scatrans 0.9.4.dev0__tar.gz → 0.9.5.dev0__tar.gz

scatrans-0.9.5.dev0/.github/workflows/ci.yml

@@ -0,0 +1,70 @@
+name: CI
+
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        install-extra:
+          - ""
+          - "advanced"
+          - "pseudobulk"
+          - "gene_features"
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: "pip"
+
+      - name: Install package with extras
+        run: |
+          pip install --upgrade pip
+          EXTRA="${{ matrix.install-extra }}"
+          if [ -n "$EXTRA" ]; then
+            pip install -e ".[dev,$EXTRA]"
+          else
+            pip install -e ".[dev]"
+          fi
+
+      - name: Ruff lint
+        run: |
+          ruff check src/scatrans tests
+          ruff format --check src/scatrans tests
+
+      - name: Run fast tests
+        run: PYTHONPATH=src:. python -m pytest -m "not plot and not slow" -q
+
+      - name: Run slow tests (core / Python 3.11 only)
+        if: matrix.python-version == '3.11' && matrix.install-extra == ''
+        run: PYTHONPATH=src:. python -m pytest -m "slow and not plot" -q
+
+      - name: Run plot tests (core / Python 3.11 only)
+        if: matrix.python-version == '3.11' && matrix.install-extra == ''
+        run: PYTHONPATH=src:. python -m pytest -m plot -q
+
+      - name: Coverage report (core / Python 3.11 only)
+        if: matrix.python-version == '3.11' && matrix.install-extra == ''
+        run: |
+          PYTHONPATH=src:. python -m pytest -m "not plot" --cov=src/scatrans --cov-report=xml -q \
+            || PYTHONPATH=src:. python -m pytest -m "not plot" -q
+
+      - name: Upload coverage (optional)
+        if: matrix.python-version == '3.11' && matrix.install-extra == ''
+        uses: codecov/codecov-action@v4
+        with:
+          files: ./coverage.xml
+          fail_ci_if_error: false

{scatrans-0.9.4.dev0 → scatrans-0.9.5.dev0}/.gitignore

@@ -21,6 +21,8 @@ sdist/
 var/
 wheels/
 *.egg-info/
+scatrans.egg-info/
+src/scatrans.egg-info/
 .installed.cfg
 *.egg
 MANIFEST

scatrans-0.9.5.dev0/CITATION.cff

@@ -0,0 +1,20 @@
+cff-version: 1.2.0
+title: "scATrans: Single-cell Active Transcription Analysis"
+message: >-
+  If you use this software, please cite it using the metadata below.
+type: software
+authors:
+  - name: "scATrans Developers"
+repository-code: "https://github.com/scATrans/scatrans"
+url: "https://github.com/scATrans/scatrans"
+license: Apache-2.0
+version: 0.9.2
+keywords:
+  - single-cell
+  - RNA-seq
+  - unspliced RNA
+  - nascent RNA
+  - active transcription
+  - bioinformatics
+  - differential expression
+  - gene set enrichment

{scatrans-0.9.4.dev0 → scatrans-0.9.5.dev0}/MANIFEST.in

@@ -7,6 +7,11 @@ include README.md
 include CHANGELOG.md
 include CITATION.cff
 include pyproject.toml
+include conftest.py
+include conftest_fixtures.py
+
+# Include the full test suite so that `pytest` can be run from sdist/unpacked source
+graft tests
 
 # Include the GitHub Actions workflows (requested)
 include .github/workflows/ci.yml

{scatrans-0.9.4.dev0 → scatrans-0.9.5.dev0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: scatrans
-Version: 0.9.4.dev0
+Version: 0.9.5.dev0
 Summary: Single-cell Active Transcription Analysis
 Author: scATrans Developers
 License: Apache-2.0

scatrans-0.9.5.dev0/conftest.py

@@ -0,0 +1,15 @@
+"""Root-level conftest.py.
+
+Ensures project root and src/ are on sys.path (CI, --cov, editable installs,
+unpacked sdists) and registers shared test fixtures via pytest_plugins.
+"""
+
+import sys
+from pathlib import Path
+
+root = Path(__file__).resolve().parent
+for p in (str(root), str(root / "src")):
+    if p not in sys.path:
+        sys.path.insert(0, p)
+
+pytest_plugins = ["conftest_fixtures"]

