scfair 0.5.0__tar.gz

scfair-0.5.0/.github/workflows/publish.yml

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+name: Publish to PyPI
+
+# Manual only — creating a GitHub Release / tag does NOT upload to PyPI.
+# Publish via: Actions → "Publish to PyPI" → Run workflow
+on:
+  workflow_dispatch:
+
+concurrency:
+  group: publish-pypi-${{ github.run_id }}
+  cancel-in-progress: false
+
+jobs:
+  build:
+    name: Build distribution 📦
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Install build tools
+        run: python -m pip install --upgrade build
+
+      - name: Build source and wheel distributions
+        # Version is read from src/scfair/_version.py (single source of truth).
+        run: python -m build
+
+      - name: Upload distribution artifacts
+        uses: actions/upload-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/
+
+  publish:
+    name: Publish to PyPI
+    needs: build
+    runs-on: ubuntu-latest
+
+    # Trusted Publishing (OIDC). Configure the "pypi" environment in repo
+    # Settings → Environments with required reviewers before first publish.
+    permissions:
+      id-token: write
+
+    environment:
+      name: pypi
+
+    steps:
+      - name: Download all dists
+        uses: actions/download-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/
+
+      - name: Publish distribution 📦 to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        # For publishing to TestPyPI instead (for testing the workflow):
+        # with:
+        #   repository-url: https://test.pypi.org/legacy/
+        #   verbose: true

scfair-0.5.0/.github/workflows/tests.yml

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+name: tests
+
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        # Must stay in sync with requires-python in pyproject.toml (">=3.10").
+        # 3.9 was dropped rather than left declared-but-untested: recent scanpy
+        # releases no longer support it, so a 3.9 job would have pinned an old
+        # scanpy and tested a configuration nobody runs.
+        python-version: ["3.10", "3.11", "3.12"]
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: pip
+          cache-dependency-path: pyproject.toml
+
+      - name: Install
+        run: |
+          python -m pip install --upgrade pip
+          pip install -e ".[dev]"
+
+      - name: Import check
+        # Catches a missing runtime dependency that the test suite might mask by
+        # importing something else first.
+        run: python -c "import scfair; print(scfair.__version__)"
+
+      - name: Leiden backend check
+        # Every balanced method needs sc.tl.leiden(flavor="igraph"). This failed
+        # once because igraph was not a declared dependency.
+        run: python -c "import igraph; print('igraph', igraph.__version__)"
+
+      - name: Direct sklearn / skmisc import check
+        # Function-local imports; package import alone does not exercise them.
+        run: |
+          python -c "import sklearn; from sklearn.cluster import KMeans; from sklearn.metrics import adjusted_rand_score; print('sklearn', sklearn.__version__)"
+          python -c "from skmisc.loess import loess; print('skmisc loess OK')"
+
+      - name: Tests
+        run: pytest -q --cov=scfair --cov-report=term-missing
+
+  min-versions:
+    # Installs the exact floors declared in pyproject.toml and runs the suite
+    # against them. Without this the floors are assertions, not facts — and two of
+    # them were wrong before this job existed: `scanpy>=1.9` could not run
+    # sc.tl.leiden(flavor="igraph") at all (1.10+ only), and `scikit-misc` was
+    # missing entirely while being required by the default flavor="seurat_v3".
+    # If this job fails, raise the floor in pyproject.toml — do not delete the job.
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+      - name: Install declared floors
+        run: |
+          python -m pip install --upgrade pip
+          pip install \
+            "anndata==0.10.*" "numpy==1.24.*" "pandas==2.0.*" \
+            "scanpy==1.10.*" "scipy==1.10.*" "igraph==0.10.*" \
+            "scikit-misc==0.3.*" "scikit-learn==1.2.*"
+          pip install --no-deps -e .
+          pip install "pytest>=7.0" "pytest-cov>=4.0"
+      - name: Show resolved versions
+        run: pip list | grep -Ei "anndata|scanpy|numpy|pandas|scipy|igraph|scikit-misc|scikit-learn"
+      - name: seurat_v3 must really be available at the floor
+        # scFair falls back to flavor="seurat" if seurat_v3 raises, so a missing
+        # skmisc would look like a pass. Assert the real path is reachable.
+        run: python -c "from skmisc.loess import loess; print('skmisc loess OK')"
+      - name: Leiden flavor must exist at the floor
+        run: |
+          python -c "
+          import inspect, scanpy as sc
+          assert 'flavor' in inspect.signature(sc.tl.leiden).parameters, \
+              'sc.tl.leiden lacks flavor= at the declared scanpy floor'
+          print('leiden flavor OK')"
+      - name: Tests
+        run: pytest -q
+
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+          cache: pip
+          cache-dependency-path: pyproject.toml
+      # Pin ruff major.minor: unpinned installs pick latest defaults and break
+      # lint when the rule set expands. Rule set is also explicit in pyproject.toml.
+      - run: pip install "ruff>=0.4.0,<0.17"
+      # examples/ is optional in slim checkouts / release zips; only lint if present.
+      - run: |
+          if [ -d examples ]; then
+            ruff check src tests examples
+          else
+            ruff check src tests
+          fi
+      # `ruff format --check` is deliberately NOT gated yet: the existing source
+      # predates the formatter and enforcing it would mean a repo-wide reformat.
+      # To adopt it, run `ruff format src tests` once, review that diff on its
+      # own, then add the check here.

