Bump numpy from 1.26.4 to 2.2.0 (#677)

* Bump numpy from 1.26.4 to 2.2.0

Bumps [numpy](https://github.com/numpy/numpy) from 1.26.4 to 2.2.0.
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst)
- [Commits](numpy/numpy@v1.26.4...v2.2.0)

---
updated-dependencies:
- dependency-name: numpy
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>

* use older numpy for older python

* better reqs parsing

* install petsc from pypi

* wip

* wip

* wip

* wip

* wip

* cleanup

---------

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Dion Häfner <dion.haefner@simulation.science>

.github/workflows/test-all.yml

@@ -23,9 +23,7 @@ jobs:
 
     env:
       PYOM2_DIR: /home/runner/pyom2
-      PETSC_VERSION: "3.20.0"
-      PETSC_DIR: /home/runner/petsc
-      PETSC_ARCH: arch-linux-c-opt
+      PETSC_VERSION: "3.22.1"
       OMPI_MCA_rmaps_base_oversubscribe: "1"
       OMPI_MCA_mpi_yield_when_idle: "1"
       VEROS_REQUIRE_CYTHON_EXT: "1"
@@ -57,13 +55,6 @@ jobs:
           path: ${{ env.PYOM2_DIR }}/py_src/*.so
           key: ${{ matrix.os }}-${{ matrix.python-version }}-${{ hashFiles('vendor/pyom2/**/*') }}-${{ hashFiles('requirements.txt') }}
 
-      - name: Restore PETSc build cache
-        uses: actions/cache@v2
-        id: petsc-cache
-        with:
-          path: ${{ env.PETSC_DIR }}
-          key: ${{ matrix.os }}-${{ env.PETSC_VERSION }}
-
       - name: Setup Python environment
         run: |
           python -m pip install --upgrade pip
@@ -75,26 +66,22 @@ jobs:
           sudo apt-get update
           sudo apt-get install libopenmpi-dev liblapack-dev libblas-dev
 
-      - name: Build PETSc
-        if: steps.petsc-cache.outputs.cache-hit != 'true'
-        run: |
-          git clone -b v$PETSC_VERSION --depth 1 https://gitlab.com/petsc/petsc.git $PETSC_DIR
-          pushd $PETSC_DIR
-          ./configure --with-debugging=0 -with-shared-libraries --with-precision=double
-          make all
-          popd
-
       - name: Install Veros
         run: |
-          pip install mpi4py
           if [ ${{ matrix.backend }} == "jax" ]
           then
-            pip install mpi4jax
             pip install -e .[test,jax]
           else
             pip install -e .[test]
           fi
-          pip install petsc4py==$PETSC_VERSION --no-deps --no-build-isolation
+
+      - name: Install optional requirements
+        run: |
+          # PETSc has issues with mpi4py v4
+          pip install "mpi4py<4"
+          pip install mpi4jax --no-build-isolation
+          pip install petsc==$PETSC_VERSION --no-build-isolation
+          pip install petsc4py==$PETSC_VERSION --no-build-isolation
 
       # Build PyOM2 after Veros to make sure we have compatible versions of NumPy / f2py
       - name: Build PyOM2

requirements.txt

@@ -1,7 +1,8 @@
 click==8.1.7
 entrypoints==0.4
 requests==2.32.3
-numpy==1.26.4
+numpy==2.2.0
+numpy==1.26.4; python_version < '3.10'
 scipy==1.14.1
 h5netcdf==1.4.1
 h5py==3.12.1

setup.py

@@ -61,16 +61,21 @@ def parse_requirements(reqfile):
     with open(os.path.join(here, reqfile), encoding="utf-8") as f:
         for line in f:
             line = line.strip()
-            pkg = re.match(r"(\w+)\b.*", line).group(1)
+            parsed = re.match(r"(\w+)(.*?)(;.*)?$", line)
+            pkg, deps, extra = parsed.groups()
+            if extra is None:
+                extra = ""
+            deps = deps.replace("==", "<=")
             if pkg in MINIMUM_VERSIONS:
-                line = "".join([line, ",>=", MINIMUM_VERSIONS[pkg]])
-            line = line.replace("==", "<=")
+                deps = f"{deps},>={MINIMUM_VERSIONS[pkg]}"
+            line = "".join([pkg, deps, extra])
             requirements.append(line)
 
     return requirements
 
 
 INSTALL_REQUIRES = parse_requirements("requirements.txt")
+print(INSTALL_REQUIRES)
 
 
 jax_req = parse_requirements("requirements_jax.txt")