pydreg 0.1.0__tar.gz

pydreg-0.1.0/.gitattributes

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+# Auto detect text files and perform LF normalization
+* text=auto

pydreg-0.1.0/.github/workflows/ci.yml

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+name: CI
+
+on:
+  pull_request:
+  push:
+    branches:
+      - main
+  workflow_dispatch:
+
+concurrency:
+  group: ci-${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  test:
+    name: Python ${{ matrix.python-version }}
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version:
+          - "3.11"
+          - "3.12"
+
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
+        with:
+          enable-cache: true
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: uv sync --locked --group dev
+
+      - name: Run tests
+        run: uv run pytest tests/ -q
+
+  build:
+    name: Build distribution
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
+        with:
+          enable-cache: true
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Build package
+        run: uv build
+
+      - name: Upload distribution artifacts
+        uses: actions/upload-artifact@v4
+        with:
+          name: dist
+          path: dist/*

pydreg-0.1.0/.github/workflows/publish.yml

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+name: Publish
+
+on:
+  release:
+    types:
+      - published
+  workflow_dispatch:
+
+permissions:
+  contents: read
+  id-token: write
+
+jobs:
+  publish:
+    name: Publish to PyPI
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/pydreg
+
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
+        with:
+          enable-cache: true
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Build package
+        run: uv build
+
+      - name: Publish package
+        uses: pypa/gh-action-pypi-publish@release/v1

pydreg-0.1.0/.gitignore

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+**/.DS_Store
+**/.vscode
+_reference/
+_models/
+
+# 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
+
+# UV
+#   Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#uv.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/latest/usage/project/#working-with-version-control
+.pdm.toml
+.pdm-python
+.pdm-build/
+
+# 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/
+
+# Ruff stuff:
+.ruff_cache/
+
+# PyPI configuration file
+.pypirc
+
+# Cursor  
+#  Cursor is an AI-powered code editor.`.cursorignore` specifies files/directories to 
+#  exclude from AI features like autocomplete and code analysis. Recommended for sensitive data
+#  refer to https://docs.cursor.com/context/ignore-files
+.cursorignore
+.cursorindexingignore

pydreg-0.1.0/CONTRIBUTING.md

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+# Contributing to pydreg
+
+## Setup
+
+```bash
+git clone https://github.com/adamyhe/pydreg.git
+cd pydreg
+uv sync --extra gpu --group dev
+uv run pytest tests/ -q
+```
+
+`uv sync --extra gpu` is safe on any platform: the `gpu` extra (cuML) only
+resolves on Linux with a matching architecture, and is a no-op elsewhere
+rather than a failure.
+
+## Tests
+
+```bash
+uv run pytest tests/ -q
+```
+
+The suite (40 tests as of this writing) covers each module in isolation
+plus a full synthetic end-to-end pipeline run. Model-dependent tests are
+skipped (not failed) if the Hugging Face repo hosting the pretrained
+weights is unreachable.
+
+## Before making changes
+
+- **Algorithmic/structural changes**: read `docs/PLANNING.md` first. It's
+  the comprehensive design record — module boundaries, exact algorithm
+  specs, and, importantly, a full list of upstream R quirks that are
+  reproduced deliberately rather than "fixed," because the pretrained
+  model's expected output depends on them. Breaking one of those
+  intentionally-kept quirks is a correctness regression, not a cleanup.
+- **Performance changes**: read `docs/PERF_LOG.md` first, and append a new
+  dated entry for any change you make. Its ground rule applies to any PR
+  touching performance: a change must not alter the pipeline's output
+  (same scores, same peaks), verified against the test suite and, ideally,
+  a full CLI diff — "looks right" isn't sufficient. `docs/OPTIMIZATION.md`
+  has the plain-language summary of the design choices already in place if
+  you want the short version first.
+- For a plain-language overview of the algorithm itself (not the
+  implementation), see `docs/METHODS.md`.
+
+## Pull requests
+
+Keep changes scoped and include tests for new behavior. If a change
+affects scores or peak calls in any way, say so explicitly and explain why
+(e.g. a genuine bug fix vs. an intentional behavior change) — silent output
+changes are the one thing this project can't tolerate, given how much of
+it exists specifically to match a pretrained model's expected input/output
+distribution.