feat(converters): add OpenMS QPX enrichment and MuData export support

.dockerignore

@@ -0,0 +1,36 @@
+# Exclude non-essential content from the Docker build context.
+# Keep only what ``pip install .`` needs: pyproject.toml, README.md, LICENSE, qpx/.
+
+.git/
+.github/
+.pytest_cache/
+.hypothesis/
+.ruff_cache/
+.tmp/
+.vscode/
+.windsurf/
+.idea/
+__pycache__/
+*.pyc
+*.pyo
+*.egg-info/
+build/
+dist/
+.coverage
+coverage.xml
+.DS_Store
+.venv/
+venv/
+env/
+
+# Project-specific large/non-essential dirs
+tests/
+docs/
+site/
+benchmarks/
+scripts/
+data/
+
+# Docker-related files are not needed inside the image
+Dockerfile
+.dockerignore

.github/workflows/docker-publish.yml

@@ -0,0 +1,88 @@
+# Build and publish the QPX container image to GitHub Container Registry (GHCR).
+#
+# Triggers:
+#   - push to main            -> publishes the `dev` tag (floating)
+#   - push tag v*.*.*         -> publishes semantic version tags + `latest`
+#   - pull_request to main    -> build only (smoke-test the Dockerfile)
+#   - workflow_dispatch       -> manual run
+#
+# Image:    ghcr.io/${owner}/qpx        (expands to ghcr.io/bigbio/qpx)
+# Platform: linux/amd64                 (multi-arch can be added later)
+#
+# Repo settings required:
+#   Settings -> Actions -> General -> Workflow permissions -> "Read and write permissions"
+#   (the default GITHUB_TOKEN is used to authenticate against GHCR)
+
+name: Publish Docker image
+
+on:
+  push:
+    branches: [main]
+    tags: ["v*.*.*"]
+  pull_request:
+    branches: [main]
+  workflow_dispatch:
+
+permissions:
+  contents: read
+  packages: write
+  id-token: write
+
+jobs:
+  docker:
+    name: Build and push to GHCR
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+          fetch-tags: true
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+
+      - name: Log in to GHCR
+        if: github.event_name != 'pull_request'
+        uses: docker/login-action@v3
+        with:
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Resolve QPX version for build-arg
+        id: ver
+        run: |
+          if [[ "${GITHUB_REF}" == refs/tags/v* ]]; then
+            echo "qpx_version=${GITHUB_REF#refs/tags/v}" >> "$GITHUB_OUTPUT"
+          else
+            echo "qpx_version=0.0.0.dev0+$(git rev-parse --short HEAD)" >> "$GITHUB_OUTPUT"
+          fi
+
+      - name: Extract image metadata
+        id: meta
+        uses: docker/metadata-action@v5
+        with:
+          images: ghcr.io/${{ github.repository_owner }}/qpx
+          tags: |
+            type=semver,pattern={{version}}
+            type=semver,pattern={{major}}.{{minor}}
+            type=ref,event=pr
+            type=raw,value=dev,enable=${{ github.ref == 'refs/heads/main' && github.event_name == 'push' }}
+            type=raw,value=latest,enable=${{ startsWith(github.ref, 'refs/tags/v') }}
+            type=sha,format=short
+
+      - name: Build and push
+        uses: docker/build-push-action@v6
+        with:
+          context: .
+          platforms: linux/amd64
+          push: ${{ github.event_name != 'pull_request' }}
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
+          build-args: |
+            QPX_VERSION=${{ steps.ver.outputs.qpx_version }}
+          provenance: true
+          cache-from: type=gha
+          cache-to: type=gha,mode=max

