Temporary solution to installation issues.

.github/workflows/publish_release.yml

@@ -1,24 +1,23 @@
 name: Publish release
 on:
-  push:
-    tags:
-      - 'v[0-9]+.[0-9]+.[0-9]+.[0-9]+'
+    push:
+        tags:
+            - "v[0-9]+.[0-9]+.[0-9]+.[0-9]+"
 jobs:
-  publish-release:
-    runs-on: ubuntu-22.04
-    env:
-      VERSION: ${{ github.ref_name }}
-    steps:
-      - uses: actions/checkout@v3
-      - uses: actions/setup-python@v4
-        with:
-          python-version: "3.11"
-          cache: "pip"
-      - run: pip install -e '.[dev]'
-      - run: python -m build
-      - name: Publish
-        run:
-          twine upload
-          -u ${{ secrets.PYPI_USERNAME }}
-          -p ${{ secrets.PYPI_PASSWORD }}
-          dist/*
+    publish-release:
+        runs-on: ubuntu-latest
+        env:
+            VERSION: ${{ github.ref_name }}
+        steps:
+            - uses: actions/checkout@v3
+            - uses: actions/setup-python@v4
+              with:
+                  python-version: "3.11"
+                  cache: "pip"
+            - run: pip install -e '.[dev]'
+            - run: python -m build
+            - name: Publish
+              run: twine upload
+                  -u ${{ secrets.PYPI_USERNAME }}
+                  -p ${{ secrets.PYPI_PASSWORD }}
+                  dist/*

.github/workflows/tests.yml

@@ -7,7 +7,7 @@ on:
     workflow_dispatch:
 jobs:
     ruff:
-        runs-on: ubuntu-22.04
+        runs-on: ubuntu-latest
         steps:
             - uses: actions/checkout@v3
             - uses: actions/setup-python@v4
@@ -18,7 +18,7 @@ jobs:
             - run: ruff check .
 
     mypy:
-        runs-on: ubuntu-22.04
+        runs-on: ubuntu-latest
         steps:
             - uses: actions/checkout@v3
             - uses: actions/setup-python@v4
@@ -29,7 +29,7 @@ jobs:
             - run: mypy src examples
 
     ruff-format:
-        runs-on: ubuntu-22.04
+        runs-on: ubuntu-latest
         steps:
             - uses: actions/checkout@v3
             - uses: actions/setup-python@v4
@@ -41,7 +41,7 @@ jobs:
 
     pytest:
         # https://ericmjl.github.io/blog/2021/12/30/better-conda-environments-on-github-actions/
-        runs-on: ubuntu-22.04
+        runs-on: ubuntu-latest
         defaults:
             run:
                 shell: bash -l {0}
@@ -67,7 +67,7 @@ jobs:
 
     example-tests:
         # https://ericmjl.github.io/blog/2021/12/30/better-conda-environments-on-github-actions/
-        runs-on: ubuntu-22.04
+        runs-on: ubuntu-latest
         defaults:
             run:
                 shell: bash -l {0}
@@ -92,7 +92,7 @@ jobs:
               run: python examples/testable_example.py
 
     doctest:
-        runs-on: ubuntu-22.04
+        runs-on: ubuntu-latest
         defaults:
             run:
                 shell: bash -l {0}

.readthedocs.yml

@@ -1,19 +1,19 @@
 version: 2
 
 build:
-  os: "ubuntu-22.04"
-  tools:
-    python: "mambaforge-latest"
+    os: "ubuntu-lts-latest"
+    tools:
+        python: "mambaforge-latest"
 
 sphinx:
-  configuration: "docs/source/conf.py"
+    configuration: "docs/source/conf.py"
 
 conda:
-  environment: "docs/environment.yml"
+    environment: "docs/environment.yml"
 
 python:
-  install:
-    - method: pip
-      path: .
-      extra_requirements:
-        - dev
+    install:
+        - method: pip
+          path: .
+          extra_requirements:
+              - dev

