From b96176ae090f3478faca4217a1d65619b85e288e Mon Sep 17 00:00:00 2001
From: Hofer-Julian <julianhofer@gnome.org>
Date: Wed, 13 Sep 2023 10:27:31 +0200
Subject: [PATCH] Move from mamba to pixi

---
 .github/workflows/core_tests.yml   |   22 +-
 .github/workflows/docs.yml         |   37 +-
 .github/workflows/python_lint.yml  |   24 +-
 .github/workflows/python_tests.yml |   25 +-
 docs/contribute/addnode.qmd        |    3 -
 docs/contribute/core.qmd           |   25 +-
 docs/contribute/python.qmd         |  105 +-
 pixi.lock                          | 8519 ++++++++++++++++++++++++++++
 pixi.toml                          |   73 +
 python/ribasim/tests/conftest.py   |   17 -
 utils/generate-testmodels.py       |   16 +
 11 files changed, 8660 insertions(+), 206 deletions(-)
 create mode 100644 pixi.lock
 create mode 100644 pixi.toml
 create mode 100644 utils/generate-testmodels.py

diff --git a/.github/workflows/core_tests.yml b/.github/workflows/core_tests.yml
index 04822cfae..9d3053953 100644
--- a/.github/workflows/core_tests.yml
+++ b/.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:
@@ -29,18 +26,17 @@ jobs:
           - x64
     steps:
       - uses: actions/checkout@v4
-      - name: Setup Micromamba
-        uses: mamba-org/setup-micromamba@v1
+      - uses: prefix-dev/setup-pixi@v0.2.0
         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: "0.3.0"
+          cache: true
+      - name: Prepare pixi
+        run: |
+          pixi install
+          pixi run post-install
       - 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 }}
diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
index 26a58be4e..34e84a938 100644
--- a/.github/workflows/docs.yml
+++ b/.github/workflows/docs.yml
@@ -14,9 +14,6 @@ jobs:
     runs-on: ubuntu-latest
     permissions:
       contents: write
-    defaults:
-      run:
-        shell: bash -l {0}
     strategy:
       matrix:
         julia_version:
@@ -40,37 +37,23 @@ jobs:
           cache-compiled: "true"
           cache-registries: "true"
 
-      - name: Setup Micromamba
-        uses: mamba-org/setup-micromamba@v1
+      - uses: prefix-dev/setup-pixi@v0.2.0
         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: "0.3.0"
+          cache: true
+      - name: Prepare pixi
+        run: |
+          pixi install
+          pixi run post-install
 
       - 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: Publish Quarto Project
         if: github.ref == 'refs/heads/main'
diff --git a/.github/workflows/python_lint.yml b/.github/workflows/python_lint.yml
index 859391309..94b5db0f8 100644
--- a/.github/workflows/python_lint.yml
+++ b/.github/workflows/python_lint.yml
@@ -14,28 +14,22 @@ jobs:
     name: Mypy
     runs-on: ubuntu-latest
     continue-on-error: true
-    defaults:
-      run:
-        shell: bash -l {0}
     steps:
       - uses: actions/checkout@v4
-      - name: Setup Micromamba
-        uses: mamba-org/setup-micromamba@v1
+      - uses: prefix-dev/setup-pixi@v0.2.0
         with:
-          cache-downloads: true
-          cache-environment: true
-          environment-file: ./environment.yml
-      - name: Install python packages
+          pixi-version: "0.3.0"
+          cache: true
+      - name: Prepare pixi
         run: |
-          pip install python/ribasim
-          pip install python/ribasim_testmodels
-          pip install python/ribasim_api
+          pixi install
+          pixi run post-install
       - 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
diff --git a/.github/workflows/python_tests.yml b/.github/workflows/python_tests.yml
index 1400ea31b..4bb713ef9 100644
--- a/.github/workflows/python_tests.yml
+++ b/.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:
@@ -32,23 +29,17 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
-      - name: Setup Micromamba
-        uses: mamba-org/setup-micromamba@v1
+      - uses: prefix-dev/setup-pixi@v0.2.0
         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: "0.3.0"
+          cache: true
+      - name: Prepare pixi
+        run: |
+          pixi install
+          pixi run post-install
 
