shapely fix + license (#12)

* shapely update: exterior --> boundary

* add license

* precommit

* bump shapely

* undo version downgrade

* just return hull coords

* lint

* mypy and numpy types

* add missing black dependence

* and add missing pydocstyle...

* reroll dependency

---------

Co-authored-by: Patrick Huck <[email protected]>

Author: esoteric-ephemera

.github/workflows/testing.yml

@@ -30,4 +30,4 @@ jobs:
         pip install -e .
     - name: pytest
       run: |
-        pytest --cov=pymatgen.analysis.diffusion --durations=30 pymatgen
+        pytest --cov=pymatgen.analysis.alloys --durations=30 pymatgen

LICENSE

@@ -0,0 +1,13 @@
+Copyright 2025 The Regents of the University of California, through Lawrence Berkeley National Laboratory (subject to receipt of any required approvals from the U.S. Dept. of Energy).
+
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS “AS IS” AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

pymatgen/analysis/alloys/__init__.py

@@ -1,4 +1,3 @@
-"""
-This module defines classes useful for representation of alloy systems and is
+"""This module defines classes useful for representation of alloy systems and is
 intended for semiconductor alloys specifically.
 """

pymatgen/analysis/alloys/core.py

@@ -5,6 +5,7 @@
 # You can find this script at https://github.com/rsmith-nl/wavelength_to_rgb
 # The algorithm is based on Dan Bruton's work in
 # http://www.physics.sfasu.edu/astro/color/spectra.html
+from __future__ import annotations
 
 import base64
 import zlib
@@ -29,10 +30,10 @@
 
 
 def rgb(nm) -> tuple[int, int, int]:
-    """
-    Converts a wavelength between 380 and 780 nm to an RGB color tuple.
+    """Converts a wavelength between 380 and 780 nm to an RGB color tuple.
     Argument:
         nm: Wavelength in nanometers. It is rounded to the nearest integer.
+
     Returns:
         a 3-tuple (red, green, blue) of integers in the range 0-255.
     """

pymatgen/analysis/alloys/rgb.py

@@ -31,7 +31,9 @@ test = [
   "pytest-mock",
   "pytest-xdist",
   "flake8",
+  "black",
   "pycodestyle",
+  "pydocstyle",
   "mypy",
   "mypy-extensions",
   "typing-extensions",
@@ -56,8 +58,7 @@ xfail_strict = true
 filterwarnings = ["default"]
 testpaths = ["pymatgen/analysis/alloys/tests"]
 
-[tool.ruff]
-target-version = "py38"
+[tool.ruff.lint]
 select = [
   "B",   # flake8-bugbear
   "D",   # pydocstyle
@@ -95,7 +96,7 @@ pydocstyle.convention = "google"
 flake8-unused-arguments.ignore-variadic-names = true
 isort.required-imports = ["from __future__ import annotations"]
 
-[tool.ruff.per-file-ignores]
+[tool.ruff.lint.per-file-ignores]
 "*/__init__.py" = ["F401"] # F401: imported but unused
 
 [tool.black]

