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bioconda / bioconda-recipes

Conda recipes for the bioconda channel.
https://bioconda.github.io
MIT License
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Setuputils changed the filenames of sdist tarballs: need migration #48971

Open corneliusroemer opened 3 days ago

corneliusroemer commented 3 days ago

I noticed that the filenames of sdist source tarballs for python packages changed around December 2023 for packages containing hyphens (if they are packaged with setuptools and use the latest version).

This means that autobumps fail for such packages.

I noticed this on the example of nextstrain-cli, see this issue for a discussion of the issue and its background genesis: https://github.com/nextstrain/cli/issues/378

Long story short, we need to check the pypi urls for a bunch of recipes.

Here's a lit of recipes to check, I got them using the rg query: rg "url:.*pypi.io.*/.*-.*-\{\{ version \}\}.tar.gz"

recipes/hic-straw/meta.yaml:  url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/hic-straw-{{ version }}.tar.gz
recipes/clinvar-this/meta.yaml:  url: https://pypi.io/packages/source/c/clinvar-this/clinvar-this-{{ version }}.tar.gz
recipes/jms-metabolite-services/meta.yaml:  url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/jms-metabolite-services-{{ version }}.tar.gz
recipes/cami-opal/meta.yaml:  url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/cami-opal-{{ version }}.tar.gz
recipes/bio_hansel/meta.yaml:  url: https://pypi.io/packages/source/{{ name[0] }}/{{ name | replace("_", "-") }}/{{ name }}-{{ version }}.tar.gz
recipes/moods/meta.yaml:  url: https://pypi.io/packages/source/{{ name[0] }}/mira-moods/mira-moods-{{ version }}.tar.gz
recipes/beacon2-import/meta.yaml:  url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/beacon2-import-{{ version }}.tar.gz
recipes/feature_merge/meta.yaml:  url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name | replace('_', '-') }}/{{ name }}-{{ version }}.tar.gz"
recipes/vcfkit/meta.yaml:  url: https://pypi.io/packages/source/V/VCF-kit/VCF-kit-{{ version }}.tar.gz
recipes/primer3-py/meta.yaml:  url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/primer3-py-{{ version }}.tar.gz
recipes/fastq-anonymous/meta.yaml:  url: https://pypi.io/packages/source/f/fastq-anonymous/fastq-anonymous-{{ version }}.tar.gz
recipes/mage-tab-merger/meta.yaml:  url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/MAGE-Tab merger-{{ version }}.tar.gz"
recipes/pyquant-ms/meta.yaml:  url: https://pypi.io/packages/source/p/pyquant-ms/pyquant-ms-{{ version }}.tar.gz
recipes/mira-multiome/meta.yaml:  url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/mira-multiome-{{ version }}.tar.gz
recipes/nda-tools/meta.yaml:  url: https://pypi.io/packages/source/{{ name[0] }}/{{ name|replace("-", "_") }}/{{ name|replace("-", "_") }}-{{ version }}.tar.gz
recipes/tides-ml/meta.yaml:  url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/TIdeS-ML-{{ version }}.tar.gz
recipes/snakemake-wrapper-utils/meta.yaml:  url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name|replace("-", "_") }}-{{ version }}.tar.gz"
recipes/noah-cli/meta.yaml:  url: https://pypi.io/packages/source/n/noah-cli/noah_cli-{{ version }}.tar.gz
recipes/nanosim-h/meta.yaml:  url: https://pypi.io/packages/source/N/NanoSim-H/NanoSim-H-{{ version }}.tar.gz
recipes/avro-cwl/meta.yaml:  url: https://pypi.io/packages/source/a/avro-cwl/avro-cwl-{{ version }}.tar.gz
recipes/bio-ting/meta.yaml:  url: "https://pypi.io/packages/source/b/bio-ting/bio-ting-{{ version }}.tar.gz"
recipes/galaxy-objectstore/meta.yaml:  url: https://pypi.io/packages/source/g/galaxy-objectstore/galaxy-objectstore-{{ version }}.tar.gz
recipes/wes-service-client/meta.yaml:  #url: https://pypi.io/packages/source/w/wes-service/wes-service-{{ version }}.tar.gz
recipes/anglerfish/meta.yaml:  url: "https://pypi.io/packages/source/b/bio-{{ name }}/bio-{{ name }}-{{ version }}.tar.gz"
recipes/eagle/meta.yaml:  url: https://pypi.io/packages/source/g/gi-eagle/gi-eagle-{{ version }}.tar.gz
