Merge pull request #113265 from SuperSandro2000/fix-collection13

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Sandro 2021-02-17 03:14:49 +01:00 committed by GitHub
commit 0d44c7989c
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62 changed files with 119 additions and 193 deletions

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@ -1,5 +1,4 @@
{ lib, fetchgit, buildPythonPackage { lib, fetchgit, buildPythonPackage
, python
, buildGoModule , buildGoModule
, srht, redis, celery, pyyaml, markdown }: , srht, redis, celery, pyyaml, markdown }:

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@ -1,5 +1,4 @@
{ lib, fetchgit, buildPythonPackage { lib, fetchgit, buildPythonPackage
, python
, srht, pyyaml, PyGithub }: , srht, pyyaml, PyGithub }:
buildPythonPackage rec { buildPythonPackage rec {

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@ -1,5 +1,4 @@
{ lib, fetchgit, buildPythonPackage { lib, fetchgit, buildPythonPackage
, python
, buildGoModule , buildGoModule
, srht, minio, pygit2, scmsrht }: , srht, minio, pygit2, scmsrht }:

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@ -1,5 +1,4 @@
{ lib, fetchhg, buildPythonPackage { lib, fetchhg, buildPythonPackage
, python
, srht, hglib, scmsrht, unidiff }: , srht, hglib, scmsrht, unidiff }:
buildPythonPackage rec { buildPythonPackage rec {

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@ -1,5 +1,4 @@
{ lib, fetchgit, buildPythonPackage { lib, fetchgit, buildPythonPackage
, python
, srht }: , srht }:
buildPythonPackage rec { buildPythonPackage rec {

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@ -1,5 +1,4 @@
{ lib, fetchgit, buildPythonPackage { lib, fetchgit, buildPythonPackage
, python
, srht, asyncpg, aiosmtpd, pygit2, emailthreads }: , srht, asyncpg, aiosmtpd, pygit2, emailthreads }:
buildPythonPackage rec { buildPythonPackage rec {

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@ -1,5 +1,4 @@
{ lib, fetchgit, buildPythonPackage { lib, fetchgit, buildPythonPackage
, python
, srht, pygit2 }: , srht, pygit2 }:
buildPythonPackage rec { buildPythonPackage rec {

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@ -1,5 +1,4 @@
{ lib, fetchgit, buildPythonPackage { lib, fetchgit, buildPythonPackage
, python
, buildGoModule , buildGoModule
, pgpy, srht, redis, bcrypt, qrcode, stripe, zxcvbn, alembic, pystache , pgpy, srht, redis, bcrypt, qrcode, stripe, zxcvbn, alembic, pystache
, sshpubkeys, weasyprint }: , sshpubkeys, weasyprint }:

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@ -1,5 +1,4 @@
{ lib, fetchgit, buildPythonPackage { lib, fetchgit, buildPythonPackage
, python
, srht, pyyaml }: , srht, pyyaml }:
buildPythonPackage rec { buildPythonPackage rec {

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@ -1,7 +1,6 @@
{ lib, fetchgit, buildPythonPackage { lib, fetchgit, buildPythonPackage
, python
, srht, redis, alembic, pystache , srht, redis, alembic, pystache
, pytest, factory_boy, writeText }: , pytest, factory_boy }:
buildPythonPackage rec { buildPythonPackage rec {
pname = "todosrht"; pname = "todosrht";

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@ -1,6 +1,5 @@
{ lib, stdenv, fetchurl, graalvm11-ce, glibcLocales }: { lib, stdenv, fetchurl, graalvm11-ce, glibcLocales }:
with lib;
stdenv.mkDerivation rec { stdenv.mkDerivation rec {
pname = "babashka"; pname = "babashka";
version = "0.2.10"; version = "0.2.10";
@ -25,7 +24,7 @@ stdenv.mkDerivation rec {
native-image \ native-image \
-jar ${src} \ -jar ${src} \
-H:Name=bb \ -H:Name=bb \
${optionalString stdenv.isDarwin ''-H:-CheckToolchain''} \ ${lib.optionalString stdenv.isDarwin ''-H:-CheckToolchain''} \
-H:+ReportExceptionStackTraces \ -H:+ReportExceptionStackTraces \
-J-Dclojure.spec.skip-macros=true \ -J-Dclojure.spec.skip-macros=true \
-J-Dclojure.compiler.direct-linking=true \ -J-Dclojure.compiler.direct-linking=true \

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@ -38,5 +38,7 @@ stdenv.mkDerivation rec {
homepage = "https://beltoforion.de/en/muparserx/"; homepage = "https://beltoforion.de/en/muparserx/";
license = licenses.bsd2; license = licenses.bsd2;
maintainers = with maintainers; [ drewrisinger ]; maintainers = with maintainers; [ drewrisinger ];
# selftest fails
broken = stdenv.isDarwin;
}; };
} }

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@ -3,7 +3,6 @@
, buildPythonPackage , buildPythonPackage
, pythonOlder , pythonOlder
, fetchFromGitHub , fetchFromGitHub
, fetchpatch
, freezegun , freezegun
, google-api-core , google-api-core
, matplotlib , matplotlib

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@ -46,11 +46,6 @@ buildPythonPackage rec {
ipython ipython
]; ];
postPatch = ''
substituteInPlace setup.py \
--replace "'numba==0.43'" "'numba'"
'';
# avoid collecting local files # avoid collecting local files
preCheck = '' preCheck = ''
cd clifford/test cd clifford/test

