feat(converters): add OpenMS QPX enrichment and MuData export support by Shen-YuFei · Pull Request #204 · bigbio/qpx

Shen-YuFei · 2026-04-25T09:03:49Z

This pull request introduces comprehensive support for OpenMS QPX enrichment and improves DIA-NN conversion accuracy in the QPX toolkit. The most significant changes are the addition of a new Docker build and publishing workflow, a Dockerfile for containerization, and enhancements to the DIA-NN and OpenMS conversion pipelines. These updates make it easier to deploy QPX as a container, expand supported workflows, and improve provenance tracking.

Dockerization and CI/CD:

Added a .dockerignore file to exclude non-essential files from Docker build context, ensuring smaller and more secure images.
Introduced a Dockerfile for building a minimal QPX image with the necessary dependencies and CLI tool, supporting the [mudata] extra.
Added a GitHub Actions workflow .github/workflows/docker-publish.yml to automate building and publishing the QPX Docker image to GHCR, triggered on pushes, tags, PRs, and manual runs.

OpenMS QPX Enrichment Support:

Added a new convert openms command to the CLI (qpx/cli/convert.py), which enriches OpenMS ProteomicsLFQ -out_qpx Parquet files into a full QPX dataset using SDRF metadata. [1] [2]
Implemented and exposed OpenMSConverter in the codebase, including module exports and new converter logic. [1] [2] [3]

DIA-NN Conversion Improvements:

Enhanced DIA-NN conversion to accept a --diann-log option, auto-detecting and recording the DIA-NN version from the provided log file for improved provenance. [1] [2] [3] [4] [5] [6] [7]
Improved DIA-NN protein group adapter to robustly strip common file extensions from run column names, supporting more file types and ensuring consistency. [1] [2] [3] [4] [5]

Dependency Management:

Added a new mudata extra to pyproject.toml and included it in the all and dev extras to support MuData export in Docker and development environments.

These changes collectively improve QPX's usability, reproducibility, and compatibility with modern proteomics workflows.

…tection

…ction

coderabbitai · 2026-04-25T09:03:56Z

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codacy-production · 2026-04-25T09:07:22Z

Not up to standards ⛔

🔴 Issues 1 medium · 7 minor

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⚠ 8 issues (≤ 0 issues of at least minor severity)

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8 new issues

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BestPractice 1 medium

Documentation 7 minor

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🟢 Metrics 46 complexity · 6 duplication

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Complexity 46

Duplication 6

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ypriverol · 2026-04-25T09:24:24Z

@Shen-YuFei Why do we need a DockerFile?

Copilot

Pull request overview

Adds OpenMS -out_qpx enrichment support and improves dataset provenance/export ergonomics across QPX, including containerization for easier deployment.

Changes:

Introduce OpenMSConverter + qpxc convert openms to enrich OpenMS -out_qpx core tables into a full QPX dataset (metadata + provenance + ontology + dataset tables).
Improve MuData export robustness (NA filtering in uns, per-table intensity label detection, and h5py-safe string sanitization).
Enhance DIA-NN conversion provenance (auto-detect DIA-NN version from log) and broaden run column extension stripping; add Docker image + GHCR publish workflow.

Reviewed changes

Copilot reviewed 13 out of 13 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
`qpx/converters/openms/converter.py`	New OpenMS enrichment orchestrator: discover/validate/copy core parquet files and generate metadata/provenance/ontology/dataset outputs.
`qpx/converters/openms/__init__.py`	Export `OpenMSConverter` from the OpenMS converters module.
`qpx/cli/convert.py`	Add `qpxc convert openms` command; add `--diann-log` option for DIA-NN provenance enrichment.
`qpx/converters/diann/converter.py`	Parse DIA-NN version from a summary log and record it in provenance + dataset metadata.
`qpx/converters/diann/pg_adapter.py`	Make run column detection/normalization more robust by stripping multiple common raw-file extensions.
`qpx/mudata.py`	Fix MuData export edge cases: handle `pd.NA`/`pd.NaT`, detect intensity labels per table, and sanitize string-like columns for h5mu serialization.
`qpx/converters/__init__.py`	Expose `OpenMSConverter` at the top-level converters package.
`tests/converters/test_openms_converter.py`	Add tests for OpenMS enrichment: file discovery, full bundle output, schema validation, provenance, and SDRF/no-SDRF behavior.
`tests/unit/test_mudata.py`	Add regression tests for MuData export metadata attachment and per-table intensity label detection.
`pyproject.toml`	Add `mudata` optional extra and include it in `all`/`dev` dependency sets.
`Dockerfile`	Provide a slim container build that installs QPX with `[mudata]` extra and sets version fallback for SCM-based versioning.
`.github/workflows/docker-publish.yml`	Add GHCR build/publish workflow for Docker image (push/tag/PR/manual triggers).
`.dockerignore`	Reduce Docker build context by excluding tests, docs, and other non-essential directories/files.

