pysam: init at 0.13 #34532

unode · 2018-02-02T16:16:37Z

A python library to interact with SAM/BAM/CRAM files

Things done

Tested using sandboxing (nix.useSandbox on NixOS, or option build-use-sandbox in nix.conf on non-NixOS)
Built on platform(s)
- 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 nox --run "nox-review wip"
Tested execution of all binary files (usually in ./result/bin/)
Fits CONTRIBUTING.md.

dotlambda · 2018-02-02T19:59:25Z

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

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


no name here as well

dotlambda · 2018-02-02T20:45:06Z

@GrahamcOfBorg build python2.pkgs.pysam python3.pkgs.pysam

GrahamcOfBorg · 2018-02-02T20:50:03Z

Failure on x86_64-linux (full log)

Partial log (click to expand)

    self.run_command(cmd)
  File "/nix/store/53dyjh7xjhnbibqllr7j27lk2h98n7j7-python3-3.6.4/lib/python3.6/distutils/dist.py", line 974, in run_command
    cmd_obj.run()
  File "/nix/store/514aqfsmhlmf4lw4vg6k2sj1dgh3zd62-python3.6-bootstrapped-pip-9.0.1/lib/python3.6/site-packages/setuptools/command/test.py", line 226, in run
    self.run_tests()
  File "/nix/store/514aqfsmhlmf4lw4vg6k2sj1dgh3zd62-python3.6-bootstrapped-pip-9.0.1/lib/python3.6/site-packages/setuptools/command/test.py", line 233, in run_tests
    module = self.test_suite.split('.')[0]
AttributeError: 'NoneType' object has no attribute 'split'
builder for ‘/nix/store/xiavzdlf0fj7jafhglyn5l29s5zrsvfg-python3.6-pysam-0.13.drv’ failed with exit code 1
error: build of ‘/nix/store/xiavzdlf0fj7jafhglyn5l29s5zrsvfg-python3.6-pysam-0.13.drv’ failed

GrahamcOfBorg · 2018-02-02T20:55:16Z

Failure on aarch64-linux (full log)

Partial log (click to expand)

    self.run_command(cmd)
  File "/nix/store/mn2c28fa7mp8ck3p74n80nls6g2w7flw-python3-3.6.4/lib/python3.6/distutils/dist.py", line 974, in run_command
    cmd_obj.run()
  File "/nix/store/msg48xf1xm0j024mgxwsccrzpyrry0bj-python3.6-bootstrapped-pip-9.0.1/lib/python3.6/site-packages/setuptools/command/test.py", line 226, in run
    self.run_tests()
  File "/nix/store/msg48xf1xm0j024mgxwsccrzpyrry0bj-python3.6-bootstrapped-pip-9.0.1/lib/python3.6/site-packages/setuptools/command/test.py", line 233, in run_tests
    module = self.test_suite.split('.')[0]
AttributeError: 'NoneType' object has no attribute 'split'
builder for '/nix/store/sd67s81cyyqq9p44jb277k60d3bl1phb-python3.6-pysam-0.13.drv' failed with exit code 1
error: build of '/nix/store/sd67s81cyyqq9p44jb277k60d3bl1phb-python3.6-pysam-0.13.drv' failed

unode · 2018-02-02T21:04:23Z

Unsure how to fix this. Doesn't seem like build_ext is supported upstream.

dotlambda · 2018-02-02T21:04:31Z

Ran 0 tests in 0.000s

Please specify an appropriate checkPhase, probably checkPhase = "py.test"

unode · 2018-02-02T21:11:42Z

Trying your suggestion

unode · 2018-02-02T21:26:36Z

@GrahamcOfBorg build python2.pkgs.pysam python3.pkgs.pysam

dotlambda · 2018-02-02T21:27:15Z

Well, it won't work unless you include pytest in checkInputs. Please test locally before pushing.

