commit 4e37a233b7de53c4d51672e404db4804329821e8 · pyrox.dev/nixpkgs

+52

pkgs/development/python-modules/h5io/default.nix

···

       1
       +
       { lib

     

       2
       +
       , buildPythonPackage

     

       3
       +
       , fetchFromGitHub

     

       4
       +
       , pythonOlder

     

       5
       +
       , setuptools

     

       6
       +
       , numpy

     

       7
       +
       , h5py

     

       8
       +
       , pytestCheckHook

     

       9
       +
       }:

     

       10
       +
       

     

       11
       +
       buildPythonPackage rec {

     

       12
       +
         pname = "h5io";

     

       13
       +
         version = "0.2.1";

     

       14
       +
         pyproject = true;

     

       15
       +
       

     

       16
       +
         disabled = pythonOlder "3.7";

     

       17
       +
       

     

       18
       +
         src = fetchFromGitHub {

     

       19
       +
           owner = "h5io";

     

       20
       +
           repo = "h5io";

     

       21
       +
           rev = "refs/tags/h5io-${version}";

     

       22
       +
           hash = "sha256-3mrHIkfaXq06mMzUwudRO81DWTk0TO/e15IQA5fxxNc=";

     

       23
       +
         };

     

       24
       +
       

     

       25
       +
         postPatch = ''

     

       26
       +
           substituteInPlace pyproject.toml  \

     

       27
       +
             --replace "--cov-report=" ""  \

     

       28
       +
             --replace "--cov-branch" ""  \

     

       29
       +
             --replace "--cov=h5io" ""

     

       30
       +
         '';

     

       31
       +
       

     

       32
       +
         nativeBuildInputs = [ setuptools ];

     

       33
       +
       

     

       34
       +
         propagatedBuildInputs = [

     

       35
       +
           numpy

     

       36
       +
           h5py

     

       37
       +
         ];

     

       38
       +
       

     

       39
       +
         nativeCheckInputs = [

     

       40
       +
           pytestCheckHook

     

       41
       +
         ];

     

       42
       +
       

     

       43
       +
         pythonImportsCheck = [ "h5io" ];

     

       44
       +
       

     

       45
       +
         meta = with lib; {

     

       46
       +
           description = "Read and write simple Python objects using HDF5";

     

       47
       +
           homepage = "https://github.com/h5io/h5io";

     

       48
       +
           changelog = "https://github.com/h5io/h5io/releases/tag/${src.rev}";

     

       49
       +
           license = licenses.bsd3;

     

       50
       +
           maintainers = with maintainers; [ mbalatsko ];

     

       51
       +
         };

     

       52
       +
       }

+44 -25

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

···

       1
        
       { lib

     

       2
        
       , buildPythonPackage

     

       3
        
       , fetchFromGitHub

     

       0
        
       
     

       0
        
       
     

       4
        
       , numpy

     

       5
        
       , scipy

     

       6
        
       , pytestCheckHook

     

       7
        
       , pytest-timeout

     

       8
       -
       , h5py

     

       9
        
       , matplotlib

     

       10
       -
       , nibabel

     

       11
       -
       , pandas

     

       12
       -
       , scikit-learn

     

       13
        
       , decorator

     

       14
        
       , jinja2

     

       15
        
       , pooch

     

       16
        
       , tqdm

     

       17
       -
       , setuptools

     

       0
        
       
     

       0
        
       
     

       0
        
       
     

       0
        
       
     

       18
        
       , pythonOlder

     

       19
        
       }:

     

       20
        
       

     

       21
        
       buildPythonPackage rec {

     

       22
        
         pname = "mne-python";

     

       23
       -
         version = "1.6.0";

     

       24
       -
         format = "setuptools";

     

       25
        
       

     

       26
       -
         disabled = pythonOlder "3.7";

     

       27
        
       

     

       28
        
         src = fetchFromGitHub {

     

       29
        
           owner = "mne-tools";

     

       30
       -
           repo = pname;

     

       31
        
           rev = "refs/tags/v${version}";

     

       32
       -
           hash = "sha256-OoaXNHGL2svOpNL5GHcVRfQc9GxIRpZRhpZ5Hi1JTzM=";

     

       33
        
         };

     

       34
        
       

     

       0
        
       
     

       0
        
       
     

       0
        
       
     

       0
        
       
     

       0
        
       
     

       0
        
       
     

       0
        
       
     

       0
        
       
     

       0
        
       
     

       0
        
       
     

       0
        
       
     

       35
        
         propagatedBuildInputs = [

     

       36
       -
           decorator

     

       37
       -
           jinja2

     

       38
       -
           matplotlib

     

       39
        
           numpy

     

       40
       -
           pooch

     

       41
        
           scipy

     

       42
       -
           setuptools

     

       43
        
           tqdm

     

       0
        
       
     

       0
        
       
     

       0
        
       
     

       0
        
       
     

       0
        
       
     

       0
        
       
     

       0
        
       
     

       44
        
         ];

     

       45
        
       

     

       0
        
       
     

       0
        
       
     

       0
        
       
     

       0
        
       
     

       0
        
       
     

       0
        
       
     

       0
        
       
     

       46
        
         nativeCheckInputs = [

     

       47
       -
           h5py

     

       48
       -
           nibabel

     

       49
       -
           pandas

     

       50
        
           pytestCheckHook

     

       51
       -
           scikit-learn

     

       52
        
           pytest-timeout

     

       53
       -
         ];

     

       0
        
       
     

       54
        
       

     

       55
        
         preCheck = ''

     

       56
       -
           export HOME=$TMP

     

       57
        
           export MNE_SKIP_TESTING_DATASET_TESTS=true

     

       58
        
           export MNE_SKIP_NETWORK_TESTS=1

     

       59
        
         '';

     

       60
        
       

     

       61
       -
         # All tests pass, but Pytest hangs afterwards - probably some thread hasn't terminated

     

       62
       -
         doCheck = false;

     

       63
       -
       

     

       64
        
         pythonImportsCheck = [

     

       65
        
           "mne"

     

       66
        
         ];

     
···

       68
        
         meta = with lib; {

     

       69
        
           description = "Magnetoencephelography and electroencephalography in Python";

     

       70
        
           homepage = "https://mne.tools";

     

       0
        
       
     

       71
        
           license = licenses.bsd3;

     

       72
       -
           maintainers = with maintainers; [ bcdarwin ];

     

       73
        
         };

     

       74
        
       }

···

       1
        
       { lib

     

       2
        
       , buildPythonPackage

     

       3
        
       , fetchFromGitHub

     

       4
       +
       , setuptools

     

       5
       +
       , setuptools-scm

     

       6
        
       , numpy

     

       7
        
       , scipy

     

       8
        
       , pytestCheckHook

     

       9
        
       , pytest-timeout

     

       10
       +
       , pytest-harvest

     

       11
        
       , matplotlib

     

       0
        
       
     

       0
        
       
     

       0
        
       
     

       12
        
       , decorator

     

       13
        
       , jinja2

     

       14
        
       , pooch

     

       15
        
       , tqdm

     

       16
       +
       , packaging

     

       17
       +
       , importlib-resources

     

       18
       +
       , lazy-loader

     

       19
       +
       , h5io

     

       20
       +
       , pymatreader

     

       21
        
       , pythonOlder

     

       22
        
       }:

     

       23
        
       

     

       24
        
       buildPythonPackage rec {

     

       25
        
         pname = "mne-python";

     

       26
       +
         version = "1.6.1";

     

       27
       +
         pyproject = true;

     

       28
        
       

     

       29
       +
         disabled = pythonOlder "3.8";

     

       30
        
       

     

       31
        
         src = fetchFromGitHub {

     

       32
        
           owner = "mne-tools";

     

       33
       +
           repo = "mne-python";

     

       34
        
           rev = "refs/tags/v${version}";

     

       35
       +
           hash = "sha256-U1aMqcUZ3BcwqwOYh/qfG5PhacwBVioAgNc52uaoJL0";

     

       36
        
         };

     

       37
        
       

     

       38
       +
         postPatch = ''

     

       39
       +
           substituteInPlace pyproject.toml  \

     

       40
       +
             --replace "--cov-report=" ""  \

     

       41
       +
             --replace "--cov-branch" ""

     

       42
       +
         '';

     

       43
       +
       

     

       44
       +
         nativeBuildInputs = [

     

       45
       +
           setuptools

     

       46
       +
           setuptools-scm

     

       47
       +
         ];

     

       48
       +
       

     

       49
        
         propagatedBuildInputs = [

     

       0
        
       
     

       0
        
       
     

       0
        
       
     

       50
        
           numpy

     

       0
        
       
     

       51
        
           scipy

     

       52
       +
           matplotlib

     

       53
        
           tqdm

     

       54
       +
           pooch

     

       55
       +
           decorator

     

       56
       +
           packaging

     

       57
       +
           jinja2

     

       58
       +
           lazy-loader

     

       59
       +
         ] ++ lib.optionals (pythonOlder "3.9") [

     

       60
       +
           importlib-resources

     

       61
        
         ];

     

       62
        
       

     

       63
       +
         passthru.optional-dependencies = {

     

       64
       +
           hdf5 = [

     

       65
       +
             h5io

     

       66
       +
             pymatreader

     

       67
       +
           ];

     

       68
       +
         };

     

       69
       +
       

     

       70
        
         nativeCheckInputs = [

     

       0
        
       
     

       0
        
       
     

       0
        
       
     

       71
        
           pytestCheckHook

     

       0
        
       
     

       72
        
           pytest-timeout

     

       73
       +
           pytest-harvest

     

       74
       +
         ] ++ lib.flatten (builtins.attrValues passthru.optional-dependencies);

     

       75
        
       

     

       76
        
         preCheck = ''

     

       77
       +
           export HOME=$(mktemp -d)

     

       78
        
           export MNE_SKIP_TESTING_DATASET_TESTS=true

     

       79
        
           export MNE_SKIP_NETWORK_TESTS=1

     

       80
        
         '';

     

       81
        
       

     

       0
        
       
     

       0
        
       
     

       0
        
       
     

       82
        
         pythonImportsCheck = [

     

       83
        
           "mne"

     

       84
        
         ];

     
···

       86
        
         meta = with lib; {

     

       87
        
           description = "Magnetoencephelography and electroencephalography in Python";

     

       88
        
           homepage = "https://mne.tools";

     

       89
       +
           changelog = "https://mne.tools/stable/changes/v${version}.html";

     

       90
        
           license = licenses.bsd3;

     

       91
       +
           maintainers = with maintainers; [ bcdarwin mbalatsko ];

     

       92
        
         };

     

       93
        
       }

+46

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

···

       1
       +
       { lib

     

       2
       +
       , buildPythonPackage

     

       3
       +
       , fetchFromGitLab

     

       4
       +
       , setuptools

     

       5
       +
       , h5py

     

       6
       +
       , numpy

     

       7
       +
       , scipy

     

       8
       +
       , xmltodict

     

       9
       +
       , pytestCheckHook

     

       10
       +
       }:

     

       11
       +
       

     

       12
       +
       buildPythonPackage rec {

     

       13
       +
         pname = "pymatreader";

     

       14
       +
         version = "0.0.31";

     

       15
       +
         pyproject = true;

     

       16
       +
       

     

       17
       +
         src = fetchFromGitLab {

     

       18
       +
           owner = "obob";

     

       19
       +
           repo = "pymatreader";

     

       20
       +
           rev = "refs/tags/v${version}";

     

       21
       +
           hash = "sha256-pYObmvqA49sHjpZcwXkN828R/N5CSpmr0OyyxzDiodQ=";

     

       22
       +
         };

     

       23
       +
       

     

       24
       +
         nativeBuildInputs = [ setuptools ];

     

       25
       +
       

     

       26
       +
         propagatedBuildInputs = [

     

       27
       +
           h5py

     

       28
       +
           numpy

     

       29
       +
           scipy

     

       30
       +
           xmltodict

     

       31
       +
         ];

     

       32
       +
       

     

       33
       +
         nativeCheckInputs = [

     

       34
       +
           pytestCheckHook

     

       35
       +
         ];

     

       36
       +
       

     

       37
       +
         pythonImportsCheck = [ "pymatreader" ];

     

       38
       +
       

     

       39
       +
         meta = with lib; {

     

       40
       +
           description = "A python package to read all kinds and all versions of Matlab mat files";

     

       41
       +
           homepage = "https://gitlab.com/obob/pymatreader/";

     

       42
       +
           changelog = "https://gitlab.com/obob/pymatreader/-/blob/${src.rev}/CHANGELOG.md";

     

       43
       +
           license = licenses.bsd2;

     

       44
       +
           maintainers = with maintainers; [ mbalatsko ];

     

       45
       +
         };

     

       46
       +
       }

+68

pkgs/development/python-modules/pytest-harvest/default.nix

···

       1
       +
       { lib

     

       2
       +
       , buildPythonPackage

     

       3
       +
       , fetchFromGitHub

     

       4
       +
       , setuptools-scm

     

       5
       +
       , pytest-runner

     

       6
       +
       , pytest

     

       7
       +
       , decopatch

     

       8
       +
       , makefun

     

       9
       +
       , six

     

       10
       +
       , pytestCheckHook

     

       11
       +
       , numpy

     

       12
       +
       , pandas

     

       13
       +
       , tabulate

     

       14
       +
       , pytest-cases

     

       15
       +
       , pythonOlder

     

       16
       +
       }:

     

       17
       +
       

     

       18
       +
       buildPythonPackage rec {

     

       19
       +
         pname = "pytest-harvest";

     

       20
       +
         version = "1.10.4";

     

       21
       +
         pyproject = true;

     

       22
       +
       

     

       23
       +
         disabled = pythonOlder "3.6";

     

       24
       +
       

     

       25
       +
         src = fetchFromGitHub {

     

       26
       +
           owner = "smarie";

     

       27
       +
           repo = "python-pytest-harvest";

     

       28
       +
           rev = "refs/tags/${version}";

     

       29
       +
           hash = "sha256-ebzE63d7zt9G9HgbLHaE/USZZpUd3y3vd0kNdT/wWw0=";

     

       30
       +
         };

     

       31
       +
       

     

       32
       +
         # create file, that is created by setuptools_scm

     

       33
       +
         # we disable this file creation as it touches internet

     

       34
       +
         postPatch = ''

     

       35
       +
           echo "version = '${version}'" > pytest_harvest/_version.py

     

       36
       +
         '';

     

       37
       +
       

     

       38
       +
         nativeBuildInputs = [

     

       39
       +
           setuptools-scm

     

       40
       +
           pytest-runner

     

       41
       +
         ];

     

       42
       +
       

     

       43
       +
         buildInputs = [ pytest ];

     

       44
       +
       

     

       45
       +
         propagatedBuildInputs = [

     

       46
       +
           decopatch

     

       47
       +
           makefun

     

       48
       +
           six

     

       49
       +
         ];

     

       50
       +
       

     

       51
       +
         nativeCheckInputs = [

     

       52
       +
           pytestCheckHook

     

       53
       +
           numpy

     

       54
       +
           pandas

     

       55
       +
           tabulate

     

       56
       +
           pytest-cases

     

       57
       +
         ];

     

       58
       +
       

     

       59
       +
         pythonImportsCheck = [ "pytest_harvest" ];

     

       60
       +
       

     

       61
       +
         meta = with lib; {

     

       62
       +
           description = "Store data created during your `pytest` tests execution, and retrieve it at the end of the session, e.g. for applicative benchmarking purposes";

     

       63
       +
           homepage = "https://github.com/smarie/python-pytest-harvest";

     

       64
       +
           changelog = "https://github.com/smarie/python-pytest-harvest/releases/tag/${src.rev}";

     

       65
       +
           license = licenses.bsd3;

     

       66
       +
           maintainers = with maintainers; [ mbalatsko ];

     

       67
       +
         };

     

       68
       +
       }

pkgs/top-level/python-packages.nix

···

       5055
        
           inherit (pkgs) h3;

     

       5056
        
         };

     

       5057
        
       

     

       0
        
       
     

       0
        
       
     

       5058
        
         h5netcdf = callPackage ../development/python-modules/h5netcdf { };

     

       5059
        
       

     

       5060
        
         h5py = callPackage ../development/python-modules/h5py { };

     
···

       10813
        
       

     

       10814
        
         pymatgen = callPackage ../development/python-modules/pymatgen { };

     

       10815
        
       

     

       0
        
       
     

       0
        
       
     

       10816
        
         pymatting = callPackage ../development/python-modules/pymatting { };

     

       10817
        
       

     

       10818
        
         pymaven-patch = callPackage ../development/python-modules/pymaven-patch { };

     
···

       11584
        
         pytest-golden = callPackage ../development/python-modules/pytest-golden { };

     

       11585
        
       

     

       11586
        
         pytest-grpc = callPackage ../development/python-modules/pytest-grpc { };

     

       0
        
       
     

       0
        
       
     

       11587
        
       

     

       11588
        
         pytest-helpers-namespace = callPackage ../development/python-modules/pytest-helpers-namespace { };

     

       11589

···

       5055
        
           inherit (pkgs) h3;

     

       5056
        
         };

     

       5057
        
       

     

       5058
       +
         h5io = callPackage ../development/python-modules/h5io { };

     

       5059
       +
       

     

       5060
        
         h5netcdf = callPackage ../development/python-modules/h5netcdf { };

     

       5061
        
       

     

       5062
        
         h5py = callPackage ../development/python-modules/h5py { };

     
···

       10815
        
       

     

       10816
        
         pymatgen = callPackage ../development/python-modules/pymatgen { };

     

       10817
        
       

     

       10818
       +
         pymatreader = callPackage ../development/python-modules/pymatreader { };

     

       10819
       +
       

     

       10820
        
         pymatting = callPackage ../development/python-modules/pymatting { };

     

       10821
        
       

     

       10822
        
         pymaven-patch = callPackage ../development/python-modules/pymaven-patch { };

     
···

       11588
        
         pytest-golden = callPackage ../development/python-modules/pytest-golden { };

     

       11589
        
       

     

       11590
        
         pytest-grpc = callPackage ../development/python-modules/pytest-grpc { };

     

       11591
       +
       

     

       11592
       +
         pytest-harvest = callPackage ../development/python-modules/pytest-harvest { };

     

       11593
        
       

     

       11594
        
         pytest-helpers-namespace = callPackage ../development/python-modules/pytest-helpers-namespace { };

     

       11595