snakemake: init at 5.2.2 #45730

Helkafen · 2018-08-29T03:31:16Z

Motivation for this change

Snakemake is a workflow management system. Useful in bio-informatics and HPC, where reproducibility is appreciated.
Also add dependency: ratelimiter (init at 1.2.0.post0)

Things done

Tested using sandboxing (nix.useSandbox on NixOS, or option sandbox in nix.conf on non-NixOS)
Built on platform(s)
- NixOS
- macOS
- other Linux distributions (Ubuntu 18.04)
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 nox --run "nox-review wip"
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)
Fits CONTRIBUTING.md.

jtojnar

Please move the packages to pkgs/development/python-modules/<name>/default.nix, as per the comment on top of pkgs/top-level/python-packages.nix. It would be also nice if you could have one commit per package, and use python.pkgs.<name> in the commit message, instead of just <name>.

Helkafen · 2018-08-29T16:15:01Z

Hi Jan. Thanks for the review! The packages are moved to separate default.nix files and I updated the commit messages.

ryantm · 2018-08-31T03:55:29Z

Related: #45828

jtojnar · 2018-08-31T05:30:19Z

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

+  '';
+
+  meta = with stdenv.lib; {
+    homepage = "https://github.com/RazerM/ratelimiter";


Plain URLs do not need to be quoted.

jtojnar · 2018-08-31T05:30:56Z

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

+    sed -i -e 's/\x9d//g' README.rst
+  '';
+
+  doCheck = true;


No need for explicit doCheck – python pakages are checked automatically.

jtojnar · 2018-08-31T05:34:35Z

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

+}:
+
+buildPythonPackage rec {
+  name = "${pname}-${version}";


name is not necessary in python packages.

jtojnar · 2018-08-31T05:34:41Z

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

+  pname = "ratelimiter";
+  version = "1.2.0.post0";
+
+  propagatedBuildInputs = [];


Why keep this?

jtojnar · 2018-08-31T05:34:59Z

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

+
+  doCheck = true;
+
+  buildInputs = [ pytest ];


You can use checkInputs.

jtojnar · 2018-08-31T05:35:52Z

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

+
+  meta = with stdenv.lib; {
+    homepage = "http://snakemake.bitbucket.io";
+    license = "MIT";


Use licenses.mit.

jtojnar · 2018-08-31T05:38:17Z

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

+  meta = with stdenv.lib; {
+    homepage = "http://snakemake.bitbucket.io";
+    license = "MIT";
+    description = "A workflow management system that aims to reduce the complexity of creating workflows by providing a fast and comfortable execution environment, together with a clean and modern specification language in python style. Snakemake workflows are essentially Python scripts extended by declarative code to define rules. Rules describe how to create output files from input files";


This is too long for description, move it to longDescription and use something shorter for description. You can get inspiration on Repology.

jtojnar · 2018-08-31T05:45:37Z

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

+      sha256 = "5c395dcabdbbde2e5178ef3f89b568a3066454a6ddc223b76473dac22f89b4f7";
+  };
+
+  prePatch = ''


Unfortunately, Python < 3.7 requires glibcLocales in nativeBuildInputs and something like LC_ALL = "en_US.UTF-8"; in the expression. But it is still better than seding.

Helkafen · 2018-08-31T13:07:10Z

All your suggestions have been applied. The locales thing makes more sense indeed!

Helkafen · 2018-08-31T13:44:49Z

Added "disabledIf (!isPy3k)" because Snakemake is no longer supported on Python 2.

renatoGarcia · 2018-08-31T16:17:43Z

The Snakemake is more a standalone application that a Python library. IMO it should be better placed at pkgs/applications/science/misc/snakemake/ for example that at pkgs/development/python-modules/snakemake/.

Helkafen · 2018-09-01T13:21:06Z

Moved to pkgs/applications/science/misc/snakemake, and added the long description by Renato.

ryantm · 2018-09-02T14:50:22Z

@GrahamcOfBorg build snakemake

GrahamcOfBorg · 2018-09-02T14:51:21Z

Success on aarch64-linux (full log)

Attempted: snakemake

Partial log (click to expand)

/build/snakemake-5.2.2
post-installation fixup
shrinking RPATHs of ELF executables and libraries in /nix/store/0h631fx7pqfkx3grv5g6d5m0b0jrxzlz-python3.6-snakemake-5.2.2
strip is /nix/store/y4ymnvgxygpq05h03kyzbj572zmh6zla-binutils-2.30/bin/strip
stripping (with command strip and flags -S) in /nix/store/0h631fx7pqfkx3grv5g6d5m0b0jrxzlz-python3.6-snakemake-5.2.2/lib  /nix/store/0h631fx7pqfkx3grv5g6d5m0b0jrxzlz-python3.6-snakemake-5.2.2/bin
patching script interpreter paths in /nix/store/0h631fx7pqfkx3grv5g6d5m0b0jrxzlz-python3.6-snakemake-5.2.2
checking for references to /build in /nix/store/0h631fx7pqfkx3grv5g6d5m0b0jrxzlz-python3.6-snakemake-5.2.2...
wrapping `/nix/store/0h631fx7pqfkx3grv5g6d5m0b0jrxzlz-python3.6-snakemake-5.2.2/bin/snakemake-bash-completion'...
wrapping `/nix/store/0h631fx7pqfkx3grv5g6d5m0b0jrxzlz-python3.6-snakemake-5.2.2/bin/snakemake'...
/nix/store/0h631fx7pqfkx3grv5g6d5m0b0jrxzlz-python3.6-snakemake-5.2.2

GrahamcOfBorg · 2018-09-02T14:51:33Z

Success on x86_64-linux (full log)

Attempted: snakemake

Partial log (click to expand)