Dockerfile

@@ -0,0 +1,39 @@
+# syntax=docker/dockerfile:1.6
+#
+# QPX container image
+# -------------------
+# Provides the ``qpxc`` CLI built from this repository's source, with the
+# optional ``[mudata]`` extras pre-installed for MuData export.
+#
+# Build:
+#   docker build -t ghcr.io/bigbio/qpx:dev .
+#
+# Run:
+#   docker run --rm -v $(pwd):/data ghcr.io/bigbio/qpx:dev convert diann --help
+
+FROM python:3.11-slim-bookworm
+
+# Runtime system deps required by pyOpenMS (see environment.yml).
+RUN apt-get update \
+ && apt-get install -y --no-install-recommends libglib2.0-0=2.74.6-2+deb12u8 procps=2:4.0.2-3 \
+ && rm -rf /var/lib/apt/lists/*
+
+# hatch-vcs derives the version from git history; when the build context lacks
+# a .git directory (typical Docker builds), fall back to this placeholder.
+ARG QPX_VERSION=0.0.0.dev0
+ENV SETUPTOOLS_SCM_PRETEND_VERSION=${QPX_VERSION}
+
+# Minimal build inputs required by ``pip install .`` under hatchling.
+WORKDIR /src
+COPY pyproject.toml README.md LICENSE ./
+COPY qpx ./qpx
+
+RUN pip install --no-cache-dir --upgrade pip==24.0 \
+ && pip install --no-cache-dir ".[mudata]" \
+ && rm -rf /src
+
+LABEL org.opencontainers.image.source="https://github.com/bigbio/qpx"
+LABEL org.opencontainers.image.description="QPX: Quantitative Proteomics Parquet toolkit (qpxc CLI) with MuData export"
+LABEL org.opencontainers.image.licenses="Apache-2.0"
+
+WORKDIR /data

pyproject.toml

@@ -28,13 +28,15 @@ mzidentml = ["lxml>=4.9.0"]
 transforms = ["biopython", "mygene>=1.0.0", "anndata>=0.9.0"]
 plotting = ["plotly>=5.0.0", "scikit-learn>=1.5.0"]
 quantify = ["mokume>=0.1.0", "directlfq"]
-all = ["lxml>=4.9.0", "biopython", "mygene>=1.0.0", "anndata>=0.9.0", "plotly>=5.0.0", "scikit-learn>=1.5.0", "mokume>=0.1.0", "directlfq"]
+mudata = ["mudata>=0.2.4", "anndata>=0.9.0"]
+all = ["lxml>=4.9.0", "biopython", "mygene>=1.0.0", "anndata>=0.9.0", "plotly>=5.0.0", "scikit-learn>=1.5.0", "mokume>=0.1.0", "directlfq", "mudata>=0.2.4"]
 dev = [
     "pytest",
     "pytest-timeout",
     "hypothesis",
     "lxml>=4.9.0",
     "anndata",
+    "mudata>=0.2.4",
     "scikit-learn",
     "plotly>=5.0.0",
     "pre-commit",

qpx/cli/convert.py

@@ -9,6 +9,7 @@
     qpxc convert maxquant   — MaxQuant output to QPX
     qpxc convert fragpipe   — FragPipe output to QPX
     qpxc convert mzidentml  — mzIdentML (incl. XL-MS 1.3) to QPX
+    qpxc convert openms     — OpenMS -out_qpx enrichment to full QPX
     qpxc convert sdrf       — SDRF to sample.parquet + run.parquet
 """
 
@@ -20,6 +21,8 @@
 
 import click
 
+from qpx.converters.openms import OpenMSConverter
+
 logger = logging.getLogger("qpx.cli.convert")
 
 
@@ -263,6 +266,11 @@
     show_default=True,
     help="Parquet compression codec.",
 )
+@click.option(
+    "--diann-log",
+    help="DIA-NN summary log file (version auto-detected from first line)",
+    type=click.Path(exists=True, dir_okay=False, path_type=Path),
+)
 @click.option("--verbose", help="Enable verbose logging", is_flag=True)
 def convert_diann_cmd(
     report_path: Path,
@@ -281,6 +289,7 @@
     project_accession: Optional[str],
     enrich_pride: bool,
     compression: str,
+    diann_log: Optional[Path],
     verbose: bool,
 ):
     """Convert DIA-NN report to QPX format.
@@ -321,6 +330,7 @@
         duckdb_max_memory=duckdb_max_memory,
         duckdb_threads=duckdb_threads,
         compression=compression,
+        diann_log=str(diann_log) if diann_log else None,
     )
     converter.convert_features(
         mzml_info_folder=mzml_info_folder,
@@ -779,6 +789,103 @@
     click.echo(f"mzIdentML conversion complete. Output: {output_folder}")
 