       - 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
diff --git a/docs/contribute/addnode.qmd b/docs/contribute/addnode.qmd
index 3c15e841f..0ddb5f3a7 100644
--- a/docs/contribute/addnode.qmd
+++ b/docs/contribute/addnode.qmd
@@ -253,8 +253,5 @@ To generate the Python module `models.py` from the JSON Schemas, run:
 datamodel-codegen --use-title-as-name --input docs/schema/root.schema.json --output python/ribasim/ribasim/models.py
 ```
 
-Run [Black](python.qmd#sec-black) to format the generated code.
-To catch possible Python issues run [Ruff](python.qmd#sec-ruff).
-
 Since adding a node type touches both the Python and Julia code,
 it is a good idea to run both the [Python test suite](python.qmd#test) and [Julia test suite](core.qmd#test) locally before creating a pull request.
diff --git a/docs/contribute/core.qmd b/docs/contribute/core.qmd
index 9e0d35064..bd8d4ae38 100644
--- a/docs/contribute/core.qmd
+++ b/docs/contribute/core.qmd
@@ -24,11 +24,6 @@ pkg> add Revise TestEnv
 Revise.jl is a library that allows you to modify code and use the changes without restarting Julia.
 You can let it start automatically by following these [instructions](https://timholy.github.io/Revise.jl/stable/config/#Using-Revise-by-default-1).
 
-## Install Quarto
-
-Quarto is the publishing system that builds our documentation.
-The installation instructions can be found on their [web page](https://quarto.org/docs/get-started/).
-
 ## Clone Ribasim
 
 In order to have the Ribasim repository locally available, you can clone it with Git.
@@ -107,24 +102,10 @@ That way you don't have to type `activate core` every time you open the REPL.
 ## Render documentation
 
 Example models are created and simulated as part of the rendering of the documentation.
-Therefore you need to have both the `ribasim` Python package and the Julia `Ribasim` package
-installed. Furthermore you need these 3 Python packages installed: `jupyter quartodoc xarray`.
-
-The Python API reference is created using quartodoc by running this command from the `docs/`
-folder:
-
-```bash
-quartodoc build
-```
-
-You typically only have to run this once, or if you want to check out how it looks after
-changing Python docstrings.
-
-The Julia API reference is created using Documenter.jl by running this command from the `docs/` folder:
+The Julia API reference is created using Documenter.jl by running this command:
 
 ```bash
-julia --project -e "using Pkg; Pkg.instantiate()"  # needed once
-julia --project make.jl  # after changing the Julia docstrings
+pixi run build-julia-docs
 ```
 
 In order to preview documentation you can run the following command from the `docs/` folder.
@@ -132,7 +113,7 @@ Afterwards, a browser tab will open with the rendered documentation, updating it
 make changes.
 
 ```bash
-quarto preview
+pixi run quarto-preview
 ```
 
 The documentation also includes [Jupyter notebooks](https://jupyter.org/).
diff --git a/docs/contribute/python.qmd b/docs/contribute/python.qmd
index 6e7e29dc4..7e51ea0b7 100644
--- a/docs/contribute/python.qmd
+++ b/docs/contribute/python.qmd
@@ -4,89 +4,26 @@ title: "Python tooling development"
 
 # Set up the developer environment
 
-## Setting up conda
+## Setting up pixi
 
-In order to develop on `ribasim` locally, please follow the following steps:
+First, set up pixi as described on their getting started [page](https://prefix.dev/docs/pixi/overview).
 
-- Download and install [miniconda](https://docs.conda.io/en/latest/miniconda.html).
+Then set up the environment by running the following commands:
 
-- Initialize `conda` by running the following in the `Miniconda prompt`:
-
-```
-conda init
-```
-
-- Depending on your company settings, you might also have to run the following in a Powershell terminal as administrator:
-
-```
-Set-ExecutionPolicy -ExecutionPolicy RemoteSigned
 ```
-
-## Creating (or updating) the environment
-
-- Create (or update) the environment by executing the following in your terminal:
-
-```
-conda env create --file=environment.yml --force
-```
-
-## Installing Python packages
-
-- Activate the environment
-
-```
-conda activate ribasim
-```
-
-In order to develop on `ribasim` locally, execute the following line inside your virtual environment with the repo root as your working directory:
-
-```bash
-pip install --editable python/ribasim
-pip install --editable python/ribasim_testmodels
-pip install --editable python/ribasim_api
-```
-
-## Install the pre-commit hook {#sec-precommit}
-
-If not already done, activate the environment:
-
-```
-conda activate ribasim
-```
-
-Pre-commit ensures that all linters are happy with your code before you commit your files.
-In order to install the pre-commit hook run:
-
-```bash
-pre-commit install
+pixi install
+pixi run post-install
 ```
 
 
 ## Running the tests {#sec-test}
 
-If not already done, activate the environment:
-
-```
-conda activate ribasim
-```
-
-To run the tests call `pytest` with the path to the Python package.
-Here the the root of the repository is the working directory:
+In order to run tests on Ribasim Python execute
 
