Code 2: Fix the error with Python >=3.9. Handle ruff and mypy

docs/source/_autosummary/pywindow.DLPOLY.rst

@@ -0,0 +1,25 @@
+pywindow.DLPOLY
+===============
+
+.. currentmodule:: pywindow
+
+.. autoclass:: DLPOLY
+   :members:
+   :inherited-members:
+   :undoc-members:
+   :show-inheritance:
+
+
+
+
+   .. rubric:: Methods
+
+   .. autosummary::
+      :nosignatures:
+
+
+
+
+
+
+

docs/source/_autosummary/pywindow.Input.rst

@@ -0,0 +1,27 @@
+pywindow.Input
+==============
+
+.. currentmodule:: pywindow
+
+.. autoclass:: Input
+   :members:
+   :inherited-members:
+   :undoc-members:
+   :show-inheritance:
+
+
+
+
+   .. rubric:: Methods
+
+   .. autosummary::
+      :nosignatures:
+
+      ~Input.load_file
+      ~Input.load_rdkit_mol
+
+
+
+
+
+

docs/source/_autosummary/pywindow.MolecularSystem.rst

@@ -0,0 +1,35 @@
+pywindow.MolecularSystem
+========================
+
+.. currentmodule:: pywindow
+
+.. autoclass:: MolecularSystem
+   :members:
+   :inherited-members:
+   :undoc-members:
+   :show-inheritance:
+
+
+
+
+   .. rubric:: Methods
+
+   .. autosummary::
+      :nosignatures:
+
+      ~MolecularSystem.decipher_atom_keys
+      ~MolecularSystem.dump_system
+      ~MolecularSystem.dump_system_json
+      ~MolecularSystem.load_file
+      ~MolecularSystem.load_rdkit_mol
+      ~MolecularSystem.load_system
+      ~MolecularSystem.make_modular
+      ~MolecularSystem.rebuild_system
+      ~MolecularSystem.swap_atom_keys
+      ~MolecularSystem.system_to_molecule
+
+
+
+
+
+

docs/source/_autosummary/pywindow.Molecule.rst

@@ -0,0 +1,39 @@
+pywindow.Molecule
+=================
+
+.. currentmodule:: pywindow
+
+.. autoclass:: Molecule
+   :members:
+   :inherited-members:
+   :undoc-members:
+   :show-inheritance:
+
+
+
+
+   .. rubric:: Methods
+
+   .. autosummary::
+      :nosignatures:
+
+      ~Molecule.calculate_average_diameter
+      ~Molecule.calculate_centre_of_mass
+      ~Molecule.calculate_maximum_diameter
+      ~Molecule.calculate_pore_diameter
+      ~Molecule.calculate_pore_diameter_opt
+      ~Molecule.calculate_pore_volume
+      ~Molecule.calculate_pore_volume_opt
+      ~Molecule.calculate_windows
+      ~Molecule.dump_molecule
+      ~Molecule.dump_properties_json
+      ~Molecule.full_analysis
+      ~Molecule.load_rdkit_mol
+      ~Molecule.molecular_weight
+      ~Molecule.shift_to_origin
+
+
+
+
+
+

docs/source/_autosummary/pywindow.PDB.rst

@@ -0,0 +1,25 @@
+pywindow.PDB
+============
+
+.. currentmodule:: pywindow
+
+.. autoclass:: PDB
+   :members:
+   :inherited-members:
+   :undoc-members:
+   :show-inheritance:
+
+
+
+
+   .. rubric:: Methods
+
+   .. autosummary::
+      :nosignatures:
+
+
+
+
+
+
+

docs/source/_autosummary/pywindow.XYZ.rst

@@ -0,0 +1,25 @@
+pywindow.XYZ
+============
+
+.. currentmodule:: pywindow
+
+.. autoclass:: XYZ
+   :members:
+   :inherited-members:
+   :undoc-members:
+   :show-inheritance:
+
+
+
+
+   .. rubric:: Methods
+
+   .. autosummary::
+      :nosignatures:
+
+
+
+
+
+
+

