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make sure the notebook runs
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‎.gitignore‎

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# PyInstaller
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# Usually these files are written by a python script from a template

‎CHANGELOG.md‎

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- Fixed `get_hcop_orthologs` to use the HGNC Google Cloud Storage bucket instead of the defunct EBI FTP mirror, resolving 404 errors in CI.
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- Added `target_organism` parameter (default `"mouse"`) to `get_hcop_orthologs`, enabling homology mapping to any of the 19 species available in the HCOP database.
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- Updated documentation notebook (`prior_knowledge.ipynb`) to use the new `target_organism` API.
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- Updated `sc_multi.ipynb` metabolite-receptor section for decoupler v2: renamed `pd_net`/`t_net` columns to `source`/`target`/`weight` and removed deprecated `source`/`target`/`weight`/`min_n` kwargs from `estimate_metalinks` (replaced by `tmin`).
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- Standardized all public docstrings to NumPy format and added type annotations across public modules (#219).
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- Added mypy type-checking to pre-commit hooks (`--no-strict-optional --ignore-missing-imports`).
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- Added `build.yaml` CI workflow: validates the package build with `uv build` + `twine check --strict` on every push and pull request.
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- Renamed `.github/workflows/main.yml` → `test.yml`.
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## 1.7.1 (24.01.2026)
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‎docs/notebooks/prior_knowledge.ipynb‎

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"/Users/b260-admin/miniforge3/envs/liana311/lib/python3.11/site-packages/tqdm/auto.py:21: TqdmWarning: IProgress not found. Please update jupyter and ipywidgets. See https://ipywidgets.readthedocs.io/en/stable/user_install.html\n",
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"/Users/b260-admin/miniforge3/envs/liana313/lib/python3.13/site-packages/tqdm/auto.py:21: TqdmWarning: IProgress not found. Please update jupyter and ipywidgets. See https://ipywidgets.readthedocs.io/en/stable/user_install.html\n",
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"source": "## Homology Mapping\n\nSimilarly, LIANA+ provides on demand homology mapping beyond mouse symbols. It utilises the [HCOP database](https://www.genenames.org/help/hcop/) to obtain homologous genes across species. Files are downloaded from the HGNC Google Cloud Storage bucket.\n\nThe homology mapping is accessible through the `resource` module:"
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"## Homology Mapping\n",
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"\n",
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"Similarly, LIANA+ provides on demand homology mapping beyond mouse symbols. It utilises the [HCOP database](https://www.genenames.org/help/hcop/) to obtain homologous genes across species. Files are downloaded from the HGNC Google Cloud Storage bucket.\n",
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"source": "# let's say we are interested in zebrafish homologs of human genes\nmap_df = li.rs.get_hcop_orthologs(target_organism='zebrafish',\n columns=['human_symbol', 'zebrafish_symbol'],\n # NOTE: HCOP integrates multiple resource, so we can filter out mappings in at least 3 of them for confidence\n min_evidence=3\n )\n# rename the columns to source and target, respectively for the original organism and the target organism\nmap_df = map_df.rename(columns={'human_symbol':'source', 'zebrafish_symbol':'target'})\nmap_df.tail()"
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