diff --git a/pkgs/development/python-modules/dask-glm/default.nix b/pkgs/development/python-modules/dask-glm/default.nix new file mode 100644 index 00000000000..13af6d9da8a --- /dev/null +++ b/pkgs/development/python-modules/dask-glm/default.nix @@ -0,0 +1,35 @@ +{ stdenv +, buildPythonPackage +, fetchPypi +, cloudpickle +, dask +, numpy, toolz # dask[array] +, multipledispatch +, scipy +, scikitlearn +, pytest +}: + +buildPythonPackage rec { + version = "0.1.0"; + pname = "dask-glm"; + + src = fetchPypi { + inherit pname version; + sha256 = "5a38d17538558fe6a3457cd67eed0a90a5dff51a9eaebb496efb68fc432ed89a"; + }; + + checkInputs = [ pytest ]; + propagatedBuildInputs = [ cloudpickle dask numpy toolz multipledispatch scipy scikitlearn ]; + + checkPhase = '' + py.test dask_glm + ''; + + meta = with stdenv.lib; { + homepage = http://github.com/dask/dask-glm/; + description = "Generalized Linear Models with Dask"; + license = licenses.bsd3; + maintainers = [ maintainers.costrouc ]; + }; +} diff --git a/pkgs/development/python-modules/dask-image/default.nix b/pkgs/development/python-modules/dask-image/default.nix new file mode 100644 index 00000000000..15a13b2ff71 --- /dev/null +++ b/pkgs/development/python-modules/dask-image/default.nix @@ -0,0 +1,30 @@ +{ stdenv +, buildPythonPackage +, fetchPypi +, dask +, numpy, toolz # dask[array] +, scipy +, pims +, pytest +, scikitimage +}: + +buildPythonPackage rec { + version = "0.1.1"; + pname = "dask-image"; + + src = fetchPypi { + inherit pname version; + sha256 = "e6294ac577a8fc0abec2b97a2c42d404f599feac61d6899bdf1bf2b7cfb0e015"; + }; + + checkInputs = [ pytest scikitimage ]; + propagatedBuildInputs = [ dask numpy toolz scipy pims ]; + + meta = with stdenv.lib; { + homepage = https://github.com/dask/dask-image; + description = "Distributed image processing"; + license = licenses.bsdOriginal; + maintainers = [ maintainers.costrouc ]; + }; +} diff --git a/pkgs/development/python-modules/dask-jobqueue/default.nix b/pkgs/development/python-modules/dask-jobqueue/default.nix new file mode 100644 index 00000000000..e6ac86660c1 --- /dev/null +++ b/pkgs/development/python-modules/dask-jobqueue/default.nix @@ -0,0 +1,33 @@ +{ stdenv +, buildPythonPackage +, fetchPypi +, dask +, distributed +, docrep +, pytest +}: + +buildPythonPackage rec { + version = "0.4.0"; + pname = "dask-jobqueue"; + + src = fetchPypi { + inherit pname version; + sha256 = "c73dae82b2a1d2a9f4ef17778f0de7a9237671a7fd3374aadd9d2bc07e92e848"; + }; + + checkInputs = [ pytest ]; + propagatedBuildInputs = [ dask distributed docrep ]; + + # do not run entire tests suite (requires slurm, sge, etc.) + checkPhase = '' + py.test dask_jobqueue/tests/test_jobqueue_core.py + ''; + + meta = with stdenv.lib; { + homepage = https://github.com/dask/dask-jobqueue; + description = "Deploy Dask on job schedulers like PBS, SLURM, and SGE"; + license = licenses.bsd3; + maintainers = [ maintainers.costrouc ]; + }; +} diff --git a/pkgs/development/python-modules/dask-ml/default.nix b/pkgs/development/python-modules/dask-ml/default.nix new file mode 100644 index 00000000000..0f53bcc225d --- /dev/null +++ b/pkgs/development/python-modules/dask-ml/default.nix @@ -0,0 +1,43 @@ +{ stdenv +, buildPythonPackage +, fetchPypi +, dask +, numpy, toolz # dask[array] +, numba +, pandas +, scikitlearn +, scipy +, dask-glm +, six +, multipledispatch +, packaging +, pytest +, xgboost +, tensorflow +, joblib +, distributed +}: + +buildPythonPackage rec { + version = "0.10.0"; + pname = "dask-ml"; + + src = fetchPypi { + inherit pname version; + sha256 = "4b6ca548c7282c1b6983e696e4bdfa0a2d7b51b168928b9322ea7a4b9a9f20f9"; + }; + + checkInputs = [ pytest xgboost tensorflow joblib distributed ]; + propagatedBuildInputs = [ dask numpy toolz numba pandas scikitlearn scipy dask-glm six multipledispatch packaging ]; + + # dask-ml has some heavy test requirements + # and requires some very new packages + doCheck = false; + + meta = with stdenv.lib; { + homepage = https://github.com/dask/dask-ml; + description = "Scalable Machine Learn with Dask"; + license = licenses.bsd3; + maintainers = [ maintainers.costrouc ]; + }; +} diff --git a/pkgs/development/python-modules/dask-xgboost/default.nix b/pkgs/development/python-modules/dask-xgboost/default.nix new file mode 100644 index 00000000000..06b5e762852 --- /dev/null +++ b/pkgs/development/python-modules/dask-xgboost/default.nix @@ -0,0 +1,36 @@ +{ stdenv +, buildPythonPackage +, fetchPypi +, xgboost +, dask +, distributed +, pytest +, scikitlearn +, scipy +}: + +buildPythonPackage rec { + version = "0.1.5"; + pname = "dask-xgboost"; + + src = fetchPypi { + inherit pname version; + sha256 = "1860d06965fe68def1c83b9195130a92050fd4bc28bf2be689898a3a74ee1316"; + }; + + checkInputs = [ pytest scikitlearn ]; + propagatedBuildInputs = [ xgboost dask distributed ]; + + checkPhase = '' + py.test dask_xgboost/tests/test_core.py + ''; + + doCheck = false; + + meta = with stdenv.lib; { + homepage = https://github.com/dask/dask-xgboost; + description = "Interactions between Dask and XGBoost"; + license = licenses.bsd3; + maintainers = [ maintainers.costrouc ]; + }; +} diff --git a/pkgs/development/python-modules/distributed/default.nix b/pkgs/development/python-modules/distributed/default.nix index 987b64439a5..694bc2ce4f9 100644 --- a/pkgs/development/python-modules/distributed/default.nix +++ b/pkgs/development/python-modules/distributed/default.nix @@ -1,6 +1,6 @@ { lib , buildPythonPackage -, fetchFromGitHub +, fetchPypi , pytest , pytest-repeat , pytest-faulthandler @@ -26,14 +26,12 @@ buildPythonPackage rec { pname = "distributed"; - version = "1.22.1"; + version = "1.23.1"; # get full repository need conftest.py to run tests - src = fetchFromGitHub { - owner = "dask"; - repo = pname; - rev = version; - sha256 = "0xvx55rhbhlyys3kjndihwq6y6260qzy9mr3miclh5qddaiw2d5z"; + src = fetchPypi { + inherit pname version; + sha256 = "9d4693442efe40e05e4304fe6d8174989c6eb4bad1afe70480c98263ef8e1cdb"; }; checkInputs = [ pytest pytest-repeat pytest-faulthandler pytest-timeout mock joblib ]; diff --git a/pkgs/development/python-modules/pims/default.nix b/pkgs/development/python-modules/pims/default.nix new file mode 100644 index 00000000000..4e45d5203e6 --- /dev/null +++ b/pkgs/development/python-modules/pims/default.nix @@ -0,0 +1,34 @@ +{ stdenv +, buildPythonPackage +, fetchPypi +, slicerator +, scikitimage +, six +, numpy +, tifffile +, pytest +, nose +}: + +buildPythonPackage rec { + version = "0.4.1"; + pname = "PIMS"; + + src = fetchPypi { + inherit pname version; + sha256 = "6a53a155e900b44e71127a1e1fccbfbaed7eec3c2b52497c40c23a05f334c9dd"; + }; + + checkInputs = [ nose ]; + propagatedBuildInputs = [ slicerator six numpy tifffile scikitimage ]; + + # not everything packaged with pypi release + doCheck = false; + + meta = with stdenv.lib; { + homepage = https://github.com/soft-matter/pims; + description = "Python Image Sequence: Load video and sequential images in many formats with a simple, consistent interface"; + license = licenses.bsdOriginal; + maintainers = [ maintainers.costrouc ]; + }; +} diff --git a/pkgs/development/python-modules/slicerator/default.nix b/pkgs/development/python-modules/slicerator/default.nix new file mode 100644 index 00000000000..6af7fafdddf --- /dev/null +++ b/pkgs/development/python-modules/slicerator/default.nix @@ -0,0 +1,32 @@ +{ stdenv +, buildPythonPackage +, fetchPypi +, python +, six +}: + +buildPythonPackage rec { + version = "0.9.8"; + pname = "slicerator"; + + src = fetchPypi { + inherit pname version; + sha256 = "b91dd76a415fd8872185cbd6fbf1922fe174359053d4694983fc719e4a0f5667"; + }; + + propagatedBuildInputs = [ six ]; + + checkPhase = '' + ${python.interpreter} run_tests.py + ''; + + # run_tests.py not packaged with pypi release + doCheck = false; + + meta = with stdenv.lib; { + homepage = http://github.com/soft-matter/slicerator; + description = "A lazy-loading, fancy-sliceable iterable"; + license = licenses.bsdOriginal; + maintainers = [ maintainers.costrouc ]; + }; +} diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix index 59324f7ab2f..2efbdf88a57 100644 --- a/pkgs/top-level/python-packages.nix +++ b/pkgs/top-level/python-packages.nix @@ -388,6 +388,8 @@ in { phonopy = callPackage ../development/python-modules/phonopy { }; + pims = callPackage ../development/python-modules/pims { }; + plantuml = callPackage ../tools/misc/plantuml { }; pymysql = callPackage ../development/python-modules/pymysql { }; @@ -568,6 +570,8 @@ in { slackclient = callPackage ../development/python-modules/slackclient { }; + slicerator = callPackage ../development/python-modules/slicerator { }; + spglib = callPackage ../development/python-modules/spglib { }; statistics = callPackage ../development/python-modules/statistics { }; @@ -1986,6 +1990,16 @@ in { dask = callPackage ../development/python-modules/dask { }; + dask-glm = callPackage ../development/python-modules/dask-glm { }; + + dask-image = callPackage ../development/python-modules/dask-image { }; + + dask-jobqueue = callPackage ../development/python-modules/dask-jobqueue { }; + + dask-ml = callPackage ../development/python-modules/dask-ml { }; + + dask-xgboost = callPackage ../development/python-modules/dask-xgboost { }; + datrie = callPackage ../development/python-modules/datrie { }; heapdict = callPackage ../development/python-modules/heapdict { };