docs/source/_autosummary/pywindow.compare_properties_dict.rst

@@ -0,0 +1,6 @@
+pywindow.compare\_properties\_dict
+==================================
+
+.. currentmodule:: pywindow
+
+.. autofunction:: compare_properties_dict

docs/source/_autosummary/pywindow.make_supercell.rst

@@ -0,0 +1,6 @@
+pywindow.make\_supercell
+========================
+
+.. currentmodule:: pywindow
+
+.. autofunction:: make_supercell

docs/source/_autosummary/pywindow.rst

@@ -0,0 +1,47 @@
+pywindow
+========
+
+.. automodule:: pywindow
+
+
+
+
+
+
+
+   .. rubric:: Classes
+
+   .. autosummary::
+      :toctree:
+      :template: class.rst
+      :nosignatures:
+
+      DLPOLY
+      Input
+      MolecularSystem
+      Molecule
+      PDB
+      XYZ
+
+
+
+
+
+
+   .. rubric:: Functions
+
+   .. autosummary::
+      :toctree:
+      :nosignatures:
+
+      compare_properties_dict
+      make_supercell
+
+
+
+
+
+
+
+
+

docs/source/_static/PUDXES_out.json

@@ -1 +1 @@
-{"no_of_atoms": 168, "pore_volume_opt": 82.31154385154417, "maximum_diameter": {"atom_2": 54, "diameter": 22.179369990077188, "atom_1": 12}, "pore_diameter": {"atom": 29, "diameter": 5.397020177310022}, "windows": {"diameters": [3.6377874601388167, 3.6356210328430296, 3.628965122399882, 3.637072370444723], "centre_of_mass": [[10.77105704516109, 10.770977067030907, 14.028939562935404], [14.015448457684588, 14.015412600374392, 14.015398449539077], [13.929655242102346, 10.87029766244962, 10.870341633949108], [10.775422358465416, 14.024532168906696, 10.775466335429106]]}, "pore_volume": 82.31154385154417, "pore_diameter_opt": {"diameter": 5.397020177310022, "centre_of_mass": [12.400000000000011, 12.399999999999991, 12.399999999999991], "atom_1": 29}, "centre_of_mass": [12.400000000000011, 12.399999999999991, 12.399999999999991]}
+{"no_of_atoms": 168, "centre_of_mass": [12.400000000000011, 12.399999999999991, 12.399999999999991], "maximum_diameter": {"diameter": 22.179369990077188, "atom_1": 12, "atom_2": 54}, "average_diameter": 13.83201751425547, "pore_diameter": {"diameter": 5.397020177310022, "atom": 29}, "pore_volume": 82.31154385154417, "pore_diameter_opt": {"diameter": 5.397020177310022, "atom_1": 29, "centre_of_mass": [12.400000000000011, 12.399999999999991, 12.399999999999991]}, "pore_volume_opt": 82.31154385154417, "windows": {"diameters": [3.637787460138805, 3.6356210328430296, 3.628965122470937, 3.6370723704447188], "centre_of_mass": [[10.771057045161115, 10.77097706703093, 14.028939562935376], [14.015448457686624, 14.015412600376724, 14.015398449541088], [13.92965526405877, 10.870297640397817, 10.87034161195557], [10.775422358465452, 14.024532168906662, 10.775466335429137]]}}

docs/source/conf.py

@@ -48,4 +48,4 @@
 html_theme = "furo"
 html_static_path = ["_static"]
 html_logo = "_static/pyWINDOW_logo.png"
-html_theme_options = {}
+html_theme_options = {}  # type: ignore[var-annotated]

examples/__init__.py

@@ -0,0 +1 @@
+"""Examples for pywindow."""

justfile

@@ -26,7 +26,7 @@ check:
   ( set -x; uv run ruff format --check . )
 
   echo
-  ( set -x; uv run mypy src/ tests/ examples/ )
+  ( set -x; uv run mypy src/ tests/ examples/ docs/source/ )
 
   echo
   ( set -x; uv run pytest --cov=src --cov-report term-missing )