ci: refactor pixi config and usages (MODFLOW-USGS#1703)

* add version to pixi.toml * include doc/Doxyfile and pixi.toml in update_version.py * consolidate tasks * refactor custom install as pypi dependencies * remove branch filters from push trigger in commit.yml * update dev docs: keep conda language, tidying * ignore pixi beta feature warning in ci * restore vscode config to avoid breaking contributor workflow — when vscode python * supports pixi I think we can update the tasks to use "command": "${command:python.interpreterPath}"
wpbonelli · Apr 4, 2024 · f31f84f · f31f84f
1 parent 7bca1de
commit f31f84f
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Showing 20 changed files with 565 additions and 251 deletions.
diff --git a/.build_rtd_docs/update_doxyfile_version.py b/.build_rtd_docs/update_doxyfile_version.py
diff --git a/.github/actions/test-par/action.yml b/.github/actions/test-par/action.yml
@@ -51,9 +51,9 @@ runs:
       shell: bash
       working-directory: modflow6
       run: |
-        pixi run setup-release-parallel builddir
-        pixi run install-build builddir
-        pixi run test-build builddir
+        pixi run setup -Dparallel=true builddir
+        pixi run build builddir
+        pixi run test builddir
 
     - name: Show Meson logs
       if: failure()
@@ -78,4 +78,4 @@ runs:
       working-directory: modflow6
       env:
         REPOS_PATH: ${{ github.workspace }}
-      run: pixi run autotest-parallel
+      run: pixi run autotest --parallel -k "test_par"
diff --git a/.github/common/compile_modflow6.bat b/.github/common/compile_modflow6.bat
@@ -1,5 +1,5 @@
 set FC=ifort
 cd "%GITHUB_WORKSPACE%\modflow6"
-pixi run setup-release-parallel builddir
-pixi run install-build builddir
-pixi run test-build builddir
+pixi run setup -Dparallel=true builddir
+pixi run build builddir
+pixi run test builddir
diff --git a/.github/common/test_modflow6.bat b/.github/common/test_modflow6.bat
@@ -1,4 +1,4 @@
 cd "%GITHUB_WORKSPACE%\modflow6\autotest"
 where libpetsc.dll
 ldd ..\bin\mf6
-pixi run autotest-parallel
+pixi run autotest --parallel -k "test_par"
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -1,8 +1,6 @@
 name: MODFLOW 6 continuous integration
 on:
   push:
-    branches: [master, develop, update/pixi-lock]
-    tags: ["*"]
     paths-ignore:
       - '**.md'
       - '**.pdf'
@@ -40,6 +38,8 @@ on:
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
+env:
+  PIXI_BETA_WARNING_OFF: true
 jobs:
   lint:
     name: Check format
@@ -84,17 +84,17 @@ jobs:
           pixi-version: "latest"
 
       - name: Meson setup
-        run: pixi run setup-strict builddir
+        run: pixi run setup -Dwerror=true builddir
 
       - name: Meson compile
-        run: pixi run compile-build builddir
+        run: pixi run build builddir
 
       - name: Show build log
         if: failure()
         run: cat builddir/meson-logs/meson-log.txt
 
       - name: Meson test
-        run: pixi run test-build builddir
+        run: pixi run test builddir
 
   smoke_test:
     name: Smoke test
@@ -123,14 +123,11 @@ jobs:
           compiler: gcc
           version: ${{ env.FC_V }}
 
-      - uses: prefix-dev/[email protected]
+      - name: Setup pixi
+        uses: prefix-dev/[email protected]
         with:
           pixi-version: "latest"
           manifest-path: "modflow6/pixi.toml"
-
-      - name: Setup pixi
-        working-directory: modflow6
-        run: pixi run install
 
       - name: Build test-drive
         working-directory: test-drive
@@ -142,8 +139,8 @@ jobs:
       - name: Build modflow6
         working-directory: modflow6
         run: |
-          pixi run setup-release builddir
-          pixi run install-build builddir
+          pixi run setup builddir
+          pixi run build builddir
 
       - name: Show build log
         if: failure()
@@ -152,7 +149,7 @@ jobs:
 
       - name: Unit test programs
         working-directory: modflow6
-        run: pixi run test-build builddir
+        run: pixi run test builddir
 
       - name: Update flopy
         working-directory: modflow6
@@ -168,7 +165,7 @@ jobs:
         working-directory: modflow6
         run: |
           if [ "${{ github.ref_name }}" == "master" ]; then
-            pixi run autotest-marker "not slow and not regression and not developmode"
+            pixi run autotest -m "not slow and not regression and not developmode"
           else
             pixi run autotest
           fi
@@ -221,20 +218,17 @@ jobs:
           compiler: gcc
           version: ${{ env.FC_V }}
 
-      - uses: prefix-dev/[email protected]
+      - name: Setup pixi
+        uses: prefix-dev/[email protected]
         with:
           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: |
-          pixi run setup-release builddir
-          pixi run install-build builddir
+          pixi run setup builddir
+          pixi run build builddir
 
       - name: Show build log
         if: failure()
@@ -243,7 +237,7 @@ jobs:
 
       - name: Unit test programs
         working-directory: modflow6
-        run: pixi run test-build builddir
+        run: pixi run test builddir
 
