College of Medicine for the distributed processing and management of large volumes of data streaming from regular experiments. Starting in 2011, DataJoint has been available as an open-source project adopted by other labs and improved through contributions from several developers.
+Presently, the primary developer of DataJoint open-source software is the company [DataJoint](https://datajoint.com){:target="_blank"}.
+
+## Data Pipeline Example
+
+![pipeline](https://raw.githubusercontent.com/datajoint/datajoint-python/master/images/pipeline.png)
+
+[Yatsenko et al., bioRxiv 2021](https://doi.org/10.1101/2021.03.30.437358){:target="_blank"}
+
+## Getting Started
+
+- Install from PyPI
+
+     ```bash
+     pip install datajoint
+     ```
+
+- [Detailed Getting Started Guide](./getting-started)
+
+- [Interactive Tutorials](https://github.com/datajoint/datajoint-tutorials){:target="_blank"} on GitHub Codespaces
+
+- [DataJoint Elements](../../elements/) - Catalog of example pipelines for neuroscience experiments
+
+- Contribute
+  - [Development Environment](./develop)
+
+  - [Guidelines](../../community/contribute/)
+
+- Legacy Resources (To be replaced by above)
+  - [Documentation](https://docs.datajoint.org)
+
+  - [Tutorials](https://tutorials.datajoint.org)
diff --git a/images/pipeline.drawio b/images/pipeline.drawio
diff --git a/images/pipeline.png b/images/pipeline.png
