Patch release preparation (#35)

* Bump numpy version, update CI pip cache

* Try intalling newer PETSc/SLEPc versions on CI

* Pin versions in tox.ini

* Fix pins

* Remove redundant CI step

* Try remove arpack for macOS

* Try using 3.9 on macOS

* Temp. disable PETSc/SLEPc on macOS

Author: michalk8

.github/workflows/ci.yml

@@ -13,23 +13,7 @@ on:
         -   main
 
 jobs:
-    init:
-        runs-on: ubuntu-latest
-        outputs:
-            skip: ${{ steps.ci-skip-step.outputs.ci-skip }}
-        steps:
-        -   uses: actions/checkout@v2
-            with:
-                fetch-depth: 0
-        -   id: ci-skip-step
-            uses: mstachniuk/ci-skip@master
-            with:
-                commit-filter: '[ci skip];[ci-skip];[skip ci];[skip-ci]'
-                commit-filter-separator: ';'
-
     lint:
-        needs: init
-        if: ${{ github.event_name == 'schedule' || needs.init.outputs.skip == 'false' }}
         runs-on: ubuntu-latest
         steps:
         -   uses: actions/checkout@v2
@@ -43,7 +27,7 @@ jobs:
         -   uses: actions/cache@v2
             with:
                 path: ~/.cache/pre-commit
-                key: precommit-${{ env.pythonLocation }}-${{ hashFiles('.pre-commit-config.yaml') }}
+                key: precommit-${{ env.pythonLocation }}-${{ hashFiles('**/.pre-commit-config.yaml') }}
                 restore-keys: |
                     precommit-${{ env.pythonLocation }}-
 
@@ -58,8 +42,6 @@ jobs:
                 tox -e lint,check-docs,readme
 
     test:
-        needs: init
-        if: ${{ github.event_name == 'schedule' || needs.init.outputs.skip == 'false' }}
         runs-on: ${{ matrix.os }}
         strategy:
             fail-fast: false
@@ -73,15 +55,16 @@ jobs:
                     python: 3.8
                     use_slepc: true
                 -   os: macos-latest
-                    python: 3.7
-                    use_slepc: true
+                    python: 3.9
+                    # TODO(michalk8): enable this in the future (problem/missing mpif90)
+                    use_slepc: false
                 -   os: macos-latest
                     python: 3.8
                     use_slepc: false
         env:
-            # for macOS only, make sure to pin this in tox.ini as well
-            PC_VERSION: 3.13.5  # PETSc version
-            SC_VERSION: 3.13.2  # SLEPc version
+            # make sure to pin this in tox.ini as well
+            PC_VERSION: 3.15.4  # PETSc version
+            SC_VERSION: 3.15.2  # SLEPc version
 
         steps:
         -   uses: actions/checkout@v2
@@ -93,11 +76,11 @@ jobs:
                 python-version: ${{ matrix.python }}
 
         -   name: Export environment variables
-            if: matrix.use_slepc == true && runner.os == 'macOS'
+            if: matrix.use_slepc == true
             run: |
                 echo "PETSC_DIR=$HOME/petsc-$PC_VERSION" >> $GITHUB_ENV
                 echo "SLEPC_DIR=$HOME/slepc-$SC_VERSION" >> $GITHUB_ENV
-                echo "PETSC_ARCH=arch-darwin-c-opt" >> $GITHUB_ENV
+                echo "PETSC_ARCH=arch-$RUNNER_OS-c-opt" >> $GITHUB_ENV
         -   name: Install PETSc/SLEPc dev dependencies
             if: matrix.use_slepc == true
             run: |
@@ -112,8 +95,6 @@ jobs:
             with:
                 path: ${{ steps.pip-cache-dir.outputs.dir }}
                 key: pip-${{ runner.os }}-${{ env.pythonLocation }}-${{ hashFiles('**/requirements.txt') }}
-                restore-keys: |
-                    pip-${{ runner.os }}-${{ env.pythonLocation }}-
 