 ```bash
-pytest python/ribasim
-```
-
-## Building the documentation
-
-Run in the docs folder:
-
-```
-quartodoc build
+pixi run test-ribasim-python
 ```
 
-This will generate the `.qmd` files in `docs/python/reference` for inspection.
-
 ## Updating example notebooks
 
 Make sure to run `Clear All Outputs` on the notebook before committing.
@@ -136,30 +73,12 @@ twine check dist/*
 twine upload dist/*
 ```
 
-## Automatic code formatting with Black {#sec-black}
-
-We use the [Black](https://black.readthedocs.io/en/stable/) code formatter.
-Code only passes the continuous integration checks if it is fully formatted according to the Black code style.
-When working in VS Code the settings suggested in @sec-vscode run Black automatically when saving Python files.
-
-If you want to run Black manually, you can run it from the command line.
-To run it on the entire repository, use the command below.
-Here the repository root is the working directory.
-
-```
-black .
-```
-
-## Code linting with Ruff {#sec-ruff}
-
-We use the [Ruff](https://github.com/charliermarsh/ruff) linter to help finding issues with Python code.
-Code only passes the continuous integration checks if Ruff does not find any issues.
+## Linting
 
-To run Ruff on the entire repository, use the command below.
-Here the repository root is the working directory.
+To run our linting suite locally, execute:
 
 ```
-ruff .
+pixi run lint
 ```
 
 # Code maintenance {#sec-codecov}
@@ -167,11 +86,13 @@ ruff .
 For new features new tests have to be added. To monitor how much of the code is covered by the tests we use [Codecov](https://about.codecov.io/).
 For a simple overview of the local code coverage run
 ```
+pixi shell
 pytest --cov=ribasim tests/
 ```
 from  `python/ribasim`. For an extensive overview in `html` format use
 ```
-ytest --cov=ribasim --cov-report=html tests/
+pixi shell
+pytest --cov=ribasim --cov-report=html tests/
 ```
 which creates a folder `htmlcov` in the working directory. To see te contents open `htmlcov/index.html` in a browser.
 
