public/nixpkgs
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity
229,934 Commits 1 Branch 0 Tags
4162b7b08166327c6922d04d044eece291e45839
Commit Graph
100 Commits
This Branch
This Branch
All Branches
Author SHA1 Message Date
Ben Darwin 7547926b81 ocamlPackages.biocaml: patch for -safe-string compilation with Ocaml 4.10 2020-05-28 09:08:51 +02:00
Ben Darwin 203d0644b4 ocamlPackages.owl: 0.8.0 -> 0.9.0 2020-05-28 09:08:51 +02:00
Ben Darwin 45cd7beeb2 bppsuite: init at 2.4.1 2020-05-25 21:13:02 -04:00
Ben Darwin 7f656f3ef6 bpp-popgen: init at 2.4.1 2020-05-25 21:12:17 -04:00
Ben Darwin a53b27829c bpp-phyl: init at 2.4.1 2020-05-25 21:10:59 -04:00
Ben Darwin 8d712ccc16 bpp-seq: init at 2.4.1 2020-05-25 21:09:52 -04:00
Ben Darwin adc7b4c979 bpp-core: init at 2.4.1 2020-05-25 21:08:31 -04:00
Ben Darwin b20f22d4cd python3Packages.pytorch-metric-learning: init at 0.9.81 2020-05-25 20:56:03 -04:00
Ben Darwin 710a48751a skorch: init at 0.8.0 2020-05-25 20:31:11 -04:00
Ben Darwin 5e716bf469 vtk: 7.1.1 -> 8.2.0 
- also create vtk_7 as several packages don't build with 8.x:
  - itk5: vtkVersion.h header not found at compile time
  - ants: version in tree (2.2.0) is incompatible with 8.2
  - itk4: ants depends on both vtk and itk4, so use vtk_7
  - gdcm: vtk header issue
  - python3Packages.vtk: Python C API compilation error with Python 3.8

- upgrade vtkWithQt4 -> vtkWithQt5
 2020-05-11 17:54:29 -04:00
Ben Darwin 1e0912d772 ocamlPackages.torch: init at 0.8 2020-05-09 19:29:47 -04:00
Ben Darwin 43d6898ea2 python3Packages.livelossplot: init at 0.5.0 2020-05-09 17:43:31 -04:00
Ben Darwin d78ba41a56 python3Packages.ipydatawidgets: init at 4.0.1 2020-05-08 07:43:25 +02:00
Ben Darwin 7ecde8b92b python3Packages.traittypes: init at unstable-2019-06-23 2020-05-08 07:43:25 +02:00
Ben DarwinandJon 81be227423 python3Packages.heudiconv: init at 0.8.0 (#86984) 
* python3Packages.heudiconv: init at 0.8.0

*python3Packages.heudiconv: rfc 45, quote homepage

Co-authored-by: Jon <jonringer@users.noreply.github.com>
 2020-05-07 11:30:16 -07:00
Ben Darwin 34807336e8 python3Packages.dicom2nifti: init at 2.2.8 2020-05-06 13:36:03 -07:00
Ben Darwin 4e2322ae7a python3Packages.neo: init at 0.8.0 2020-05-06 09:47:34 -07:00
Ben Darwin d737f310ff ocamlPackages.owl: unbreak by reversing previous edits 
- package was broken by 1c8aba83 (#83888)
 - fixes #85915
 2020-05-06 09:21:58 +02:00
Ben Darwin 5caa76705b elastix: update for ITK 5.1.0 
- fetch patches to build elastix 5.0 with ITK 5.1
- update 'platforms': builds on Darwin, fails on aarch64
 2020-05-05 00:08:04 -04:00
Ben Darwin 6f1430a802 ezminc: switch from itk5 to itk4 branch 
- itk5 branch currently lacks support for itk 5.1
 2020-05-05 00:08:04 -04:00
Ben Darwin 20cf206a09 simpleitk: itk -> itk4 
- simpleitk 1.2.4 is incompatible with ITK 5.1, so this can be reverted when 2.x is released.
