Adding `seqlike`, `weblogo` and `python-codon-tables` from PyPI #17283

sugatoray · 2021-12-17T05:43:13Z

Checklist

Title of this PR is meaningful: e.g. "Adding my_nifty_package", not "updated meta.yaml".
License file is packaged (see here for an example).
Source is from official source.
Package does not vendor other packages. (If a package uses the source of another package, they should be separate packages or the licenses of all packages need to be packaged).
If static libraries are linked in, the license of the static library is packaged.
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.
When in trouble, please check our knowledge base documentation before pinging a team.

- seqlike (U) - weblogo (A)

sugatoray · 2021-12-17T07:15:13Z

Request for review. @BastianZim

sugatoray · 2021-12-17T07:15:48Z

Ready for review.

cc: @conda-forge/help-python

sugatoray · 2021-12-17T07:20:24Z

Notes on Build Error

The windows build fails for some reason I am not sure why.

same place for linux build: (report)

windows build: (error)

search for 'seqlike.egg-info in the build log-output to compare what happened immediately afterward:

(a) when successful run,

(b) when failed run.

This does not impact anything

But this will not matter as linux-build successfully completes and all three packages are labeled as noarch: python. Once the packages are built on linux, they should be usable on any platform: win, osx, linux.

Notes on Build Status

On linux and osx all three builds pass: seqlike, weblogo and python-codon-tables.
On Windows only two builds pass: weblogo and python-codon-tables.

sugatoray · 2021-12-23T19:02:31Z

Current License Status for `python-codon-tables`

The following question was asked on conda-forge gitter (gitter.im/conda-forge/question-sugatoray).

The following was the suggestions made by @beckermr in the forum.

https://wiki.spdx.org/view/Legal_Team/Decisions/Dealing_with_Public_Domain_within_SPDX_Files

cc: @conda-forge/core Please see the license related issue above and advise.

recipes/python-codon-tables/LICENSE

recipes/python-codon-tables/meta.yaml

recipes/seqlike/meta.yaml

- `seqlike`: removed extra script (commands) - `python-codon-tables`: changed license type - using license "LicenseRef-PublicDomain"

conda-forge-linter · 2021-12-23T19:58:07Z

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/python-codon-tables, recipes/seqlike, recipes/weblogo) and found it was in an excellent condition.

I do have some suggestions for making it better though...

For recipes/python-codon-tables:

Recipe with the same name exists in bioconda: please discuss with @conda-forge/bioconda-recipes.

For recipes/seqlike:

Recipe with the same name exists in bioconda: please discuss with @conda-forge/bioconda-recipes.

For recipes/weblogo:

Recipe with the same name exists in bioconda: please discuss with @conda-forge/bioconda-recipes.

sugatoray · 2021-12-23T20:03:25Z

Looks like someone has already added all three recipes to bioconda-recipes! It wasn't (seqlike) a few days ago though (when I started). What do you suggest?

bioconda seqlike: (recipe)
bioconda weblogo: (recipe)
bioconda python-codon-tables: (recipe)
- uses license: NIST-PD (See details)

@BastianZim

BastianZim · 2021-12-23T20:31:16Z

Are all of them the same? Meaning not by name but also by source? In that case you can ask Bioconda to transfer the packages here (Best to talk to the maintainer there). Bioconda also uses conda-forge so anything that is available here will also be available there.

sugatoray · 2021-12-23T20:34:41Z

Are all of them the same? Meaning not by name but also by source? In that case you can ask Bioconda to transfer the packages here (Best to talk to the maintainer there). Bioconda also uses conda-forge so anything that is available here will also be available there.

What if these packages are published here and bioconda has it's own? Could that work (since these are two separate channels after all)? Also, the maintainers of seqlike want to have it on conda-forge (issue: modernatx/seqlike#4).

BastianZim · 2021-12-23T20:48:52Z

What if these packages are published here and bioconda has it's own?

Being a good neighbour, this is generally not preferred (As it makes a mess on Bioconda side as far as I know) so it's better to ask them to bring the packages here. You can also ping the team above and ask them.

beckermr · 2021-12-23T20:50:56Z

Yes we prefer to move things from bioconda if they are needed for stuff in conda-forge. Since bioconda uses conda-forge packages typically, this is generally not an issue.

sugatoray · 2021-12-23T20:53:43Z

Who do you contact for such issues typically? Just the maintainers of the packages on bioconda? Or, is there a core team of bioconda, which is also a necessary intermediary for the handover?

beckermr · 2021-12-23T20:58:55Z

See the linter above: @conda-forge/bioconda-recipes.

sugatoray · 2021-12-23T21:06:41Z

Summary for porting/transferring `bioconda` recipes over to `conda-forge`

The three libraries that are being packaged here are now available on bioconda. However, the library-maintainers of seqlike would like to have the library available on conda-forge. It will be helpful if you could kindly transfer those over to conda-forge. The current maintainers of each library will also be added to the recipes here.