scatrans-0.9.5.dev0/conftest_fixtures.py

@@ -0,0 +1,146 @@
+"""Pytest plugin: shared AnnData fixtures for the scATrans test suite.
+
+Loaded via ``pytest_plugins`` from root ``conftest.py`` (and ``tests/conftest.py``)
+so fixtures are registered even when nested conftest discovery fails in CI.
+"""
+
+import numpy as np
+import pandas as pd
+import pytest
+import scanpy as sc
+
+
+@pytest.fixture(scope="module")
+def adata_basic():
+    """AnnData with spliced/unspliced layers + gene features."""
+    np.random.seed(42)
+    n_cells, n_genes = 120, 250
+    X = np.random.negative_binomial(4, 0.45, size=(n_cells, n_genes)).astype(float)
+    ad = sc.AnnData(X)
+    ad.obs["condition"] = ["Disease"] * 60 + ["Control"] * 60
+    ad.obs["sample"] = ["s" + str(i % 8) for i in range(n_cells)]
+    ad.layers["spliced"] = X.copy()
+    ad.layers["unspliced"] = X * 0.55
+    ad.var["gene_length"] = np.random.randint(700, 4500, n_genes)
+    ad.var["intron_number"] = np.random.randint(0, 12, n_genes)
+    return ad
+
+
+@pytest.fixture(scope="module")
+def adata_de_only():
+    """Count AnnData without velocity layers (pure DE path)."""
+    np.random.seed(99)
+    n_cells, n_genes = 80, 120
+    X = np.random.negative_binomial(5, 0.4, size=(n_cells, n_genes)).astype(float)
+    ad = sc.AnnData(X)
+    ad.obs["condition"] = ["Disease"] * 40 + ["Control"] * 40
+    ad.obs["sample"] = ["s" + str(i % 6) for i in range(n_cells)]
+    return ad
+
+
+@pytest.fixture(scope="module")
+def adata_small_reference():
+    """Synthetic data with a small reference group (empirical Bayes gamma)."""
+    np.random.seed(123)
+    n_ref, n_tgt, n_genes = 18, 80, 200
+    n_cells = n_ref + n_tgt
+    X = np.random.negative_binomial(4, 0.45, size=(n_cells, n_genes)).astype(float)
+    ad = sc.AnnData(X)
+    ad.obs["condition"] = ["Control"] * n_ref + ["Disease"] * n_tgt
+    ad.layers["spliced"] = X.copy()
+    ad.layers["unspliced"] = X * 0.5
+    ad.var["gene_length"] = np.random.randint(700, 4500, n_genes)
+    ad.var["intron_number"] = np.random.randint(0, 12, n_genes)
+    return ad
+
+
+@pytest.fixture(scope="module")
+def adata_high_unspliced():
+    """Very high unspliced fraction for qc warning path."""
+    np.random.seed(7)
+    n_cells, n_genes = 40, 50
+    X = np.random.negative_binomial(3, 0.5, size=(n_cells, n_genes)).astype(float)
+    ad = sc.AnnData(X)
+    ad.obs["condition"] = ["A"] * 20 + ["B"] * 20
+    ad.layers["spliced"] = X * 0.2
+    ad.layers["unspliced"] = X * 2.0
+    return ad
+
+
+@pytest.fixture(scope="module")
+def adata_mature_nascent():
+    """kb_python style layer names."""
+    np.random.seed(123)
+    n_cells, n_genes = 80, 180
+    X = np.random.negative_binomial(3, 0.5, size=(n_cells, n_genes)).astype(float)
+    ad = sc.AnnData(X)
+    ad.obs["condition"] = ["GA"] * 40 + ["Ctrl"] * 40
+    ad.layers["mature"] = X.copy()
+    ad.layers["nascent"] = X * 0.5
+    ad.var["gene_length"] = np.random.randint(800, 4000, n_genes)
+    ad.var["intron_number"] = np.random.randint(1, 9, n_genes)
+    return ad
+
+
+@pytest.fixture(scope="module")
+def adata_mixed_small():
+    """Small fixture for mixed-model + filter_active_genes tests."""
+    np.random.seed(42)
+    n_cells, n_genes = 60, 70
+    X = np.random.negative_binomial(3, 0.5, size=(n_cells, n_genes)).astype(float)
+    ad = sc.AnnData(X)
+    ad.obs["condition"] = ["Disease"] * 30 + ["Control"] * 30
+    ad.obs["sample"] = ["s" + str(i % 6) for i in range(n_cells)]
+    ad.layers["spliced"] = X.copy()
+    ad.layers["unspliced"] = X * 0.45
+    ad.var["gene_length"] = np.random.randint(600, 3500, n_genes)
+    ad.var["intron_number"] = np.random.randint(0, 8, n_genes)
+    return ad
+
+
+@pytest.fixture(scope="module")
+def adata_pb():
+    """Pseudobulk-oriented fixture (4 samples per group)."""
+    np.random.seed(11)
+    n_cells, n_genes = 96, 80
+    X = np.random.negative_binomial(6, 0.35, size=(n_cells, n_genes)).astype(float)
+    ad = sc.AnnData(X)
+    ad.obs["condition"] = ["Disease"] * 48 + ["Control"] * 48
+    ad.obs["sample"] = [f"S{i // 12}" for i in range(n_cells)]
+    ad.layers["spliced"] = X.copy()
+    ad.layers["unspliced"] = X * 0.5
+    return ad
+
+
+@pytest.fixture(scope="module")
+def results_df(adata_basic):
+    """Shared active_score table for plotting tests (one run per module)."""
+    import scatrans as scat
+
+    _, _, allr = scat.active_score(
+        adata_basic,
+        groupby="condition",
+        target_group="Disease",
+        reference_group="Control",
+        use_permutation=False,
+        show_plot=False,
+    )
+    return allr
+
+
+@pytest.fixture(scope="module")
+def enrich_df():
+    """Minimal enrichment result for plotting smoke tests."""
+    return pd.DataFrame(
+        {
+            "Term": ["T1", "T2", "T3"],
+            "Description": ["desc1", "desc2", "desc3"],
+            "Count": [5, 3, 8],
+            "GeneRatio": [0.1, 0.05, 0.2],
+            "FoldEnrichment": [2.0, 1.5, 3.0],
+            "pvalue": [0.001, 0.01, 0.0001],
+            "p.adjust": [0.01, 0.05, 0.001],
+            "neg_log10_padj": [2.0, 1.3, 3.0],
+            "Genes": ["G1;G2", "G2;G3", "G4;G5;G6"],
+        }
+    )

