Migrate docs and compilers CI

Hofer-Julian · Apr 3, 2024 · 782e2a6 · 782e2a6
1 parent a12d404
commit 782e2a6
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diff --git a/.build_rtd_docs/update_doxyfile_version.py b/.build_rtd_docs/update_doxyfile_version.py
@@ -0,0 +1,14 @@
+import sys
+import os
+sys.path.insert(0, os.path.abspath(os.path.join("..", "doc")))
+from version import __version__
+print("Update the Doxyfile with the latest version number")
+with open("Doxyfile", "r") as fp:
+    lines = fp.readlines()
+
+tag = "PROJECT_NUMBER"
+with open("Doxyfile", "w") as fp:
+    for line in lines:
+        if tag in line:
+            line = '{}         = "version {}"\n'.format(tag, __version__)
+        fp.write(line)
diff --git a/.github/workflows/compilers.yml.disabled → .github/workflows/compilers.yml b/.github/workflows/compilers.yml.disabled → .github/workflows/compilers.yml
@@ -132,7 +132,7 @@ jobs:
           - {os: windows-2022, compiler: intel-classic, version: 2021.6}
     defaults:
       run:
-        shell: bash -l {0}
+        shell: bash
     steps:
       - name: Checkout modflow6
         uses: actions/checkout@v4
@@ -157,21 +157,20 @@ jobs:
           compiler: ${{ matrix.compiler}}
           version: ${{ matrix.version }}
 
-      - name: Setup Micromamba
-        uses: mamba-org/setup-micromamba@v1
+      - uses: prefix-dev/setup-pixi@v0.5.1
         with:
-          environment-file: modflow6/environment.yml
-          init-shell: >-
-              bash
-              powershell
-          cache-environment: true
-          cache-downloads: true
+          pixi-version: "latest"
+          manifest-path: "modflow6/pixi.toml"
+
+      - name: Setup pixi
+        working-directory: modflow6
+        run: pixi run install
 
       - name: Build modflow6
         working-directory: modflow6
         run: |
-          meson setup builddir -Ddebug=false --prefix=$(pwd) --libdir=bin
-          meson install -C builddir
+          pixi run setup-release builddir
+          pixi run install-build builddir
 
       - name: Show build log
         if: failure()
@@ -188,7 +187,7 @@ jobs:
       - name: Unit test programs
         if: success()
         working-directory: modflow6
-        run: meson test --verbose --no-rebuild -C builddir
+        run: pixi run test-build builddir
 
       - name: Create compile report
         if: success() || failure()
@@ -207,21 +206,21 @@ jobs:
       - name: Update flopy
         if: success()
         working-directory: modflow6/autotest
-        run: python update_flopy.py
+        run: pixi run update-flopy
 
       - name: Get executables
         if: success()
         working-directory: modflow6/autotest
         env:
           GITHUB_TOKEN: ${{ github.token }}
-        run: pytest -v --durations 0 get_exes.py
+        run: pixi run get-exes
 
       - name: Test modflow6
         if: success()
-        working-directory: modflow6/autotest
+        working-directory: modflow6
         env:
           REPOS_PATH: ${{ github.workspace }}
-        run: pytest -v -n auto --durations 0
+        run: pixi run autotest
 
       - name: Create test report
         if: success() || failure()
@@ -354,4 +353,4 @@ jobs:
 
           # open PR
           cat <(echo '### Compile') <(echo) .github/compat/comp.md <(echo) <(echo '### Test') <(echo) .github/compat/test.md > compat.md
-          gh pr create -B "${{ github.event.repository.default_branch }}" -H "$head" --title "Update compile/test compatibility tables" --body-file compat.md
+          gh pr create -B "${{ github.event.repository.default_branch }}" -H "$head" --title "Update compile/test compatibility tables" --body-file compat.md
diff --git a/.github/workflows/docs.yml.disabled → .github/workflows/docs.yml b/.github/workflows/docs.yml.disabled → .github/workflows/docs.yml
@@ -40,19 +40,20 @@ jobs:
           repository: MODFLOW-USGS/usgslatex
           path: usgslatex
 
-      - name: Install Conda environment from environment.yml
-        uses: mamba-org/setup-micromamba@v1
+      - uses: prefix-dev/setup-pixi@v0.5.1
         with:
-          environment-file: modflow6/environment.yml
-          cache-environment: true
-          cache-downloads: true
-
+          pixi-version: "latest"
+          manifest-path: "modflow6/pixi.toml"
+
+      - name: Setup pixi
+        working-directory: modflow6
+        run: pixi run install
       - name: Install additional packages for Sphinx using pip
         working-directory: modflow6/.build_rtd_docs
-        run: pip install -r requirements.rtd.txt
+        run: pixi run pip install -r requirements.rtd.txt
 
       - name: Print python package versions
-        run: pip list
+        run: pixi run pip list
 
       - name: Install TeX Live
         run: |
@@ -65,7 +66,7 @@ jobs:
 
       - name: Test building files from dfn's for LaTeX
         working-directory: modflow6/autotest
-        run: pytest -v build_mfio_tex.py
+        run: pixi run pytest -v build_mfio_tex.py
 
       - name: Setup ${{ env.FC }} ${{ env.FC_V }}
         uses: fortran-lang/setup-fortran@v1
@@ -84,19 +85,19 @@ jobs:
         if: steps.cache-examples.outputs.cache-hit != 'true'
         working-directory: modflow6-examples/etc
         run: |
-          pip install -r requirements.pip.txt
-          pip install -r requirements.usgs.txt
+          pixi run pip install -r requirements.pip.txt
+          pixi run pip install -r requirements.usgs.txt
 
