From 7bca1de46f1d83a45998662ef46e6f2a8a5a13e4 Mon Sep 17 00:00:00 2001
From: Hofer-Julian <30049909+Hofer-Julian@users.noreply.github.com>
Date: Wed, 3 Apr 2024 21:58:39 +0200
Subject: [PATCH] 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 |   14 +
 .gitattributes                             |    3 +
 .github/actions/test-par-win/action.yml    |    8 +-
 .github/actions/test-par/action.yml        |   26 +-
 .github/common/compile_modflow6.bat        |    6 +-
 .github/common/test_modflow6.bat           |    2 +-
 .github/workflows/ci.yml                   |  180 +-
 .github/workflows/compilers.yml            |   33 +-
 .github/workflows/docs.yml                 |   79 +-
 .github/workflows/large.yml                |   30 +-
 .github/workflows/pixi_auto_update.yml     |   32 +
 .github/workflows/release.yml              |  109 +-
 .github/workflows/release_dispatch.yml     |   35 +-
 .gitignore                                 |    3 +
 .vscode/README.md                          |    4 +-
 .vscode/build_vscode.py                    |   18 +-
 .vscode/run_python.cmd                     |    3 +-
 .vscode/run_python.sh                      |    5 +-
 CONTRIBUTING.md                            |    2 +-
 DEVELOPER.md                               |   68 +-
 distribution/README.md                     |    4 +-
 pixi.lock                                  | 9495 ++++++++++++++++++++
 pixi.toml                                  |   72 +
 23 files changed, 9915 insertions(+), 316 deletions(-)
 create mode 100644 .build_rtd_docs/update_doxyfile_version.py
 create mode 100644 .github/workflows/pixi_auto_update.yml
 create mode 100644 pixi.lock
 create mode 100644 pixi.toml

diff --git a/.build_rtd_docs/update_doxyfile_version.py b/.build_rtd_docs/update_doxyfile_version.py
new file mode 100644
index 00000000000..8755cc54c9e
--- /dev/null
+++ 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/.gitattributes b/.gitattributes
index 9134554730d..36ea1f56347 100644
--- a/.gitattributes
+++ b/.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
+
diff --git a/.github/actions/test-par-win/action.yml b/.github/actions/test-par-win/action.yml
index 643805d4f45..7710c058b70 100644
--- a/.github/actions/test-par-win/action.yml
+++ b/.github/actions/test-par-win/action.yml
@@ -8,16 +8,16 @@ 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 
@@ -25,4 +25,4 @@ runs:
         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"
\ No newline at end of file
+        "%ONEAPI_ROOT%\setvars.bat" intel64 vs2022 && "%TEMP%\test_modflow6.bat"
diff --git a/.github/actions/test-par/action.yml b/.github/actions/test-par/action.yml
index fb643ca9f81..b68a6da3137 100644
--- a/.github/actions/test-par/action.yml
+++ b/.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
\ No newline at end of file
+      run: pixi run autotest-parallel
diff --git a/.github/common/compile_modflow6.bat b/.github/common/compile_modflow6.bat
index 874a255488b..179bbc01959 100644
--- a/.github/common/compile_modflow6.bat
+++ b/.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
\ No newline at end of file
+pixi run setup-release-parallel builddir
+pixi run install-build builddir
+pixi run test-build builddir
diff --git a/.github/common/test_modflow6.bat b/.github/common/test_modflow6.bat
index 8fe57923c32..68dcf45f727 100644
--- 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
-micromamba run -r "C:\Users\runneradmin\micromamba" -n modflow6 pytest -v -n auto --parallel -k "test_par" --durations 0 --keep-failed .failed
\ No newline at end of file
+pixi run autotest-parallel
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index cf4337f7b43..ae52964dc0d 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -1,6 +1,8 @@
 name: MODFLOW 6 continuous integration
 on:
   push:
+    branches: [master, develop, update/pixi-lock]
+    tags: ["*"]
     paths-ignore:
       - '**.md'
       - '**.pdf'
@@ -35,30 +37,27 @@ on:
       - 'doc/**.sh'
       - 'doc/**.xlsx'
       - '.hpc/**'
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
 jobs:
   lint:
     name: Check format
     runs-on: ubuntu-latest
-    defaults:
-      run:
-        shell: bash -l {0}
     steps:
 
       - name: Checkout modflow6
         uses: actions/checkout@v4
 
-      - name: Setup Micromamba
-        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"
 
       - name: Check Fortran source formatting
-        run: python .github/common/fortran_format_check.py
+        run: pixi run fortran-format-check
 
       - name: Check MSVS project files
-        run: python .github/common/msvs_vfproj_check.py
+        run: pixi run msvs-vfproj-check 
       
       - name: Check CITATION.cff
         uses: dieghernan/cff-validator@v3
@@ -66,9 +65,6 @@ jobs:
   build:
     name: Build
     runs-on: ubuntu-22.04
-    defaults:
-      run:
-        shell: bash -l {0}
     env:
       FC: gfortran
       FC_V: 13
@@ -83,32 +79,29 @@ jobs:
           compiler: gcc
           version: ${{ env.FC_V }}
 
-      - name: Setup Micromamba
-        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"
 
       - name: Meson setup
-        run: meson setup builddir -Ddebug=false -Dwerror=true
+        run: pixi run setup-strict builddir
 
       - name: Meson compile
-        run: meson compile -C builddir
+        run: pixi run compile-build builddir
 
       - name: Show build log
         if: failure()
         run: cat builddir/meson-logs/meson-log.txt
 
       - name: Meson test
-        run: meson test --verbose --no-rebuild -C builddir
+        run: pixi run test-build builddir
 
   smoke_test:
     name: Smoke test
     runs-on: ubuntu-22.04
     defaults:
       run:
-        shell: bash -l {0}
+        shell: bash
     env:
       FC: gfortran
       FC_V: 13
@@ -130,25 +123,27 @@ jobs:
           compiler: gcc
           version: ${{ env.FC_V }}
 
-      - name: Setup Micromamba
-        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: Build test-drive
         working-directory: test-drive
         run: |
-          meson setup builddir --prefix=$(pwd) --libdir=lib
-          meson install -C builddir
+          pixi run --manifest-path=../modflow6/pixi.toml meson setup builddir --prefix=$(pwd) --libdir=lib
+          pixi run --manifest-path=../modflow6/pixi.toml meson install -C builddir
           echo "PKG_CONFIG_PATH=$(pwd)/lib/pkgconfig:$PKG_CONFIG_PATH" >> $GITHUB_ENV
 
       - 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()
@@ -157,25 +152,25 @@ jobs:
     
       - name: Unit test programs
         working-directory: modflow6
-        run: meson test --verbose --no-rebuild -C builddir
+        run: pixi run test-build builddir
 
       - name: Update flopy
-        working-directory: modflow6/autotest
-        run: python update_flopy.py
+        working-directory: modflow6
+        run: pixi run update-flopy
 
       - name: Get executables
-        working-directory: modflow6/autotest
+        working-directory: modflow6
         env:
           GITHUB_TOKEN: ${{ github.token }}
-        run: pytest -v --durations 0 get_exes.py
+        run: pixi run get-exes
 