{scatrans-0.9.4.dev0/.github → scatrans-0.9.5.dev0/github}/workflows/ci.yml

@@ -13,7 +13,6 @@ jobs:
       fail-fast: false
       matrix:
         python-version: ["3.9", "3.10", "3.11", "3.12"]
-        # Core + each optional extra (some may be heavy / have native deps)
         install-extra:
           - ""
           - "advanced"
@@ -23,7 +22,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
         with:
-          fetch-depth: 0  # Good practice for setuptools_scm (version detection)
+          fetch-depth: 0
 
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v5
@@ -46,13 +45,24 @@ jobs:
           ruff check src/scatrans tests
           ruff format --check src/scatrans tests
 
-      - name: Run tests (with coverage when possible)
-        run: |
-          pytest --cov=src/scatrans --cov-report=xml -q || pytest -q
+      - name: Run fast tests
+        run: PYTHONPATH=src:. python -m pytest -m "not plot and not slow" -q
+
+      - name: Run slow tests (core / Python 3.11 only)
+        if: matrix.python-version == '3.11' && matrix.install-extra == ''
+        run: PYTHONPATH=src:. python -m pytest -m "slow and not plot" -q
+
+      - name: Run plot tests (core / Python 3.11 only)
+        if: matrix.python-version == '3.11' && matrix.install-extra == ''
+        run: PYTHONPATH=src:. python -m pytest -m plot -q
+
+      - name: Coverage report (core / Python 3.11 only)
+        if: matrix.python-version == '3.11' && matrix.install-extra == ''
+        run: PYTHONPATH=src:. python -m pytest -m "not plot" --cov=src/scatrans --cov-report=xml -q
 
       - name: Upload coverage (optional)
         if: matrix.python-version == '3.11' && matrix.install-extra == ''
         uses: codecov/codecov-action@v4
         with:
           files: ./coverage.xml
-          fail_ci_if_error: false
+          fail_ci_if_error: false

scatrans-0.9.5.dev0/github/workflows/publish.yml

@@ -0,0 +1,74 @@
+name: Publish to PyPI
+
+on:
+  push:
+    tags:
+      - "v*"
+  release:
+    types: [published]
+  workflow_dispatch:
+    inputs:
+      version:
+        description: "Force a specific version (SETUPTOOLS_SCM_PRETEND_VERSION). Useful for dev releases when not on a tag."
+        required: false
+        default: ""
+
+jobs:
+  build:
+    name: Build distribution 📦
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0  # Critical for setuptools_scm to detect tags and produce correct version
+
+      - 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
+        run: |
+          if [ -n "${{ github.event.inputs.version }}" ]; then
+            echo "Using forced version: ${{ github.event.inputs.version }}"
+            SETUPTOOLS_SCM_PRETEND_VERSION="${{ github.event.inputs.version }}" python -m build
+          else
+            python -m build
+          fi
+
+      - 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
+
+    # Required for Trusted Publishing (OIDC) - no API token secret needed
+    permissions:
+      id-token: write
+
+    # Recommended: tie to a protected GitHub Environment (create "pypi" environment in repo settings)
+    # You can add required reviewers or branch restrictions in the environment settings.
+    # 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