         -   name: Install pip dependencies
             run: |

.scripts/ci/install_dependencies.sh

@@ -2,7 +2,7 @@
 
 set -euo pipefail
 
-function install_petsc_macos {
+function install_petsc {
     curl -O "https://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-lite-$PC_VERSION.tar.gz"
     tar -xzf "petsc-lite-$PC_VERSION.tar.gz"
     pushd "petsc-$PC_VERSION"
@@ -15,42 +15,41 @@ function install_petsc_macos {
     popd
 }
 
-function install_slepc_macos {
+function install_slepc {
     curl -O "https://slepc.upv.es/download/distrib/slepc-$SC_VERSION.tar.gz"
     tar -xzf "slepc-$SC_VERSION.tar.gz"
     pushd "slepc-$SC_VERSION"
 
-    ./configure --with-arpack-dir=/usr/local/Cellar/arpack
+    ./configure
     make all
     make check
     # make install  # only to move into the appropriate location
 
     popd
 }
 
-
 if [[ "$RUNNER_OS" == "Linux" ]]; then
     echo "Installing PETSc/SLEPc dependencies for Linux"
     sudo apt-get update -y
-    sudo apt-get install gcc gfortran libopenmpi-dev libblas-dev liblapack-dev petsc-dev slepc-dev -y
+    sudo apt-get install gcc gfortran libopenmpi-dev libblas-dev liblapack-dev -y
 elif [[ "$RUNNER_OS" == "macOS" ]]; then
-    echo "Installing PETSc/SLEPc with SLEPc dir: '$SLEPC_DIR', PETSc dir: '$PETSC_DIR', PETSc arch: '$PETSC_ARCH'"
-    pushd "$HOME"
-
     brew install gcc open-mpi openblas lapack arpack
-    install_petsc_macos
-    install_slepc_macos
-
-    popd
-
-    # this seems to be only necessary on the CI
-    echo "Symlinking numpy"
-    python -m pip install --upgrade pip
-    pip install numpy
-
-    NUMPY_INCLUDE="$(python -c 'import numpy; print(numpy.get_include())')"
-    ln -sfv "$NUMPY_INCLUDE/numpy" "$PETSC_DIR/$PETSC_ARCH/include"
 else
-    echo "Invalid OS for PETSc/SLEPc dependencies: $OS"
+    echo "Invalid OS for PETSc/SLEPc dependencies: '$OS'"
     exit 42
 fi
+
+echo "Installing PETSc/SLEPc with SLEPc dir: '$SLEPC_DIR', PETSc dir: '$PETSC_DIR', PETSc arch: '$PETSC_ARCH'"
+
+pushd "$HOME"
+install_petsc
+install_slepc
+popd
+
+# this seems to be only necessary on the CI
+echo "Installing and symlinking numpy"
+python -m pip install --upgrade pip
+pip install numpy
+
+NUMPY_INCLUDE="$(python -c 'import numpy; print(numpy.get_include())')"
+ln -sfv "$NUMPY_INCLUDE/numpy" "$PETSC_DIR/$PETSC_ARCH/include"

requirements.txt

@@ -1,5 +1,5 @@
 docrep>=0.3.1
 # https://numpy.org/neps/nep-0029-deprecation_policy.html#drop-schedule
-numpy>=1.15.0
+numpy>=1.17.0
 # https://github.com/scipy/scipy/releases/tag/v1.5.0
 scipy>=1.5.0

tox.ini

@@ -109,11 +109,11 @@ deps =
     pytest-cov
     pytest-mock
     # we manually install PETSc and SLEPc on the CI from source and the [dev] installation causes problems
-    macos-slepc: mpi4py>=3.0.3,<3.1
-    macos-slepc: petsc4py>=3.13,<3.14
-    macos-slepc: slepc4py>=3.13,<3.14
-extras =
-    linux-slepc: slepc
+    slepc: mpi4py>=3.0.3
+    slepc: petsc==3.15.4
+    slepc: petsc4py==3.15.1
+    slepc: slepc==3.15.2
+    slepc: slepc4py==3.15.1
 passenv = TOXENV CI CODECOV_* GITHUB_ACTIONS PETSC_* SLEPC_*
 usedevelop = true
 commands = python -m pytest --cov --cov-append --cov-report=term-missing --cov-config={toxinidir}/tox.ini --ignore docs/ {posargs:-vv}