ci: move from mamba to pixi (#1696)

* add pixi.toml environment file, equivalent to conda environment.yml
* pixi.toml also defines tasks: aliases for development commands
* checkin pixi lock file, add ci workflow to update it monthly
* use pixi tasks in ci actions, scripts, workflows
* update developer docs with pixi info

.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)

.gitattributes

@@ -18,3 +18,6 @@
 *.inc linguist-language=Fortran
 .build_rtd_docs/** linguist-documentation
 .doc/** linguist-documentation
+# GitHub syntax highlighting
+pixi.lock linguist-language=YAML
+

.github/actions/test-par-win/action.yml

@@ -8,21 +8,21 @@ runs:
       uses: ./modflow6/.github/actions/build-par-win
 
     - name: Update flopy
-      working-directory: modflow6/autotest
+      working-directory: modflow6
       shell: cmd
-      run: micromamba run -r "C:\Users\runneradmin\micromamba" -n modflow6 python update_flopy.py
+      run: pixi run update-flopy
 
     - name: Get executables
       working-directory: modflow6/autotest
       shell: cmd
       env:
         GITHUB_TOKEN: ${{ github.token }}
-      run: micromamba run -r "C:\Users\runneradmin\micromamba" -n modflow6 pytest -v --durations 0 get_exes.py
+      run: pixi run get-exes
 
     - name: Test programs
       shell: cmd 
       env:
         REPOS_PATH: ${{ github.workspace }}
       run: |
         unix2dos -n "%GITHUB_WORKSPACE%\modflow6\.github\common\test_modflow6.bat" "%TEMP%\test_modflow6.bat"
-        "%ONEAPI_ROOT%\setvars.bat" intel64 vs2022 && "%TEMP%\test_modflow6.bat"
+        "%ONEAPI_ROOT%\setvars.bat" intel64 vs2022 && "%TEMP%\test_modflow6.bat"

.github/actions/test-par/action.yml

@@ -48,12 +48,12 @@ runs:
         sudo make all
 
     - name: Build modflow6
-      shell: bash -l {0}
+      shell: bash
       working-directory: modflow6
       run: |
-        meson setup builddir -Ddebug=false -Dparallel=true --prefix=$(pwd) --libdir=bin
-        meson install -C builddir
-        meson test --verbose --no-rebuild -C builddir
+        pixi run setup-release-parallel builddir
+        pixi run install-build builddir
+        pixi run test-build builddir
 
     - name: Show Meson logs
       if: failure()
@@ -62,20 +62,20 @@ runs:
       run: cat builddir/meson-logs/meson-log.txt
 
     - name: Update flopy
-      shell: bash -l {0}
-      working-directory: modflow6/autotest
-      run: python update_flopy.py
+      shell: bash
+      working-directory: modflow6
+      run: pixi run update-flopy
 
     - name: Get executables
-      shell: bash -l {0}
-      working-directory: modflow6/autotest
+      shell: bash
+      working-directory: modflow6
       env:
         GITHUB_TOKEN: ${{ github.token }}
-      run: pytest -v --durations 0 get_exes.py
+      run: pixi run get-exes
 
     - name: Test programs
-      shell: bash -l {0}
-      working-directory: modflow6/autotest
+      shell: bash
+      working-directory: modflow6
       env:
         REPOS_PATH: ${{ github.workspace }}
-      run: pytest -v -n auto --parallel --durations 0 -k "test_par" --keep-failed .failed
+      run: pixi run autotest-parallel

.github/common/compile_modflow6.bat

@@ -1,5 +1,5 @@
 set FC=ifort
 cd "%GITHUB_WORKSPACE%\modflow6"
-micromamba run -r "C:\Users\runneradmin\micromamba" -n modflow6 meson setup builddir -Ddebug=false -Dparallel=true --prefix=%CD% --libdir=bin
-micromamba run -r "C:\Users\runneradmin\micromamba" -n modflow6 meson install -C builddir
-micromamba run -r "C:\Users\runneradmin\micromamba" -n modflow6 meson test --verbose --no-rebuild -C builddir
+pixi run setup-release-parallel builddir
+pixi run install-build builddir
+pixi run test-build builddir

.github/common/test_modflow6.bat

@@ -1,4 +1,4 @@
 cd "%GITHUB_WORKSPACE%\modflow6\autotest"
 where libpetsc.dll
 ldd ..\bin\mf6
-micromamba run -r "C:\Users\runneradmin\micromamba" -n modflow6 pytest -v -n auto --parallel -k "test_par" --durations 0 --keep-failed .failed
+pixi run autotest-parallel