deeptools: init at 3.3.1 #70995

scalavision · 2019-10-11T21:17:18Z

Motivation for this change

Things done

[x ] Tested using sandboxing (nix.useSandbox on NixOS, or option sandbox in nix.conf on non-NixOS)
Built on platform(s)
- [x ] NixOS
- macOS
- other Linux distributions
Tested via one or more NixOS test(s) if existing and applicable for the change (look inside nixos/tests)
Tested compilation of all pkgs that depend on this change using nix-shell -p nix-review --run "nix-review wip"
[ x] Tested execution of all binary files (usually in ./result/bin/)
Determined the impact on package closure size (by running nix path-info -S before and after)
[ x] Ensured that relevant documentation is up to date
[ x] Fits CONTRIBUTING.md.

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scalavision · 2019-10-11T21:29:34Z

deepTools have a lot of small, very useful tools for manipulating bam files etc.

jonringer · 2019-10-19T02:35:44Z

do you mind rebasing on top of master? you got conflicts now :(

jonringer · 2019-10-19T02:36:43Z

Also, to be compliant with CONTRIBUTING.md, you should have roughly 1 commit relate to one package

pkgs/applications/science/biology/deeptools/default.nix

pkgs/development/python-modules/pybigwig/default.nix

pkgs/development/python-modules/py2bit/default.nix

pkgs/applications/science/biology/deeptools/default.nix

jonringer · 2019-10-19T02:39:34Z

pkgs/applications/science/biology/deeptools/default.nix

+}:
+
+buildPythonPackage rec {
+


Suggested change

Thank you for your help on this @jonringer.

I've removed most of the blank lines I hope. Is there any guidelines for this? I seem to always want more blank lines than necessary.

I kept the package within the biology folder. Any special reason you want to move it to science? It is a bioinformatic tool alongside samtools, bedtools etc.

The reasoning behind moving it from python-packages, is that it's meant to be used a standalone application and not imported by other python packages. It's to avoid the situation in which someone will try to do propagatedBuildInputs = [ deeptools ]; in another python packages, which is probably not what you want.

Another reason for doing this, is that some applications have very specific package versions which may deviate greatly from what's available in python-modules, #71797 for example

pkgs/top-level/all-packages.nix

pkgs/development/python-modules/deeptoolsintervals/default.nix

pkgs/applications/science/biology/deeptools/default.nix

pkgs/development/python-modules/deeptoolsintervals/default.nix

pkgs/development/python-modules/pybigwig/default.nix

pkgs/top-level/all-packages.nix

pkgs/applications/science/biology/deeptools/default.nix

scalavision · 2019-10-30T22:01:46Z

Thanks again for helping me out with this one @jonringer . I've added python3 as a parameter, and used with to retrieve back the python dependencies in the build. Hope this was what you meant ?

I also wonder if I should do something like this:

{ lib
, python
}:
let
  py = python.pkgs;
in
py.buildPythonApplication rec {
 /* .. */
}

Or if that is too much? Anyways, learned a lot playing around with this :-)

jonringer · 2019-10-30T22:14:40Z

Yea, since you're only referencing pythonPackages, I would be fine with a top-level with python.pkgs; but if you also needed native inputs, then I would do something very similar to what you did. Since you already did a lot of tedious work, I would say just keep as is. (at least for python.pkgs usage)

scalavision · 2019-10-31T09:14:04Z

of course, I didn't think about that. Will do that next time :-) this have been a great journey!

jonringer

To adhere to contributing guidelines, do you mind breaking each package addition into it's own commit, it should follow:

pythonPackages.deeptoolsintervals: init at 0.1.9
.....

and so on for the git log history

scalavision · 2019-10-31T18:40:48Z

Trying again :-) I have to work on my git skill I think, this was really good practice. I also changed, so that I use with python.pkgs at the top of the function body of deeptools. That also seems to work pretty well. Just let me know if there are more things that could be improved :-)

Just hope I did everything correctly here!

jonringer · 2019-10-31T21:36:39Z

to help you out in the future, you can use git add --patch to iterate over what changes you want to stage, discard, edit, etc.

Generally when doing multiple packages, I iterate over the whole change set in un-staged. Then when im making the commits, I'll just git add path/to/fil and use git add -p python-modules/all-packages to select the smaller changes that I want.

For editing a particular commit in a series, you should use git rebase -i, which will allow for you go to to a commit, make changes, then re apply the other commits on top of it

scalavision · 2019-11-03T12:19:54Z

Thanks again @jonringer, I've used git rebase -i extensively during this PR, and it was really helpful also for work, hehe. Will look into the other things you mention. Probably very helpful too :-)

jonringer

nix-review passes on NixOS
diff LGTM
deeptools seems to wokr

[15 built, 1 copied (7.8 MiB), 2.1 MiB DL]
https://github.com/NixOS/nixpkgs/pull/70995
10 package were build:
deeptools python27Packages.deeptoolsintervals python27Packages.py2bit python27Packages.pybigwig python37Packages.deeptoolsintervals python37Packages.py2bit python37Packages.pybigwig python38Packages.deeptoolsintervals python38Packages.py2bit python38Packages.pybigwig

jonringer · 2019-11-04T10:18:28Z

@GrahamcOfBorg build deeptools python27Packages.deeptoolsintervals python27Packages.py2bit python27Packages.pybigwig python37Packages.deeptoolsintervals python37Packages.py2bit python37Packages.pybigwig python38Packages.deeptoolsintervals python38Packages.py2bit python38Packages.pybigwig

scalavision requested a review from FRidh as a code owner October 11, 2019 21:17

ofborg bot added the 6.topic: python label Oct 11, 2019

ofborg bot added 8.has: package (new) 11.by: package-maintainer 10.rebuild-darwin: 1-10 10.rebuild-linux: 1-10 labels Oct 11, 2019

jonringer reviewed Oct 19, 2019

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scalavision force-pushed the add-deeptools-to-biology branch from 7d9a50f to 363ab82 Compare October 27, 2019 10:10

FRidh reviewed Oct 27, 2019

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jonringer reviewed Oct 27, 2019

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scalavision force-pushed the add-deeptools-to-biology branch from 363ab82 to 90afd74 Compare October 30, 2019 21:07

jonringer suggested changes Oct 31, 2019

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scalavision added 4 commits October 31, 2019 19:36

pythonPackages.py2bit: init at 0.3.0

d4fe16b

pythonPackages.pybigwig: init at 0.3.17

97d4cd1

pythonPackages.deeptoolsIntervals: init at 0.1.9

3ba856b

deeptools: init at 3.3.1

b46d4ea

scalavision force-pushed the add-deeptools-to-biology branch from 90afd74 to b46d4ea Compare October 31, 2019 18:37

jonringer approved these changes Nov 4, 2019

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jonringer merged commit d9b40f6 into NixOS:master Nov 4, 2019

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deeptools: init at 3.3.1 #70995

deeptools: init at 3.3.1 #70995

scalavision commented Oct 11, 2019

scalavision commented Oct 11, 2019

jonringer commented Oct 19, 2019

jonringer commented Oct 19, 2019

jonringer Oct 19, 2019

scalavision Oct 27, 2019

jonringer Oct 30, 2019

scalavision commented Oct 30, 2019 •

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jonringer commented Nov 4, 2019

		}:

		buildPythonPackage rec {

deeptools: init at 3.3.1 #70995

deeptools: init at 3.3.1 #70995

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scalavision commented Oct 11, 2019

Motivation for this change

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