cellprofiler 3.1.9 #9538

sunyi000 · 2019-09-13T09:02:29Z

Checklist

License file is packaged (see here for an example)
Source is from official source
Package does not vend other packages
Build number is 0
A tarball (url) rather than a repo (e.g. git_url) is used in your
recipe (see
here
for more details)
GitHub users listed in the maintainer section have posted a comment confirming they are willing to be listed there

conda-forge-linter · 2019-09-13T09:02:39Z

Hi! This is the friendly automated conda-forge-linting service.

I wanted to let you know that I linted all conda-recipes in your PR (recipes/cellprofiler) and found some lint.

Here's what I've got...

For recipes/cellprofiler:

The home item is expected in the about section.
The license item is expected in the about section.
The recipe could do with some maintainers listed in the extra/recipe-maintainers section.
Selectors are suggested to take a <two spaces>#<one space>[<expression>] form. See lines [14, 15]
requirements: run: matplotlib==2.2.3 must contain a space between the name and the pin, i.e. matplotlib ==2.2.3
requirements: run: pyzmq=15.3.0 must contain a space between the name and the pin, i.e. pyzmq =15.3.0
requirements: run: scikit-image=0.14.0 must contain a space between the name and the pin, i.e. scikit-image =0.14.0
requirements: run: networkx==2.2 must contain a space between the name and the pin, i.e. networkx ==2.2

bgruening · 2019-09-13T09:20:33Z

recipes/cellprofiler/meta.yaml

+    - wxpython
+    - joblib
+    - mahotas
+    - matplotlib==2.2.3


I don't think this strict pin is necessary.

yes, it needs to be > 2.0.0, so I will change it to >=2.0

bgruening · 2019-09-13T09:20:41Z

recipes/cellprofiler/meta.yaml

+    - javabridge
+    - prokaryote
+    - python-bioformats
+    - pyzmq=15.3.0


relax the pin?

I will try relax it see what happens. it builds find locally for now.

bgruening · 2019-09-13T09:21:16Z

recipes/cellprofiler/meta.yaml

+    - pyzmq=15.3.0
+    - raven
+    - requests
+    - scikit-image=0.14.0


- scikit-image 0.14.*

bgruening · 2019-09-13T09:21:34Z

recipes/cellprofiler/meta.yaml

+    - scipy
+      #    - six==1.11.0
+    - pillow
+    - networkx==2.2


- networkx 2.2.*

bgruening · 2019-09-13T09:21:46Z

recipes/cellprofiler/meta.yaml

+    - pillow
+    - networkx==2.2
+    - vigra
+    - pytest


Is pytest really a runtime dependency?

i moved it to host: as I can see setup.py requires it

bgruening · 2019-09-13T09:22:07Z

recipes/cellprofiler/meta.yaml

+    - cellprofiler
+
+about:
+  summary: "CellProfiler is free, open-source software"


Please add license, doc_url etc and under extras you as a maintainer.

added. I have not pushed the actual license file with the correct content yet. I will do that soon

bgruening · 2019-09-13T09:23:44Z

please also have a look at #7701

ping @drpatelh

conda-forge-linter · 2019-09-13T09:38:34Z

Hi! This is the friendly automated conda-forge-linting service.

I wanted to let you know that I linted all conda-recipes in your PR (recipes/cellprofiler) and found some lint.

Here's what I've got...

For recipes/cellprofiler:

Selectors are suggested to take a <two spaces>#<one space>[<expression>] form. See lines [14, 15]
There are 1 too many lines. There should be one empty line at the end of the file.
requirements: run: pyzmq=15.3.0 must contain a space between the name and the pin, i.e. pyzmq =15.3.0

conda-forge-linter · 2019-09-13T14:20:58Z

Hi! This is the friendly automated conda-forge-linting service.

I wanted to let you know that I linted all conda-recipes in your PR (recipes/cellprofiler) and found some lint.

Here's what I've got...

For recipes/cellprofiler:

Selectors are suggested to take a <two spaces>#<one space>[<expression>] form. See lines [14, 15]
The recipe license should not include the word "License".
There are 1 too many lines. There should be one empty line at the end of the file.

For recipes/cellprofiler:

license_file entry is missing, but is expected.

sunyi000 · 2019-09-13T14:28:04Z

I have made another commit and it builds fine locally.

but I still used the javabridge package from the old 'free' channel.

I will have a look at #7701 see what I can do.

Yi

conda-forge-linter · 2019-09-13T14:35:08Z

Hi! This is the friendly automated conda-forge-linting service.

I just wanted to let you know that I linted all conda-recipes in your PR (recipes/cellprofiler) and found it was in an excellent condition.

sunyi000 · 2019-09-16T10:11:19Z

Hi @bgruening ,

a couple of questions,

I tried to install javabridge to local channel using its own conda recipe mentioned in #7710, then build and install cellprofiler. It seems ok, so is this the correct approach for now, since javabridge is not yet in conda-forge?

is that possible to write the javabridge installation from source within cellprofiler's meta.yaml?
for exmaple, create a build.sh for cellprofiler ,download javabridge source, and do python setup.py install within it?

