Use tactus in surfExp

.github/workflows/documentation.yaml

@@ -0,0 +1,83 @@
+#.github/workflows/documentation.yaml
+name: Create documentation
+
+on:
+  pull_request:
+    branches:
+      - master
+  push:
+    branches:
+      - '**' # Every branch
+
+env:
+  USER: "github_runner"
+  HOME: "/tmp"
+
+jobs:
+  tests:
+    name: "Create documentation"
+    runs-on: "ubuntu-latest"
+
+    steps:
+      #----------------------------------------------
+      #           check-out repo
+      #----------------------------------------------
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+      - uses: mamba-org/setup-micromamba@v2
+        with:
+          environment-file: environment.yml
+          init-shell: >-
+            bash
+          cache-environment: true
+          post-cleanup: 'all'
+
+      - name: Set PATH
+        run: |
+          echo "/tmp/micromamba/envs/surfExp/bin" >> $GITHUB_PATH
+
+      - name: Set python
+        run: |
+          poetry env use /tmp/micromamba/envs/surfExp/bin/python
+
+      #- name: Load cached venv (if cache exists)
+      #  id: cached-poetry-dependencies
+      #  uses: actions/cache@v4
+      #  with:
+      #    path: .venv
+      #    key: venv-${{ hashFiles('pyproject.toml') }}
+
+      - name: Install dependencies (if venv cache is not found)
+        if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
+        run: |
+          poetry install --no-interaction --no-root --all-extras
+
+      - name: Install the project itself
+        run: |
+          poetry install --no-interaction --only-root
+
+      - name: Create documentation
+        run: |
+          poetry run sphinx-build . docs/build/html
+
+      - name: Commit documentation changes
+        if: ${{ github.repository_owner == 'metno' && github.event_name != 'pull_request' }}
+        run: |
+          git clone https://github.com/metno/surfExp.git --branch gh-pages --single-branch gh-pages
+          cp -r docs/build/html/* gh-pages/
+          cd gh-pages
+          git config --local user.email "action@github.com"
+          git config --local user.name "GitHub Action"
+          git add .
+          git commit -m "Update documentation" -a || true
+          # The above command will fail if no changes were present, so we ignore
+          # the return code.
+
+      - name: Push changes
+        if: ${{ github.repository_owner == 'metno' && github.event_name != 'pull_request' }}
+        uses: ad-m/github-push-action@master
+        with:
+          branch: gh-pages
+          directory: gh-pages
+          github_token: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/linting.yaml

@@ -5,66 +5,61 @@ on:
   pull_request:
     branches:
       - master
-      - develop
-    paths:
-      - '**.py'
   push:
     branches:
       - '**' # Every branch
-    paths:
-      - '**.py'
+
+env:
+  USER: "github_runner"
+  HOME: "/tmp"
 
 jobs:
   linting:
-    if: github.repository_owner == 'destination-earth-digital-twins'
     name: Run Linters
     runs-on: ubuntu-latest
-    environment: staging
+
     steps:
       #----------------------------------------------
-      #       check-out repo and set-up python
+      #           check-out repo
       #----------------------------------------------
       - name: Check out repository
         uses: actions/checkout@v4
-      - name: Set up python
-        id: setup-python
-        uses: actions/setup-python@v5
-        with:
-          python-version: '3.11'
 
-      #----------------------------------------------
-      #  --- configure poetry & install project  ----
-      #----------------------------------------------
-      - name: Install Poetry
-        uses: snok/install-poetry@v1
+      - uses: mamba-org/setup-micromamba@v2
         with:
-          virtualenvs-create: true
-          virtualenvs-in-project: true
+          environment-file: environment.yml
+          init-shell: >-
+            bash
+          cache-environment: true
+          post-cleanup: 'all'
 
-      - name: Load cached venv (if cache exists)
-        id: cached-poetry-dependencies
-        uses: actions/cache@v4
-        with:
-          path: .venv
-          key: venv-${{ runner.os }}-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/pyproject.toml') }}
+      - name: Set PATH
+        run: |
+          echo "/tmp/micromamba/envs/surfExp/bin" >> $GITHUB_PATH
+
+      - name: Set python
+        run: |
+          poetry env use /tmp/micromamba/envs/surfExp/bin/python
+
+      #- name: Load cached venv (if cache exists)
+      #  id: cached-poetry-dependencies
+      #  uses: actions/cache@v4
+      #  with:
+      #    path: .venv
+      #    key: venv-${{ hashFiles('pyproject.toml') }}
 
       - name: Install dependencies (if venv cache is not found)
         if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
-        run: poetry install --no-interaction --no-root --only linting
+        run: |
+          poetry install -vvv --no-interaction --no-root --only linting
 
       - name: Install the project itself
-        run: poetry install --no-interaction --only-root
+        run: |
+          poetry install -vvv --no-interaction --only-root
 
