Merge pull request #175 from lukasturcani/lukas/optimizer

Make ruff stricter and clean up doc strings throughout src and examples directories. mypy fails due to issue with rdkit version: rdkit/rdkit#7401 We will wait till that is solved to fix.
JelfsMaterialsGroup · May 15, 2024 · 8e71823 · 8e71823
2 parents 3cb09ca + d4d9216
commit 8e71823
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diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -25,8 +25,8 @@ jobs:
           python-version: "3.11"
           cache: "pip"
       - run: "pip install -e '.[dev]'"
-      - run: mypy src
-  black:
+      - run: mypy src examples
+  ruff-format:
     runs-on: ubuntu-22.04
     steps:
       - uses: actions/checkout@v3
@@ -35,7 +35,7 @@ jobs:
           python-version: "3.11"
           cache: "pip"
       - run: "pip install -e '.[dev]'"
-      - run: black --check .
+      - run: ruff format --check .
   pytest:
     runs-on: ubuntu-22.04
     steps:
@@ -45,4 +45,4 @@ jobs:
           python-version: "3.11"
           cache: "pip"
       - run: "pip install -e '.[dev]'"
-      - run: pytest
+      - run: pytest
diff --git a/docs/source/_templates/class.rst b/docs/source/_templates/class.rst
@@ -8,26 +8,32 @@
    :undoc-members:
    :show-inheritance:
 
-   {% block methods %}
-   {% if methods %}
-   .. rubric:: {{ _('Methods') }}
+   {% block attributes %}
+   {% if attributes %}
+   .. rubric:: {{ _('Attributes') }}
 
    .. autosummary::
-      :nosignatures:
-   {% for item in methods %}
-      {%- if not item.startswith('_') %}
+   {% for item in attributes %}
       ~{{ name }}.{{ item }}
-      {%- endif -%}
    {%- endfor %}
    {% endif %}
    {% endblock %}
 
-   {% block attributes %}
-   {% if attributes %}
-   .. rubric:: {{ _('Attributes') }}
+   {% block methods %}
+
+   {% set public_methods = [] %}
+   {% for item in methods %}
+   {% if not item.startswith('_') %}
+   {% set public_methods = public_methods.append(item) %}
+   {% endif %}
+   {% endfor %}
+
+   {% if public_methods %}
+   .. rubric:: {{ _('Methods') }}
 
    .. autosummary::
-   {% for item in attributes %}
+      :nosignatures:
+   {% for item in public_methods %}
       ~{{ name }}.{{ item }}
    {%- endfor %}
    {% endif %}

diff --git a/docs/source/cage_analysis.rst b/docs/source/cage_analysis.rst
@@ -19,7 +19,6 @@ like all other methods in :mod:`stko`.
   DitopicThreeSiteAnalyser <_autosummary/stko.molecule_analysis.DitopicThreeSiteAnalyser>
   ConstructedAnalyser <_autosummary/stko.molecule_analysis.ConstructedAnalyser>
   GeometryAnalyser <_autosummary/stko.molecule_analysis.GeometryAnalyser>
-  PoreAnalyser <_autosummary/stko.molecule_analysis.PoreAnalyser>
 
 
 There is an example script with some of the analyses

diff --git a/docs/source/calculators.rst b/docs/source/calculators.rst
@@ -17,4 +17,3 @@ Calculators
   MatchedTorsionCalculator <_autosummary/stko.MatchedTorsionCalculator>
   PlanarityCalculator <_autosummary/stko.PlanarityCalculator>
   GeometryAnalyser <_autosummary/stko.molecule_analysis.GeometryAnalyser>
-  PoreAnalyser <_autosummary/stko.molecule_analysis.PoreAnalyser>
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -9,7 +9,7 @@
 # -- Project information ----------------------------------------------
 
 project = "stko"
-copyright = "2023, Steven Bennett, Andrew Tarzia, Lukas Turcani"
+project_copyright = "2023, Steven Bennett, Andrew Tarzia, Lukas Turcani"
 author = "Steven Bennett, Andrew Tarzia, Lukas Turcani"
 
 # -- General configuration ---------------------------------------------------
@@ -29,7 +29,7 @@
 
 autodoc_typehints = "description"
 autodoc_member_order = "groupwise"
-autoclass_content = "both"
+autoclass_content = "class"
 
 intersphinx_mapping = {
     "python": ("https://docs.python.org/3", None),

diff --git a/docs/source/helpers.rst b/docs/source/helpers.rst
@@ -0,0 +1,8 @@
+Helpers
+=======
+
+.. toctree::
+  :maxdepth: 1
+
+  MAEExtractor <_autosummary/stko.MAEExtractor>
+  XTBExtractor <_autosummary/stko.XTBExtractor>
diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -7,6 +7,7 @@
    Calculators <calculators>
    Optimizers <optimizers>
    Cage analysis <cage_analysis>
+   Helpers <helpers>
 
