Unpin rdkit, handle a few other installation issues.

.github/workflows/tests.yml

@@ -12,7 +12,7 @@ jobs:
             - uses: actions/checkout@v3
             - uses: actions/setup-python@v4
               with:
-                  python-version: "3.11"
+                  python-version: "3.13"
                   cache: "pip"
             - run: "pip install '.[dev]'"
             - run: ruff check .
@@ -23,7 +23,7 @@ jobs:
             - uses: actions/checkout@v3
             - uses: actions/setup-python@v4
               with:
-                  python-version: "3.11"
+                  python-version: "3.13"
                   cache: "pip"
             - run: "pip install -e '.[dev]'"
             - run: mypy src examples
@@ -34,7 +34,7 @@ jobs:
             - uses: actions/checkout@v3
             - uses: actions/setup-python@v4
               with:
-                  python-version: "3.11"
+                  python-version: "3.13"
                   cache: "pip"
             - run: "pip install -e '.[dev]'"
             - run: ruff format --check .
@@ -52,17 +52,16 @@ jobs:
 
               with:
                   miniforge-version: latest
-                  python-version: 3.11
+                  python-version: 3.13
                   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]'
+                  conda install -c conda-forge openff-toolkit
             - run: pytest
 
     example-tests:
@@ -77,17 +76,16 @@ jobs:
 
               with:
                   miniforge-version: latest
-                  python-version: 3.11
+                  python-version: 3.13
                   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]'
+                  conda install -c conda-forge openff-toolkit
             - name: Run script
               run: python examples/testable_example.py
 
@@ -103,15 +101,14 @@ jobs:
 
               with:
                   miniforge-version: latest
-                  python-version: 3.11
+                  python-version: 3.13
                   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]'
+                  conda install -c conda-forge openff-toolkit
             - run: make -C docs doctest

README.rst

@@ -6,16 +6,15 @@
 
 .. figure:: docs/source/_static/stko.png
 
-.. image:: https://readthedocs.org/projects/stko-docs/badge/?version=latest
-    :target: https://stko-docs.readthedocs.io/en/latest/?badge=latest
-    :alt: Documentation Status
-
 Overview
 ========
 
-``stko`` is a Python library which allows for the optimisation and
-property calculation of molecules constructed using the library
-``stk`` https://github.com/lukasturcani/stk. There is a Discord server
+`stko <https://github.com/JelfsMaterialsGroup/stko>`_ is a Python library for
+performing optimizations and calculations on complex molecules built using
+`stk <https://github.com/lukasturcani/stk>`_. In the case of
+optimizations, a clone of ``stk.Molecule`` is returned. For
+calculators, a ``Results`` class are used to calculate and extract
+properties of an ``stk.Molecule``. There is a Discord server
 for ``stk``, which can be joined through https://discord.gg/zbCUzuxe2B.
 
 
@@ -34,10 +33,9 @@ Some optional dependencies are only available through conda:
 
   # for xtb
   mamba install xtb
-  # for openbabel
+  # for openbabel, assuming you are not using Python >= 3.13!
   mamba install openbabel
-  # for mdanalysis
-  mamba install mdanalysis
+
 
 With OpenMM
 -----------
@@ -48,16 +46,26 @@ 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
+  mamba install -c conda-forge openff-toolkit
 
-Then install ``stko`` with pip:
+Then install ``stko`` with pip, but with the cuda variant to take advantage
+of GPU speed up (note that this is a heavy installation!).
 
 .. code-block:: bash
 
-  pip install stko
+  pip install stko[cuda]
+
+We also removed the default installation of ``espaloma_charge`` that provides
+the ML-based ``espaloma-am1bcc`` partial charges method. If users want this
+package, create a new environment and install their dependancies (if this
+fails, please check their
+`instructions <https://github.com/choderalab/espaloma-charge>`_), then install
+``stko``:
+
+.. code-block:: bash
+
+    mamba install -c conda-forge espaloma_charge openff-toolkit
+    pip install stko[cuda]
 
 
 Developer Setup
@@ -86,7 +94,7 @@ and maintain examples in the doc strings of ``Calculator`` and
 ``Optimizer`` classes.
 
 ``examples/basic_examples.py`` highlights basic optimisation with
-``rdkit``, ``openbabel`` and ``xtb`` (if you have ``xtb`` available).
+``rdkit``, and ``xtb`` (if you have ``xtb`` available).
 
 
 How To Contribute

docs/Makefile

@@ -16,4 +16,4 @@ help:
 # Catch-all target: route all unknown targets to Sphinx using the new
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
 %: Makefile
-	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/environment.yml

@@ -1,15 +1,8 @@
 channels:
-  - conda-forge
-  - defaults
+    - conda-forge
+    - defaults
 dependencies:
-  - openff-toolkit
-  - openmm
-  - openmmtools
-  - dgl
-  - python=3.11
-  - pip
-  - rdkit==2024.3.4
-  - espaloma_charge
-  - mdanalysis
-  - openbabel
-
+    - openff-toolkit
+    - python=3.13
+    - pip
+    - rdkit