scatrans 0.7.0.dev0__tar.gz → 0.9.1.dev0__tar.gz

{scatrans-0.7.0.dev0 → scatrans-0.9.1.dev0}/.github/workflows/ci.yml

@@ -22,6 +22,8 @@ jobs:
 
     steps:
       - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0  # Good practice for setuptools_scm (version detection)
 
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v5

scatrans-0.9.1.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-0.7.0.dev0 → scatrans-0.9.1.dev0}/CHANGELOG.md

@@ -5,6 +5,71 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [0.9.0] - 2026-06-19
+
+### Added
+- `run_gsea(ranked_genes, gene_sets=..., nperm=..., ...)` — pre-ranked GSEA (via gseapy.prerank wrapper).
+  Reuses the same gene-set loading, `gene_case`, diagnostics, and `.attrs` system as ORA.
+  Returns DataFrame with `NES`, `ES`, `pvalue`, `p.adjust`, `leading_edge`, etc.
+  Optional dependency: `pip install "scatrans[gsea]"`.
+- `scat.pl.gseaplot(ranked_genes, gsea_result, term=...)` — classic GSEA running enrichment score plot.
+  Automatically uses pre-computed RES curves + hits stored in `run_gsea` results (`.attrs["gsea_details"]`).
+- `enrich_dotplot` now auto-detects GSEA results (defaults `x="NES"`, uses diverging colormap when `color_by="NES"`).
+- Added `gsea` extra in `pyproject.toml`.
+
+### Changed
+- Minor internal cleanups and test coverage for the new GSEA path.
+- All new functions follow the existing consistent signatures (`ax=`, `use_style=`, `save_path=`, etc.).
+
+## [0.8.0] - 2026-06-14
+
+### Added (enrichment module — major paper-readiness upgrade)
+- `run_go(ontology="BP"|"CC"|"MF"|"ALL", ...)` — direct wrapper analogous to clusterProfiler `enrichGO`. Supports `adjust_across_all=True` for a single BH correction across all GO terms when using "ALL".
+- `save_enrichment_report(res, prefix=..., save_excel=True, save_csv=True, save_tsv=True, save_metadata=True, save_term_gene_table=True)` — one-call export of main table, term-gene long table (via `expand_enrichment_genes`), and rich `metadata.json` + xlsx sheet. Auto-creates parent directories. List columns (e.g. `Genes_list`) are sanitized to `;` strings for clean export.
+- `expand_enrichment_genes(res)` — expands the `Genes` (semicolon) column into a long-format Term–Gene table (one row per gene). Preserves `Ontology` column when input came from `run_go(..., "ALL")`.
+- Rich provenance in every result `.attrs` (success and empty):
+  - `analysis_info`: package, version, timestamp, module
+  - `gene_set_info`: `requested`/`resolved`, `requested_source` vs `actual_source` ("bundled", "gseapy", "gmt", "dict"), `library_name`, `n_terms`, `n_unique_genes`
+  - `universe_info`: full details of background handling (provided size, restricted, dropped_by_annotation, force_universe, mapping counts)
+  - Empty results now carry `reason` ("gene_list_empty", "universe_empty", "no_term_overlap_after_filters", ...) + the above fields so users can diagnose why nothing came back.
+- New `run_enrichment` / `run_kegg` / `run_go` parameters: `padj_cutoff` (preferred modern name), `include_gene_list` (adds `Genes_list` python-list column), `adjust_across_all`.
+- `list_bundled_gene_sets()` now clearly documents the 2026 organism-specific defaults.
+- Improved low-mapping-rate warning (includes input examples + gene-set examples).
+- `background` is now a documented deprecated alias of `universe`; passing both raises immediately.
+- All empty-result DataFrames preserve consistent columns (including optional `Genes_list` when requested) and full diagnostic attrs.
+
+### Changed / Improved
+- `_load_gene_sets` now returns `(term_to_genes, term_to_desc, load_info)` so `actual_source` is always recorded accurately (even on gseapy fallback after bundled attempt).
+- `run_kegg` fully synchronized with new parameters (`padj_cutoff`, `include_gene_list`, etc.).
+- `enrich_dotplot` (pl.py) and various tl.py flows updated for new columns/attrs.
+- Version unified to 0.8.0 for this release.
+- README and docstrings extensively updated with manuscript-export examples, `run_go`, provenance details, and `adjust_across_all` guidance.
+- Full test coverage for new paths (per-ontology attrs, within_ontology p.adjust, save+tsv+dir creation, expand with Ontology, dual-cutoff warning, etc.). All tests pass.
+
+## [0.9.0] - 2026-06-18
+
+### Added
+- **Independent permutation statistics for unspliced excess**: `unspliced_excess_pval` and `unspliced_excess_fdr` (one-sided test on bias-corrected `unspliced_excess_residual`). Computed alongside existing `active_score_pval` / `active_score_fdr` when `use_permutation=True`.
+- New parameter `unspliced_excess_fdr_cutoff` (default 0.05) for the built-in `significant` gene list and `filter_active_genes`.
+- `filter_active_genes` parameters `unspliced_excess_residual_cutoff` and `unspliced_excess_fdr_cutoff`; heuristic/pseudobulk presets updated accordingly.
+- `adata.uns["scatrans"]["significant_criteria"]` metadata documenting the built-in significance conjunction.
+
+### Changed
+- **Terminology**: primary result columns renamed from velocity to unspliced/nascent excess:
+  - `unspliced_excess_delta` (was `velocity_delta_raw`)
+  - `unspliced_excess_residual` (was `velocity_residual`)
+  - Legacy `velocity_*` columns remain in `adata.var` as deprecated aliases.
+- **Built-in `significant` gene list** now requires:
+  - `logFC > logfc_cutoff`, `p_adj < pval_cutoff`, `unspliced_excess_residual > 0`, `unspliced_excess_fdr < unspliced_excess_fdr_cutoff`
+  - `active_score` is no longer used for significance (ranking/visualization only).
+  - Without `use_permutation=True`, the built-in `significant` list is empty (logged warning).
+- Plotting functions accept primary or legacy column names; axis labels updated.
+- README rewritten for the new significance model and column names.
+
+### Deprecated
+- `active_fdr_cutoff` (no longer used for built-in significance; use `unspliced_excess_fdr_cutoff`).
+- `velocity_residual_cutoff` in `filter_active_genes` (use `unspliced_excess_residual_cutoff`).
+
 ## [Unreleased]
 
 ### Added

scatrans-0.9.1.dev0/MANIFEST.in

@@ -0,0 +1,24 @@
+# Control what goes into the source distribution (sdist).
+# The wheel only contains the runtime package (src/scatrans + data).
+
+# Standard important files
+include LICENSE
+include README.md
+include CHANGELOG.md
+include pyproject.toml
+
+# Include the GitHub Actions workflows (requested)
+include .github/workflows/ci.yml
+include .github/workflows/publish.yml
+
+# If more workflows are added in the future, this will catch them:
+include .github/workflows/*.yml
+
+# Never ship generated metadata directories inside the sdist
+recursive-exclude src/scatrans.egg-info *
+prune build
+prune dist
+global-exclude *.pyc
+global-exclude __pycache__/*
+global-exclude *.egg-info
+global-exclude *.egg-info/*