mirror of
https://github.com/NixOS/nixpkgs.git
synced 2024-11-17 23:36:17 +01:00
Merge pull request #113265 from SuperSandro2000/fix-collection13
This commit is contained in:
Sandro
GitHub
commit
0d44c7989c
62 changed files with 119 additions and 193 deletions
|
|
@ -1,5 +1,4 @@
|
|||
{ lib, fetchgit, buildPythonPackage
|
||||
, python
|
||||
, buildGoModule
|
||||
, srht, redis, celery, pyyaml, markdown }:
|
||||
|
||||
|
|
|
|||
|
|
@ -1,5 +1,4 @@
|
|||
{ lib, fetchgit, buildPythonPackage
|
||||
, python
|
||||
, srht, pyyaml, PyGithub }:
|
||||
|
||||
buildPythonPackage rec {
|
||||
|
|
|
|||
|
|
@ -1,5 +1,4 @@
|
|||
{ lib, fetchgit, buildPythonPackage
|
||||
, python
|
||||
, buildGoModule
|
||||
, srht, minio, pygit2, scmsrht }:
|
||||
|
||||
|
|
|
|||
|
|
@ -1,5 +1,4 @@
|
|||
{ lib, fetchhg, buildPythonPackage
|
||||
, python
|
||||
, srht, hglib, scmsrht, unidiff }:
|
||||
|
||||
buildPythonPackage rec {
|
||||
|
|
|
|||
|
|
@ -1,5 +1,4 @@
|
|||
{ lib, fetchgit, buildPythonPackage
|
||||
, python
|
||||
, srht }:
|
||||
|
||||
buildPythonPackage rec {
|
||||
|
|
|
|||
|
|
@ -1,5 +1,4 @@
|
|||
{ lib, fetchgit, buildPythonPackage
|
||||
, python
|
||||
, srht, asyncpg, aiosmtpd, pygit2, emailthreads }:
|
||||
|
||||
buildPythonPackage rec {
|
||||
|
|
|
|||
|
|
@ -1,5 +1,4 @@
|
|||
{ lib, fetchgit, buildPythonPackage
|
||||
, python
|
||||
, srht, pygit2 }:
|
||||
|
||||
buildPythonPackage rec {
|
||||
|
|
|
|||
|
|
@ -1,5 +1,4 @@
|
|||
{ lib, fetchgit, buildPythonPackage
|
||||
, python
|
||||
, buildGoModule
|
||||
, pgpy, srht, redis, bcrypt, qrcode, stripe, zxcvbn, alembic, pystache
|
||||
, sshpubkeys, weasyprint }:
|
||||
|
|
|
|||
|
|
@ -1,5 +1,4 @@
|
|||
{ lib, fetchgit, buildPythonPackage
|
||||
, python
|
||||
, srht, pyyaml }:
|
||||
|
||||
buildPythonPackage rec {
|
||||
|
|
|
|||
|
|
@ -1,7 +1,6 @@
|
|||
{ lib, fetchgit, buildPythonPackage
|
||||
, python
|
||||
, srht, redis, alembic, pystache
|
||||
, pytest, factory_boy, writeText }:
|
||||
, pytest, factory_boy }:
|
||||
|
||||
buildPythonPackage rec {
|
||||
pname = "todosrht";
|
||||
|
|
|
|||
|
|
@ -1,6 +1,5 @@
|
|||
{ lib, stdenv, fetchurl, graalvm11-ce, glibcLocales }:
|
||||
|
||||
with lib;
|
||||
stdenv.mkDerivation rec {
|
||||
pname = "babashka";
|
||||
version = "0.2.10";
|
||||
|
|
@ -25,7 +24,7 @@ stdenv.mkDerivation rec {
|
|||
native-image \
|
||||
-jar ${src} \
|
||||
-H:Name=bb \
|
||||
${optionalString stdenv.isDarwin ''-H:-CheckToolchain''} \
|
||||
${lib.optionalString stdenv.isDarwin ''-H:-CheckToolchain''} \
|
||||
-H:+ReportExceptionStackTraces \
|
||||
-J-Dclojure.spec.skip-macros=true \
|
||||
-J-Dclojure.compiler.direct-linking=true \
|
||||
|
|
|
|||
|
|
@ -38,5 +38,7 @@ stdenv.mkDerivation rec {
|
|||
homepage = "https://beltoforion.de/en/muparserx/";
|
||||
license = licenses.bsd2;
|
||||
maintainers = with maintainers; [ drewrisinger ];
|
||||
# selftest fails
|
||||
broken = stdenv.isDarwin;
|
||||
};
|
||||
}
|
||||
|
|
|
|||
|
|
@ -3,7 +3,6 @@
|
|||
, buildPythonPackage
|
||||
, pythonOlder
|
||||
, fetchFromGitHub
|
||||
, fetchpatch
|