pyproject.toml

@@ -10,12 +10,16 @@ babel==2.17.0
     # via sphinx
 bibtexparser==1.4.3
     # via pymatgen
+black==25.9.0
+    # via pymatgen-analysis-alloys (pyproject.toml)
 certifi==2025.10.5
     # via requests
 cfgv==3.4.0
     # via pre-commit
 charset-normalizer==3.4.4
     # via requests
+click==8.3.0
+    # via black
 contourpy==1.3.3
     # via matplotlib
 coverage[toml]==7.11.0
@@ -62,6 +66,7 @@ mypy==1.18.2
     # via pymatgen-analysis-alloys (pyproject.toml)
 mypy-extensions==1.1.0
     # via
+    #   black
     #   mypy
     #   pymatgen-analysis-alloys (pyproject.toml)
 narwhals==2.10.1
@@ -84,6 +89,7 @@ orjson==3.11.4
     # via pymatgen
 packaging==25.0
     # via
+    #   black
     #   matplotlib
     #   plotly
     #   pytest
@@ -93,11 +99,15 @@ palettable==3.3.3
 pandas==2.3.3
     # via pymatgen
 pathspec==0.12.1
-    # via mypy
+    # via
+    #   black
+    #   mypy
 pillow==12.0.0
     # via matplotlib
 platformdirs==4.5.0
-    # via virtualenv
+    # via
+    #   black
+    #   virtualenv
 plotly==6.3.1
     # via pymatgen
 pluggy==1.6.0
@@ -110,6 +120,8 @@ pycodestyle==2.14.0
     # via
     #   flake8
     #   pymatgen-analysis-alloys (pyproject.toml)
+pydocstyle==6.3.0
+    # via pymatgen-analysis-alloys (pyproject.toml)
 pyflakes==3.4.0
     # via flake8
 pygments==2.19.2
@@ -141,6 +153,8 @@ python-dateutil==2.9.0.post0
     # via
     #   matplotlib
     #   pandas
+pytokens==0.2.0
+    # via black
 pytz==2025.2
     # via pandas
 pyyaml==6.0.3
@@ -164,7 +178,9 @@ shapely==2.1.2
 six==1.17.0
     # via python-dateutil
 snowballstemmer==3.0.1
-    # via sphinx
+    # via
+    #   pydocstyle
+    #   sphinx
 spglib==2.6.0
     # via pymatgen
 sphinx==8.2.3

requirements/requirements-ubuntu-latest_py3.11_extras.txt

@@ -10,12 +10,16 @@ babel==2.17.0
     # via sphinx
 bibtexparser==1.4.3
     # via pymatgen
+black==25.9.0
+    # via pymatgen-analysis-alloys (pyproject.toml)
 certifi==2025.10.5
     # via requests
 cfgv==3.4.0
     # via pre-commit
 charset-normalizer==3.4.4
     # via requests
+click==8.3.0
+    # via black
 contourpy==1.3.3
     # via matplotlib
 coverage[toml]==7.11.0
@@ -62,6 +66,7 @@ mypy==1.18.2
     # via pymatgen-analysis-alloys (pyproject.toml)
 mypy-extensions==1.1.0
     # via
+    #   black
     #   mypy
     #   pymatgen-analysis-alloys (pyproject.toml)
 narwhals==2.10.1
@@ -84,6 +89,7 @@ orjson==3.11.4
     # via pymatgen
 packaging==25.0
     # via
+    #   black
     #   matplotlib
     #   plotly
     #   pytest
@@ -93,11 +99,15 @@ palettable==3.3.3
 pandas==2.3.3
     # via pymatgen
 pathspec==0.12.1
-    # via mypy
+    # via
+    #   black
+    #   mypy
 pillow==12.0.0
     # via matplotlib
 platformdirs==4.5.0
-    # via virtualenv
+    # via
+    #   black
+    #   virtualenv
 plotly==6.3.1
     # via pymatgen
 pluggy==1.6.0
@@ -110,6 +120,8 @@ pycodestyle==2.14.0
     # via
     #   flake8
     #   pymatgen-analysis-alloys (pyproject.toml)
+pydocstyle==6.3.0
+    # via pymatgen-analysis-alloys (pyproject.toml)
 pyflakes==3.4.0
     # via flake8
 pygments==2.19.2
@@ -141,6 +153,8 @@ python-dateutil==2.9.0.post0
     # via
     #   matplotlib
     #   pandas
+pytokens==0.2.0
+    # via black
 pytz==2025.2
     # via pandas
 pyyaml==6.0.3
@@ -164,7 +178,9 @@ shapely==2.1.2
 six==1.17.0
     # via python-dateutil
 snowballstemmer==3.0.1
-    # via sphinx
+    # via
+    #   pydocstyle
+    #   sphinx
 spglib==2.6.0
     # via pymatgen
 sphinx==8.2.3

requirements/requirements-ubuntu-latest_py3.12_extras.txt

@@ -9,6 +9,8 @@
 
 bibtexparser==1.4.3
     # via pymatgen
+black==25.9.0
+pydocstyle==6.3.0
 certifi==2025.10.5
     # via requests
 charset-normalizer==3.4.4