Migrate to tox 4

.github/workflows/build_upload_pypi_wheels.yml

@@ -89,8 +89,8 @@ jobs:
 
           CIBW_REPAIR_WHEEL_COMMAND_MACOS: ""
 
-          CIBW_TEST_EXTRAS: "test,brille,phonopy_reader,matplotlib"
-          CIBW_TEST_COMMAND: "python {package}/tests_and_analysis/test/run_tests.py"
+          CIBW_TEST_EXTRAS: "test,brille,phonopy-reader,matplotlib"
+          CIBW_TEST_COMMAND: python {package}/tests_and_analysis/test/run_tests.py
 
         with:
           output-dir: wheelhouse
@@ -169,7 +169,7 @@ jobs:
 
       - name: Install from sdist
         shell: bash -l {0}
-        run: python -m pip install $(find dist -name 'euphonic-*.tar.gz')[matplotlib,phonopy_reader,brille,test]
+        run: python -m pip install $(find dist -name 'euphonic-*.tar.gz')[matplotlib,phonopy-reader,brille,test]
 
       - name: Checkout repository (for tests and test data)
         uses: actions/checkout@v4

.github/workflows/run_tests.yml

@@ -73,16 +73,13 @@ jobs:
         if: github.event_name != 'workflow_dispatch'
         env:
           TOX_SKIP_ENV: '.*?(py311).*?'
-          TOX_PARALLEL_NO_SPINNER: 1
         shell: bash -l {0}
-        run: python -m tox --parallel
+        run: python -m tox run-parallel
 
       - name: Run tests, workflow dispatch so test all Python versions
         if: github.event_name == 'workflow_dispatch'
-        env:
-          TOX_PARALLEL_NO_SPINNER: 1
         shell: bash -l {0}
-        run: python -m tox --parallel
+        run: python -m tox run-parallel
 
       - name: Upload test results
         if: always()
@@ -115,7 +112,7 @@ jobs:
           python -m pip install --upgrade pip
           python -m pip install -r tests_and_analysis/ci_requirements.txt
           python -m pip install -r doc/requirements.txt
-          python -m pip install .[matplotlib,phonopy_reader,brille]
+          python -m pip install .[matplotlib,phonopy-reader,brille]
       - name: Run Sphinx doctests
         working-directory: ./doc
         shell: bash -l {0}

.github/workflows/test_release.yml

@@ -15,12 +15,15 @@ jobs:
     runs-on: ${{ matrix.os }}
     steps:
       - uses: actions/checkout@v4
-      - uses: conda-incubator/setup-miniconda@v3
         with:
-          python-version: '3.10'
-          channels: conda-forge,defaults
-          channel-priority: true
-      - name: Install llvm on Macos
+          fetch-depth: 0 # Ensure tags are fetched for versioning
+      - uses: actions/setup-python@v5
+        with:
+          python-version: |
+              3.10
+              3.11
+              3.12
+      - name: Install llvm on MacOS
         if: startsWith(matrix.os, 'macos')
         shell: bash -l {0}
         env:

.readthedocs.yml

@@ -23,5 +23,5 @@ python:
         path: .
         extra_requirements:
            - matplotlib
-           - phonopy_reader
+           - phonopy-reader
            - brille

build_utils/release_tox.ini

@@ -1,74 +1,52 @@
 [tox]
 # Use conda to set up the python environments to run in
-requires = tox-conda
+requires = tox>=4
 # The python environments to run the tests in
 envlist = pypi-py310-min,conda-py310-old-np,{pypi,conda}-{py310,py311,py312},pypisource-{py310,py312}
-# Skip the execution of setup.py as we do it with the correct version in commands_pre below
-skipsdist = True
+skip_install = True
 
 [testenv]
 changedir = tests_and_analysis/test
 test_command = python {toxinidir}/../tests_and_analysis/test/run_tests.py --report
 requirements_dir = {toxinidir}/../tests_and_analysis
+passenv =
+    EUPHONIC_VERSION
+# The name "extras" is reserved and has its own format with newlines:
+# we need a token to inject into custom commands_pre, so call it extras_str
+extras_str = [test,matplotlib,phonopy-reader,brille]
 
 # Test PyPI source distribution
 [testenv:pypisource-{py310,py312}]
-passenv = CC CC_LD LDFLAGS CPPFLAGS
-install_command = python -m pip install {opts} {packages}
-deps =
-    numpy
-    spglib  # Not interested here in whether source builds of spglib work
-    -r{[testenv]requirements_dir}/tox_requirements.txt
+passenv =
+    CC
+    CC_LD
+    LDFLAGS
+    CPPFLAGS
 commands_pre =
     python -m pip install \
     --force-reinstall \
-    'euphonic[matplotlib,phonopy_reader,brille]=={env:EUPHONIC_VERSION}' \
+    euphonic{[testenv]extras_str}=={env:EUPHONIC_VERSION} \
     --no-binary 'euphonic'
 commands = {[testenv]test_command}
 
-
 [testenv:pypi-{py310,py311,py312}]
-install_command = python -m pip install {opts} {packages}
-deps =
-    numpy
-    -r{[testenv]requirements_dir}/tox_requirements.txt
 commands_pre =
     python -m pip install \
     --force-reinstall \
-    'euphonic[matplotlib,phonopy_reader,brille]=={env:EUPHONIC_VERSION}' \
+    euphonic{[testenv]extras_str}=={env:EUPHONIC_VERSION} \
     --only-binary 'euphonic'
 commands = {[testenv]test_command}
 
-[testenv:pypi-py310-min-win-linux]
-install_command = python -m pip install --force-reinstall {opts} {packages}
-platform =
-    linux: linux
-    windows: win32
+[testenv:pypi-py310-min]
+platform = (linux)|(win32)
 deps =
-    numpy==1.24.0
+    numpy==1.24
+    -r{toxinidir}/../tests_and_analysis/tox_requirements.txt
 commands_pre =
     python -m pip install --force-reinstall \
-        -r{[testenv]requirements_dir}/minimum_euphonic_requirements.txt
-    python -m pip install --force-reinstall \
-        -r{[testenv]requirements_dir}/tox_requirements.txt
+        -r{toxinidir}/../tests_and_analysis/minimum_euphonic_requirements.txt
     python -m pip install \
-    'euphonic[matplotlib,phonopy_reader,brille]=={env:EUPHONIC_VERSION}' \
-    --only-binary 'euphonic'
-commands = {[testenv]test_command}
-
-[testenv:pypi-py310-min-mac]
-install_command = python -m pip install --force-reinstall {opts} {packages}
-platform =
-    mac: darwin
-deps =
-    numpy==1.24.0
-commands_pre =
-    python -m pip install --force-reinstall \
-        -r{[testenv]requirements_dir}/minimum_euphonic_requirements_mac.txt
-    python -m pip install --force-reinstall \
-        -r{[testenv]requirements_dir}/tox_requirements.txt
-    python -m pip install \
-    'euphonic[matplotlib,phonopy_reader,brille]=={env:EUPHONIC_VERSION}' \
+    euphonic{[testenv]extras_str}=={env:EUPHONIC_VERSION} \
     --only-binary 'euphonic'
 commands = {[testenv]test_command}
 
@@ -78,10 +56,13 @@ install_command = conda install {packages}
 conda_channels =
     conda-forge
     default
-conda_deps =
-    --file={[testenv]requirements_dir}/tox_requirements.txt
+extras =
+    test
+    matplotlib
+    phonopy-reader
+
 commands_pre =
-    conda install -c conda-forge euphonic={env:EUPHONIC_VERSION} matplotlib-base pyyaml h5py
+    conda install -c conda-forge euphonic={env:EUPHONIC_VERSION}
 # Brille not available on conda
 commands = {[testenv]test_command} -m "not brille"
 
