several MINC additions/updates in separate commits: libminc, minc-tools, minc-widgets, N3, inormalize, EBTKS, mni_autoreg, and some Perl modules #29782

bcdarwin · 2017-09-25T19:29:05Z

Motivation for this change

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
- Linux
[NA] Tested via one or more NixOS test(s) if existing and applicable for the change (look inside nixos/tests)
[NA] 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.

…sion)

mention-bot · 2017-09-25T19:29:08Z

@bcdarwin, thanks for your PR! By analyzing the history of the files in this pull request, we identified @obadz to be a potential reviewer.

vyp

Despite the number of comments, nothing major here, these are really all just nitpicks regarding version numbers, licenses etc. 👍 🙂

vyp · 2017-09-26T05:21:52Z

pkgs/applications/science/biology/N3/default.nix

+    description = "MRI non-uniformity correction for MINC files";
+    maintainers = with maintainers; [ bcdarwin ];
+    platforms = platforms.unix;
+  };


I'm not sure what the exact license is, but it seems to be free software, so can you add a license field here? license = licenses.free;

vyp · 2017-09-26T05:31:46Z

pkgs/applications/science/biology/N3/default.nix

+
+stdenv.mkDerivation rec {
+  pname = "N3";
+  name  = "${pname}-1.0.20";


Where did you get this version number?

vyp · 2017-09-26T05:42:56Z

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

+
+stdenv.mkDerivation rec {
+  pname = "inormalize";
+  name  = "${pname}-1.0.20";


This version number doesn't correspond to the git revision. For the 79cea9c revision, a date version should be used: "${pname}-2014-10-21". Or if you want to use this version:

{ pname = "inormalize"; version = "1.0.20"; name = "${pname}-${version}"; src = fetchFromGitHub { # ... rev = "release-${version}"; # ... }; }

vyp · 2017-09-26T05:43:46Z

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

+    description = "Program to normalize intensity of MINC files";
+    maintainers = with maintainers; [ bcdarwin ];
+    platforms = platforms.unix;
+  };


license = licenses.free;

vyp · 2017-09-26T05:46:18Z

pkgs/applications/science/biology/minc-tools/default.nix

+    for prog in minccomplete minchistory mincpik; do
+      wrapProgram $out/bin/$prog --prefix PERL5LIB : $PERL5LIB
+    done
+  '';

  meta = with stdenv.lib; {


Could you also add a license = licenses.free; field for meta in this update too?

vyp · 2017-09-26T06:16:13Z

pkgs/development/libraries/libminc/default.nix

+  checkPhase = ''
+    export LD_LIBRARY_PATH="$(pwd)"  # see #22060
+    ctest -E ezminc_rw_test --output-on-failure   # ezminc_rw_test can't find libminc_io.so.5.2.0
+  '';
  doCheck = true;

  meta = with stdenv.lib; {


Could you also add a license = licenses.free; field for this package too while you're at it?

vyp · 2017-09-26T06:17:39Z

pkgs/development/libraries/science/biology/EBTKS/default.nix

+    description = "Library for working with MINC files";
+    maintainers = with maintainers; [ bcdarwin ];
+    platforms = platforms.unix;
+  };


license = licenses.free;

vyp · 2017-09-26T06:18:39Z

pkgs/development/libraries/science/biology/EBTKS/default.nix

+
+  cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/" "-DBUILD_TESTING=FALSE" ];
+
+  checkPhase = "ctest --output-on-failure";  # but there are no tests ...


Isn't testing/ebtks_test_fft.cc a test file?

vyp · 2017-09-26T06:21:22Z

pkgs/development/libraries/science/biology/EBTKS/default.nix

+
+stdenv.mkDerivation rec {
+  pname = "EBTKS";
+  name  = "${pname}-1.6.50";


Version number doesn't correspond to the git revision.

vyp · 2017-09-26T06:22:58Z

pkgs/top-level/perl-packages.nix

+      homepage = http://www.shlomifish.org/open-source/projects/Text-Format/;
+      description = "Format text";
+      license = with stdenv.lib.licenses; [ artistic1 gpl1Plus ];
+    };


Did you want to maintain this package as well?

bcdarwin · 2017-09-26T17:24:36Z

@vyp all addressed.

bcdarwin · 2017-09-26T19:20:41Z

The minc-widgets maintainers have updated the license information to confirm that they're indeed free software; I used 'licenses.free' in the packages so everything's fine.

vyp · 2017-09-27T03:29:11Z

pkgs/top-level/perl-packages.nix

+      homepage = http://www.shlomifish.org/open-source/projects/Text-Format/;
+      description = "Format text";
+      license = with stdenv.lib.licenses; [ artistic1 gpl1Plus ];
+      maintainer = with maintainers; [ bcdarwin ];


with stdenv.lib.maintainers;

perl-packages has stdenv.lib.maintainers in scope

My bad, thanks.

vyp · 2017-09-27T03:30:19Z

The EBTKS version number still doesn't correspond to the git revision. Everything else except for the above review comment looks good though, thanks! 👍

bcdarwin · 2017-09-27T03:54:17Z

EBTKS version also now updated.

bcdarwin · 2017-09-27T15:14:00Z

travis build is failing for unrelated reasons

bcdarwin · 2017-12-30T19:40:29Z

as far as I can tell everything is good here; is there a way to notify someone who could merge it or should I open a new PR?