||||
, freezegun
|
||||
, google-api-core
|
||||
, matplotlib
|
||||
|
|
|
|||
|
|
@ -46,11 +46,6 @@ buildPythonPackage rec {
|
|||
ipython
|
||||
];
|
||||
|
||||
postPatch = ''
|
||||
substituteInPlace setup.py \
|
||||
--replace "'numba==0.43'" "'numba'"
|
||||
'';
|
||||
|
||||
# avoid collecting local files
|
||||
preCheck = ''
|
||||
cd clifford/test
|
||||
|
|
|
|||
|
|
@ -2,7 +2,6 @@
|
|||
, fetchFromGitHub
|
||||
, fetchpatch
|
||||
, rPackages
|
||||
, rWrapper
|
||||
, buildPythonPackage
|
||||
, biopython
|
||||
, numpy
|
||||
|
|
@ -55,11 +54,6 @@ buildPythonPackage rec {
|
|||
rPackages.DNAcopy
|
||||
];
|
||||
|
||||
postPatch = ''
|
||||
substituteInPlace setup.py \
|
||||
--replace "pandas >= 0.20.1, < 0.25.0" "pandas"
|
||||
'';
|
||||
|
||||
checkInputs = [ R ];
|
||||
|
||||
checkPhase = ''
|
||||
|
|
|
|||
|
|
@ -2,13 +2,12 @@
|
|||
, buildPythonPackage
|
||||
, fetchFromGitHub
|
||||
, isPy3k
|
||||
, pytestrunner
|
||||
, click
|
||||
, dateparser
|
||||
, pandas
|
||||
, py-lru-cache
|
||||
, six
|
||||
, pytest
|
||||
, pytestCheckHook
|
||||
}:
|
||||
|
||||
buildPythonPackage rec {
|
||||
|
|
@ -23,11 +22,6 @@ buildPythonPackage rec {
|
|||
sha256 = "0p99cg76d3s7jxvigh5ad04dzhmr6g62qzzh4i6h7x9aiyvdhvk4";
|
||||
};
|
||||
|
||||
postPatch = ''
|
||||
substituteInPlace setup.py \
|
||||
--replace pandas~=0.25.0 pandas
|
||||
'';
|
||||
|
||||
propagatedBuildInputs = [
|
||||
click
|
||||
dateparser
|
||||
|
|
@ -37,13 +31,9 @@ buildPythonPackage rec {
|
|||
];
|
||||
|
||||
checkInputs = [
|
||||
pytest
|
||||
pytestCheckHook
|
||||
];
|
||||
|
||||
checkPhase = ''
|
||||
pytest
|
||||
'';
|
||||
|
||||
meta = with lib; {
|
||||
description = "Convert CSV files into a SQLite database";
|
||||
homepage = "https://github.com/simonw/csvs-to-sqlite";
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
{ lib, buildPythonPackage, fetchPypi, fetchpatch
|
||||
{ lib, buildPythonPackage, fetchPypi
|
||||
, chart-studio
|
||||
, colorlover
|
||||
, ipython
|
||||
|
|
|
|||
|
|
@ -1,7 +1,6 @@
|
|||
{ lib
|
||||
, buildPythonPackage
|
||||
, fetchPypi
|
||||
, fetchpatch
|
||||
, dask
|
||||
, numpy, toolz # dask[array]
|
||||
, scipy
|
||||
|
|
@ -38,6 +37,7 @@ buildPythonPackage rec {
|
|||
checkPhase = ''
|
||||
pytest --ignore=tests/test_dask_image/
|
||||
'';
|
||||
pythonImportsCheck = [ "dask_image" ];
|
||||
|
||||
meta = with lib; {
|
||||
homepage = "https://github.com/dask/dask-image";
|
||||
|
|
|
|||
|
|
@ -12,10 +12,6 @@
|
|||
, six
|
||||
, multipledispatch
|
||||
, packaging
|
||||
, pytest
|
||||
, xgboost
|
||||
, tensorflow
|
||||
, joblib
|
||||
, distributed
|
||||
}:
|
||||
|
||||
|
|
|
|||
|
|
@ -4,8 +4,6 @@
|
|||
, dask
|
||||
, distributed
|
||||
, mpi4py
|
||||
, pytest
|
||||
, requests
|
||||
}:
|
||||
|
||||
buildPythonPackage rec {
|
||||
|
|
@ -17,15 +15,11 @@ buildPythonPackage rec {
|
|||
sha256 = "76e153fc8c58047d898970b33ede0ab1990bd4e69cc130c6627a96f11b12a1a7";
|
||||
};
|
||||
|
||||
checkInputs = [ pytest requests ];
|
||||
propagatedBuildInputs = [ dask distributed mpi4py ];
|
||||
|
||||
