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AdamNogellAdamNogell
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Release v1.3.0
1 parent cdbc862 commit 071c486

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‎.dockerignore‎

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.git
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.github
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.pytest_cache
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__pycache__
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*.pyc
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.DS_Store
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data
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dist
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docs
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tests
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exp_heatmap.egg-info

‎.github/workflows/tests.yml‎

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name: tests
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on:
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push:
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branches:
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- main
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pull_request:
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jobs:
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pytest:
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runs-on: ubuntu-latest
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env:
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MPLCONFIGDIR: /tmp/matplotlib
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strategy:
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fail-fast: false
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matrix:
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python-version: ["3.10", "3.11", "3.12"]
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steps:
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- uses: actions/checkout@v4
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- uses: actions/setup-python@v5
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install package and test dependencies
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run: |
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python -m pip install --upgrade pip
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pip install -e .[dev]
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- name: Run tests
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run: python -m pytest -q

‎.gitignore‎

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.vscode
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data/
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dist/
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build/
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__pycache__/
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exp_heatmap.egg-info/
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*.py[cod]
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*.egg-info/
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.pytest_cache/
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.coverage
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.mypy_cache/
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.ruff_cache/
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.DS_Store
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adam/testing/.DS_Store
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local_data/
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.claude_resources.json
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.env
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.venv/
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venv/

‎Dockerfile‎

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FROM python:3.11-slim
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ENV PYTHONDONTWRITEBYTECODE=1 \
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PYTHONUNBUFFERED=1 \
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PIP_NO_CACHE_DIR=1 \
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MPLCONFIGDIR=/tmp/matplotlib
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WORKDIR /app
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RUN apt-get update \
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&& apt-get install -y --no-install-recommends vcftools \
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&& rm -rf /var/lib/apt/lists/*
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COPY pyproject.toml README.md LICENSE ./
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COPY src ./src
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RUN python -m pip install --upgrade pip \
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&& pip install .
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ENTRYPOINT ["exp_heatmap"]

‎README.md‎

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‎environment.yml‎

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name: exp-heatmap-dev
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channels:
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- conda-forge
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- bioconda
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dependencies:
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- python=3.11
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- pip
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- vcftools
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- pip:
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- -e .[dev]

‎pyproject.toml‎

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[project]
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name = "exp_heatmap"
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version = "1.2.0"
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version = "1.3.0"
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authors = [
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{name = "Edvard Ehler", email = "edvard.ehler@img.cas.cz"},
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{name = "Ondřej Moravčík"}
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]
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maintainers = [
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{name = "Adam Nógell", email = "adam.nogell@img.cas.cz"}
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]
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description = "Computing and drawing ExP heatmap for displaying complex cross-population data"
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description = "Ordered-pair workflow for regional cross-population genomic visualization (VCF -> empirical rank-score heatmaps)"
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readme = "README.md"
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requires-python = ">=3.8"
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requires-python = ">=3.10"
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license = "MIT"
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keywords = [
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"bioinformatics",
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"population-genetics",
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"selection-scan",
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"xpehh",
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"xpnsl",
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"fst",
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"tajima-d",
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"heatmap",
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"visualization",
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"1000-genomes",
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"ggvp"
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]
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classifiers = [
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"Development Status :: 5 - Production/Stable",
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"Intended Audience :: Science/Research",
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"Programming Language :: Python :: 3",
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"Programming Language :: Python :: 3.10",
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"Programming Language :: Python :: 3.11",
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"Programming Language :: Python :: 3.12",
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"Operating System :: OS Independent",
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"Topic :: Scientific/Engineering :: Bio-Informatics"
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"Topic :: Scientific/Engineering :: Bio-Informatics",
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"Topic :: Scientific/Engineering :: Visualization"
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]
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dependencies = [
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"scikit-allel",
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"zarr<3.0.0",
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"numpy",
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"pandas",
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"matplotlib",
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"seaborn",
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"click",
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"plotly",
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"tqdm"
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"scikit-allel>=1.3.7",
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"zarr>=2.10,<3.0.0",
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"numpy>=1.22",
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"pandas>=1.4",
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"matplotlib>=3.5",
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"seaborn>=0.12",
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"click>=8.0",
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"plotly>=5.10",
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"tqdm>=4.60"
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]
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[project.optional-dependencies]
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dev = [
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"pytest>=7.0",
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"pytest-cov>=4.0"
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]
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benchmarks = [
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"psutil>=5.9",
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"pysam>=0.22"
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]
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all = [
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"pytest>=7.0",
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"pytest-cov>=4.0",
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"psutil>=5.9",
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"pysam>=0.22"
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]
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[project.urls]
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Homepage = "https://github.com/bioinfocz/exp_heatmap"
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Repository = "https://github.com/bioinfocz/exp_heatmap"
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"Bug Tracker" = "https://github.com/bioinfocz/exp_heatmap/issues"
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Documentation = "https://github.com/bioinfocz/exp_heatmap#readme"
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[project.scripts]
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exp-selection = "exp_heatmap.cli:cli"
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exp_heatmap = "exp_heatmap.cli:cli"
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exp-heatmap = "exp_heatmap.cli:cli"
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[tool.setuptools.package-dir]
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"" = "src"
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[tool.pytest.ini_options]
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testpaths = ["tests"]
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python_files = ["test_*.py"]

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