Add ability to build out unit cells from CIF files (#11)

* Add _str2num and _deg2rad _utils * Add cif file keys list to sample data * Add key_value_pairs reader and cell_params reader to parse * Add tests for key reader * Add tests for new utils * Reorder test_key_reader * Improve documentation for regex * Add warnings and tests to read_key_value_pairs * Restore trailing spaces to downloaded CIF files * Properly track keys containing "-" * Improved tests for key value pair reader * Add key-value tests for INTENTIONALLY_BAD_CIF.cif * Fix docs * Enable top of page button * Update brand primary colors * Improve docs for parse.py * Add __future__.annotations imports to relevant files * Fix typo * Seperate _errors from _templates * Clean up docstring return types * Add PDB cif to test suite * Fix test in test_key_reader * Clean up patterns.py and add remove_nondelimiting_whitespace * Update table_reader to use remove_nondelimiting_whitespace * Allow value reader to read mmCIF files * Update test_table_reader.py * Remove seperate mmCIF reader * Add docs for patterns module * Fix cast_to_float default value * Update docs * Add documentation for __call__ * Update regex_filter param documentation * Fix typo * Remove unneeded comment * Fix default values in docs * Fix typo * Minor doc fix * Fix typo * Remove duplicate Introduction from index * Remove duplicate entries from toc * Add source for PDB cif * Add mmCIF flag to read_cell_params * Add quickstart.rst * Fix comment in quickstart * Remove unnecessary line in quickstart * Fix image path in README.rst * Update regex documentation * Fix CI * Update __init__.py * Add unitcells module * Add documentation links * Fix doc file naming * Remove resolved TODO * Add top level description to unitcells * Default regex filters to None * Fix default setting for nondelimiting_whitespace_replacement * Remove outdated comment * Fix tests * Add tests for symmetry operations * Fix precision issues * Increase string lines threshold * Remove in-file tests * Return unrounded values * Add test_extract_unit_cell * Add distance calculation util for uniqueness comparison * Add function to build basis vector matrix from box * Update unitcell builder and rename to extract_atomic_positions * Update docstrings * Clarify function naming * Change space group for IncStrDb_Ccmm.cif to standard format * Remove unnecessary transpose in basis vector function * Update unitcell tests to use ase * Filter out ase warnings * Switch catch_warnings to filterwarnings for python 3.9 compat * Add pytest to test requirements * Fix top of page buttons and add view link * Fix logo on README.rst * Add readable assertion error in unitcells.py * Improve assertion error in _safe_eval * Remove unused distance-merge code * Improve CI resilience * Remove dependabot * Add requirements.txt for py3.6 and py3.7 * Update requirements.yaml CI action * Remove temporary lines from ci * Add future-annotations package * Fix annotations * Disable testing on py3.6 * Update doc requirements * Decapitalize changelog and credits * Swap tests to us UV * Fix uv version * Clean up CI script * Activate venv * Remove setup.py * Fix CI * Clean up CI * Simplify CI * Clean up overview
glotzerlab · Dec 20, 2024 · 844578f · 844578f
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commit 844578f
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diff --git a/.github/dependabot.yml b/.github/dependabot.yml
diff --git a/.github/requirements-3.10.txt b/.github/requirements-3.10.txt
@@ -0,0 +1,47 @@
+# This file was autogenerated by uv via the following command:
+#    uv pip compile --python-version=3.10 pyproject.toml tests/requirements.in
+ase==3.23.0
+    # via -r tests/requirements.in
+contourpy==1.3.1
+    # via matplotlib
+cycler==0.12.1
+    # via matplotlib
+exceptiongroup==1.2.2
+    # via pytest
