Migrate project meta code

.github/workflows/python-publish.yaml

@@ -0,0 +1,54 @@
+name: Publish Python packages to PyPI
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  build:
+    name: Build distribution
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          fetch-depth: 0  # required for setuptools_scm to determine version from git tags
+
+      - name: Set up Python
+        uses: actions/setup-python@v6
+        with:
+          python-version: "3.12"
+
+      - name: Install build
+        run: python -m pip install build
+
+      - name: Build package
+        run: |
+          cd packages/python/openproblems
+          python -m build
+
+      - name: Upload distribution artifacts
+        uses: actions/upload-artifact@v4
+        with:
+          name: python-package-distributions
+          path: packages/python/openproblems/dist/
+
+  publish-to-pypi:
+    name: Publish to PyPI
+    needs: build
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/openproblems
+    permissions:
+      id-token: write  # required for OIDC trusted publishing
+
+    steps:
+      - name: Download distribution artifacts
+        uses: actions/download-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

packages/python/openproblems/CHANGELOG.md

@@ -1,3 +1,27 @@
+# openproblems core Python v0.2.0
+
+## NEW FUNCTIONALITY
+
+* `project`:
+  - `resolve_path`: Resolve a path relative to a parent path or project root.
+
+* `project.component_tests`:
+  - `run_check_config` / `check_config`: Validate a component's Viash config (namespace, type, metadata, normalization, variants, Nextflow runner).
+  - `run_and_check_output`: Run a component executable and validate its output files against format specifications.
+
+* `project.docs`:
+  - `read_task_config`: Read a task-level configuration file.
+  - `read_task_metadata`: Read and assemble full task metadata by traversing the task's component graph.
+  - `read_component_spec`: Read a component API specification.
+  - `read_file_format`: Read a file format specification.
+  - `render_task_readme_qmd`: Render a Quarto README document for a task.
+  - `render_component_spec`: Render a component specification as a Markdown section.
+  - `render_file_format`: Render a file format specification as a Markdown section.
+
+## MINOR CHANGES
+
+* Improve diagnostic print messages in `check_config` and `run_and_check_output` to be more descriptive.
+
 # openproblems core Python v0.1.1
 
 ## NEW FUNCTIONALITY

packages/python/openproblems/README.md

@@ -0,0 +1,56 @@
+# openproblems
+
+[![PyPI](https://img.shields.io/pypi/v/openproblems)](https://pypi.org/project/openproblems/)
+[![Python Versions](https://img.shields.io/pypi/pyversions/openproblems)](https://pypi.org/project/openproblems/)
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+
+Core Python helper functions for [OpenProblems](https://openproblems.bio) benchmarking tasks.
+
+## Installation
+
+```bash
+pip install openproblems
+```
+
+## Modules
+
+### `openproblems.project`
+
+Utilities for working with Viash projects.
+
+- `find_project_root`: Find the root of a Viash project.
+- `read_nested_yaml`: Read a nested YAML file.
+- `read_viash_config`: Read a Viash configuration file.
+- `resolve_path`: Resolve a path relative to a parent or project path.
+
+#### `openproblems.project.component_tests`
+
+Helpers for writing component tests.
+
+- `run_check_config` / `check_config`: Validate a component's Viash configuration.
+- `run_and_check_output`: Run a component and validate its output files against format specs.
+
+#### `openproblems.project.docs`
+
+Utilities for generating task documentation.
+
+- `read_task_config`: Read a task-level configuration file.
+- `read_task_metadata`: Read and assemble full task metadata.
+- `read_component_spec`: Read a component API specification.
+- `read_file_format`: Read a file format specification.
+- `render_task_readme_qmd`: Render a Quarto README for a task.
+- `render_component_spec`: Render a component specification as Markdown.
+- `render_file_format`: Render a file format specification as Markdown.
+
+### `openproblems.utils`
+
+General-purpose utilities.
+
+- `strip_margin`: Strip leading margin characters from a multiline string.
+- `deep_merge`: Recursively merge two dictionaries.
+
+## Links
+
+- **Documentation**: <https://openproblems.bio/documentation>
+- **Repository**: <https://github.com/openproblems-bio/core>
+- **Issue tracker**: <https://github.com/openproblems-bio/core/issues>