diff --git a/pixi.lock b/pixi.lock
new file mode 100644
index 000000000..84e592e1e
--- /dev/null
+++ b/pixi.lock
@@ -0,0 +1,8519 @@
+metadata:
+  content_hash:
+    win-64: e90c2ee71ad70fc0a1c8302029533a7d1498f2bffcd0eaa8d2934700e775dc1d
+  channels:
+  - url: https://conda.anaconda.org/conda-forge/
+    used_env_vars: []
+  platforms:
+  - win-64
+  sources: []
+  time_metadata: null
+  git_metadata: null
+  inputs_metadata: null
+  custom_metadata: null
+package:
+- name: anyio
+  version: 4.0.0
+  manager: conda
+  platform: win-64
+  dependencies:
+    exceptiongroup: '*'
+    idna: '>=2.8'
+    python: '>=3.8'
+    sniffio: '>=1.1'
+  url: https://conda.anaconda.org/conda-forge/noarch/anyio-4.0.0-pyhd8ed1ab_0.conda
+  hash:
+    md5: 3c4e99d3ae4ec033d4dd99fb5220e540
+    sha256: 64125775b2e724db5c72e431dd180495d5d509d0a2d1228a122e6af9f1b60e33
+  optional: false
+  category: main
+  build: pyhd8ed1ab_0
+  arch: x86_64
+  subdir: win-64
+  build_number: 0
+  constrains:
+  - trio >=0.22
+  license: MIT
+  license_family: MIT
+  noarch: python
+  size: 98958
+  timestamp: 1693488730301
+- name: argcomplete
+  version: 3.1.1
+  manager: conda
+  platform: win-64
+  dependencies:
+    python: '>=3.8'
+  url: https://conda.anaconda.org/conda-forge/noarch/argcomplete-3.1.1-pyhd8ed1ab_0.conda
+  hash:
+    md5: 964bace0c38ce4733851a2a29679e3f9
+    sha256: 1fe9b55d3daeb26ac404ec51f106ce8792d7d6548810ca87600cd9b9e9cfbd6e
+  optional: false
+  category: main
+  build: pyhd8ed1ab_0
+  arch: x86_64
+  subdir: win-64
+  build_number: 0
+  license: Apache-2.0
+  license_family: Apache
+  noarch: python
+  size: 39430
+  timestamp: 1686587564613
+- name: argon2-cffi
+  version: 23.1.0
+  manager: conda
+  platform: win-64
+  dependencies:
+    argon2-cffi-bindings: '*'
+    python: '>=3.7'
+    typing-extensions: '*'
+  url: https://conda.anaconda.org/conda-forge/noarch/argon2-cffi-23.1.0-pyhd8ed1ab_0.conda
+  hash:
+    md5: 3afef1f55a1366b4d3b6a0d92e2235e4
+    sha256: 130766446f5507bd44df957b6b5c898a8bd98f024bb426ed6cb9ff1ad67fc677
+  optional: false
+  category: main
+  build: pyhd8ed1ab_0
+  arch: x86_64
+  subdir: win-64
+  build_number: 0
+  constrains:
+  - argon2_cffi ==999
+  license: MIT
+  license_family: MIT
+  noarch: python
+  size: 18602
+  timestamp: 1692818472638
+- name: argon2-cffi-bindings
+  version: 21.2.0
+  manager: conda
+  platform: win-64
+  dependencies:
+    cffi: '>=1.0.1'
+    python: '>=3.11,<3.12.0a0'
+    python_abi: 3.11.* *_cp311
+    ucrt: '>=10.0.20348.0'
+    vc: '>=14.2,<15'
+    vs2015_runtime: '>=14.29.30139'
+  url: https://conda.anaconda.org/conda-forge/win-64/argon2-cffi-bindings-21.2.0-py311ha68e1ae_3.tar.bz2
+  hash:
+    md5: c321cd825b72a2073dfb3f92ce1507fb
+    sha256: 641dd4b9d7714d28a2dbc3f80e9f3503acabd5706454d54e8c04578035cb22e7
+  optional: false
+  category: main
+  build: py311ha68e1ae_3
+  arch: x86_64
+  subdir: win-64
+  build_number: 3
+  license: MIT
+  license_family: MIT
+  size: 36208
+  timestamp: 1666851014828
+- name: arrow
+  version: 1.2.3
+  manager: conda
+  platform: win-64
+  dependencies:
+    python: '>=3.6'
+    python-dateutil: '>=2.7.0'
+    typing_extensions: '*'
+  url: https://conda.anaconda.org/conda-forge/noarch/arrow-1.2.3-pyhd8ed1ab_0.tar.bz2
+  hash:
+    md5: fd1967c76eda3a3dd9e8e6cb7a15a028
+    sha256: a0434c2770cf5b0ab5a33913c0b202b1521bc13f755b762d16a86b110425cdc2
