Merge branch 'RMeli:develop' into develop

.codecov.yml

@@ -11,4 +11,4 @@ comment:
   branches: null
   behavior: default
   flags: null
-  paths: null
+  paths: null

.coveragerc

@@ -1,6 +1,6 @@
 [run]
 source = spyrmsd
-omit = 
+omit =
     spyrmsd/_version.py
     spyrmsd/due.py
 
@@ -13,6 +13,3 @@ exclude_lines =
     # Don't complain if non-runnable code isn't run:
     if 0:
     if __name__ == .__main__.:
-
-    # OpenBabel2
-    except ImportError:

.github/CONTRIBUTING.md

@@ -1,7 +1,7 @@
 # How to contribute
 
 We welcome contributions from external contributors, and this document
-describes how to merge code changes into `spyrmsd`. 
+describes how to merge code changes into `spyrmsd`.
 
 ## Getting Started
 

.github/ISSUE_TEMPLATE/bug-report.md

@@ -29,7 +29,7 @@ A clear and concise description of what you expected to happen.
 **Environment**
  - OS:
  - Python:
- - Package Manager [e.g. `pip`, `conda`]: 
+ - Package Manager [e.g. `pip`, `conda`]:
 
 **Additional Context**
 <!--

.github/ISSUE_TEMPLATE/empty-issue.md

@@ -6,5 +6,3 @@ labels: ''
 assignees: ''
 
 ---
-
-

.github/workflows/flake8.yml

@@ -13,21 +13,22 @@ jobs:
 
     strategy:
       matrix:
-        python-version: [3.6, 3.7, 3.8]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v1
       with:
           python-version: ${{ matrix.python-version }}
     - 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
-    - name: Lint with flake8 
+    - name: Lint with flake8
       run: |
-        flake8 . --count --show-source --statistics
+        flake8 . --count --show-source --statistics

.github/workflows/mypy.yml

@@ -13,18 +13,19 @@ jobs:
 
     strategy:
       matrix:
-        python-version: [3.6, 3.7, 3.8]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v1
       with:
           python-version: ${{ matrix.python-version }}
     - 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
@@ -33,4 +34,4 @@ jobs:
         python setup.py develop --no-deps
     - name: Lint with mypy
       run: |
-        mypy
+        mypy

.github/workflows/pre-commit.yml

@@ -0,0 +1,24 @@
+name: pre-commit
+
+on:
+  push:
+    branches: [ master, develop ]
+  pull_request:
+    branches: [ master, develop ]
+
+jobs:
+  main:
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
+
+    steps:
+    - uses: actions/checkout@v3
+    - uses: actions/setup-python@v4
+      with:
+        python-version: '3.x'
+    - uses: pre-commit/[email protected]
+    - uses: pre-commit-ci/[email protected]
+      if: always()

.github/workflows/pypi.yml

@@ -11,9 +11,9 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: Set up Python
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v4
       with:
         python-version: '3.x'
     - name: Install dependencies
@@ -25,5 +25,6 @@ jobs:
         FLIT_USERNAME: ${{ secrets.FLIT_USERNAME }}
         FLIT_PASSWORD: ${{ secrets.FLIT_PASSWORD }}
       run: |
+        python -m pip install . --no-deps
         flit build
         flit publish

.github/workflows/pytest.yml

@@ -24,15 +24,18 @@ jobs:
     strategy:
       matrix:
         os: [macOS-latest, ubuntu-latest, windows-latest]
-        python-version: [3.7, 3.8, 3.9]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
         chemlib: [obabel, rdkit]
         graphlib: [nx, gt]
-        # graph-tools does not work on Windows
         exclude:
+        # graph-tools does not work on Windows
         - {os: "windows-latest", graphlib: "gt"}
+        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@v1
+    - uses: actions/checkout@v3
 
     - name: Info
       shell: bash
@@ -41,27 +44,30 @@ 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: |
         pytest -v --benchmark --cov=spyrmsd --cov-report=xml --color=yes tests/
 
     - name: CodeCov
-      uses: codecov/codecov-action@v1
+      uses: codecov/codecov-action@v3
       with:
         file: ./coverage.xml
         flags: unittests