scfair-0.5.0/.gitignore

@@ -0,0 +1,71 @@
+# --- Python ---
+__pycache__/
+*.py[cod]
+*.egg-info/
+*.egg
+.eggs/
+dist/
+build/
+.pytest_cache/
+.mypy_cache/
+.ruff_cache/
+.coverage
+coverage.xml
+htmlcov/
+.venv/
+venv/
+.ipynb_checkpoints/
+
+# --- Third-party datasets: never committed, cited instead ---
+# These come from 10x Genomics, CELLxGENE, figshare/scIB, Zenodo (Zhao et al.
+# 2025), CraftedExperiment (Liu et al. 2025) and CellBRF. We have no right to
+# redistribute them, several files exceed GitHub's 100 MB per-file limit, and the
+# tree is ~5.6 GB. Sources and accessions: docs/DATA_SOURCES.md
+data/
+examples/data/
+
+# Belt and braces: raw matrix / archive formats anywhere in the tree.
+*.h5ad
+*.h5
+*.rds
+*.RData
+*.mtx
+*.mtx.gz
+*.loom
+*.zip
+*.tar
+*.tar.gz
+*.tgz
+*.txt.gz
+*.csv.gz
+*.xlsx
+
+# --- Locally generated outputs: not committed ---
+# Every table, figure and log under here is produced by the benchmark scripts.
+examples/results/
+
+# --- Local research notes (not part of the public docs site / release) ---
+# Keep on disk for development; do not publish to GitHub / RTD / PyPI sdist.
+docs/PAPER_*
+docs/DEVELOPMENT_LOG.md
+docs/PACKAGE_VALUE.md
+docs/gold.md
+docs/review.md
+docs/AUTO_N_*
+docs/CELLBRF_*
+docs/DATA_SOURCES.md
+docs/**/*.csv
+
+# Sphinx build products
+docs/_build/
+docs/api/generated/
+
+# --- Editors / OS ---
+.DS_Store
+*.swp
+*~
+.idea/
+.vscode/
+
+# Claude Code harness internals
+.claude/

scfair-0.5.0/.readthedocs.yaml

@@ -0,0 +1,20 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+version: 2
+
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"
+
+sphinx:
+  configuration: docs/conf.py
+  fail_on_warning: false
+
+python:
+  install:
+    - requirements: docs/requirements.txt
+    - method: pip
+      path: .

