Add cython-lint

.github/workflows/build.yml

@@ -7,6 +7,11 @@ on:
     branches: [ "master" ]
   workflow_dispatch:
 
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 jobs:
 
   linux:
@@ -33,6 +38,8 @@ 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 +52,7 @@ 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 +84,53 @@ 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
 
@@ -157,7 +165,7 @@ jobs:
         key: ccache-${{ runner.os }}-${{ matrix.py-version }}
 
     - name: Setup GNU Fortran
-      uses: modflowpy/install-gfortran-action@v1
+      uses: fortran-lang/setup-fortran@v1
 
     - uses: actions/setup-python@v4
       with:
@@ -173,6 +181,10 @@ jobs:
       if: always()
       run: ccache --show-config
 
+    - name: Augment path
+      run: |
+        echo "$HOME/.local/bin" >> $GITHUB_PATH
+
     - name: Install Python dependencies
       run: make prereq && make prereq-extra
 
@@ -204,18 +216,34 @@ 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

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
@@ -45,6 +45,8 @@ RUN echo "alias ls='ls --color=auto -FN'" >> /root/.bashrc \
 # allow running MPI as root in the container
 # bind MPI ranks to hwthreads
 ENV OMPI_MCA_hwloc_base_binding_policy=hwthread \
-    MPIEXEC_FLAGS=--allow-run-as-root
+    MPIEXEC_FLAGS=--allow-run-as-root \
+    OMPI_ALLOW_RUN_AS_ROOT=1 \
+    OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
 
 RUN python -m ipykernel install --name=PyNucleus

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

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

base/PyNucleus_base/LinearOperator_{SCALAR}.pxi

@@ -651,14 +651,12 @@ cdef class {SCALAR_label}Transpose_Linear_Operator({SCALAR_label}LinearOperator)
     cdef INDEX_t matvec(self,
                         {SCALAR}_t[::1] x,
                         {SCALAR}_t[::1] y) except -1:
-        self.A.matvecTrans(x, y)
-        return 0
+        return self.A.matvecTrans(x, y)
 
     cdef INDEX_t matvec_no_overwrite(self,
                                      {SCALAR}_t[::1] x,
                                      {SCALAR}_t[::1] y) except -1:
-        self.A.matvecTrans_no_overwrite(x, y)
-        return 0
+        return self.A.matvecTrans_no_overwrite(x, y)
 
     def isSparse(self):
         return self.A.isSparse()
@@ -677,7 +675,10 @@ cdef class {SCALAR_label}Transpose_Linear_Operator({SCALAR_label}LinearOperator)
             return Bcsr
 
     def toarray(self):
-        return self.A.transpose().toarray()
+        try:
+            return self.A.transpose().toarray()
+        except AttributeError:
+            return np.ascontiguousarray(self.A.toarray().T)
 
     def get_diagonal(self):
         return np.array(self.A.diagonal, copy=False)

base/PyNucleus_base/linear_operators.pyx

@@ -1213,26 +1213,57 @@ cdef class sumMultiplyOperator(LinearOperator):
         cdef:
             INDEX_t i
             LinearOperator op
+            int ret
         op = self.ops[0]
-        op.matvec(x, y)
+        ret = op.matvec(x, y)
         scaleScalar(y, self.coeffs[0])
         for i in range(1, self.coeffs.shape[0]):
             op = self.ops[i]
-            op.matvec(x, self.z)
+            ret = min(ret, op.matvec(x, self.z))
             assign3(y, y, 1.0, self.z, self.coeffs[i])
-        return 0
+        return ret
 
