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Update to plantcv v3.3.0 #15539

Merged
merged 25 commits into from
May 25, 2019
Merged

Update to plantcv v3.3.0 #15539

merged 25 commits into from
May 25, 2019

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nfahlgren
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  • 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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biocondabot bot commented May 22, 2019

No artifacts found on recent CircleCI builds.

@nfahlgren
Merge branch 'master' into update-plantcv-3.3.0
0e6de70
@nfahlgren
Updated opencv version
bf95649
@nfahlgren
Create yum_requirements.txt
0f2711b
@nfahlgren
Revert "Create yum_requirements.txt"
3b24ced 
This reverts commit 0f2711b.
@nfahlgren
Add libGL requirements to build
7f76c30
@nfahlgren
Add jasper to host
a71958e
@nfahlgren
Revert "Add jasper to host"
db29c40 
This reverts commit a71958e.
@nfahlgren
Revert "Revert "Create yum_requirements.txt""
659e690 
This reverts commit 3b24ced.
@nfahlgren
Revert "Revert "Revert "Create yum_requirements.txt"""
4c27e04 
This reverts commit 659e690.
@nfahlgren
Add mesa-libgl to test requirements
7c40786
@nfahlgren
added xorg libfixes
34124ae
@nfahlgren
added libGL requirements to build
ed2dda8
@nfahlgren
Build from source
12ea3e4
@nfahlgren
Fix sha256 hash value
e8c29d2
@nfahlgren
Add setuptools
435aa1e
@nfahlgren
Change back to build script
36ec3bd
@nfahlgren
Revert "Change back to build script"
423a4a3 
This reverts commit 36ec3bd.
@nfahlgren
Revert "Add setuptools"
d00bc3e 
This reverts commit 435aa1e.
@nfahlgren
Revert "Fix sha256 hash value"
f974568 
This reverts commit e8c29d2.
@nfahlgren
Revert "Build from source"
98e7e5f 
This reverts commit 12ea3e4.
@nfahlgren nfahlgren mentioned this pull request May 23, 2019
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@npavlovikj
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@nfahlgren , your recipe is failing at the Liniting step, and not while building. The error is:
NotImplementedError: overlap in comment [None, [CommentToken('# [linux]\n', line: 20)]] [None, [CommentToken('# [linux]\n', line: 21)]]

I am not sure what the error exactly means, but I would try removing noarch: python - noarch packages are for architecture-independent packages, while yours need to use libGL on linux, and not osx, which is not independent.

Regarding "libGL", I believe just using the extended-base should work, and you will see if that gives you any error during build afer the linting step is fixed.

@npavlovikj
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Ah, please ignore what I said earlier @nfahlgren - I didn't notice that you were not using any compilers...
In that case, please keep noarch: python, and remove # [linux] from the build section, so you have something like in https://github.com/bioconda/bioconda-recipes/blob/0c10b43ca0b7acdba91527f8573e872507bb4d5c/recipes/bioconductor-rdrtoolbox/meta.yaml.

@nfahlgren
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Thanks @npavlovikj, the comments were definitely causing linting to fail. I updated the PR and the CircleCI log now shows the build error I was talking about.

@epruesse epruesse requested a review from npavlovikj May 25, 2019 03:09
@nfahlgren
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Awesome, thanks @npavlovikj!

@npavlovikj
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@BiocondaBot merge

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biocondabot bot commented May 25, 2019 •
edited

Upload & Merge started. Reload page to view progress.

  • Checks OK
  • Fetching 1 packages and 1 images
  • Uploaded image biocontainers/plantcv:3.3.0--py_0
  • Uploaded package noarch/plantcv-3.3.0-py_0.tar.bz2
  • Creating squash merge (with co-authors @npavlovikj)

@biocondabot biocondabot bot merged commit 6082a99 into master May 25, 2019
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biocondabot bot commented May 25, 2019

@npavlovikj, your request to merge succeeded: Pull Request successfully merged

@dpryan79 dpryan79 deleted the update-plantcv-3.3.0 branch May 25, 2019 11:52
epruesse added a commit to epruesse/bioconda-recipes that referenced this pull request May 25, 2019
@epruesse
Merge branch 'master' into colinbrislawn-patch-2
d8eda61 
* master: (336 commits)
  Rebuild libgtextutils (bioconda#14659)
  set minced=0.3 (bioconda#15575)
  Update to plantcv v3.3.0 (bioconda#15539)
  add cami-opal recipe (bioconda#15573)
  Tango (bioconda#15570)
  stacks: bump version 2.4 (bioconda#15546)
  Bump segtools build for newer python versions (bioconda#15572)
  Update blast to 2.9.0 (bioconda#15550)
  add fastqsplitter recipe (bioconda#15568)
  Update xopen (bioconda#15566)
  r-probmetab - fix conda getting stuck on solving environment (bioconda#15519)
  Change sha256 for PGCGAP (bioconda#15565)
  Update PGCGAP to v1.0.2 (bioconda#15562)
  pb-falcon-0.3.3 (bioconda#15559)
  Spoa (bioconda#15555)
  seqbuster: bump to latest version (bioconda#15558)
  update irida uploader 0.2.1 (bioconda#15557)
  Super distance (bioconda#15551)
  Fix nanoplotter (bioconda#15548)
  Pycoqc requires h5py (bioconda#15545)
  ...
kpalin pushed a commit to kpalin/bioconda-recipes that referenced this pull request Aug 7, 2019
@nfahlgren @kpalin
Update to plantcv v3.3.0 (bioconda#15539)
88eb249 
Package uploads complete: [ci skip]
 - biocontainers/plantcv:3.3.0--py_0
 - noarch/plantcv-3.3.0-py_0.tar.bz2

Co-authored-by: Natasha Pavlovikj <npavlovikj2@unl.edu>
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