Merge branch 'main' into numerics

.gitattributes

@@ -1,5 +1 @@
-* text=auto
-
-**/Project.toml eol=lf
-**/Manifest.toml eol=lf
-**/*.json eol=lf
+* text=auto eol=lf

.github/pull_request_template.md

@@ -1,36 +1 @@
 Fixes #
-
-# Description
-
-
-
-
----
-text below is for instruction and can be removed
-
-# New node types
-Typically new node types require an update of:
-
-- `core/src/create.jl`
-- `core/src/validation.jl`
-- `core/src/solve.jl`
-
-Updating other julia files may be required.
-
-
-## ribasim_python
-- `new_node_type.py` with associated implementation in `python/ribasim/ribasim`.
-- add/update nodetype to `python/ribasim/ribasim/model.py`
-- add/update nodetype to `python/ribasim/tests/conftest.py`
-- add/update nodetype to `python/ribasim_api/tests/conftest.py`
-
-## documentation
-
-- update `docs/core/equations.qmd`
-- update `docs/core/usage.qmd`
-- update `docs/python/examples.ipynb`  # or start a new example model
-- update `docs/schema*.json` by running `julia --project=docs docs/gen_schema.jl` and `datamodel-codegen --use-title-as-name --input docs/schema/root.schema.json --output python/ribasim/ribasim/models.py`
-- update the instructions in `docs/contribute/*.qmd` if something changes there, e.g. something changes in how a new node type must be defined.
-
-## QGIS
-- update `qgis/core/nodes.py`

.github/workflows/core_tests.yml

@@ -13,9 +13,6 @@ jobs:
   test:
     name: Julia ${{ matrix.julia_version }} - ${{ matrix.os }} - ${{ matrix.arch }}
     runs-on: ${{ matrix.os }}
-    defaults:
-      run:
-        shell: bash -l {0}
     strategy:
       fail-fast: false
       matrix:
@@ -28,19 +25,16 @@ jobs:
         arch:
           - x64
     steps:
-      - uses: actions/checkout@v3
-      - name: Setup Micromamba
-        uses: mamba-org/setup-micromamba@v1
+      - uses: actions/checkout@v4
+      - uses: prefix-dev/[email protected]
         with:
-          cache-downloads: true
-          cache-environment: true
-          environment-file: ./environment.yml
-      - name: Install ribasim
-        run: pip install --editable python/ribasim
-      - name: Install ribasim_testmodels
-        run: pip install --editable python/ribasim_testmodels
+          pixi-version: "v0.3.0"
+          cache: true
+      - name: Prepare pixi
+        run: pixi run post-install-without-pre-commit
       - name: Prepare model input
-        run: python python/ribasim/tests/conftest.py
+        run: |
+          pixi run generate-testmodels
       - uses: julia-actions/setup-julia@v1
         with:
           version: ${{ matrix.julia_version }}

.github/workflows/docs.yml

@@ -14,17 +14,14 @@ jobs:
     runs-on: ubuntu-latest
     permissions:
       contents: write
-    defaults:
-      run:
-        shell: bash -l {0}
     strategy:
       matrix:
         julia_version:
           - "1.9"
         arch:
           - x64
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: julia-actions/setup-julia@v1
         with:
@@ -40,38 +37,24 @@ jobs:
           cache-compiled: "true"
           cache-registries: "true"
 
-      - name: Setup Micromamba
-        uses: mamba-org/setup-micromamba@v1
+      - uses: prefix-dev/[email protected]
         with:
-          cache-downloads: true
-          cache-environment: true
-          environment-file: ./environment.yml
-
-      - name: Install ribasim-python
-        run: pip install --editable python/ribasim
-
-      - name: Set up Quarto
-        uses: quarto-dev/quarto-actions/setup@v2
+          pixi-version: "v0.3.0"
+          cache: true
+      - name: Prepare pixi
+        run: pixi run post-install-without-pre-commit
 
