Merge branch 'RMeli:master' into master

.github/workflows/flake8.yml

@@ -13,7 +13,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
 
     steps:
     - uses: actions/checkout@v3
@@ -24,7 +24,8 @@ jobs:
     - name: Install Dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install flake8
+        python -m pip install setuptools
+        python -m pip install flake8
     - name: Install  package
       run: |
         python setup.py develop --no-deps

.github/workflows/mypy.yml

@@ -13,7 +13,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
 
     steps:
     - uses: actions/checkout@v3
@@ -24,7 +24,8 @@ jobs:
     - name: Install Dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install mypy
+        python -m pip install setuptools
+        python -m pip install mypy
     - name: Install Types
       run: |
         python -m pip install types-requests

.github/workflows/pre-commit.yml

@@ -12,7 +12,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
 
     steps:
     - uses: actions/checkout@v3

.github/workflows/pytest.yml

@@ -24,14 +24,17 @@ jobs:
     strategy:
       matrix:
         os: [macOS-latest, ubuntu-latest, windows-latest]
-        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
         chemlib: [obabel, rdkit]
-        graphlib: [nx, gt]
+        graphlib: [nx, gt, rx, all]
         exclude:
         # graph-tools does not work on Windows
         - {os: "windows-latest", graphlib: "gt"}
-        # FIXME: Keeps failing in CI for unknown reasons during miniconda setup
-        - {os: "ubuntu-latest", graphlib: "gt", chemlib: "rdkit", python-version: "3.7"}
+        - {os: "windows-latest", graphlib: "all"}
+        - {graphlib: "all", chemlib: "obabel"}
+        include:
+        - {os: "macOS-14", graphlib: "gt", chemlib: "obabel", python-version: "3.12"}
+        - {os: "macOS-14", graphlib: "nx", chemlib: "rdkit", python-version: "3.12"}
 
     steps:
     - uses: actions/checkout@v3
@@ -43,20 +46,23 @@ jobs:
         df -h
         ulimit -a
 
-    - uses: conda-incubator/setup-miniconda@v2
+    - uses: conda-incubator/setup-miniconda@v3
       with:
         python-version: ${{ matrix.python-version }}
         environment-file: devtools/conda-envs/spyrmsd-test-${{ matrix.chemlib }}-${{ matrix.graphlib }}.yaml
-        channels: conda-forge,defaults
+        miniforge-version: "latest"
         activate-environment: spyrmsd
+        miniforge-variant: Mambaforge
+        use-mamba: true
         auto-update-conda: true
         auto-activate-base: false
         show-channel-urls: true
 
     - name: Install
       run: |
         python -m pip install . --no-deps
-        conda list
+        mamba info
+        mamba list
 
     - name: Test
       run: |

.pre-commit-config.yaml

@@ -25,6 +25,7 @@ repos:
     rev: 5.12.0
     hooks:
     -   id: isort
+        args: ["--profile", "black"]
 -   repo: https://github.com/pre-commit/mirrors-mypy
     rev: v1.5.1
     hooks:

.readthedocs.yml

@@ -1,16 +1,20 @@
-# .readthedocs.yml
-# Read the Docs configuration file
+# Read the Docs configuration file for Sphinx projects
 # See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
 
 version: 2
 
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "mambaforge-22.9"
+
 sphinx:
   builder: html
   configuration: docs/source/conf.py
 
 formats:
-  - epub
   - pdf
+  - epub
 
 conda:
   environment: devtools/conda-envs/spyrmsd-docs.yaml

CHANGELOG.md

@@ -3,6 +3,38 @@
 
 ------------------------------------------------------------------------------
 
+## Version 0.7.0
+
+Date:            05/04/2024
+Contributors:    @RMeli, @takluyver, @Jnelen
+
+### Added
+
+* Support for `rustworkx` graph library [PR 111 | @RMeli]
+* Functionality to manually select the backend from CLI [PR #108 | @RMeli]
+* Functionality to manually select the backend [PR  #107 | @Jnelen]
+* Python `3.12` to CI [PR  #102 | @RMeli]
+* macOS M1 (`macoOS-14`) to CI [PR  #102 | @RMeli]
+
+### Changed
+
+* Molecular graphs cache to cache by backend [PR  #107 | @Jnelen]
+* Python build system to use flit_core directly [PR #103 | @takluyver]
+* Minimum version of Python to `3.9` (to reduce CI matrix) [PR  #102 | @RMeli]
+
+### Fixed
+
+* Failing tests with `pytest=8.0.0` [PR #101 | @RMeli]
+
+### Improved
+
+* Messages for `NotImplementedError` exceptions [PR #90 | @RMeli]
+
+### Removed
+
+* `.gitattributes` and `.lgtm.yaml` stale files
+* `versioneer` [PR #91 | @RMeli]
+
 ## Version 0.6.0
 