       - name: Update flopy
         working-directory: modflow6
@@ -261,9 +255,9 @@ jobs:
           REPOS_PATH: ${{ github.workspace }}
         run: |
           if [ "${{ github.ref_name }}" == "master" ]; then
-            pixi run autotest-marker "not large and not developmode"
+            pixi run autotest -m "not large and not developmode"
           else
-            pixi run autotest-marker "not large"
+            pixi run autotest -m "not large"
           fi
       
       - name: Upload failed test output
@@ -299,7 +293,7 @@ jobs:
         working-directory: modflow6
         env:
           GITHUB_TOKEN: ${{ github.token }}
-        run: pixi run test-distribution
+        run: pixi run test-dist-scripts
 
   test_intel_fortran:
     name: Test intel fortran
@@ -337,14 +331,11 @@ jobs:
           repository: MODFLOW-USGS/modflow6-examples
           path: modflow6-examples
 
-      - uses: prefix-dev/[email protected]
+      - name: Setup pixi
+        uses: prefix-dev/[email protected]
         with:
           pixi-version: "latest"
           manifest-path: "modflow6/pixi.toml"
-
-      - name: Setup pixi
-        working-directory: modflow6
-        run: pixi run install
 
       - name: Setup ${{ env.FC }} ${{ env.FC_V }}
         uses: fortran-lang/setup-fortran@v1
@@ -359,8 +350,8 @@ jobs:
       - name: Build modflow6
         working-directory: modflow6
         run: |
-          pixi run setup-release builddir
-          pixi run install-build builddir
+          pixi run setup builddir
+          pixi run build builddir
 
       - name: Show build log
         if: failure()
@@ -369,7 +360,7 @@ jobs:
 
       - name: Unit test programs
         working-directory: modflow6
-        run: pixi run test-build builddir
+        run: pixi run test builddir
 
       - name: Update flopy
         working-directory: modflow6
@@ -387,9 +378,9 @@ jobs:
           REPOS_PATH: ${{ github.workspace }}
         run: |
           if [ "${{ github.ref_name }}" == "master" ]; then
-            pixi run autotest-marker "not large and not developmode"
+            pixi run autotest -m "not large and not developmode"
           else
-            pixi run autotest-marker "not large"
+            pixi run autotest -m "not large"
           fi
       
       - name: Upload failed test output
@@ -403,7 +394,7 @@ jobs:
         working-directory: modflow6
         env:
           GITHUB_TOKEN: ${{ github.token }}
-        run: pixi run test-distribution
+        run: pixi run test-dist-scripts
 
   parallel_test:
     name: Parallel testing
@@ -427,14 +418,11 @@ jobs:
         with:
           path: modflow6
 
-      - uses: prefix-dev/[email protected]
+      - name: Setup pixi
+        uses: prefix-dev/[email protected]
         with:
           pixi-version: "latest"
           manifest-path: "modflow6/pixi.toml"
-
-      - name: Setup pixi
-        working-directory: modflow6
-        run: pixi run install
 
       - name: Test parallel MF6
         if: runner.os != 'Windows'

diff --git a/.github/workflows/compilers.yml b/.github/workflows/compilers.yml
@@ -3,6 +3,8 @@ on:
   # workflow_dispatch trigger to start release via GitHub UI or CLI, see
   # https://docs.github.com/en/actions/managing-workflow-runs/manually-running-a-workflow
   workflow_dispatch:
+env:
+  PIXI_BETA_WARNING_OFF: true
 jobs:
   test:
     name: Test
@@ -157,20 +159,17 @@ jobs:
           compiler: ${{ matrix.compiler}}
           version: ${{ matrix.version }}
 
-      - uses: prefix-dev/[email protected]
+      - name: Setup pixi
+        uses: prefix-dev/[email protected]
         with:
           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: |
-          pixi run setup-release builddir
-          pixi run install-build builddir
+          pixi run setup builddir
+          pixi run build builddir
 
       - name: Show build log
         if: failure()
@@ -187,7 +186,7 @@ jobs:
       - name: Unit test programs
         if: success()
         working-directory: modflow6
-        run: pixi run test-build builddir
+        run: pixi run test builddir
 
       - name: Create compile report
         if: success() || failure()

diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
@@ -12,6 +12,8 @@ on:
     paths-ignore:
       - '.github/workflows/release.yml'
       - '.hpc/**'
+env:
+  PIXI_BETA_WARNING_OFF: true
 jobs:
   rtd_build:
     name: Build ReadTheDocs
@@ -40,14 +42,11 @@ jobs:
           repository: MODFLOW-USGS/usgslatex
           path: usgslatex
 
-      - uses: prefix-dev/[email protected]
+      - name: Setup pixi
+        uses: prefix-dev/[email protected]
         with:
           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
@@ -185,22 +184,17 @@ jobs:
           sudo apt-get update
           sudo apt-get install doxygen graphviz
 
-      - uses: prefix-dev/[email protected]
+      - name: Setup pixi
+        uses: prefix-dev/[email protected]
         with:
           pixi-version: "latest"
-
-      - name: Setup pixi
-        run: pixi run install
 
       - name: Print python package versions
         run: pixi run pip list
 
       - name: update MODFLOW 6 version
         run: pixi run update-version
 
-      - name: update MODFLOW 6 version in Doxyfile
-        run: pixi run update-doxyfile-version
-
       - name: run doxygen
         run: doxygen
         working-directory: ${{env.working-directory}}