mxlmodels 1.0.0__tar.gz

mxlmodels-1.0.0/.gitattributes

@@ -0,0 +1,9 @@
+# GitHub syntax highlighting
+pixi.lock linguist-language=YAML
+
+# proper line endings
+* text=auto eol=lf
+*.{cmd,[cC][mM][dD]} text eol=crlf
+*.{bat,[bB][aA][tT]} text eol=crlf
+# SCM syntax highlighting & preventing 3-way merges
+pixi.lock merge=binary linguist-language=YAML linguist-generated=true

mxlmodels-1.0.0/.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,7 @@
+---
+name: "\U0001F41B Bug report"
+about: "Create a report to help us improve"
+title: ''
+labels: bug
+assignees: ''
+---

mxlmodels-1.0.0/.github/ISSUE_TEMPLATE/discussion.md

@@ -0,0 +1,9 @@
+---
+name: "\U0001F5E8 Discussion"
+about: "Create a discussion"
+title: ''
+labels: bug
+assignees: ''
+---
+
+## Discussion

mxlmodels-1.0.0/.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,8 @@
+---
+name: "\U0001F680 Feature Request"
+about: "I have a suggestion (and may want to implement it \U0001F642)!"
+title: ''
+labels: 'enhancement'
+assignees: ''
+
+---

mxlmodels-1.0.0/.github/dependabot.yml

@@ -0,0 +1,17 @@
+version: 2
+
+updates:
+  - package-ecosystem: "uv"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+      day: "monday"
+      time: "05:00"
+    assignees:
+      - "marvinvanaalst"
+    commit-message:
+      prefix: "build(deps): "
+    groups:
+      dependencies:
+        patterns:
+          - "*"

mxlmodels-1.0.0/.github/workflows/docs.yml

@@ -0,0 +1,43 @@
+name: documentation
+
+on:
+  release:
+    types: [published]
+  workflow_dispatch: {}
+
+permissions:
+  contents: write
+
+jobs:
+  build-documentation:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0 # fetch all commits/branches
+
+      - name: Configure Git Credentials
+        run: |
+          git config user.name github-actions[bot]
+          git config user.email 41898282+github-actions[bot]@users.noreply.github.com
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v4
+
+      - name: Set up Python
+        run: uv python install 3.13
+
+      - name: Set Python version
+        run: uv venv --python 3.13
+
+      - run: echo "cache_id=$(date --utc '+%V')" >> $GITHUB_ENV
+      - uses: actions/cache@v4
+        with:
+          key: mkdocs-material-${{ env.cache_id }}
+          path: .cache
+          restore-keys: |
+            mkdocs-material-
+      - run: uv sync --all-extras --all-groups
+      - run: uv run python -c "import toml;print('VERSION={}'.format(toml.load(open('pyproject.toml'))['project']['version']))" >> $GITHUB_ENV
+      - run: uv run mike deploy --update-aliases --push ${{ env.VERSION }} latest
+      - run: uv run mike set-default --push latest

mxlmodels-1.0.0/.github/workflows/python-publish.yml

@@ -0,0 +1,55 @@
+name: Upload Python Package
+
+on:
+  release:
+    types: [published]
+  workflow_dispatch: {}
+
+permissions:
+  contents: read
+
+jobs:
+  release-build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v4
+
+      - name: Set up Python
+        run: uv python install 3.13
+
+      - name: Set Python version
+        run: uv venv --python 3.13
+
+      - name: Build release distribution
+        run: uv build
+
+      - name: Upload distributions
+        uses: actions/upload-artifact@v4
+        with:
+          name: release-dists
+          path: dist/
+
+  pypi-publish:
+    runs-on: ubuntu-latest
+    needs:
+      - release-build
+    permissions:
+      id-token: write
+
+    environment:
+      name: pypi
+
+    steps:
+      - name: Retrieve release distributions
+        uses: actions/download-artifact@v4
+        with:
+          name: release-dists
+          path: dist/
+
+      - name: Publish release distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          packages-dir: dist/

