Convert packaging to pyproject.toml, rebase onto stable (v0.11.1, Python 3.14)

.github/workflows/build_conda.yaml

@@ -1,35 +1,35 @@
-
-name: Conda
-
-on:
-  release:
-    types: ['released', 'prereleased']
-
-# workflow_dispatch:        # Un comment line if you also want to trigger action manually
-
-jobs:
-  conda_deployment_with_new_tag:
-    name: Conda deployment of package for platform ${{ matrix.os }} with Python ${{ matrix.python-version }}
-    runs-on: ubuntu-latest
-
-    steps:
-      - name: Checkout
-        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683
-      - name: Conda environment creation and activation
-        uses: conda-incubator/setup-miniconda@505e6394dae86d6a5c7fbb6e3fb8938e3e863830
-        with:
-          python-version: "3.12"
-          environment-file: recipe/build-env.yml
-          activate-environment: build-environment
-          auto-update-conda: true
-          auto-activate-base: false
-          show-channel-urls: true
-      - name: Build and upload the conda packages
-        uses: uibcdf/action-build-and-upload-conda-packages@4940704d2be7906d3bda5b00e3c3e4472fd7808f
-        with:
-          meta_yaml_dir: recipe
-          overwrite: true
-          python-version: "3.12"
-          user: phygbu
-          label: main
-          token: ${{ secrets.ANACONDA }} # Replace with the right name of your secret
+
+name: Conda
+
+on:
+  release:
+    types: ['released', 'prereleased']
+
+# workflow_dispatch:        # Un comment line if you also want to trigger action manually
+
+jobs:
+  conda_deployment_with_new_tag:
+    name: Conda deployment of package for platform ${{ matrix.os }} with Python ${{ matrix.python-version }}
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
+      - name: Conda environment creation and activation
+        uses: mamba-org/setup-micromamba@add3a49764cedee8ee24e82dfde87f5bc2914462 # v2.0.7
+        with:
+          environment-file: recipe/build-env.yml
+          environment-name: build-environment
+          create-args: python=3.12
+          init-shell: bash
+      - name: Build and upload the conda packages
+        uses: uibcdf/action-build-and-upload-conda-packages@4940704d2be7906d3bda5b00e3c3e4472fd7808f
+        with:
+          meta_yaml_dir: recipe
+          overwrite: true
+          python-version: "3.12"
+          user: phygbu
+          label: main
+          token: ${{ secrets.ANACONDA }} # Replace with the right name of your secret

