dynestyx 0.0.3__tar.gz

dynestyx-0.0.3/.github/workflows/build_docs.yml

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+name: Build docs
+
+on:
+  push:
+    branches: [main]
+    tags: ["v*"]
+  workflow_dispatch:
+    inputs:
+      target_ref:
+        description: Git ref to build from (e.g. main, v0.0.1, feature/my-docs)
+        required: true
+        default: main
+      version:
+        description: Mike version id to publish (e.g. 0.0.1, dev, manual-preview-build)
+        required: true
+        default: manual-preview-build
+      alias:
+        description: Mike alias to update (e.g. stable, latest, manual-preview)
+        required: true
+        default: manual-preview
+      title:
+        description: Human-readable title in version switcher
+        required: true
+        default: manual preview
+      set_default:
+        description: Also set this alias as the default site root
+        required: true
+        default: "false"
+
+permissions:
+  contents: write
+
+concurrency:
+  group: ${{ github.event_name == 'workflow_dispatch' && format('docs-manual-{0}', inputs.version) || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+          ref: ${{ github.event_name == 'workflow_dispatch' && inputs.target_ref || github.ref }}
+
+      - name: Setup Python
+        uses: actions/setup-python@v5
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+        with:
+          version: "0.6.3"
+          enable-cache: true
+
+      - name: Install dependencies
+        run: uv sync --all-extras --dev
+
+      - name: Configure Git for mike
+        run: |
+          git config user.name "github-actions[bot]"
+          git config user.email "41898282+github-actions[bot]@users.noreply.github.com"
+
+      - name: Build latest docs
+        if: github.ref == 'refs/heads/main' && github.event_name == 'push'
+        run: |
+          uv run mike deploy --push --title "latest" dev latest
+
+      - name: Build stable docs
+        if: startsWith(github.ref, 'refs/tags/v') && github.event_name == 'push'
+        env:
+          TAG: ${{ github.ref_name }}
+        run: |
+          VERSION="${TAG#v}"
+          uv run mike deploy --push --update-aliases --title "$VERSION" "$VERSION" stable
+          uv run mike set-default --push stable
+
+      - name: Build manual docs
+        if: github.event_name == 'workflow_dispatch'
+        run: |
+          uv run mike deploy --push \
+            --title "${{ inputs.title }}" \
+            "${{ inputs.version }}" \
+            "${{ inputs.alias }}"
+          if [ "${{ inputs.set_default }}" = "true" ]; then
+            uv run mike set-default --push "${{ inputs.alias }}"
+          fi

dynestyx-0.0.3/.github/workflows/lint.yml

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+name: Lint
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches:
+      - main
+      - "staging-*"
+      - "*"
+  workflow_dispatch:
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version-file: "pyproject.toml"
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+        with:
+          version: "0.6.3"
+          enable-cache: true
+
+      - name: Install dependencies
+        run: |
+          uv sync --all-extras --dev
+
+      - name: Lint
+        run: uv run ./scripts/lint.sh
+
+      - name: Build docs
+        run: |
+          source .venv/bin/activate && mkdocs build

dynestyx-0.0.3/.github/workflows/python-publish.yml

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+# This workflow will upload a Python Package using Twine when a release is created
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python#publishing-to-package-registries
+
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+name: Upload Python Package
+
+on:
+  release:
+    types: [published]
+
+permissions:
+  contents: read
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    environment: pypi
+    permissions:
+      id-token: write  # IMPORTANT: mandatory for trusted publishing
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version-file: "pyproject.toml"
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install build
+    - name: Build package
+      run: python -m build
+    - name: Publish package
+      uses: pypa/gh-action-pypi-publish@release/v1

dynestyx-0.0.3/.github/workflows/test.yml

@@ -0,0 +1,37 @@
+name: Test
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches:
+      - main
+      - 'staging-*'
+      - '*'
+  workflow_dispatch:
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version-file: "pyproject.toml"
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+        with:
+          version: "0.6.3"
+          enable-cache: true
+
+      - name: Install Python dependencies
+        run: |
+          uv sync --all-extras --dev
+
+      - name: Run tests
+        env:
+          MKL_NUM_THREADS: 1
+        run: uv run ./scripts/test.sh

dynestyx-0.0.3/.gitignore

@@ -0,0 +1,184 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+__pycache__/
+docs/_build/
+build/
+dist/
+
+*egg-info
+*.ipynb_checkpoints
+
+# ignore figures unless manually added
+*.png
+*.jpg
+*.pdf
+*-dot
+*.DS_Store
+.vscode/
+.venv
+
+# Test output directories
+.output/
+
+*.ttf
+
+uv.lock