       - name: Check Quarto installation and all engines
-        run: quarto check all
-
-      - name: Generate API pages
-        working-directory: docs
-        # objects.json: https://github.com/machow/quartodoc/issues/63
-        run: |
-          quartodoc build
-          rm objects.json
+        run: pixi run quarto-check
 
       - name: Generate Julia docs
-        working-directory: docs
-        run: |
-          julia --project -e "using Pkg; Pkg.instantiate()"
-          julia --project make.jl
+        run: pixi run build-julia-docs
 
       - name: Render Quarto Project
-        run: "quarto render docs --to html --execute"
+        run: pixi run quarto-render
 
+      - name: Set up Quarto for publish
+        uses: quarto-dev/quarto-actions/setup@v2
       - name: Publish Quarto Project
         if: github.ref == 'refs/heads/main'
         uses: quarto-dev/quarto-actions/publish@v2

.github/workflows/pre-commit_auto_update.yml

@@ -11,7 +11,7 @@ jobs:
   auto-update:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           ssh-key: ${{ secrets.SSH_PRIVATE_KEY }}
       - uses: actions/setup-python@v4

.github/workflows/pre-commit_check.yml

@@ -10,7 +10,7 @@ jobs:
   check:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: actions/setup-python@v4
         with:
           python-version: "3.11"

.github/workflows/python_lint.yml

@@ -14,28 +14,20 @@ jobs:
     name: Mypy
     runs-on: ubuntu-latest
     continue-on-error: true
-    defaults:
-      run:
-        shell: bash -l {0}
     steps:
-      - uses: actions/checkout@v3
-      - name: Setup Micromamba
-        uses: mamba-org/setup-micromamba@v1
+      - uses: actions/checkout@v4
+      - uses: prefix-dev/[email protected]
         with:
-          cache-downloads: true
-          cache-environment: true
-          environment-file: ./environment.yml
-      - name: Install python packages
-        run: |
-          pip install python/ribasim
-          pip install python/ribasim_testmodels
-          pip install python/ribasim_api
+          pixi-version: "latest"
+          cache: true
+      - name: Prepare pixi
+        run: pixi run post-install-without-pre-commit
       - name: Run mypy on python/ribasim
         run: |
-          mypy --ignore-missing-imports python/ribasim/ribasim
+          pixi run mypy-ribasim-python
       - name: Run mypy on python/ribasim_testmodels
         run: |
-          mypy --ignore-missing-imports python/ribasim_testmodels/ribasim_testmodels
+          pixi run mypy-ribasim-testmodels
       - name: Run mypy on python/ribasim_api
         run: |
-          mypy --ignore-missing-imports python/ribasim_api/ribasim_api
+          pixi run mypy-ribasim-api

.github/workflows/python_tests.yml

@@ -13,9 +13,6 @@ jobs:
   test:
     name: Python ${{ matrix.python_version }} - ${{ matrix.os }} - ${{ matrix.arch }}
     runs-on: ${{ matrix.os }}
-    defaults:
-      run:
-        shell: bash -l {0}
     strategy:
       fail-fast: false
       matrix:
@@ -30,25 +27,17 @@ jobs:
         arch:
           - x86
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
-      - name: Setup Micromamba
-        uses: mamba-org/setup-micromamba@v1
+      - uses: prefix-dev/[email protected]
         with:
-          cache-downloads: true
-          cache-environment: true
-          environment-file: ./environment.yml
-          create-args: >-
-            python=${{ matrix.python_version }}
-
-      - name: Install ribasim
-        run: pip install --editable python/ribasim
-
-      - name: Install ribasim_testmodels
-        run: pip install --editable python/ribasim_testmodels
+          pixi-version: "v0.3.0"
+          cache: true
+      - name: Prepare pixi
+        run: pixi run post-install-without-pre-commit
 
       - name: Run tests
-        run: pytest --cov=ribasim --cov-report=xml python/ribasim/tests
+        run: pixi run test-ribasim-python-cov
 
       - name: Upload coverage to Codecov
         uses: codecov/codecov-action@v3

.github/workflows/qgis.yml

@@ -17,7 +17,7 @@ jobs:
         steps:
 