 Date:            08/09/2023

CITATION.cff

@@ -4,8 +4,11 @@ authors:
 - family-names: "Meli"
   given-names: "Rocco"
   orcid: "https://orcid.org/0000-0002-2845-3410"
+- family-names: "Nelen"
+  given-names: "Jochem"
+  orcid: "https://orcid.org/0000-0002-9970-4950"
 title: "spyrmsd"
-version: 0.6.0
+version: 0.7.0
 doi: 10.5281/zenodo.3631876
 date-released: 2021-06-21
 url: "https://github.com/RMeli/spyrmsd"

MANIFEST.in

@@ -1,6 +1,5 @@
 include LICENSE
 include MANIFEST.in
-include versioneer.py
 
 graft spyrmsd
 global-exclude *.py[cod] __pycache__ *.so

README.md

@@ -9,7 +9,7 @@
 [![Documentation Status](https://readthedocs.org/projects/spyrmsd/badge/?version=develop)](https://spyrmsd.readthedocs.io/en/develop/?badge=develop)
 
 [![License](https://img.shields.io/github/license/RMeli/pyrmsd?color=%2333BBFF)](https://opensource.org/licenses/MIT)
-[![PyPI](https://img.shields.io/badge/PyPI-v0.6.0%20-ff69b4)](https://pypi.org/project/spyrmsd/)
+[![PyPI](https://img.shields.io/badge/PyPI-v0.7.0%20-ff69b4)](https://pypi.org/project/spyrmsd/)
 [![Conda Version](https://img.shields.io/conda/vn/conda-forge/spyrmsd.svg)](https://anaconda.org/conda-forge/spyrmsd)
 
 [![J. Cheminform.](https://img.shields.io/badge/J.%20Cheminform.-10.1186%2Fs13321--020--00455--2-blue)](https://doi.org/10.1186/s13321-020-00455-2)
@@ -38,7 +38,7 @@ If you find `spyrmsd` useful, please consider citing the following paper:
 `spyrmsd` is available on [PyPI](https://pypi.org/project/spyrmsd/) and [conda-forge](https://github.com/conda-forge/spyrmsd-feedstock) and can be easily installed from source. See [Dependencies](###Dependencies) for a description of all the dependencies.
 
 > [!NOTE]
-> `spyrmsd` will install [NetworkX](https://networkx.github.io/) (multi-platform). You can install [graph-tool](https://graph-tool.skewed.de/) on macOS and Linux for higher performance.
+> `spyrmsd` will install [NetworkX](https://networkx.github.io/) (multi-platform). You can install the other backends for higher performance.
 
 > [!WARNING]
 > If `spyrmsd` is used as a standalone tool, it is required to install either [RDKit](https://rdkit.org/) or [Open Babel](http://openbabel.org/). Neither is automatically installed with `pip` nor `conda`.
@@ -71,12 +71,16 @@ pip install .
 
 The following packages are required to use `spyrmsd` as a module:
 
-* [graph-tool](https://graph-tool.skewed.de/) or [NetworkX](https://networkx.github.io/)
 * [numpy](https://numpy.org/)
 * [scipy](https://www.scipy.org/)
 
+One of the following graph libraries is required:
+* [graph-tool]
+* [NetworkX]
+* [rustworkx]
+
 > [!NOTE]
-> `spyrmsd` uses [graph-tool](https://graph-tool.skewed.de/) by default but will fall back to [NetworkX](https://networkx.github.io/) if the former is not installed (e.g. on Windows). However, in order to support cross-platform installation [NetworkX](https://networkx.github.io/) is installed by default, and [graph-tool](https://graph-tool.skewed.de/) needs to be installed manually.
+> `spyrmsd` uses the following priority when multiple graph libraries are present: [graph-tool], [NetworkX], [rustworkx]. *This order might change. Use `set_backend` to ensure you are always using the same backend, if needed.* However, in order to support cross-platform installation [NetworkX](https://networkx.github.io/) is installed by default, and the other graph library need to be installed manually.
 