dynestyx-0.0.3/.python-version

@@ -0,0 +1 @@
+3.12

dynestyx-0.0.3/CONTRIBUTING.md

@@ -0,0 +1,123 @@
+# Contributing to dynestyx
+
+Thanks for contributing. This guide explains the two main ways to contribute: (a) open an issue describing a bug/idea, and/or (b) open a PR with a proposed fix or implementation. We strongly encourage the combined path (A+B): open an issue, then address it yourself and submit a PR.
+
+## 0) Pick a contribution path
+
+Preferred path: **A + B** (open an issue, then open a PR that addresses it).
+
+### Option A: Open an issue
+
+Use this when you want feedback before coding, or to report a bug/request.
+
+1. Go to the [dynestyx Issues page](https://github.com/BasisResearch/dynestyx/issues).
+2. Click **New issue**.
+3. Use a clear title.
+4. Include:
+   - expected behavior
+   - observed behavior
+   - minimal reproduction (if bug)
+   - environment details (OS, Python, key package versions)
+5. Submit the issue.
+
+### Option B: Open a Pull Request
+
+Use this when you already have a concrete proposed change. Follow the steps below.
+
+## 1) Setup
+
+Fork `dynestyx` to your GitHub account first:
+
+1. Go to [github.com/BasisResearch/dynestyx](https://github.com/BasisResearch/dynestyx).
+2. Click **Fork** (top-right).
+3. Choose your GitHub account as the destination.
+
+Then in your terminal, clone your fork and add the original repo as `upstream`:
+
+```bash
+git clone https://github.com/<your-username>/dynestyx.git
+cd dynestyx
+git remote add upstream https://github.com/BasisResearch/dynestyx.git
+git remote -v
+uv venv
+source .venv/bin/activate
+uv sync --dev --all-extras
+```
+
+You should see:
+- `origin` -> `https://github.com/<your-username>/dynestyx.git`
+- `upstream` -> `https://github.com/BasisResearch/dynestyx.git`
+
+## 2) Create a branch
+
+```bash
+git checkout main
+git pull upstream main
+git checkout -b <type>/<short-description>
+```
+
+Examples: `feature/add-ode-example`, `fix/filter-shape-bug`, `docs/update-quickstart`.
+
+## 3) Before opening a PR, run project scripts
+
+From repo root:
+
+```bash
+uv run scripts/clean.sh
+uv run scripts/lint.sh
+uv run scripts/test.sh
+```
+
+If you changed a lot or touched core inference code, also run:
+
+```bash
+uv run scripts/test_full.sh
+```
+
+`scripts/test_full.sh` writes run artifacts and logs under `.output`. To inspect results:
+
+```bash
+ls .output
+```
+
+Open relevant files in `.output` to review test summaries/logs for failures.
+
+If you edited docs, also build docs locally:
+
+```bash
+uv run mkdocs build
+```
+
+To preview docs locally while editing:
+
+```bash
+uv run mkdocs serve
+```
+
+Then open `http://127.0.0.1:8000` in your browser.
+
+Published docs on GitHub Pages are **versioned with [mike](https://github.com/jimporter/mike)** (`latest` = `main`, `stable` = newest `v*` tag). Maintainers deploy via CI; see [docs/versioning.md](docs/versioning.md). When you change tutorials (notebooks), remember readers on **stable** may still use an older install—add an optional banner (template in that page). For versioned local previews (`stable` vs `latest`) and manual backfills from historical tags, use the commands in [docs/versioning.md](docs/versioning.md).
+
+## 4) Commit and push
+
+```bash
+git add .
+git commit -m "Short imperative message"
+git push -u origin <type>/<short-description>
+```
+
+## 5) Open the Pull Request
+
+1. Go to [github.com/BasisResearch/dynestyx](https://github.com/BasisResearch/dynestyx).
+2. If prompted with your recently pushed branch, click **Compare & pull request**.
+   - If not prompted, go to the **Pull requests** tab and click **New pull request**.
+3. Set **base** to `BasisResearch/dynestyx:main`.
+4. Set **compare** to your branch (`<type>/<short-description>`).
+5. Add title + description (template below), then click **Create pull request**.
+
+Use this PR description format:
+
+- **Summary**: what changed and why
+- **Notes**: any caveats, follow-ups, or breaking behavior
+
+Keep PRs focused. If your change is user-facing, include doc updates in the same PR.