+fonttools==4.55.3
+    # via matplotlib
+gemmi==0.7.0
+    # via -r tests/requirements.in
+iniconfig==2.0.0
+    # via pytest
+kiwisolver==1.4.7
+    # via matplotlib
+matplotlib==3.10.0
+    # via ase
+numpy==2.2.0
+    # via
+    #   parsnip (pyproject.toml)
+    #   ase
+    #   contourpy
+    #   matplotlib
+    #   scipy
+packaging==24.2
+    # via
+    #   matplotlib
+    #   pytest
+pillow==11.0.0
+    # via matplotlib
+pluggy==1.5.0
+    # via pytest
+pyparsing==3.2.0
+    # via matplotlib
+pytest==8.3.4
+    # via -r tests/requirements.in
+python-dateutil==2.9.0.post0
+    # via matplotlib
+scipy==1.14.1
+    # via ase
+six==1.17.0
+    # via python-dateutil
+tomli==2.2.1
+    # via pytest
diff --git a/.github/requirements-3.11.txt b/.github/requirements-3.11.txt
@@ -0,0 +1,43 @@
+# This file was autogenerated by uv via the following command:
+#    uv pip compile --python-version=3.11 pyproject.toml tests/requirements.in
+ase==3.23.0
+    # via -r tests/requirements.in
+contourpy==1.3.1
+    # via matplotlib
+cycler==0.12.1
+    # via matplotlib
+fonttools==4.55.3
+    # via matplotlib
+gemmi==0.7.0
+    # via -r tests/requirements.in
+iniconfig==2.0.0
+    # via pytest
+kiwisolver==1.4.7
+    # via matplotlib
+matplotlib==3.10.0
+    # via ase
+numpy==2.2.0
+    # via
+    #   parsnip (pyproject.toml)
+    #   ase
+    #   contourpy
+    #   matplotlib
+    #   scipy
+packaging==24.2
+    # via
+    #   matplotlib
+    #   pytest
+pillow==11.0.0
+    # via matplotlib
+pluggy==1.5.0
+    # via pytest
+pyparsing==3.2.0
+    # via matplotlib
+pytest==8.3.4
+    # via -r tests/requirements.in
+python-dateutil==2.9.0.post0
+    # via matplotlib
+scipy==1.14.1
+    # via ase
+six==1.17.0
+    # via python-dateutil
diff --git a/.github/requirements-3.12.txt b/.github/requirements-3.12.txt
@@ -0,0 +1,43 @@
+# This file was autogenerated by uv via the following command:
+#    uv pip compile --python-version=3.12 pyproject.toml tests/requirements.in
+ase==3.23.0
+    # via -r tests/requirements.in
+contourpy==1.3.1
+    # via matplotlib
+cycler==0.12.1
+    # via matplotlib
+fonttools==4.55.3
+    # via matplotlib
+gemmi==0.7.0
+    # via -r tests/requirements.in
+iniconfig==2.0.0
+    # via pytest
+kiwisolver==1.4.7
+    # via matplotlib
+matplotlib==3.10.0
+    # via ase
+numpy==2.2.0
+    # via
+    #   parsnip (pyproject.toml)
+    #   ase
+    #   contourpy
+    #   matplotlib
+    #   scipy
+packaging==24.2
+    # via
+    #   matplotlib
+    #   pytest
+pillow==11.0.0
+    # via matplotlib
+pluggy==1.5.0
+    # via pytest
+pyparsing==3.2.0
+    # via matplotlib
+pytest==8.3.4
+    # via -r tests/requirements.in
+python-dateutil==2.9.0.post0
+    # via matplotlib
+scipy==1.14.1
+    # via ase
+six==1.17.0
+    # via python-dateutil
diff --git a/.github/requirements-3.13.txt b/.github/requirements-3.13.txt
@@ -0,0 +1,43 @@
+# This file was autogenerated by uv via the following command:
+#    uv pip compile --python-version=3.13 pyproject.toml tests/requirements.in
+ase==3.23.0
+    # via -r tests/requirements.in
+contourpy==1.3.1
+    # via matplotlib
+cycler==0.12.1
+    # via matplotlib
+fonttools==4.55.3
+    # via matplotlib
+gemmi==0.7.0
+    # via -r tests/requirements.in
+iniconfig==2.0.0
+    # via pytest
+kiwisolver==1.4.7
+    # via matplotlib
+matplotlib==3.10.0
+    # via ase
+numpy==2.2.0
+    # via
+    #   parsnip (pyproject.toml)
+    #   ase
+    #   contourpy
+    #   matplotlib
+    #   scipy
+packaging==24.2
+    # via
+    #   matplotlib
+    #   pytest
+pillow==11.0.0
+    # via matplotlib
+pluggy==1.5.0
+    # via pytest
+pyparsing==3.2.0
+    # via matplotlib
+pytest==8.3.4
+    # via -r tests/requirements.in
+python-dateutil==2.9.0.post0
+    # via matplotlib
+scipy==1.14.1
+    # via ase
+six==1.17.0
+    # via python-dateutil
