group dependabot updates

.github/dependabot.yml

@@ -4,6 +4,10 @@ updates:
     directory: "/"
     schedule:
       interval: "daily"
+    groups:
+      actions-deps:
+        patterns:
+          - "*"
 
   - package-ecosystem: "docker"
     directory: "/"

.github/workflows/build.yml

@@ -51,23 +51,23 @@ jobs:
 
     steps:
     - name: Harden Runner
-      uses: step-security/harden-runner@f4a75cfd619ee5ce8d5b864b0d183aff3c69b55a # v2.13.1
+      uses: step-security/harden-runner@5ef0c079ce82195b2a36a210272d6b661572d83e # v2.14.2
       with:
         egress-policy: audit
 
     - name: Check out repo
       if: always()
-      uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5.0.0
+      uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
 
     - name: Pull ccache cache
       if: always()
       id: ccache-restore
-      uses: actions/cache/restore@0057852bfaa89a56745cba8c7296529d2fc39830 # v4.3.0
+      uses: actions/cache/restore@cdf6c1fa76f9f475f3d7449005a359c84ca0f306 # v5.0.3
       with:
         path: /home/runner/.cache/ccache
         key: ccache-${{ env.BUILD_IDENTIFIER }}
 
-    - uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6.0.0
+    - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0
       if: always()
       with:
         python-version: ${{ matrix.py-version }}
@@ -89,7 +89,7 @@ jobs:
 
     - name: Install
       if: always()
-      run: python -m pip list && make install PIP_INSTALL_FLAGS="--no-use-pep517 -vvv"
+      run: python -m pip list && make install PIP_INSTALL_FLAGS="--no-build-isolation -vvv"
 
     - name: Remove ccache cache
       if: ${{ steps.ccache-restore.outputs.cache-hit }}
@@ -103,7 +103,7 @@ jobs:
 
     - name: Push ccache cache
       if: always()
-      uses: actions/cache/save@0057852bfaa89a56745cba8c7296529d2fc39830 # v4.3.0
+      uses: actions/cache/save@cdf6c1fa76f9f475f3d7449005a359c84ca0f306 # v5.0.3
       with:
         path: /home/runner/.cache/ccache
         key: ccache-${{ env.BUILD_IDENTIFIER }}
@@ -129,7 +129,7 @@ jobs:
         mv cython-lint.xml cython-lint-${{ env.BUILD_IDENTIFIER }}.xml
 
     - name: Archive results
-      uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4.6.2
+      uses: actions/upload-artifact@b7c566a772e6b6bfb58ed0dc250532a479d7789f # v6.0.0
       if: always()
       with:
         name: Results (${{ env.BUILD_PRETTY_IDENTIFIER }})
@@ -139,7 +139,7 @@ jobs:
           cython-lint-${{ env.BUILD_IDENTIFIER }}.xml
 
     - name: Report results
-      uses: dorny/test-reporter@dc3a92680fcc15842eef52e8c4606ea7ce6bd3f3 # v1
+      uses: dorny/test-reporter@b082adf0eced0765477756c2a610396589b8c637 # v1
       if: always()
       with:
         name: Report (${{ env.BUILD_PRETTY_IDENTIFIER }})
@@ -156,7 +156,7 @@ jobs:
       fail-fast: false
     name: Mac clang Python ${{ matrix.py-version }}
 
-    runs-on: macos-13
+    runs-on: macos-15
     timeout-minutes: 180
     env:
       MPIEXEC_FLAGS: "--allow-run-as-root --oversubscribe"
@@ -169,34 +169,35 @@ jobs:
 
     steps:
     - name: Harden Runner
-      uses: step-security/harden-runner@f4a75cfd619ee5ce8d5b864b0d183aff3c69b55a # v2.13.1
+      uses: step-security/harden-runner@5ef0c079ce82195b2a36a210272d6b661572d83e # v2.14.2
       with:
         egress-policy: audit
 
     - name: Check out repo
-      uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5.0.0
+      uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
 
     - name: Pull ccache cache
       if: always()
       id: ccache-restore
-      uses: actions/cache/restore@0057852bfaa89a56745cba8c7296529d2fc39830 # v4.3.0
+      uses: actions/cache/restore@cdf6c1fa76f9f475f3d7449005a359c84ca0f306 # v5.0.3
       with:
         path: /Users/runner/Library/Caches/ccache
         key: ccache-${{ runner.os }}-${{ matrix.py-version }}
 