     cdef INDEX_t matvec_no_overwrite(self,
                                      REAL_t[::1] x,
                                      REAL_t[::1] y) except -1:
+        cdef:
+            INDEX_t i
+            LinearOperator op = 0
+            int ret = 0
+        for i in range(self.coeffs.shape[0]):
+            op = self.ops[i]
+            ret = min(op.matvec(x, self.z), ret)
+            assign3(y, y, 1.0, self.z, self.coeffs[i])
+        return ret
+
+    cdef INDEX_t matvecTrans(self,
+                             REAL_t[::1] x,
+                             REAL_t[::1] y) except -1:
         cdef:
             INDEX_t i
             LinearOperator op
+            int ret
+        op = self.ops[0]
+        ret = op.matvecTrans(x, y)
+        scaleScalar(y, self.coeffs[0])
+        for i in range(1, self.coeffs.shape[0]):
+            op = self.ops[i]
+            ret = min(ret, op.matvecTrans(x, self.z))
+            assign3(y, y, 1.0, self.z, self.coeffs[i])
+        return ret
+
+    cdef INDEX_t matvecTrans_no_overwrite(self,
+                                          REAL_t[::1] x,
+                                          REAL_t[::1] y) except -1:
+        cdef:
+            INDEX_t i
+            LinearOperator op
+            int ret = 0
         for i in range(self.coeffs.shape[0]):
             op = self.ops[i]
-            op.matvec(x, self.z)
+            ret = min(ret, op.matvecTrans(x, self.z))
             assign3(y, y, 1.0, self.z, self.coeffs[i])
-        return 0
+        return ret
 
     def toarray(self):
         return sum([c*op.toarray() for c, op in zip(self.coeffs, self.ops)])
@@ -1436,8 +1467,34 @@ cdef class multiIntervalInterpolationOperator(LinearOperator):
             interpolationOperator op
         assert self.selected != -1
         op = self.ops[self.selected]
-        op.matvec(x, y)
-        return 0
+        return op.matvec(x, y)
+
+    cdef INDEX_t matvec_no_overwrite(self,
+                                     REAL_t[::1] x,
+                                     REAL_t[::1] y) except -1:
+        cdef:
+            interpolationOperator op
+        assert self.selected != -1
+        op = self.ops[self.selected]
+        return op.matvec_no_overwrite(x, y)
+
+    cdef INDEX_t matvecTrans(self,
+                             REAL_t[::1] x,
+                             REAL_t[::1] y) except -1:
+        cdef:
+            interpolationOperator op
+        assert self.selected != -1
+        op = self.ops[self.selected]
+        return op.matvecTrans(x, y)
+
+    cdef INDEX_t matvecTrans_no_overwrite(self,
+                                          REAL_t[::1] x,
+                                          REAL_t[::1] y) except -1:
+        cdef:
+            interpolationOperator op
+        assert self.selected != -1
+        op = self.ops[self.selected]
+        return op.matvecTrans_no_overwrite(x, y)
 
     def toarray(self):
         assert self.selected != -1
@@ -1521,8 +1578,25 @@ cdef class delayedConstructionOperator(LinearOperator):
                         REAL_t[::1] x,
                         REAL_t[::1] y) except -1:
         self.assure_constructed()
-        self.A.matvec(x, y)
-        return 0
+        return self.A.matvec(x, y)
+
+    cdef INDEX_t matvec_no_overwrite(self,
+                                     REAL_t[::1] x,
+                                     REAL_t[::1] y) except -1:
+        self.assure_constructed()
+        return self.A.matvec_no_overwrite(x, y)
+
+    cdef INDEX_t matvecTrans(self,
+                             REAL_t[::1] x,
+                             REAL_t[::1] y) except -1:
+        self.assure_constructed()
+        return self.A.matvecTrans(x, y)
+
+    cdef INDEX_t matvecTrans_no_overwrite(self,
+                                          REAL_t[::1] x,
+                                          REAL_t[::1] y) except -1:
+        self.assure_constructed()
+        return self.A.matvecTrans_no_overwrite(x, y)
 
     def toarray(self):
         self.assure_constructed()

base/PyNucleus_base/utilsFem.py

@@ -646,7 +646,7 @@ def diff(self, d):
                             result[p.label] = (p.value, d[p.label])
                     elif isinstance(p.value, (int, INDEX, REAL, float)):
                         if not np.allclose(p.value, d[p.label],
-                                           rtol=rTol, atol=aTol):
+                                           rtol=rTol, atol=aTol) and not (np.isnan(p.value) and np.isnan(d[p.label])):
                             print(p.label, p.value, d[p.label], rTol, aTol, p.rTol, p.aTol)
                             result[p.label] = (p.value, d[p.label])
                     else:

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: .