 #### Standalone Tool
 
@@ -89,27 +93,12 @@ Additionally, one of the following packages is required to use `spyrmsd` as a st
 
 ### Standalone Tool
 
+`spyrmsd` provides a convenient CLI tool. See `spyrmsd`'s `--help` for the usage:
+
 ```bash
 python -m spyrmsd -h
 ```
 
-```text
-usage: python -m spyrmsd [-h] [-m] [-c] [--hydrogens] [-n] reference molecules [molecules ...]
-
-Symmetry-corrected RMSD calculations in Python.
-
-positional arguments:
-  reference       Reference file
-  molecules       Input file(s)
-
-optional arguments:
-  -h, --help      show this help message and exit
-  -m, --minimize  Minimize (fit)
-  -c, --center    Center molecules at origin
-  --hydrogens     Keep hydrogen atoms
-  -n, --nosymm    No graph isomorphism
-```
-
 ### Module
 
 ```python
@@ -133,7 +122,7 @@ def rmsd(
 ```
 
 > [!NOTE]
-> Atomic properties (`aprops`) can be any Python object when using [NetworkX](https://networkx.github.io/), or integers, floats, or strings when using [graph-tool](https://graph-tool.skewed.de/).
+> Atomic properties (`aprops`) can be any Python object when using [NetworkX] and [rustworkx], or integers, floats, or strings when using [graph-tool].
 
 #### Symmetry-Corrected RMSD
 
@@ -157,7 +146,31 @@ def symmrmsd(
 ```
 
 > [!NOTE]
-> Atomic properties (`aprops`) can be any Python object when using [NetworkX](https://networkx.github.io/), or integers, floats, or strings when using [graph-tool](https://graph-tool.skewed.de/).
+> Atomic properties (`aprops`) can be any Python object when using [NetworkX] and [rustworkx], or integers, floats, or strings when using [graph-tool](https://graph-tool.skewed.de/).
+
+#### Select Backend
+
+`spyrmsd` supports the following graph libraries for the calculation of graph isomorphisms:
+* [graph-tool]
+* [NetworkX]
+* [rustworkx]
+
+ You can check which backend is being used with
+
+```python
+spyrmsd.get_backend()
+```
+
+You can also manually select your preferred backend with
+
+```python
+spyrmsd.set_backend("networkx")
+# spyrmsd uses NetworkX
+spyrmsd.set_backend("graph_tool")
+# spyrmsd uses graph_tool
+```
+
+The available backends (which depend on the installed dependencies) are stored in `spyrmsd.available_backends`.
 
 ## Development
 
@@ -172,7 +185,7 @@ Pre-commit `git` hooks can be installed with [pre-commit](https://pre-commit.com
 
 ## Copyright
 
-Copyright (c) 2019-2021, Rocco Meli.
+Copyright (c) 2019-2024, Rocco Meli.
 
 ## References
 
@@ -181,3 +194,7 @@ References are tracked with [duecredit](https://github.com/duecredit/duecredit/)
 ### Acknowledgements
 
 Project based on the [Computational Molecular Science Python Cookiecutter](https://github.com/molssi/cookiecutter-cms) version `1.1`.
+
+[rustworkx]: https://www.rustworkx.org
+[NetworkX]: https://networkx.github.io/
+[graph-tool]: https://graph-tool.skewed.de/

devtools/conda-envs/spyrmsd-all.yaml

@@ -7,6 +7,7 @@ dependencies:
   - python
   - pip
   - ipython
+  - setuptools
 
   # Jupyter
   - jupyterlab

devtools/conda-envs/spyrmsd-docs.yaml

@@ -5,6 +5,7 @@ channels:
 dependencies:
   # Base
   - python
+  - setuptools
 
   # Maths
   - numpy

devtools/conda-envs/spyrmsd-test-obabel-gt.yaml

@@ -4,6 +4,7 @@ channels:
 dependencies:
   # Base
   - python
+  - setuptools
 
   # Maths
   - numpy

devtools/conda-envs/spyrmsd-test-obabel-nx.yaml

@@ -4,6 +4,7 @@ channels:
 dependencies:
   # Base
   - python
+  - setuptools
 
   # Maths
   - numpy

devtools/conda-envs/spyrmsd-test-obabel-rx.yaml

@@ -0,0 +1,26 @@
+name: spyrmsd
+channels:
+  - conda-forge
+dependencies:
+  # Base
+  - python
+  - setuptools
+
+  # Maths
+  - numpy
+  - scipy
+  - rustworkx
+
+  # Chemistry
+  - openbabel
+
+  # Testing
+  - pytest
+  - pytest-cov
+  - pytest-benchmark
+
+  # Dev
+  - mypy
+  - flake8
+  - black
+  - codecov