recipes/genomics-data-index/meta.yaml:  url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/genomics-data-index-{{ version }}.tar.gz
recipes/nextstrain-cli/meta.yaml:  url: https://pypi.io/packages/source/n/nextstrain-cli/nextstrain_cli-{{ version }}.tar.gz
recipes/arvados-python-client/meta.yaml:  url: https://pypi.io/packages/source/a/arvados-python-client/arvados-python-client-{{ version }}.tar.gz
recipes/chia-rep/meta.yaml:  url: "https://pypi.io/packages/source/c/chia-rep/ChIA-Rep-{{ version }}.tar.gz"
recipes/galaxy-data/meta.yaml:  url: https://pypi.io/packages/source/g/galaxy-data/galaxy-data-{{ version }}.tar.gz
recipes/ipython-cluster-helper/meta.yaml:  url: https://pypi.io/packages/source/i/ipython-cluster-helper/ipython-cluster-helper-{{ version }}.tar.gz
recipes/galaxy-files/meta.yaml:  url: https://pypi.io/packages/source/g/galaxy-files/galaxy-files-{{ version }}.tar.gz
recipes/khipu-metabolomics/meta.yaml:  url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/khipu-metabolomics-{{ version }}.tar.gz
recipes/ncbi-datasets-pylib/meta.yaml:  url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/ncbi-datasets-pylib-{{ version }}.tar.gz
recipes/sevenbridges-python/meta.yaml:  url: https://pypi.io/packages/source/s/sevenbridges-python/sevenbridges-python-{{ version }}.tar.gz
recipes/thapbi-pict/meta.yaml:  url: https://pypi.io/packages/source/{{ name[0] }}/{{ name | replace("-", "_") }}/{{ name | replace("-", "_") }}-{{ version }}.tar.gz
recipes/rich-msa/meta.yaml:  url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/rich-msa-{{ version }}.tar.gz
recipes/allo/meta.yaml:  url: https://pypi.io/packages/source/b/bio-{{ name }}/bio_allo-{{ version }}.tar.gz
recipes/ncbi-acc-download/meta.yaml:  url: https://pypi.io/packages/source/n/ncbi-acc-download/ncbi-acc-download-{{ version }}.tar.gz
recipes/mira-moods/meta.yaml:  url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/mira-moods-{{ version }}.tar.gz
recipes/bel-resources/meta.yaml:  url: https://pypi.io/packages/source/{{ name[0] }}/{{ name|replace("-", "_") }}/{{ name|replace("-", "_") }}-{{ version }}.tar.gz
recipes/cellprofiler-core/meta.yaml:  url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/cellprofiler-core-{{ version }}.tar.gz
recipes/bx-python/meta.yaml:  url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/bx-python-{{ version }}.tar.gz
recipes/phip-stat/meta.yaml:  url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/phip-stat-{{ version }}.tar.gz
recipes/htseq-clip/meta.yaml:  url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/htseq-clip-{{ version }}.tar.gz
recipes/galaxy-ml/meta.yaml:  url: https://pypi.io/packages/source/G/Galaxy-ML/Galaxy-ML-{{ version }}.tar.gz
recipes/sam-algorithm/meta.yaml:  url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/sam-algorithm-{{ version }}.tar.gz
recipes/illumina-utils/meta.yaml:  url: https://pypi.io/packages/source/i/illumina-utils/illumina-utils-{{ version }}.tar.gz
recipes/card_trick/meta.yaml:  url: https://pypi.io/packages/source/c/card-trick/card-trick-{{ version }}.tar.gz
recipes/interval-binning/meta.yaml:  url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/interval-binning-{{ version }}.tar.gz
recipes/happy-python/meta.yaml:  url: https://pypi.io/packages/source/{{ name[0] }}/happy-AntoineHo/happy-AntoineHo-{{ version }}.tar.gz
recipes/arvados-cwl-runner/meta.yaml:  url: https://pypi.io/packages/source/a/arvados-cwl-runner/arvados-cwl-runner-{{ version }}.tar.gz
recipes/cami-amber/meta.yaml:  url:  https://pypi.io/packages/source/c/cami-amber/cami-amber-{{ version }}.tar.gz
recipes/ngs-chew/meta.yaml:  url: https://pypi.io/packages/source/n/ngs-chew/ngs-chew-{{ version }}.tar.gz
recipes/ncbi-genome-download/meta.yaml:  url: https://pypi.io/packages/source/n/ncbi-genome-download/ncbi-genome-download-{{ version }}.tar.gz
recipes/magic-impute/meta.yaml:  url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/magic-impute-{{ version }}.tar.gz
corneliusroemer commented 3 days ago

