Merge pull request #102 from RMeli/ci

RMeli · Feb 3, 2024 · d50f203 · d50f203
2 parents c65aa6d + c6396f3
commit d50f203
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Showing 14 changed files with 36 additions and 14 deletions.
diff --git a/.github/workflows/flake8.yml b/.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

diff --git a/.github/workflows/mypy.yml b/.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

diff --git a/.github/workflows/pre-commit.yml b/.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

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
@@ -24,14 +24,15 @@ 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]
         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"}
+        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 +44,23 @@ 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: |

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -12,10 +12,19 @@ Contributors:    @RMeli
 
 * Failing tests with `pytest=8.0.0` [PR #101 | @RMeli]
 
+### Changed
+
+* 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
 
 * `versioneer` [PR #91 | @RMeli]

diff --git a/devtools/conda-envs/spyrmsd-all.yaml b/devtools/conda-envs/spyrmsd-all.yaml
@@ -7,6 +7,7 @@ dependencies:
   - python
   - pip
   - ipython
+  - setuptools
 
   # Jupyter
   - jupyterlab

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

diff --git a/devtools/conda-envs/spyrmsd-test-obabel-gt.yaml b/devtools/conda-envs/spyrmsd-test-obabel-gt.yaml
@@ -4,6 +4,7 @@ channels:
 dependencies:
   # Base
   - python
+  - setuptools
 
   # Maths
   - numpy

diff --git a/devtools/conda-envs/spyrmsd-test-obabel-nx.yaml b/devtools/conda-envs/spyrmsd-test-obabel-nx.yaml
@@ -4,6 +4,7 @@ channels:
 dependencies:
   # Base
   - python
+  - setuptools
 
   # Maths
   - numpy

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

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

diff --git a/devtools/conda-envs/spyrmsd.yaml b/devtools/conda-envs/spyrmsd.yaml
@@ -4,8 +4,9 @@ channels:
 dependencies:
   # Base
   - python
+  - setuptools
 
   # Maths
   - numpy
   - scipy
-  - graph-tool
+  - networkx
diff --git a/pyproject.toml b/pyproject.toml
@@ -12,5 +12,5 @@ home-page = "https://spyrmsd.readthedocs.io"
 classifiers = [
     "License :: OSI Approved :: MIT License",
     "Programming Language :: Python :: 3",]
-requires-python = ">=3.7"
+requires-python = ">=3.9"
 requires = ["numpy", "scipy", "networkx>=2"]
diff --git a/setup.py b/setup.py
@@ -35,5 +35,5 @@
         "openbabel": ["openbabel"],
     },
     platforms=["Linux", "Mac OS-X", "Unix", "Windows"],
-    python_requires=">=3.7",
+    python_requires=">=3.9",
 )
-Original file line number
+Diff line change
@@ Expand Up / @@ -7,6 +7,7 @@ dependencies: @@
       - python
       - pip
       - ipython
+      - setuptools
       # Jupyter
       - jupyterlab
@@ Expand Down @@