pythonPackages.sumo: init at 1.0.9 ( And other packages that sumo depends on) #43260

PsyanticY · 2018-07-09T16:02:34Z

sumo: init at 1.0.9, phonopy: init at 1.13.2.13, pymatgen: init at 2018.6.27, palettable:init at 3.1.1
For pymatgen, test are available in Github repo but the repo is 150 MB of size. I also had a problem running them because of an issue i couldn't understand. if any one can take a look and help me understand the issue would be great.

Motivation for this change

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
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.

dotlambda · 2018-07-09T22:51:52Z

Please create one commit per package.

PsyanticY · 2018-07-11T17:28:48Z

@dotlambda Done.

dotlambda · 2018-07-12T06:56:26Z

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

+  '';
+
+  meta = with stdenv.lib; {
+    description = "Palettable (formerly brewer2mpl) is a library of color palettes for Python";


https://nixos.org/nixpkgs/manual/#sec-standard-meta-attributes

dotlambda · 2018-07-12T06:57:27Z

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

+  meta = with stdenv.lib; {
+    description = "Palettable (formerly brewer2mpl) is a library of color palettes for Python";
+    homepage = https://jiffyclub.github.io/palettable/;
+    license = licenses.free;


MIT: https://github.com/jiffyclub/palettable/blob/master/license.txt

dotlambda · 2018-07-12T06:57:39Z

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

+  '';
+
+  meta = with stdenv.lib; {
+    description = "Phonopy is an open source package for phonon calculations at harmonic and quasi-harmonic levels.";


https://nixos.org/nixpkgs/manual/#sec-standard-meta-attributes

dotlambda · 2018-07-12T06:59:02Z

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

+
+  checkPhase = ''
+    cd test/phonopy
+    ${python.interpreter} -m unittest discover -b


You should be able to specify the directory using -s test/phonopy.

@dotlambda I think we can keep it that way ? (couldn't get it to work with -s ....)

dotlambda · 2018-07-12T06:59:46Z

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

+  doCheck = false;
+
+  meta = with stdenv.lib; {
+    description = "A robust materials analysis code that defines core object representations for structures and molecules with support for many electronic structure codes.";


https://nixos.org/nixpkgs/manual/#sec-standard-meta-attributes
I also think this is too long.

dotlambda · 2018-07-12T07:01:18Z

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

+  propagatedBuildInputs = [ numpy scipy spglib pymatgen h5py matplotlib seekpath phonopy ];
+
+  meta = with stdenv.lib; {
+    description = "Toolkit for plotting and analysis of ab initio solid-state calculation data.";


https://nixos.org/nixpkgs/manual/#sec-standard-meta-attributes

PsyanticY · 2018-07-13T10:44:31Z

@dotlambda Hi, Thanks for the review. Should I push the fix in one commit or I need to rebase and push each fix for each package in a separate commit?

dotlambda · 2018-07-13T11:12:49Z

You should use git rebase -i to make the changes in the existing commit appropriate to the respective package.

PsyanticY · 2018-07-27T12:59:16Z

@dotlambda I updated the commits as you mentioned but it seems that some merging conflicts was introduced as this was open for some time now. Any idea on how to fix that or should i create a new PR?

dotlambda · 2018-07-30T17:11:41Z

Just do git rebase upstream/master, supposed you added https://github.com/NixOS/nixpkgs.git as upstream remote. Then you can git rebase -i to adjust the appropriate commits.

PsyanticY · 2018-07-31T16:52:06Z

@dotlambda Done, Thanks for the help

dotlambda · 2018-07-31T16:54:05Z

@Assassinkin There still seems to be a conflict. I forgot to say that you need to do git fetch upstream beforehand.

