Changelog

v1.3.2.2 — 2026-06

Fixes

Cleaned up the authors / maintainers fields in pyproject.toml so that the package’s Author metadata renders cleanly as Ayushman Mallick on PyPI and pepy.tech. The Plant Signaling Lab, IISER Tirupati attribution is now carried in the Maintainer field, eliminating comma-driven truncation issues on third-party indexes.

Fixes

Replaced broken shields.io pypi/dt downloads badge with the pepy.tech all-time downloads badge in the README, ensuring the downloads counter renders correctly on both GitHub and PyPI.

Fixes

Corrected PyPI author metadata — Author field now correctly displays the authors on PyPI and pypistats.org.

Fixes

Highlights

Multi-species batch mode — new cis-gs batch subcommand accepts a tab-separated manifest file (species, FASTA path, GFF3 path, optional upstream bp) and runs promoter extraction + motif search for every species in a single automated pass, writing per-species hit CSVs and a combined batch_hits.csv with a species column.
Batch wizard — cis-gs wizard batch provides a step-by-step interactive guide for the new batch workflow, consistent with all other wizard commands.

Documentation

Added cis-gs batch to the CLI command reference.
Rewrote the Wizard page with a full workflow table and dedicated multi-species batch section.
Added missing cis-gs logo command to the CLI reference (was implemented but not documented).

Highlights

37× faster Louvain clustering — replaced the O(N²) Python double loop for co-expression graph construction with NumPy vectorised masking (np.triu), and switched the community-detection backend from python-louvain + NetworkX to the igraph C-library (community_multilevel). Louvain time for A. hypogaea (56 513 genes) dropped from ~150 s to ~4 s.
igraph added as a dependency — igraph >= 0.11 added to pyproject.toml; python-louvain retained as fallback.
PyInstaller bundle updated — igraph and igraph._igraph added to hiddenimports in Cis-GS.spec; Windows .exe rebuilt and uploaded to the v1.2.0 GitHub release.

Performance (benchmarked)

Promoter extraction: 11–87 s across four genome assemblies (O(C) disk reads, where C = chromosome count).
Motif scanning: 6–18 s scaling linearly with sequence count.
KEGG REST retrieval: 5–8 s on first use; < 30 ms on subsequent calls via local disk cache (229–311× speedup).
Full co-expression pipeline (normalisation → Pearson → Louvain → k-means): 77–159 s per species.

Fixes

All em dashes replaced with hyphens throughout GUI and CLI output.
scan_fasta_for_motifs import aligned with the canonical function name in cis_gs.app.

Highlights

Live KEGG organism dropdown (11 700+ organisms, fetched via REST).
Live NCBI Taxonomy search in both GUI and CLI.
60× faster MyGene.info ID conversion via batched POST.
Interactive CLI wizard plus -i / --interactive on every command.
Fuzzy “did you mean…?” for CLI typos.
Modern single-colour theme (#16A085 teal) with instant theme swap (pre-cached stylesheet, setUpdatesEnabled freeze).
First-run NCBI email prompt.
Three Gene-ID-Mapping methods (column swap, mapping CSV, GFF3 Dbxref expansion).
Real brand-icon Contact tab.

Removed

Fixes

Initial public release.

Seven-step pipeline: Promoters → Motifs → Logos → Expression → Coexpression → K-means → Enrichment.
PlantTFDB importer.
PyQt5 GUI + first-cut CLI.
Standalone Windows .exe via PyInstaller.