+  optional: false
+  category: main
+  build: pyhd8ed1ab_0
+  arch: x86_64
+  subdir: win-64
+  build_number: 0
+  license: Apache-2.0
+  license_family: Apache
+  noarch: python
+  size: 93703
+  timestamp: 1662382594353
+- name: asttokens
+  version: 2.4.0
+  manager: conda
+  platform: win-64
+  dependencies:
+    python: '>=3.5'
+    six: '>=1.12.0'
+  url: https://conda.anaconda.org/conda-forge/noarch/asttokens-2.4.0-pyhd8ed1ab_0.conda
+  hash:
+    md5: 056f04e51dd63337e8d7c425c18c86f1
+    sha256: e7e91e3fa26abe502be690371893f205d87a82c225668ea6e9a1ba26870388ee
+  optional: false
+  category: main
+  build: pyhd8ed1ab_0
+  arch: x86_64
+  subdir: win-64
+  build_number: 0
+  license: Apache-2.0
+  license_family: Apache
+  noarch: python
+  size: 28819
+  timestamp: 1694046538391
+- name: async-lru
+  version: 2.0.4
+  manager: conda
+  platform: win-64
+  dependencies:
+    python: '>=3.8'
+    typing_extensions: '>=4.0.0'
+  url: https://conda.anaconda.org/conda-forge/noarch/async-lru-2.0.4-pyhd8ed1ab_0.conda
+  hash:
+    md5: 3d081de3a6ea9f894bbb585e8e3a4dcb
+    sha256: 7ed83731979fe5b046c157730e50af0e24454468bbba1ed8fc1a3107db5d7518
+  optional: false
+  category: main
+  build: pyhd8ed1ab_0
+  arch: x86_64
+  subdir: win-64
+  build_number: 0
+  license: MIT
+  license_family: MIT
+  noarch: python
+  size: 15342
+  timestamp: 1690563152778
+- name: attrs
+  version: 23.1.0
+  manager: conda
+  platform: win-64
+  dependencies:
+    python: '>=3.7'
+  url: https://conda.anaconda.org/conda-forge/noarch/attrs-23.1.0-pyh71513ae_1.conda
+  hash:
+    md5: 3edfead7cedd1ab4400a6c588f3e75f8
+    sha256: 063639cd568f5c7a557b0fb1cc27f098598c0d8ff869088bfeb82934674f8821
+  optional: false
+  category: main
+  build: pyh71513ae_1
+  arch: x86_64
+  subdir: win-64
+  build_number: 1
+  license: MIT
+  license_family: MIT
+  noarch: python
+  size: 55022
+  timestamp: 1683424195402
+- name: aws-c-auth
+  version: 0.7.3
+  manager: conda
+  platform: win-64
+  dependencies:
+    aws-c-cal: '>=0.6.2,<0.6.3.0a0'
+    aws-c-common: '>=0.9.0,<0.9.1.0a0'
+    aws-c-http: '>=0.7.12,<0.7.13.0a0'
+    aws-c-io: '>=0.13.32,<0.13.33.0a0'
+    aws-c-sdkutils: '>=0.1.12,<0.1.13.0a0'
+    ucrt: '>=10.0.20348.0'
+    vc: '>=14.2,<15'
+    vc14_runtime: '>=14.29.30139'
+  url: https://conda.anaconda.org/conda-forge/win-64/aws-c-auth-0.7.3-hd125877_3.conda
+  hash:
+    md5: eb7328f112a1e015c508de9cd241f990
+    sha256: 4c790ff7a2699abb8651679a20df7461e3966d46960eb5584e5ca24af8ac2849
+  optional: false
+  category: main
+  build: hd125877_3
+  arch: x86_64
+  subdir: win-64
+  build_number: 3
+  license: Apache-2.0
+  license_family: Apache
+  size: 97721
+  timestamp: 1692935709843
+- name: aws-c-cal
+  version: 0.6.2
+  manager: conda
+  platform: win-64
+  dependencies:
+    aws-c-common: '>=0.9.0,<0.9.1.0a0'
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diff --git a/pixi.toml b/pixi.toml
new file mode 100644
index 000000000..7847d39b1
--- /dev/null
+++ b/pixi.toml
@@ -0,0 +1,73 @@
+[project]
+name = "Ribasim"
+version = "0.1.0"
+description = "Add a short description here"
+authors = ["Hofer-Julian <julianhofer@gnome.org>"]
+channels = ["conda-forge"]
+platforms = ["win-64"]
+
+[tasks]
+install-ribasim-python = "pip install --no-deps --editable python/ribasim"
+install-ribasim-api = "pip install --no-deps --editable python/ribasim_api"
