phenoradar 0.1.0__tar.gz

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

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+name: ci
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+
+concurrency:
+  group: ci-${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+permissions:
+  contents: read
+
+env:
+  OPENBLAS_NUM_THREADS: "1"
+  OMP_NUM_THREADS: "1"
+  MKL_NUM_THREADS: "1"
+  NUMEXPR_NUM_THREADS: "1"
+  POLARS_MAX_THREADS: "1"
+
+jobs:
+  test:
+    name: test / py${{ matrix.python-version }}
+    runs-on: ubuntu-latest
+    timeout-minutes: 30
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.12", "3.13", "3.14"]
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - uses: astral-sh/setup-uv@v5
+      - name: Cache uv
+        uses: actions/cache@v4
+        with:
+          path: ~/.cache/uv
+          key: uv-${{ runner.os }}-py${{ matrix.python-version }}-${{ hashFiles('uv.lock') }}
+          restore-keys: |
+            uv-${{ runner.os }}-py${{ matrix.python-version }}-
+            uv-${{ runner.os }}-
+      - name: Install dependencies
+        run: uv sync --extra dev --frozen
+      - name: Ruff
+        run: uv run ruff check .
+      - name: Mypy
+        run: uv run mypy src
+      - name: Pytest
+        run: uv run pytest -q

phenoradar-0.1.0/.github/workflows/release-please.yml

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+name: release-please
+
+on:
+  push:
+    branches: [main]
+
+concurrency:
+  group: release-please-${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+permissions:
+  contents: write
+  pull-requests: write
+
+jobs:
+  release-please:
+    runs-on: ubuntu-latest
+    timeout-minutes: 15
+    steps:
+      - name: Run release-please
+        uses: googleapis/release-please-action@v4
+        with:
+          token: ${{ secrets.RELEASE_PLEASE_TOKEN || github.token }}
+          release-type: python
+          package-name: phenoradar
+          include-component-in-tag: false
+          include-v-in-tag: true

phenoradar-0.1.0/.github/workflows/release.yml

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+name: release
+
+on:
+  push:
+    tags:
+      - "v*"
+
+concurrency:
+  group: release-${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+permissions:
+  contents: read
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    timeout-minutes: 30
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+      - uses: astral-sh/setup-uv@v5
+      - name: Cache uv
+        uses: actions/cache@v4
+        with:
+          path: ~/.cache/uv
+          key: uv-${{ runner.os }}-release-${{ hashFiles('uv.lock') }}
+          restore-keys: |
+            uv-${{ runner.os }}-release-
+            uv-${{ runner.os }}-
+      - name: Validate tag version matches pyproject
+        run: |
+          python - <<'PY'
+          import os
+          import sys
+          import tomllib
+          from pathlib import Path
+
+          pyproject = tomllib.loads(Path("pyproject.toml").read_text(encoding="utf-8"))
+          version = pyproject["project"]["version"]
+          tag = os.environ["GITHUB_REF_NAME"]
+          expected_tag = f"v{version}"
+          if tag != expected_tag:
+              print(
+                  f"Tag/version mismatch: got {tag}, expected {expected_tag} from pyproject.toml",
+                  file=sys.stderr,
+              )
+              sys.exit(1)
+          print(f"Validated release tag: {tag}")
+          PY
+      - name: Build distributions
+        run: uv run --with build python -m build
+      - name: Check distributions
+        run: uv run --with twine twine check dist/*
+      - name: Upload dist artifacts
+        uses: actions/upload-artifact@v4
+        with:
+          name: dist
+          path: dist/*
+          if-no-files-found: error
+
+  publish-pypi:
+    needs: build
+    runs-on: ubuntu-latest
+    timeout-minutes: 15
+    permissions:
+      id-token: write
+    steps:
+      - name: Download dist artifacts
+        uses: actions/download-artifact@v4
+        with:
+          name: dist
+          path: dist
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          packages-dir: dist
+
+  github-release:
+    needs: [build, publish-pypi]
+    runs-on: ubuntu-latest
+    timeout-minutes: 15
+    permissions:
+      contents: write
+    steps:
+      - name: Download dist artifacts
+        uses: actions/download-artifact@v4
+        with:
+          name: dist
+          path: dist
+      - name: Upload dist assets to GitHub release
+        uses: softprops/action-gh-release@v2
+        with:
+          files: dist/*
+          fail_on_unmatched_files: true

phenoradar-0.1.0/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[codz]
+*$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
+#poetry.toml
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#   pdm recommends including project-wide configuration in pdm.toml, but excluding .pdm-python.
+#   https://pdm-project.org/en/latest/usage/project/#working-with-version-control
+#pdm.lock
+#pdm.toml
+.pdm-python
+.pdm-build/
+
+# pixi
+#   Similar to Pipfile.lock, it is generally recommended to include pixi.lock in version control.
+#pixi.lock
+#   Pixi creates a virtual environment in the .pixi directory, just like venv module creates one
+#   in the .venv directory. It is recommended not to include this directory in version control.
+.pixi
+
+# 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
+.envrc
+.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/
+
+# Abstra
+# Abstra is an AI-powered process automation framework.
+# Ignore directories containing user credentials, local state, and settings.
+# Learn more at https://abstra.io/docs
+.abstra/
+
+# Visual Studio Code
+#  Visual Studio Code specific template is maintained in a separate VisualStudioCode.gitignore 
+#  that can be found at https://github.com/github/gitignore/blob/main/Global/VisualStudioCode.gitignore
+#  and can be added to the global gitignore or merged into this file. However, if you prefer, 
+#  you could uncomment the following to ignore the entire vscode folder
+# .vscode/
+
+# 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
+
+# Marimo
+marimo/_static/
+marimo/_lsp/
+__marimo__/
+
+# Local datasets
+c4_dataset/
+
+# PhenoRadar generated artifacts
+runs/
+reports/

phenoradar-0.1.0/.pre-commit-config.yaml

@@ -0,0 +1,13 @@
+repos:
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.6.9
+    hooks:
+      - id: ruff-check
+      - id: ruff-format
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.11.2
+    hooks:
+      - id: mypy
+        additional_dependencies:
+          - pydantic>=2.9.2,<3.0.0
+          - typer>=0.12.5,<1.0.0

phenoradar-0.1.0/CHANGELOG.md

@@ -0,0 +1,13 @@
+# Changelog
+
+## 0.1.0 (2026-02-28)
+
+
+### Features
+
+* PhenoRadar baseline ([0081f23](https://github.com/mkrg01/phenoradar/commit/0081f2384339810ec449288c5532dad5ad104338))
+
+
+### Documentation
+
+* update Python badge for supported versions ([c9f9417](https://github.com/mkrg01/phenoradar/commit/c9f9417516f4b840d029460828f000ea6977ccf8))

phenoradar-0.1.0/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2025 Tomoya Nishiguchi
+
+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.

