Version 0.8.0 (#124)

RMeli · May 28, 2024 · 98c5752 · 98c5752
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diff --git a/.github/workflows/flake8.yml b/.github/workflows/flake8.yml
@@ -16,9 +16,9 @@ jobs:
         python-version: ["3.9", "3.10", "3.11", "3.12"]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v5
       with:
           python-version: ${{ matrix.python-version }}
     - name: Install Dependencies

diff --git a/.github/workflows/mypy.yml b/.github/workflows/mypy.yml
@@ -16,9 +16,9 @@ jobs:
         python-version: ["3.9", "3.10", "3.11", "3.12"]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v5
       with:
           python-version: ${{ matrix.python-version }}
     - name: Install Dependencies

diff --git a/.github/workflows/pypi.yml b/.github/workflows/pypi.yml
@@ -11,9 +11,9 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Python
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: '3.x'
     - name: Install dependencies

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
@@ -26,18 +26,19 @@ jobs:
         os: [macOS-latest, ubuntu-latest, windows-latest]
         python-version: ["3.9", "3.10", "3.11", "3.12"]
         chemlib: [obabel, rdkit]
-        graphlib: [nx, gt, rx, all]
+        graphlib: [nogt, all]
         exclude:
-        # graph-tools does not work on Windows
-        - {os: "windows-latest", graphlib: "gt"}
-        - {os: "windows-latest", graphlib: "all"}
-        - {graphlib: "all", chemlib: "obabel"}
+          # graph-tool does not work on Windows
+          - {os: "windows-latest", graphlib: "all"}
+          # Don't run without graph-tool on Ubuntu and macOS
+          - {os: "ubuntu-latest", graphlib: "nogt"}
+          - {os: "macOS-latest", graphlib: "nogt"}
         include:
-        - {os: "macOS-14", graphlib: "gt", chemlib: "obabel", python-version: "3.12"}
-        - {os: "macOS-14", graphlib: "nx", chemlib: "rdkit", python-version: "3.12"}
+          - {os: "macOS-14", graphlib: "all", chemlib: "obabel", python-version: "3.12"}
+          - {os: "macOS-14", graphlib: "all", chemlib: "rdkit", python-version: "3.12"}
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Info
       shell: bash
@@ -69,7 +70,7 @@ jobs:
         pytest -v --benchmark --cov=spyrmsd --cov-report=xml --color=yes tests/
 
     - name: CodeCov
-      uses: codecov/codecov-action@v3
+      uses: codecov/codecov-action@v4
       with:
         file: ./coverage.xml
         flags: unittests

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -4,7 +4,7 @@ exclude: |
             )$
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.6.0
     hooks:
     - id: check-json
     - id: check-merge-conflict
@@ -14,20 +14,20 @@ repos:
     - id: end-of-file-fixer
     - id: trailing-whitespace
 -   repo: https://github.com/psf/black
-    rev: 23.7.0
+    rev: 24.4.0
     hooks:
     -   id: black
 -   repo: https://github.com/PyCQA/flake8
-    rev: 6.1.0
+    rev: 7.0.0
     hooks:
     -   id: flake8
 -   repo: https://github.com/PyCQA/isort
-    rev: 5.12.0
+    rev: 5.13.2
     hooks:
     -   id: isort
         args: ["--profile", "black"]
 -   repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.5.1
+    rev: v1.9.0
     hooks:
     -   id: mypy
         additional_dependencies: [types-requests]
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,14 +3,40 @@
 
 ------------------------------------------------------------------------------
 
+## Version 0.8.0
+
+Date:            28/05/2024
+Contributors:    @RMeli
+
+### Added
+
+* Warnings filter for tests of multiple backends [PR #118 | @RMeli]
+* Parametrized fixture to run tests with all available backends [PR #118 | @RMeli]
+
+### Improved
+
+* Test IDs [PR #117 | @RMeli]
+
+### Changed
+
+* the default backend for `pip` installations to `rustworkx` [PR#122 | @RMeli]
+* `pre-commit` versions [PR #120 | @RMeli]
+* Versions of several GitHub Actions [PR #120 | @RMeli]
+* Location of backend tests to standalone file [PR #118 | @RMeli]
+
+### Removed
+
+* Many CI configurations in favour of running tests for all available backends [PR #118 | @RMeli]
+* `tests/molecule.py` in favour of fixtures [PR #118 | @RMeli]
+
 ## Version 0.7.0
 
 Date:            05/04/2024
 Contributors:    @RMeli, @takluyver, @Jnelen
 
 ### Added
 
-* Support for `rustworkx` graph library [PR 111 | @RMeli]
+* 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]
@@ -19,7 +45,7 @@ Contributors:    @RMeli, @takluyver, @Jnelen
 ### Changed
 