mxlmodels-1.0.0/.github/workflows/release-to-slack.yml

@@ -0,0 +1,77 @@
+name: Notify Slack on Release
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  notify:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Send release notification to Slack
+        env:
+          SLACK_WEBHOOK_URL: ${{ secrets.SLACK_WEBHOOK_URL }}
+          RELEASE_NAME: ${{ github.event.release.name }}
+          RELEASE_TAG: ${{ github.event.release.tag_name }}
+          RELEASE_BODY: ${{ github.event.release.body }}
+          RELEASE_URL: ${{ github.event.release.html_url }}
+          REPO: ${{ github.repository }}
+        run: |
+          payload=$(jq -n \
+            --arg text "*New Release Published* :tada:" \
+            --arg repo "$REPO" \
+            --arg name "$RELEASE_NAME" \
+            --arg tag "$RELEASE_TAG" \
+            --arg body "$RELEASE_BODY" \
+            --arg url "$RELEASE_URL" \
+            '{
+              text: $text,
+              blocks: [
+                {
+                  type: "section",
+                  text: {
+                    type: "mrkdwn",
+                    text: "*New Release Published* :tada:"
+                  }
+                },
+                {
+                  type: "section",
+                  fields: [
+                    { type: "mrkdwn", text: "*Repository:*\n\($repo)" },
+                    { type: "mrkdwn", text: "*Tag:*\n\($tag)" }
+                  ]
+                },
+                {
+                  type: "section",
+                  text: {
+                    type: "mrkdwn",
+                    text: "*Release:*\n\($name)"
+                  }
+                },
+                {
+                  type: "section",
+                  text: {
+                    type: "mrkdwn",
+                    text: "*Notes:*\n\($body)"
+                  }
+                },
+                {
+                  type: "actions",
+                  elements: [
+                    {
+                      type: "button",
+                      text: {
+                        type: "plain_text",
+                        text: "View Release"
+                      },
+                      url: $url
+                    }
+                  ]
+                }
+              ]
+            }')
+
+          curl -X POST -H 'Content-type: application/json' \
+            --data "$payload" \
+            "$SLACK_WEBHOOK_URL"

mxlmodels-1.0.0/.github/workflows/tests.yml

@@ -0,0 +1,30 @@
+name: ci
+
+on:
+  pull_request:
+    branches:
+      - main
+
+permissions:
+  contents: write
+
+jobs:
+  default-tests:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v4
+
+      - name: Set up Python
+        run: uv python install 3.13
+
+      - name: Set Python version
+        run: uv venv --python 3.13
+
+      - name: Set up environment
+        run: uv sync --all-extras --all-groups
+
+      - name: Run tests
+        run: uv run pytest -m "not extensive" --disable-warnings tests/

mxlmodels-1.0.0/.gitignore

@@ -0,0 +1,15 @@
+# Python-generated files
+__pycache__/
+*.py[oc]
+build/
+dist/
+wheels/
+*.egg-info
+
+# Virtual environments
+.venv
+
+# AI config files
+.github/copilot-instructions.md
+.claude
+CLAUDE.md

mxlmodels-1.0.0/.pre-commit-config.yaml

@@ -0,0 +1,10 @@
+repos:
+  # Lint & format
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.12.0
+    hooks:
+      - id: ruff
+        types_or: [ python, pyi, jupyter ]
+        args: [ --fix ]
+      - id: ruff-format
+        types_or: [ python, pyi, jupyter ]