Also, another issue is with the package wxPython, conda-forge only has version 4.0.6, but cellprofiler only works with 3.0.2 for the release3.1.8

thanks very much,
Yi

conda-forge-linter · 2020-03-06T11:52:54Z

Hi! This is the friendly automated conda-forge-linting service.

I wanted to let you know that I linted all conda-recipes in your PR (recipes/cellprofiler) and found some lint.

Here's what I've got...

For recipes/cellprofiler:

Non noarch packages should have python requirement without any version constraints.
Non noarch packages should have python requirement without any version constraints.

conda-forge-linter · 2020-03-06T13:13:55Z

Hi! This is the friendly automated conda-forge-linting service.

I was trying to look for recipes to lint for you, but it appears we have a merge conflict.
Please try to merge or rebase with the base branch to resolve this conflict.

Please ping the 'conda-forge/core' team (using the @ notation in a comment) if you believe this is a bug.

bgruening · 2020-03-06T13:54:02Z

recipes/cellprofiler/meta.yaml

+  version: "{{ version }}"
+
+source:
+    git_url: "https://github.com/CellProfiler/CellProfiler.git"


here you should use a tarball

conda-forge-linter · 2020-03-06T14:02:03Z

Hi! This is the friendly automated conda-forge-linting service.

I wanted to let you know that I linted all conda-recipes in your PR (recipes/cellprofiler) and found some lint.

Here's what I've got...

For recipes/cellprofiler:

Non noarch packages should have python requirement without any version constraints.
Non noarch packages should have python requirement without any version constraints.

conda-forge-linter · 2020-03-06T14:03:36Z

Hi! This is the friendly automated conda-forge-linting service.

I just wanted to let you know that I linted all conda-recipes in your PR (recipes/cellprofiler) and found it was in an excellent condition.

conda-forge-linter · 2020-03-09T12:11:21Z

Hi! This is the friendly automated conda-forge-linting service.

I wanted to let you know that I linted all conda-recipes in your PR (recipes/cellprofiler) and found some lint.

Here's what I've got...

For recipes/cellprofiler:

requirements: run: matplotlib!=2.1.0,>2.0.0,<3 must contain a space between the name and the pin, i.e. matplotlib! =2.1.0,>2.0.0,<3

conda-forge-linter · 2020-03-09T12:12:52Z

Hi! This is the friendly automated conda-forge-linting service.

I just wanted to let you know that I linted all conda-recipes in your PR (recipes/cellprofiler) and found it was in an excellent condition.

stale · 2020-08-06T17:20:17Z

Hi friend!

We really, really, really appreciate that you have taken the time to make a PR on conda-forge/staged-recipes! conda-forge only exists because people like you donate their time to build and maintain conda recipes for use by the community.

In an effort to maintain this repository and increase the signal-to-noise for open PRs, the maintainers of staged-recipes close excessively old PRs after six months. This PR will remain open for another month, and then will be closed.

If you'd like to keep it open, please comment/push and we will be happy to oblige! Note that very old PRs will likely need to be rebased on master so that they can be rebuilt with the most recent CI scripts. If you have any trouble, or we missed reviewing this PR in the first place (sorry!), feel free to ping the team using a special command in a comment on the PR to get the attention of the staged-recipes team.

Cheers and thank you for contributing to this community effort!

drpatelh · 2020-08-06T19:27:21Z

Hi @bgruening ! Sorry, I completely missed your ping and just saw this again 😏 The javabridge issue seemed insurmountable at the time so I ended up using Docker containers directly provided by CellProfiler in the end. Hope you and loved ones are well.

bgruening · 2020-08-06T19:45:54Z

All good @drpatelh!

Conda: https://anaconda.org/bioconda/cellprofiler
Container: https://quay.io/repository/biocontainers/cellprofiler?tag=latest&tab=tags
Galaxy Integration: https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/bgruening/cp_cellprofiler/cp_cellprofiler/3.1.9

Thanks to @sunyi000 and @beatrizserrano!

initial commit

1f7903a

bgruening reviewed Sep 13, 2019

View reviewed changes

added license, extras etc

21b0bb8

sunyi000 and others added 3 commits September 13, 2019 11:48

Update meta.yaml

d11f042

Delete LICENSE.txt

5e7af31

unpinned some packages; added additional dependencies

72b81c4

added license file

873f13b

Yi Sun added 2 commits November 25, 2019 16:59

update to v3.1.9, install from git

db7dc39

add future library

b56d7a0

sunyi000 changed the title ~~initial commit~~ cellprofiler 3.1.9 Mar 6, 2020

test cp with javabridge1.0.14

e5acc9e

bgruening reviewed Mar 6, 2020

View reviewed changes

add example back; replace git_url with tarball url and checksum

bdfa032

fix noach warning

a8bdac1

bgruening and others added 2 commits March 6, 2020 20:20

Update meta.yaml

56d74d5

add version pining back to matplotlib

3fa8b4a

add space between name and the pin

234f877

change pin verison for matplotlib

6c6f81f

stale bot added the stale will be closed in 30 days label Aug 6, 2020

bgruening closed this Aug 6, 2020

hmaarrfk mentioned this pull request Feb 3, 2023

Package request: CellProfiler #21949

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cellprofiler 3.1.9 #9538

cellprofiler 3.1.9 #9538

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cellprofiler 3.1.9 #9538

cellprofiler 3.1.9 #9538

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