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More blacklist updates #18999

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wants to merge 5 commits into from
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More blacklist updates #18999

wants to merge 5 commits into from

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dpryan79
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@dpryan79 dpryan79 commented Nov 29, 2019

Bioconda requires reviews prior to merging pull-requests (PRs). To facilitate this, once your PR is passing tests and ready to be merged, please add the please review & merge label so other members of the bioconda community can have a look at your PR and either make suggestions or merge it. Note that if you are not already a member of the bioconda project (meaning that you can't add this label), please ping @bioconda/core so that your PR can be reviewed and merged (please note if you'd like to be added to the bioconda project). Please see #15332 for more details.

  • I have read the guidelines for bioconda recipes.
  • This PR adds a new recipe.
  • AFAIK, this recipe is directly relevant to the biological sciences (otherwise, please submit to the more general purpose conda-forge channel).
  • This PR updates an existing recipe.
  • This PR does something else (explain below).

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@bioconda-bot please fetch artifacts

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Package(s) built on CircleCI are ready for inspection:

Arch Package Repodata
linux-64 glimmerhmm-3.0.4-pl526he1b5a44_4.tar.bz2 repodata.json
noarch groopm-0.3.4-py_1.tar.bz2 repodata.json
noarch qiimetomaaslin-1.1.0-py_2.tar.bz2 repodata.json
osx-64 glimmerhmm-3.0.4-pl526h6de7cb9_4.tar.bz2 repodata.json

You may also use conda to install these:

  • For packages on noarch:
conda install -c https://84836-42372094-gh.circle-artifacts.com/0/tmp/artifacts/packages <package name>
conda install -c https://84836-42372094-gh.circle-artifacts.com/0/tmp/artifacts/packages <package name>
  • For packages on linux-64:
conda install -c https://84836-42372094-gh.circle-artifacts.com/0/tmp/artifacts/packages <package name>
  • For packages on osx-64:
conda install -c https://84845-42372094-gh.circle-artifacts.com/0/tmp/artifacts/packages <package name>

Docker image(s) built:

Package Tag Install with docker
glimmerhmm 3.0.4--pl526he1b5a44_4
showcurl "https://84836-42372094-gh.circle-artifacts.com/0/tmp/artifacts/images/glimmerhmm%3A3.0.4--pl526he1b5a44_4.tar.gz" | gzip -dc | docker load
groopm 0.3.4--py_1
showcurl "https://84836-42372094-gh.circle-artifacts.com/0/tmp/artifacts/images/groopm%3A0.3.4--py_1.tar.gz" | gzip -dc | docker load
qiimetomaaslin 1.1.0--py_2
showcurl "https://84836-42372094-gh.circle-artifacts.com/0/tmp/artifacts/images/qiimetomaaslin%3A1.1.0--py_2.tar.gz" | gzip -dc | docker load

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@bioconda-bot please add label

@BiocondaBot BiocondaBot added the please review & merge set to ask for merge label Nov 29, 2019
@@ -7,6 +7,8 @@ package:
source:
url: https://pypi.io/packages/source/G/GroopM/GroopM-{{ version }}.tar.gz
sha256: 48bdaeb9010e7d81785697a55edc394ef36c2646b310d625a24bec740f1b6080
patches:
- patch
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I think we should better use MPLBACKEND=Agg in the tests than patching this in, right?

Something like this:

test:
  commands:
    - MPLBACKEND=Agg python -c 'import groopm'
    - MPLBACKEND=Agg groopm

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No, since we need it to run everywhere and it'll fail on most clusters and in containers at the moment.

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I understand the reasoning, but I don't agree. It's up to the user to set it. Or, in rarer cases, up to the upstream developers to decide. We should only patch it if it's not maintained upstream anymore and there is a clear intend to only want the Agg backend.

No matter the decision on the above, it most likely makes sense to change the dependency from matplotlib to matplotlib-base in all cases.

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A compromise would be to scan the env and if nothing is in there fallback to Agg? This would provide people a way to overwrite our defaults.

@dpryan79 dpryan79 closed this Jan 31, 2020
@dpryan79 dpryan79 deleted the blacklist_291119B branch January 31, 2020 11:28
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