       #----------------------------------------------
       #         Run the linting checks
       #----------------------------------------------
-      - name: isort
-        run: |
-          poetry run isort --check-only .
-      - name: black
-        run: |
-          poetry run black --check --diff .
-      - name: flakeheaven
+      - name: Linting
         run: |
-          export FLAKEHEAVEN_CACHE="${TMPDIR:-${TEMP:-${TMP:-/tmp}}}/flakeheaven_cache.$(openssl rand -hex 12)"
-          poetry run flakeheaven lint .
+          poetry run poetry devtools lint

.github/workflows/tests.yml

@@ -15,21 +15,9 @@ env:
 
 jobs:
   tests:
-    if: github.repository_owner == 'destination-earth-digital-twins'
-    strategy:
-      fail-fast: true
-      matrix:
-        os: [ "ubuntu-latest" ]
-        env: [ "pytest" ]
-        python-version: [ "3.11" ]
 
-    name: "${{ matrix.os }}, python=${{ matrix.python-version }}"
-    runs-on: ${{ matrix.os }}
-
-    container:
-      image: python:${{ matrix.python-version }}-bullseye
-      env:
-        COVERAGE_FILE: ".coverage.${{ matrix.env }}.${{ matrix.python-version }}"
+    name: "Install and test surfExp"
+    runs-on: "ubuntu-latest"
 
     steps:
       #----------------------------------------------
@@ -46,88 +34,33 @@ jobs:
           cache-environment: true
           post-cleanup: 'all'
 
-      #----------------------------------------------
-      #  --- configure poetry & install project  ----
-      #----------------------------------------------
-      - name: Install Poetry
-        uses: snok/install-poetry@v1
-        with:
-          virtualenvs-create: true
-          virtualenvs-in-project: true
+      - name: Set PATH
+        run: |
+          echo "/tmp/micromamba/envs/surfExp/bin" >> $GITHUB_PATH
+
+      - name: Set python
+        run: |
+          poetry env use /tmp/micromamba/envs/surfExp/bin/python
 
       - name: Load cached venv (if cache exists)
         id: cached-poetry-dependencies
         uses: actions/cache@v4
         with:
           path: .venv
-          key: venv-${{ runner.os }}-${{ matrix.python-version }}-${{ hashFiles('**/pyproject.toml') }}
+          key: venv-${{ hashFiles('pyproject.toml') }}
 
-      - name: Modify pyproject.toml
-        env:
-          GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}}
-        run: |
-          #export GITHUB_TOKEN=${{ secrets.GH_REPO_READ_TOKEN }}
-          #export GITHUB_TOKEN="trygve"
-          sed -i "s#https://github.com/destination-earth-digital-twins/Deode-Workflow#https://${GITHUB_TOKEN}@github.com/destination-earth-digital-twins/Deode-Workflow#g" pyproject.toml
-
       - name: Install dependencies (if venv cache is not found)
         if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
         run: |
-          cat pyproject.toml
           poetry install --no-interaction --no-root --only main,test
-        shell: micromamba-shell {0}       
-
+
       - name: Install the project itself
         run: |
-          # poetry config http-basic.deode x-token-auth ${{secrets.DEODE_WORKFLOW_ACCESS}}
           poetry install --no-interaction --only-root
-        shell: micromamba-shell {0}
 
       #----------------------------------------------
       #      run test suite and report coverage
       #----------------------------------------------
       - name: Run tests
         run: |
           poetry run pytest
-        shell: micromamba-shell {0}
-
-      #- name: Upload test coverage report to Codecov
-      #  uses: codecov/codecov-action@v3
-      #  with:
-      #    token: ${{ secrets.CODECOV_TOKEN }}
-      #    files: ./.coverage.xml
-
-      - name: Coveralls
-        if: ${{ matrix.python-version == 3.11 }}
-        env:
-          GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}}
-        run: |
-          export COVERALLS_REPO_TOKEN=${{secrets.COVERALLS_REPO_TOKEN}}
-          poetry run coveralls
-        shell: micromamba-shell {0}
-
-      - name: Create documentation
-        if: ${{ matrix.python-version == 3.11 }}
-        run: |
-          poetry run sphinx-build . docs/build/html
-        shell: micromamba-shell {0}
-      - name: Commit documentation changes
-        if: ${{ matrix.python-version == 3.11 && github.event_name != 'pull_request' }}
-        run: |
-          git clone https://github.com/metno/surfExp.git --branch gh-pages --single-branch gh-pages
-          cp -r docs/build/html/* gh-pages/
-          cd gh-pages
-          git config --local user.email "action@github.com"
-          git config --local user.name "GitHub Action"
-          git add .
-          git commit -m "Update documentation" -a || true
-          # The above command will fail if no changes were present, so we ignore
-          # the return code.
-
-      - name: Push changes
-        if: ${{ matrix.python-version == 3.11 && github.event_name != 'pull_request' }}
-        uses: ad-m/github-push-action@master
-        with:
-          branch: gh-pages
-          directory: gh-pages
-          github_token: ${{ secrets.GITHUB_TOKEN }}

README.rst

@@ -10,7 +10,7 @@ This repository is a setup to create and run offline SURFEX experiments.
 
