Improve Freud integration (#30)

* WIP on doctests

* Add sphinx-copybutton and notfound

* messy wip on sybil

* Further wip

* Remove .doctrees

* Remove CIFTEST

* Swap to pytest-doctestplus

* Remove unused files

* Clean up settings

* Fix read_cell_params interaction with cast_values

* Clean up conf.py

* Update filepath for docstrings

* Clean up pyproject.toml

* Fix formatting for doctests

* Finalize indentation for quickstart.rst

* Update requirements.in files

* Update doc/requirements.txt

* Update requirements files

* Fix return None example

* Lint

* Fix pytest-doctestplus version

* Update `cell` to return box-like

* Clarify docs for CifFile.cell

* Final cleanup of freud tests

* Install freud on ubuntu-latest tests

* Add missing doctest: +SKIP

* Use pytest importorskip

* Remove freud from ci

* Fix doctest-requires block

* Standardize spelling of angstrom

* Rename cell to box

Author: janbridley

.github/requirements-3.10.txt

@@ -18,7 +18,7 @@ kiwisolver==1.4.8
     # via matplotlib
 matplotlib==3.10.0
     # via ase
-more-itertools==10.5.0
+more-itertools==10.6.0
     # via parsnip (pyproject.toml)
 numpy==2.2.1
     # via
@@ -32,7 +32,8 @@ packaging==24.2
     # via
     #   matplotlib
     #   pytest
-pillow==11.0.0
+    #   pytest-doctestplus
+pillow==11.1.0
     # via matplotlib
 pluggy==1.5.0
     # via pytest
@@ -43,10 +44,14 @@ pycifrw==4.4.6
 pyparsing==3.2.1
     # via matplotlib
 pytest==8.3.4
+    # via
+    #   -r tests/requirements.in
+    #   pytest-doctestplus
+pytest-doctestplus==1.3.0
     # via -r tests/requirements.in
 python-dateutil==2.9.0.post0
     # via matplotlib
-scipy==1.14.1
+scipy==1.15.1
     # via ase
 six==1.17.0
     # via python-dateutil

.github/requirements-3.11.txt

@@ -16,7 +16,7 @@ kiwisolver==1.4.8
     # via matplotlib
 matplotlib==3.10.0
     # via ase
-more-itertools==10.5.0
+more-itertools==10.6.0
     # via parsnip (pyproject.toml)
 numpy==2.2.1
     # via
@@ -30,7 +30,8 @@ packaging==24.2
     # via
     #   matplotlib
     #   pytest
-pillow==11.0.0
+    #   pytest-doctestplus
+pillow==11.1.0
     # via matplotlib
 pluggy==1.5.0
     # via pytest
@@ -41,10 +42,14 @@ pycifrw==4.4.6
 pyparsing==3.2.1
     # via matplotlib
 pytest==8.3.4
+    # via
+    #   -r tests/requirements.in
+    #   pytest-doctestplus
+pytest-doctestplus==1.3.0
     # via -r tests/requirements.in
 python-dateutil==2.9.0.post0
     # via matplotlib
-scipy==1.14.1
+scipy==1.15.1
     # via ase
 six==1.17.0
     # via python-dateutil

.github/requirements-3.12.txt

@@ -16,7 +16,7 @@ kiwisolver==1.4.8
     # via matplotlib
 matplotlib==3.10.0
     # via ase
-more-itertools==10.5.0
+more-itertools==10.6.0
     # via parsnip (pyproject.toml)
 numpy==2.2.1
     # via
@@ -30,7 +30,8 @@ packaging==24.2
     # via
     #   matplotlib
     #   pytest
-pillow==11.0.0
+    #   pytest-doctestplus
+pillow==11.1.0
     # via matplotlib
 pluggy==1.5.0
     # via pytest
@@ -41,10 +42,14 @@ pycifrw==4.4.6
 pyparsing==3.2.1
     # via matplotlib
 pytest==8.3.4
+    # via
+    #   -r tests/requirements.in
+    #   pytest-doctestplus
+pytest-doctestplus==1.3.0
     # via -r tests/requirements.in
 python-dateutil==2.9.0.post0
     # via matplotlib
-scipy==1.14.1
+scipy==1.15.1
     # via ase
 six==1.17.0
     # via python-dateutil

.github/requirements-3.13.txt

@@ -16,7 +16,7 @@ kiwisolver==1.4.8
     # via matplotlib
 matplotlib==3.10.0
     # via ase
-more-itertools==10.5.0
+more-itertools==10.6.0
     # via parsnip (pyproject.toml)
 numpy==2.2.1
     # via
@@ -30,7 +30,8 @@ packaging==24.2
     # via
     #   matplotlib
     #   pytest
-pillow==11.0.0
+    #   pytest-doctestplus
+pillow==11.1.0
     # via matplotlib
 pluggy==1.5.0
     # via pytest
@@ -41,10 +42,14 @@ pycifrw==4.4.6
 pyparsing==3.2.1
     # via matplotlib
 pytest==8.3.4
+    # via
+    #   -r tests/requirements.in
+    #   pytest-doctestplus
+pytest-doctestplus==1.3.0
     # via -r tests/requirements.in
 python-dateutil==2.9.0.post0
     # via matplotlib
-scipy==1.14.1
+scipy==1.15.1
     # via ase
 six==1.17.0
     # via python-dateutil

.github/requirements-3.7.txt

@@ -44,9 +44,11 @@ pycifrw==4.4.6
 pyparsing==3.1.4
     # via matplotlib
 pytest==7.4.4
+    # via matplotlib
+pytest-doctestplus==1.0.0
     # via -r tests/requirements.in
 python-dateutil==2.9.0.post0
-    # via matplotlib
+    # via -r tests/requirements.in
 scipy==1.7.3
     # via ase
 six==1.17.0