packages/python/openproblems/pyproject.toml

@@ -12,8 +12,23 @@ authors = [
 license = { text = "MIT" }
 readme = "README.md"
 requires-python = ">= 3.9"
+keywords = ["openproblems", "benchmarking", "bioinformatics", "viash"]
+classifiers = [
+  "Development Status :: 4 - Beta",
+  "Intended Audience :: Science/Research",
+  "License :: OSI Approved :: MIT License",
+  "Operating System :: OS Independent",
+  "Programming Language :: Python :: 3",
+  "Programming Language :: Python :: 3.9",
+  "Programming Language :: Python :: 3.10",
+  "Programming Language :: Python :: 3.11",
+  "Programming Language :: Python :: 3.12",
+  "Programming Language :: Python :: 3.13",
+  "Topic :: Scientific/Engineering :: Bio-Informatics",
+]
 dependencies = [
-  'PyYAML'
+  'PyYAML',
+  'networkx',
 ]
 
 [project.optional-dependencies]
@@ -22,8 +37,10 @@ test = [
 ]
 
 [project.urls]
-homepage = "https://openproblems.bio/documentation"
-repository = "https://github.com/openproblems-bio/core"
+Homepage = "https://openproblems.bio/documentation"
+Repository = "https://github.com/openproblems-bio/core"
+"Bug Tracker" = "https://github.com/openproblems-bio/core/issues"
+Changelog = "https://github.com/openproblems-bio/core/blob/main/packages/python/openproblems/CHANGELOG.md"
 
 [tool.setuptools.packages.find]
 where = ["src"]

packages/python/openproblems/src/openproblems/__init__.py

@@ -2,6 +2,6 @@
 from . import utils
 
 __all__ = [
-  "project",
-  "utils",
+    "project",
+    "utils",
 ]

packages/python/openproblems/src/openproblems/project/__init__.py

@@ -1,9 +1,17 @@
 from .find_project_root import find_project_root
 from .read_viash_config import read_viash_config
 from .read_nested_yaml import read_nested_yaml
+from .component_tests.check_config import run_check_config as check_config
+from .component_tests.run_and_check_output import run_and_check_output
+from .docs.read_task_metadata import read_task_metadata
+from .docs.render_task_readme_qmd import render_task_readme_qmd
 
 __all__ = [
     "find_project_root",
     "read_viash_config",
     "read_nested_yaml",
-]
+    "check_config",
+    "run_and_check_output",
+    "read_task_metadata",
+    "render_task_readme_qmd",
+]

packages/python/openproblems/src/openproblems/project/component_tests/__init__.py

@@ -0,0 +1,41 @@
+from .check_config import (
+    check_info,
+    check_links,
+    check_references,
+    check_url,
+    run_check_config,
+)
+from .run_and_check_output import (
+    check_anndata,
+    check_dataframe,
+    check_dictionary,
+    check_format,
+    check_input_files,
+    check_output_files,
+    check_spatialdata,
+    generate_cmd_args,
+    get_argument_sets,
+    run_and_check_output,
+    run_component,
+)
+
+__all__ = [
+    # check_config
+    "check_info",
+    "check_links",
+    "check_references",
+    "check_url",
+    "run_check_config",
+    # run_and_check_output
+    "check_anndata",
+    "check_dataframe",
+    "check_dictionary",
+    "check_format",
+    "check_input_files",
+    "check_output_files",
+    "check_spatialdata",
+    "generate_cmd_args",
+    "get_argument_sets",
+    "run_and_check_output",
+    "run_component",
+]