       - name: Test programs
-        working-directory: modflow6/autotest
+        working-directory: modflow6
         run: |
           if [ "${{ github.ref_name }}" == "master" ]; then
-            pytest -v -n auto --durations 0 -m "not slow and not regression and not developmode" --keep-failed .failed
+            pixi run autotest-marker "not slow and not regression and not developmode"
           else
-            pytest -v -n auto --durations 0 -S --keep-failed .failed
+            pixi run autotest
           fi
 
       - name: Upload failed test output
@@ -198,7 +193,7 @@ jobs:
         os: [ ubuntu-22.04, macos-12, windows-2022 ]
     defaults:
       run:
-        shell: bash -l {0}
+        shell: bash
     env:
       FC: gfortran
       FC_V: 13
@@ -226,23 +221,20 @@ jobs:
           compiler: gcc
           version: ${{ env.FC_V }}
 
-      - name: Setup Micromamba
-        uses: mamba-org/setup-micromamba@v1
+      - uses: prefix-dev/setup-pixi@v0.5.1
         with:
-          environment-file: modflow6/environment.yml
-          create-args: >-
-            python=3.9
-          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()
@@ -251,27 +243,27 @@ jobs:
       
       - name: Unit test programs
         working-directory: modflow6
-        run: meson test --verbose --no-rebuild -C builddir
+        run: pixi run test-build builddir
 
       - name: Update flopy
-        working-directory: modflow6/autotest
-        run: python update_flopy.py
+        working-directory: modflow6
+        run: pixi run update-flopy
 
       - name: Get executables
         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
-        working-directory: modflow6/autotest
+        working-directory: modflow6
         env:
           REPOS_PATH: ${{ github.workspace }}
         run: |
           if [ "${{ github.ref_name }}" == "master" ]; then
-            pytest -v -n auto --durations 0 -m "not large and not developmode" --keep-failed .failed
+            pixi run autotest-marker "not large and not developmode"
           else
-            pytest -v -n auto --durations 0 -m "not large" --keep-failed .failed
+            pixi run autotest-marker "not large"
           fi
       
       - name: Upload failed test output
@@ -304,10 +296,10 @@ jobs:
         run: sudo ./install.sh --all-users
      
       - name: Test distribution scripts
-        working-directory: modflow6/distribution
+        working-directory: modflow6
         env:
           GITHUB_TOKEN: ${{ github.token }}
-        run: pytest -v --durations 0
+        run: pixi run test-distribution
 
   test_intel_fortran:
     name: Test intel fortran
@@ -325,7 +317,7 @@ jobs:
         os: [ubuntu-22.04, macos-12, windows-2022]
     defaults:
       run:
-        shell: bash -l {0}
+        shell: bash
     steps:
 
       - name: Checkout modflow6
@@ -345,15 +337,14 @@ jobs:
           repository: MODFLOW-USGS/modflow6-examples
           path: modflow6-examples
 
-      - 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: Setup ${{ env.FC }} ${{ env.FC_V }}
         uses: fortran-lang/setup-fortran@v1
@@ -362,14 +353,14 @@ jobs:
           version: ${{ env.FC_V }}
 
       - name: Update version files
-        working-directory: modflow6/distribution
-        run: python update_version.py
+        working-directory: modflow6
+        run: pixi run update-version
 
       - 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()
@@ -378,27 +369,27 @@ jobs:
 
       - name: Unit test programs
         working-directory: modflow6
-        run: meson test --verbose --no-rebuild -C builddir
+        run: pixi run test-build builddir
 
       - name: Update flopy
-        working-directory: modflow6/autotest
-        run: python update_flopy.py
+        working-directory: modflow6
+        run: pixi run update-flopy
 
       - name: Get executables
-        working-directory: modflow6/autotest
+        working-directory: modflow6
         env:
           GITHUB_TOKEN: ${{ github.token }}
-        run: pytest -v --durations 0 get_exes.py
+        run: pixi run get-exes
 
       - name: Test programs
-        working-directory: modflow6/autotest
+        working-directory: modflow6
         env:
           REPOS_PATH: ${{ github.workspace }}
         run: |
           if [ "${{ github.ref_name }}" == "master" ]; then
-            pytest -v -n auto --durations 0 -m "not large and not developmode" --keep-failed .failed
+            pixi run autotest-marker "not large and not developmode"
           else
-            pytest -v -n auto --durations 0 -m "not large" --keep-failed .failed
+            pixi run autotest-marker "not large"
           fi
       
       - name: Upload failed test output
@@ -409,10 +400,10 @@ jobs:
           path: modflow6/autotest/.failed
 
       - name: Test scripts
-        working-directory: modflow6/distribution
+        working-directory: modflow6
         env:
           GITHUB_TOKEN: ${{ github.token }}
-        run: pytest -v --durations 0
+        run: pixi run test-distribution
         
   parallel_test:
     name: Parallel testing
@@ -427,7 +418,7 @@ jobs:
         os: [ ubuntu-22.04, macos-12, windows-2022 ]
     defaults:
       run:
-        shell: bash -l {0}
+        shell: bash
     
     steps:
 
@@ -436,17 +427,14 @@ jobs:
         with:
           path: modflow6
 
-      - name: Setup Micromamba
-        uses: mamba-org/setup-micromamba@v1
+      - uses: prefix-dev/setup-pixi@v0.5.1
         with:
-          environment-file: modflow6/environment.yml
-          create-args: >-
-            python=3.9
-          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: Test parallel MF6
         if: runner.os != 'Windows'
@@ -461,4 +449,4 @@ jobs:
         uses: actions/upload-artifact@v4
         with:
           name: failed-${{ matrix.os }}
-          path: modflow6/autotest/.failed
\ No newline at end of file
+          path: modflow6/autotest/.failed
diff --git a/.github/workflows/compilers.yml b/.github/workflows/compilers.yml
index 4f91d47df30..bf73aa7d719 100644
--- a/.github/workflows/compilers.yml
+++ b/.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
\ No newline at end of file
+          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 b/.github/workflows/docs.yml
index 37743f39fc4..d31b26d4e12 100644
--- a/.github/workflows/docs.yml
+++ b/.github/workflows/docs.yml
@@ -40,19 +40,22 @@ 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
+        working-directory: modflow6
+        run: pixi run pip list
 
       - name: Install TeX Live
         run: |
@@ -65,7 +68,7 @@ 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
@@ -82,26 +85,26 @@ jobs:
 
       - name: Install extra Python packages
         if: steps.cache-examples.outputs.cache-hit != 'true'
-        working-directory: modflow6-examples/etc
+        working-directory: modflow6
         run: |
-          pip install -r requirements.pip.txt
-          pip install -r requirements.usgs.txt
+          pixi run pip install -r ../modflow6-examples/etc/requirements.pip.txt
+          pixi run pip install -r ../modflow6-examples/etc/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
-        working-directory: modflow6/distribution
-        run: python benchmark.py
+        working-directory: modflow6
+        run: pixi run benchmark
         env:
           GITHUB_TOKEN: ${{ github.token }}
       
@@ -116,8 +119,8 @@ jobs:
           path: modflow6/distribution/run-time-comparison.md
 
       - name: Collect deprecations
-        working-directory: modflow6/doc/mf6io/mf6ivar
-        run: python deprecations.py
+        working-directory: modflow6
+        run: pixi run deprecations
 
       - name: Show deprecations
         working-directory: modflow6/doc/mf6io/mf6ivar/md
@@ -130,8 +133,8 @@ jobs:
           path: modflow6/doc/mf6io/mf6ivar/md/deprecations.md
 
       - name: Run sphinx
-        working-directory: modflow6/.build_rtd_docs
-        run: make html
+        working-directory: modflow6
+        run: pixi run sphinx
       
       - name: Upload results
         uses: actions/upload-artifact@v3
@@ -165,12 +168,11 @@ jobs:
     runs-on: ubuntu-22.04
     env:
       working-directory: .build_rtd_docs
-      distribution-directory: distribution
       common-directory: .github/common
       branch-name: ${GITHUB_REF##*/}
     defaults:
       run:
-        shell: bash -l {0}
+        shell: bash
 
     steps:
       - uses: actions/checkout@v4
@@ -183,38 +185,21 @@ 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"
+      
+      - name: Setup pixi
+        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/.github/workflows/large.yml b/.github/workflows/large.yml
index 25aad3fd825..a52b35b20c3 100644
--- a/.github/workflows/large.yml
+++ b/.github/workflows/large.yml
@@ -64,12 +64,14 @@ jobs:
           repository: MODFLOW-USGS/modflow6-largetestmodels
           path: modflow6-largetestmodels
 
-      - name: Setup Micromamba
-        uses: mamba-org/setup-micromamba@v1
+      - uses: prefix-dev/setup-pixi@v0.5.1
         with:
-          environment-file: modflow6/environment.yml
-          cache-downloads: true
-          cache-environment: true
+          pixi-version: "latest"
+          manifest-path: "modflow6/pixi.toml"
+      
+      - name: Setup pixi
+        working-directory: modflow6
+        run: pixi run install
 
       - name: Setup ${{ matrix.compiler }} ${{ matrix.version }}
         uses: fortran-lang/setup-fortran@v1
@@ -80,26 +82,26 @@ jobs:
       - name: Build modflow6
         working-directory: modflow6
         run: |
-          meson setup builddir --prefix=$(pwd) --libdir=bin
-          meson install -C builddir
+          pixi run setup-release builddir
+          pixi run install-build builddir
 
       - name: Get executables
-        working-directory: modflow6/autotest
+        working-directory: modflow6
         env:
           GITHUB_TOKEN: ${{ github.token }}
-        run: pytest -v --durations 0 get_exes.py
+        run: pixi run get-exes
 
       - name: Update flopy
-        working-directory: modflow6/autotest
-        run: python update_flopy.py
+        working-directory: modflow6
+        run: pixi run update-flopy
 
       - name: Run tests
-        working-directory: modflow6/autotest
-        run: pytest -v -n auto --durations 0 test_largetestmodels.py --keep-failed .failed
+        working-directory: modflow6
+        run: pixi run autotest-large
       
       - name: Upload failed test output
         if: failure()
         uses: actions/upload-artifact@v4
         with:
           name: failed-${{ runner.os }}-${{ matrix.compiler }}-${{ matrix.version }}
-          path: modflow6/autotest/.failed
\ No newline at end of file
+          path: modflow6/autotest/.failed
diff --git a/.github/workflows/pixi_auto_update.yml b/.github/workflows/pixi_auto_update.yml
new file mode 100644
index 00000000000..0b909659944
--- /dev/null
+++ b/.github/workflows/pixi_auto_update.yml
@@ -0,0 +1,32 @@
+name: Pixi auto update
+
+on:
+  schedule:
+  # At 03:00 on day 3 of the month
+    - cron: "0 3 3 * *"
+  # on demand
+  workflow_dispatch:
+
+jobs:
+  auto-update:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          ssh-key: ${{ secrets.SSH_PRIVATE_KEY }}
+      - uses: prefix-dev/setup-pixi@v0.5.1
+        with:
+          pixi-version: "latest"
+          cache: false
+      - name: Update pixi lock file
+        run: |
+          rm pixi.lock
+          pixi install
+      - uses: peter-evans/create-pull-request@v6
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          branch: update/pixi-lock
+          title: Update pixi lock file
+          commit-message: "Update `pixi.lock`"
+          body: Update pixi dependencies to the latest version.
+          author: "GitHub <noreply@github.com>"
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index 733c8cfa7d8..59b91e24e46 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -96,15 +96,14 @@ jobs:
           path: modflow6
           ref: ${{ inputs.branch }}
 
-      - name: Setup Micromamba
-        uses: mamba-org/setup-micromamba@v1
+      - uses: prefix-dev/setup-pixi@v0.5.1
         with:
-          environment-file: modflow6/environment.yml
-          cache-downloads: true
-          cache-environment: true
-          init-shell: >-
-            bash
-            powershell
+          pixi-version: "latest"
+          manifest-path: "modflow6/pixi.toml"
+      
+      - name: Setup pixi
+        working-directory: modflow6
+        run: pixi run install
 
       - name: Setup ${{ matrix.compiler }} ${{ matrix.version }}
         if: (!(runner.os == 'Windows' && matrix.parallel))
@@ -129,6 +128,7 @@ jobs:
       - name: Update version
         id: update_version
         working-directory: modflow6/distribution
+        shell: pixi run bash -e {0}
         run: |
           ver="${{ steps.set_version.outputs.version }}"
           cmd="python update_version.py -v $ver"
@@ -142,6 +142,7 @@ jobs:
 
       - name: Get OS tag
         id: ostag
+        shell: pixi run bash -e {0}
         run: |
           ostag=$(python -c "from modflow_devtools.ostags import get_ostag; print(get_ostag())")
           if [[ "${{ matrix.parallel }}" == "true" ]]; then
@@ -169,9 +170,9 @@ jobs:
         if: (!(runner.os == 'Windows' && matrix.parallel))
         working-directory: modflow6
         run: |
-          meson setup builddir -Ddebug=false --prefix=$(pwd) --libdir=bin
-          meson install -C builddir
-          meson test --verbose --no-rebuild -C builddir
+          pixi run setup-release builddir
+          pixi run install-build builddir
+          pixi run test-build builddir
 
       - name: Check architecture (macOS)
         working-directory: modflow6/bin
@@ -242,19 +243,19 @@ jobs:
 
       - name: Update flopy
         if: inputs.run_tests == true && runner.os != 'Windows'
-        working-directory: modflow6/autotest
-        run: python update_flopy.py
+        working-directory: modflow6
+        run: pixi run update-flopy
 
       - name: Get executables
         if: inputs.run_tests == true && runner.os != 'Windows'
         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: inputs.run_tests == true && runner.os != 'Windows'
-        working-directory: modflow6/autotest
+        working-directory: modflow6
         env:
           REPOS_PATH: ${{ github.workspace }}
         run: |
@@ -262,7 +263,7 @@ jobs:
           if [[ "${{ inputs.developmode }}" == "false" ]]; then
             markers="$markers and not developmode"
           fi
-          pytest -v -n auto --durations 0 -m "$markers"
+          pixi run autotest-markers "$markers"
       
       - name: Upload failed test output
         if: failure()
@@ -300,7 +301,7 @@ jobs:
         working-directory: modflow6/distribution
         env:
           GITHUB_TOKEN: ${{ github.token }}
-        run: pytest -v --durations 0
+        run: pixi run test-distribution
 
   docs:
     name: Build docs
@@ -343,12 +344,14 @@ jobs:
         working-directory: usgslatex/usgsLaTeX
         run: sudo ./install.sh --all-users
 
-      - name: Setup Micromamba
-        uses: mamba-org/setup-micromamba@v1
+      - uses: prefix-dev/setup-pixi@v0.5.1
         with:
-          environment-file: modflow6/environment.yml
-          cache-downloads: true
-          cache-environment: true
+          pixi-version: "latest"
+          manifest-path: "modflow6/pixi.toml"
+      
+      - name: Setup pixi
+        working-directory: modflow6
+        run: pixi run install
 
       - name: Setup ${{ inputs.compiler_toolchain }} ${{ inputs.compiler_version }}
         uses: fortran-lang/setup-fortran@v1
@@ -359,6 +362,7 @@ jobs:
       - name: Update version
         id: update_version
         working-directory: modflow6/distribution
+        shell: pixi run bash -e {0}
         run: |
           ver="${{ needs.build.outputs.version }}"
           cmd="python update_version.py -v $ver"
@@ -371,8 +375,8 @@ jobs:
           eval "$cmd"
 
       - name: Update FloPy classes
-        working-directory: modflow6/autotest
-        run: python update_flopy.py
+        working-directory: modflow6
+        run: pixi run update-flopy
 
       - name: Get OS tag
         id: ostag
@@ -396,18 +400,23 @@ jobs:
     
       - name: Install dependencies for building models
         if: inputs.full == true
-        working-directory: modflow6-examples/etc
+        shell: pixi run bash -e {0}
+        working-directory: modflow6
         env:
           GITHUB_TOKEN: ${{ github.token }}
         run: |
+          cd ../modflow6-examples/etc
           pip install -r requirements.pip.txt
           echo "${{ github.workspace }}/bin" >> $GITHUB_PATH
           get-modflow "${{ github.workspace }}/bin" --subset mf2005,triangle,gridgen
 
       - name: Build example models
         if: inputs.full == true
-        working-directory: modflow6-examples/autotest
-        run: pytest -v -n auto test_scripts.py --init
+        working-directory: modflow6
+        shell: pixi run bash -e {0}
+        run: |
+          cd ../modflow6-examples/autotest
+          pytest -v -n auto test_scripts.py --init
       
       - name: Create folder structure
         if: inputs.full == true
@@ -426,13 +435,12 @@ jobs:
           cp -r modflow6/utils/zonebudget "$distname/utils/zonebudget"
           
           # create LaTeX file describing the folder structure
-          cd modflow6/doc/ReleaseNotes
-          python mk_folder_struct.py -dp "${{ github.workspace }}/$distname"
+          pixi run mk-folder-struct -dp "${{ github.workspace }}/$distname"
 
       - name: Collect deprecations
         working-directory: modflow6/doc/mf6io/mf6ivar
         run: |
-          python deprecations.py
+          pixi run deprecations
           cat md/deprecations.md
 
       - name: Upload deprecations
@@ -442,12 +450,15 @@ jobs:
           path: modflow6/doc/mf6io/mf6ivar/md/deprecations.md
 
       - name: Build documentation
+        working-directory: modflow6
+        shell: pixi run bash -e {0}
         env:
           # this step is lazy about building the mf6 examples PDF document, first
           # trying to download a prebuilt PDF from MODFLOW-USGS/modflow6-examples,
           # so it needs a GITHUB_TOKEN.
           GITHUB_TOKEN: ${{ github.token }}
         run: |
+          cd ..
           mkdir -p "${{ needs.build.outputs.distname }}/doc"
           cmd="python modflow6/distribution/build_docs.py -b bin -o doc"
           if [[ "${{ inputs.full }}" == "true" ]]; then
@@ -496,15 +507,14 @@ jobs:
           repository: MODFLOW-USGS/modflow6-examples
           path: modflow6-examples
 
-      - name: Setup Micromamba
-        uses: mamba-org/setup-micromamba@v1
+      - uses: prefix-dev/setup-pixi@v0.5.1
         with:
-          environment-file: modflow6/environment.yml
-          cache-downloads: true
-          cache-environment: true
-          init-shell: >-
-            bash
-            powershell
+          pixi-version: "latest"
+          manifest-path: "modflow6/pixi.toml"
+      
+      - name: Setup pixi
+        working-directory: modflow6
+        run: pixi run install
 
       - name: Setup ${{ inputs.compiler_toolchain }} ${{ inputs.compiler_version }}
         uses: fortran-lang/setup-fortran@v1
@@ -514,8 +524,10 @@ jobs:
       
       - name: Update version
         id: update_version
-        working-directory: modflow6/distribution
+        working-directory: modflow6
+        shell: pixi run bash -e {0}
         run: |
+          cd distribution
           ver="${{ needs.build.outputs.version }}"
           cmd="python update_version.py -v $ver"
           if [[ "${{ inputs.approve }}" == "true" ]]; then
@@ -528,7 +540,10 @@ jobs:
  
       - name: Get OS tag
         id: ostag
+        working-directory: modflow6
+        shell: pixi run bash -e {0}
         run: |
+          cd ..
           ostag=$(python -c "from modflow_devtools.ostags import get_ostag; print(get_ostag())")
           if [[ "${{ matrix.parallel }}" == "true" ]]; then
             ostag="${ostag}par"
@@ -559,7 +574,10 @@ jobs:
       - name: Install dependencies for example models
         env:
           GITHUB_TOKEN: ${{ github.token }}
+        working-directory: modflow6
+        shell: pixi run bash -e {0}
         run: |
+          cd ..
           pip install -r modflow6-examples/etc/requirements.pip.txt
           distname="${{ needs.build.outputs.distname }}_${{ steps.ostag.outputs.ostag }}"
           echo "$distname/bin" >> $GITHUB_PATH
@@ -576,14 +594,19 @@ jobs:
 
       - name: Update Flopy
         working-directory: modflow6/autotest
-        run: python update_flopy.py
+        run: pixi run update-flopy
   
       - name: Build example models
         if: inputs.full == true
-        working-directory: modflow6-examples/autotest
-        run: pytest -v -n auto test_scripts.py --init
+        working-directory: modflow6
+        shell: pixi run bash -e {0}
+        run: |
+          cd ../modflow6-examples/autotest
+          pytest -v -n auto test_scripts.py --init
 
       - name: Build distribution
+        working-directory: modflow6
+        shell: pixi run bash -e {0}
         env:
           GITHUB_TOKEN: ${{ github.token }}
         run: |
@@ -704,4 +727,4 @@ jobs:
           if [[ "${{ inputs.full }}" == "true" ]]; then
             cmd="$cmd --full"
           fi
-          eval "$cmd"
\ No newline at end of file
+          eval "$cmd"
diff --git a/.github/workflows/release_dispatch.yml b/.github/workflows/release_dispatch.yml
index 77d159d0f46..e889d1c2486 100644
--- a/.github/workflows/release_dispatch.yml
+++ b/.github/workflows/release_dispatch.yml
@@ -149,7 +149,7 @@ jobs:
       pull-requests: write
     defaults:
       run:
-        shell: bash -l {0}
+        shell: bash
     steps:
       - name: Checkout modflow6
         uses: actions/checkout@v4
@@ -157,12 +157,14 @@ jobs:
           repository: ${{ github.repository_owner }}/modflow6
           ref: ${{ github.ref }}
 
-      - name: Setup Micromamba
-        uses: mamba-org/setup-micromamba@v1
+      - uses: prefix-dev/setup-pixi@v0.5.1
         with:
-          environment-file: environment.yml
-          cache-downloads: true
-          cache-environment: true
+          pixi-version: "latest"
+          manifest-path: "modflow6/pixi.toml"
+      
+      - name: Setup pixi
+        working-directory: modflow6
+        run: pixi run install
 
       - name: Update version
         working-directory: distribution
@@ -172,13 +174,13 @@ jobs:
           # approve will be empty if workflow was triggered by pushing a release branch
           # todo: pull approve into set_options job/output?
           if [[ ("${{ inputs.approve }}" == "true") || ("${{ inputs.approve }}" == "") ]]; then
-            python update_version.py -v "$ver" --approve
+            pixi run update-version -v "$ver" --approve
           else
-            python update_version.py -v "$ver"
+            pixi run update-version -v "$ver"
           fi
           
           # lint version.f90
-          fprettify -c ../.fprettify.yaml ../src/Utilities/version.f90
+          pixi run fprettify -c ../.fprettify.yaml ../src/Utilities/version.f90
           
           # commit and push
           git config core.sharedRepository true
@@ -209,7 +211,7 @@ jobs:
     runs-on: ubuntu-22.04
     defaults:
       run:
-        shell: bash -l {0}
+        shell: bash
     steps:
       - name: Checkout modflow6
         uses: actions/checkout@v4
@@ -217,12 +219,14 @@ jobs:
           repository: ${{ github.repository_owner }}/modflow6
           path: modflow6
 
-      - name: Setup Micromamba
-        uses: mamba-org/setup-micromamba@v1
+      - uses: prefix-dev/setup-pixi@v0.5.1
         with:
-          environment-file: modflow6/environment.yml
-          cache-downloads: true
-          cache-environment: true
+          pixi-version: "latest"
+          manifest-path: "modflow6/pixi.toml"
+      
+      - name: Setup pixi
+        working-directory: modflow6
+        run: pixi run install
 
       - name: Download artifacts
         uses: dawidd6/action-download-artifact@v3
@@ -231,6 +235,7 @@ jobs:
         working-directory: modflow6
         env:
           GITHUB_TOKEN: ${{ github.token }}
+        shell: pixi run bash -e {0}
         run: |
           # create draft release
           version=$(python distribution/update_version.py -g)
diff --git a/.gitignore b/.gitignore
index 67be4780390..a45b2864baa 100644
--- a/.gitignore
+++ b/.gitignore
@@ -134,6 +134,7 @@ modflow6.code-workspace
 
 # unittests
 unittests/
+autotest/.failed
 
 **/__pycache__
 **/.benchmarks
@@ -142,3 +143,5 @@ unittests/
 .github/compat/*.md
 
 **.DS_Store
+# pixi environments
+.pixi
diff --git a/.vscode/README.md b/.vscode/README.md
index 962fe1d07b2..93941be54b3 100644
--- a/.vscode/README.md
+++ b/.vscode/README.md
@@ -41,10 +41,10 @@ In general, to determine the path of an installed tool in your environment run:
 - cmd: `where <toolname>`, e.g. `where python`
 - PowerShell: `Get-Command <toolname>` e.g. `Get-Command fprettify`
 
-1. Activate the conda environment:
+1. Activate the pixi environment:
 
 ```bash
-conda activate modflow6
+pixi shell
 ```
 
 2. Determine the path of `fortls` and `fprettify`
diff --git a/.vscode/build_vscode.py b/.vscode/build_vscode.py
index d222cc7c772..654e70fca42 100644
--- a/.vscode/build_vscode.py
+++ b/.vscode/build_vscode.py
@@ -21,22 +21,8 @@
 if args.action == "rebuild" and os.path.isdir(builddir):
     shutil.rmtree(builddir)
 
-if args.buildtype == "release":
-    setup_flag = ["-Doptimization=2"]
-elif args.buildtype == "debug":
-    setup_flag = ["-Ddebug=true", "-Doptimization=0"]
-
 if not os.path.isdir(builddir):
-    command = [
-        "meson",
-        "setup",
-        builddir,
-        "--prefix",
-        os.getcwd(),
-        "--libdir",
-        "bin",
-        arg_parallel,
-    ] + setup_flag
+    command = ["pixi", "run", f"setup-{args.buildtype}", builddir, arg_parallel]
     print("Run:", shlex.join(command))
     subprocess.run(
         command,
@@ -51,6 +37,6 @@
         if os.path.isfile(path):
             os.remove(path)
 
-command = ["meson", "install", "-C", builddir]
+command = ["pixi", "run", "install-build", builddir]
 print("Run:", shlex.join(command))
 subprocess.run(command, check=True)
diff --git a/.vscode/run_python.cmd b/.vscode/run_python.cmd
index 87c6f3de58b..43318bc5015 100644
--- a/.vscode/run_python.cmd
+++ b/.vscode/run_python.cmd
@@ -4,7 +4,6 @@ if "%3" == "ifort" (
  call "C:\Program Files (x86)\Intel\oneAPI\setvars.bat"
 )
 
-call conda activate modflow6
 
 rem run python script
-python %1 %2 %3 %4 %5 %6
+pixi run python %1 %2 %3 %4 %5 %6
diff --git a/.vscode/run_python.sh b/.vscode/run_python.sh
index cbd3b27fcc9..6977d7a2fe1 100755
--- a/.vscode/run_python.sh
+++ b/.vscode/run_python.sh
@@ -5,8 +5,5 @@ then
     source /opt/intel/oneapi/setvars.sh
 fi
 
-eval "$(conda shell.bash hook)"
-conda activate modflow6
-
 # run python script
-python $1 $2 $3 $4 $5 $6
+pixi run python $1 $2 $3 $4 $5 $6
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index e751d48539d..5845a06f4b6 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -141,7 +141,7 @@ To ensure consistency throughout the source code, keep these rules in mind as yo
 ## <a name="format"></a> Format Rules
 
 Fortran souce code format rules are met by running the
-[fprettify formatter](https://github.com/pseewald/fprettify) while specifying the [MODFLOW 6 fprettify configuration](.fprettify.yaml). `fprettify` is included in the Conda `environment.yml` and can be run on the command line or integrated into a [VSCode](.vscode/README.md) or Visual Studio environment.
+[fprettify formatter](https://github.com/pseewald/fprettify) while specifying the [MODFLOW 6 fprettify configuration](.fprettify.yaml). `fprettify` is included in the pixi environment and can be run on the command line or integrated into a [VSCode](.vscode/README.md) or Visual Studio environment.
 
 The configuration file reflects the current minimum standard for Fortran source
 formatting.  The main goal, however, is consistent and readable Fortran source code and as such pay particular attention to consistency within and across files. As the formatting tool may at times shift code in unexpected ways, check for formatting consistency after running.
diff --git a/DEVELOPER.md b/DEVELOPER.md
index cc6c233b2df..61d5f3ec853 100644
--- a/DEVELOPER.md
+++ b/DEVELOPER.md
@@ -51,7 +51,6 @@ To build and test a parallel version of the program, first read the instructions
   - [Updating extra and excluded files](#updating-extra-and-excluded-files)
   - [Testing makefiles](#testing-makefiles)
   - [Installing `make` on Windows](#installing-make-on-windows)
-    - [Using Conda from Git Bash](#using-conda-from-git-bash)
 - [Branching model](#branching-model)
   - [Overview](#overview)
   - [Managing long-lived branches](#managing-long-lived-branches)
@@ -180,16 +179,12 @@ The following tables are automatically generated by [a CI workflow](.github/work
 
 ### Python
 
-Python 3.8+ is required to run MODFLOW 6 tests. A Conda distribution (e.g. [miniconda](https://docs.conda.io/en/latest/miniconda.html) or [Anaconda](https://www.anaconda.com/products/individual) is recommended. Python dependencies are specified in `environment.yml`. To create an environment, run from the project root:
+Python 3.8+ is required to run MODFLOW 6 tests. Using Python from the pixi environment is recommended.
+The installation docs can be found [here](https://pixi.sh).
+After installing pixi, you can trigger the installation process as follows:
 
 ```
-conda env create -f environment.yml
-```
-
-To update an existing environment:
-
-```shell
-conda env update -f environment.yml
+pixi run install
 ```
 
 #### Dependencies
@@ -201,19 +196,19 @@ This project depends critically on a few Python packages for building, linting a
 - `pymake`
 - `flopy`
 
-These are each described briefly below. The Conda `environment.yml` contains a number of other dependencies also required for various development tasks, but they are not described in detail here.
+These are each described briefly below. The `pixi.toml` contains a number of other dependencies also required for various development tasks, but they are not described in detail here.
 
 ##### `meson`
 
-[Meson](https://mesonbuild.com/index.html) is recommended for building MODFLOW 6 and is included in `environment.yml`. It can also be [installed independently](https://mesonbuild.com/Getting-meson.html) &mdash; note that if you do so you will need to manually add the executable to the [PATH](https://en.wikipedia.org/wiki/PATH_(variable)).
+[Meson](https://mesonbuild.com/index.html) is recommended for building MODFLOW 6 and is included in `pixi.toml`. It can also be [installed independently](https://mesonbuild.com/Getting-meson.html) &mdash; note that if you do so you will need to manually add the executable to the [PATH](https://en.wikipedia.org/wiki/PATH_(variable)).
 
 ##### `fprettify`
 
-[`fprettify`](https://github.com/pseewald/fprettify) can be used to format Fortran source code and in combination with the [MODFLOW 6 fprettify configuration](.fprettify.yaml) establishes a contribution standard for properly formatted MODFLOW 6 Fortran source. This tool can be installed with `pip` or `conda` and used from the command line or integrated with a [VSCode](.vscode/README.md) or Visual Studio development environment. The `fprettify` package is included in the Conda environment in `environment.yml`. See [contribution guidelines](CONTRIBUTING.md) for additional information.
+[`fprettify`](https://github.com/pseewald/fprettify) can be used to format Fortran source code and in combination with the [MODFLOW 6 fprettify configuration](.fprettify.yaml) establishes a contribution standard for properly formatted MODFLOW 6 Fortran source. This tool can be installed with `pip` or `conda` and used from the command line or integrated with a [VSCode](.vscode/README.md) or Visual Studio development environment. The `fprettify` package is included in the Pixi environment in `pixi.toml`. See [contribution guidelines](CONTRIBUTING.md) for additional information.
 
 ##### `mfpymake`
 
-The `mfpymake` package can build MODFLOW 6 and related programs and artifacts (e.g. makefiles), and is used in particular by the `distribution/build_makefiles.py` script. `mfpymake` is included in the Conda environment in `environment.yml`. To install separately, follow the instructions as explained on the README of the [repository](https://github.com/modflowpy/pymake). The README also demonstrates basic usage.
+The `mfpymake` package can build MODFLOW 6 and related programs and artifacts (e.g. makefiles), and is used in particular by the `distribution/build_makefiles.py` script. `mfpymake` is included in `pixi.toml`. To install separately, follow the instructions as explained on the README of the [repository](https://github.com/modflowpy/pymake). The README also demonstrates basic usage.
 
 ##### `flopy`
 
@@ -223,7 +218,7 @@ Like MODFLOW 6, `flopy` is modular &mdash; for each MODFLOW 6 package there is g
 
 ##### `modflow-devtools`
 
-The tests use a set of shared fixtures and utilities provided by the [`modflow-devtools`](https://github/com/MODFLOW-USGS/modflow-devtools) package. This package is included in the Conda environment in `environment.yml`.
+The tests use a set of shared fixtures and utilities provided by the [`modflow-devtools`](https://github/com/MODFLOW-USGS/modflow-devtools) package. This package is included in the Pixi environment in `pixi.toml`.
 
 ### Optional tools
 
@@ -264,7 +259,7 @@ git remote add upstream https://github.com/MODFLOW-USGS/modflow6.git
 
 ## Building
 
-Meson is the recommended build tool for MODFLOW 6. [Meson](https://mesonbuild.com/Getting-meson.html) must be installed and on your [PATH](https://en.wikipedia.org/wiki/PATH_(variable)). Creating and activating the Conda environment `environment.yml` should be sufficient for this.
+Meson is the recommended build tool for MODFLOW 6. [Meson](https://mesonbuild.com/Getting-meson.html) must be installed and on your [PATH](https://en.wikipedia.org/wiki/PATH_(variable)). Creating and activating the Pixi environment `pixi.toml` should be sufficient for this.
 
 Meson build configuration files are provided for MODFLOW 6, for the ZONEBUDGET and MODFLOW 2005 to 6 converter utility programs, and for Fortran unit tests (see [Testing](#testing) section below).
 
@@ -273,28 +268,29 @@ Meson build configuration files are provided for MODFLOW 6, for the ZONEBUDGET a
 - `utils/mf5to6/meson.build`
 - `autotest/meson.build`
 
-To build MODFLOW 6, first configure the build directory. By default Meson uses compiler flags for a release build. To create a debug build, add `-Doptimization=0` to the following `setup` command.
+To build MODFLOW 6, first configure the build directory.
+Depending on which task you use, meson will configure a debug or release build.
 
