Updating typing, handle issues with actions.

.github/workflows/tests.yml

@@ -1,118 +1,117 @@
 name: Tests
 on:
-  push:
-    branches:
-      - master
-  pull_request:
-  workflow_dispatch:
+    push:
+        branches:
+            - master
+    pull_request:
+    workflow_dispatch:
 jobs:
-  ruff:
-    runs-on: ubuntu-22.04
-    steps:
-      - uses: actions/checkout@v3
-      - uses: actions/setup-python@v4
-        with:
-          python-version: "3.11"
-          cache: "pip"
-      - run: "pip install '.[dev]'"
-      - run: ruff check .
+    ruff:
+        runs-on: ubuntu-22.04
+        steps:
+            - uses: actions/checkout@v3
+            - uses: actions/setup-python@v4
+              with:
+                  python-version: "3.11"
+                  cache: "pip"
+            - run: "pip install '.[dev]'"
+            - run: ruff check .
 
-  mypy:
-    runs-on: ubuntu-22.04
-    steps:
-      - uses: actions/checkout@v3
-      - uses: actions/setup-python@v4
-        with:
-          python-version: "3.11"
-          cache: "pip"
-      - run: "pip install -e '.[dev]'"
-      - run: mypy src examples
+    mypy:
+        runs-on: ubuntu-22.04
+        steps:
+            - uses: actions/checkout@v3
+            - uses: actions/setup-python@v4
+              with:
+                  python-version: "3.11"
+                  cache: "pip"
+            - run: "pip install -e '.[dev]'"
+            - run: mypy src examples
 
-  ruff-format:
-    runs-on: ubuntu-22.04
-    steps:
-      - uses: actions/checkout@v3
-      - uses: actions/setup-python@v4
-        with:
-          python-version: "3.11"
-          cache: "pip"
-      - run: "pip install -e '.[dev]'"
-      - run: ruff format --check .
+    ruff-format:
+        runs-on: ubuntu-22.04
+        steps:
+            - uses: actions/checkout@v3
+            - uses: actions/setup-python@v4
+              with:
+                  python-version: "3.11"
+                  cache: "pip"
+            - run: "pip install -e '.[dev]'"
+            - run: ruff format --check .
 
-  pytest:
-    # https://ericmjl.github.io/blog/2021/12/30/better-conda-environments-on-github-actions/
-    runs-on: ubuntu-22.04
-    defaults:
-      run:
-        shell: bash -l {0}
-    steps:
-      - uses: actions/checkout@v3
-      - uses: conda-incubator/setup-miniconda@v2
-        with:
-          auto-update-conda: true
-          miniforge-variant: Mambaforge
-          channels: conda-forge,defaults
-          python-version: 3.11
-          activate-environment: pytest
-          use-mamba: true
-      - name: Build environment
-        run: |
-          conda activate pytest
-          conda install -c conda-forge openff-toolkit openmm openmmtools dgl rdkit==2024.3.4 espaloma_charge
-          conda install -c conda-forge mdanalysis openbabel
-          python -m pip install --upgrade pip
-          python -m pip install --upgrade setuptools
-          python -m pip install -e '.[dev]'
-      - run: pytest
+    pytest:
+        # https://ericmjl.github.io/blog/2021/12/30/better-conda-environments-on-github-actions/
+        runs-on: ubuntu-22.04
+        defaults:
+            run:
+                shell: bash -l {0}
 
-  example-tests:
-    # https://ericmjl.github.io/blog/2021/12/30/better-conda-environments-on-github-actions/
-    runs-on: ubuntu-22.04
-    defaults:
-      run:
-        shell: bash -l {0}
-    steps:
-      - uses: actions/checkout@v3
-      - uses: conda-incubator/setup-miniconda@v2
-        with:
-          auto-update-conda: true
-          miniforge-variant: Mambaforge
-          channels: conda-forge,defaults
-          python-version: 3.11
-          activate-environment: pytest
-          use-mamba: true
-      - name: Build environment
-        run: |
-          conda activate pytest
-          conda install -c conda-forge openff-toolkit openmm openmmtools dgl rdkit==2024.3.4 espaloma_charge
-          conda install -c conda-forge mdanalysis openbabel
-          python -m pip install --upgrade pip
-          python -m pip install --upgrade setuptools
-          python -m pip install -e '.[dev]'
-      - name: Run script
-        run: python examples/testable_example.py
+        steps:
+            - uses: actions/checkout@v4
+            - uses: conda-incubator/setup-miniconda@v3
 