scfair-0.5.0/CHANGELOG.md

@@ -0,0 +1,82 @@
+# Changelog
+
+All notable changes to this project are documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/).
+Versions follow [Semantic Versioning](https://semver.org/). While the package
+is in the `0.x` series, defaults may still change in a minor release when new
+evidence warrants it.
+
+## [0.5.0] - 2026-08-02
+
+First public release prepared for PyPI and Read the Docs.
+
+### Added
+
+- `scfair.pp.highly_variable_genes` — fair / balanced HVG selection with a short
+  product surface and optional research knobs via `HVGOptions`.
+  - Default `balance_method="append"`: freeze the global top-`k` list, then
+    append the next `append_budget` genes from the same ranking (default 200).
+  - `balance_method="none"` reproduces a single global scanpy-style pass.
+  - Opt-in cluster-aware methods: `hybrid`, `score`, `reweight`.
+  - `n_top_genes="auto"` (structure-aware) and product `mode` presets
+    (`compact` / `balanced` / `fine`, or `mode="auto"`).
+- `scfair.pp.HVGOptions` — secondary controls (append budget, clustering pool,
+  neighbor contrast, raw-count snapshot policy, and related fields).
+- `scfair.pp.diagnose_from_labels` — pre-call imbalance tips from known labels
+  (does not run HVG).
+- `scfair.pp.estimate_n_populations` — label-free estimate of how many
+  populations a density field supports (advisory).
+- Downstream helpers: `recommend_cluster_resolution`,
+  `resolve_cluster_resolution`, `resolve_hvg_mode`, and structure-based auto-`k`
+  utilities under `scfair.pp`.
+- Sphinx documentation (installation, quickstart, user guide, API, FAQ,
+  changelog) and a PBMC 10k tutorial comparing standard HVG with scFair.
+- CI matrix for Python 3.10–3.12, a min-versions job for declared dependency
+  floors, and a manual PyPI publish workflow (Trusted Publishing).
+
+### Changed
+
+- Default path is append-on-global-rank (no intermediate clustering). Final
+  list size is `n_top_genes + append_budget`, capped at `n_vars`.
+- Intermediate clustering (when used) scales genes before PCA by default
+  (`HVGOptions.scale_clustering=True`).
+- Structure auto-`k` applies a soft buffer and an anti-SHORT floor when density
+  confidence is low, so under-powered short lists are less common on large,
+  multi-type PBMCs.
+- Non-selected genes use `NaN` in `var["highly_variable_rank"]` (scanpy
+  seurat_v3 convention).
+
+### Fixed
+
+- Count-layer handling no longer overwrites a user `layers["counts"]` when it
+  disagrees with integer `.X`; staging uses an internal layer and is cleaned up
+  after the call.
+- Repeated HVG calls on the same object do not leak scanpy score columns or
+  redirect later default calls to a previous `layer=`.
+- Explicit `append_budget` (including `0`) is never replaced by mode defaults.
+- seurat_v3 loess path falls back on tiny gene sets before a hard crash.
+- Empty or all-zero counts raise a clear error before PCA.
+- Ribosomal filter no longer matches kinase names such as `RPS6KA*`.
+- Failed HVG runs roll back partial `var` HVG columns and record
+  `uns["scfair"]["hvg_failed"]`.
+
+### Documentation
+
+- README oriented for PyPI / GitHub (install, first run, status).
+- User-facing docs in American English; research notes and paper tables stay
+  local and are not part of the published documentation tree.
+
+## [0.3.0] - 2026-08-01
+
+Internal pre-release: API hygiene, structure auto-`k` anti-SHORT floor, scaled
+intermediate PCA, and reliability fixes for empty counts and filter rules.
+
+## [0.2.0] - 2026-08-01
+
+Internal pre-release: product default moved to append, `HVGOptions` introduced,
+and the experimental `cap` allocation path removed.
+
+## [0.1.0] - 2026-07-29
+
+Initial private package scaffold and core HVG entry point.