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Copilot · 2026-04-25T09:28:23Z

+                if score and "name" in score and score["name"]:
+                    names.add(score["name"])


In _collect_score_names, the code looks for a name key inside each additional_scores entry, but the QPX score struct uses score_name (see qpx/core/data/schemas/types.yaml). As written, this will fail to collect any score names and will silently omit score-derived ontology entries. Update the extraction to read score_name (and consider guarding for both keys if you need backward compatibility).

Suggested change

if score and "name" in score and score["name"]:

names.add(score["name"])

if score:

score_name = score.get("score_name") or score.get("name")

if score_name:

names.add(score_name)

Copilot · 2026-04-25T09:28:24Z

+                "tool_uri": None,
+                "parameters": None,
+                "config": None,
+                "output_views": [SAMPLE, RUN, ONTOLOGY],
+            },


_build_provenance() always lists SAMPLE and RUN in output_views, but convert() can skip SDRF conversion (and thus never create sample/run files). This makes provenance inaccurate for runs without sdrf_path. Consider building output_views dynamically based on whether SDRF conversion actually ran (and whether ontology was written).

Copilot · 2026-04-25T09:28:24Z

+    help="SDRF metadata file path (for sample/run generation)",
+    required=True,


The openms CLI command requires --sdrf-file, but OpenMSConverter supports running without SDRF (and there’s a test asserting sample/run are skipped when SDRF is absent). Either make --sdrf-file optional (and update help/examples accordingly), or remove the no-SDRF codepath/tests so the CLI and converter behavior stay consistent.

Suggested change

help="SDRF metadata file path (for sample/run generation)",

required=True,

help="Optional SDRF metadata file path; if omitted, sample/run generation is skipped",

required=False,

Shen-YuFei · 2026-04-25T09:42:56Z

@Shen-YuFei Why do we need a DockerFile?

@ypriverol QPX is not on BioConda yet, so there's no BioContainers image available. The Dockerfile is currently the only way to build the ghcr.io/bigbio/qpx image that quantms depends on. If you plan to publish QPX to BioConda, we can remove it afterwards.

Shen-YuFei added 6 commits April 21, 2026 15:34

feat(mudata): add MuData extras, Docker image, and per-table label de…

f3c7545

…tection

feat(converters): add OpenMS QPX converter for -out_qpx enrichment

a98668c

fix(pg_adapter): support non-mzML extensions in pg_matrix column dete…

c99da01

…ction

Merge branch 'dev' of https://github.com/Shen-YuFei/qpx into dev

1ca82f2

feat(diann): auto-detect DIA-NN version from summary log

69c378f

fix(mudata): stem-based run matching and NaN serialization in h5mu

3becbc7

Copilot AI review requested due to automatic review settings April 25, 2026 09:03

Shen-YuFei requested review from ypriverol and removed request for Copilot April 25, 2026 09:03

Copilot started reviewing on behalf of Shen-YuFei April 25, 2026 09:04 View session

ypriverol requested review from Copilot and timosachsenberg April 25, 2026 09:24

Copilot started reviewing on behalf of ypriverol April 25, 2026 09:24 View session

Copilot AI reviewed Apr 25, 2026

View reviewed changes

fix(codacy): pin versions and resolve codacy warnings

eacb586

fix(codacy): NumPy docstring style and eliminate SQL string construction

1832f32

ypriverol merged commit dc2a252 into bigbio:dev Apr 28, 2026
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feat(converters): add OpenMS QPX enrichment and MuData export support#204

feat(converters): add OpenMS QPX enrichment and MuData export support#204
ypriverol merged 8 commits intobigbio:devfrom
Shen-YuFei:dev

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		if score and "name" in score and score["name"]:
		names.add(score["name"])

-                if score and "name" in score and score["name"]:
-                    names.add(score["name"])
+                if score:
+                    score_name = score.get("score_name") or score.get("name")
+                    if score_name:
+                        names.add(score_name)

		help="SDRF metadata file path (for sample/run generation)",
		required=True,

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