diff --git a/pkgs/development/python-modules/batchgenerators/default.nix b/pkgs/development/python-modules/batchgenerators/default.nix index 336c6b2e5134..a20d0c696cd6 100644 --- a/pkgs/development/python-modules/batchgenerators/default.nix +++ b/pkgs/development/python-modules/batchgenerators/default.nix @@ -1,12 +1,12 @@ { lib , buildPythonPackage -, isPy27 +, pythonOlder , fetchFromGitHub , pytestCheckHook -, unittest2 , future , numpy , pillow +, fetchpatch , scipy , scikit-learn , scikitimage @@ -16,27 +16,53 @@ buildPythonPackage rec { pname = "batchgenerators"; version = "0.21"; + format = "setuptools"; - disabled = isPy27; + disabled = pythonOlder "3.7"; src = fetchFromGitHub { owner = "MIC-DKFZ"; repo = pname; rev = "v${version}"; - sha256 = "16bk4r0q3m2c9fawpmj4l7kz0x3fyv1spb92grf44gmyricq3jdb"; - + hash = "sha256-q8mBWcy+PkJcfiKtq8P2bnTw56FE1suVS0zUgUEmc5k="; }; propagatedBuildInputs = [ - future numpy pillow scipy scikit-learn scikitimage threadpoolctl + future + numpy + pillow + scipy + scikit-learn + scikitimage + threadpoolctl ]; - checkInputs = [ pytestCheckHook unittest2 ]; + checkInputs = [ + pytestCheckHook + ]; - meta = { + patches = [ + # Remove deprecated unittest2, https://github.com/MIC-DKFZ/batchgenerators/pull/78 + (fetchpatch { + name = "remove-unittest2.patch"; + url = "https://github.com/MIC-DKFZ/batchgenerators/commit/87a9437057df8a7550aa3b3eaf840871cc0d5cef.patch"; + sha256 = "sha256-vozBK7g2dLxx9din/R2vU28Mm+LoGAO/BmQlt/ShmEo="; + }) + ]; + + postPatch = '' + substituteInPlace setup.py \ + --replace '"unittest2",' "" + ''; + + pythonImportsCheck = [ + "batchgenerators" + ]; + + meta = with lib; { description = "2D and 3D image data augmentation for deep learning"; homepage = "https://github.com/MIC-DKFZ/batchgenerators"; - license = lib.licenses.asl20; - maintainers = with lib.maintainers; [ bcdarwin ]; + license = licenses.asl20; + maintainers = with maintainers; [ bcdarwin ]; }; } diff --git a/pkgs/development/python-modules/bibtexparser/default.nix b/pkgs/development/python-modules/bibtexparser/default.nix index d69b2d6ce4ca..2c24578f4581 100644 --- a/pkgs/development/python-modules/bibtexparser/default.nix +++ b/pkgs/development/python-modules/bibtexparser/default.nix @@ -1,33 +1,49 @@ { lib -, buildPythonPackage, fetchFromGitHub -, future, pyparsing -, glibcLocales, nose, unittest2 +, buildPythonPackage +, fetchFromGitHub +, future +, pyparsing +, pytestCheckHook +, pythonOlder }: buildPythonPackage rec { pname = "bibtexparser"; - version = "1.1.0"; + version = "1.2.0"; + format = "setuptools"; + + disabled = pythonOlder "3.7"; - # PyPI tarball does not ship tests src = fetchFromGitHub { owner = "sciunto-org"; repo = "python-${pname}"; rev = "v${version}"; - sha256 = "1yj3hqnmkjh0sjjhmlm4097mmz98kna8rn0dd9g8zaw9g1a35h8c"; + hash = "sha256-M9fDI28Yq0uUHPx51wiuRPmRTLkjVqj7ixapbSftnJc="; }; - propagatedBuildInputs = [ future pyparsing ]; + propagatedBuildInputs = [ + future + pyparsing + ]; - checkInputs = [ nose unittest2 glibcLocales ]; + checkInputs = [ + pytestCheckHook + ]; - checkPhase = '' - LC_ALL="en_US.UTF-8" nosetests + postPatch = '' + # https://github.com/sciunto-org/python-bibtexparser/pull/259 + substituteInPlace bibtexparser/tests/test_crossref_resolving.py \ + --replace "import unittest2 as unittest" "import unittest" ''; - meta = { - description = "Bibtex parser for python 2.7 and 3.3 and newer"; + pythonImportsCheck = [ + "bibtexparser" + ]; + + meta = with lib; { + description = "Bibtex parser for Python"; homepage = "https://github.com/sciunto-org/python-bibtexparser"; - license = with lib.licenses; [ gpl3 bsd3 ]; - maintainers = with lib.maintainers; [ fridh ]; + license = with licenses; [ lgpl3Only /* or */ bsd3 ]; + maintainers = with maintainers; [ fridh ]; }; } diff --git a/pkgs/development/python-modules/tifffile/default.nix b/pkgs/development/python-modules/tifffile/default.nix index 2e4676267215..fdd4c2bf0b2f 100644 --- a/pkgs/development/python-modules/tifffile/default.nix +++ b/pkgs/development/python-modules/tifffile/default.nix @@ -1,53 +1,55 @@ { lib -, fetchPypi , buildPythonPackage -, isPy27 -, isPy3k +, dask +, fetchPypi +, fsspec +, lxml , numpy -, imagecodecs-lite -, enum34 ? null -, futures ? null -, pathlib ? null -, pytest +, pytestCheckHook +, pythonOlder +, zarr }: buildPythonPackage rec { pname = "tifffile"; version = "2021.11.2"; + format = "setuptools"; + + disabled = pythonOlder "3.7"; src = fetchPypi { inherit pname version; - sha256 = "153e31fa1d892f482fabb2ae9f2561fa429ee42d01a6f67e58cee13637d9285b"; + hash = "sha256-FT4x+h2JL0gvq7KunyVh+kKe5C0BpvZ+WM7hNjfZKFs="; }; - patches = lib.optional isPy27 ./python2-regex-compat.patch; - - # Missing dependencies: imagecodecs, czifile, cmapfile, oiffile, lfdfiles - # and test data missing from PyPI tarball - doCheck = false; - - checkInputs = [ - pytest - ]; - - checkPhase = '' - pytest - ''; - propagatedBuildInputs = [ numpy - ] ++ lib.optionals isPy3k [ - imagecodecs-lite - ] ++ lib.optionals isPy27 [ - futures - enum34 - pathlib + ]; + + checkInputs = [ + dask + fsspec + lxml + pytestCheckHook + zarr + ]; + + disabledTests = [ + # Test require network access + "test_class_omexml" + "test_write_ome" + # Test file is missing + "test_write_predictor" + ]; + + pythonImportsCheck = [ + "tifffile" ]; meta = with lib; { - description = "Read and write image data from and to TIFF files."; - homepage = "https://www.lfd.uci.edu/~gohlke/"; - maintainers = [ maintainers.lebastr ]; + description = "Read and write image data from and to TIFF files"; + homepage = "https://github.com/cgohlke/tifffile/"; license = licenses.bsd3; + maintainers = with maintainers; [ lebastr ]; }; }