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@ -2,7 +2,6 @@
, fetchFromGitHub , fetchFromGitHub
, fetchpatch , fetchpatch
, rPackages , rPackages
, rWrapper
, buildPythonPackage , buildPythonPackage
, biopython , biopython
, numpy , numpy
@ -55,11 +54,6 @@ buildPythonPackage rec {
rPackages.DNAcopy rPackages.DNAcopy
]; ];
postPatch = ''
substituteInPlace setup.py \
--replace "pandas >= 0.20.1, < 0.25.0" "pandas"
'';
checkInputs = [ R ]; checkInputs = [ R ];
checkPhase = '' checkPhase = ''

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@ -2,13 +2,12 @@
, buildPythonPackage , buildPythonPackage
, fetchFromGitHub , fetchFromGitHub
, isPy3k , isPy3k
, pytestrunner
, click , click
, dateparser , dateparser
, pandas , pandas
, py-lru-cache , py-lru-cache
, six , six
, pytest , pytestCheckHook
}: }:
buildPythonPackage rec { buildPythonPackage rec {
@ -23,11 +22,6 @@ buildPythonPackage rec {
sha256 = "0p99cg76d3s7jxvigh5ad04dzhmr6g62qzzh4i6h7x9aiyvdhvk4"; sha256 = "0p99cg76d3s7jxvigh5ad04dzhmr6g62qzzh4i6h7x9aiyvdhvk4";
}; };
postPatch = ''
substituteInPlace setup.py \
--replace pandas~=0.25.0 pandas
'';
propagatedBuildInputs = [ propagatedBuildInputs = [
click click
dateparser dateparser
@ -37,13 +31,9 @@ buildPythonPackage rec {
]; ];
checkInputs = [ checkInputs = [
pytest pytestCheckHook
]; ];
checkPhase = ''
pytest
'';
meta = with lib; { meta = with lib; {
description = "Convert CSV files into a SQLite database"; description = "Convert CSV files into a SQLite database";
homepage = "https://github.com/simonw/csvs-to-sqlite"; homepage = "https://github.com/simonw/csvs-to-sqlite";

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@ -1,4 +1,4 @@
{ lib, buildPythonPackage, fetchPypi, fetchpatch { lib, buildPythonPackage, fetchPypi
, chart-studio , chart-studio
, colorlover , colorlover
, ipython , ipython

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@ -1,7 +1,6 @@
{ lib { lib
, buildPythonPackage , buildPythonPackage
, fetchPypi , fetchPypi
, fetchpatch
, dask , dask
, numpy, toolz # dask[array] , numpy, toolz # dask[array]
, scipy , scipy
@ -38,6 +37,7 @@ buildPythonPackage rec {
checkPhase = '' checkPhase = ''
pytest --ignore=tests/test_dask_image/ pytest --ignore=tests/test_dask_image/
''; '';
pythonImportsCheck = [ "dask_image" ];
meta = with lib; { meta = with lib; {
homepage = "https://github.com/dask/dask-image"; homepage = "https://github.com/dask/dask-image";

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@ -12,10 +12,6 @@
, six , six
, multipledispatch , multipledispatch
, packaging , packaging
, pytest
, xgboost
, tensorflow
, joblib
, distributed , distributed
}: }:

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@ -4,8 +4,6 @@
, dask , dask
, distributed , distributed
, mpi4py , mpi4py
, pytest
, requests
}: }:
buildPythonPackage rec { buildPythonPackage rec {
@ -17,15 +15,11 @@ buildPythonPackage rec {
sha256 = "76e153fc8c58047d898970b33ede0ab1990bd4e69cc130c6627a96f11b12a1a7"; sha256 = "76e153fc8c58047d898970b33ede0ab1990bd4e69cc130c6627a96f11b12a1a7";
}; };
checkInputs = [ pytest requests ];
propagatedBuildInputs = [ dask distributed mpi4py ]; propagatedBuildInputs = [ dask distributed mpi4py ];
checkPhase = ''
py.test dask_mpi
'';
# hardcoded mpirun path in tests # hardcoded mpirun path in tests
doCheck = false; doCheck = false;
pythonImportsCheck = [ "dask_mpi" ];
meta = with lib; { meta = with lib; {
homepage = "https://github.com/dask/dask-mpi"; homepage = "https://github.com/dask/dask-mpi";

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@ -4,8 +4,6 @@
, xgboost , xgboost
, dask , dask
, distributed , distributed
, pytest
, scikitlearn
}: }:
buildPythonPackage rec { buildPythonPackage rec {
@ -17,19 +15,17 @@ buildPythonPackage rec {
sha256 = "3fbe1bf4344dc74edfbe9f928c7e3e6acc26dc57cefd8da8ae56a15469c6941c"; sha256 = "3fbe1bf4344dc74edfbe9f928c7e3e6acc26dc57cefd8da8ae56a15469c6941c";
}; };
checkInputs = [ pytest scikitlearn ];
propagatedBuildInputs = [ xgboost dask distributed ]; propagatedBuildInputs = [ xgboost dask distributed ];
checkPhase = ''
py.test dask_xgboost/tests/test_core.py
'';
doCheck = false; doCheck = false;
pythonImportsCheck = [ "dask_xdgboost" ];
meta = with lib; { meta = with lib; {
homepage = "https://github.com/dask/dask-xgboost"; homepage = "https://github.com/dask/dask-xgboost";
description = "Interactions between Dask and XGBoost"; description = "Interactions between Dask and XGBoost";
license = licenses.bsd3; license = licenses.bsd3;
maintainers = [ maintainers.costrouc ]; maintainers = [ maintainers.costrouc ];
# TypeError: __init__() got an unexpected keyword argument 'iid'
broken = true;
}; };
} }

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@ -78,7 +78,7 @@ buildPythonPackage rec {
# dask doesn't do well with large core counts # dask doesn't do well with large core counts
checkPhase = '' checkPhase = ''
pytest -n $NIX_BUILD_CORES datashader -k 'not dask.array' pytest -n $NIX_BUILD_CORES datashader -k 'not dask.array and not test_simple_nested'
''; '';
meta = with lib; { meta = with lib; {