scatrans-0.9.5.dev0/gitignore

@@ -0,0 +1,174 @@
+# 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/
+*.egg-info/
+scatrans.egg-info/
+src/scatrans.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+*.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
+.python-version
+
+# pipenv
+Pipfile.lock
+
+# poetry
+poetry.lock
+
+# pdm
+.pdm.toml
+.pdm-python
+.pdm-build/
+
+# PEP 582
+__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/
+
+# Ruff
+.ruff_cache/
+
+# IDE / editors
+.idea/
+.vscode/
+*.swp
+*.swo
+*~
+
+# OS generated files
+.DS_Store
+.DS_Store?
+._*
+.Spotlight-V100
+.Trashes
+ehthumbs.db
+Thumbs.db
+
+# Project specific
+# Bundled large data is committed intentionally (gene features)
+# but do not add user-generated .parquet outputs here by mistake
+*.h5ad
+*.loom
+*.zarr
+# Keep source data/ but ignore generated outputs at root
+gene_features.parquet
+*_gene_features.parquet
+*_features.parquet
+# Temporary analysis outputs
+*.pdf
+*.png
+*.svg
+active_results/

scatrans-0.9.5.dev0/pre-commit-config.yaml

@@ -0,0 +1,34 @@
+# Pre-commit hooks for scATrans
+# Install: pip install pre-commit
+# Setup: pre-commit install
+# Run manually: pre-commit run --all-files
+
+repos:
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.4.4
+    hooks:
+      - id: ruff
+        args: [--fix, --exit-non-zero-on-fix]
+      - id: ruff-format
+
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.10.0
+    hooks:
+      - id: mypy
+        additional_dependencies: []
+        args: [--ignore-missing-imports, --no-error-summary]
+        # mypy on the src layout; relax for now to avoid blocking on third-party stubs
+        exclude: |
+          (?x)^(
+            tests/|
+            backup/|
+            src/scatrans/_version.py
+          )
+
+  # Optional pyright (static type checker, often stricter). Requires node + pyright.
+  # Uncomment if you have pyright in your env (npm i -g pyright or via pyright package).
+  # - repo: https://github.com/RobertCraigie/pyright-python
+  #   rev: v1.1.367
+  #   hooks:
+  #     - id: pyright
+  #       additional_dependencies: [".[dev]"]

{scatrans-0.9.4.dev0 → scatrans-0.9.5.dev0}/pyproject.toml

@@ -108,6 +108,9 @@ indent-style = "space"
 [tool.pytest.ini_options]
 minversion = "7.0"
 testpaths = ["tests"]
+# Ensure the project root is on sys.path for fixture discovery and src-layout editable installs
+# (helps in CI, zip extractions, and when cwd differs slightly)
+pythonpath = ["src", "."]
 # Daily dev: skip plot + slow. Override examples:
 #   pytest -m "not plot"          # include slow integration tests
 #   pytest -m plot              # plotting only

{scatrans-0.9.4.dev0 → scatrans-0.9.5.dev0}/scatrans.egg-info/SOURCES.txt

@@ -1,9 +1,15 @@
 .gitignore
 CHANGELOG.md
+CITATION.cff
 LICENSE
 MANIFEST.in
 PKG-INFO
 README.md
+conftest.py
+conftest_fixtures.py
+coverage
+gitignore
+pre-commit-config.yaml
 pyproject.toml
 setup.cfg
 .github/workflows/ci.yml
@@ -11,8 +17,9 @@ setup.cfg
 examples/memento_de_example.py
 examples/real_data_template.py
 examples/synthetic_active_transcription.py
+github/workflows/ci.yml
+github/workflows/publish.yml
 src/scatrans/__init__.py
-src/scatrans/_bias.py
 src/scatrans/_de.py
 src/scatrans/_permutation.py
 src/scatrans/_utils.py
@@ -31,4 +38,14 @@ src/scatrans/data/Mm_KEGG_2026.txt
 src/scatrans/data/Mus_musculus.GRCm39.115_gene_features.parquet
 src/scatrans/data/README.md
 src/scatrans/data/mouse_2020A_gene_features.parquet
-tests/test_basic.py
+tests/__init__.py
+tests/conftest.py
+tests/test_basic.py
+tests/test_de_backends.py
+tests/test_enrich_api.py
+tests/test_enrich_go.py
+tests/test_pl_coverage.py
+tests/test_pl_extended.py
+tests/test_pp_bias_cli.py
+tests/test_public_api.py
+tests/test_tl_coverage.py