See (comment here).

cc: @conda-forge/bioconda-recipes

💡 I reached out to bioconda on their gitter. (gitter.im/bioconda)

sugatoray · 2021-12-23T21:10:12Z

Are all of them the same? Meaning not by name but also by source? In that case you can ask Bioconda to transfer the packages here (Best to talk to the maintainer there). Bioconda also uses conda-forge so anything that is available here will also be available there.

@BastianZim Just checked and found that the source of weblogo is github on bioconda. For the other two it is PyPI. So, does it (weblogo) require a transfer over to conda-forge?

BastianZim · 2021-12-23T21:11:31Z

Yes. Sometimes they have the same name but are completely different packages. Just wanted to make sure that’s not the case. So yes, all require transfer.

conda-forge-linter · 2022-01-11T04:57:30Z

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/python-codon-tables, recipes/seqlike, recipes/weblogo) and found it was in an excellent condition.

I do have some suggestions for making it better though...

For recipes/python-codon-tables:

Recipe with the same name exists in bioconda: please discuss with @conda-forge/bioconda-recipes.

For recipes/seqlike:

Recipe with the same name exists in bioconda: please discuss with @conda-forge/bioconda-recipes.

For recipes/weblogo:

Recipe with the same name exists in bioconda: please discuss with @conda-forge/bioconda-recipes.
Jinja2 variable references are suggested to take a {{<one space><variable name><one space>}} form. See lines [80].

conda-forge-linter · 2022-01-11T04:59:05Z

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/python-codon-tables, recipes/seqlike, recipes/weblogo) and found it was in an excellent condition.

I do have some suggestions for making it better though...

For recipes/python-codon-tables:

Recipe with the same name exists in bioconda: please discuss with @conda-forge/bioconda-recipes.

For recipes/seqlike:

Recipe with the same name exists in bioconda: please discuss with @conda-forge/bioconda-recipes.

For recipes/weblogo:

Recipe with the same name exists in bioconda: please discuss with @conda-forge/bioconda-recipes.

sugatoray · 2022-01-11T21:28:35Z

Added licenses for weblogo

I have included the licenses for weblogo after scanning the library.

cc: @jaimergp @beckermr

sugatoray · 2022-01-11T21:29:02Z

Windows build failure for `seqlike`

Interestingly, the windows build for seqlike fails: (error)

This was the case even before as well. (see comment)

  running install_scripts
  error: [WinError 2] The system cannot find the file specified
  Building wheel for seqlike (pyproject.toml): finished with status 'error'
  ERROR: Failed building wheel for seqlike
ERROR: Could not build wheels for seqlike, which is required to install pyproject.toml-based projects
Failed to build seqlike

cc: @BastianZim @beckermr

jaimergp · 2022-01-12T09:53:34Z

recipes/weblogo/meta.yaml

+    - cp -r ${RECIPE_DIR}/licenses licenses  # [not win]
+    - xcopy /s /e /q /i %RECIPE_DIR%\licenses licenses  # [win]


You don't need this. conda-build will also look for paths in RECIPE_DIR.

Tested already. Thank you. Will remove this.

recipes/weblogo/meta.yaml

- attempt to read-in license filenames

conda-forge-linter · 2022-01-12T21:10:52Z

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/python-codon-tables, recipes/seqlike, recipes/weblogo) and found some lint.

Here's what I've got...

For recipes/python-codon-tables:

Recipe with the same name exists in bioconda: please discuss with @conda-forge/bioconda-recipes.

For recipes/seqlike:

Recipe with the same name exists in bioconda: please discuss with @conda-forge/bioconda-recipes.

For recipes/weblogo:

Failed to even lint the recipe, probably because of a conda-smithy bug 😢. This likely indicates a problem in your meta.yaml, though. To get a traceback to help figure out what's going on, install conda-smithy and run conda smithy recipe-lint . from the recipe directory.

For recipes/weblogo:

Recipe with the same name exists in bioconda: please discuss with @conda-forge/bioconda-recipes.

- try without copying "licenses" folder from recipe_dir

conda-forge-linter · 2022-01-13T11:05:23Z

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/python-codon-tables, recipes/seqlike, recipes/weblogo) and found some lint.

Here's what I've got...

For recipes/python-codon-tables:

Recipe with the same name exists in bioconda: please discuss with @conda-forge/bioconda-recipes.

For recipes/seqlike:

Recipe with the same name exists in bioconda: please discuss with @conda-forge/bioconda-recipes.

For recipes/weblogo:

Jinja2 variable definitions are suggested to take a {%<one space>set<one space><variable name><one space>=<one space><expression><one space>%} form. See lines [21]

For recipes/weblogo:

Recipe with the same name exists in bioconda: please discuss with @conda-forge/bioconda-recipes.

conda-forge-linter · 2022-01-13T11:07:09Z

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/python-codon-tables, recipes/seqlike, recipes/weblogo) and found it was in an excellent condition.