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@ -12,11 +12,7 @@
, lammps-cython , lammps-cython
, pymatgen-lammps , pymatgen-lammps
, pytestrunner , pytestrunner
, pytest
, pytestcov
, pytest-benchmark
, isPy3k , isPy3k
, openssh
}: }:
buildPythonPackage rec { buildPythonPackage rec {
@ -25,18 +21,27 @@ buildPythonPackage rec {
disabled = (!isPy3k); disabled = (!isPy3k);
src = fetchPypi { src = fetchPypi {
inherit pname version; inherit pname version;
sha256 = "4dcbde48948835dcf2d49d6628c9df5747a8ec505d517e374b8d6c7fe95892df"; sha256 = "4dcbde48948835dcf2d49d6628c9df5747a8ec505d517e374b8d6c7fe95892df";
}; };
buildInputs = [ pytestrunner ]; buildInputs = [ pytestrunner ];
checkInputs = [ pytest pytestcov pytest-benchmark openssh ]; propagatedBuildInputs = [
propagatedBuildInputs = [ pymatgen marshmallow pyyaml pygmo pymatgen
pandas scipy numpy scikitlearn marshmallow
lammps-cython pymatgen-lammps ]; pyyaml
pygmo
pandas
scipy
numpy
scikitlearn
lammps-cython
pymatgen-lammps
];
# tests require git lfs download. and is quite large so skip tests # tests require git lfs download. and is quite large so skip tests
doCheck = false; doCheck = false;
pythonImportsCheck = [ "dftfit" ];
meta = { meta = {
description = "Ab-Initio Molecular Dynamics Potential Development"; description = "Ab-Initio Molecular Dynamics Potential Development";

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@ -1,11 +1,6 @@
{ lib { lib
, buildPythonPackage , buildPythonPackage
, fetchPypi , fetchPypi
, pytest
, pytest-repeat
, pytest-timeout
, mock
, joblib
, click , click
, cloudpickle , cloudpickle
, dask , dask
@ -18,9 +13,6 @@
, tornado , tornado
, zict , zict
, pyyaml , pyyaml
, isPy3k
, futures
, singledispatch
, mpi4py , mpi4py
, bokeh , bokeh
, pythonOlder , pythonOlder
@ -29,6 +21,7 @@
buildPythonPackage rec { buildPythonPackage rec {
pname = "distributed"; pname = "distributed";
version = "2.30.1"; version = "2.30.1";
disabled = pythonOlder "3.6";
# get full repository need conftest.py to run tests # get full repository need conftest.py to run tests
src = fetchPypi { src = fetchPypi {
@ -36,23 +29,14 @@ buildPythonPackage rec {
sha256 = "1421d3b84a0885aeb2c4bdc9e8896729c0f053a9375596c9de8864e055e2ac8e"; sha256 = "1421d3b84a0885aeb2c4bdc9e8896729c0f053a9375596c9de8864e055e2ac8e";
}; };
disabled = pythonOlder "3.6";
checkInputs = [ pytest pytest-repeat pytest-timeout mock joblib ];
propagatedBuildInputs = [ propagatedBuildInputs = [
click cloudpickle dask msgpack psutil six click cloudpickle dask msgpack psutil six
sortedcontainers tblib toolz tornado zict pyyaml mpi4py bokeh sortedcontainers tblib toolz tornado zict pyyaml mpi4py bokeh
]; ];
# tests take about 10-15 minutes
# ignore 5 cli tests out of 1000 total tests that fail due to subprocesses
# these tests are not critical to the library (only the cli)
checkPhase = ''
py.test distributed -m "not avoid-travis" -r s --timeout-method=thread --timeout=0 --durations=20 --ignore="distributed/cli/tests"
'';
# when tested random tests would fail and not repeatably # when tested random tests would fail and not repeatably
doCheck = false; doCheck = false;
pythonImportsCheck = [ "distributed" ];
meta = { meta = {
description = "Distributed computation in Python."; description = "Distributed computation in Python.";

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@ -6,7 +6,7 @@
, pybind11 , pybind11
, setuptools_scm , setuptools_scm
, pytestrunner , pytestrunner
, pytest , pytestCheckHook
}: }:
buildPythonPackage rec { buildPythonPackage rec {
@ -31,18 +31,10 @@ buildPythonPackage rec {
pytestrunner pytestrunner
]; ];
checkInputs = [ propagatedBuildInputs = [ numpy pandas ];
pytest
];
propagatedBuildInputs = [ checkInputs = [ pytestCheckHook ];
numpy pythonImportsCheck = [ "duckdb" ];
pandas
];
checkPhase = ''
pytest
'';
meta = with lib; { meta = with lib; {
description = "DuckDB is an embeddable SQL OLAP Database Management System"; description = "DuckDB is an embeddable SQL OLAP Database Management System";