         - name: Check out repository
-          uses: actions/checkout@v3
+          uses: actions/checkout@v4
         - name: Launching docker compose
           run: ./start.sh
         - name: Running tests

.gitignore

@@ -15,7 +15,7 @@ docs/site/
 # environment.
 /core/Manifest.toml
 
-/data/
+/generated_testmodels
 build/create_binaries/ribasim_cli/
 build/create_binaries/libribasim/
 
@@ -155,3 +155,5 @@ dmypy.json
 .vscode/settings.json
 
 /.luarc.json
+build/ribasim_cli/tests/temp/
+report.xml

.teamcity/Ribasim_Ribasim/buildTypes/BuildRibasimCliWindows.xml

@@ -9,7 +9,7 @@
       <option name="publishArtifactCondition" value="SUCCESSFUL" />
     </options>
     <parameters>
-      <param name="conda_env_path" value="%system.teamcity.build.checkoutDir%/env" />
+      <param name="conda_env_path" value="%system.teamcity.build.checkoutDir%/env_build_ribasim_cli" />
       <param name="julia" value="%env.JULIA_1_9%" />
     </parameters>
     <build-runners>
@@ -33,7 +33,7 @@ call pip install --editable "python/ribasim_testmodels"]]></param>
       <runner id="RUNNER_1992" name="Prepare model input" type="simpleRunner">
         <parameters>
           <param name="script.content"><![CDATA[call conda activate "%conda_env_path%"
-call python python/ribasim/tests/conftest.py]]></param>
+call python utils/generate-testmodels.py]]></param>
           <param name="teamcity.step.mode" value="default" />
           <param name="use.custom.script" value="true" />
         </parameters>
@@ -113,4 +113,3 @@ call python python/ribasim/tests/conftest.py]]></param>
     <cleanup />
   </settings>
 </build-type>
-

.teamcity/Ribasim_Ribasim/buildTypes/Ribasim_RibasimJl_BuildLibribasimWindows.xml

@@ -12,7 +12,7 @@
       <setting-ref ref="RQ_271" />
     </disabled-settings>
     <parameters>
-      <param name="conda_env_path" value="%system.teamcity.build.checkoutDir%/env" />
+      <param name="conda_env_path" value="%system.teamcity.build.checkoutDir%/env_build_libribasim" />
       <param name="julia" value="%env.JULIA_1_9%" />
     </parameters>
     <build-runners>
@@ -36,7 +36,7 @@ call pip install --editable "python/ribasim_testmodels"]]></param>
       <runner id="RUNNER_1967" name="Prepare model input" type="simpleRunner">
         <parameters>
           <param name="script.content"><![CDATA[call conda activate "%conda_env_path%"
-call python python/ribasim/tests/conftest.py]]></param>
+call python utils/generate-testmodels.py]]></param>
           <param name="teamcity.step.mode" value="default" />
           <param name="use.custom.script" value="true" />
         </parameters>
@@ -103,4 +103,3 @@ call python python/ribasim/tests/conftest.py]]></param>
     <cleanup />
   </settings>
 </build-type>
-

.teamcity/Ribasim_Ribasim/buildTypes/Ribasim_Ribasim_BuildPythonWheels.xml

@@ -19,6 +19,7 @@ set -euxo pipefail
 . /usr/share/Modules/init/bash
 ls /opt/apps/modules/anaconda3
 module load anaconda3/miniconda
+rm --force ribasim-*.whl
 pip wheel python/ribasim --no-deps]]></param>
           <param name="teamcity.step.mode" value="default" />
           <param name="use.custom.script" value="true" />

.teamcity/Ribasim_Ribasim/buildTypes/Ribasim_Ribasim_MakeQgisPlugin.xml

@@ -10,8 +10,9 @@
     <build-runners>
       <runner id="RUNNER_2193" name="" type="simpleRunner">
         <parameters>
-          <param name="script.content"><![CDATA[cp -r qgis ribasim_qgis
-zip ribasim_qgis.zip -r ribasim_qgis]]></param>
+          <param name="script.content"><![CDATA[rsync --verbose --recursive --delete qgis/ ribasim_qgis
+rm --force ribasim_qgis.zip
+zip -r ribasim_qgis.zip ribasim_qgis]]></param>
           <param name="teamcity.step.mode" value="default" />
           <param name="use.custom.script" value="true" />
         </parameters>