-    # - name: Setup GNU Fortran
-    #   uses: fortran-lang/setup-fortran@2bbdcb313d2b7e72d1d07caf87f3ef9f376d9224 # v1.6.3
+    - name: Setup GNU Fortran
+      uses: fortran-lang/setup-fortran@47809fdb6e637da656ce9ada436527b240c1287f # v1.8.1
 
-    - uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6.0.0
+    - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0
       with:
         python-version: ${{ matrix.py-version }}
         cache: 'pip'
 
     - name: Install packages
       run: |
         brew install open-mpi ccache
-        brew tap brewsci/num
-        brew install brewsci-metis brewsci-parmetis brewsci-suite-sparse
+        # brew tap brewsci/num
+        # brew install brewsci-metis brewsci-parmetis brewsci-suite-sparse
+        brew install scotch suite-sparse
 
     - name: Get ccache config dir
       if: always()
@@ -211,7 +212,7 @@ jobs:
       run: make prereq && make prereq-extra
 
     - name: Install
-      run: PIP_INSTALL_FLAGS=-vvv make install
+      run: PIP_INSTALL_FLAGS="-vvv --no-build-isolation" make install
 
     - name: Remove ccache cache
       if: ${{ steps.ccache-restore.outputs.cache-hit }}
@@ -225,7 +226,7 @@ jobs:
 
     - name: Push ccache cache
       if: always()
-      uses: actions/cache/save@0057852bfaa89a56745cba8c7296529d2fc39830 # v4.3.0
+      uses: actions/cache/save@cdf6c1fa76f9f475f3d7449005a359c84ca0f306 # v5.0.3
       with:
         path: /Users/runner/Library/Caches/ccache
         key: ccache-${{ runner.os }}-${{ matrix.py-version }}
@@ -251,7 +252,7 @@ jobs:
         mv cython-lint.xml cython-lint-${{ runner.os }}-${{ matrix.py-version }}.xml
 
     - name: Archive results
-      uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4.6.2
+      uses: actions/upload-artifact@b7c566a772e6b6bfb58ed0dc250532a479d7789f # v6.0.0
       if: always()
       with:
         name: Results ${{ github.job }}
@@ -261,7 +262,7 @@ jobs:
           cython-lint-${{ runner.os }}-${{ matrix.py-version }}.xml
 
     - name: Report results
-      uses: dorny/test-reporter@dc3a92680fcc15842eef52e8c4606ea7ce6bd3f3 # v1
+      uses: dorny/test-reporter@b082adf0eced0765477756c2a610396589b8c637 # v1
       if: always()
       with:
         name: Report (${{ github.job }})

.github/workflows/container.yml

@@ -31,7 +31,7 @@ jobs:
 
     steps:
     - name: Harden Runner
-      uses: step-security/harden-runner@f4a75cfd619ee5ce8d5b864b0d183aff3c69b55a # v2.13.1
+      uses: step-security/harden-runner@5ef0c079ce82195b2a36a210272d6b661572d83e # v2.14.2
       with:
         egress-policy: audit
 
@@ -43,7 +43,7 @@ jobs:
 
     - name: Check out
       if: always()
-      uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5.0.0
+      uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
       with:
         fetch-depth: 0
 
@@ -117,12 +117,12 @@ jobs:
 
     steps:
     - name: Harden Runner
-      uses: step-security/harden-runner@f4a75cfd619ee5ce8d5b864b0d183aff3c69b55a # v2.13.1
+      uses: step-security/harden-runner@5ef0c079ce82195b2a36a210272d6b661572d83e # v2.14.2
       with:
         egress-policy: audit
 
     - name: Check out
-      uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5.0.0
+      uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
 
     - name: Install podman-compose
       run: pip install podman-compose
@@ -141,12 +141,12 @@ jobs:
 
     steps:
       - name: Harden Runner
-        uses: step-security/harden-runner@f4a75cfd619ee5ce8d5b864b0d183aff3c69b55a # v2.13.1
+        uses: step-security/harden-runner@5ef0c079ce82195b2a36a210272d6b661572d83e # v2.14.2
         with:
           egress-policy: audit
 