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@ -1,5 +1,5 @@
{ lib, buildPythonPackage, fetchFromGitHub, numba, numpy, pandas, pytestrunner, { lib, buildPythonPackage, fetchFromGitHub, numba, numpy, pandas, pytestrunner
thrift, pytest, python-snappy, lz4, zstd }: , thrift, pytestCheckHook, python-snappy, lz4, zstandard, zstd }:
buildPythonPackage rec { buildPythonPackage rec {
pname = "fastparquet"; pname = "fastparquet";
@ -12,15 +12,13 @@ buildPythonPackage rec {
sha256 = "17i091kky34m2xivk29fqsyxxxa7v4352n79w01n7ni93za6wana"; sha256 = "17i091kky34m2xivk29fqsyxxxa7v4352n79w01n7ni93za6wana";
}; };
postPatch = ''
# FIXME: package zstandard
# removing the test dependency for now
substituteInPlace setup.py --replace "'zstandard'," ""
'';
nativeBuildInputs = [ pytestrunner ]; nativeBuildInputs = [ pytestrunner ];
propagatedBuildInputs = [ numba numpy pandas thrift ]; propagatedBuildInputs = [ numba numpy pandas thrift ];
checkInputs = [ pytest python-snappy lz4 zstd ]; checkInputs = [ pytestCheckHook python-snappy lz4 zstandard zstd ];
# E ModuleNotFoundError: No module named 'fastparquet.speedups'
doCheck = false;
pythonImportsCheck = [ "fastparquet" ];
meta = with lib; { meta = with lib; {
description = "A python implementation of the parquet format"; description = "A python implementation of the parquet format";

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@ -1,4 +1,4 @@
{ lib, pkgs, buildPythonPackage, fetchPypi, isPy27 { lib, buildPythonPackage, fetchPypi, isPy27
, numpy , numpy
, scipy , scipy
, tables , tables

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@ -2,7 +2,6 @@
, buildPythonPackage , buildPythonPackage
, fetchFromGitHub , fetchFromGitHub
, numpy , numpy
, setuptools
, python , python
, scikitimage , scikitimage
, openjpeg , openjpeg

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@ -37,7 +37,7 @@ buildPythonPackage rec {
]; ];
checkInputs = [ pytestCheckHook pytestcov ]; checkInputs = [ pytestCheckHook pytestcov ];
pytestFlagsArray = [ "tests" "--ignore=docs" ]; pytestFlagsArray = [ "tests" "--ignore=docs" "--ignore=tests/test_sklearn.py" ];
disabledTests = [ "gridplot_outputs" ]; disabledTests = [ "gridplot_outputs" ];
meta = with lib; { meta = with lib; {

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@ -24,6 +24,7 @@ buildPythonPackage {
# tests cannot work without elasticsearch # tests cannot work without elasticsearch
doCheck = false; doCheck = false;
pythonImportsCheck = [ "image_match" ];
meta = with lib; { meta = with lib; {
homepage = "https://github.com/ascribe/image-match"; homepage = "https://github.com/ascribe/image-match";

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@ -26,6 +26,9 @@ buildPythonPackage rec {
opencv3 opencv3
]; ];
doCheck = false;
pythonImportsCheck = [ "imagecorruptions" ];
meta = with lib; { meta = with lib; {
homepage = "https://github.com/bethgelab/imagecorruptions"; homepage = "https://github.com/bethgelab/imagecorruptions";
description = "This package provides a set of image corruptions"; description = "This package provides a set of image corruptions";

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@ -3,7 +3,6 @@
, pandas , pandas
, pytestCheckHook , pytestCheckHook
, scikitlearn , scikitlearn
, tensorflow
}: }:
buildPythonPackage rec { buildPythonPackage rec {

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@ -9,10 +9,7 @@
, pymatgen , pymatgen
, ase , ase
, pytestrunner , pytestrunner
, pytest_4
, pytestcov
, isPy3k , isPy3k
, openssh
}: }:
buildPythonPackage rec { buildPythonPackage rec {
@ -26,7 +23,6 @@ buildPythonPackage rec {
}; };
buildInputs = [ cython pytestrunner ]; buildInputs = [ cython pytestrunner ];
checkInputs = [ pytest_4 pytestcov openssh ];
propagatedBuildInputs = [ mpi4py pymatgen ase numpy ]; propagatedBuildInputs = [ mpi4py pymatgen ase numpy ];
preBuild = '' preBuild = ''
@ -44,6 +40,8 @@ buildPythonPackage rec {
EOF EOF
''; '';
pythonImportsCheck = [ "lammps" ];
meta = { meta = {
description = "Pythonic Wrapper to LAMMPS using cython"; description = "Pythonic Wrapper to LAMMPS using cython";
homepage = "https://gitlab.com/costrouc/lammps-cython"; homepage = "https://gitlab.com/costrouc/lammps-cython";

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@ -35,6 +35,7 @@ buildPythonPackage rec {
# tests not included with pypi release # tests not included with pypi release
doCheck = false; doCheck = false;
pythonImportsCheck = [ "nbsmoke" ];
meta = with lib; { meta = with lib; {
description = "Basic notebook checks and linting"; description = "Basic notebook checks and linting";

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@ -1,5 +1,5 @@
{ lib, buildPythonPackage, fetchFromGitHub, geopandas, descartes, matplotlib, networkx, numpy { lib, buildPythonPackage, fetchFromGitHub, geopandas, descartes, matplotlib, networkx, numpy
, pandas, requests, Rtree, shapely, pytest, coverage, coveralls, folium, scikitlearn, scipy}: , pandas, requests, Rtree, shapely, folium, scikitlearn, scipy}:
buildPythonPackage rec { buildPythonPackage rec {
pname = "osmnx"; pname = "osmnx";
@ -14,14 +14,9 @@ buildPythonPackage rec {
propagatedBuildInputs = [ geopandas descartes matplotlib networkx numpy pandas requests Rtree shapely folium scikitlearn scipy ]; propagatedBuildInputs = [ geopandas descartes matplotlib networkx numpy pandas requests Rtree shapely folium scikitlearn scipy ];
checkInputs = [ coverage pytest coveralls ]; # requires network
#Fails when using sandboxing as it requires internet connection, works fine without it
doCheck = false; doCheck = false;
pythonImportsCheck = [ "osmnx" ];
#Check phase for the record
#checkPhase = ''
# coverage run --source osmnx -m pytest --verbose
#'';
meta = with lib; { meta = with lib; {
description = "A package to easily download, construct, project, visualize, and analyze complex street networks from OpenStreetMap with NetworkX."; description = "A package to easily download, construct, project, visualize, and analyze complex street networks from OpenStreetMap with NetworkX.";

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@ -1,7 +1,6 @@
{ lib { lib
, buildPythonPackage , buildPythonPackage
, fetchPypi , fetchPypi
, pytestCheckHook
, isPy27 , isPy27
, pandas , pandas
, lxml , lxml

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@ -23,6 +23,7 @@ buildPythonPackage rec {
# not everything packaged with pypi release # not everything packaged with pypi release
doCheck = false; doCheck = false;
pythonImportsCheck = [ "pims" ];
meta = with lib; { meta = with lib; {
homepage = "https://github.com/soft-matter/pims"; homepage = "https://github.com/soft-matter/pims";

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@ -1,4 +1,4 @@
{ lib, buildPythonPackage, python, isPy3k, arrow-cpp, cmake, cython, futures, hypothesis, numpy, pandas, pytestCheckHook, pytest-lazy-fixture, pkg-config, setuptools_scm, six }: { lib, buildPythonPackage, python, isPy3k, arrow-cpp, cmake, cython, hypothesis, numpy, pandas, pytestCheckHook, pytest-lazy-fixture, pkg-config, setuptools_scm, six }:
let let
_arrow-cpp = arrow-cpp.override { python3 = python; }; _arrow-cpp = arrow-cpp.override { python3 = python; };

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@ -1,7 +1,6 @@
{ buildPythonPackage { buildPythonPackage
, lib , lib
, fetchPypi , fetchPypi
, isPy27
, click , click
, num2words , num2words
, numpy , numpy
@ -11,8 +10,7 @@
, patsy , patsy
, bids-validator , bids-validator
, sqlalchemy , sqlalchemy
, pytest , pytestCheckHook
, pathlib
}: }:
buildPythonPackage rec { buildPythonPackage rec {
@ -36,11 +34,8 @@ buildPythonPackage rec {
sqlalchemy sqlalchemy
]; ];
checkInputs = [ pytest ] ++ lib.optionals isPy27 [ pathlib ]; checkInputs = [ pytestCheckHook ];
pythonImportsCheck = [ "bids" ];
checkPhase = ''
pytest
'';
meta = with lib; { meta = with lib; {
description = "Python tools for querying and manipulating BIDS datasets"; description = "Python tools for querying and manipulating BIDS datasets";

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@ -10,20 +10,18 @@ buildPythonPackage rec {
sha256 = "60988e823ca75808a26fd79d88dbae1de3699e72a293f812aa4534f8a0a58cb0"; sha256 = "60988e823ca75808a26fd79d88dbae1de3699e72a293f812aa4534f8a0a58cb0";
}; };
preConfigure = ''
export LDFLAGS="-L${fftw.out}/lib -L${fftwFloat.out}/lib -L${fftwLongDouble.out}/lib"
export CFLAGS="-I${fftw.dev}/include -I${fftwFloat.dev}/include -I${fftwLongDouble.dev}/include"
'';
buildInputs = [ fftw fftwFloat fftwLongDouble]; buildInputs = [ fftw fftwFloat fftwLongDouble];
propagatedBuildInputs = [ numpy scipy cython dask ]; propagatedBuildInputs = [ numpy scipy cython dask ];
# Tests cannot import pyfftw. pyfftw works fine though. # Tests cannot import pyfftw. pyfftw works fine though.
doCheck = false; doCheck = false;
pythonImportsCheck = [ "pyfftw" ];
preConfigure = ''
export LDFLAGS="-L${fftw.out}/lib -L${fftwFloat.out}/lib -L${fftwLongDouble.out}/lib"
export CFLAGS="-I${fftw.dev}/include -I${fftwFloat.dev}/include -I${fftwLongDouble.dev}/include"
'';
#+ optionalString isDarwin ''
# export DYLD_LIBRARY_PATH="${pkgs.fftw.out}/lib"
#'';
meta = with lib; { meta = with lib; {
description = "A pythonic wrapper around FFTW, the FFT library, presenting a unified interface for all the supported transforms"; description = "A pythonic wrapper around FFTW, the FFT library, presenting a unified interface for all the supported transforms";

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@ -3,14 +3,14 @@
, buildPythonPackage , buildPythonPackage
, pymatgen , pymatgen
, pytestrunner , pytestrunner
, pytest , pytestCheckHook
, isPy3k , isPy3k
}: }:
buildPythonPackage rec { buildPythonPackage rec {
pname = "pymatgen-lammps"; pname = "pymatgen-lammps";
version = "0.4.5"; version = "0.4.5";
disabled = (!isPy3k); disabled = !isPy3k;
src = fetchurl { src = fetchurl {
url = "https://gitlab.com/costrouc/${pname}/-/archive/v${version}/${pname}-v${version}.tar.gz"; url = "https://gitlab.com/costrouc/${pname}/-/archive/v${version}/${pname}-v${version}.tar.gz";
@ -18,13 +18,17 @@ buildPythonPackage rec {
}; };
buildInputs = [ pytestrunner ]; buildInputs = [ pytestrunner ];
checkInputs = [ pytest ]; checkInputs = [ pytestCheckHook ];
propagatedBuildInputs = [ pymatgen ]; propagatedBuildInputs = [ pymatgen ];
pythonImportsCheck = [ "pmg_lammps" ];
meta = { meta = {
description = "A LAMMPS wrapper using pymatgen"; description = "A LAMMPS wrapper using pymatgen";
homepage = "https://gitlab.com/costrouc/pymatgen-lammps"; homepage = "https://gitlab.com/costrouc/pymatgen-lammps";
license = lib.licenses.mit; license = lib.licenses.mit;
maintainers = with lib.maintainers; [ costrouc ]; maintainers = with lib.maintainers; [ costrouc ];
# not compatible with recent versions of pymatgen
broken = true;
}; };
} }