@@ -93,10 +74,12 @@ install_command = conda install {packages}
 conda_channels =
     conda-forge
     default
-conda_deps =
-    --file={[testenv]requirements_dir}/tox_requirements.txt
+deps = numpy==1.24
+extras =
+    test
+    matplotlib
+    phonopy-reader
 commands_pre =
-    conda install numpy=1.22
-    conda install -c conda-forge euphonic={env:EUPHONIC_VERSION} matplotlib-base pyyaml h5py
+    conda install -c conda-forge euphonic={env:EUPHONIC_VERSION}
 # Brille not available on conda
 commands = {[testenv]test_command} -m "not brille"

doc/source/installation.rst

@@ -14,14 +14,14 @@ Euphonic has optional 'extensions' which require extra dependencies for certain
 They are listed below
 
 * **matplotlib** - required for plotting
-* **phonopy_reader** - required for reading Phonopy files
+* **phonopy-reader** - required for reading Phonopy files
 * **brille** - required for performing linear interpolation with the Brille library
 
 To install euphonic with all the dependencies run:
 
 .. code-block:: bash
 
-  pip install euphonic[matplotlib,phonopy_reader,brille]
+  pip install euphonic[matplotlib,phonopy-reader,brille]
 
 The dependencies can also be installed individually:
 
@@ -69,7 +69,7 @@ To install with all dependencies use:
 
 .. code-block:: bash
 
-  pip install .[matplotlib,phonopy_reader,brille]
+  pip install .[matplotlib,phonopy-reader,brille]
 
 If you don't require the extra dependencies, just use:
 

euphonic/readers/phonopy.py

@@ -18,7 +18,7 @@ def __init__(self):
             '\n\nCannot import yaml, h5py to read Phonopy files, maybe '
             'they are not installed. To install the optional '
             'dependencies for Euphonic\'s Phonopy reader, try:\n\n'
-            'pip install euphonic[phonopy_reader]\n')
+            'pip install euphonic[phonopy-reader]\n')
 
     def __str__(self):
         return self.message

pyproject.toml

@@ -53,9 +53,11 @@ documentation = "https://euphonic.readthedocs.io/en/stable/"
 
 [project.optional-dependencies]
 matplotlib = ["matplotlib>=3.8.0"]
-phonopy_reader = ["h5py>=3.6.0", "PyYAML>=6.0"]
+phonopy_reader = ["h5py>=3.6.0", "PyYAML>=6.0"]  # Deprecated, will be removed in future versions.
+phonopy-reader = ["h5py>=3.6.0", "PyYAML>=6.0"]
 brille = ["brille>=0.7.0"]
-test = ["mock", "pytest~=7.0", "coverage", "pytest-mock", "pytest-lazy-fixture", "pytest-xvfb"]
+test = ["mock", "pytest~=7.0", "coverage", "pytest-mock", "pytest-lazy-fixture", "pytest-xvfb", "python-slugify"]
+ci = ["tox==4.32.2"]
 
 [project.scripts]
 euphonic-brille-convergence = "euphonic.cli.brille_convergence:main"

tests_and_analysis/ci_requirements.txt

@@ -1 +1 @@
-tox==3.28.0
+tox==4.23.2

tests_and_analysis/test/euphonic_test/test_force_constants_calculate_qpoint_phonon_modes.py

@@ -301,7 +301,7 @@ def test_with_use_c_false_doesnt_raise_error_or_warn(
             fc.calculate_qpoint_phonon_modes(get_test_qpts(), use_c=False)
         assert len(warn_record) == 0
 
-
+@pytest.mark.c_extension
 class TestForceConstantsCalculateQPointPhononModesWithCExtensionInstalled:
 
     @pytest.fixture

tests_and_analysis/test/pytest.ini

@@ -4,3 +4,4 @@ markers =
     matplotlib: requires euphonic[matplotlib] extra to be installed
     brille: requires euphonic[brille] extra to be installed
     multiple_extras: requires any combination of the above extras e.g. phonopy_reader and matplotlib
+    c_extension: Requires c extension compiled