Cis-GS v1.1.0

[Ayushmania2002]

Cis-GS v1.1.0

First release with PyPI distribution, full Sphinx documentation, and a unified GUI + CLI.

Install

pip install cis-gs
cis-gs --help        # CLI
cis-gs-gui           # GUI

Or grab Cis-GS.exe below — no Python install required (Windows).

Full docs: https://Ayushmania2002.github.io/Cis-GS/

Highlights

• Live KEGG organism dropdown — every one of the 11,700+ organisms KEGG knows about, fetched on demand from the REST API.
• Live NCBI Taxonomy search — type any common or Latin name; results stream back as you type.
• 60× faster ID conversion — MyGene.info batched POST + progress bar (previously 60+ minutes for 10k genes, now ~60 s).
• Interactive CLI wizards — cis-gs wizard walks you through every step with arrow-key menus. Every subcommand also accepts -i / --interactive.
• Fuzzy "did you mean…?" suggestions for CLI typos.
• Brand-icon Contact tab with real-website logos (LinkedIn, GitHub, KEGG, NCBI, PlantTFDB, AnimalTFDB, MyGene).
• Modern single-colour theme (teal #16A085) with instant light/dark toggle — no more 1-2 s freeze on swap.
• First-run NCBI email prompt — required by the Entrez API, stored only on your machine.
• Three Gene-ID-Mapping methods for the annoying NCBI-LOC ↔ species-database mismatch (column swap, mapping CSV, GFF3 Dbxref expansion).
• AnimalTFDB v4 endpoint, JASPAR 2024, HOCOMOCO v11.

Removed

• GO enrichment (KEGG-only for now — re-introducing in v1.2).
• Public RNA-seq import tab.
• All ShinyGO / iDEP attribution.

Fixes

• Dark-mode label visibility in PlantTFDB / AnimalTFDB pop-up dialogs.
• Thin rectangular ? buttons in Step 2 (now proper circles, size-locked).
• Expression-Feeding tab section overlap (wrapped in scroll area).
• Tab labels no longer clip ("NCBI Fetc", "Step 1: Promoter").
• Theme switch no longer freezes the UI for 1-2 s.
• Help-button geometry preserved across font-size changes.

Packaging & infrastructure

• New PyPI package: pip install cis-gs.
• Sphinx documentation site auto-deployed to GitHub Pages on every push.
• GitHub Actions workflows: docs build/deploy + PyPI publish on tag.
• Smoke test suite (pytest).
• Consolidated 5 BUILD_*.md files into single BUILD.md.

Full diff

v1.0.0...v1.1.0

---

If Cis-GS helps your work, please cite the repo — CITATION.cff powers the "Cite this repository" button in the sidebar.

---

This discussion was created from the release Cis-GS v1.1.0.