I do have some suggestions for making it better though...

For recipes/python-codon-tables:

Recipe with the same name exists in bioconda: please discuss with @conda-forge/bioconda-recipes.

For recipes/seqlike:

Recipe with the same name exists in bioconda: please discuss with @conda-forge/bioconda-recipes.

For recipes/weblogo:

Recipe with the same name exists in bioconda: please discuss with @conda-forge/bioconda-recipes.

jaimergp · 2022-01-13T11:33:11Z

Thanks for your submission and keeping up with the review, @sugatoray! Please remember to submit a PR at bioconda to remove their recipes there.

sugatoray · 2022-01-13T12:21:05Z

Thank you @jaimergp. I will wait until all three are available on conda-forge (also need to push an empty PR for seqlike as it depends on the other two) and then ask Bioconda folks to remove their recipes.

jaimergp · 2022-01-13T13:12:14Z

Ping me for the seqlike rebuild. We won't probably need an empty PR.

sugatoray · 2022-01-13T21:41:24Z

@jaimergp Curious to know if rebuild is possible without any empty-PR.

jaimergp · 2022-01-13T21:47:30Z

Yup, just retriggered it. You will see this "Re-run" link in when you click in the CI status of a commit:

sugatoray · 2022-01-14T19:41:09Z

Thank you for your review and help in merging the PR.

@BastianZim @beckermr @jaimergp @dpryan79

sugatoray added 5 commits December 16, 2021 21:07

Adding seqlike from PyPI

ea6bacf

Update recipe

bb36c66

updated/added recipe

c22a410

- seqlike (U) - weblogo (A)

adding python-codon-tables from PyPI

d701019

updated recipe

f767fcb

sugatoray mentioned this pull request Dec 17, 2021

Conda-forge release modernatx/seqlike#4

Closed

This was referenced Dec 17, 2021

adding CC0 license (public domain) Edinburgh-Genome-Foundry/codon-usage-tables#8

Merged

Please include a license file (repo + PyPI) Edinburgh-Genome-Foundry/codon-usage-tables#7

Closed

add a conda install option gecrooks/weblogo#124

Closed

BastianZim reviewed Dec 23, 2021

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recipes/python-codon-tables/LICENSE Outdated Show resolved Hide resolved

BastianZim reviewed Dec 23, 2021

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recipes/python-codon-tables/meta.yaml Outdated Show resolved Hide resolved

BastianZim reviewed Dec 23, 2021

View reviewed changes

recipes/seqlike/meta.yaml Outdated Show resolved Hide resolved

updated recipe

b295cbd

- `seqlike`: removed extra script (commands) - `python-codon-tables`: changed license type - using license "LicenseRef-PublicDomain"

sugatoray added 2 commits December 23, 2021 14:16

removed license file from python-codon-tables

eb1828d

updated recipe

968df5c

updated recipe: weblogo (5)

4f5ebcf

update recipe: weblogo (6)

6e51c4e

sugatoray added 2 commits January 11, 2022 00:04

update recipe: weblogo (7)

dabc78c

update recipe: weblogo (8)

dd9a609

jaimergp reviewed Jan 12, 2022

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recipes/weblogo/meta.yaml Outdated Show resolved Hide resolved

jaimergp reviewed Jan 12, 2022

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recipes/weblogo/meta.yaml Outdated Show resolved Hide resolved

update recipe: weblogo (9)

c18f61a

- attempt to read-in license filenames

sugatoray and others added 3 commits January 12, 2022 16:29

update recipe: weblogo (10)

54b1e7c

update recipe: weblogo

0159843

- try without copying "licenses" folder from recipe_dir

Update meta.yaml

ddd3a7e

satisfy linter

f6acda9

jaimergp merged commit ade8c44 into conda-forge:main Jan 13, 2022

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Adding `seqlike`, `weblogo` and `python-codon-tables` from PyPI #17283

Adding `seqlike`, `weblogo` and `python-codon-tables` from PyPI #17283

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		- cp -r ${RECIPE_DIR}/licenses licenses # [not win]
		- xcopy /s /e /q /i %RECIPE_DIR%\licenses licenses # [win]

Adding seqlike, weblogo and python-codon-tables from PyPI #17283

Adding seqlike, weblogo and python-codon-tables from PyPI #17283

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Notes on Build Error

This does not impact anything

Notes on Build Status

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Current License Status for python-codon-tables

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Summary for porting/transferring bioconda recipes over to conda-forge

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Added licenses for weblogo

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Windows build failure for seqlike

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Adding `seqlike`, `weblogo` and `python-codon-tables` from PyPI #17283

Adding `seqlike`, `weblogo` and `python-codon-tables` from PyPI #17283

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Current License Status for `python-codon-tables`

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Summary for porting/transferring `bioconda` recipes over to `conda-forge`

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Windows build failure for `seqlike`