 
 .. toctree::
@@ -80,4 +81,4 @@ Indices and Tables
 
 * :ref:`genindex`
 * :ref:`modindex`
-* :ref:`search`
+* :ref:`search`
diff --git a/docs/source/molecular.rst b/docs/source/molecular.rst
@@ -21,10 +21,9 @@ Molecular
   DecomposeMOC <_autosummary/stko.molecule_analysis.DecomposeMOC>
   DitopicThreeSiteAnalyser <_autosummary/stko.molecule_analysis.DitopicThreeSiteAnalyser>
   ConstructedAnalyser <_autosummary/stko.molecule_analysis.ConstructedAnalyser>
-  SubgroupAnalyser <_autosummary/stko.molecule_analysis.SubgroupAnalyser>
   AlkyneAngle <_autosummary/stko.molecule_analysis.AlkyneAngle>
   X5Planarity <_autosummary/stko.molecule_analysis.X5Planarity>
   C5N1Planarity <_autosummary/stko.molecule_analysis.C5N1Planarity>
   C6Planarity <_autosummary/stko.molecule_analysis.C6Planarity>
   Subgroup <_autosummary/stko.molecule_analysis.Subgroup>
-  SubgroupAnalyser <_autosummary/stko.molecule_analysis.SubgroupAnalyser>
+  SubgroupAnalyser <_autosummary/stko.molecule_analysis.SubgroupAnalyser>
diff --git a/docs/source/optimizers.rst b/docs/source/optimizers.rst
@@ -27,7 +27,5 @@ Optimizers
   XTBCREST <_autosummary/stko.XTBCREST>
   XTBFFCREST <_autosummary/stko.XTBFFCREST>
 
-
   GulpUFFMDOptimizer <_autosummary/stko.GulpUFFMDOptimizer>
   MacroModelMD <_autosummary/stko.MacroModelMD>
-  MAEExtractor <_autosummary/stko.MAEExtractor>
diff --git a/examples/aligner_example.py b/examples/aligner_example.py
@@ -1,14 +1,15 @@
-import os
+from pathlib import Path
 
 import numpy as np
 import stk
 import stko
 
 
-def main():
-    examples_output = "aligner_directory"
-    if not os.path.exists(examples_output):
-        os.mkdir(examples_output)
+def main() -> None:
+    """Run the example."""
+    examples_output = Path("aligner_directory")
+    if not examples_output.exists():
+        examples_output.mkdir()
 
     bb1 = stk.BuildingBlock("NCCN", [stk.PrimaryAminoFactory()])
     bb2 = stk.BuildingBlock(
@@ -45,20 +46,20 @@ def main():
             np.array((0, 0, 1)),
             np.array((0, 0, 0)),
         )
-        mol.write(os.path.join(examples_output, f"unaligned_{i}.mol"))
-        initial.write(os.path.join(examples_output, f"init_{i}.mol"))
+        mol.write(examples_output / f"unaligned_{i}.mol")
+        initial.write(examples_output / f"init_{i}.mol")
         aligner = stko.Aligner(
             initial_molecule=initial,
             matching_pairs=pairs,
         )
         if uff_opt:
-            mol = aligner.optimize(_opt.optimize(mol))
+            aligned_mol = aligner.optimize(_opt.optimize(mol))
         else:
-            mol = aligner.optimize(mol)
-        mol.write(os.path.join(examples_output, f"aligned_{i}.mol"))
+            aligned_mol = aligner.optimize(mol)
+        aligned_mol.write(examples_output / f"aligned_{i}.mol")
         rmsd_calculator = stko.RmsdMappedCalculator(initial)
         rmsd = rmsd_calculator.get_results(mol).get_rmsd()
-        print(f"molecule {i} RMSD: {rmsd}")
+        print(f"molecule {i} RMSD: {rmsd}")  # noqa: T201
 
 
 if __name__ == "__main__":

diff --git a/examples/basic_example.py b/examples/basic_example.py
@@ -1,10 +1,11 @@
-import os
+from pathlib import Path
 
 import stk
 import stko
 
 
-def main():
+def main() -> None:
+    """Run the example."""
     bb1 = stk.BuildingBlock("NCCNCCN", [stk.PrimaryAminoFactory()])
     bb2 = stk.BuildingBlock("O=CCCC=O", [stk.AldehydeFactory()])
     polymer = stk.ConstructedMolecule(
@@ -16,20 +17,20 @@ def main():
         )
     )
 