       - name: Update FloPy
         if: steps.cache-examples.outputs.cache-hit != 'true'
         working-directory: modflow6/autotest
-        run: python update_flopy.py
+        run: pixi run update-flopy
 
       - name: Build example models
         if: steps.cache-examples.outputs.cache-hit != 'true'
         working-directory: modflow6-examples/autotest
         run: |
-          pytest -v -n auto test_scripts.py --init
+          pixi run pytest -v -n auto test_scripts.py --init
           ls -lh ../examples/
 
       - name: Run benchmarks
@@ -117,7 +118,7 @@ jobs:
 
       - name: Collect deprecations
         working-directory: modflow6/doc/mf6io/mf6ivar
-        run: python deprecations.py
+        run: pixi run deprecations
 
       - name: Show deprecations
         working-directory: modflow6/doc/mf6io/mf6ivar/md
@@ -165,7 +166,6 @@ jobs:
     runs-on: ubuntu-22.04
     env:
       working-directory: .build_rtd_docs
-      distribution-directory: distribution
       common-directory: .github/common
       branch-name: ${GITHUB_REF##*/}
     defaults:
@@ -183,38 +183,23 @@ jobs:
           sudo apt-get update
           sudo apt-get install doxygen graphviz
 
-      - name: Install Conda environment from environment.yml
-        uses: mamba-org/setup-micromamba@v1
+      - uses: prefix-dev/setup-pixi@v0.5.1
         with:
-            environment-file: environment.yml
-            cache-environment: true
-            cache-downloads: true
+          pixi-version: "latest"
+          manifest-path: "modflow6/pixi.toml"
+
+      - name: Setup pixi
+        working-directory: modflow6
+        run: pixi run install
 
       - name: Print python package versions
-        run: pip list
+        run: pixi run pip list
 
       - name: update MODFLOW 6 version
-        run: python update_version.py
-        working-directory: ${{env.distribution-directory}}
+        run: pixi run update-version
 
       - name: update MODFLOW 6 version in Doxyfile
-        run: |
-          import sys
-          import os
-          sys.path.insert(0, os.path.abspath(os.path.join("..", "doc")))
-          from version import __version__
-          print("Update the Doxyfile with the latest version number")
-          with open("Doxyfile", "r") as fp:
-              lines = fp.readlines()
-
-          tag = "PROJECT_NUMBER"
-          with open("Doxyfile", "w") as fp:
-              for line in lines:
-                  if tag in line:
-                      line = '{}         = "version {}"\n'.format(tag, __version__)
-                  fp.write(line)
-        shell: python
-        working-directory: ${{env.working-directory}}
+        run: pixi run update-doxyfile-version
 
       - name: run doxygen
         run: doxygen

diff --git a/DEVELOPER.md b/DEVELOPER.md
@@ -300,7 +300,7 @@ The binaries can then be found in the `bin` folder. `meson install` also trigger
 
 MODFLOW 6 unit tests are written in Fortran with [`test-drive`](https://github.com/fortran-lang/test-drive).
 
-MODFLOW 6 integration tests are written in Python with [`pytest`](https://docs.pytest.org/en/7.1.x/). Integration testing dependencies are included in the Conda environment `environment.yml`.
+MODFLOW 6 integration tests are written in Python with [`pytest`](https://docs.pytest.org/en/7.1.x/). Integration testing dependencies are included in the Pixi environment `pixi.toml`.
 
 **Note:** the entire test suite should pass before a pull request is submitted. Tests run in GitHub Actions CI and a PR can only be merged with passing tests. See [`CONTRIBUTING.md`](CONTRIBUTING.md) for more information.
 

diff --git a/distribution/README.md b/distribution/README.md
@@ -58,7 +58,7 @@ Both nightly builds and official distributions are created automatically with Gi
 
 ## Requirements
 
-This document assumes a MODFLOW 6 development environment has been configured as per the [developer documentation](../DEVELOPER.md), including a Fortran compiler (either `ifort` or `gfortran`) as well as a Conda environment as specified in `environment.yml`. Official distributions are currently prepared with Intel Fortran (`ifort`).
+This document assumes a MODFLOW 6 development environment has been configured as per the [developer documentation](../DEVELOPER.md), including a Fortran compiler (either `ifort` or `gfortran`) as well as a Pixi environment as specified in `pixi.toml`. Official distributions are currently prepared with Intel Fortran (`ifort`).
 
 ## Steps
 
@@ -242,4 +242,4 @@ To dispatch the release workflow, navigate to the Actions tab of this repository
 - `branch`: the branch to release from
 - `development`: whether to build a minimal development distribution or a full distribution
 - `run_tests`: whether to run autotests after building binaries
-- `version`: the version number of the release
+- `version`: the version number of the release
diff --git a/pixi.toml b/pixi.toml
@@ -21,8 +21,10 @@ fortran-format-check = "python .github/common/fortran_format_check.py"
 msvs-vfproj-check = "python .github/common/msvs_vfproj_check.py"
 update-flopy = { cmd = "python update_flopy.py", cwd = "autotest" }
 update-version = { cmd = "python update_version.py", cwd = "distribution" }
+update-doxyfile-version = { cmd = "python update_doxyfile_version", cwd = ".build_rtd_docs"}
 get-exes = { cmd = "pytest -v --durations 0 get_exes.py", cwd = "autotest" }
 build-makefiles = "python build_makefiles.py"
+deprecations = "python deprecations.py"
 
 # CI
 setup-strict = "meson setup -Ddebug=false -Dwerror=true"