GrahamcOfBorg · 2018-02-02T21:28:42Z

Failure on x86_64-linux (full log)

Partial log (click to expand)

shrinking /nix/store/mbf876p0wyrqvz02q92jdnkvcq4ajap0-python3.6-pysam-0.13/lib/python3.6/site-packages/pysam/libcutils.cpython-36m-x86_64-linux-gnu.so
shrinking /nix/store/mbf876p0wyrqvz02q92jdnkvcq4ajap0-python3.6-pysam-0.13/lib/python3.6/site-packages/pysam/libcvcf.cpython-36m-x86_64-linux-gnu.so
strip is /nix/store/mdyy001q67hiks0g24ra53z7ckm4jfr4-binutils-2.28.1/bin/strip
stripping (with command strip and flags -S) in /nix/store/mbf876p0wyrqvz02q92jdnkvcq4ajap0-python3.6-pysam-0.13/lib 
patching script interpreter paths in /nix/store/mbf876p0wyrqvz02q92jdnkvcq4ajap0-python3.6-pysam-0.13
checking for references to /tmp/nix-build-python3.6-pysam-0.13.drv-0 in /nix/store/mbf876p0wyrqvz02q92jdnkvcq4ajap0-python3.6-pysam-0.13...
running install tests
/nix/store/4zaswd1lyncz1jmjkfd3hjz33vakpwx7-stdenv/setup: line 1222: py.test: command not found
builder for ‘/nix/store/yhcz6xw95m6pban19a3lvm4qvz2g7kzj-python3.6-pysam-0.13.drv’ failed with exit code 127
error: build of ‘/nix/store/3xv20aymh719hkhkvw2an0hg45gpbm9b-python2.7-pysam-0.13.drv’, ‘/nix/store/yhcz6xw95m6pban19a3lvm4qvz2g7kzj-python3.6-pysam-0.13.drv’ failed

dotlambda · 2018-02-02T21:33:26Z

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

+
+  meta = {
+    homepage = http://pysam.readthedocs.io/;
+    description = "a python module for reading, manipulating and writing genome data sets";


Captialize fist character please: https://nixos.org/nixpkgs/manual/#sec-standard-meta-attributes

GrahamcOfBorg · 2018-02-02T21:36:20Z

Failure on aarch64-linux (full log)

Partial log (click to expand)

shrinking /nix/store/a8k2zbm86lmx5cz2mi29mwsr3bm17ymd-python3.6-pysam-0.13/lib/python3.6/site-packages/pysam/libcutils.cpython-36m-aarch64-linux-gnu.so
shrinking /nix/store/a8k2zbm86lmx5cz2mi29mwsr3bm17ymd-python3.6-pysam-0.13/lib/python3.6/site-packages/pysam/libcvcf.cpython-36m-aarch64-linux-gnu.so
strip is /nix/store/jwz859pxqj7sl2dbwvmxkx68jp774izb-binutils-2.28.1/bin/strip
stripping (with command strip and flags -S) in /nix/store/a8k2zbm86lmx5cz2mi29mwsr3bm17ymd-python3.6-pysam-0.13/lib
patching script interpreter paths in /nix/store/a8k2zbm86lmx5cz2mi29mwsr3bm17ymd-python3.6-pysam-0.13
checking for references to /build in /nix/store/a8k2zbm86lmx5cz2mi29mwsr3bm17ymd-python3.6-pysam-0.13...
running install tests
/nix/store/aci5ir60cxnl692vx652y4sawm592igr-stdenv/setup: line 1222: py.test: command not found
builder for '/nix/store/0q8qlbn11bk7vjpvka1022yyi230y957-python3.6-pysam-0.13.drv' failed with exit code 127
error: build of '/nix/store/0q8qlbn11bk7vjpvka1022yyi230y957-python3.6-pysam-0.13.drv', '/nix/store/0z51frnycwz59wjvkid454vgcrbdsk08-python2.7-pysam-0.13.drv' failed

unode · 2018-02-05T23:40:06Z

@GrahamcOfBorg build python2.pkgs.pysam python3.pkgs.pysam

GrahamcOfBorg · 2018-02-05T23:40:59Z

Failure on aarch64-linux (full log)

Partial log (click to expand)