-    examples_output = "output_directory"
-    if not os.path.exists(examples_output):
-        os.mkdir(examples_output)
+    examples_output = Path("output_directory")
+    if not examples_output.exists():
+        examples_output.mkdir()
 
     # Run optimisations.
     uff = stko.UFF()
     polymer = uff.optimize(polymer)
-    polymer.write(os.path.join(examples_output, "poly_uff.mol"))
+    polymer.write(examples_output / "poly_uff.mol")
     mmff = stko.MMFF()
     polymer = mmff.optimize(polymer)
-    polymer.write(os.path.join(examples_output, "poly_mmff.mol"))
+    polymer.write(examples_output / "poly_mmff.mol")
     etkdg = stko.ETKDG()
     polymer = etkdg.optimize(polymer)
-    polymer.write(os.path.join(examples_output, "poly_etkdg.mol"))
+    polymer.write(examples_output / "poly_etkdg.mol")
 
 
 if __name__ == "__main__":

diff --git a/examples/cage_analysis_example.py b/examples/cage_analysis_example.py
@@ -1,3 +1,4 @@
+# ruff: noqa: T201
 import logging
 from collections import defaultdict
 
@@ -6,7 +7,8 @@
 import stko
 
 
-def main():
+def main() -> None:
+    """Run the example."""
     logging.warning(
         "This code is only present in the latest versions of stko that "
         "require Python 3.11!"
@@ -15,9 +17,9 @@ def main():
     pd = stk.BuildingBlock(
         smiles="[Pd+2]",
         functional_groups=(
-            stk.SingleAtom(stk.Pd(0, charge=2)) for i in range(4)
+            stk.SingleAtom(stk.Pd(0, charge=2)) for _ in range(4)
         ),
-        position_matrix=[[0.0, 0.0, 0.0]],
+        position_matrix=np.array([[0.0, 0.0, 0.0]]),
     )
     ditopic_bb = stk.BuildingBlock(
         smiles="C1=NC=CC(C2=CC=CC(C3=CC=NC=C3)=C2)=C1",
@@ -99,8 +101,8 @@ def main():
     # on the constructed molecule or maintain building block chemistry.
     # It simply extracts the parts of building blocks still present in
     # the molecule.
-    analyser = stko.molecule_analysis.ConstructedAnalyser()
-    centroids = analyser.get_building_block_centroids(apdcage)
+    constructed_analyser = stko.molecule_analysis.ConstructedAnalyser()
+    centroids = constructed_analyser.get_building_block_centroids(apdcage)
     print("building block centroids:")
     print(centroids)
     print()

diff --git a/examples/calculators_example.py b/examples/calculators_example.py
@@ -1,16 +1,14 @@
-import os
-import sys
+# ruff: noqa: T201
+import argparse
+from pathlib import Path
 
 import stk
 import stko
 
 
-def main():
-    if len(sys.argv) > 1:
-        xtb_path = sys.argv[1]
-    else:
-        xtb_path = None
-
+def main() -> None:
+    """Run the example."""
+    args = _parse_args()
     bb1 = stk.BuildingBlock("NCCNCCN", [stk.PrimaryAminoFactory()])
 
     # Run calculations.
@@ -39,11 +37,11 @@ def main():
         mmff.get_energy(bb1),
     )
 
-    if xtb_path is not None:
+    if args.xtb_path is not None:
         print("doing XTB calculation.")
         xtb = stko.XTBEnergy(
-            xtb_path=xtb_path,
-            output_dir=os.path.join("output_directory", "example_xtb_out"),
+            xtb_path=args.xtb_path,
+            output_dir=Path("output_directory") / "example_xtb_out",
             unlimited_memory=True,
             calculate_ip_and_ea=True,
         )
@@ -76,7 +74,7 @@ def main():
             print("Expected fail")
 
         # Try yielded option.
-        calculations.append(xtb.calculate((bb1)))
+        calculations.append(xtb.calculate(bb1))
 
     # Run through yield statements using the `.calculate` method
     # all in once.
@@ -98,5 +96,16 @@ def main():
         )
 
 
+def _parse_args() -> argparse.Namespace:
+    parser = argparse.ArgumentParser()
+    parser.add_argument(
+        "--xtb_path",
+        type=Path,
+        help="Path to xtb binary.",
+        default=None,
+    )
+    return parser.parse_args()
+
+
 if __name__ == "__main__":
     main()