diff --git a/.github/requirements-3.6.txt b/.github/requirements-3.6.txt
@@ -0,0 +1,56 @@
+    # manual, required to use __future__ annotations style in py3.6
+ase==3.22.1
+    # via -r tests/requirements.in
+cycler==0.11.0
+    # via matplotlib
+exceptiongroup==0.0.0a0
+    # via pytest
+fonttools==4.27.1
+# This file was MANUALLY MODIFIED based on an initial state generated via the following command:
+#    uv pip compile --python-version=3.7 pyproject.toml tests/requirements.in
+future-annotations==1.0.0
+    # via matplotlib
+gemmi==0.6.3
+    # via -r tests/requirements.in
+importlib-metadata==4.8.3
+    # via
+    #   pluggy
+    #   pytest
+iniconfig==1.1.1
+    # via pytest
+kiwisolver==1.3.1
+    # via matplotlib
+matplotlib==3.3.4
+    # via ase
+numpy==1.19.5
+    # via
+    #   parsnip (pyproject.toml)
+    #   ase
+    #   matplotlib
+    #   scipy
+packaging==21.3
+    # via
+    #   matplotlib
+    #   pytest
+pillow==8.4.0
+    # via matplotlib
+pluggy==1.0.0
+    # via pytest
+pyparsing==3.1.4
+    # via matplotlib
+pytest==7.0.1
+    # via -r tests/requirements.in
+python-dateutil==2.9.0.post0
+    # via matplotlib
+scipy==1.5.4
+    # via ase
+six==1.17.0
+    # via python-dateutil
+tomli==1.2.3
+    # via pytest
+typing-extensions==4.1.1
+    # via
+    #   importlib-metadata
+    #   kiwisolver
+zipp==3.6.0
+    # via importlib-metadata
diff --git a/.github/requirements-3.7.txt b/.github/requirements-3.7.txt
@@ -0,0 +1,54 @@
+# This file was autogenerated by uv via the following command:
+#    uv pip compile --python-version=3.7 pyproject.toml tests/requirements.in
+ase==3.22.1
+    # via -r tests/requirements.in
+cycler==0.11.0
+    # via matplotlib
+exceptiongroup==1.2.2
+    # via pytest
+fonttools==4.38.0
+    # via matplotlib
+gemmi==0.6.7
+    # via -r tests/requirements.in
+importlib-metadata==6.7.0
+    # via
+    #   pluggy
+    #   pytest
+iniconfig==2.0.0
+    # via pytest
+kiwisolver==1.4.5
+    # via matplotlib
+matplotlib==3.5.3
+    # via ase
+numpy==1.21.6
+    # via
+    #   parsnip (pyproject.toml)
+    #   ase
+    #   matplotlib
+    #   scipy
+packaging==24.0
+    # via
+    #   matplotlib
+    #   pytest
+pillow==9.5.0
+    # via matplotlib
+pluggy==1.2.0
+    # via pytest
+pyparsing==3.1.4
+    # via matplotlib
+pytest==7.4.4
+    # via -r tests/requirements.in
+python-dateutil==2.9.0.post0
+    # via matplotlib
+scipy==1.7.3
+    # via ase
+six==1.17.0
+    # via python-dateutil
+tomli==2.0.1
+    # via pytest
+typing-extensions==4.7.1
+    # via
+    #   importlib-metadata
+    #   kiwisolver
+zipp==3.15.0
+    # via importlib-metadata
diff --git a/.github/requirements-3.8.txt b/.github/requirements-3.8.txt
@@ -0,0 +1,51 @@
+# This file was autogenerated by uv via the following command:
+#    uv pip compile --python-version=3.8 pyproject.toml tests/requirements.in
+ase==3.23.0
+    # via -r tests/requirements.in
+contourpy==1.1.1
+    # via matplotlib
+cycler==0.12.1
+    # via matplotlib
+exceptiongroup==1.2.2
+    # via pytest
+fonttools==4.55.3
+    # via matplotlib
+gemmi==0.7.0
+    # via -r tests/requirements.in
+importlib-resources==6.4.5
+    # via matplotlib
+iniconfig==2.0.0
+    # via pytest
+kiwisolver==1.4.7
+    # via matplotlib
+matplotlib==3.7.5
+    # via ase
+numpy==1.24.4
+    # via
+    #   parsnip (pyproject.toml)
+    #   ase
+    #   contourpy
+    #   matplotlib
+    #   scipy
+packaging==24.2
+    # via
+    #   matplotlib
+    #   pytest
+pillow==10.4.0
+    # via matplotlib
+pluggy==1.5.0
+    # via pytest
+pyparsing==3.1.4
+    # via matplotlib
+pytest==8.3.4
+    # via -r tests/requirements.in
+python-dateutil==2.9.0.post0
+    # via matplotlib
+scipy==1.10.1
+    # via ase
+six==1.17.0
+    # via python-dateutil
+tomli==2.2.1
+    # via pytest
+zipp==3.20.2
+    # via importlib-resources