Report redesign + --always-top-n/--class search options + MkDocs docs site

.github/workflows/docs.yml

@@ -0,0 +1,37 @@
+name: docs
+
+on:
+  push:
+    branches: [main]
+  workflow_dispatch:
+
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+concurrency:
+  group: pages
+  cancel-in-progress: true
+
+jobs:
+  build-deploy:
+    runs-on: ubuntu-latest
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0  # hatch-vcs needs full history for the version
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+      - run: pip install -e ".[docs]"
+      - run: mkdocs build
+      - uses: actions/configure-pages@v5
+      - uses: actions/upload-pages-artifact@v3
+        with:
+          path: site
+      - id: deployment
+        uses: actions/deploy-pages@v4

.gitignore

@@ -12,6 +12,8 @@ data/*html
 !data/ref_data/Gibbs_motifs_mouse/motif/*.png 
 output/*
 .DS_Store
+# MkDocs build output
+/site/
 cli/*__pycache__
 test_output
 poetry.lock

README.md

@@ -110,3 +110,30 @@ src/mhc_tp/
   tui/              Rich console banner, logging, results table
 tests/              pytest suite
 ```
+
+---
+
+## Citation
+
+If you use MHC-TP in your work, please cite:
+
+> Munday PR, Krishna SSG, Fehring J, Croft NP, Purcell AW, Li C, Braun A.
+> Immunolyser 2.0: An advanced computational pipeline for comprehensive analysis
+> of immunopeptidomic data. *Comput Struct Biotechnol J.* 2025;29:296–304.
+> doi:[10.1016/j.csbj.2025.10.007](https://doi.org/10.1016/j.csbj.2025.10.007).
+> PMID: [41209766](https://pubmed.ncbi.nlm.nih.gov/41209766/); PMCID: PMC12590289.
+
+```bibtex
+@article{Munday2025Immunolyser2,
+  title   = {Immunolyser 2.0: An advanced computational pipeline for comprehensive analysis of immunopeptidomic data},
+  author  = {Munday, Prithvi Raj and Krishna, Sanjay S. G. and Fehring, Joshua and Croft, Nathan P. and Purcell, Anthony W. and Li, Chen and Braun, Asolina},
+  journal = {Computational and Structural Biotechnology Journal},
+  volume  = {29},
+  pages   = {296--304},
+  year    = {2025},
+  doi     = {10.1016/j.csbj.2025.10.007},
+  pmid    = {41209766},
+  pmcid   = {PMC12590289}
+}
+```
+

docs/api.md

@@ -0,0 +1,19 @@
+# API reference
+
+Auto-generated from the package docstrings.
+
+## Search engine
+
+::: mhc_tp.engine.search
+
+::: mhc_tp.engine.kernels
+
+## Reference data
+
+::: mhc_tp.refdata.fetch
+
+## Report
+
+::: mhc_tp.report.render
+
+::: mhc_tp.naming