Add cython-lint, fix bugs

sandialabs · Dec 10, 2023 · 07da094 · 07da094
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commit 07da094
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Showing 6 changed files with 62 additions and 35 deletions.
diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -33,6 +33,8 @@ jobs:
       PYNUCLEUS_BUILD_PARALLELISM: 2
       OMPI_CC: ${{ matrix.c-compiler }}
       OMPI_CXX: ${{ matrix.cxx-compiler }}
+      BUILD_PRETTY_IDENTIFIER: "Linux ${{ matrix.c-compiler }} Python ${{ matrix.py-version }}"
+      BUILD_IDENTIFIER: "Linux-${{ matrix.c-compiler }}-${{ matrix.py-version }}"
 
     steps:
     - name: Check out repo
@@ -45,7 +47,7 @@ jobs:
       uses: actions/cache/restore@v3
       with:
         path: /home/runner/.cache/ccache
-        key: ccache-${{ runner.os }}-${{ matrix.c-compiler }}-${{ matrix.py-version }}
+        key: ccache-${{ env.BUILD_IDENTIFIER }}
 
     - uses: actions/setup-python@v4
       if: always()
@@ -77,52 +79,53 @@ jobs:
         GH_TOKEN: ${{ github.token }}
       run: |
         gh extension install actions/gh-actions-cache
-        gh actions-cache delete ccache-${{ runner.os }}-${{ matrix.c-compiler}}-${{ matrix.py-version }} --confirm
+        gh actions-cache delete ccache-${{ env.BUILD_IDENTIFIER }} --confirm
       continue-on-error: true
 
     - name: Push ccache cache
       if: always()
       uses: actions/cache/save@v3
       with:
         path: /home/runner/.cache/ccache
-        key: ccache-${{ runner.os }}-${{ matrix.c-compiler }}-${{ matrix.py-version }}
+        key: ccache-${{ env.BUILD_IDENTIFIER }}
 
     - name: Ccache report
       if: always()
       run: ccache -s
 
     - name: Run tests
       if: always()
-      run: python3 -m pytest --junit-xml=test-results-${{ runner.os }}-${{ matrix.c-compiler }}-${{ matrix.py-version }}.xml tests/
+      run: python3 -m pytest --junit-xml=test-results-${{ env.BUILD_IDENTIFIER }}.xml tests/
 
     - name: Run flake8
       if: always()
       run: |
         make flake8
-        mv flake8.xml flake8-${{ runner.os }}-${{ matrix.c-compiler }}-${{ matrix.py-version }}.xml
+        mv flake8.xml flake8-${{ env.BUILD_IDENTIFIER }}.xml
 
-    - name: Archive test results
-      uses: actions/upload-artifact@v3
+    - name: Run cython-lint
       if: always()
-      with:
-        name: Test results
-        path: test-results-${{ runner.os }}-${{ matrix.c-compiler }}-${{ matrix.py-version }}.xml
+      run: |
+        make cython-lint
+        mv cython-lint.xml cython-lint-${{ env.BUILD_IDENTIFIER }}.xml
 
-    - name: Report test results
-      uses: dorny/test-reporter@v1
+    - name: Archive results
+      uses: actions/upload-artifact@v3
       if: always()
       with:
-        name: Test report (${{ runner.os }}, ${{ matrix.c-compiler }}, Python ${{ matrix.py-version }})
-        path: test-results-${{ runner.os }}-${{ matrix.c-compiler }}-${{ matrix.py-version }}.xml
-        reporter: java-junit
-        fail-on-error: true
+        name: Results (${{ env.BUILD_PRETTY_IDENTIFIER }})
+        path: |
+          test-results-${{ env.BUILD_IDENTIFIER }}.xml
+          flake8-${{ env.BUILD_IDENTIFIER }}.xml
+          cython-lint-${{ env.BUILD_IDENTIFIER }}.xml
 
-    - name: Report flake8 results
+    - name: Report results
       uses: dorny/test-reporter@v1
       if: always()
       with:
-        name: Flake8 report (${{ runner.os }}, ${{ matrix.c-compiler }}, Python ${{ matrix.py-version }})
-        path: flake8-${{ runner.os }}-${{ matrix.c-compiler }}-${{ matrix.py-version }}.xml
+        name: Report (${{ env.BUILD_PRETTY_IDENTIFIER }})
+        path: |
+          *-${{ env.BUILD_IDENTIFIER }}.xml
         reporter: java-junit
         fail-on-error: false
 
@@ -204,18 +207,34 @@ jobs:
       if: always()
       run: python3 -m pytest --junit-xml=test-results-${{ runner.os }}-${{ matrix.py-version }}.xml tests/
 
-    - name: Archive test results
+    - name: Run flake8
+      if: always()
+      run: |
+        make flake8
+        mv flake8.xml flake8-${{ runner.os }}-${{ matrix.py-version }}.xml
+
+    - name: Run cython-lint
+      if: always()
+      run: |
+        make cython-lint
+        mv cython-lint.xml cython-lint-${{ runner.os }}-${{ matrix.py-version }}.xml
+
+    - name: Archive results
       uses: actions/upload-artifact@v3
       if: always()
       with:
-        name: Test results
-        path: test-results-${{ runner.os }}-${{ matrix.py-version }}.xml
+        name: Results ${{ github.job }}
+        path: |
+          test-results-${{ runner.os }}-${{ matrix.py-version }}.xml
+          flake8-${{ runner.os }}-${{ matrix.py-version }}.xml
+          cython-lint-${{ runner.os }}-${{ matrix.py-version }}.xml
 