@vyp

bcdarwin added 9 commits September 24, 2017 17:28

libminc: 2.3.00 -> 2.3.01 (develop branch)

27da553

perlPackages.TextFormat: init at 0.60

8ecd95e

minc-tools: 2.3.00 -> 2.3.01 (develop branch)

579d1c8

EBTKS: init at 1.6.50 (develop branch)

3b0f8aa

perlPackages.MNI-Perllib: init at 0.08

75e296f

mni_autoreg: init at 0.99.70

117d0a0

minc-widgets: init at "1.0.0" (package seems to lack a consistent ver…

12ea730

…sion)

n3: init at 1.0.20

1facbf4

inormalize: init at 1.0.20 (develop branch)

b55216d

vyp reviewed Sep 26, 2017

View reviewed changes

address license/version issues for PR NixOS#29782

82a0996

bcdarwin added 3 commits September 26, 2017 17:59

itk: enable more MINC support

3fcb47b

bicpl: init at 2017-09-10

0419655

ezminc: init at 2017-08-29

773b609

bcdarwin force-pushed the mni-autoreg branch from 9d75e04 to 773b609 Compare September 26, 2017 22:44

vyp reviewed Sep 27, 2017

View reviewed changes

fix EBTKS version naming

4cf407f

bcdarwin added 2 commits September 29, 2017 14:03

arguments: init at 2015-11-30

016afb0

oobicpl: init at 2016-03-02

5a70944

vyp approved these changes Sep 30, 2017

View reviewed changes

bcdarwin added a commit to bcdarwin/nixpkgs that referenced this pull request Apr 10, 2018

address license/version issues for PR NixOS#29782

cf2aac6

bcdarwin mentioned this pull request Apr 10, 2018

MINC ecosystem #38664

Merged

6 tasks

bcdarwin closed this Apr 10, 2018

bcdarwin deleted the mni-autoreg branch February 14, 2020 16:51

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

several MINC additions/updates in separate commits: libminc, minc-tools, minc-widgets, N3, inormalize, EBTKS, mni_autoreg, and some Perl modules #29782

several MINC additions/updates in separate commits: libminc, minc-tools, minc-widgets, N3, inormalize, EBTKS, mni_autoreg, and some Perl modules #29782

bcdarwin commented Sep 25, 2017 •

edited

mention-bot commented Sep 25, 2017

vyp left a comment

vyp Sep 26, 2017

vyp Sep 26, 2017

vyp Sep 26, 2017

vyp Sep 26, 2017

vyp Sep 26, 2017

vyp Sep 26, 2017

vyp Sep 26, 2017

vyp Sep 26, 2017

vyp Sep 26, 2017

vyp Sep 26, 2017

bcdarwin commented Sep 26, 2017

bcdarwin commented Sep 26, 2017

vyp Sep 27, 2017

bcdarwin Sep 27, 2017

vyp Sep 27, 2017

vyp commented Sep 27, 2017 •

edited

bcdarwin commented Sep 27, 2017

bcdarwin commented Sep 27, 2017

bcdarwin commented Dec 30, 2017


		cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/" "-DBUILD_TESTING=FALSE" ];

		checkPhase = "ctest --output-on-failure"; # but there are no tests ...

several MINC additions/updates in separate commits: libminc, minc-tools, minc-widgets, N3, inormalize, EBTKS, mni_autoreg, and some Perl modules #29782

several MINC additions/updates in separate commits: libminc, minc-tools, minc-widgets, N3, inormalize, EBTKS, mni_autoreg, and some Perl modules #29782

Conversation

bcdarwin commented Sep 25, 2017 • edited

Motivation for this change

Things done

mention-bot commented Sep 25, 2017

vyp left a comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

bcdarwin commented Sep 26, 2017

bcdarwin commented Sep 26, 2017

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

vyp commented Sep 27, 2017 • edited

bcdarwin commented Sep 27, 2017

bcdarwin commented Sep 27, 2017

bcdarwin commented Dec 30, 2017

bcdarwin commented Sep 25, 2017 •

edited

vyp commented Sep 27, 2017 •

edited