.pre-commit-config.yaml

@@ -1,6 +1,10 @@
+exclude: |
+            (?x)^(
+                docs/source/conf.py
+            )$
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.0.1
+    rev: v4.4.0
     hooks:
     - id: check-json
     - id: check-merge-conflict
@@ -10,18 +14,19 @@ repos:
     - id: end-of-file-fixer
     - id: trailing-whitespace
 -   repo: https://github.com/psf/black
-    rev: 21.7b0
+    rev: 23.7.0
     hooks:
     -   id: black
 -   repo: https://github.com/PyCQA/flake8
-    rev: 3.9.2
+    rev: 6.1.0
     hooks:
     -   id: flake8
 -   repo: https://github.com/PyCQA/isort
-    rev: 5.9.3
+    rev: 5.12.0
     hooks:
     -   id: isort
 -   repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v0.910
+    rev: v1.5.1
     hooks:
     -   id: mypy
+        additional_dependencies: [types-requests]

.readthedocs.yml

@@ -13,4 +13,4 @@ formats:
   - pdf
 
 conda:
-  environment: devtools/conda-envs/spyrmsd-docs.yaml
+  environment: devtools/conda-envs/spyrmsd-docs.yaml

CHANGELOG.md

@@ -3,9 +3,70 @@
 
 ------------------------------------------------------------------------------
 
-## Version 0.5.x
+## Version X.Y.Z
 
-Date:            XX/YY/20ZZ
+Date:            XX/YY/ZZZZ
+Contributors:    @RMeli, @takluyver
+
+### Fixed
+
+* Failing tests with `pytest=8.0.0` [PR #101 | @RMeli]
+
+### Changed
+
+* Updated 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]
+
+### Improved
+
+* Messages for `NotImplementedError` exceptions [PR #90 | @RMeli]
+
+### Added
+
+* Python `3.12` to CI [PR  #102 | @RMeli]
+* macOS M1 (`macoOS-14`) to CI [PR  #102 | @RMeli]
+
+### Removed
+
+* `.gitattributes` and `.lgtm.yaml` stale files
+* `versioneer` [PR #91 | @RMeli]
+
+## Version 0.6.0
+
+Date:            08/09/2023
+Contributors:    @RMeli
+
+### Improved
+
+* Documentation on loading RDKit and Open Babel molecules [PR #77 | @RMeli]
+
+### Changed
+
+* Versions of `pre-commit` hooks tools [PR #85 | @RMeli]
+* Version of several GitHub actions [PR #76 | @RMeli]
+* Versioneer to `0.28` [PR #76 | @RMeli]
+* Minimum Python version to `3.7` to match CI [PR #76 | @RMeli]
+* Code according to `black==23.3.0` [PR #76 | @RMeli]
+
+### Added
+
+* `pre-commit` CI action [PR #85 | @RMeli]
+* `extras_require` to `setup.py` for RDKit and Open Babel [PR #84 | @RMeli]
+* Error message when `spyrmsd` is used as module but neither OpenBabel nor RDKit are installed [PR #81 | @RMeli]
+* Pin to `sphinx<7` to avoid compatibility with RTD theme [PR #77 | @RMeli]
+
+### Removed
+
+* `ubuntu-latest-3.7-rdkit-gt` configuration from CI due to continuous failures [PR #84 | @RMeli]
+* Outdated information about RDKit from the documentation [PR #84 | @RMeli]
+* Support for Open Babel 2 [PR #84 | @RMeli]
+* LGTM badge and code annotations [PR #76 | @RMeli]
+
+------------------------------------------------------------------------------
+
+## Version 0.5.2
+
+Date:            23/02/2022
 Contributors:    @RMeli
 
 ### Fixed
@@ -16,6 +77,10 @@ Contributors:    @RMeli
 
 * Support for more types of node properties (including strings) with `graph-tool` [PR #64 | @RMeli]
 
+### Changed
+
+* `ValueError` exception into `NonIsomorphicGraphs(ValueError)` exception [PR #65 | @RMeli]
+
 ### Added
 
 * Warning for disconnected graphs [PR #61| @RMeli]

CITATION.cff

@@ -5,7 +5,7 @@ authors:
   given-names: "Rocco"
   orcid: "https://orcid.org/0000-0002-2845-3410"
 title: "spyrmsd"
-version: 0.5.1
+version: 0.6.0
 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
+global-exclude *.py[cod] __pycache__ *.so