 * Molecular graphs cache to cache by backend [PR  #107 | @Jnelen]
-* Python build system to use flit_core directly [PR #103 | @takluyver]
+* 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

diff --git a/CITATION.cff b/CITATION.cff
@@ -8,7 +8,7 @@ authors:
   given-names: "Jochem"
   orcid: "https://orcid.org/0000-0002-9970-4950"
 title: "spyrmsd"
-version: 0.7.0
+version: 0.8.0
 doi: 10.5281/zenodo.3631876
 date-released: 2021-06-21
 url: "https://github.com/RMeli/spyrmsd"

diff --git a/README.md b/README.md
@@ -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 the other backends for higher performance.
+> `spyrmsd` will install [rustworkx] (multi-platform) when using `pip` or `conda`. You can install other backends manually.
 
 > [!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`.
@@ -76,11 +76,11 @@ The following packages are required to use `spyrmsd` as a module:
 
 One of the following graph libraries is required:
 * [graph-tool]
-* [NetworkX]
 * [rustworkx]
+* [NetworkX]
 
 > [!NOTE]
-> `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.
+> `spyrmsd` uses the following priority when multiple graph libraries are present: [graph-tool], [rustworkx], [NetworkX]. *This order might change. Use `set_backend` to ensure you are always using the same backend, if needed.*
 
 #### Standalone Tool
 
@@ -178,10 +178,10 @@ To ensure code quality and consistency the following tools are used during devel
 
 * [black](https://black.readthedocs.io/en/stable/)
 * [Flake 8](http://flake8.pycqa.org/en/latest/) (CI)
-* [isort]()
+* [isort](https://pycqa.github.io/isort/)
 * [mypy](http://mypy-lang.org/) (CI)
 
-Pre-commit `git` hooks can be installed with [pre-commit](https://pre-commit.com/).
+Pre-commit `git` hooks can be installed with [pre-commit].
 
 ## Copyright
 
@@ -198,3 +198,4 @@ Project based on the [Computational Molecular Science Python Cookiecutter](https
 [rustworkx]: https://www.rustworkx.org
 [NetworkX]: https://networkx.github.io/
 [graph-tool]: https://graph-tool.skewed.de/
+[pre-commit]: https://pre-commit.com/
diff --git a/devtools/conda-envs/spyrmsd-all.yaml b/devtools/conda-envs/spyrmsd-all.yaml
@@ -16,8 +16,9 @@ dependencies:
   - numpy
   - pandas
   - scipy
-  - networkx>=2
   - graph-tool
+  - rustworkx
+  - networkx>=2
   - scikit-learn
 
   # Chemistry

diff --git a/devtools/conda-envs/spyrmsd-docs.yaml b/devtools/conda-envs/spyrmsd-docs.yaml
@@ -12,6 +12,7 @@ dependencies:
   - scipy
   - networkx>=2
   - graph-tool
+  - rustworkx
 
   # Chemistry
   - openbabel

diff --git a/...ls/conda-envs/spyrmsd-test-obabel-gt.yaml → ...s/conda-envs/spyrmsd-test-obabel-all.yaml b/...ls/conda-envs/spyrmsd-test-obabel-gt.yaml → ...s/conda-envs/spyrmsd-test-obabel-all.yaml
@@ -4,12 +4,15 @@ channels:
 dependencies:
   # Base
   - python
+  - pip
   - setuptools
 
   # Maths
   - numpy
   - scipy
   - graph-tool
+  - networkx>=2
+  - rustworkx
 
   # Chemistry
   - openbabel

diff --git a/...ls/conda-envs/spyrmsd-test-obabel-nx.yaml → .../conda-envs/spyrmsd-test-obabel-nogt.yaml b/...ls/conda-envs/spyrmsd-test-obabel-nx.yaml → .../conda-envs/spyrmsd-test-obabel-nogt.yaml
@@ -4,12 +4,14 @@ channels:
 dependencies:
   # Base
   - python
+  - pip
   - setuptools
 
   # Maths
   - numpy
   - scipy
   - networkx>=2
+  - rustworkx
 
   # Chemistry
   - openbabel

diff --git a/devtools/conda-envs/spyrmsd-test-rdkit-all.yaml b/devtools/conda-envs/spyrmsd-test-rdkit-all.yaml
@@ -5,6 +5,7 @@ channels:
 dependencies:
   # Base
   - python
+  - pip
   - setuptools
 
