Add rustworkx backend (#111)

* Update graph.py to support set_backend function I also made a fuction to see the available backends and get the current backend * Apply private _available_backends suggestions from code review This commit contains the suggested changes regarding making the available_backends variable private, and refactoring the get_available_backends method to available_backends Co-authored-by: Rocco Meli <r.meli@bluemail.ch> * Print warning when backend is already set + make sure we use _available_backends everywhere where possible * remove reliance on environment variables * make _validate_backend function print warning when a certain backend isn't installed * Use precommit hooks add __all__ back refactor _alias_backendDict to _alias_to_backend * Update ValueError message Co-authored-by: Rocco Meli <r.meli@bluemail.ch> * Don't return the backend when setting it Co-authored-by: Rocco Meli <r.meli@bluemail.ch> * Add dummy function to make mypy happy remove __all__ assignment * fist play with rustworkx backend * add documentation for backend selection * add cli backend selection * cleanup * changelog * apply @Jnelen suggestion and add warning filter * make molecule test also more robust * add rx to ci * add rustworkx to all backends tests * add back graphtool * add rx to test all backends and add verbose mode * Update test_molecule.py --------- Co-authored-by: jnelen <jnelen@ucam.edu> Co-authored-by: Jochem Nelen <78348388+Jnelen@users.noreply.github.com>
RMeli · Mar 11, 2024 · f250c3e · f250c3e
1 parent fbff4a3
commit f250c3e
Show file tree

Hide file tree

Showing 12 changed files with 307 additions and 11 deletions.
diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
@@ -26,7 +26,7 @@ jobs:
         os: [macOS-latest, ubuntu-latest, windows-latest]
         python-version: ["3.9", "3.10", "3.11", "3.12"]
         chemlib: [obabel, rdkit]
-        graphlib: [nx, gt, all]
+        graphlib: [nx, gt, rx, all]
         exclude:
         # graph-tools does not work on Windows
         - {os: "windows-latest", graphlib: "gt"}

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -10,6 +10,7 @@ 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]

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 [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
 
@@ -118,7 +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
 
@@ -142,11 +146,16 @@ 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 both [NetworkX](https://networkx.github.io/) and [graph-tool](https://graph-tool.skewed.de/) for the calculation of graph isomorphisms. You can check which backend is being used with
+`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()
@@ -176,7 +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
 
@@ -185,3 +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/
diff --git a/devtools/conda-envs/spyrmsd-test-obabel-rx.yaml b/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
diff --git a/devtools/conda-envs/spyrmsd-test-rdkit-all.yaml b/devtools/conda-envs/spyrmsd-test-rdkit-all.yaml
@@ -12,6 +12,7 @@ dependencies:
   - scipy
   - graph-tool
   - networkx>=2
+  - rustworkx
 
   # Chemistry
   - rdkit

diff --git a/devtools/conda-envs/spyrmsd-test-rdkit-rx.yaml b/devtools/conda-envs/spyrmsd-test-rdkit-rx.yaml
@@ -0,0 +1,27 @@
+name: spyrmsd
+channels:
+  - conda-forge
+  - rdkit
+dependencies:
+  # Base
+  - python
+  - setuptools
+
+  # Maths
+  - numpy
+  - scipy
+  - rustworkx
+
+  # Chemistry
+  - rdkit
+
+  # Testing
+  - pytest
+  - pytest-cov
+  - pytest-benchmark
+
+  # Dev
+  - mypy
+  - flake8
+  - black
+  - codecov
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -23,7 +23,7 @@
 
 project = "spyrmsd"
 copyright = (
-    "2019-2021, Rocco Meli. Project structure based on the "
+    "2019-2024, Rocco Meli. Project structure based on the "
     "Computational Molecular Science Python Cookiecutter version 1.1"
 )
 author = "Rocco Meli"

diff --git a/spyrmsd/__main__.py b/spyrmsd/__main__.py
@@ -34,6 +34,9 @@
         default=None,
         help="Graph library (backend)",
     )
+    parser.add_argument(
+        "-v", "--verbose", action="store_true", help="Enable verbose mode"
+    )
 
     args = parser.parse_args()
 
@@ -63,6 +66,9 @@
             warnings.simplefilter("ignore")
             spyrmsd.set_backend(args.graph_backend)
 
+            if args.verbose:
+                print(f"Graph library: {spyrmsd.get_backend()}")
+
     # Loop over molecules within fil
     RMSDlist = rmsdwrapper(
         ref,

diff --git a/spyrmsd/graph.py b/spyrmsd/graph.py
@@ -5,14 +5,15 @@
 
 from spyrmsd import constants
 
-_supported_backends = ("graph_tool", "networkx")
+_supported_backends = ("graph_tool", "networkx", "rustworkx")
 
 _available_backends = []
 _current_backend = None
 
 _backend_to_alias = {
     "graph_tool": ["graph_tool", "graphtool", "graph-tool", "graph tool", "gt"],
     "networkx": ["networkx", "nx"],
+    "rustworkx": ["rustworkx", "rx"],
 }
 
 _alias_to_backend = {}
@@ -141,6 +142,25 @@ def _set_backend(backend):
         num_vertices = nx_num_vertices
         vertex_property = nx_vertex_property
 
+    elif backend == "rustworkx":
+        from spyrmsd.graphs.rx import cycle as rx_cycle
+        from spyrmsd.graphs.rx import (
+            graph_from_adjacency_matrix as rx_graph_from_adjacency_matrix,
+        )
+        from spyrmsd.graphs.rx import lattice as rx_lattice
+        from spyrmsd.graphs.rx import match_graphs as rx_match_graphs
+        from spyrmsd.graphs.rx import num_edges as rx_num_edges
+        from spyrmsd.graphs.rx import num_vertices as rx_num_vertices
+        from spyrmsd.graphs.rx import vertex_property as rx_vertex_property
+
+        cycle = rx_cycle
+        graph_from_adjacency_matrix = rx_graph_from_adjacency_matrix
+        lattice = rx_lattice
+        match_graphs = rx_match_graphs
+        num_edges = rx_num_edges
+        num_vertices = rx_num_vertices
+        vertex_property = rx_vertex_property
+
     _current_backend = backend