-  doctest:
-    runs-on: ubuntu-22.04
-    defaults:
-      run:
-        shell: bash -l {0}
-    steps:
-      - uses: actions/checkout@v3
-      - uses: conda-incubator/setup-miniconda@v2
-        with:
-          auto-update-conda: true
-          miniforge-variant: Mambaforge
-          channels: conda-forge,defaults
-          python-version: 3.11
-          activate-environment: pytest
-          use-mamba: true
-      - name: Build environment
-        run: |
-          conda activate pytest
-          conda install -c conda-forge openff-toolkit openmm openmmtools dgl rdkit==2024.3.4 espaloma_charge
-          conda install -c conda-forge mdanalysis openbabel
-          python -m pip install --upgrade pip
-          python -m pip install --upgrade setuptools
-          python -m pip install -e '.[dev]'
-      - run: make -C docs doctest
+              with:
+                  miniforge-version: latest
+                  python-version: 3.11
+                  activate-environment: pytest
+
+            - name: Build environment
+              run: |
+                  conda activate pytest
+                  conda install -c conda-forge pytorch==2.3.1 torchdata==0.7.1 openff-toolkit openmm openmmtools dgl rdkit==2024.3.4 espaloma_charge
+                  conda install -c conda-forge mdanalysis openbabel
+                  python -m pip install --upgrade pip
+                  python -m pip install --upgrade setuptools
+                  python -m pip install -e '.[dev]'
+            - run: pytest
+
+    example-tests:
+        # https://ericmjl.github.io/blog/2021/12/30/better-conda-environments-on-github-actions/
+        runs-on: ubuntu-22.04
+        defaults:
+            run:
+                shell: bash -l {0}
+        steps:
+            - uses: actions/checkout@v4
+            - uses: conda-incubator/setup-miniconda@v3
+
+              with:
+                  miniforge-version: latest
+                  python-version: 3.11
+                  activate-environment: pytest
+
+            - name: Build environment
+              run: |
+                  conda activate pytest
+                  conda install -c conda-forge pytorch==2.3.1 torchdata==0.7.1 openff-toolkit openmm openmmtools dgl rdkit==2024.3.4 espaloma_charge
+                  conda install -c conda-forge mdanalysis openbabel
+                  python -m pip install --upgrade pip
+                  python -m pip install --upgrade setuptools
+                  python -m pip install -e '.[dev]'
+            - name: Run script
+              run: python examples/testable_example.py
+
+    doctest:
+        runs-on: ubuntu-22.04
+        defaults:
+            run:
+                shell: bash -l {0}
+
+        steps:
+            - uses: actions/checkout@v4
+            - uses: conda-incubator/setup-miniconda@v3
+
+              with:
+                  miniforge-version: latest
+                  python-version: 3.11
+                  activate-environment: pytest
+
+            - name: Build environment
+              run: |
+                  conda activate pytest
+                  conda install -c conda-forge pytorch==2.3.1 torchdata==0.7.1 openff-toolkit openmm openmmtools dgl rdkit==2024.3.4 espaloma_charge
+                  conda install -c conda-forge mdanalysis openbabel
+                  python -m pip install --upgrade pip
+                  python -m pip install --upgrade setuptools
+                  python -m pip install -e '.[dev]'
+            - run: make -C docs doctest

.gitignore

@@ -22,3 +22,4 @@ tests/failures.txt
 /examples/.model.pt
 
 /examples/*/md_optimisation
+.model.pt

README.rst

@@ -35,14 +35,32 @@ Some optional dependencies are only available through conda:
   # for OpenMM and espaloma charge
   # note the temporary issue with rdkit versions and conda will overwrite pip
   # installed software
-  mamba install -c conda-forge openff-toolkit openmm openmmtools dgl rdkit==2024.3.4 espaloma_charge
+  mamba install -c conda-forge pytorch==2.3.1 torchdata==0.7.1 openff-toolkit openmm openmmtools dgl rdkit==2024.3.4 espaloma_charge
   # for xtb
   mamba install xtb
   # for openbabel
   mamba install openbabel
   # for mdanalysis
   mamba install mdanalysis
 
+Developer Setup
+---------------
+
+1. Install `just`_.
+2. In a new virtual environment run:
+
+.. code-block:: bash
+
+  just dev
+
+3. Run code checks:
+
+.. code-block:: bash
+
+  just check
+
+.. _`just`: https://github.com/casey/just
+
 Examples
 ========
 

docs/source/cage_analysis.rst

@@ -257,7 +257,7 @@ We can get measures of pore size and cage geometry.
 .. testcode:: analysing-cage
     :hide:
 
-    assert analyser.get_min_centroid_distance(apdcage) == 6.612215150137052
+    assert np.isclose(analyser.get_min_centroid_distance(apdcage), 6.612215150137052)
 
 Giving:
 
@@ -274,4 +274,4 @@ Giving:
 
     import shutil
 
-    shutil.rmtree('cage_output')
+    shutil.rmtree('cage_output')

docs/source/index.rst

@@ -23,8 +23,12 @@
 Welcome to stko's documentation!
 ================================
 