.github/workflows/run-tests-action.yaml

@@ -1,92 +1,100 @@
-name: pytest
-on: push
-jobs:
-  run_pytest:
-    name: run-tests (${{ matrix.python-version }}, ${{ matrix.os }})
-    runs-on: ${{ matrix.os }}
-    defaults:
-      run:
-        shell: bash -l {0}
-    strategy:
-      fail-fast: false
-      matrix:
-        python-version: ["3.11", "3.12","3.13", "3.14"]
-        os: ["ubuntu-latest"]
-    steps:
-      - name: Check out repository code
-        uses: actions/checkout@v4
-      - name: Install Conda environment with Micromamba
-        uses: conda-incubator/setup-miniconda@v3
-        with:
-          environment-file: tests/test-env.yml
-          python: ${{ matrix.python-version }}
-          channels: conda-forge,phygbu
-          channel-priority: flexible
-          activate-environment: test-environment
-          auto-activate-base: false
-      - name: Conda information
-        run: |
-          conda info
-          conda list
-          conda config --show-sources
-          conda config --show
-      - name: install package
-        run: pip install --no-deps .
-      - name: Install headless server
-        run: |
-           sudo apt-get update
-           sudo apt-get install xvfb
-           sudo apt-get install qtbase5-dev
-      - name: Test with xvfb
-        run: |
-           xvfb-run --auto-servernum /usr/share/miniconda/envs/test-environment/bin/pytest  -n 2 --cov-report= --cov=Stoner --junitxml pytest.xml
-           coverage xml
-        env:
-            TZ: Europe/London
-            LC_CTYPE: en_GB.UTF-8
-            GH_ACTION: True
-      - name: Cleanup X11 server
-        uses: bcomnes/cleanup-xvfb@v1
-      - name: Coveralls Parallel
-        uses: coverallsapp/github-action@v2
-        with:
-          flag-name: run-${{ join(matrix.*, '-') }}
-          format: cobertura
-          github-token: ${{ secrets.GITHUB_TOKEN }}
-      - name: Upload Unit Test Results
-        if: always()
-        uses: actions/upload-artifact@v4
-        with:
-          name: Unit Test Results (Python ${{ matrix.python-version }})
-          path: pytest.xml
-      - name: Post Coveraage result to Codacy
-        run: |
-          export CODACY_PROJECT_TOKEN=${{ secrets.CODACY_PROJECT_TOKEN }}
-          bash <(curl -Ls https://coverage.codacy.com/get.sh) report -r coverage.xml
-
-  publish-test-results:
-    name: "Publish Unit Tests Results"
-    needs: run_pytest
-    runs-on: ubuntu-latest
-    if: always()
-
-    steps:
-      - name: Download Artifacts
-        uses: actions/download-artifact@v4
-        with:
-          path: artifacts
-
-      - name: Publish Unit Test Results
-        uses: EnricoMi/publish-unit-test-result-action@v2
-        with:
-          files: artifacts/**/*.xml
-
-  coverage-finish:
-    needs: run_pytest
-    runs-on: ubuntu-latest
-    steps:
-    - name: Coveralls Finished
-      uses: coverallsapp/github-action@v2
-      with:
-        parallel-finished: true
-        carryforward: "run-1,run-2"
+name: pytest
+on: push
+jobs:
+  run_pytest:
+    name: run-tests (${{ matrix.python-version }}, ${{ matrix.os }})
+    runs-on: ${{ matrix.os }}
+    permissions:
+      contents: read
+      checks: write
+    defaults:
+      run:
+        shell: bash -l {0}
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.11", "3.12","3.13", "3.14"]
+        os: ["ubuntu-latest"]
+    steps:
+      - name: Check out repository code
+        uses: actions/checkout@34e114876b0b11c390a56381ad16ebd13914f8d5 # v4.3.1
+      - name: Install Mamba environment
+        uses: mamba-org/setup-micromamba@add3a49764cedee8ee24e82dfde87f5bc2914462 # v2.0.7
+        with:
+          environment-file: tests/test-env.yml
+          environment-name: test-environment
+          create-args: >-
+            python=${{ matrix.python-version }}
+            --channel-priority flexible
+          init-shell: bash
+          cache-downloads: true
+          cache-environment: true
+      - name: Mamba information
+        run: |
+          micromamba info
+          micromamba list
+      - name: install package
+        run: pip install --no-deps .
+      - name: Install headless server
+        run: |
+           sudo apt-get update
+           sudo apt-get install xvfb
+           sudo apt-get install qtbase5-dev
+      - name: Test with xvfb
+        run: |
+           xvfb-run --auto-servernum pytest -n 2 --cov-report= --cov=Stoner --junitxml pytest.xml
+           coverage xml
+        env:
+            TZ: Europe/London
+            LC_CTYPE: en_GB.UTF-8
+            GH_ACTION: True
+      - name: Cleanup X11 server
+        uses: bcomnes/cleanup-xvfb@9e016c43bb8d73fe7d5933d2ef00fd770c1a7c50 # v1.0.9
+      - name: Coveralls Parallel
+        uses: coverallsapp/github-action@5cbfd81b66ca5d10c19b062c04de0199c215fb6e # v2.3.7
+        with:
+          flag-name: run-${{ join(matrix.*, '-') }}
+          format: cobertura
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+      - name: Upload Unit Test Results
+        if: always()
+        uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4.6.2
+        with:
+          name: Unit Test Results (Python ${{ matrix.python-version }})
+          path: pytest.xml
+      - name: Post Coveraage result to Codacy
+        run: |
+          export CODACY_PROJECT_TOKEN=${{ secrets.CODACY_PROJECT_TOKEN }}
+          bash <(curl -Ls https://coverage.codacy.com/get.sh) report -r coverage.xml
+
+  publish-test-results:
+    name: "Publish Unit Tests Results"
+    needs: run_pytest
+    runs-on: ubuntu-latest
+    if: always()
+    permissions:
+      checks: write
+      pull-requests: write
+
+    steps:
+      - name: Download Artifacts
+        uses: actions/download-artifact@d3f86a106a0bac45b974a628896c90dbdf5c8093 # v4.3.0
+        with:
+          path: artifacts
+
+      - name: Publish Unit Test Results
+        uses: EnricoMi/publish-unit-test-result-action@c950f6fb443cb5af20a377fd0dfaa78838901040 # v2.23.0
+        with:
+          files: artifacts/**/*.xml
+
+  coverage-finish:
+    needs: run_pytest
+    runs-on: ubuntu-latest
+    permissions:
+      checks: write
+    steps:
+    - name: Coveralls Finished
+      uses: coverallsapp/github-action@5cbfd81b66ca5d10c19b062c04de0199c215fb6e # v2.3.7
+      with:
+        parallel-finished: true
+        carryforward: "run-1,run-2"

.ipynb_checkpoints/Makefile-checkpoint

@@ -0,0 +1,57 @@
+ifeq ($(OS),"Windows_NT")
+	SPHINX_BUILD	=	sphinx-build.bat
+else
+	SPHINX_BUILD	=	sphinx-build
+endif
+PYTHON_SETUP	=	python setup.py
+
+BRANCH		=	`git branch | grep '*' | cut -d ' ' -f 2`
+
+clean:
+	$(MAKE) -C doc clean
+	- rm dist/*
+	- rm -rf build/*
+	- find -name '__pycache__' -exec rm -rf {} \;
+
+test:
+	pytest -n `python -c 'import os;print(min(8,os.cpu_count()))'`
+
+check:
+	prospector -E -0 --profile-path=. -P .landscape.yml Stoner > prospector-report.txt
+
+black:
+	find Stoner -name '*.py' | xargs -d "\n" black -l 119
+	find doc/samples -name '*.py' | xargs  -d "\n" black -l 80
+	find scripts -name '*.py' | xargs -d "\n" black -l 80
+
+commit: black
+	$(MAKE) -C doc readme
+	git add tests
+	git add Stoner
+	git add doc/samples
+	git commit -a
+	git push origin $(BRANCH)
+
+_build_wheel:
+	$(MAKE) -C doc readme
+	$(PYTHON_SETUP) sdist bdist_wheel --universal
+	twine upload dist/*
+
+wheel: clean test _build_wheel
+
+docbuild: FORCE
+	$(MAKE) -C doc clean
+	$(MAKE) -C doc html
+	( cd ../gh-pages; git pull )
+	rsync -rcm --perms --chmod=ugo=rwX --delete  --filter="P .git" --filter="P .nojekyll" doc/_build/html/ ../gh-pages/
+
+conda:
+	conda build --python=3.6 recipe &
+	conda build --python=3.7 recipe &
+	conda build --python 3.8 recipe &
+
+
+rtdbuild: export READTHEDOCS=1
+rtdbuild: docbuild
+
+FORCE: