Update to v2.0.0-alpha.1

.flake8.cfg

@@ -0,0 +1,16 @@
+[flake8]
+# https://pep8.readthedocs.io/en/latest/intro.html#error-codes
+ignore =
+    # line break after operator
+    W504
+# Max width of GitHub code review is 79 characters
+max-line-length = 79
+max-complexity = 18
+per-file-ignores =
+    */__init__.py: F401
+exclude =
+    .git,
+    docs,
+    .idea,
+    .mypy_cache,
+    .pytest_cache,

.github/workflows/build_workflow.yml

@@ -12,7 +12,7 @@ on:
 env:
   CANCEL_OTHERS: false
   PATHS_IGNORE: '["**/README.md", "**/docs/**"]'
-  PYTHON_VERSION: "3.13"
+  PYTHON_VERSION: "3.14"
 
 jobs:
   pre-commit-hooks:
@@ -60,7 +60,7 @@ jobs:
         shell: bash -l {0}
     strategy:
       matrix:
-        python-version: ["3.10", "3.11", "3.12", "3.13"]
+        python-version: ["3.11", "3.12", "3.13", "3.14"]
       fail-fast: false
     steps:
       - id: skip_check
@@ -73,43 +73,56 @@ jobs:
         uses: actions/checkout@v6
 
       - if: ${{ steps.skip_check.outputs.should_skip != 'true' }}
-        name: Set up Conda Environment
-        uses: mamba-org/setup-micromamba@v3
+        name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v6
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - if: ${{ steps.skip_check.outputs.should_skip != 'true' }}
+        name: Cache pixi packages
+        uses: actions/cache@v5
+        env:
+          # Increase this value to reset cache if deploy inputs have not changed in the workflow
+          CACHE_NUMBER: 0
         with:
-          environment-name: compass_test
-          init-shell: bash
-          condarc: |
-            channel_priority: strict
-            channels:
-                - conda-forge
-                - e3sm/label/compass
-          create-args: >-
-            python=${{ matrix.python-version }}
+          path: |
+            ~/.cache/rattler/cache
+            ~/.pixi/bin
+          key: ${{ runner.os }}-${{ matrix.python-version }}-pixi-${{ env.CACHE_NUMBER }}-${{ hashFiles('deploy.py', 'deploy/**', 'pyproject.toml') }}
 
       - if: ${{ steps.skip_check.outputs.should_skip != 'true' }}
         name: Install compass
         run: |
           git config --global url."https://github.com/".insteadOf "git@github.com:"
-          ./conda/configure_compass_env.py \
-            --env_name compass_test \
-            --python=${{ matrix.python-version }} \
-            --mpi=mpich \
-            --verbose
-          source load_compass_test_mpich.sh
+          ./deploy.py \
+            --mache-fork xylar/mache --mache-branch add-target-software-cli-flags \
+            --no-spack \
+            --python ${{ matrix.python-version }} \
+            --recreate
+          load_script=$(find . -maxdepth 1 -type f -name 'load_compass*.sh' | sort | tail -n 1)
+          if [ -z "$load_script" ]; then
+            echo "ERROR: no generated Compass load script found" >&2
+            exit 1
+          fi
+          source "$load_script"
+          python -c "import compass; import compass.version; print(compass.version.__version__)"
+          compass --help
 
       - if: ${{ steps.skip_check.outputs.should_skip != 'true' }}
         name: Build Sphinx Docs
         run: |
-          source load_compass_test_mpich.sh
+          load_script=$(find . -maxdepth 1 -type f -name 'load_compass*.sh' | sort | tail -n 1)
+          source "$load_script"
           cd docs
-          make html
+          make html-strict
 
       - if: ${{ steps.skip_check.outputs.should_skip != 'true' }}
         name: Run Tests
         env:
           CHECK_IMAGES: False
         run: |
-          source load_compass_test_mpich.sh
+          load_script=$(find . -maxdepth 1 -type f -name 'load_compass*.sh' | sort | tail -n 1)
+          source "$load_script"
           python -c "import compass"
           compass list
           compass list --machines

.github/workflows/docs_workflow.yml

@@ -8,63 +8,61 @@ on:
     types: [published]
 
 env:
-  PYTHON_VERSION: "3.13"
+  PYTHON_VERSION: "3.14"
 
 jobs:
   publish-docs:
     runs-on: ubuntu-latest
     defaults:
       run:
         shell: bash -l {0}
-    env:
-      docs_version: "latest"
     timeout-minutes: 20
     steps:
       - uses: actions/checkout@v6
         with:
           persist-credentials: false
           fetch-depth: 0
 
-      - if: ${{ steps.skip_check.outputs.should_skip != 'true' }}
-        name: Set up Conda Environment
-        uses: mamba-org/setup-micromamba@v3
+      - name: Set up Python ${{ env.PYTHON_VERSION }}
+        uses: actions/setup-python@v6
         with:
-          environment-name: compass_test
-          init-shell: bash
-          condarc: |
-            channel_priority: strict
-            channels:
-                - conda-forge
-                - e3sm/label/compass
-          create-args: >-
-            python=${{ env.PYTHON_VERSION }}
+          python-version: ${{ env.PYTHON_VERSION }}
 
-      - if: ${{ steps.skip_check.outputs.should_skip != 'true' }}
-        name: Install compass
+      - name: Cache pixi packages
+        uses: actions/cache@v5
+        env:
+          # Increase this value to reset cache if deploy inputs have not changed in the workflow
+          CACHE_NUMBER: 0
+        with:
+          path: |
+            ~/.cache/rattler/cache
+            ~/.pixi/bin
+          key: ${{ runner.os }}-${{ env.PYTHON_VERSION }}-pixi-${{ env.CACHE_NUMBER }}-${{ hashFiles('deploy.py', 'deploy/**', 'pyproject.toml') }}
+
+      - name: Install compass
         run: |
           git config --global url."https://github.com/".insteadOf "git@github.com:"
-          ./conda/configure_compass_env.py \
-            --env_only \
-            --env_name compass_test \
-            --python=${{ env.PYTHON_VERSION }} \
-            --verbose
-          source load_compass_test.sh
+          ./deploy.py \
+            --no-spack \
+            --python ${{ env.PYTHON_VERSION }} \
+            --recreate
+          load_script=$(find . -maxdepth 1 -type f -name 'load_compass*.sh' | sort | tail -n 1)
+          if [ -z "$load_script" ]; then
+            echo "ERROR: no generated Compass load script found" >&2
+            exit 1
+          fi
+          source "$load_script"
 
       - name: Build Sphinx Docs
         run: |
-          source load_compass_test.sh
+          load_script=$(find . -maxdepth 1 -type f -name 'load_compass*.sh' | sort | tail -n 1)
+          source "$load_script"
           cd docs
-          if [[ $GITHUB_REF_NAME == "main" ]]; then
-              export DOCS_VERSION="latest"
-          else
-              export DOCS_VERSION=${GITHUB_REF_NAME}
-          fi
-          echo "Docs version: $DOCS_VERSION"
-          echo "docs_version=$DOCS_VERSION" >> $GITHUB_ENV
           make html
       - name: Copy Docs and Commit
         run: |
-          source load_compass_test.sh
+          load_script=$(find . -maxdepth 1 -type f -name 'load_compass*.sh' | sort | tail -n 1)
+          source "$load_script"
           cd docs
           # gh-pages branch must already exist
           git clone https://github.com/MPAS-Dev/compass.git --branch gh-pages --single-branch gh-pages
@@ -74,8 +72,8 @@ jobs:
           touch .nojekyll
           # Add `index.html` to point to the `main` branch automatically.
           printf '<meta http-equiv="refresh" content="0; url=./main/index.html" />' > index.html
-          # Only replace `main` docs with latest changes. Docs for releases should be untouched.
-          export DOCS_VERSION="${{ env.docs_version }}"
+          # Replace the docs for the current branch or tag with the latest build.
+          export DOCS_VERSION="${GITHUB_REF_NAME}"
           rm -rf ${DOCS_VERSION}
           mkdir ${DOCS_VERSION}
           cp -r ../_build/html/* ${DOCS_VERSION}

.github/workflows/gis_coarse_meshgen.yml

@@ -15,24 +15,52 @@ jobs:
   gis-coarse-meshgen:
     name: GIS Coarse Mesh Generation
     runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
     steps:
       - uses: actions/checkout@v6
+
+      - name: Set up Python 3.14
+        uses: actions/setup-python@v6
         with:
-          submodules: recursive
-          path: compass
-      - name: setup_and_run_step
-        run: |
-          # create top level working directory
-          root=$PWD
-          pushd compass
+          python-version: "3.14"
 
-          # create the compass environment
-          ./conda/configure_compass_env.py --conda $root/mambaForge --env_name compass_test --mpi mpich
+      - name: Cache pixi packages
+        uses: actions/cache@v5
+        env:
+          # Increase this value to reset cache if deploy inputs have not changed in the workflow
+          CACHE_NUMBER: 0
+        with:
+          path: |
+            ~/.cache/rattler/cache
+            ~/.pixi/bin
+          key: ${{ runner.os }}-3.14-pixi-${{ env.CACHE_NUMBER }}-${{ hashFiles('deploy.py', 'deploy/**', 'pyproject.toml') }}
 
