MPC working by grpinto · Pull Request #136 · lueckenlab/patpy

grpinto · 2026-05-04T11:46:14Z

Gonçalo Pinto :

Going to work on MCPs for Patpy

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Fix/gloscope_py

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…entation_tutorial - Add the tutorials for the GloScope reimplementation - Fix R implementation of GloScope

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Fix/negative distances

Adds a markdown skill library (Claude Code per-folder SKILL.md layout) that mirrors the public API surface (pp / tl / pl / datasets), so coding agents can use patpy without rediscovering the API from source each session. Pure additive change: no module behavior is altered. Skills ship with the wheel via the default hatchling include for files under src/patpy/. Co-Authored-By: Claude Opus 4.7 <[email protected]>

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Fix KNN score

Feature/agent skills

Adds a BioContextAI Registry-compatible MCP server that exposes dataset search and download from CellxGene Discover so any MCP-capable agent (Claude Desktop, Cursor, mcp-cli + Ollama, ...) can fetch single-cell datasets by disease, tissue, or ontology term. The server complements (instead of duplicating) the existing MaxMLang/cxg-census-mcp and biocontext-ai/anndata-mcp registry servers. - New src/patpy/mcp/ package with a multi-source plugin architecture (DataSource protocol) and a CellxGene Discover REST source with pagination, retries, 24 h on-disk index cache, and streaming download with SHA-256 verification. - New mcp/ directory with a schema-validated meta.yaml ready to be PR'd into biocontext-ai/registry, plus a Dockerfile and .dockerignore. - Documentation in docs/mcp.md (linked from docs/index.md and a new section in README.md) covering install, agent config snippets, and a chaining recipe with cxg-census-mcp and anndata-mcp. - Test suite under tests/: server tool registration check, twelve discover-client unit tests with a hand-rolled fake session, and registry-schema validation against the upstream schema.json (committed offline as a fixture). Co-authored-by: Cursor <[email protected]>

VladimirShitov · 2026-05-04T20:20:38Z

Thanks, looks interesting, I'll review the content soon. But the main question is how to keep it relevant? Could you add prompts that you used to generate it, or come up with a way to update the skills on new code updates? It would be cool to have a GitHub action, backed by Claude, that updates skills on pull requests.

For more effective prompting, point the agent to CHANGELOG.md

grpinto · 2026-05-05T06:35:18Z

Will do it today, thanks Vlad

VladimirShitov · 2026-05-05T07:39:40Z

Claude tells that these skills will be available to patpy developers, but not users.

Should we also create and publish a plugin? Looks super easy, but would be helpful to have a clear workflow on how to keep it updated and what needs to be done on a new package release

grpinto · 2026-05-05T07:43:16Z

Sounds good, I am trying to finish fetching datasets from cellXgene

Grpinto branch

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…caches Aligns the mcp/ subproject with biocontext-ai/mcp-server-cookiecutter and keeps test caches out of git going forward. mcp/ subproject (cookiecutter alignment): - Add mcp/mcp.json (BioContextAI Registry client snippet, mirrors biocontext-ai-anndata-mcp and MaxMLang-cxg-census-mcp siblings). - Add .github/workflows/test-patpy-mcp.yaml and build-patpy-mcp.yaml so mcp/tests/ runs on every PR (was previously only at release-tag time) and a broken mcp/pyproject.toml is caught before tagging. Both are path-filtered to mcp/** so they don't run on parent-only changes. - Enrich mcp/README.md with the cookiecutter's four canonical install patterns (uvx PyPI / uvx git / uvx local / pip) plus copyable mcp.json snippets, and document the two-file registry submission. Skills (correct API divergences surfaced by an end-to-end run): - sample_representation/SKILL.md: Pseudobulk's cell_group_key is a required positional arg (not optional); document that explicitly with an inline TypeError example, and update the minimal example to pass it. - supervised_methods/SKILL.md: PULSAR is zero-shot inference using a pretrained HuggingFace model on UCE foundation-model embeddings, not a trainable classifier on PCA features. Split the "common signature" into trainable (MixMIL/PaSCient) vs zero-shot (PULSAR), document layer="X_uce", device="cuda", and the HF-model download. Add the mixmil + torch-scatter install gotcha. Repo hygiene: - Tighten .gitignore: ignore .cache-*/, .venv-*/, /outputs/, /run_*.py, /.cellxgene-test-target.json, and /mcp/dist/. Prevents the patpy-mcp test cache and any future scratch from being committed. - Remove already-committed scratch from HEAD: 62.7 MB Slide-seq h5ad, 9.5 MB CellxGene catalog dump, the test-target sidecar, and the /.cellxgene-test-target.json probe file. Historical blobs will be evicted from .git/objects via a follow-up git filter-repo run. AGENTS.md: document the new mcp.json + workflows so future agents see them in the layout tree. Co-authored-by: Cursor <[email protected]>

review-notebook-app · 2026-05-05T14:00:44Z

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- Pack patpy skill modules (datasets, preprocessing, sample_representation, supervised_methods, evaluation, plotting) for export to Claude Code, Codex, and BioContext layouts via patpy-export-skills / patpy-export-biocontext - Add patpy.mcp FastMCP server (patpy-skills-mcp console script) exposing dataset_summary, preprocess_dataset, build_representation, evaluate_representation, run_supervised_prediction, generate_plot, simulate_dataset as MCP tools - Add example client configs under examples/mcp/ - Add tests for skill export bundles and MCP tool wrappers - Add [mcp] optional dependency group