-    - name: Report test results
+    - name: Report results
       uses: dorny/test-reporter@v1
       if: always()
       with:
-        name: Test report (${{ runner.os }}, Python ${{ matrix.py-version }})
-        path: test-results-${{ runner.os }}-${{ matrix.py-version }}.xml
+        name: Report (${{ github.job }})
+        path: |
+          *-${{ runner.os }}-${{ matrix.py-version }}.xml
         reporter: java-junit
-        fail-on-error: true
+        fail-on-error: false
diff --git a/Dockerfile b/Dockerfile
@@ -33,8 +33,8 @@ ENV VIRTUAL_ENV=/pynucleus/venv
 RUN python3 -m venv $VIRTUAL_ENV
 ENV PATH="$VIRTUAL_ENV/bin:$PATH"
 WORKDIR /pynucleus
-RUN make prereq && \
-    make prereq-extra && \
+RUN make prereq PIP_FLAGS=--no-cache-dir && \
+    make prereq-extra PIP_FLAGS=--no-cache-dir && \
     make install && \
     python -m pip install --no-cache-dir ipykernel && \
     rm -rf build packageTools/build base/build metisCy/build fem/build multilevelSolver/build nl/build

diff --git a/Makefile b/Makefile
@@ -169,8 +169,16 @@ prereq:
 	$(PYTHON) -m pip install $(PIP_FLAGS) $(PIP_INSTALL_FLAGS) scikit-sparse
 
 prereq-extra:
-	$(PYTHON) -m pip install $(PIP_FLAGS) pytest pytest-html pytest-xdist Sphinx sphinxcontrib-programoutput flake8 flake8-junit-report
+	$(PYTHON) -m pip install $(PIP_FLAGS) pytest pytest-html pytest-xdist Sphinx sphinxcontrib-programoutput flake8 flake8-junit-report cython-lint
 
 flake8:
-	$(PYTHON) -m flake8 --output-file=flake8.txt --exit-zero drivers packageTools base metisCy fem multilevelSolver nl tests
+	$(PYTHON) -m flake8 --output-file=flake8.txt --exit-zero drivers examples packageTools base metisCy fem multilevelSolver nl tests
 	flake8_junit flake8.txt flake8.xml
+	rm flake8.txt
+
+cython-lint:
+	- cython-lint --max-line-length=160 drivers examples packageTools base metisCy fem multilevelSolver nl tests > cython-lint.txt 2>&1
+	flake8_junit cython-lint.txt cython-lint.xml
+	rm cython-lint.txt
+	sed 's/name="flake8"/name="cython-lint"/g' cython-lint.xml > cython-lint2.xml
+	mv cython-lint2.xml cython-lint.xml
diff --git a/README.rst b/README.rst
@@ -99,7 +99,7 @@ For example, on Ubuntu podman can be installed with
 
 Instructions for other platforms can be found here: https://podman.io/docs/installation
 
-Once podman is installed, we can download a copy of https://github.com/sandialabs/PyNucleus/compose.yaml and save it to an empty directory.
+Once podman is installed, we can download a copy of https://github.com/sandialabs/PyNucleus/blob/master/compose.yaml and save it to an empty directory.
 In that directory we then run
 
 .. code-block:: shell
@@ -121,7 +121,7 @@ For development using PyNucleus it can be useful to launch a Jupyter notebook se
 
    podman compose up pynucleus-jupyter
 
-and then open the access the Jupyter notebook interface at https://localhost:8889
+and then open the Jupyter notebook interface at https://localhost:8889
 
 
 Spack install

diff --git a/compose.yaml b/compose.yaml
@@ -25,7 +25,7 @@ services:
 
   # Launch with:
   # docker compose up
-  # Then open localhost:8888 in your browser
+  # Then open localhost:8889 in your browser
   pynucleus-jupyter:
     image: ghcr.io/sandialabs/pynucleus:latest
     build: .

diff --git a/docs/installation.rst b/docs/installation.rst
@@ -28,7 +28,7 @@ For example, on Ubuntu podman can be installed with
 
 Instructions for other platforms can be found here: https://podman.io/docs/installation
 
-Once podman is installed, we can download a copy of https://github.com/sandialabs/PyNucleus/compose.yaml and save it to an empty directory.
+Once podman is installed, we can download a copy of https://github.com/sandialabs/PyNucleus/blob/master/compose.yaml and save it to an empty directory.
 In that directory we then run
 
 .. code-block:: shell
@@ -50,7 +50,7 @@ For development using PyNucleus it can be useful to launch a Jupyter notebook se
 
    podman compose up pynucleus-jupyter
 
-and then open the access the Jupyter notebook interface at https://localhost:8889
+and then open the Jupyter notebook interface at https://localhost:8889
 
 
 Spack install