 See online documentation in https://metno.github.io/surfExp/
 
-The setup is dependent of pysurfex (https://metno.github.io/pysurfex) and deode workflow (https://github.com/destination-earth-digital-twins/Deode-Workflow).
+The setup is dependent of pysurfex (https://metno.github.io/pysurfex) and tactus (https://github.com/ACCORD-NWP/tactus).
 
 
 
@@ -76,9 +76,9 @@ In addition you can add optional arguments like the start and end times and if y
 
 The surfex binaries executed from surfExp are of course depending on source code version.
 This means the fortran namelists must correspond to the binaries being run.
-There are two ways to generate the fortran namelists. Since surfexp is a plugin to deode
-the first way is to create the namelists is with the deode namelist generator.
-This is achieved by setting ldeode = true for the surfex binary sections.
+There are two ways to generate the fortran namelists. Since surfexp is a plugin to tactus
+the first way is to create the namelists is with the tactus namelist generator.
+This is achieved by setting tactus = true for the surfex binary sections.
 
 The other method is using the pysurfex namelist generator and is handled by the keyword blocks in the settings for the different binaries.
 Please note that since this is a list, it is not merged between diffentent configuration inputs,
@@ -110,7 +110,7 @@ from the config file.
  surfExp -o my_config.toml --case-name LDAS --plugin-home $PWD surfexp/data/config/configurations/metno_ldas.toml surfexp/data/config/mods/cy46_aa_offline/ppi.toml
 
  # To start you experiment
- deode start suite --config-file my_config.toml
+ tactus start suite --config-file my_config.toml
 
 
 
@@ -164,10 +164,10 @@ Extra environment on PPI-RHEL8 needed to start experiments
  export ECF_SSL=1
 
  # Set HOST
- export DEODE_HOST="ppi_rhel8_b1"
+ export TACTUS_HOST="ppi_rhel8_b1"
 
  # Start suite (modify dates)
- deode start suite --config-file exps/LDAS.toml
+ tactus start suite --config-file exps/LDAS.toml
 
  # MET-Norway LDAS single decade
  surfExp -o exps/LDAS_decade.toml --case-name LDAS_decade \
@@ -179,5 +179,5 @@ Extra environment on PPI-RHEL8 needed to start experiments
  surfexp/data/config/scheduler/ecflow_ppi_rhel8-$USER.toml
 
  # Start the suite
- deode start suite  --config-file exps/LDAS_decade.toml
+ tactus start suite  --config-file exps/LDAS_decade.toml
 

docs/example.rst

@@ -36,8 +36,8 @@ To detect the proper host on MET-Norway PPI you need to export one of the follow
 
 .. code-block:: bash
 
-  export DEODE_HOST="ppi_rhel8_b1"
-  export DEODE_HOST="ppi_rhel8_a1"
+  export TACTUS_HOST="ppi_rhel8_b1"
+  export TACTUS_HOST="ppi_rhel8_a1"
 
 The variables below are needed for ecflow for MET-Norway PPI
 
@@ -62,14 +62,13 @@ South-Norway domain
 
     surfExp -o dt_offline_drammen.toml \
     --case-name CY49DT_OFFLINE_DRAMMEN \
-    --plugin-home /home/$USER/projects/surfExp \
+    --plugin-home $PWD \
     --troika troika \
-
     surfexp/data/config/configurations/dt.toml \
     surfexp/data/config/domains/DRAMMEN.toml \
     surfExp/surfexp/data/config/mods/dev-CY49T2h_deode/dt.toml
 
-    deode start suite --config-file dt_offline_drammen.toml
+    tactus start suite --config-file dt_offline_drammen.toml
 
 
 DT_2_5_2500x2500
@@ -85,7 +84,7 @@ DT_2_5_2500x2500
     surfexp/data/config/domains/dt_2_5_2500x2500.toml \
     surfexp/data/config/mods/dev-CY49T2h_deode/dt.toml
 
-    deode start suite --config-file dt_offline_dt_2_5_2500x2500.toml
+    tactus start suite --config-file dt_offline_dt_2_5_2500x2500.toml
 
 DT_2_5_2500x2500 Initial conditions from namelist
 -------------------------
@@ -101,5 +100,5 @@ DT_2_5_2500x2500 Initial conditions from namelist
     surfexp/data/config/mods/dev-CY49T2h_deode/dt.toml \
     surfexp/data/config/mods/dev-CY49T2h_deode/dt_prep_from_namelist.toml
 
-    deode start suite --config-file dt_offline_dt_2_5_2500x2500.toml
+    tactus start suite --config-file dt_offline_dt_2_5_2500x2500.toml