-Meson `setup` on linux and macOS:
+Setup a debug build:
 ```shell
-meson setup builddir --prefix=$(pwd) --libdir=bin
+pixi run setup-debug builddir
 ```
 
-Meson `setup` on windows:
+Or alternatively, setup a release build
 ```shell
-meson setup builddir --prefix=%CD% --libdir=bin
+pixi run setup-release builddir
 ```
 
 Compile MODFLOW 6 by executing:
 
 ```shell
-meson compile -C builddir
+pixi run compile-build builddir
 ```
 
 In order to run the tests the binaries have to be installed:
 
 ```shell
-meson install -C builddir
+pixi run install-build builddir
 ```
 
 The binaries can then be found in the `bin` folder. `meson install` also triggers a compilation if necessary, so executing `meson install` is enough to get up-to-date binaries in the `bin` folder.
@@ -305,7 +301,7 @@ 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.
 
@@ -359,13 +355,7 @@ As mentioned above, binaries live in the `bin` subdirectory of the project root.
 Tests require the latest official MODFLOW 6 release to be compiled in develop mode with the same Fortran compiler as the development version. A number of binaries distributed from the [executables repo](https://github.com/MODFLOW-USGS/executables) must also be installed. The script `autotest/get_exes.py` does both of these things. It can be run from the project root with:
 
 ```shell
-python autotest/get_exes.py
-```
-
-Alternatively, with `pytest` from the `autotest` directory:
-
-```shell
-pytest get_exes.py
+pixi run get-exes
 ```
 
 As above, binaries are placed in the `bin` subdirectory of the project root, with nested `bin/downloaded` and `bin/rebuilt` subdirectories containing the rebuilt latest release and downloaded binaries, respectively.
@@ -379,8 +369,8 @@ FloPy packages should be regenerated from DFN files before running tests for the
 There is a single optional argument, the path to the folder containing definition files. By default DFN files are assumed to live in `doc/mf6io/mf6ivar/dfn`, making the following functionally identical:
 
 ```shell
-python autotest/update_flopy.py
-python autotest/update_flopy.py doc/mf6io/mf6ivar/dfn
+pixi run update-flopy
+pixi run update-flopy doc/mf6io/mf6ivar/dfn
 ```
 
 ##### Installing external models
@@ -402,15 +392,14 @@ MODFLOW 6 has two kinds of tests: Fortran unit tests, driven with Meson, and Pyt
 Unit tests must be run from the project root. To run unit tests in verbose mode:
 
 ```shell
-meson test -C builddir --no-rebuild --verbose
+pixi run test-build builddir
 ```
 
-Without the `--no-rebuild` options, Meson will rebuild the project before running tests.
 
 Unit tests can be selected by module name (as listed in `autotest/tester.f90`). For instance, to test the `ArrayHandlersModule`:
 
 ```shell
-meson test -C builddir --no-rebuild --verbose ArrayHandlers
+pixi run test-build builddir --verbose ArrayHandlers
 ```
 
 To run a test module in the `gdb` debugger, just add the `--gdb` flag to the test command.
@@ -420,12 +409,14 @@ To run a test module in the `gdb` debugger, just add the `--gdb` flag to the tes
 Integration tests must be run from the `autotest/` folder. To run tests in a particular file, showing verbose output, use:
 
 ```shell
+pixi shell
 pytest -v <file>
 ```
 
 Tests can be run in parallel with the `-n` option, which accepts an integer argument for the number of parallel processes. If the value `auto` is provided, `pytest-xdist` will use one worker per available processor.
 
 ```shell
+pixi shell
 pytest -v -n auto
 ```
 
@@ -441,12 +432,14 @@ Markers can be used to select subsets of tests. Markers provided in `pytest.ini`
 Markers can be used with the `-m <marker>` option, and can be applied in boolean combinations with `and`, `or` and `not`. For instance, to run fast tests in parallel, excluding regression tests:
 
 ```shell
+pixi shell
 pytest -v -n auto -m "not slow and not regression"
 ```
 
 The `--smoke` (short `-S`) flag, provided by `modflow-devtools` is an alias for the above:
 
 ```shell
+pixi shell
 pytest -v -n auto -S
 ```
 
@@ -455,12 +448,14 @@ pytest -v -n auto -S
 Tests using models from external repositories can be selected with the `repo` marker:
 
 ```shell
+pixi shell
 pytest -v -n auto -m "repo"
 ```
 
 The `large` marker is a subset of the `repo` marker. To test models excluded from commit-triggered CI and only run on GitHub Actions nightly:
 
 ```shell
+pixi shell
 pytest -v -n auto -m "large"
 ```
 
@@ -596,7 +591,7 @@ After running the reference and comparison models, the framework will try to fin
 Run `build_makefiles.py` in the `distribution/` directory after adding, removing, or renaming source files. This script uses [Pymake](https://github.com/modflowpy/pymake) to regenerate makefiles. For instance:
 
 ```shell
-python build_makefiles.py
+pixi run build-makefiles
 ```
 
 ### Updating extra and excluded files
@@ -610,6 +605,7 @@ Module dependencies for features still under development should be added to `exc
 Makefile generation and usage can be tested from the `distribution` directory by running the `build_makefiles.py` script with Pytest:
 
 ```shell
+pixi shell
 pytest -v build_makefiles.py
 ```
 