mxlmodels-1.0.0/.python-version

@@ -0,0 +1 @@
+3.13

mxlmodels-1.0.0/.vscode/settings.json

@@ -0,0 +1,63 @@
+{
+    "[python]": {
+        "editor.rulers": [
+            88
+        ]
+    },
+    "[toml]": {
+        "editor.defaultFormatter": "tamasfe.even-better-toml"
+    },
+    "evenBetterToml.formatter.alignComments": true,
+    "evenBetterToml.formatter.alignEntries": true,
+    "evenBetterToml.formatter.allowedBlankLines": 2,
+    "evenBetterToml.formatter.columnWidth": 79,
+    "evenBetterToml.formatter.crlf": false,
+    "evenBetterToml.formatter.indentTables": false,
+    "evenBetterToml.formatter.indentEntries": false,
+    "evenBetterToml.formatter.reorderInlineTables": true,
+    "evenBetterToml.formatter.trailingNewline": true,
+    "evenBetterToml.formatter.arrayAutoCollapse": false,
+    "evenBetterToml.formatter.arrayAutoExpand": true,
+    "evenBetterToml.formatter.arrayTrailingComma": true,
+    "evenBetterToml.formatter.reorderKeys": true,
+    "files.exclude": {
+        "**/__pycache__": true,
+        "**/_minted-main": true,
+        "**/*.aux": true,
+        "**/*.bbl": true,
+        "**/*.bcf": true,
+        "**/*.blg": true,
+        "**/*.dvi": true,
+        "**/*.egg-info": true,
+        "**/*.fdb_latexmk": true,
+        "**/*.fls": true,
+        "**/*.glsdefs": true,
+        "**/*.lof": true,
+        "**/*.log": true,
+        "**/*.lot": true,
+        "**/*.mypy_cache": true,
+        "**/*.out": true,
+        "**/*.pixi": true,
+        "**/*.pytest_cache": true,
+        "**/*.ruff_cache": true,
+        "**/*.run.xml": true,
+        "**/*.synctex.gz": true,
+        "**/*.toc": true,
+        // envs
+        "**/*.venv": true,
+        "**/*dist": true,
+        "**/*synctex(busy)": true
+    },
+    "notebook.output.textLineLimit": 50,
+    "python.defaultInterpreterPath": "${workspaceFolder}/.venv/bin/python",
+    "python.terminal.activateEnvironment": false,
+    "ruff.interpreter": [
+        "${workspaceFolder}/.venv/bin/python"
+    ],
+    "terminal.integrated.env.linux": {
+        "UV_PROJECT_ENVIRONMENT": "${workspaceFolder}/.venv"
+    },
+    "terminal.integrated.env.osx": {
+        "UV_PROJECT_ENVIRONMENT": "${workspaceFolder}/.venv"
+    }
+}

mxlmodels-1.0.0/CONTRIBUTING.md

@@ -0,0 +1,17 @@
+All contributions, bug reports, bug fixes, documentation improvements, enhancements and ideas are welcome.
+In order to contribute:
+
+1. [Fork the project](https://github.com/Computational-Biology-Aachen/mxlpy)
+2. Improve or extend the project
+3. Create unit tests for your added / improved features in the respective [test directory](https://github.com/Computational-Biology-Aachen/mxlpy/tree/main/tests). The old test suite mostly uses the standard [unittest](https://docs.python.org/3/library/unittest.html) library, however new tests are written with [pytest](https://docs.pytest.org/en/latest/). If you are not familiar with pytest you can still use the unittest interface, as pytest supports both test styles.
+4. Create a [pull request](https://docs.github.com/de/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/creating-a-pull-request)
+
+Your work will then be reviewed as soon as possible (suggestions about some changes, improvements or alternatives may be given).
+
+## Coding standards
+
+In order for your improvements to be accepted, please make sure that you added tests in the respective subfolder of the [test directory](https://github.com/Computational-Biology-Aachen/mxlpy/tree/main/tests).
+We also ask you to write proper documentation in the [NumPy / SciPy style](https://docs.scipy.org/doc/numpy/docs/howto_document.html) and
+that you name your functions according to [pep8](http://pep8.org/). Further, please use the supplied [pre-commit](https://pre-commit.com/) hook, to make sure that your code passes our guidelines.
+
+Thank you for participating!