   # Maths

diff --git a/devtools/conda-envs/spyrmsd-test-rdkit-gt.yaml b/devtools/conda-envs/spyrmsd-test-rdkit-gt.yaml
diff --git a/...ols/conda-envs/spyrmsd-test-rdkit-nx.yaml → ...s/conda-envs/spyrmsd-test-rdkit-nogt.yaml b/...ols/conda-envs/spyrmsd-test-rdkit-nx.yaml → ...s/conda-envs/spyrmsd-test-rdkit-nogt.yaml
@@ -5,12 +5,14 @@ channels:
 dependencies:
   # Base
   - python
+  - pip
   - setuptools
 
   # Maths
   - numpy
   - scipy
   - networkx>=2
+  - rustworkx
 
   # Chemistry
   - rdkit

diff --git a/devtools/conda-envs/spyrmsd.yaml b/devtools/conda-envs/spyrmsd.yaml
@@ -9,4 +9,5 @@ dependencies:
   # Maths
   - numpy
   - scipy
+  - rustworkx
   - networkx
diff --git a/docs/source/installation.rst b/docs/source/installation.rst
@@ -44,12 +44,12 @@ Module
 
 The following packages are required to use ``spyrmsd`` as a module:
 
-* graph-tool_ or NetworkX_
+* graph-tool_, rustworkx_, or NetworkX_
 * numpy_
 * scipy_
 
 .. note::
-   ``spyrmsd`` uses graph-tool_ by default but will  fall back  to NetworkX_ if the former is not installed (e.g. on Windows).
+   ``spyrmsd`` uses graph-tool_ by default but will fall back to either rustworkx_ or NetworkX_ if the former is not installed (e.g. on Windows).
 
 Standalone Tool
 ~~~~~~~~~~~~~~~
@@ -67,3 +67,4 @@ Additionally, one of the following packages is required to use ``spyrmsd`` as a
 .. _NetworkX: https://networkx.github.io/
 .. _numpy: https://numpy.org/
 .. _scipy: https://www.scipy.org/
+.. _rustworkx: https://www.rustworkx.org
diff --git a/pyproject.toml b/pyproject.toml
@@ -13,4 +13,4 @@ classifiers = [
     "License :: OSI Approved :: MIT License",
     "Programming Language :: Python :: 3",]
 requires-python = ">=3.9"
-requires = ["numpy", "scipy", "networkx>=2"]
+requires = ["numpy", "scipy", "rustworkx"]
diff --git a/setup.py b/setup.py
@@ -23,16 +23,17 @@
     description=short_description[0],
     long_description=long_description,
     long_description_content_type="text/markdown",
-    version="0.7.0-dev",
+    version="0.8.0",
     license="MIT",
     packages=find_packages(),
     include_package_data=True,
     url="https://spyrmsd.readthedocs.io",
-    install_requires=["numpy", "scipy", "networkx>=2"],
+    install_requires=["numpy", "scipy", "rustworkx"],
     extras_require={
         "bib": ["duecredit"],
         "rdkit": ["rdkit"],
         "openbabel": ["openbabel"],
+        "networkx": ["networkx"],
     },
     platforms=["Linux", "Mac OS-X", "Unix", "Windows"],
     python_requires=">=3.9",

diff --git a/spyrmsd/__init__.py b/spyrmsd/__init__.py
@@ -10,7 +10,7 @@
 from .graph import _get_backend as get_backend  # noqa: F401
 from .graph import _set_backend as set_backend  # noqa: F401
 
-__version__ = "0.7.0"
+__version__ = "0.8.0"
 
 # This will print latest Zenodo version
 due.cite(

diff --git a/spyrmsd/__main__.py b/spyrmsd/__main__.py
@@ -66,8 +66,8 @@
             warnings.simplefilter("ignore")
             spyrmsd.set_backend(args.graph_backend)
 
-            if args.verbose:
-                print(f"Graph library: {spyrmsd.get_backend()}")
+    if args.verbose:
+        print(f"Graph library: {spyrmsd.get_backend()}")
 
     # Loop over molecules within fil
     RMSDlist = rmsdwrapper(

diff --git a/spyrmsd/graph.py b/spyrmsd/graph.py
@@ -5,7 +5,10 @@
 
 from spyrmsd import constants
 
-_supported_backends = ("graph_tool", "networkx", "rustworkx")
+# The first backend found from this list is set as default
+# TODO: Need to determine if graph_tool or rustworkx is better
+# NetworkX is slow, therefore it is the last resort
+_supported_backends = ("graph_tool", "rustworkx", "networkx")
 
 _available_backends = []
 _current_backend = None