diff --git a/distribution/README.md b/distribution/README.md
index 66d74f805fb..7bafeb8d437 100644
--- 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
\ No newline at end of file
+- `version`: the version number of the release
diff --git a/pixi.lock b/pixi.lock
new file mode 100644
index 00000000000..adf4f04e1ca
--- /dev/null
+++ b/pixi.lock
@@ -0,0 +1,9495 @@
+version: 4
+environments:
+  default:
+    channels:
+    - url: https://conda.anaconda.org/conda-forge/
+    packages:
+      linux-64:
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/alsa-lib-1.2.11-hd590300_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/appdirs-1.4.4-pyh9f0ad1d_0.tar.bz2
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/atk-1.0-2.38.0-hd4edc92_1.tar.bz2
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/attr-2.5.1-h166bdaf_1.tar.bz2
+      - conda: https://conda.anaconda.org/conda-forge/noarch/attrs-23.2.0-pyh71513ae_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/black-24.3.0-py39hf3d152e_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/bmipy-2.0.1-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/brotli-1.1.0-hd590300_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/brotli-bin-1.1.0-hd590300_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/brotli-python-1.1.0-py39h3d6467e_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hd590300_5.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.2.2-hbcca054_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/cairo-1.18.0-h3faef2a_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/certifi-2024.2.2-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/charset-normalizer-3.3.2-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/click-8.1.7-unix_pyh707e725_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/colorama-0.4.6-pyhd8ed1ab_0.tar.bz2
+      - conda: https://conda.anaconda.org/conda-forge/noarch/configargparse-1.7-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/contourpy-1.2.0-py39h7633fee_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/cycler-0.12.1-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/dbus-1.13.6-h5008d03_3.tar.bz2
+      - conda: https://conda.anaconda.org/conda-forge/noarch/editables-0.5-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/exceptiongroup-1.2.0-pyhd8ed1ab_2.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/execnet-2.0.2-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/expat-2.6.2-h59595ed_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/filelock-3.13.3-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/flaky-3.8.1-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/font-ttf-dejavu-sans-mono-2.37-hab24e00_0.tar.bz2
+      - conda: https://conda.anaconda.org/conda-forge/noarch/font-ttf-inconsolata-3.000-h77eed37_0.tar.bz2
+      - conda: https://conda.anaconda.org/conda-forge/noarch/font-ttf-source-code-pro-2.038-h77eed37_0.tar.bz2
+      - conda: https://conda.anaconda.org/conda-forge/noarch/font-ttf-ubuntu-0.83-h77eed37_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/fontconfig-2.14.2-h14ed4e7_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/fonts-conda-ecosystem-1-0.tar.bz2
+      - conda: https://conda.anaconda.org/conda-forge/noarch/fonts-conda-forge-1-0.tar.bz2
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/fonttools-4.50.0-py39hd1e30aa_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/fortran-language-server-1.12.0-pyhd8ed1ab_0.tar.bz2
+      - conda: https://conda.anaconda.org/conda-forge/noarch/fprettify-0.3.7-pyhd8ed1ab_0.tar.bz2
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/freetype-2.12.1-h267a509_2.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/fribidi-1.0.10-h36c2ea0_0.tar.bz2
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/gdk-pixbuf-2.42.10-h829c605_5.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/geos-3.12.1-h59595ed_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/gettext-0.21.1-h27087fc_0.tar.bz2
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/giflib-5.2.1-h0b41bf4_3.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/glib-2.80.0-hf2295e7_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/glib-tools-2.80.0-hde27a5a_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/graphite2-1.3.13-h59595ed_1003.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/graphviz-2.50.0-h5abf519_3.tar.bz2
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/gst-plugins-base-1.22.9-hfa15dee_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/gstreamer-1.22.9-h98fc4e7_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/gtk2-2.24.33-h280cfa0_4.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/gts-0.7.6-h977cf35_4.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/harfbuzz-8.3.0-h3d44ed6_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/hatchling-1.22.4-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/icu-73.2-h59595ed_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/idna-3.6-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/importlib-metadata-7.1.0-pyha770c72_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/importlib-resources-6.4.0-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/importlib_resources-6.4.0-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/iniconfig-2.0.0-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/jinja2-3.1.3-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/jsonschema-4.21.1-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/jsonschema-specifications-2023.12.1-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/jupyter_core-5.7.2-py39hf3d152e_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/jupytext-1.16.1-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/keyutils-1.6.1-h166bdaf_0.tar.bz2
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/kiwisolver-1.4.5-py39h7633fee_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/krb5-1.21.2-h659d440_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/lame-3.100-h166bdaf_1003.tar.bz2
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/lcms2-2.16-hb7c19ff_0.conda
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+  - xorg-libxt >=1.3.0,<2.0a0
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+  - xorg-xproto
+  license: MIT
+  license_family: MIT
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+- kind: conda
+  name: xorg-libxrender
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+  build: hd590300_0
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+  - xorg-renderproto
+  license: MIT
+  license_family: MIT
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+  timestamp: 1688300707994
+- kind: conda
+  name: xorg-libxt
+  version: 1.3.0
+  build: hcd874cb_1
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+  url: https://conda.anaconda.org/conda-forge/win-64/xorg-libxt-1.3.0-hcd874cb_1.conda
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+  - xorg-libsm >=1.2.4,<2.0a0
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+  license: MIT
+  license_family: MIT
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diff --git a/pixi.toml b/pixi.toml
new file mode 100644
index 00000000000..88227d2033d
--- /dev/null
+++ b/pixi.toml
@@ -0,0 +1,72 @@
+[project]
+name = "modflow6"
+channels = ["conda-forge"]
+platforms = ["win-64", "linux-64", "osx-arm64", "osx-64"]
+
+[tasks]
+# Install
+install-flopy = "pip install --no-build-isolation --no-deps --disable-pip-version-check git+https://github.com/modflowpy/flopy.git"
+install-pymake = "pip install --no-build-isolation --no-deps --disable-pip-version-check git+https://github.com/modflowpy/pymake.git"
+install-modflowapi = "pip install --no-build-isolation --no-deps --disable-pip-version-check git+https://github.com/MODFLOW-USGS/modflowapi.git"
+install-modflow-devtools = "pip install --no-build-isolation --no-deps --disable-pip-version-check git+https://github.com/MODFLOW-USGS/modflow-devtools.git"
+install = { depends_on = [
+    "install-flopy",
+    "install-pymake",
+    "install-modflowapi",
+    "install-modflow-devtools",
+] }
+
+# Utils
+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.py", cwd = ".build_rtd_docs" }
+get-exes = { cmd = "pytest -v --durations 0 get_exes.py", cwd = "autotest" }
+build-makefiles = "python build_makefiles.py"
+deprecations = { cmd = "python deprecations.py", cwd = "doc/mf6io/mf6ivar" }
+benchmark = { cmd = "python benchmark.py", cwd = "distribution" }
+mk-folder-struct = { cmd = "python mk_folder_struct.py", cwd = "doc/ReleaseNotes" }
+
+# CI
+setup-strict = "meson setup -Ddebug=false -Dwerror=true"
+setup-debug = "meson setup -Doptimization=0 --prefix=$(pwd) --libdir=bin"
+setup-release = "meson setup -Ddebug=false --prefix=$(pwd) --libdir=bin"
+setup-release-parallel = "meson setup -Ddebug=false -Dparallel=true --prefix=$(pwd) --libdir=bin"
+compile-build = "meson compile -C"
+install-build = "meson install -C"
+test-build = "meson test --verbose --no-rebuild -C"
+test-distribution = { cmd = "pytest -v --durations 0", cwd = "distribution" }
+autotest = { cmd = "pytest -v -n auto --durations 0 --keep-failed .failed", cwd = "autotest" }
+autotest-marker = { cmd = "pytest -v -n auto --durations 0 --keep-failed .failed -m", cwd = "autotest" }
+autotest-parallel = { cmd = "pytest -v -n auto --parallel --durations 0 -k \"test_par\" --keep-failed .failed", cwd = "autotest" }
+autotest-large = { cmd = "pytest -v -n auto --durations 0 test_largetestmodels.py --keep-failed .failed", cwd = "autotest" }
+sphinx = { cmd = "make html", cwd = ".build_rtd_docs" }
+
+[dependencies]
+appdirs = "*"
+filelock = "*"
+flaky = "*"
+fortran-language-server = "*"
+fprettify = "*"
+hatchling = "*"
+jupytext = "*"
+matplotlib = "*"
+meson = "1.3.0"
+networkx = "*"
+ninja = "*"
+numpy = "*"
+pandas = "*"
+pip = "*"
+pydotplus = "*"
+pyshp = "*"
+pytest = "!=8.1.0"
+pytest-benchmark = "*"
+pytest-dotenv = "*"
+pytest-order = "*"
+pytest-xdist = "*"
+python = "3.9.*"
+requests = "*"
+scipy = "*"
+shapely = "*"
+xmipy = "*"