PsyanticY · 2018-08-01T10:18:30Z

@dotlambda We should be good now.

dotlambda · 2018-08-01T14:58:12Z

@GrahamcOfBorg build python2.pkgs.sumo python3.pkgs.sumo

GrahamcOfBorg · 2018-08-01T15:02:08Z

Failure on x86_64-linux (full log)

Attempted: python2.pkgs.sumo, python3.pkgs.sumo

Partial log (click to expand)


trying https://github.com/SMTG-UCL/sumo/archive/v1.0.9.tar.gz
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100   121    0   121    0     0    311      0 --:--:-- --:--:-- --:--:--   311
100 11.3M  100 11.3M    0     0  7406k      0  0:00:01  0:00:01 --:--:-- 11.6M
unpacking source archive /build/v1.0.9.tar.gz
cannot build derivation '/nix/store/1w172m9zvpxlgldaw7dr9zpbirzww04d-python2.7-sumo-1.0.9.drv': 3 dependencies couldn't be built
cannot build derivation '/nix/store/ag783ikscqwlcb35z91p1c45b74fjfwg-python3.6-sumo-1.0.9.drv': 3 dependencies couldn't be built
error: build of '/nix/store/1w172m9zvpxlgldaw7dr9zpbirzww04d-python2.7-sumo-1.0.9.drv', '/nix/store/ag783ikscqwlcb35z91p1c45b74fjfwg-python3.6-sumo-1.0.9.drv' failed

GrahamcOfBorg · 2018-08-01T15:58:16Z

Failure on aarch64-linux (full log)

Attempted: python2.pkgs.sumo, python3.pkgs.sumo

Partial log (click to expand)

tests/groupby/test_filters.py::test_filter_and_transform_with_non_unique_float_index
  /nix/store/fpbrms71s182h8q8rppkkaqc9b9i21kl-python3.6-pandas-0.23.3/lib/python3.6/site-packages/pandas/core/indexes/base.py:3078: FutureWarning: elementwise comparison failed; returning scalar instead, but in the future will perform elementwise comparison
    return self._engine.get_loc(key)

-- Docs: http://doc.pytest.org/en/latest/warnings.html
 5 failed, 16889 passed, 1036 skipped, 11894 deselected, 37 xfailed, 2 xpassed, 6 warnings in 1520.75 seconds
builder for '/nix/store/v9g5l67xxd9vna2qljywd6kzkyihzkd7-python3.6-pandas-0.23.3.drv' failed with exit code 1
cannot build derivation '/nix/store/6rab20k1f0rk299i0aidan0fnqds6fad-python3.6-pymatgen-2018.6.27.drv': 2 dependencies couldn't be built
cannot build derivation '/nix/store/zv5hmdh1iqfmmgz9xk480hq54m313d5i-python3.6-sumo-1.0.9.drv': 3 dependencies couldn't be built
error: build of '/nix/store/nw9fz5nnk4i4kpfwfcr679r786izy0bi-python2.7-sumo-1.0.9.drv', '/nix/store/zv5hmdh1iqfmmgz9xk480hq54m313d5i-python3.6-sumo-1.0.9.drv' failed

PsyanticY · 2018-08-01T17:05:45Z

spglib tests are failing in the new version https://github.com/atztogo/spglib/issues/63 . Will update that package then update this one.

dotlambda · 2018-08-02T12:31:15Z

@GrahamcOfBorg build python2.pkgs.sumo python3.pkgs.sumo

GrahamcOfBorg · 2018-08-02T12:34:31Z

Success on x86_64-linux (full log)

Attempted: python2.pkgs.sumo, python3.pkgs.sumo

Partial log (click to expand)

Check path format conversion from seekpath ... ok
test_seekpath_kpath_load (tests_symmetry.test_seekpath_kpath.SeekpathKpathTestCase)
Check path generation from structure with seekpath ... ok

----------------------------------------------------------------------
Ran 14 tests in 1.457s

OK
/nix/store/cymp8m5xm8kh1aqi5c3pigzgmsqih0zc-python2.7-sumo-1.0.9
/nix/store/jsqjxvnq1642hk381gcjrrhcm0d9720n-python3.6-sumo-1.0.9

GrahamcOfBorg · 2018-08-02T13:31:27Z

Failure on aarch64-linux (full log)