README.rst

@@ -32,17 +32,34 @@ Some optional dependencies are only available through conda:
 
 .. code-block:: bash
 
-  # for OpenMM and espaloma charge
-  # note the temporary issue with rdkit versions and conda will overwrite pip
-  # installed software
-  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
 
+With OpenMM
+-----------
+
+To get ``stko`` and use ``OpenMM``, we had some installation issues. The
+current solution is to first, in a new environment, install the ``OpenMM``
+requirements:
+
+.. code-block:: bash
+
+  # for OpenMM and espaloma charge
+  # note the temporary issue with rdkit versions and conda will overwrite pip
+  # installed software
+  mamba install -c conda-forge pytorch==2.3.1 torchdata==0.7.1 openff-toolkit openmm openmmtools dgl rdkit==2024.3.4 espaloma_charge
+
+Then install ``stko`` with pip:
+
+.. code-block:: bash
+
+  pip install stko
+
+
 Developer Setup
 ---------------
 

docs/source/index.rst

@@ -43,17 +43,33 @@ Some optional dependencies are only available through conda:
 
 .. code-block:: bash
 
-  # for OpenMM and espaloma charge
-  # note the temporary issue with rdkit versions and conda will overwrite pip
-  # installed software
-  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
 
+With OpenMM
+-----------
+
+To get :mod:`.stko` and use ``OpenMM``, we had some installation issues. The
+current solution is to first, in a new environment, install the ``OpenMM``
+requirements:
+
+.. code-block:: bash
+
+  # for OpenMM and espaloma charge
+  # note the temporary issue with rdkit versions and conda will overwrite pip
+  # installed software
+  mamba install -c conda-forge pytorch==2.3.1 torchdata==0.7.1 openff-toolkit openmm openmmtools dgl rdkit==2024.3.4 espaloma_charge
+
+Then install :mod:`.stko` with pip:
+
+.. code-block:: bash
+
+  pip install stko
+
 Developer Setup
 ---------------
 

examples/cage_analysis_example.py

@@ -7,10 +7,12 @@
 
 import stko
 
+logger = logging.getLogger(__name__)
+
 
 def main() -> None:
     """Run the example."""
-    logging.warning(
+    logger.warning(
         "This code is only present in the latest versions of stko that "
         "require Python 3.11!"
     )

examples/cage_openmm_example.py

@@ -10,6 +10,8 @@
 
 import stko
 
+logger = logging.getLogger(__name__)
+
 
 def integrator(
     *,
@@ -118,14 +120,14 @@ def main() -> None:
             ),
         ),
     )
-    logging.info("starting calculations...")
+    logger.info("starting calculations...")
     st = time.time()
     optimised_cage = optimisation_sequence.optimize(cage)
     et = time.time()
-    logging.info("calculations done!")
+    logger.info("calculations done!")
 
     optimised_cage.write(output_directory / "opt_cage.mol")
-    logging.info(
+    logger.info(
         "cage energy: %s kJmol-1 in %s s",
         stko.OpenMMEnergy(
             force_field=ForceField("openff_unconstrained-2.1.0.offxml"),

examples/intermediates_example.py

@@ -5,6 +5,8 @@
 
 import stko
 
+logger = logging.getLogger(__name__)
+
 
 def main() -> None:
     """Run the example."""
@@ -23,16 +25,14 @@ def main() -> None:
     cage_graphs = stko.topology_functions.UnreactedTopologyGraph(
         stk.cage.FourPlusSix((bb1, bb2))
     )
-    logging.info(
+    logger.info(
         "there are %s possible reactions",
         len(cage_graphs.get_available_reactions()),
     )
 