       - name: Checkout binder branch
-        uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5.0.0
+        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
         with:
           ref: binder
 
@@ -155,7 +155,7 @@ jobs:
           python generateDockerfile.py ${{ env.IMAGE_REGISTRY }}/${{ env.IMAGE_NAME }}:${{ env.TEST_IMAGE_TAG }}
 
       - name: Create PR
-        uses: peter-evans/create-pull-request@271a8d0340265f705b14b6d32b9829c1cb33d45e # v7.0.8
+        uses: peter-evans/create-pull-request@c0f553fe549906ede9cf27b5156039d195d2ece0 # v8.1.0
         with:
           token: ${{ secrets.GITHUB_TOKEN }}
           commit-message: "Update Dockerfile"

.github/workflows/dependency-review.yml

@@ -17,11 +17,11 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Harden Runner
-        uses: step-security/harden-runner@f4a75cfd619ee5ce8d5b864b0d183aff3c69b55a # v2.13.1
+        uses: step-security/harden-runner@5ef0c079ce82195b2a36a210272d6b661572d83e # v2.14.2
         with:
           egress-policy: audit
 
       - name: 'Checkout Repository'
-        uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5.0.0
+        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
       - name: 'Dependency Review'
-        uses: actions/dependency-review-action@40c09b7dc99638e5ddb0bfd91c1673effc064d8a # v4.8.1
+        uses: actions/dependency-review-action@3c4e3dcb1aa7874d2c16be7d79418e9b7efd6261 # v4.8.2

.github/workflows/documentation-ci.yml

@@ -24,21 +24,21 @@ jobs:
 
     steps:
     - name: Harden Runner
-      uses: step-security/harden-runner@f4a75cfd619ee5ce8d5b864b0d183aff3c69b55a # v2.13.1
+      uses: step-security/harden-runner@5ef0c079ce82195b2a36a210272d6b661572d83e # v2.14.2
       with:
         egress-policy: audit
 
     - name: Check out repo
-      uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5.0.0
+      uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
 
     - name: Pull ccache cache
       id: ccache-restore
-      uses: actions/cache/restore@0057852bfaa89a56745cba8c7296529d2fc39830 # v4.3.0
+      uses: actions/cache/restore@cdf6c1fa76f9f475f3d7449005a359c84ca0f306 # v5.0.3
       with:
         path: /home/runner/.cache/ccache
         key: ccache-documentation-ci
 
-    - uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6.0.0
+    - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0
       with:
         python-version: '3.13'
         cache: 'pip'
@@ -52,7 +52,7 @@ jobs:
       run: make prereq && make prereq-extra
 
     - name: Install
-      run: make install PIP_INSTALL_FLAGS="--no-use-pep517 -vvv"
+      run: make dev
 
     - name: Remove ccache cache
       if: ${{ steps.ccache-restore.outputs.cache-hit }}
@@ -65,7 +65,7 @@ jobs:
       continue-on-error: true
 
     - name: Push ccache cache
-      uses: actions/cache/save@0057852bfaa89a56745cba8c7296529d2fc39830 # v4.3.0
+      uses: actions/cache/save@cdf6c1fa76f9f475f3d7449005a359c84ca0f306 # v5.0.3
       with:
         path: /home/runner/.cache/ccache
         key: ccache-documentation-ci
@@ -75,6 +75,6 @@ jobs:
         make docs
 
     - name: Upload artifact
-      uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4.6.2
+      uses: actions/upload-artifact@b7c566a772e6b6bfb58ed0dc250532a479d7789f # v6.0.0
       with:
         path: 'docs/build'

.github/workflows/documentation.yml

@@ -25,21 +25,21 @@ jobs:
 
     steps:
     - name: Harden Runner
-      uses: step-security/harden-runner@f4a75cfd619ee5ce8d5b864b0d183aff3c69b55a # v2.13.1
+      uses: step-security/harden-runner@5ef0c079ce82195b2a36a210272d6b661572d83e # v2.14.2
       with:
         egress-policy: audit
 
     - name: Check out repo
-      uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5.0.0
+      uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
 
     - name: Pull ccache cache
       id: ccache-restore
-      uses: actions/cache/restore@0057852bfaa89a56745cba8c7296529d2fc39830 # v4.3.0
+      uses: actions/cache/restore@cdf6c1fa76f9f475f3d7449005a359c84ca0f306 # v5.0.3
       with:
         path: /home/runner/.cache/ccache
         key: ccache
 