Attempted: python2.pkgs.sumo, python3.pkgs.sumo

Partial log (click to expand)

tests/groupby/test_filters.py::test_filter_and_transform_with_non_unique_float_index
  /nix/store/fpbrms71s182h8q8rppkkaqc9b9i21kl-python3.6-pandas-0.23.3/lib/python3.6/site-packages/pandas/core/indexes/base.py:3078: FutureWarning: elementwise comparison failed; returning scalar instead, but in the future will perform elementwise comparison
    return self._engine.get_loc(key)

-- Docs: http://doc.pytest.org/en/latest/warnings.html
 5 failed, 16889 passed, 1036 skipped, 11894 deselected, 37 xfailed, 2 xpassed, 6 warnings in 1524.88 seconds
builder for '/nix/store/v9g5l67xxd9vna2qljywd6kzkyihzkd7-python3.6-pandas-0.23.3.drv' failed with exit code 1
cannot build derivation '/nix/store/r0qb5bxdhly50jdgjbw612iiq832717n-python3.6-pymatgen-2018.6.27.drv': 1 dependencies couldn't be built
cannot build derivation '/nix/store/r1a79yfax3g7w5jkr65xzi0i8qph9267-python3.6-sumo-1.0.9.drv': 1 dependencies couldn't be built
error: build of '/nix/store/62lmjjw5mcxg96wv7yxq2g8qgkhlfxjn-python2.7-sumo-1.0.9.drv', '/nix/store/r1a79yfax3g7w5jkr65xzi0i8qph9267-python3.6-sumo-1.0.9.drv' failed

PsyanticY requested a review from FRidh as a code owner July 9, 2018 16:02

GrahamcOfBorg added 6.topic: python 8.has: package (new) 10.rebuild-darwin: 1-10 10.rebuild-linux: 1-10 labels Jul 9, 2018

PsyanticY force-pushed the sumo branch from 59626bb to 04bdc7a Compare July 11, 2018 17:28

dotlambda reviewed Jul 12, 2018

View reviewed changes

FRidh added the 2.status: work-in-progress label Jul 21, 2018

PsyanticY force-pushed the sumo branch from 04bdc7a to 3f425b1 Compare July 27, 2018 12:57

GrahamcOfBorg added the 2.status: merge conflict label Jul 27, 2018

PsyanticY force-pushed the sumo branch from 3f425b1 to fbca925 Compare July 31, 2018 16:51

PsyanticY added 4 commits August 1, 2018 10:57

pythonPackages.palettable:init at 3.1.1

7487510

pythonPackages.phonopy:init at 1.13.2.13

1e1cf4f

pythonPackages.pymatgen:init at 2018.6.27

791d50f

pythonPackages.sumo:init at 1.0.9

6ee997a

PsyanticY force-pushed the sumo branch from fbca925 to 6ee997a Compare August 1, 2018 09:58

GrahamcOfBorg removed the 2.status: merge conflict label Aug 1, 2018

dotlambda merged commit de880be into NixOS:master Aug 2, 2018

PsyanticY deleted the sumo branch August 2, 2018 12:58

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pythonPackages.sumo: init at 1.0.9 ( And other packages that sumo depends on) #43260

pythonPackages.sumo: init at 1.0.9 ( And other packages that sumo depends on) #43260

PsyanticY commented Jul 9, 2018

dotlambda commented Jul 9, 2018

PsyanticY commented Jul 11, 2018

dotlambda Jul 12, 2018

dotlambda Jul 12, 2018

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dotlambda Jul 12, 2018

PsyanticY Jul 27, 2018 •

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GrahamcOfBorg commented Aug 2, 2018

pythonPackages.sumo: init at 1.0.9 ( And other packages that sumo depends on) #43260

pythonPackages.sumo: init at 1.0.9 ( And other packages that sumo depends on) #43260

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PsyanticY commented Jul 9, 2018

Motivation for this change

Things done

dotlambda commented Jul 9, 2018

PsyanticY commented Jul 11, 2018

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