     # With up to N reactions performed.
     intermediate_pool = cage_graphs.get_named_intermediates(n=4)
-    logging.info(
-        "there are %s structures with n=%s", len(intermediate_pool), 4
-    )
+    logger.info("there are %s structures with n=%s", len(intermediate_pool), 4)
     for named_intermediate in intermediate_pool.intermediates:
         named_intermediate.molecule.write(
             examples_output / f"{named_intermediate.intermediate_name}.mol"
@@ -41,7 +41,7 @@ def main() -> None:
     # Now iterate over all possible reactions with varying amounts of
     # completeness and get their smiles.
     all_possible_smiles = cage_graphs.get_reacted_smiles()
-    logging.info("there are %s unique smiles", len(all_possible_smiles))
+    logger.info("there are %s unique smiles", len(all_possible_smiles))
 
 
 if __name__ == "__main__":

examples/openmm_hg_example.py

@@ -10,6 +10,8 @@
 
 import stko
 
+logger = logging.getLogger(__name__)
+
 
 def integrator(
     *,
@@ -116,14 +118,14 @@ def main() -> None:
             ),
         ),
     )
-    logging.info("starting calculations...")
+    logger.info("starting calculations...")
     st = time.time()
     optimised_complex = optimisation_sequence.optimize(hg_complex)
     et = time.time()
-    logging.info("calculations done!")
+    logger.info("calculations done!")
 
     optimised_complex.write(output / "opt_complex.mol")
-    logging.info(
+    logger.info(
         "hgcomplex energy: %s kJmol-1 in %s s",
         stko.OpenMMEnergy(
             force_field=ForceField("openff_unconstrained-2.1.0.offxml"),

examples/optwrite_example.py

@@ -7,6 +7,8 @@
 
 import stko
 
+logger = logging.getLogger(__name__)
+
 
 def main() -> None:
     """Run the example."""

examples/testable_example.py

@@ -20,6 +20,8 @@
 
 from stko import WrapperNotInstalledError
 
+logger = logging.getLogger(__name__)
+
 
 def main() -> None:
     """Run the example."""
@@ -43,7 +45,7 @@ def main() -> None:
         torsion_example.main()
         zmatrix_example.main()
         optwrite_example.main()
-        logging.info("all examples ran, at least!")
+        logger.info("all examples ran, at least!")
 
     finally:
         os.chdir(init_dir)

pyproject.toml

@@ -9,7 +9,7 @@ maintainers = [
     { name = "Lukas Turcani", email = "lukasturcani93@gmail.com" },
 ]
 dependencies = [
-    "numpy",
+    "numpy<2",
     # Pinned while rdkit changes stk results.
     "rdkit == 2024.3.4",
     "stk",

src/stko/_internal/optimizers/xtb.py

@@ -437,7 +437,7 @@ def _run_optimizations(
                     # case, exit optimization loop and warn.
                     self.incomplete.add(mol)
                     msg = f"Small negative frequencies present in {mol}."
-                    logging.warning(msg)
+                    logger.warning(msg)
                     return mol, opt_complete
             else:
                 # Optimization is complete.
@@ -482,7 +482,7 @@ def optimize(self, mol: MoleculeT) -> MoleculeT:
         if not complete:
             self.incomplete.add(mol)
             msg = f"Optimization is incomplete for {mol}."
-            logging.warning(msg)
+            logger.warning(msg)
 
         return mol
 
@@ -881,7 +881,7 @@ def optimize(self, mol: MoleculeT) -> MoleculeT:
 
         if not complete:
             msg = f"CREST run is incomplete for {mol}."
-            logging.warning(msg)
+            logger.warning(msg)
 
         return mol
 
@@ -1122,7 +1122,7 @@ def optimize(self, mol: MoleculeT) -> MoleculeT:
 
         if not complete:
             msg = f"Optimization is incomplete for {mol}."
-            logging.warning(msg)
+            logger.warning(msg)
 
         return mol
 
@@ -1473,6 +1473,6 @@ def optimize(self, mol: MoleculeT) -> MoleculeT:
 
         if not complete:
             msg = f"CREST run is incomplete for {mol}."
-            logging.warning(msg)
+            logger.warning(msg)
 
         return mol