-          # enable the compass environment
-          source load_compass_test_mpich.sh
+      - name: Install compass
+        run: |
+          git config --global url."https://github.com/".insteadOf "git@github.com:"
+          ./deploy.py \
+            --mache-fork xylar/mache --mache-branch add-target-software-cli-flags \
+            --no-spack \
+            --python 3.14 \
+            --recreate
+          load_script=$(find . -maxdepth 1 -type f -name 'load_compass*.sh' | sort | tail -n 1)
+          if [ -z "$load_script" ]; then
+            echo "ERROR: no generated Compass load script found" >&2
+            exit 1
+          fi
+          source "$load_script"
+          # only update the MALI-Dev submodule, not others
+          git submodule update --init MALI-Dev
 
-          popd
+      - name: Setup and run step
+        run: |
+          load_script=$(find . -maxdepth 1 -type f -name 'load_compass*.sh' | sort | tail -n 1)
+          source "$load_script"
+
+          # create top level working directory
+          root=$PWD
 
           # download the input GIS coarse mesh
           tarball=gis4kmSubSampled_01302025.tgz
@@ -71,4 +99,3 @@ jobs:
           # run the test case
           cd $testDir
           compass run
-

.gitignore

@@ -120,3 +120,21 @@ ENV/
 
 # activation scripts
 /load_*.sh
+
+# pixi
+.pixi/
+pixi.lock
+pixi-env/
+
+# vs code
+.vscode/
+
+# mypy
+.mypy_cache/
+
+# ruff
+.ruff_cache/
+
+# mache
+.mache_cache/
+deploy_tmp

.pre-commit-config.yaml

@@ -22,7 +22,7 @@ repos:
     rev: 7.3.0
     hooks:
       - id: flake8
-        args: ["--config=setup.cfg"]
+        args: ["--config=.flake8.cfg"]
         additional_dependencies: [flake8-isort]
 
 # https://pre-commit.ci/#configuration

compass/landice/tests/dome/albany_input.yaml

@@ -11,7 +11,7 @@ ANONYMOUS:
 
 # Discretization Description
   Discretization:
-    Exodus Output File Name: albany_output.exo
+#    Exodus Output File Name: albany_output.exo
 
   Piro:
 #   Nonlinear Solver Information

compass/landice/tests/ensemble_generator/branch_ensemble/branch_run.py

@@ -4,8 +4,8 @@
 import netCDF4
 
 import compass.namelist
-from compass.io import symlink
 from compass.job import write_job_script
+from compass.load_script import symlink_load_script
 from compass.model import run_model
 from compass.step import Step
 
@@ -166,14 +166,7 @@ def setup(self):
                          pre_run_commands=pre_run_cmd,
                          post_run_commands=post_run_cmd)
 
-        # COMPASS does not create symlinks for the load script in step dirs,
-        # so use the standard approach for creating that symlink in each
-        # step dir.
-        if 'LOAD_COMPASS_ENV' in os.environ:
-            script_filename = os.environ['LOAD_COMPASS_ENV']
-            # make a symlink to the script for loading the compass conda env.
-            symlink(script_filename, os.path.join(self.work_dir,
-                                                  'load_compass_env.sh'))
+        symlink_load_script(self.work_dir)
 
     def run(self):
         """

compass/landice/tests/ensemble_generator/ensemble_member.py

@@ -6,9 +6,9 @@
 import netCDF4
 import yaml
 
-from compass.io import symlink
 from compass.job import write_job_script
 from compass.landice.extrapolate import extrapolate_variable
+from compass.load_script import symlink_load_script
 from compass.model import make_graph_file, run_model
 from compass.step import Step
 
@@ -262,14 +262,7 @@ def setup(self):
                          target_cores=self.ntasks, min_cores=self.min_tasks,
                          work_dir=self.work_dir)
 
-        # COMPASS does not create symlinks for the load script in step dirs,
-        # so use the standard approach for creating that symlink in each
-        # step dir.
-        if 'LOAD_COMPASS_ENV' in os.environ:
-            script_filename = os.environ['LOAD_COMPASS_ENV']
-            # make a symlink to the script for loading the compass conda env.
-            symlink(script_filename, os.path.join(self.work_dir,
-                                                  'load_compass_env.sh'))
+        symlink_load_script(self.work_dir)
 
         # save run info for analysis/viz
         with open(os.path.join(self.work_dir, 'run_info.cfg'), 'w') \

compass/landice/tests/greenland/albany_input.yaml

@@ -3,7 +3,7 @@
 ANONYMOUS:
 # Discretization Description
   Discretization:
-    Exodus Output File Name: albany_output.exo
+#    Exodus Output File Name: albany_output.exo
 
   Problem:
     Cubature Degree: 4