Here's the list of packages with latest releases:

Package: hic-straw, Latest Version: 1.3.1, Release Date: 2022-05-27T22:31:02
Package: clinvar-this, Latest Version: 0.9.0, Release Date: 2023-09-08T12:12:17
Package: jms-metabolite-services, Latest Version: 0.5.8, Release Date: 2024-04-15T19:44:17
Package: cami-opal, Latest Version: 1.0.9, Release Date: 2021-02-01T12:39:37
Package: bio-hansel, Latest Version: 2.6.1, Release Date: 2021-03-05T18:33:01
Package: mira-moods, Latest Version: 1.9.4.2, Release Date: 2023-08-29T21:12:12
Package: beacon2-import, Latest Version: 1.0.8, Release Date: 2024-05-13T13:29:18
Package: feature-merge, Latest Version: 1.3.0, Release Date: 2020-12-01T22:29:57
Package: VCF-kit, Latest Version: 0.2.9, Release Date: 2020-12-20T21:37:14
Package: primer3-py, Latest Version: 2.0.3, Release Date: 2024-02-16T03:00:45
Package: fastq-anonymous, Latest Version: 1.0.1, Release Date: 2017-10-19T09:01:45
Package: MAGE-Tab merger, No release information found.
Package: pyquant-ms, Latest Version: 0.2.4, Release Date: 2019-03-24T01:11:00
Package: mira-multiome, Latest Version: 2.1.1a6, Release Date: 2024-02-11T23:28:10
Package: nda-tools, Latest Version: 0.2.8, Release Date: 2021-09-03T14:02:02
Package: TIdeS-ML, Latest Version: 1.3.0, Release Date: 2024-06-30T16:52:19
Package: snakemake-wrapper-utils, Latest Version: 0.6.2, Release Date: 2023-07-06T13:04:50
Package: noah-cli, Latest Version: 0.2.0, Release Date: 2023-08-28T14:27:36
Package: NanoSim-H, Latest Version: 1.1.0.4, Release Date: 2018-08-07T17:55:30
Package: avro-cwl, Latest Version: 1.8.9, Release Date: 2018-11-27T10:33:48
Package: bio-ting, Latest Version: 1.1.0, Release Date: 2020-11-06T08:16:34
Package: galaxy-objectstore, Latest Version: 24.1.1, Release Date: 2024-07-03T13:09:53
Package: wes-service, Latest Version: 4.0, Release Date: 2022-04-01T14:57:00
Package: anglerfish, Latest Version: 2.5.0, Release Date: 2017-05-16T17:27:44
Package: gi-eagle, Latest Version: 0.9.4.6, Release Date: 2018-10-01T13:48:29
Package: genomics-data-index, Latest Version: 0.9.2, Release Date: 2022-12-07T17:03:47
Package: nextstrain-cli, Latest Version: 8.5.0, Release Date: 2024-06-18T22:38:06
Package: arvados-python-client, Latest Version: 2.7.3rc2, Release Date: 2024-05-28T17:54:54
Package: ChIA-Rep, Latest Version: 3.1.1, Release Date: 2021-06-13T12:45:25
Package: galaxy-data, Latest Version: 24.1.1, Release Date: 2024-07-03T13:10:09
Package: ipython-cluster-helper, Latest Version: 0.6.4, Release Date: 2019-09-24T21:27:27
Package: galaxy-files, Latest Version: 24.1.1, Release Date: 2024-07-03T13:09:44
Package: khipu-metabolomics, Latest Version: 2.0.1, Release Date: 2024-05-29T21:24:30
Package: ncbi-datasets-pylib, Latest Version: 9.1.0, Release Date: 2020-10-09T11:51:54
Package: sevenbridges-python, Latest Version: 2.9.2, Release Date: 2023-07-11T12:56:34
Package: thapbi-pict, Latest Version: 1.0.9, Release Date: 2024-02-12T16:10:24
Package: rich-msa, Latest Version: 0.1.0, Release Date: 2022-05-12T11:28:33
Package: bio_allo, Latest Version: 1.1.1, Release Date: 2024-05-09T21:45:23
Package: ncbi-acc-download, Latest Version: 0.2.8, Release Date: 2021-10-22T07:24:38
Package: bel-resources, Latest Version: 0.0.3, Release Date: 2019-11-15T13:44:04
Package: cellprofiler-core, Latest Version: 4.2.6, Release Date: 2023-08-08T15:00:39
Package: bx-python, Latest Version: 0.9.0, Release Date: 2022-08-28T15:43:58
Package: phip-stat, Latest Version: 0.5.1, Release Date: 2021-12-05T17:10:00
Package: htseq-clip, Latest Version: 2.9.0b0, Release Date: 2021-12-06T13:59:43
Package: Galaxy-ML, Latest Version: 0.9.1, Release Date: 2021-10-15T04:00:40
Package: sam-algorithm, Latest Version: 1.0.2, Release Date: 2022-11-04T00:44:02
Package: illumina-utils, Latest Version: 2.9, Release Date: 2021-01-19T17:36:43
Package: card-trick, Latest Version: 0.2.1, Release Date: 2020-07-01T13:24:05
Package: interval-binning, Latest Version: 1.0.0, Release Date: 2015-10-28T20:27:01
Package: happy-AntoineHo, Latest Version: 0.2.1rc0, Release Date: 2020-12-15T14:50:26
Package: arvados-cwl-runner, Latest Version: 2.7.3rc2, Release Date: 2024-05-28T17:54:45
Package: cami-amber, Latest Version: 2.0.4, Release Date: 2023-05-19T14:14:26
Package: ngs-chew, Latest Version: 0.9.4, Release Date: 2024-02-21T16:11:01
Package: ncbi-genome-download, Latest Version: 0.3.3, Release Date: 2023-07-28T12:49:20
Package: magic-impute, Latest Version: 3.0.0, Release Date: 2021-03-11T17:49:40
corneliusroemer commented 3 days ago

Todo list: