build: update dependencies storage and setup.py extras

Signed-off-by: David Hart <[email protected]>

.github/workflows/codeql.yml

@@ -59,7 +59,7 @@ jobs:
           objects.githubusercontent.com:443
           pypi.org:443
           uploads.github.com:443
-    
+
     - name: Checkout repository
       uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
 
@@ -85,8 +85,8 @@ jobs:
     - if: matrix.build-mode == 'manual'
       shell: bash
       run: |
-        python -m pip install pybind11 setuptools
-        python setup.py build_ext
+        python3 -m pip install pybind11 setuptools
+        python3 setup.py build_ext
 
     - name: Perform CodeQL Analysis
       uses: github/codeql-action/analyze@6db8d6351fd0be61f9ed8ebd12ccd35dcec51fea # v3.26.11

.github/workflows/continuous-integration.yml

@@ -54,10 +54,13 @@ jobs:
           python-version: ~${{ matrix.version }}
 
       - name: Install development dependencies
-        run: python3 -m pip install --upgrade pip
+        run: |
+          python3 -m pip install --upgrade pip
+          python3 -m pip install -r requirements.txt
+          python3 -m pip install -r tests/requirements.txt
 
       - name: Test install
-        run: python3 -m pip install .[tests,formats]
+        run: python3 -m pip install .[formats]
 
       - name: Test with pytest
         run: python3 -m pytest --nbmake --cov=sansmic --cov=tests examples/ tests/

.github/workflows/continuous-testing.yml

@@ -47,9 +47,11 @@ jobs:
       - name: Install development dependencies
         run: |
           python3 -m pip install --upgrade pip
+          python3 -m pip install -r tests/requirements.txt
 
       - name: Test install
-        run: python3 -m pip install .[tests,formats]
+        run: python3 -m pip install .
+
 
       - name: Test with pytest
         run: |

.github/workflows/gh-pages.yml

@@ -48,11 +48,13 @@ jobs:
       - uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5.2.0
         with:
           python-version: '3.11'
-      - name: Install package
+      - name: Install dependencies
         run: |
           sudo apt-get install -y doxygen graphviz
-          pip install -e .[docs]
-          pip install -r requirements.txt
+          python3 -m pip install --upgrade pip
+          python3 -m pip install -r docs/requirements.txt
+      - name: Install package
+        run:  pip install -e .
       - name: Build documentation
         run: sphinx-build docs/ docs/_build/html
       - name: Upload artifact

docs/requirements.txt

@@ -0,0 +1,7 @@
+Sphinx==8.0.0
+pydata-sphinx-theme==0.15.4
+sphinx_design==0.6.0
+sphinxcontrib-bibtex==2.6.3
+breathe==4.35.0
+exhale==0.3.7
+sphinx-argparse==0.5.2

pyproject.toml

@@ -25,35 +25,8 @@ classifiers = [
 ]
 
 [project.optional-dependencies]
-formats = ['h5py', 'openpyxl', 'tabulate', 'pyyaml', 'lasio', 'matplotlib']
-docs = [
-    'Sphinx',
-    'pydata-sphinx-theme',
-    'sphinx_design',
-    'sphinxcontrib-bibtex',
-    'breathe',
-    'exhale',
-    'sphinx-argparse',
-]
-dev = [
-    'pre-commit',
-    'pyproject_hooks',
-    'black',
-    'pybind11',
-    'pytest',
-    'pytest-cov',
-]
-tests = [
-    'pytest',
-    'pytest-cov',
-    'h5py',
-    'openpyxl',
-    'tabulate',
-    'pyyaml',
-    'lasio',
-    'nbmake',
-    'matplotlib',
-]
+formats = ['h5py', 'openpyxl', 'tabulate', 'pyyaml', 'lasio']
+examples = ['nbmake', 'matplotlib']
 
 [project.urls]
 Documentation = "https://sandialabs.github.io/sansmic"

requirements.txt

@@ -1,10 +1,11 @@
-numpy
-pandas
-pyyaml
-pre-commit
-pytest
-pytest-cov
-black
-pybind11
-nbmake
-matplotlib
+numpy>=2.1.0
+pandas>=2.2.0
+pyyaml>=6.0.0
+pre-commit>=3.8.0
+pyproject_hooks>=1.2.0
+pytest>=8.0.0
+pytest-cov>=5.0.0
+black>=24.0.0
+pybind11>=2.13.0
+nbmake>=1.5.0
+matplotlib>=3.9.0

tests/requirements.txt

@@ -0,0 +1,9 @@
+pytest==8.3.3
+pytest-cov==5.0.0
+h5py==3.12.1
+openpyxl==3.1.0
+tabulate==0.9.0
+pyyaml==6.0.2
+lasio==0.3.1
+nbmake==1.5.4
+matplotlib==3.9.2