-GitHub: https://github.com/JelfsMaterialsGroup/stko
+| GitHub: https://github.com/JelfsMaterialsGroup/stko
+| Discord: https://discord.gg/zbCUzuxe2B
 
+.. tip::
+
+  ⭐ Star us on `GitHub <https://github.com/JelfsMaterialsGroup/stko>`_! ⭐
 
 Install
 =======
@@ -42,14 +46,27 @@ Some optional dependencies are only available through conda:
   # for OpenMM and espaloma charge
   # note the temporary issue with rdkit versions and conda will overwrite pip
   # installed software
-  mamba install -c conda-forge openff-toolkit openmm openmmtools dgl rdkit==2024.3.4  espaloma_charge
+  mamba install -c conda-forge pytorch==2.3.1 torchdata==0.7.1 openff-toolkit openmm openmmtools dgl rdkit==2024.3.4  espaloma_charge
   # for xtb
   mamba install xtb
   # for openbabel
   mamba install openbabel
   # for mdanalysis
   mamba install mdanalysis
 
+Developer Setup
+---------------
+
+#. Install `just`_.
+#. In a new virtual environment run::
+
+    $ just dev
+
+#. Run code checks::
+
+    $ just check
+
+.. _`just`: https://github.com/casey/just
 
 Dependencies
 ------------

docs/source/molecular.rst

@@ -16,6 +16,16 @@ Atoms, Functional Groups and Molecules
   ThreeSiteFactory <_autosummary/stko.functional_groups.ThreeSiteFactory>
 
 
+Molecular utilities
+-------------------
+
+.. toctree::
+  :maxdepth: 1
+
+  separate_molecule <_autosummary/stko.molecular_utilities.separate_molecule>
+  merge_stk_molecules <_autosummary/stko.molecular_utilities.merge_stk_molecules>
+  update_stk_from_rdkit_conformer <_autosummary/stko.molecular_utilities.update_stk_from_rdkit_conformer>
+
 Molecular Analysis
 ------------------
 

examples/cage_analysis_example.py

@@ -82,20 +82,14 @@ def main() -> None:
     # Distance between binders in the organic linkers?
     print(f"avg. binder distance: {np.mean(ligand_dict['binder_dist'])}")
     # How twisted is the molecule, or aligned are the binding groups?
-    print(
-        "avg. binder binder angle: " f"{np.mean(ligand_dict['binder_binder'])}"
-    )
+    print(f"avg. binder binder angle: {np.mean(ligand_dict['binder_binder'])}")
     # How twisted is the molecule, or what is the torsion between
     # the binding groups?
-    print(
-        "avg. binder adjacent torsion: " f"{np.mean(ligand_dict['torsion'])}"
-    )
+    print(f"avg. binder adjacent torsion: {np.mean(ligand_dict['torsion'])}")
     # What is the angle made by the binders?
     print(f"avg. binder angles: {np.mean(ligand_dict['binder_angle'])}")
     # And the resultant bite-angle [caution!]?
-    print(
-        "avg. bite angle [caution]: " f"{np.mean(ligand_dict['bite_angle'])}"
-    )
+    print(f"avg. bite angle [caution]: {np.mean(ligand_dict['bite_angle'])}")
 
     # Get the centroid and atom ids of distinct building blocks.
     # This is similar to the above, but does not perform any disconnections
@@ -133,11 +127,11 @@ def main() -> None:
     # And some geometrical measures.
     print(
         f"avg. N-Pd bond length:"
-        f' {np.mean(analyser.calculate_bonds(apdcage)[("N", "Pd")])}'
+        f" {np.mean(analyser.calculate_bonds(apdcage)[('N', 'Pd')])}"
     )
     print(
         f"N-Pd-N angles: "
-        f'{analyser.calculate_angles(apdcage)[("N", "Pd", "N")]}'
+        f"{analyser.calculate_angles(apdcage)[('N', 'Pd', 'N')]}"
     )
 
 

examples/obabel_example.py

@@ -74,7 +74,7 @@ def main() -> None:
 
     # Define spacer building block.
     bb3 = stk.BuildingBlock(
-        smiles=("C1=CC(C2=CC=C(Br)C=C2)=C" "C=C1Br"),
+        smiles=("C1=CC(C2=CC=C(Br)C=C2)=CC=C1Br"),
         functional_groups=[stk.BromoFactory()],
     )
 

justfile

@@ -11,7 +11,7 @@ docs:
 # Install development environment.
 dev:
   pip install -e '.[dev]'
-  mamba install -y -c conda-forge openff-toolkit openmm openmmtools rdkit==2024.3.4 dgl espaloma_charge
+  mamba install -y -c conda-forge pytorch==2.3.1 torchdata==0.7.1 openff-toolkit openmm openmmtools rdkit!=2024.3.5 dgl espaloma_charge
   mamba install -y xtb
   mamba install -y openbabel
   mamba install -y mdanalysis