mxlmodels-1.0.0/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) [2025] [Marvin van Aalst, Anna Matuszyńska]
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

mxlmodels-1.0.0/PKG-INFO

@@ -0,0 +1,68 @@
+Metadata-Version: 2.4
+Name: mxlmodels
+Version: 1.0.0
+Summary: MxlModels is a Python package of reference mechanistic models.
+Author-email: Marvin van Aalst <marvin.vanaalst@gmail.com>
+Maintainer-email: Marvin van Aalst <marvin.vanaalst@gmail.com>
+License-Expression: MIT
+License-File: LICENSE
+Keywords: metabolic,modelling,ode
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Environment :: Console
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: MacOS
+Classifier: Operating System :: Microsoft :: Windows
+Classifier: Operating System :: OS Independent
+Classifier: Operating System :: POSIX
+Classifier: Operating System :: Unix
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Topic :: Scientific/Engineering
+Classifier: Topic :: Software Development
+Requires-Python: >=3.13
+Requires-Dist: mxlpy>=0.38.0
+Description-Content-Type: text/markdown
+
+<p align="center">
+    <img src="https://raw.githubusercontent.com/Computational-Biology-Aachen/mxl-models/refs/heads/main/docs/assets/logo.png" width="400px" alt='mxlmodels-logo'>
+</p>
+
+# MxlModels
+
+`MxlModels` is a Python package of reference mechanistic models.
+It contains the same models as in the [MxlBricks](https://github.com/Computational-Biology-Aachen/mxl-bricks) repo, but written as single, flat files to make inspection easier.
+
+Usually, these here will be created by codegen from [MxlBricks](https://github.com/Computational-Biology-Aachen/mxl-bricks).
+
+## Installation
+
+You can install mxlpy using pip: `pip install mxlmodels`.
+
+Done. Simple as that.
+
+## Models
+
+| Name                 | Description                                                                 |
+| -------------------- | --------------------------------------------------------------------------- |
+| Yokota 1985          | Photorespiration                                                            |
+| Poolman 2000         | CBB cycle, based on Pettersson & Ryde-Pettersson 1988                       |
+| Ebenhöh 2011         | PSII & two-state quencher & ATP synthase                                    |
+| Ebenhöh 2014         | PETC & state transitions & ATP synthase from Ebenhoeh 2011                  |
+| Matuszyńska 2016 NPQ | 2011 + PSII & four-state quencher                                           |
+| Matuszyńska 2016 PhD | ?                                                                           |
+| Matuszyńska 2019     | Merges PETC (Ebenhöh 2014), NPQ (Matuszynska 2016) and CBB (Poolman 2000)   |
+| Saadat 2021          | 2019 + Mehler (Valero ?) & Thioredoxin & extendend PSI states & consumption |
+| Ebeling 2026         | unpublishd                                                                  |
+
+
+## Tool family 🏠
+
+`MxlModels` is part of a larger family of tools that are designed with a similar set of abstractions. Check them out!
+
+- [MxlPy](https://github.com/Computational-Biology-Aachen/MxlPy) is a Python package for mechanistic learning (Mxl)
+- [MxlBricks](https://github.com/Computational-Biology-Aachen/mxl-bricks) is a Python package to build mechanistic models composed of pre-defined reactions (bricks)
+- [MxlWeb](https://github.com/Computational-Biology-Aachen/mxl-web) brings simulation of mechanistic models to the browser!
+- [pysbml](https://github.com/Computational-Biology-Aachen/pysbml) simplifies SBML models for import/export with MxlPy
+- [Parameteriser](https://gitlab.com/marvin.vanaalst/parameteriser) looks up kinetic parameters from BRENDA and other databases

