Add ChEBI web service converter

.flake8

@@ -0,0 +1,7 @@
+[flake8]
+# uv creates the virtual environment inside the repository, so a bare `flake8 .`
+# would otherwise descend into the installed dependencies and report their issues.
+extend-exclude =
+    .venv
+    build
+    dist

.github/workflows/publish_pypi.yaml

@@ -10,7 +10,12 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v6
-      - name: Build and publish to pypi
-        uses: JRubics/poetry-publish@v2.1
+      - name: Install uv
+        uses: astral-sh/setup-uv@v10.3.3
+      - name: Build sdist and wheel
+        run: |
+          uv build
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
         with:
-          pypi_token: ${{ secrets.PYPI_API_TOKEN }}
+          password: ${{ secrets.PYPI_API_TOKEN }}

.github/workflows/test-package.yml

@@ -13,23 +13,22 @@ jobs:
 
     steps:
       - uses: actions/checkout@v6
-      - name: Set up Python 3.12
-        uses: actions/setup-python@v6
+      - name: Install uv
+        uses: astral-sh/setup-uv@v10.3.3
         with:
-          python-version: 3.12
+          python-version: "3.12"
       - name: Install dependencies
         run: |
-          pip install poetry
-          poetry install --with=dev
+          uv sync --frozen
       - name: Lint with ruff
         run: |
-          poetry run ruff check . --fix --exit-non-zero-on-fix
+          uv run ruff check . --fix --exit-non-zero-on-fix
       - name: Lint with flake8
         run: |
           # stop the build if there are Python syntax errors or undefined names
-          poetry run flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+          uv run flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
           # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-          poetry run flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+          uv run flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
       - name: Test with pytest
         run: |
-          poetry run pytest --cov --cov-report term --cov-report xml --junitxml=xunit-result.xml
+          uv run pytest --cov --cov-report term --cov-report xml --junitxml=xunit-result.xml

.gitignore

@@ -5,4 +5,9 @@ MSMetaEnhancer_*.log
 dist
 MSMetaEnhancer.egg-info
 .vscode
-poetry.lock
+.venv
+# copied into the docs source tree by docs/source/conf.py at build time
+docs/source/readme.md
+docs/source/CHANGELOG.md
+docs/source/CONTRIBUTING.md
+docs/build

.readthedocs.yaml

@@ -10,17 +10,15 @@ build:
   os: ubuntu-22.04
   tools:
     python: "3.12"
-  jobs:
-    post_create_environment:
-      # Install poetry
-      # https://python-poetry.org/docs/#installing-manually
-      - pip install poetry
-    post_install:
-      # Install dependencies with 'docs' dependency group
-      # https://python-poetry.org/docs/managing-dependencies/#dependency-groups
-      # VIRTUAL_ENV needs to be set manually for now.
-      # See https://github.com/readthedocs/readthedocs.org/pull/11152/
-      - VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH poetry install --with docs
+
+# Install the project and the 'docs' dependency group with uv.
+# https://docs.readthedocs.com/platform/stable/config-file/v2.html#python-install
+python:
+  install:
+    - method: uv
+      command: sync
+      groups:
+        - docs
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:

CHANGELOG.md

@@ -7,6 +7,22 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## Unreleased
 
+### Added
+- Added a `ChEBI` web converter querying the ChEBI service (https://www.ebi.ac.uk/chebi/)
+  - Supports `compound_name`, `iupac_name`, `inchikey`, `inchi`, `smiles`, and `chebiid` as source attributes and returns `chebiid`, `compound_name`, `iupac_name`, `inchikey`, `inchi`, `smiles`, and `formula`
+  - Structure search from SMILES uses the ChEBI `structure_search` endpoint with `type=similarity` and a similarity threshold of 1
+- Declared `pytest-asyncio` explicitly instead of relying on it arriving transitively, and moved `myst-parser` from the `dev` to the `docs` group so the documentation dependencies are self-contained
+
+### Changed
+- Project management moved from Poetry to [uv](https://docs.astral.sh/uv/): metadata converted to PEP 621, `uv_build` is the build backend, and `uv` now handles virtual environments, tests, linting, the docs build, and the package build
+- `uv.lock` is committed and used as the source of truth; CI installs with `uv sync --frozen`, so a dependency change without a refreshed lock now fails instead of silently re-resolving
+- Read the Docs installs with uv natively, which removes the `pip install poetry` step and its `VIRTUAL_ENV` workaround
+- PyPI publishing builds with `uv build` and uploads with `pypa/gh-action-pypi-publish` in place of `JRubics/poetry-publish`
+- `docs/source/conf.py` resolves its paths relative to itself rather than to the working directory, so the documentation also builds from the repository root
+
+### Fixed
+- Normalize unhyphenated CAS numbers in the `Wikidata` converter before querying: Wikidata stores `P231` hyphenated only, so a source `casno` such as `50782` previously matched nothing. `fix_cas_number` moved to `libs.utils.Generic` and now leaves values that cannot be CAS numbers untouched instead of inserting dashes into them
+
 ## [0.6.1] - 2026-10-22
 
 ### Added

CONTRIBUTING.md

@@ -29,7 +29,7 @@ In case you feel like you've made a valuable contribution, but you don't know ho
 1. (**important**) announce your plan to the rest of the community *before you start working*. This announcement should be in the form of a (new) issue;
 1. (**important**) wait until some kind of consensus is reached about your idea being a good idea;
 1. if needed, fork the repository to your own Github profile and create your own feature branch off of the latest master commit. While working on your feature branch, make sure to stay up to date with the main branch by pulling in changes, possibly from the 'upstream' repository (follow the instructions [here](https://help.github.com/articles/configuring-a-remote-for-a-fork/) and [here](https://help.github.com/articles/syncing-a-fork/));
-1. make sure the existing tests still work by running ``pytest``;
+1. make sure the existing tests still work by running ``uv run pytest`` (see the [setup instructions](README.md#developer-documentation));
 1. add your own tests (if necessary);
 1. update or expand the documentation;
 1. update the [CHANGELOG](CHANGELOG.md) file with change;
@@ -259,12 +259,12 @@ After implementing your converter:
 
 1. Run the existing tests to ensure you haven't broken anything:
    ```bash
-   pytest tests/
+   uv run pytest tests/
    ```
 
 2. Run your specific tests:
    ```bash
-   pytest tests/test_YourService.py -v
+   uv run pytest tests/test_YourService.py -v
    ```
 
 3. Test the integration by using the converter in a real scenario

MSMetaEnhancer/libs/Curator.py

@@ -4,6 +4,7 @@
     is_valid_inchikey,
 )
 from MSMetaEnhancer.libs.utils.Errors import InvalidAttributeFormat
+from MSMetaEnhancer.libs.utils.Generic import fix_cas_number as add_cas_dashes
 
 
 # Example usage
@@ -55,10 +56,7 @@ def fix_cas_number(cas_number):
         :param cas_number: given CAS number
         :return: CAS number enriched by dashes (if needed)
         """
-        if isinstance(cas_number, str):
-            if "-" not in cas_number:
-                return f"{cas_number[:-3]}-{cas_number[-3:-1]}-{cas_number[-1]}"
-        return cas_number
+        return add_cas_dashes(cas_number)
 
     @staticmethod
     def filter_invalid_metadata(metadata, log, job):