.teamcity/Ribasim_Ribasim/buildTypes/Ribasim_Ribasim_TestLibribasimWindows.xml

@@ -6,36 +6,32 @@
     <options>
       <option name="artifactRules" value="python\ribasim_api\tests\temp =&gt; test_output.zip" />
     </options>
-    <disabled-settings>
-      <setting-ref ref="RQ_436" />
-    </disabled-settings>
     <parameters>
       <param name="conda_env_path" value="%system.teamcity.build.checkoutDir%/libribasim_test_env" />
     </parameters>
     <build-runners>
       <runner id="RUNNER_1501" name="Set up virtual environment" type="simpleRunner">
         <parameters>
           <param name="script.content"><![CDATA[if exist "%conda_env_path%" rd /q /s "%conda_env_path%"
-call conda create --prefix "%conda_env_path%" python=3.10]]></param>
-          <param name="teamcity.build.workingDir" value="imod_coupler" />
+call conda env create --file environment.yml -p "%conda_env_path%"]]></param>
           <param name="teamcity.step.mode" value="default" />
           <param name="use.custom.script" value="true" />
         </parameters>
       </runner>
       <runner id="RUNNER_1502" name="Install Python packages" type="simpleRunner">
         <parameters>
           <param name="script.content"><![CDATA[call conda activate "%conda_env_path%"
-call pip install --editable "python/ribasim"
-call pip install --editable "python/ribasim_testmodels"
-call pip install --editable "python/ribasim_api[tests]"]]></param>
+pip install "python/ribasim"
+pip install "python/ribasim_testmodels"
+pip install "python/ribasim_api"]]></param>
           <param name="teamcity.step.mode" value="default" />
           <param name="use.custom.script" value="true" />
         </parameters>
       </runner>
       <runner id="RUNNER_1503" name="Run tests" type="simpleRunner">
         <parameters>
           <param name="script.content"><![CDATA[call conda activate "%conda_env_path%"
-call pytest tests --basetemp=tests/temp --junitxml="report.xml"]]></param>
+pytest tests --basetemp=tests/temp --junitxml="report.xml"]]></param>
           <param name="teamcity.build.workingDir" value="python/ribasim_api" />
           <param name="teamcity.step.mode" value="default" />
           <param name="use.custom.script" value="true" />
@@ -46,8 +42,7 @@ call pytest tests --basetemp=tests/temp --junitxml="report.xml"]]></param>
       <vcs-entry-ref root-id="Ribasim_Ribasim_Ribasim" />
     </vcs-settings>
     <requirements>
-      <equals id="RQ_436" name="teamcity.agent.jvm.os.name" value="Windows 10" />
-      <does-not-equal id="RQ_96" name="system.agent.name" value="c-teamcity0358" />
+      <equals id="RQ_315" name="env.OS" value="Windows_NT" />
     </requirements>
     <build-triggers>
       <build-trigger id="TRIGGER_64" type="buildDependencyTrigger">
@@ -78,7 +73,7 @@ call pytest tests --basetemp=tests/temp --junitxml="report.xml"]]></param>
     </build-extensions>
     <artifact-dependencies>
       <dependency id="ARTIFACT_DEPENDENCY_570" sourceBuildTypeId="Ribasim_RibasimJl_BuildLibribasimWindows" cleanDestination="true">
-        <revisionRule name="lastSuccessful" revision="latest.lastSuccessful" />
+        <revisionRule name="lastSuccessful" revision="latest.lastSuccessful" branch="+:&lt;default&gt;&#xD;&#xA;+:ref" />
         <artifact sourcePath="libribasim.zip!** =&gt; build/create_binaries/libribasim&#xD;&#xA;" />
       </dependency>
     </artifact-dependencies>