-    - uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6.0.0
+    - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0
       with:
         python-version: '3.13'
         cache: 'pip'
@@ -53,7 +53,7 @@ jobs:
       run: make prereq && make prereq-extra
 
     - name: Install
-      run: make install PIP_INSTALL_FLAGS="--no-use-pep517 -vvv"
+      run: make dev
 
     - name: Remove ccache cache
       if: ${{ steps.ccache-restore.outputs.cache-hit }}
@@ -66,7 +66,7 @@ jobs:
       continue-on-error: true
 
     - name: Push ccache cache
-      uses: actions/cache/save@0057852bfaa89a56745cba8c7296529d2fc39830 # v4.3.0
+      uses: actions/cache/save@cdf6c1fa76f9f475f3d7449005a359c84ca0f306 # v5.0.3
       with:
         path: /home/runner/.cache/ccache
         key: ccache

.github/workflows/scorecard.yml

@@ -29,12 +29,12 @@ jobs:
 
     steps:
       - name: Harden Runner
-        uses: step-security/harden-runner@f4a75cfd619ee5ce8d5b864b0d183aff3c69b55a # v2.13.1
+        uses: step-security/harden-runner@5ef0c079ce82195b2a36a210272d6b661572d83e # v2.14.2
         with:
           egress-policy: audit
 
       - name: "Checkout code"
-        uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5.0.0
+        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
         with:
           persist-credentials: false
 
@@ -46,13 +46,13 @@ jobs:
           publish_results: true
 
       - name: "Upload artifact"
-        uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4.6.2
+        uses: actions/upload-artifact@b7c566a772e6b6bfb58ed0dc250532a479d7789f # v6.0.0
         with:
           name: SARIF file
           path: results.sarif
           retention-days: 5
 
       - name: "Upload to code-scanning"
-        uses: github/codeql-action/upload-sarif@16140ae1a102900babc80a33c44059580f687047 # v3.29.5
+        uses: github/codeql-action/upload-sarif@45cbd0c69e560cd9e7cd7f8c32362050c9b7ded2 # v3.29.5
         with:
           sarif_file: results.sarif

Dockerfile

@@ -30,7 +30,6 @@ RUN sed -i 's/Components: main/Components: main contrib non-free/' /etc/apt/sour
 # allow running MPI as root in the container
 # bind MPI ranks to hwthreads
 ENV OMPI_MCA_hwloc_base_binding_policy=hwthread \
-    PRTE_MCA_rmaps_default_mapping_policy=:oversubscribe \
     MPIEXEC_FLAGS=--allow-run-as-root \
     OMPI_ALLOW_RUN_AS_ROOT=1 \
     OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 \
@@ -52,7 +51,7 @@ RUN \
 # Build PyNucleus
 # RUN --mount=type=cache,target=/root/.ccache --mount=type=cache,target=/root/.cache/pip \
 RUN \
-    make install PIP_INSTALL_FLAGS=" --break-system-packages" \
+    make install PIP_INSTALL_FLAGS=" --break-system-packages --no-build-isolation" \
     && find . -type f -name '*.c' -exec rm {} + \
     && find . -type f -name '*.cpp' -exec rm {} + \
     && rm -rf build packageTools/build base/build metisCy/build fem/build multilevelSolver/build nl/build \

Makefile

@@ -1,7 +1,7 @@
 PYTHON ?= python3
 VIRTUAL_ENV ?=
 ifeq ($(VIRTUAL_ENV),)
-  FLAGS ?= --no-use-pep517 -e
+  FLAGS ?= --no-build-isolation
   PIP_FLAGS ?= --user
 else
   PYTHON ?= python

base/PyNucleus_base/CSR_LinearOperator_{SCALAR}.pxi

@@ -306,6 +306,7 @@ cdef class {SCALAR_label}CSR_LinearOperator({SCALAR_label}LinearOperator):
     def copy(self):
         data = np.array(self.data, copy=True)
         other = {SCALAR_label}CSR_LinearOperator(self.indices, self.indptr, data)
+        other.num_columns = self.num_columns
         return other
 
     def sort_indices(self):