 2020-05-05 00:08:04 -04:00
Ben Darwin 404834334b itk: 5.0.1 -> 5.1.0 2020-05-05 00:08:00 -04:00
Ben Darwin 5d88b43f58 python3Packages.pydicom: 1.4.1 -> 1.4.2 2020-05-04 23:19:44 -04:00
Ben Darwin e72b2beab0 vtk: unbreak on OS X 2020-05-04 10:47:27 -04:00
Ben Darwin dca8b1bdd0 python3Packages.transforms3d: init at unstable-2019-12-17 2020-05-01 09:35:06 +02:00
Ben Darwin 948b38300d vtkWithQt4: actually build QVTK libs/headers (#84772) 
- VTK_USE_QT is obsolete and didn't have the intended effect
 2020-04-29 19:11:14 -04:00
Ben Darwin cc89b93798 python3Packages.batchgenerators: 0.19.7 -> 0.20.0 2020-04-28 09:31:12 -07:00
Ben Darwin 70171d321e mrtrix: 3.0_RC3_latest -> 3.0.0 2020-04-28 10:37:06 -04:00
Ben Darwin fe07e2b2ac elastix: enable tests 2020-04-21 07:54:59 +02:00
Ben Darwin 30cafee8b6 elastix: python -> python3 2020-04-21 07:54:59 +02:00
Ben Darwin ad7b7367b6 beluga: 20180403 -> unstable-2020-03-11 2020-04-19 21:54:06 -04:00
Ben Darwin c62428963a ocamlPackages.sedlex_2: fix dependencies (as per 77901a9) 2020-04-19 21:50:37 -04:00
Ben Darwin 3a9f743605 ocamlPackages.linenoise: 1.1.0 -> 1.3.0 2020-04-19 21:50:37 -04:00
Ben Darwin 261d7c2f66 ocamlPackages.dune-build-info: init at 2.4.0 2020-04-19 21:50:37 -04:00
Ben Darwin 9b83c440f6 python3Packages.mayavi: build for Python 3 instead of Python 2 
- switch from wxPython to Qt5
 2020-04-14 12:43:56 -04:00
Ben Darwin 2d8f346c7c python3Packages.envisage: update and disable for Python 2 
- next release will drop support for Python 2
 2020-04-13 14:04:50 -04:00
Ben Darwin 5ac182265e python3Packages.pyface: remove optional wxPython dep 2020-04-13 12:33:51 -04:00
Ben Darwin 21f191cddb python3Packages.apptools: fix build 2020-04-13 12:32:37 -04:00
Ben Darwin 0dd910d470 python3Packages.graspy: init at 0.2 2020-04-10 00:08:42 -07:00
Ben Darwin 0473d4d62e python2Packages.traitsui: remove optional wxPython dependency 2020-04-09 10:04:04 -07:00
Ben Darwin e67d840931 python2Packages.apptools: 4.4.0 -> 4.5.0 2020-04-09 10:01:58 -07:00
Ben Darwin 92763dd8f1 python3Packages.nitime: quote homepage URL 2020-04-09 10:45:09 -04:00
Ben Darwin 7e2f26ea05 python3Packages.nilearn: quote homepage URL 2020-04-09 10:44:55 -04:00
Ben Darwin 8073255e47 python3Packages.nibabel: quote homepage URL 2020-04-09 10:44:40 -04:00
Ben Darwin e31f63b45a python3Packages.nipy: quote homepage URL 2020-04-09 10:43:53 -04:00
Ben Darwin 77901a96da ocamlPackages.sedlex: fix dependencies 2020-04-06 10:48:42 -04:00
Ben Darwin 2d50f3e27e python3Packages.spyder: unbreak package 
- by removed removed "Editor" category from categories arg to
  makeDesktopItem
 2020-04-01 17:16:05 -07:00
Ben Darwin 4aaa18b64b python3Packages.dcmstack: init at 0.8 2020-03-30 18:01:07 -07:00
Ben Darwin 17611f14c2 python3Packages.dipy: init at 1.1.1 2020-03-27 14:43:56 -07:00
Ben Darwin 6f9f91d331 python3Packages.cufflinks: add nose to checkInputs 2020-03-27 10:53:07 -07:00
Ben Darwin 93c9cb09bd python3Packages.deap: add nose to checkInputs 2020-03-27 10:53:07 -07:00
Ben Darwin ca2cf66f10 python3Packages.bayespy: add nose to checkInputs 2020-03-27 10:53:07 -07:00
Ben Darwin 78d5faba5e python3Packages.nilearn: add nose to checkInputs 2020-03-27 10:53:07 -07:00
Ben Darwin 5842ec9368 python3Packages.matplotlib: remove nose from propagatedBuildInputs 2020-03-27 10:53:07 -07:00
Ben Darwin 5df826fb11 python3Packages.rope: 0.14.0 -> 0.16.0 2020-03-26 13:43:10 -07:00
Ben Darwin 353c6c948e python37Packages.spyder: 4.0.1 -> 4.1.1 (and unbreak for Python3.7) 2020-03-23 10:50:45 -07:00
Ben Darwin ac17611354 python3Packages.python-language-server: 0.31.8 -> 0.31.9 2020-03-23 10:50:45 -07:00
Ben Darwin 3d0410e769 python38Packages.rope: disable for Python>=3.8 
- browsing the github page suggests the upcoming 0.17 release should support 3.8
 2020-03-23 08:40:29 -04:00
Ben Darwin 8e44423a96 ocamlPackages.lacaml: 11.0.3 -> 11.0.6 2020-03-18 08:32:39 +01:00
Ben Darwin 61b61ed087 python3Packages.batchgenerators: init at 0.19.7 2020-03-14 22:56:38 +01:00
Ben Darwin 45d0109512 python3Packages.threadpoolctl: init at 2.0.0 2020-03-14 22:56:38 +01:00
Ben Darwin b5d0ffcab1 python3Packages.hickle: 3.4.5 -> 3.4.6 2020-03-13 19:49:18 +00:00
Ben Darwin fd9b40d076 ocamlPackages_latest.phylogenetics: dune2/fix meta 2020-02-27 12:22:14 -05:00
Ben Darwin 290b09847a ocamlPackages.owl: 0.7.2 -> 0.8.0 2020-02-27 12:05:21 -05:00
Ben Darwin 5fc6b34dba ocamlPackages.eigen: 0.1.5 -> 0.2.0 2020-02-27 12:03:28 -05:00
Ben Darwin 65461ea1f2 python3Packages.nitime: init at 0.8.1 2020-02-26 13:19:28 -05:00
Ben Darwin 9a2cd20478 mrtrix: init at 3.0_RC3_latest 
This package consists mostly of command-line tools, but there are also two qt5-based image viewers (`mrview` and `shview`). I have provided an option `withGui = true` to allow users to disable these viewers. They work on NixOS but unlikely to work out-of-the box on non-NixOS Linux (see #62169), but I've refrained from asserting that they shouldn't be built since a user might want to fiddle with runtime GL stuff.

Some programs rely on FSL and/or ANTs backends; I have somewhat heavy-handedly wrapped all binaries to point to ANTs, while FSL is not available in Nix at the moment and has a non-commercial license so would be convenient to disable by default for Hydra builds.
 2020-02-16 22:25:25 -05:00
Ben Darwin 6dca90784a python3Packages.pywick: init at 0.5.6 2020-02-14 16:42:52 -08:00
Ben Darwin 931f47304f python3Packages.hickle: init at 3.4.5 2020-02-14 16:42:52 -08:00
Ben Darwin 1112bcc75e c3d: unbreak via stdenv -> gcc8Stdenv 2020-02-13 17:45:18 -05:00
Ben Darwin c81a2e6a1e ocamlPackages.npy: init at unstable-2019-04-02 2020-02-11 07:33:42 +01:00
Ben Darwin c79d6d0430 c3d: 2018-10-04 -> unstable-2019-10-22; mark unbroken 2020-02-10 20:58:35 +01:00
Ben Darwin 7059f44440 python3Packages.tensorly: init at 0.4.5 2020-02-10 20:21:28 +01:00
Ben Darwin 35bfcc98c9 python3Packages.sparse: mark unbroken (package has been previously updated) 2020-02-10 20:21:28 +01:00
Ben Darwin 39f0e3b32b minc_tools: enable building conversion tools 2020-02-10 19:53:25 +01:00
Ben Darwin bcad453bcf minc_tools: 2017-09-11 -> unstable-2019-12-04 2020-02-10 19:53:25 +01:00
Ben Darwin 134b645343 python3Packages.nilearn: unbreak package 2020-02-06 19:59:14 +01:00
Ben Darwin f5c191739b pythonPackages.pydicom: 1.3.0 -> 1.4.1 
- routine update; unbreaks with Python 3.8 (not supported before 1.4.1)
 2020-02-06 19:59:14 +01:00
Ben Darwin 83bdc1d989 python3Packages.nibabel: 3.0.0 -> 3.0.1 
- this unbreaks the package due to erroring tests in 3.0.0
- remove obsolete (mostly Python2-related) deps
- add deps to support MINC, DICOM, and SPM formats
- only build on x64 due to a dtype bug on Arm64
 2020-02-06 19:59:14 +01:00
Ben Darwin d55c1b09ce ocamlPackages.bistro: propagate buildInputs 2020-02-06 09:39:25 +01:00
Ben Darwin 00cd1d0f21 ocamlPackages.parmap: init at 1.1 2020-02-04 17:49:45 +01:00
Ben Darwin 3ac3677876 octave: build without qscintilla by default 
- qscintilla is used for IDE features in the GUI, which is not built since qt support isn't enabled
- this removes qt from the Octave closure
 2020-02-03 10:29:17 -05:00
Ben Darwin 24bd88ce5a ocamlPackages.biocaml: 0.10.0 -> 0.10.1 2020-01-30 17:05:33 -05:00
Ben Darwin 29bc26113c ocamlPackages.cfstream: 1.3.0 -> 1.3.1 2020-01-30 17:04:54 -05:00
Ben Darwin 046730ebdb pythonPackages.pydicom: init at 1.3.0 2020-01-16 12:34:09 -08:00
Ben Darwin 54c409eb01 pythonPackages.pyezminc: remove 
- package supports Python 2 only
- develop-python3 branch exists but datatype tests fail
- not updated since 2018
 2020-01-16 12:14:49 -08:00
Ben Darwin 1dc14208f5 python3Packages.ignite: init at 0.2.1 2020-01-14 14:26:56 -05:00
Ben Darwin 1c613434c5 python3Packages.pynvml: init at 8.0.4 2020-01-14 14:26:50 -05:00
Ben Darwin 8f1994c2cc pythonPackages.pynrrd: init at 0.4.2 2020-01-14 10:33:55 -08:00
Ben Darwin ee7d45c638 pythonPackages.hydra: init at 1.4.1 2020-01-09 22:54:16 -08:00
Ben Darwin 60c03fb380 pythonPackages.omegaconf: init at 1.4.1 2020-01-09 22:54:16 -08:00
Ben Darwin b4615c3b6a python3Packages.pycm: init at 2.5 2020-01-08 16:19:47 -08:00
Ben Darwin 81179a4d56 pythonPackages.crc32c: init at 2.0 2020-01-07 20:55:18 -08:00
Ben Darwin d255365342 ocamlPackages.parany: 7.0.0 -> 8.0.0 2019-12-26 17:31:16 -05:00
Ben Darwin f1958523e3 ocamlPackages.cpu: setcore 1.0.1 -> cpu 2.0.0 2019-12-26 17:30:49 -05:00
Ben Darwin 80da0a626e functoria: 2.0.2 -> 3.0.3 2019-12-22 20:45:12 -05:00
Ben Darwin 2ea7b81750 netcdf: 4.6.1 -> 4.7.3 
and enable tests as per unmerged #56830
 2019-12-20 13:56:53 +01:00
Ben Darwin 52d15ab28b libminc: 2018-01-17 -> 2.4.03 and disable broken checkPhase on OSX 2019-12-09 14:19:15 -05:00
Ben Darwin bfe5d1cc96 ocamlPackages.owl: 0.7.1 -> 0.7.2 
- also enable tests (except on OSX) due to upstream fixes
 2019-12-09 11:00:11 -05:00
Ben Darwin e85fe01325 plplot: init at 5.15.0 2019-12-06 14:41:39 -05:00