scfair-0.5.0/CITATION.cff

@@ -0,0 +1,21 @@
+cff-version: 1.2.0
+title: "scFair: Fair highly variable gene selection for single-cell RNA-seq"
+message: >-
+  If you use this software, please cite it using the metadata below.
+type: software
+authors:
+  # Display form used elsewhere: Zhao Li (李钊)
+  - family-names: "Li"
+    given-names: "Zhao (李钊)"
+    email: "leelieber@gmail.com"
+repository-code: "https://github.com/leelieber2025/scFair"
+url: "https://github.com/leelieber2025/scFair"
+license: Apache-2.0
+version: 0.5.0
+keywords:
+  - single-cell
+  - RNA-seq
+  - HVG
+  - highly variable genes
+  - fairness
+  - bioinformatics

scfair-0.5.0/LICENSE

@@ -0,0 +1,202 @@
+
+                                 Apache License
+                           Version 2.0, January 2004
+                        http://www.apache.org/licenses/
+
+   TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
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+   5. Submission of Contributions. Unless You explicitly state otherwise,
+      any Contribution intentionally submitted for inclusion in the Work
+      by You to the Licensor shall be under the terms and conditions of
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+      Notwithstanding the above, nothing herein shall supersede or modify
+      the terms of any separate license agreement you may have executed
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+
+   6. Trademarks. This License does not grant permission to use the trade
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+   7. Disclaimer of Warranty. Unless required by applicable law or
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+
+   9. Accepting Warranty or Additional Liability. While redistributing
+      the Work or Derivative Works thereof, You may choose to offer,
+      and charge a fee for, acceptance of support, warranty, indemnity,
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+      of your accepting any such warranty or additional liability.
+
+   END OF TERMS AND CONDITIONS
+
+   APPENDIX: How to apply the Apache License to your work.
+
+      To apply the Apache License to your work, attach the following
+      boilerplate notice, with the fields enclosed by brackets "[]"
+      replaced with your own identifying information. (Don't include
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+   Copyright 2026 Zhao Li (李钊)
+
+   Licensed under the Apache License, Version 2.0 (the "License");
+   you may not use this file except in compliance with the License.
+   You may obtain a copy of the License at
+
+       http://www.apache.org/licenses/LICENSE-2.0
+
+   Unless required by applicable law or agreed to in writing, software
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scfair-0.5.0/MANIFEST.in

@@ -0,0 +1,51 @@
+# Source distribution (sdist) contents for PyPI / GitHub source installs.
+# The wheel only ships the runtime package (src/scfair + package data).
+
+include LICENSE
+include README.md
+include CHANGELOG.md
+include SECURITY.md
+include CITATION.cff
+include pyproject.toml
+include MANIFEST.in
+include .gitignore
+include .readthedocs.yaml
+
+graft tests
+graft docs
+prune docs/_build
+# Local research notes and paper tables are not part of the public docs site.
+global-exclude docs/PAPER_*
+global-exclude docs/DEVELOPMENT_LOG.md
+global-exclude docs/PACKAGE_VALUE.md
+global-exclude docs/gold.md
+global-exclude docs/review.md
+global-exclude docs/AUTO_N_*
+global-exclude docs/CELLBRF_*
+global-exclude docs/DATA_SOURCES.md
+
+graft examples
+# Never ship large or regenerable example outputs / data
+prune examples/data
+prune examples/results
+global-exclude examples/**/__pycache__/*
+
+graft .github/workflows
+
+recursive-exclude src/scfair.egg-info *
+prune build
+prune dist
+prune data
+prune .git
+prune .mypy_cache
+prune .pytest_cache
+prune .ruff_cache
+prune .tox
+prune htmlcov
+global-exclude *.pyc
+global-exclude __pycache__/*
+global-exclude *.egg-info
+global-exclude *.egg-info/*
+global-exclude *.h5ad
+global-exclude *.zip
+global-exclude .DS_Store