bioconda-utils

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test: run tests on osx-arm64

3

See if all tests pass on osx-arm and resolve.

aliciaaevans

feat: Add Python 3.11 to the build matrix

14

I have no idea what all is involved in updating this and perhaps doing initial package builds on the **bulk** branch, but this PR provides a starting point for this...

jmarshall

I got this error when installing on python 3.12: ``` Collecting configparser Downloading configparser-6.0.1-py3-none-any.whl.metadata (10 kB) Downloading configparser-6.0.1-py3-none-any.whl (19 kB) Installing collected packages: configparser Successfully installed configparser-6.0.1 ❯ python setup.py...

alneberg

This takes the ideas from the code review on #953 and simplifies by refactoring how everything is configured. See https://github.com/bioconda/bioconda-utils/pull/953#issuecomment-1958104290 for the specific proposed items, which are addressed here. The...

daler

argh.exceptions.AssemblingError when using bioconda-utils

2

Hi! I'm having issues using the `bioconda-utils`: I installed mamba with https://github.com/conda-forge/miniforge#mambaforge and then ran: ``` mamba create -n bioconda -c conda-forge -c bioconda bioconda-utils mamba activate bioconda ``` However,...

matrulda

I'm trying to autobump my `viral_consensus` recipe using the ["Updating recipes" guide](https://bioconda.github.io/contributor/updating.html), and when I ran the following: ```bash bioconda-utils autobump recipes/ config.yml --packages viral_consensus --create-pr ``` it crashed as...

niemasd

Current extended-base (`quay.io/bioconda/base-glibc-debian-bash:3.0`) for container builds yields docker images unusable on some systems

10

Since docker 25.0.0 (https://docs.docker.com/engine/release-notes/25.0/#2500), * Unpacking layers with extended attributes onto an incompatible filesystem will now fail instead of silently discarding extended attributes. [moby/moby#45464](https://github.com/moby/moby/pull/45464) The current image used as extended-base...

pontus

Hi, File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/ruamel/yaml/parser.py", line 804, in move_token_comment token.move_old_comment(self.scanner.peek_token() if nt is None else nt, empty=empty) File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/ruamel/yaml/scanner.py", line 1743, in peek_token self._gather_comments() File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/ruamel/yaml/scanner.py", line 1770, in _gather_comments self.fetch_more_tokens() File...

oranges7

Make git-lfs available at cloning time ?

2

If I'm not mistaken, when running mulled-tests, there seems to be no way to retrieve github test files that are stored via git-lfs. E.g. files that after cloning appear as...

blinard-BIOINFO

autobump for GitHub releases fails - presumably because of broken regex

1

Our bioconda releases of [poseidon-trident](https://anaconda.org/bioconda/poseidon-trident) and [poseidon-xerxes](https://anaconda.org/bioconda/poseidon-xerxes) fail to autobump, forcing @stschiff, @TCLamnidis and me to open PRs manually upon every release. I can reproduce the bioconda-utils behaviour with ```bash...

nevrome