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@ -52,6 +52,7 @@ buildPythonPackage rec {
# No tests in pypi tarball. # No tests in pypi tarball.
doCheck = false; doCheck = false;
pythonImportsCheck = [ "pymatgen" ];
meta = with lib; { meta = with lib; {
description = "A robust materials analysis code that defines core object representations for structures and molecules"; description = "A robust materials analysis code that defines core object representations for structures and molecules";

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@ -17,10 +17,11 @@ buildPythonPackage rec {
sha256 = "8ccb06c57c31fa157b978a0d810de7718ee46583d28cf818250d45f36abd2faa"; sha256 = "8ccb06c57c31fa157b978a0d810de7718ee46583d28cf818250d45f36abd2faa";
}; };
doCheck = false;
propagatedBuildInputs = [ requests lxml pandas ]; propagatedBuildInputs = [ requests lxml pandas ];
doCheck = false;
pythonImportsCheck = [ "pytrends" ];
meta = with lib; { meta = with lib; {
description = "Pseudo API for Google Trends"; description = "Pseudo API for Google Trends";
homepage = "https://github.com/GeneralMills/pytrends"; homepage = "https://github.com/GeneralMills/pytrends";

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@ -2,7 +2,6 @@
, pythonOlder , pythonOlder
, buildPythonPackage , buildPythonPackage
, fetchFromGitHub , fetchFromGitHub
, fetchpatch
# C Inputs # C Inputs
, blas , blas
, catch2 , catch2

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@ -2,7 +2,6 @@
, pythonOlder , pythonOlder
, buildPythonPackage , buildPythonPackage
, fetchFromGitHub , fetchFromGitHub
, fetchpatch
, python , python
, numpy , numpy
, qiskit-terra , qiskit-terra

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@ -46,6 +46,8 @@ buildPythonPackage rec {
importlib-metadata importlib-metadata
]; ];
pythonImportsCheck = [ "quandl" ];
meta = with lib; { meta = with lib; {
description = "Quandl Python client library"; description = "Quandl Python client library";
homepage = "https://github.com/quandl/quandl-python"; homepage = "https://github.com/quandl/quandl-python";

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@ -1,8 +1,6 @@
{ stdenv { stdenv
, lib , lib
, python
, buildPythonPackage , buildPythonPackage
, fetchpatch
, fetchPypi , fetchPypi
, isPyPy , isPyPy
, R , R

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@ -32,12 +32,6 @@ buildPythonPackage rec {
checkInputs = [ coverage ]; checkInputs = [ coverage ];
propagatedBuildInputs = [ lockfile cachecontrol decorator ipython matplotlib natsort numpy pandas scipy hdmedians scikitlearn ]; propagatedBuildInputs = [ lockfile cachecontrol decorator ipython matplotlib natsort numpy pandas scipy hdmedians scikitlearn ];
# remove on when version > 0.5.4
postPatch = ''
sed -i "s/numpy >= 1.9.2, < 1.14.0/numpy/" setup.py
sed -i "s/pandas >= 0.19.2, < 0.23.0/pandas/" setup.py
'';
# cython package not included for tests # cython package not included for tests
doCheck = false; doCheck = false;
@ -45,6 +39,8 @@ buildPythonPackage rec {
${python.interpreter} -m skbio.test ${python.interpreter} -m skbio.test
''; '';
pythonImportsCheck = [ "skbio" ];
meta = with lib; { meta = with lib; {
homepage = "http://scikit-bio.org/"; homepage = "http://scikit-bio.org/";
description = "Data structures, algorithms and educational resources for bioinformatics"; description = "Data structures, algorithms and educational resources for bioinformatics";

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@ -26,6 +26,7 @@ buildPythonPackage rec {
# Computationally very demanding tests # Computationally very demanding tests
doCheck = false; doCheck = false;
pythonImportsCheck= [ "seaborn" ];
meta = { meta = {
description = "Statisitical data visualization"; description = "Statisitical data visualization";

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@ -26,10 +26,13 @@ buildPythonPackage rec {
propagatedBuildInputs = [ numpy pytorch scikitlearn scipy tabulate tqdm ]; propagatedBuildInputs = [ numpy pytorch scikitlearn scipy tabulate tqdm ];
checkInputs = [ pytest pytestcov flaky pandas pytestCheckHook ]; checkInputs = [ pytest pytestcov flaky pandas pytestCheckHook ];
# on CPU, these expect artifacts from previous GPU run
disabledTests = [ disabledTests = [
# on CPU, these expect artifacts from previous GPU run
"test_load_cuda_params_to_cpu" "test_load_cuda_params_to_cpu"
# failing tests
"test_pickle_load" "test_pickle_load"
"test_grid_search_with_slds_"
"test_grid_search_with_dict_works"
]; ];
meta = with lib; { meta = with lib; {

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@ -1,4 +1,4 @@
{ lib, buildPythonPackage, fetchPypi, fetchpatch { lib, buildPythonPackage, fetchPypi
, confluent-kafka , confluent-kafka
, distributed , distributed
, flaky , flaky

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@ -1,4 +1,4 @@
{ lib, pkgs, buildPythonPackage, fetchPypi, isPy3k, callPackage { lib, buildPythonPackage, fetchPypi, isPy3k
, opencv3 , opencv3
, pyqt5 , pyqt5
, pyqtgraph , pyqtgraph
@ -19,7 +19,7 @@
, imageio-ffmpeg , imageio-ffmpeg
, av , av
, nose , nose
, pytest , pytestCheckHook
, pyserial , pyserial
, arrayqueues , arrayqueues
, colorspacious , colorspacious
@ -37,14 +37,18 @@ buildPythonPackage rec {
inherit pname version; inherit pname version;
sha256 = "aab9d07575ef599a9c0ae505656e3c03ec753462df3c15742f1f768f2b578f0a"; sha256 = "aab9d07575ef599a9c0ae505656e3c03ec753462df3c15742f1f768f2b578f0a";
}; };
doCheck = false;
# crashes python
preCheck = ''
rm stytra/tests/test_z_experiments.py
'';
checkInputs = [ checkInputs = [
nose nose
pytest pytestCheckHook
pyserial pyserial
]; ];
propagatedBuildInputs = [ propagatedBuildInputs = [
opencv3 opencv3
pyqt5 pyqt5

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@ -2,7 +2,6 @@
, buildPythonPackage , buildPythonPackage
, fetchFromGitHub , fetchFromGitHub
, isPy27 , isPy27
, pytest
, pytestrunner , pytestrunner
, pytestCheckHook , pytestCheckHook
, pytorch , pytorch
@ -23,12 +22,11 @@ buildPythonPackage rec {
propagatedBuildInputs = [ pytorch ]; propagatedBuildInputs = [ pytorch ];
checkInputs = [ pytest pytestrunner pytestCheckHook ]; checkInputs = [ pytestrunner pytestCheckHook ];
disabledTests = [ "test_inplace_on_requires_grad" ]; disabledTests = [
# seems like a harmless failure: "test_inplace_on_requires_grad"
## AssertionError: "test_input_requiring_grad"
## Pattern 'a leaf Variable that requires grad has been used in an in-place operation.' ];
## does not match 'a leaf Variable that requires grad is being used in an in-place operation.'
meta = with lib; { meta = with lib; {
description = "GPipe implemented in Pytorch and optimized for CUDA rather than TPU"; description = "GPipe implemented in Pytorch and optimized for CUDA rather than TPU";

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@ -3,10 +3,9 @@
, fetchFromGitHub , fetchFromGitHub
, fetchpatch , fetchpatch
, isPy27 , isPy27
, pytest , pytestCheckHook
, nose , nose
, numpy , numpy
, scipy
, pandas , pandas
, xarray , xarray
, traitlets , traitlets
@ -35,7 +34,8 @@ buildPythonPackage rec {
propagatedBuildInputs = [ traitlets ]; propagatedBuildInputs = [ traitlets ];
checkInputs = [ numpy pandas xarray nose pytest ]; checkInputs = [ numpy pandas xarray nose pytestCheckHook ];
pythonImportsCheck = [ "traittypes" ];
meta = with lib; { meta = with lib; {
description = "Trait types for NumPy, SciPy, XArray, and Pandas"; description = "Trait types for NumPy, SciPy, XArray, and Pandas";

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@ -20,6 +20,7 @@ buildPythonPackage rec {
# No tests on PyPi # No tests on PyPi
doCheck = false; doCheck = false;
pythonImportsCheck = [ "uproot3_methods" ];
meta = with lib; { meta = with lib; {
homepage = "https://github.com/scikit-hep/uproot3-methods"; homepage = "https://github.com/scikit-hep/uproot3-methods";

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@ -1,5 +1,5 @@
{ lib, buildPythonPackage , fetchPypi, pythonOlder { lib, buildPythonPackage , fetchPypi, pythonOlder
, pytest, jupyter_core, pandas, ipywidgets, jupyter, altair }: , jupyter_core, pandas, ipywidgets, jupyter }:
buildPythonPackage rec { buildPythonPackage rec {
pname = "vega"; pname = "vega";
@ -11,12 +11,11 @@ buildPythonPackage rec {
sha256 = "f343ceb11add58d24cd320d69e410b111a56c98c9069ebb4ef89c608c4c1950d"; sha256 = "f343ceb11add58d24cd320d69e410b111a56c98c9069ebb4ef89c608c4c1950d";
}; };
buildInputs = [ pytest ];
propagatedBuildInputs = [ jupyter jupyter_core pandas ipywidgets ]; propagatedBuildInputs = [ jupyter jupyter_core pandas ipywidgets ];
# currently, recommonmark is broken on python3 # currently, recommonmark is broken on python3
doCheck = false; doCheck = false;
checkInputs = [ altair ]; pythonImportsCheck = [ "vega" ];
meta = with lib; { meta = with lib; {
description = "An IPython/Jupyter widget for Vega and Vega-Lite"; description = "An IPython/Jupyter widget for Vega and Vega-Lite";

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@ -6,7 +6,6 @@
, imutils , imutils
, progress , progress
, matplotlib , matplotlib
, pytest
}: }:
buildPythonPackage rec { buildPythonPackage rec {
@ -18,11 +17,11 @@ buildPythonPackage rec {
sha256 = "649a77a0c1b670d13a1bf411451945d7da439364dc0c33ee3636a23f1d82b456"; sha256 = "649a77a0c1b670d13a1bf411451945d7da439364dc0c33ee3636a23f1d82b456";
}; };
checkInputs = [ pytest ];
propagatedBuildInputs = [ numpy pandas imutils progress matplotlib ]; propagatedBuildInputs = [ numpy pandas imutils progress matplotlib ];
# tests not packaged with pypi # tests not packaged with pypi
doCheck = false; doCheck = false;
pythonImportsCheck = [ "vidstab" ];
meta = with lib; { meta = with lib; {
homepage = "https://github.com/AdamSpannbauer/python_video_stab"; homepage = "https://github.com/AdamSpannbauer/python_video_stab";

