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Cis-GS v1.1.0

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@Ayushmania2002 Ayushmania2002 released this 21 May 08:30
· 31 commits to main since this release
v1.1.0
502dff7

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.

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