/build/snakemake-5.2.2
post-installation fixup
shrinking RPATHs of ELF executables and libraries in /nix/store/8y6ivbcxq5bs92i4nbsgc2ddcnbpnb6a-python3.6-snakemake-5.2.2
strip is /nix/store/h0lbngpv6ln56hjj59i6l77vxq25flbz-binutils-2.30/bin/strip
stripping (with command strip and flags -S) in /nix/store/8y6ivbcxq5bs92i4nbsgc2ddcnbpnb6a-python3.6-snakemake-5.2.2/lib  /nix/store/8y6ivbcxq5bs92i4nbsgc2ddcnbpnb6a-python3.6-snakemake-5.2.2/bin
patching script interpreter paths in /nix/store/8y6ivbcxq5bs92i4nbsgc2ddcnbpnb6a-python3.6-snakemake-5.2.2
checking for references to /build in /nix/store/8y6ivbcxq5bs92i4nbsgc2ddcnbpnb6a-python3.6-snakemake-5.2.2...
wrapping `/nix/store/8y6ivbcxq5bs92i4nbsgc2ddcnbpnb6a-python3.6-snakemake-5.2.2/bin/snakemake'...
wrapping `/nix/store/8y6ivbcxq5bs92i4nbsgc2ddcnbpnb6a-python3.6-snakemake-5.2.2/bin/snakemake-bash-completion'...
/nix/store/8y6ivbcxq5bs92i4nbsgc2ddcnbpnb6a-python3.6-snakemake-5.2.2

GrahamcOfBorg · 2018-09-02T14:51:34Z

Success on x86_64-darwin (full log)

Attempted: snakemake

Partial log (click to expand)

  Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.
Successfully installed snakemake-5.2.2
/private/tmp/nix-build-python3.6-snakemake-5.2.2.drv-0/snakemake-5.2.2
post-installation fixup
strip is /nix/store/df6k4mgdjxciy0f637lryp7c9ln7n1m3-cctools-binutils-darwin/bin/strip
stripping (with command strip and flags -S) in /nix/store/srg5zq3qlcvyf3viz6bjp4fwl6a1yvbk-python3.6-snakemake-5.2.2/lib  /nix/store/srg5zq3qlcvyf3viz6bjp4fwl6a1yvbk-python3.6-snakemake-5.2.2/bin
patching script interpreter paths in /nix/store/srg5zq3qlcvyf3viz6bjp4fwl6a1yvbk-python3.6-snakemake-5.2.2
wrapping `/nix/store/srg5zq3qlcvyf3viz6bjp4fwl6a1yvbk-python3.6-snakemake-5.2.2/bin/snakemake'...
wrapping `/nix/store/srg5zq3qlcvyf3viz6bjp4fwl6a1yvbk-python3.6-snakemake-5.2.2/bin/snakemake-bash-completion'...
/nix/store/srg5zq3qlcvyf3viz6bjp4fwl6a1yvbk-python3.6-snakemake-5.2.2

ryantm · 2018-09-02T14:54:39Z

Looks good to me; merged. I hope @renatoGarcia submits a PR to add himself as a maintainer too.

renatoGarcia · 2018-09-05T17:03:15Z

Thanks both of you, @ryantm and @Helkafen, for the consideration.
Helkafen, you didn't add a maintainers field on snakemake expression. Would you mind if I submit a PR with both our names like at here?

Helkafen · 2018-09-05T17:30:56Z

@renatoGarcia Sure!

Helkafen requested a review from FRidh as a code owner August 29, 2018 03:31

GrahamcOfBorg added 6.topic: python 8.has: package (new) 10.rebuild-darwin: 1-10 10.rebuild-linux: 1-10 labels Aug 29, 2018

jtojnar reviewed Aug 29, 2018

View reviewed changes

Helkafen force-pushed the snakemake branch from d0d19e6 to 2f3deeb Compare August 29, 2018 16:11

jtojnar requested changes Aug 31, 2018

View reviewed changes

python.pkgs.ratelimiter: init at 1.2.0.post0

c49e507

Helkafen force-pushed the snakemake branch from 2f3deeb to 5af28b3 Compare August 31, 2018 13:02

Helkafen force-pushed the snakemake branch from 5af28b3 to ca04255 Compare August 31, 2018 13:43

renatoGarcia mentioned this pull request Aug 31, 2018

snakemake: init at 5.2.2 #45828

Closed

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python.pkgs.snakemake: init at 5.2.2

93ce77a

Helkafen force-pushed the snakemake branch from ca04255 to 93ce77a Compare September 1, 2018 13:19

ryantm merged commit 7b54a50 into NixOS:master Sep 2, 2018

renatoGarcia mentioned this pull request Sep 5, 2018

snakemake: add maintainers #46117

Merged

9 tasks

Janik-Haag added the 12. first-time contribution label Jun 12, 2023

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snakemake: init at 5.2.2 #45730

snakemake: init at 5.2.2 #45730

Helkafen commented Aug 29, 2018

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renatoGarcia commented Sep 5, 2018

Helkafen commented Sep 5, 2018

snakemake: init at 5.2.2 #45730

snakemake: init at 5.2.2 #45730

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Helkafen commented Aug 29, 2018

Motivation for this change

Things done

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Helkafen commented Aug 31, 2018

Helkafen commented Aug 31, 2018

renatoGarcia commented Aug 31, 2018

Helkafen commented Sep 1, 2018

ryantm commented Sep 2, 2018

GrahamcOfBorg commented Sep 2, 2018

GrahamcOfBorg commented Sep 2, 2018

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ryantm commented Sep 2, 2018

renatoGarcia commented Sep 5, 2018

Helkafen commented Sep 5, 2018