.github/requirements-3.8.txt

@@ -34,6 +34,7 @@ packaging==24.2
     # via
     #   matplotlib
     #   pytest
+    #   pytest-doctestplus
 pillow==10.4.0
     # via matplotlib
 pluggy==1.5.0
@@ -45,6 +46,10 @@ pycifrw==4.4.6
 pyparsing==3.1.4
     # via matplotlib
 pytest==8.3.4
+    # via
+    #   -r tests/requirements.in
+    #   pytest-doctestplus
+pytest-doctestplus==1.3.0
     # via -r tests/requirements.in
 python-dateutil==2.9.0.post0
     # via matplotlib

.github/requirements-3.9.txt

@@ -12,15 +12,15 @@ fonttools==4.55.3
     # via matplotlib
 gemmi==0.7.0
     # via -r tests/requirements.in
-importlib-resources==6.4.5
+importlib-resources==6.5.2
     # via matplotlib
 iniconfig==2.0.0
     # via pytest
 kiwisolver==1.4.7
     # via matplotlib
 matplotlib==3.9.4
     # via ase
-more-itertools==10.5.0
+more-itertools==10.6.0
     # via parsnip (pyproject.toml)
 numpy==2.0.2
     # via
@@ -34,7 +34,8 @@ packaging==24.2
     # via
     #   matplotlib
     #   pytest
-pillow==11.0.0
+    #   pytest-doctestplus
+pillow==11.1.0
     # via matplotlib
 pluggy==1.5.0
     # via pytest
@@ -45,6 +46,10 @@ pycifrw==4.4.6
 pyparsing==3.2.1
     # via matplotlib
 pytest==8.3.4
+    # via
+    #   -r tests/requirements.in
+    #   pytest-doctestplus
+pytest-doctestplus==1.3.0
     # via -r tests/requirements.in
 python-dateutil==2.9.0.post0
     # via matplotlib

ChangeLog.rst

@@ -4,7 +4,31 @@ Changelog
 The format is based on `Keep a Changelog <http://keepachangelog.com/en/1.1.0/>`__.
 This project adheres to `Semantic Versioning <http://semver.org/spec/v2.0.0.html>`__.
 
-v0.x.x - 20xx-xx-xx
+v1.0.0 - 20xx-xx-xx
+-------------------
 
 Added
 ~~~~~
+- Support for nonsimple (';'-delimited) data entries.
+- Improved support for entries containing special characters.
+- Ability to query multiple keys or columns simultaneously.
+- Additional tests for AMCSD and zeolite databases.
+- Additional documentation and examples for the new interface
+
+Changed
+~~~~~~~
+- Primary interface is now the ``CifFile`` object, which supports all previously implemented features in addition to several new methods.
+- Files are now parsed lazily, and are traversed a single time.
+
+Dependencies
+~~~~~~~~~~~~
+- Added ``more-itertools`` as a dependency for ``peekable`` iterators
+
+
+v0.1.0 - 2024-12-20
+-------------------
+
+Added
+~~~~~
+- Unitcells module
+- Function-based parsing interface for key and table reading

doc/requirements.in

@@ -2,3 +2,6 @@ autodocsumm
 furo
 numpy>=1.26.4
 sphinx>=7.3.7
+sphinx-copybutton
+sphinx-notfound-page
+pytest-doctestplus

doc/requirements.txt

@@ -10,7 +10,7 @@ beautifulsoup4==4.12.3
     # via furo
 certifi==2024.12.14
     # via requests
-charset-normalizer==3.4.0
+charset-normalizer==3.4.1
     # via requests
 docutils==0.21.2
     # via sphinx
@@ -20,20 +20,33 @@ idna==3.10
     # via requests
 imagesize==1.4.1
     # via sphinx
-jinja2==3.1.4
+iniconfig==2.0.0
+    # via pytest
+jinja2==3.1.5
     # via sphinx
 markupsafe==3.0.2
     # via jinja2
-numpy==2.2.0
+more-itertools==10.6.0
+    # via parsnip (pyproject.toml)
+numpy==2.2.1
     # via
     #   -r doc/requirements.in
     #   parsnip (pyproject.toml)
 packaging==24.2
-    # via sphinx
-pygments==2.18.0
+    # via
+    #   pytest
+    #   pytest-doctestplus
+    #   sphinx
+pluggy==1.5.0
+    # via pytest
+pygments==2.19.1
     # via
     #   furo
     #   sphinx
+pytest==8.3.4
+    # via pytest-doctestplus
+pytest-doctestplus==1.3.0
+    # via -r doc/requirements.in
 requests==2.32.3
     # via sphinx
 snowballstemmer==2.2.0
@@ -46,8 +59,14 @@ sphinx==8.1.3
     #   autodocsumm
     #   furo
     #   sphinx-basic-ng
+    #   sphinx-copybutton
+    #   sphinx-notfound-page
 sphinx-basic-ng==1.0.0b2
     # via furo
+sphinx-copybutton==0.5.2
+    # via -r doc/requirements.in
+sphinx-notfound-page==1.0.4
+    # via -r doc/requirements.in
 sphinxcontrib-applehelp==2.0.0
     # via sphinx
 sphinxcontrib-devhelp==2.0.0
@@ -60,5 +79,5 @@ sphinxcontrib-qthelp==2.0.0
     # via sphinx
 sphinxcontrib-serializinghtml==2.0.0
     # via sphinx
-urllib3==2.2.3
+urllib3==2.3.0
     # via requests