Usage: test-regidx [OPTIONS]
Options:
   -h, --help          this help message
   -s, --seed <int>    random seed
   -v, --verbose       increase verbosity by giving multiple times
make: *** [Makefile:247: test-plugins] Error 1
builder for '/nix/store/2k4xwjhxa1650x0x5gs8pf4ixhkkqzpx-bcftools-1.6.drv' failed with exit code 2
cannot build derivation '/nix/store/xdkizrhkgxqjjawd8agwnq8wy38yjm0d-python2.7-pysam-0.13.0.drv': 1 dependencies couldn't be built
cannot build derivation '/nix/store/7ig76c3587bhs2sx9y6qdvkzp27d1spk-python3.6-pysam-0.13.0.drv': 1 dependencies couldn't be built
error: build of '/nix/store/7ig76c3587bhs2sx9y6qdvkzp27d1spk-python3.6-pysam-0.13.0.drv', '/nix/store/xdkizrhkgxqjjawd8agwnq8wy38yjm0d-python2.7-pysam-0.13.0.drv' failed

GrahamcOfBorg · 2018-02-05T23:48:24Z

Success on x86_64-linux (full log)

Partial log (click to expand)


=============================== warnings summary ===============================
tests/AlignmentFile_test.py::TestTruncatedBAM::testTruncatedBam2
  /tmp/nix-build-python3.6-pysam-0.13.0.drv-0/source/tests/AlignmentFile_test.py:1757: UserWarning: no BGZF EOF marker; file may be truncated
    ignore_truncation=True)

-- Docs: http://doc.pytest.org/en/latest/warnings.html
============== 804 passed, 9 skipped, 1 warnings in 76.89 seconds ==============
/nix/store/lkxpg85asvwq7fv9zd0a4hjmf7v0j5li-python2.7-pysam-0.13.0
/nix/store/grwy2hln9rbaz52vy05y0639yzxs8r5s-python3.6-pysam-0.13.0

A python library to interact with SAM/BAM/CRAM files

unode · 2018-02-06T09:08:46Z

aarch64 failure due to bcftools not being available on that platform.
Targetting only x86 because of this.

PS: Is there any platform alias that represents both x86_64 and i686?

unode requested a review from FRidh as a code owner February 2, 2018 16:16

unode force-pushed the pysam branch 3 times, most recently from 8396b23 to 4b884bc Compare February 2, 2018 17:47

GrahamcOfBorg added 10.rebuild-darwin: 1-10 10.rebuild-linux: 1-10 labels Feb 2, 2018

dotlambda reviewed Feb 2, 2018

View reviewed changes

unode force-pushed the pysam branch from 4b884bc to 962465c Compare February 2, 2018 20:17

unode force-pushed the pysam branch from 962465c to 0f68c89 Compare February 2, 2018 21:11

unode force-pushed the pysam branch from 0f68c89 to 5677bb9 Compare February 2, 2018 21:16

dotlambda reviewed Feb 2, 2018

View reviewed changes

FRidh added the 6.topic: python label Feb 3, 2018

unode mentioned this pull request Feb 5, 2018

pypi 0.13.tar.gz is missing files (present in github 0.13.0.tar.gz) pysam-developers/pysam#616

Open

unode force-pushed the pysam branch from 5677bb9 to 0be0c5e Compare February 5, 2018 23:38

unode force-pushed the pysam branch from 0be0c5e to c630036 Compare February 5, 2018 23:41

pysam: init at 0.13.0

37680b0

A python library to interact with SAM/BAM/CRAM files

unode force-pushed the pysam branch from c630036 to 37680b0 Compare February 6, 2018 09:07

GrahamcOfBorg added 10.rebuild-darwin: 0 and removed 10.rebuild-darwin: 1-10 labels Feb 6, 2018

FRidh merged commit 712c322 into NixOS:master Feb 8, 2018

tjni mentioned this pull request Sep 16, 2022

pysam supported platforms excludes macOS #191512

Closed

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pysam: init at 0.13 #34532

pysam: init at 0.13 #34532

unode commented Feb 2, 2018

dotlambda Feb 2, 2018

dotlambda commented Feb 2, 2018

GrahamcOfBorg commented Feb 2, 2018

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unode commented Feb 2, 2018

dotlambda commented Feb 2, 2018 •

edited

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dotlambda Feb 2, 2018

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unode commented Feb 5, 2018

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GrahamcOfBorg commented Feb 5, 2018

unode commented Feb 6, 2018

pysam: init at 0.13 #34532

pysam: init at 0.13 #34532

Conversation

unode commented Feb 2, 2018

Things done

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dotlambda commented Feb 2, 2018 • edited

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edited