 
+# ---------------------------------------------------------------------------
+# OpenMS
+# ---------------------------------------------------------------------------
+
+
+@convert.command("openms")
+@click.option(
+    "--qpx-dir",
+    help="Directory containing OpenMS -out_qpx parquet files (*.psm.parquet, *.feature.parquet, *.pg.parquet)",
+    required=True,
+    type=click.Path(exists=True, file_okay=False, path_type=Path),
+)
+@click.option(
+    "--sdrf-file",
+    help="SDRF metadata file path (for sample/run generation)",
+    required=True,
+    type=click.Path(exists=True, dir_okay=False, path_type=Path),
+)
+@click.option(
+    "--output-folder",
+    help="Output directory for the full QPX dataset",
+    required=True,
+    type=click.Path(file_okay=False, path_type=Path),
+)
+@click.option(
+    "--output-prefix",
+    help="Prefix for output file names",
+    default="openms",
+)
+@click.option(
+    "--project-accession",
+    help="PRIDE / ProteomeXchange accession (e.g. PXD001819)",
+)
+@click.option(
+    "--enrich-pride",
+    help="Fetch project metadata from PRIDE API after conversion",
+    is_flag=True,
+    default=False,
+)
+@click.option(
+    "--compression",
+    type=click.Choice(["zstd", "snappy", "gzip", "none"], case_sensitive=False),
+    default="zstd",
+    show_default=True,
+    help="Parquet compression codec.",
+)
+@click.option("--verbose", help="Enable verbose logging", is_flag=True)
+def convert_openms_cmd(**kwargs):
+    r"""Enrich OpenMS ProteomicsLFQ -out_qpx output into a full QPX dataset.
+
+    Validates the existing psm/feature/pg parquet files, copies them to the
+    output folder, and generates the missing metadata tables (run, sample,
+    ontology, provenance, dataset) from the SDRF file.
+
+    \b
+    Examples:
+        # Enrich OpenMS QPX output
+        qpxc convert openms \\
+            --qpx-dir ./openms_qpx_output \\
+            --sdrf-file metadata.sdrf.tsv \\
+            --output-folder ./qpx_full
+
+        # With project accession
+        qpxc convert openms \\
+            --qpx-dir ./openms_qpx_output \\
+            --sdrf-file metadata.sdrf.tsv \\
+            --output-folder ./qpx_full \\
+            --project-accession PXD001819
+    """
+    qpx_dir = kwargs["qpx_dir"]
+    sdrf_file = kwargs["sdrf_file"]
+    output_folder = kwargs["output_folder"]
+    output_prefix = kwargs["output_prefix"]
+    project_accession = kwargs["project_accession"]
+    enrich_pride = kwargs["enrich_pride"]
+    compression = kwargs["compression"]
+    verbose = kwargs["verbose"]
+
+    if verbose:
+        logging.getLogger().setLevel(logging.DEBUG)
+
+    converter = OpenMSConverter(
+        qpx_dir=qpx_dir,
+        sdrf_path=sdrf_file,
+        compression=compression,
+    )
+    converter.convert(
+        output_folder=output_folder,
+        output_prefix=output_prefix,
+        project_accession=project_accession,
+    )
+
+    _maybe_enrich_pride(output_folder, project_accession, enrich_pride)
+
+    click.echo(f"OpenMS QPX enrichment complete. Output: {output_folder}")
+
+
 # ---------------------------------------------------------------------------
 # SDRF
 # ---------------------------------------------------------------------------

qpx/converters/__init__.py

@@ -20,6 +20,7 @@
 from qpx.converters.maxquant.pg_adapter import MaxQuantPgAdapter
 from qpx.converters.maxquant.psm_adapter import MaxQuantPsmAdapter
 from qpx.converters.mzidentml.psm_adapter import MzIdentMLPsmAdapter
+from qpx.converters.openms.converter import OpenMSConverter
 from qpx.converters.orchestrator import BaseOrchestrator, build_dataset_record
 from qpx.converters.quantms.converter import QuantMSConverter
 from qpx.converters.quantms.feature_adapter import QuantmsFeatureAdapter
@@ -55,4 +56,6 @@
     "FragPipeConverter",
     # mzIdentML
     "MzIdentMLPsmAdapter",
+    # OpenMS
+    "OpenMSConverter",
 ]