mxlmodels-1.0.0/README.md

@@ -0,0 +1,41 @@
+<p align="center">
+    <img src="https://raw.githubusercontent.com/Computational-Biology-Aachen/mxl-models/refs/heads/main/docs/assets/logo.png" width="400px" alt='mxlmodels-logo'>
+</p>
+
+# MxlModels
+
+`MxlModels` is a Python package of reference mechanistic models.
+It contains the same models as in the [MxlBricks](https://github.com/Computational-Biology-Aachen/mxl-bricks) repo, but written as single, flat files to make inspection easier.
+
+Usually, these here will be created by codegen from [MxlBricks](https://github.com/Computational-Biology-Aachen/mxl-bricks).
+
+## Installation
+
+You can install mxlpy using pip: `pip install mxlmodels`.
+
+Done. Simple as that.
+
+## Models
+
+| Name                 | Description                                                                 |
+| -------------------- | --------------------------------------------------------------------------- |
+| Yokota 1985          | Photorespiration                                                            |
+| Poolman 2000         | CBB cycle, based on Pettersson & Ryde-Pettersson 1988                       |
+| Ebenhöh 2011         | PSII & two-state quencher & ATP synthase                                    |
+| Ebenhöh 2014         | PETC & state transitions & ATP synthase from Ebenhoeh 2011                  |
+| Matuszyńska 2016 NPQ | 2011 + PSII & four-state quencher                                           |
+| Matuszyńska 2016 PhD | ?                                                                           |
+| Matuszyńska 2019     | Merges PETC (Ebenhöh 2014), NPQ (Matuszynska 2016) and CBB (Poolman 2000)   |
+| Saadat 2021          | 2019 + Mehler (Valero ?) & Thioredoxin & extendend PSI states & consumption |
+| Ebeling 2026         | unpublishd                                                                  |
+
+
+## Tool family 🏠
+
+`MxlModels` is part of a larger family of tools that are designed with a similar set of abstractions. Check them out!
+
+- [MxlPy](https://github.com/Computational-Biology-Aachen/MxlPy) is a Python package for mechanistic learning (Mxl)
+- [MxlBricks](https://github.com/Computational-Biology-Aachen/mxl-bricks) is a Python package to build mechanistic models composed of pre-defined reactions (bricks)
+- [MxlWeb](https://github.com/Computational-Biology-Aachen/mxl-web) brings simulation of mechanistic models to the browser!
+- [pysbml](https://github.com/Computational-Biology-Aachen/pysbml) simplifies SBML models for import/export with MxlPy
+- [Parameteriser](https://gitlab.com/marvin.vanaalst/parameteriser) looks up kinetic parameters from BRENDA and other databases

mxlmodels-1.0.0/SECURITY.md

@@ -0,0 +1,21 @@
+# Security Policy
+
+## Supported Versions
+
+Use this section to tell people about which versions of your project are
+currently being supported with security updates.
+
+| Version | Supported          |
+| ------- | ------------------ |
+| 5.1.x   | :white_check_mark: |
+| 5.0.x   | :x:                |
+| 4.0.x   | :white_check_mark: |
+| < 4.0   | :x:                |
+
+## Reporting a Vulnerability
+
+Use this section to tell people how to report a vulnerability.
+
+Tell them where to go, how often they can expect to get an update on a
+reported vulnerability, what to expect if the vulnerability is accepted or
+declined, etc.

