Review: python-oncoref 1.8.207-1
Package Information
| Description | curated cancer reference data and analysis tools (Python library) Oncoref provides a Python API for curated cancer reference data, including cancer-type ontologies, tumor mutational burden, incidence and mortality, checkpoint-inhibitor response, gene identifiers, and cancer-testis antigen evidence. It also provides reference plots and access to Human Protein Atlas and per-cohort expression datasets. Small curated tables are included. Larger expression matrices and external reference datasets are downloaded and cached on demand. Genome integration requires the optional pyensembl package and an installed Ensembl release. This package provides the Python library and bundled reference tables. |
|---|---|
| Maintainer | Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org> |
| Changed By | Steffen Moeller <moeller@debian.org> |
| Sponsor | moeller@debian.org |
| Distribution | unstable |
| Architecture | all |
| VCS | git: https://salsa.debian.org/med-team/python-oncoref.git (browse) |
| Closes | #1150263 |
| Tracker | https://tracker.debian.org/pkg/python-oncoref |
| Uploaded | 26 days ago |
New Package Report
.changes
| Version | 1.8.207-1 |
|---|---|
| Changed-By | Steffen Moeller <moeller@debian.org> |
| Architecture | source all |
| Distribution | unstable |
| Date | Sat, 10 Oct 2026 15:21:41 +0200 |
| Source | python-oncoref |
Changelog
python-oncoref (1.8.207-1) unstable; urgency=medium
.
* Initial release. (Closes: #1150263)
- Python library and curated tables in python3-oncoref; command-line
interface and manual page in a separate oncoref binary package.
- Offline unit tests and installed-package autopkgtests.
- Fix driver-evidence validation for retired source gene symbols..dsc
| Section | science |
|---|---|
| Priority | optional |
| Component | main |
| Package-List | oncoref deb science optional arch=all python3-oncoref deb science optional arch=all |
debian/copyright
Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Source: https://github.com/pirl-unc/oncoref Upstream-Name: oncoref Upstream-Contact: Alex Rubinsteyn <alex.rubinsteyn@unc.edu> Files: * Copyright: 2026 Alex Rubinsteyn <alex.rubinsteyn@unc.edu> License: Apache-2.0 Files: debian/* Copyright: 2026 Steffen Moeller <moeller@debian.org> License: Apache-2.0 License: Apache-2.0 Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at . https://www.apache.org/licenses/LICENSE-2.0 . Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. . On Debian systems, the complete text of the Apache License, Version 2.0, can be found in /usr/share/common-licenses/Apache-2.0.
Review Information
accepted — allocated to awm 25 days ago, started 25 days ago, completed 25 days ago.
Final Comment
Hi,
Only one minor issue noted...
validate-retired-driver-symbols.patch fixes an upstream bug but is marked Forwarded: no
Files: debian/patches/validate-retired-driver-symbols.patch
Evidence: Forwarded: no on a patch that fixes an upstream validation failure (CBWD3 -> ZNG1C) in oncoref/drivers.py.
Problem: This is a genuine upstream bug that also affects PyPI users; keeping it Debian-only adds permanent patch maintenance. (test-installed-builder-audit.patch is correctly Debian-specific.)
Fix: Submit the fix upstream (small, already regression-tested in debian/tests/test_driver_symbols.py) and update Forwarded: when accepted.
Thanks!