sasview: init at 4.1.2 #36852

rprospero · 2018-03-12T09:28:29Z

Motivation for this change

Sasview is a data fitting and analysis package for small angle scattering data.

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.

This package is a required dependency of SasView, which will be added in a later commit.

This package is used by Sasview, which will be added in a later commit.

This package is required by SasView, which will be added in a later commit.

Sasmodels provides a library of small angle scattering calculations that are needed by Sasview, which will be added in my next commit.

Sasview is a data fitting and analysis package for small angle scattering data. More information can be found at https://www.sasview.org. There is some unfortunate cruft to this commit. SasView uses the xhtml2pdf python package, which has a specific version of html5lib as a dependency. This module manually loads that version into sasview. I haven't made xhtml2pdf available as its own package due to these circumstances.

FRidh

Libraries that are in python-packages.nix should be used. If those versions are not compatible, then they can be overridden.

The licenses variable was being required by sasmoels, but licenses was already a child of the lib parameter and was redundant.

xhtml2pdf now uses the main package html5lib with just an override to pull the correct version number.

rprospero · 2018-03-21T13:50:26Z

I'm now using html5lib from python-packages and merely overriding the version. This has also allowed me to move xhtml2pdf into the python-packages.nix, instead of making it part of sasview.

I've also done just a bit of cleanup as I was manually importing licenses into a couple of the packages for no good reason.

FRidh · 2018-03-22T06:31:51Z

pkgs/applications/science/misc/sasview/default.nix

+{lib, fetchgit, gcc, python}:
+
+python.pkgs.buildPythonApplication rec {
+  name = "sasview-${version}";


The name attribute is added by buildPython* and should therefore be removed. Instead use pname for just the name.

FRidh · 2018-03-22T06:32:00Z

pkgs/applications/science/misc/sasview/default.nix

+  };
+
+  patches = [./pyparsing-fix.patch ./local_config.patch];
+  sandbox = true;


FRidh · 2018-03-22T06:32:18Z

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

+{ stdenv, buildPythonPackage, fetchPypi, six}:
+
+buildPythonPackage rec {
+  name = "${pname}-${version}";


The name attribute is added by buildPython* and should therefore be removed.

FRidh · 2018-03-22T06:32:31Z

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

+{lib, fetchgit, buildPythonPackage, pytest, numpy, scipy, matplotlib, docutils}:
+
+buildPythonPackage rec {
+  name = "sasmodels-${version}";


The name attribute is added by buildPython* and should therefore be removed.

FRidh · 2018-03-22T06:32:58Z

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

+  name = "sasmodels-${version}";
+  version = "0.96";
+
+  propagatedBuildInputs = [docutils matplotlib numpy pytest scipy];


test dependencies should not be propagated

FRidh · 2018-03-22T06:34:17Z

pkgs/development/python-modules/xhtml2pdf/default.nix

+
+let
+  #xhtml2pdf specifically requires version "1.0b10" of html5lib
+  html5 = html5lib.overrideAttrs( oldAttrs: rec{


We permit only a single version within python-packages.nix, so no overriding here.

Considering sasview is the only consumer of this package, I suggest moving the expression there.

FRidh · 2018-03-22T06:35:38Z

pkgs/top-level/python-packages.nix

@@ -12276,6 +12278,26 @@ in {
    };
  };

+  periodictable = buildPythonPackage rec{


We are moving Python expressions out of pkgs/top-level/python-packages.nix into pkgs/development/python-modules/<module>/default.nix.

Please move the expression there, and call it from pkgs/top-level/python-packages.nix using callPackage ../development/python-modules/<package> { };.

FRidh · 2018-03-22T06:35:44Z

pkgs/top-level/python-packages.nix

@@ -12276,6 +12278,26 @@ in {
    };
  };

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


The name attribute is added by buildPython* and should therefore be removed.

FRidh · 2018-03-22T06:35:59Z

pkgs/top-level/python-packages.nix

@@ -17329,6 +17353,29 @@ in {
    };
  };

+  unittest-xml-reporting = buildPythonPackage rec {


We are moving Python expressions out of pkgs/top-level/python-packages.nix into pkgs/development/python-modules/<module>/default.nix.

Please move the expression there, and call it from pkgs/top-level/python-packages.nix using callPackage ../development/python-modules/<package> { };.

FRidh · 2018-03-22T06:36:05Z

pkgs/top-level/python-packages.nix

@@ -17329,6 +17353,29 @@ in {
    };
  };

+  unittest-xml-reporting = buildPythonPackage rec {
+    name = "${pname}-${version}";


The name attribute is added by buildPython* and should therefore be removed.

rprospero · 2018-03-22T17:45:55Z

I've made your suggested changes. Thank you for your patience with this. I probably should have chosen a less finicky package for my first submission.

dotlambda · 2018-04-10T07:15:06Z

@matthewbauer This one created a conflict. I manually merged master into staging right now.

matthewbauer · 2018-04-10T07:17:14Z

Ok thanks!

rprospero added 5 commits March 9, 2018 11:53

pythonPackages.periodictable: init at 1.5.0

e1edb55

This package is a required dependency of SasView, which will be added in a later commit.

pythonPackages.unittest-xml-reporting: init at 2.1.1

db2e6b6

This package is used by Sasview, which will be added in a later commit.

pythonPackage.bumps: init at 0.7.6

242e378

This package is required by SasView, which will be added in a later commit.

pythonPackages.sasmodels: init at 0.96

27f14b5

Sasmodels provides a library of small angle scattering calculations that are needed by Sasview, which will be added in my next commit.

rprospero requested a review from FRidh as a code owner March 12, 2018 09:28

GrahamcOfBorg added 6.topic: python 8.has: package (new) 10.rebuild-darwin: 1-10 10.rebuild-linux: 1-10 labels Mar 12, 2018

FRidh requested changes Mar 17, 2018

View reviewed changes

rprospero added 2 commits March 21, 2018 13:32

Remove explicit licenses import from python package sasmodels

6093745

The licenses variable was being required by sasmoels, but licenses was already a child of the lib parameter and was redundant.

Make xhtml2pdf its own package in python-packages

01c1385

xhtml2pdf now uses the main package html5lib with just an override to pull the correct version number.

Fix typo in license for xhtml2pdf python package

068d792

GrahamcOfBorg added 10.rebuild-darwin: 11-100 10.rebuild-linux: 11-100 and removed 10.rebuild-darwin: 1-10 10.rebuild-linux: 1-10 labels Mar 21, 2018

FRidh requested changes Mar 22, 2018

View reviewed changes

Remove lint from Sasview package

392def7

GrahamcOfBorg added 10.rebuild-darwin: 1-10 10.rebuild-linux: 1-10 and removed 10.rebuild-darwin: 11-100 10.rebuild-linux: 11-100 labels Mar 22, 2018

matthewbauer merged commit 6a74718 into NixOS:master Apr 9, 2018

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sasview: init at 4.1.2 #36852

sasview: init at 4.1.2 #36852

rprospero commented Mar 12, 2018

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matthewbauer commented Apr 10, 2018

sasview: init at 4.1.2 #36852

sasview: init at 4.1.2 #36852

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rprospero commented Mar 12, 2018

Motivation for this change

Things done

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rprospero commented Mar 21, 2018

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rprospero commented Mar 22, 2018

dotlambda commented Apr 10, 2018

matthewbauer commented Apr 10, 2018