phenoradar-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: phenoradar
+Version: 0.1.0
+Summary: Macroevolutionary phenotype predictor
+Author-email: Tomoya Nishiguchi <t.nishiguchi5@gmail.com>
+License-File: LICENSE
+Requires-Python: >=3.12
+Requires-Dist: joblib<2.0.0,>=1.4.2
+Requires-Dist: matplotlib<4.0.0,>=3.9.2
+Requires-Dist: optuna<5.0.0,>=4.0.0
+Requires-Dist: polars<2.0.0,>=1.9.0
+Requires-Dist: pydantic<3.0.0,>=2.9.2
+Requires-Dist: pyyaml<7.0.0,>=6.0.2
+Requires-Dist: scikit-learn<2.0.0,>=1.5.2
+Requires-Dist: typer<1.0.0,>=0.12.5
+Provides-Extra: dev
+Requires-Dist: mypy<2.0.0,>=1.11.2; extra == 'dev'
+Requires-Dist: pre-commit<4.0.0,>=3.8.0; extra == 'dev'
+Requires-Dist: pytest-cov<6.0.0,>=5.0.0; extra == 'dev'
+Requires-Dist: pytest<9.0.0,>=8.3.3; extra == 'dev'
+Requires-Dist: ruff<1.0.0,>=0.6.9; extra == 'dev'
+Requires-Dist: types-pyyaml<7.0.0,>=6.0.12.20250915; extra == 'dev'
+Description-Content-Type: text/markdown
+
+# phenoradar
+
+[![CI](https://github.com/mkrg01/phenoradar/actions/workflows/ci.yml/badge.svg?branch=main)](https://github.com/mkrg01/phenoradar/actions/workflows/ci.yml) [![PyPI](https://img.shields.io/pypi/v/phenoradar.svg)](https://pypi.org/project/phenoradar/) [![Python](https://img.shields.io/badge/python-3.12%20%7C%203.13%20%7C%203.14-blue.svg)](https://www.python.org/downloads/) [![License](https://img.shields.io/github/license/mkrg01/phenoradar.svg)](LICENSE)
+
+## Overview
+
+PhenoRadar is a CLI tool for binary phenotype prediction from orthogroup-level TPM.
+
+## Install
+
+```bash
+pip install phenoradar
+```
+
+## Fastest Run
+
+Fetch compact test data, materialize default config, then run:
+
+```bash
+phenoradar dataset
+phenoradar config
+phenoradar run -c config.yml
+```
+
+## Documentation (Recommended Order)
+
+1. [docs/quickstart.md](docs/quickstart.md): first successful run, full run, and prediction.
+2. [docs/data-format.md](docs/data-format.md): required metadata/expression TSV schema.
+3. [docs/configuration.md](docs/configuration.md): config behavior, defaults, and key-by-key definitions.
+4. [docs/cli-reference.md](docs/cli-reference.md): all commands and options.
+5. [docs/output-artifacts.md](docs/output-artifacts.md): output files, column-level details, and interpretation guidance.
+6. [docs/pipeline-details.md](docs/pipeline-details.md): internal execution behavior.
+7. [docs/release-automation.md](docs/release-automation.md): release workflow and PyPI publishing.

phenoradar-0.1.0/README.md

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+# phenoradar
+
+[![CI](https://github.com/mkrg01/phenoradar/actions/workflows/ci.yml/badge.svg?branch=main)](https://github.com/mkrg01/phenoradar/actions/workflows/ci.yml) [![PyPI](https://img.shields.io/pypi/v/phenoradar.svg)](https://pypi.org/project/phenoradar/) [![Python](https://img.shields.io/badge/python-3.12%20%7C%203.13%20%7C%203.14-blue.svg)](https://www.python.org/downloads/) [![License](https://img.shields.io/github/license/mkrg01/phenoradar.svg)](LICENSE)
+
+## Overview
+
+PhenoRadar is a CLI tool for binary phenotype prediction from orthogroup-level TPM.
+
+## Install
+
+```bash
+pip install phenoradar
+```
+
+## Fastest Run
+
+Fetch compact test data, materialize default config, then run:
+
+```bash
+phenoradar dataset
+phenoradar config
+phenoradar run -c config.yml
+```
+
+## Documentation (Recommended Order)
+
+1. [docs/quickstart.md](docs/quickstart.md): first successful run, full run, and prediction.
+2. [docs/data-format.md](docs/data-format.md): required metadata/expression TSV schema.
+3. [docs/configuration.md](docs/configuration.md): config behavior, defaults, and key-by-key definitions.
+4. [docs/cli-reference.md](docs/cli-reference.md): all commands and options.
+5. [docs/output-artifacts.md](docs/output-artifacts.md): output files, column-level details, and interpretation guidance.
+6. [docs/pipeline-details.md](docs/pipeline-details.md): internal execution behavior.
+7. [docs/release-automation.md](docs/release-automation.md): release workflow and PyPI publishing.