+install-ribasim-testmodels = "pip install --no-deps --editable python/ribasim_testmodels"
+install-quartodoc = "pip install quartodoc"
+pre-commit-install = "pre-commit install"
+post-install = { depends_on = [
+    "install-ribasim-python",
+    "install-ribasim-api",
+    "install-ribasim-testmodels",
+    "install-quartodoc",
+    "pre-commit-install",
+] }
+instantiate-julia-docs = "cd docs && julia --project -e \"using Pkg; Pkg.instantiate()\""
+build-julia-docs = { cmd = "cd docs && julia --project make.jl", depends_on = [
+    "instantiate-julia-docs",
+] }
+quartodoc-build = "cd docs && quartodoc build && rm objects.json"
+quarto-preview = { cmd = "quarto preview docs", depends_on = ["quartodoc-build"] }
+quarto-check = { cmd = "quarto check all", depends_on = ["quartodoc-build"] }
+quarto-render = "quarto render docs --to html --execute"
+mypy-ribasim-python = "mypy --ignore-missing-imports python/ribasim/ribasim"
+mypy-ribasim-testmodels = "mypy --ignore-missing-imports python/ribasim_testmodels/ribasim_testmodels"
+mypy-ribasim-api = "mypy --ignore-missing-imports python/ribasim_api/ribasim_api"
+pre-commit = "pre-commit run --all-files"
+lint = { depends_on = [
+    "pre-commit",
+    "mypy-ribasim-python",
+    "mypy-ribasim-testmodels",
+    "mypy-ribasim-api",
+] }
+test-ribasim-python = "pytest python/ribasim/tests"
+test-ribasim-python-cov = "pytest --cov=ribasim --cov-report=xml python/ribasim/tests"
+test-ribasim-api = "pytest python/ribasim_api/tests"
+generate-testmodels = "python utils/generate-testmodels.py"
+
+
+[dependencies]
+black = "*"
+black-jupyter = "*"
+build = "*"
+datamodel-code-generator = "*"
+geopandas = "*"
+jupyterlab = "*"
+matplotlib = "*"
+mypy = "*"
+pandas = "!=2.1.0"
+pandas-stubs = "*"
+pandera = "*"
+pip = "*"
+pre-commit = "*"
+pyarrow = "*"
+pydantic = "~=1.0"
+pyogrio = "*"
+pytest = "*"
+pytest-cov = "*"
+python = ">=3.9"
+quarto = "*"
+ruff = "*"
+shapely = ">=2.0"
+tomli = "*"
+tomli-w = "*"
+twine = "*"
+xarray = "*"
+xmipy = "*"
diff --git a/python/ribasim/tests/conftest.py b/python/ribasim/tests/conftest.py
index 877cbfa4a..c2e23b670 100644
--- a/python/ribasim/tests/conftest.py
+++ b/python/ribasim/tests/conftest.py
@@ -1,5 +1,3 @@
-from pathlib import Path
-
 import pytest
 import ribasim
 import ribasim_testmodels
@@ -24,18 +22,3 @@ def tabulated_rating_curve() -> ribasim.Model:
 @pytest.fixture()
 def backwater() -> ribasim.Model:
     return ribasim_testmodels.backwater_model()
-
-
-# write models to disk for Julia tests to use
-if __name__ == "__main__":
-    datadir = Path("data")
-
-    models = [
-        model_generator()
-        for model_generator in map(
-            ribasim_testmodels.__dict__.get, ribasim_testmodels.__all__
-        )
-    ]
-
-    for model in models:
-        model.write(datadir / model.modelname)
diff --git a/utils/generate-testmodels.py b/utils/generate-testmodels.py
new file mode 100644
index 000000000..4b5f7dd39
--- /dev/null
+++ b/utils/generate-testmodels.py
@@ -0,0 +1,16 @@
+from pathlib import Path
+
+import ribasim_testmodels
+
+if __name__ == "__main__":
+    datadir = Path("data")
+
+    models = [
+        model_generator()
+        for model_generator in map(
+            ribasim_testmodels.__dict__.get, ribasim_testmodels.__all__
+        )
+    ]
+
+    for model in models:
+        model.write(datadir / model.modelname)