mxlmodels-1.0.0/pyproject.toml

@@ -0,0 +1,140 @@
+[build-system]
+build-backend = "hatchling.build"
+requires    = ["hatchling"]
+
+[dependency-groups]
+dev = [
+  "coverage>=7.6.4",
+  "jupyter>=1.1.1",
+  "mike>=2.1.3",
+  "mkdocs-jupyter>=0.25.1",
+  "mkdocs-material>=9.5.42",
+  "mkdocs>=1.6.1,<2.0.0",
+  "pre-commit>=4.0.1",
+  "pyright>=1.1.403",
+  "pytest-cov>=5.0.0",
+  "pytest>=8.3.3",
+  "ruff>=0.15.11",
+]
+
+[project]
+authors = [{ email = "marvin.vanaalst@gmail.com", name = "Marvin van Aalst" }]
+classifiers = [
+  "Development Status :: 5 - Production/Stable",
+  "Environment :: Console",
+  "Intended Audience :: Developers",
+  "Intended Audience :: Science/Research",
+  "License :: OSI Approved :: MIT License",
+  "Operating System :: MacOS",
+  "Operating System :: Microsoft :: Windows",
+  "Operating System :: OS Independent",
+  "Operating System :: POSIX",
+  "Operating System :: Unix",
+  "Programming Language :: Python :: 3",
+  "Programming Language :: Python :: 3.11",
+  "Topic :: Scientific/Engineering",
+  "Topic :: Software Development",
+]
+dependencies = ["mxlpy>=0.38.0"]
+description = "MxlModels is a Python package of reference mechanistic models."
+keywords = ["metabolic", "modelling", "ode"]
+license = "MIT"
+maintainers = [
+  { email = "marvin.vanaalst@gmail.com", name = "Marvin van Aalst" },
+]
+name = "mxlmodels"
+readme = "README.md"
+requires-python = ">=3.13"
+version = "1.0.0"
+
+[tool.hatchling]
+from  = "src"
+include = ["mxlmodels"]
+
+[tool.pyright]
+deprecateTypingAliases = true
+exclude = [
+  "**/.*",
+  "**/__pycache__",
+  "**/node_modules",
+  ".venv",
+  "tests/sbml/assets",
+  "tmp",
+]
+include = ["docs", "src", "tests", 'publication-figures']
+pythonVersion = "3.13"
+reportMissingModuleSource = "none"
+strict = []
+
+[tool.ruff]
+indent-width = 4
+line-length  = 88
+
+[tool.ruff.lint]
+fixable = ["ALL"]
+ignore = [
+  "ANN401",  # any
+  "C901",  # too complex
+  "COM812",  # missing trailing comma  # "D", # all of documentation
+  "D105",  # magic methods
+  "D203",  # blank line before docstring
+  "D213",  # multi-line summary first line
+  "D401",  # first line should be in imperative mood
+  "E501",  # line-too-long
+  "ERA001",  # commented-out code
+  "FIX001",  # line contains FIXME
+  "ISC001",  # single line implicit string concat
+  "N806",  # non-lowercase variable
+  "N818",  # Exception should end in "Error"
+  "PD010",   # pivot table
+  "PGH003",  # specific rule type ignore
+  "PLR0911", # too many statements
+  "PLR0912", # too many branches
+  "PLR0913", # max num of arguments
+  "PLR0915", # too many lines
+  "PT011",   # pytest.raises is too broad
+  "RUF022",  # unsorted all
+  "S110",  # try-except-pass
+  "S301",  # pickle usage
+  "TC006",   # cast("type")
+  "TD001",   # invalid todo tag
+  "TD002",   # missing todo author
+  "TD003",   # missing todo link
+  "TD004",   # missing todo version
+  "TD005",   # missing todo date
+  "TRY003",  # raise vanilla args
+]
+select = ["ALL"]
+
+[tool.ruff.lint.per-file-ignores]
+"*.ipynb" = [
+  "D",  # all of documentation
+  "T201", # print statements
+]
+"tests/*" = [
+  "D",     # all of documentation
+  "PD901",   # "df" name
+  "PLR2004", # magic comparisons
+  "S101",  # assert
+  "SLF",
+]
+"tmp/*" = [
+  "D",  # all of documentation
+  "I001", # unsorted imports
+  "N",  # all of naming
+  "S101", # assert
+]
+
+[tool.ruff.lint.pydocstyle]
+convention = "numpy"
+
+[tool.tomlsort]
+spaces_before_inline_comment = 2
+spaces_indent_inline_array   = 2
+trailing_comma_inline_array  = true
+
+[tool.uv]
+package = true
+
+[tool.uv.sources]
+mxlmodels = { workspace = true }