fix: various little fixes for build failure records and automatic skiplisting #894
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…n logging the commit process.
…it has changed. This is better as the commit sha needs the full git history to be reliably obtained. However, the full git history takes way too long to checkout in bioconda-recipes.
…1000 output lines on error
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There is a seemingly temporal problem with the https certificate of bioconductor that makes the test fail, which is definitely unrelated to this PR. Hence, I will merge this now. |
johanneskoester
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🤖 I have created a release \*beep\* \*boop\* --- ## [2.3.0](https://www.github.com/bioconda/bioconda-utils/compare/v2.2.1...v2.3.0) (2023-06-07) ### Features * always add a fallback archive URL to the meta.yaml when using bioconductor-skeleton ([#886](https://www.github.com/bioconda/bioconda-utils/issues/886)) ([d885495](https://www.github.com/bioconda/bioconda-utils/commit/d885495d54b177411863fdca3bdfa35ca781457f)) ### Bug Fixes * various little fixes for build failure records and automatic skiplisting ([#894](https://www.github.com/bioconda/bioconda-utils/issues/894)) ([715efc2](https://www.github.com/bioconda/bioconda-utils/commit/715efc27319afda8b7fe19a0d112a84e8b8569c9)) --- This PR was generated with [Release Please](https://github.com/googleapis/release-please). See [documentation](https://github.com/googleapis/release-please#release-please). Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Yikun
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In the bioconda#866 we introduced the `--docker-base-image` to help user to specify customized build docker image (such as Linux aarch64 build). But we noticed that it doesn’t work after the bioconda#894 , because a local var introduced and the `docker-base-image` arguments is ignored: https://github.com/bioconda/bioconda-utils/blame/9a85115ae306f58c8b4e65e5f92f6cbdb5b68f04/bioconda_utils/cli.py#L468 This PR try to recover it, if user specify the `--docker-base-image`, it will be used directly otherwise use the local var. Signed-off-by: Yikun Jiang <[email protected]>
johanneskoester
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In the #866 we introduced the `--docker-base-image` to help user to specify customized build docker image (such as Linux aarch64 build). But we noticed that it doesn’t work after the #894 , because a local var introduced and the `docker-base-image` arguments is ignored. This PR try to recover it, if user specify the `--docker-base-image`, it will be used directly otherwise use the local var. Test: ``` [root@kunpeng bioconda-recipes]# bioconda-utils build --docker --packages bamstats --docker-base-image ghcr.io/yikun/bioconda-utils-build-env-cos7-aarch64 11:50:12 BIOCONDA INFO Considering total of 1 recipes (bamstats). 11:50:12 BIOCONDA INFO Processing 1 recipes (bamstats). 11:50:12 BIOCONDA WARNING Using tag 2.3.4 for docker image, since there is no image for a not yet release version (2.3.4+0.g9a85115.dirty). 11:50:12 BIOCONDA INFO Using docker image ghcr.io/yikun/bioconda-utils-build-env-cos7-aarch64 for building. // ... ... ``` Signed-off-by: Yikun Jiang <[email protected]>
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| sys.platform = original | |||
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| def run(cmds: List[str], env: Dict[str, str]=None, mask: List[str]=None, live: bool=True, | |||
| mylogger: logging.Logger=logger, loglevel: int=logging.INFO, | |||
| def run(cmds: List[str], env: Dict[str, str]=None, mask: List[str]=None, mask_envvars: bool=False, live: bool=False, | |||
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@johanneskoester The log messages from inside docker are not getting to stdout. What was the reasoning for this change of default to live=False? Would there be an issue to pass in live=True for the docker build?
bioconda-utils/bioconda_utils/docker_utils.py
Line 477 in 88680cf
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