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@ -17,9 +17,9 @@ stdenv.mkDerivation rec {
propagatedBuildInputs = with python3.pkgs; [ python python3.pkgs.protobuf ]; propagatedBuildInputs = with python3.pkgs; [ python python3.pkgs.protobuf ];
postPatch = '' postPatch = ''
substituteInPlace ./Documentation/Makefile --replace "2>/dev/null" "" substituteInPlace ./Documentation/Makefile \
substituteInPlace ./Documentation/Makefile --replace "-m custom.xsl" "-m custom.xsl --skip-validation -x ${docbook_xsl}/xml/xsl/docbook/manpages/docbook.xsl" --replace "2>/dev/null" "" \
substituteInPlace ./criu/Makefile --replace "-I/usr/include/libnl3" "-I${libnl.dev}/include/libnl3" --replace "-m custom.xsl" "-m custom.xsl --skip-validation -x ${docbook_xsl}/xml/xsl/docbook/manpages/docbook.xsl"
substituteInPlace ./Makefile --replace "head-name := \$(shell git tag -l v\$(CRIU_VERSION))" "head-name = ${version}.0" substituteInPlace ./Makefile --replace "head-name := \$(shell git tag -l v\$(CRIU_VERSION))" "head-name = ${version}.0"
ln -sf ${protobuf}/include/google/protobuf/descriptor.proto ./images/google/protobuf/descriptor.proto ln -sf ${protobuf}/include/google/protobuf/descriptor.proto ./images/google/protobuf/descriptor.proto
''; '';

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@ -24,12 +24,6 @@ stdenv.mkDerivation rec {
# Tainted Mode disables PERL5LIB # Tainted Mode disables PERL5LIB
substituteInPlace btrbk --replace "perl -T" "perl" substituteInPlace btrbk --replace "perl -T" "perl"
# Fix btrbk-mail
substituteInPlace contrib/cron/btrbk-mail \
--replace "/bin/date" "${coreutils}/bin/date" \
--replace "/bin/echo" "${coreutils}/bin/echo" \
--replace '$btrbk' 'btrbk'
# Fix SSH filter script # Fix SSH filter script
sed -i '/^export PATH/d' ssh_filter_btrbk.sh sed -i '/^export PATH/d' ssh_filter_btrbk.sh
substituteInPlace ssh_filter_btrbk.sh --replace logger ${util-linux}/bin/logger substituteInPlace ssh_filter_btrbk.sh --replace logger ${util-linux}/bin/logger

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@ -1,4 +1,4 @@
{ stdenv, lib, darwin, fetchFromGitHub, rustPlatform }: { stdenv, lib, fetchFromGitHub, rustPlatform, Security }:
rustPlatform.buildRustPackage rec { rustPlatform.buildRustPackage rec {
pname = "kak-lsp"; pname = "kak-lsp";
@ -13,7 +13,7 @@ rustPlatform.buildRustPackage rec {
cargoSha256 = "174qy50m9487vv151vm8q6sby79dq3gbqjbz6h4326jwsc9wwi8c"; cargoSha256 = "174qy50m9487vv151vm8q6sby79dq3gbqjbz6h4326jwsc9wwi8c";
buildInputs = lib.optional stdenv.isDarwin [ darwin.apple_sdk.frameworks.Security ]; buildInputs = lib.optional stdenv.isDarwin [ Security ];
meta = with lib; { meta = with lib; {
description = "Kakoune Language Server Protocol Client"; description = "Kakoune Language Server Protocol Client";

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@ -1,6 +1,6 @@
{ lib, stdenv, fetchurl, pkg-config, zlib, kmod, which { lib, stdenv, fetchurl, pkg-config, zlib, kmod, which
, static ? stdenv.hostPlatform.isStatic , static ? stdenv.hostPlatform.isStatic
, darwin ? null , IOKit
}: }:
stdenv.mkDerivation rec { stdenv.mkDerivation rec {
@ -13,7 +13,7 @@ stdenv.mkDerivation rec {
nativeBuildInputs = [ pkg-config ]; nativeBuildInputs = [ pkg-config ];
buildInputs = [ zlib kmod which ] ++ buildInputs = [ zlib kmod which ] ++
lib.optional stdenv.hostPlatform.isDarwin darwin.apple_sdk.frameworks.IOKit; lib.optional stdenv.hostPlatform.isDarwin IOKit;
preConfigure = if stdenv.cc.isGNU then null else '' preConfigure = if stdenv.cc.isGNU then null else ''
substituteInPlace Makefile --replace 'CC=$(CROSS_COMPILE)gcc' "" substituteInPlace Makefile --replace 'CC=$(CROSS_COMPILE)gcc' ""

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@ -5505,7 +5505,9 @@ in
plugins = [ ]; # override with the list of desired plugins plugins = [ ]; # override with the list of desired plugins
}; };
kak-lsp = callPackage ../tools/misc/kak-lsp { }; kak-lsp = callPackage ../tools/misc/kak-lsp {
inherit (darwin.apple_sdk.frameworks) Security;
};
kbdd = callPackage ../applications/window-managers/kbdd { }; kbdd = callPackage ../applications/window-managers/kbdd { };
@ -7009,7 +7011,9 @@ in
pcimem = callPackage ../os-specific/linux/pcimem { }; pcimem = callPackage ../os-specific/linux/pcimem { };
pciutils = callPackage ../tools/system/pciutils { }; pciutils = callPackage ../tools/system/pciutils {
inherit (darwin.apple_sdk.frameworks) IOKit;
};
pcsclite = callPackage ../tools/security/pcsclite { pcsclite = callPackage ../tools/security/pcsclite {
inherit (darwin.apple_sdk.frameworks) IOKit; inherit (darwin.apple_sdk.frameworks) IOKit;