# Conflicts: # .gitignore # CHANGELOG.md # README.md # docs/index.md # pyproject.toml # src/patpy/skills/SKILL.md # src/patpy/skills/sample_representation/SKILL.md # src/patpy/skills/supervised_methods/SKILL.md # src/patpy/tl/evaluation.py # tests/test_evaluation.py # tests/test_skills.py

… into feature/agent-skills

Feature/agent skills

VladimirShitov · 2026-05-10T15:37:48Z

Is this ready for review?

grpinto · 2026-05-12T05:19:22Z

@VladimirShitov I am not sure yet @benjaminfreyuu did you finish what you wanted to do ? I have not refactored the code. It is something that still needs to be done, reorganize stuff and test like on a large scale.

benjaminfreyuu · 2026-05-18T11:57:27Z

The skills part is working, MCP claude code integration and biocontextAI are added as well.
Claude Code import is tested. Not tested for Claude.ai. BiocontextAI addition not completed yet.
Either test it thoroughly, could also be later added (the MCP addition of the package, not the goncalo dataset MCP stuff). Wdyt? @grpinto @VladimirShitov

VladimirShitov and others added 30 commits September 13, 2025 01:32

Update version

324266b

Fix code style

4711fe8

Change catching Exception to more specific errors

852b8ee

Merge pull request lueckenlab#110 from lueckenlab/add-spare-metrics

ee5461a

Add SPARE metrics

Fix getting layer from obsm instead of a general slot

ed070a0

Bump up the version

7a788f7

Merge pull request lueckenlab#112 from lueckenlab/Fix/gloscope_py_X

7aaba7c

Fix/gloscope_py

Add anndata2ri

55e38f0

Update R interface to use converters

30a8af6

Set negative distances to 0 in gloscope

ac245e5

Add more explanations, run all implementations

2ebd4a3

Bump up version

86e7429

Add plots for gloscope reimplementation

e4e13f3

Add a conclusion

bf98d66

Rename the notebook

1c8113e

Remove the unused tutorial

731b39a

Pt gloscope tutorial after the basic one, remove unused links

9a77ddc

Describe 0.11.2 updates

df939cd

Bump up version

0da546b

Merge branch 'main' into gloscope_reimplementation_tutorial

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[pre-commit.ci] auto fixes from pre-commit.com hooks

d28212b

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Merge pull request lueckenlab#109 from EmmaSchonner/gloscope_reimplem…

8a5a70e

…entation_tutorial - Add the tutorials for the GloScope reimplementation - Fix R implementation of GloScope

Remove negative distances from gloscope output

ec3a1a7

Bump version up

3581751

[pre-commit.ci] auto fixes from pre-commit.com hooks

360609c

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Change order of commands to save sample names correctly

15b308f

[pre-commit.ci] auto fixes from pre-commit.com hooks

0ceb6e7

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Add a test for removing negative distances

32fe7fc

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05ecbb1

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Merge pull request lueckenlab#114 from lueckenlab/Fix/negative-distances

cecd3fa

Fix/negative distances

benjaminfreyuu and others added 12 commits May 4, 2026 16:55

Add tests for the fixed bugs

7a9574e

Update version to 0.15.3

02d7f84

[pre-commit.ci] auto fixes from pre-commit.com hooks

ef64aa4

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Merge pull request lueckenlab#140 from lueckenlab/Fix/knn_score

25dc3cd

Fix KNN score

Add packaging test for bundled skills

893f848

Add packaging test for bundled skills

899fa0d

Merge branch 'lueckenlab:main' into feature/agent-skills

a05cc52

Merge branch 'lueckenlab:main' into feature/agent-skills

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Merge pull request #2 from grpinto/feature/agent-skills

2de19be

Feature/agent skills

grpinto and others added 5 commits May 5, 2026 10:30

added MCP to externally call CellXgGene

a2f3b52

Merge pull request #3 from grpinto/grpinto_branch

0e5c592

Grpinto branch

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added an agents file

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grpinto force-pushed the main branch from eb9761f to f59880f Compare May 5, 2026 14:00

benjaminfreyuu and others added 4 commits May 6, 2026 00:13

Merge branch 'feature/agent-skills' of https://github.com/grpinto/patpy…

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… into feature/agent-skills

Merge pull request #4 from grpinto/feature/agent-skills

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Feature/agent skills

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MPC working#136

MPC working#136
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