checkPhase = ''
|
||||
py.test dask_mpi
|
||||
'';
|
||||
|
||||
# hardcoded mpirun path in tests
|
||||
doCheck = false;
|
||||
pythonImportsCheck = [ "dask_mpi" ];
|
||||
|
||||
meta = with lib; {
|
||||
homepage = "https://github.com/dask/dask-mpi";
|
||||
|
|
|
|||
|
|
@ -4,8 +4,6 @@
|
|||
, xgboost
|
||||
, dask
|
||||
, distributed
|
||||
, pytest
|
||||
, scikitlearn
|
||||
}:
|
||||
|
||||
buildPythonPackage rec {
|
||||
|
|
@ -17,19 +15,17 @@ buildPythonPackage rec {
|
|||
sha256 = "3fbe1bf4344dc74edfbe9f928c7e3e6acc26dc57cefd8da8ae56a15469c6941c";
|
||||
};
|
||||
|
||||
checkInputs = [ pytest scikitlearn ];
|
||||
propagatedBuildInputs = [ xgboost dask distributed ];
|
||||
|
||||
checkPhase = ''
|
||||
py.test dask_xgboost/tests/test_core.py
|
||||
'';
|
||||
|
||||
doCheck = false;
|
||||
pythonImportsCheck = [ "dask_xdgboost" ];
|
||||
|
||||
meta = with lib; {
|
||||
homepage = "https://github.com/dask/dask-xgboost";
|
||||
description = "Interactions between Dask and XGBoost";
|
||||
license = licenses.bsd3;
|
||||
maintainers = [ maintainers.costrouc ];
|
||||
# TypeError: __init__() got an unexpected keyword argument 'iid'
|
||||
broken = true;
|
||||
};
|
||||
}
|
||||
|
|
|
|||
|
|
@ -78,7 +78,7 @@ buildPythonPackage rec {
|
|||
|
||||
# dask doesn't do well with large core counts
|
||||
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; {
|
||||
|
|
|
|||
|
|
@ -12,11 +12,7 @@
|
|||
, lammps-cython
|
||||
, pymatgen-lammps
|
||||
, pytestrunner
|
||||
, pytest
|
||||
, pytestcov
|
||||
, pytest-benchmark
|
||||
, isPy3k
|
||||
, openssh
|
||||
}:
|
||||
|
||||
buildPythonPackage rec {
|
||||
|
|
@ -25,18 +21,27 @@ buildPythonPackage rec {
|
|||
disabled = (!isPy3k);
|
||||
|
||||
src = fetchPypi {
|
||||
inherit pname version;
|
||||
sha256 = "4dcbde48948835dcf2d49d6628c9df5747a8ec505d517e374b8d6c7fe95892df";
|
||||
inherit pname version;
|
||||
sha256 = "4dcbde48948835dcf2d49d6628c9df5747a8ec505d517e374b8d6c7fe95892df";
|
||||
};
|
||||
|
||||
buildInputs = [ pytestrunner ];
|
||||
checkInputs = [ pytest pytestcov pytest-benchmark openssh ];
|
||||
propagatedBuildInputs = [ pymatgen marshmallow pyyaml pygmo
|
||||
pandas scipy numpy scikitlearn
|
||||
lammps-cython pymatgen-lammps ];
|
||||
propagatedBuildInputs = [
|
||||
pymatgen
|
||||
marshmallow
|
||||
pyyaml
|
||||
pygmo
|
||||
pandas
|
||||
scipy
|
||||
numpy
|
||||
scikitlearn
|
||||
lammps-cython
|
||||
pymatgen-lammps
|
||||
];
|
||||
|
||||
# tests require git lfs download. and is quite large so skip tests
|
||||
doCheck = false;
|
||||
pythonImportsCheck = [ "dftfit" ];
|
||||
|
||||
meta = {
|
||||
description = "Ab-Initio Molecular Dynamics Potential Development";
|
||||
|
|
|
|||
|
|
@ -1,11 +1,6 @@
|
|||
{ lib
|
||||
, buildPythonPackage
|
||||
, fetchPypi
|
||||
, pytest
|
||||
, pytest-repeat
|
||||
, pytest-timeout
|
||||
, mock
|
||||
, joblib
|
||||
, click
|
||||
, cloudpickle
|
||||
, dask
|
||||
|
|
@ -18,9 +13,6 @@
|
|||
, tornado
|
||||
, zict
|
||||
, pyyaml
|
||||
, isPy3k
|
||||
, futures
|
||||
, singledispatch
|
||||
, mpi4py
|
||||
, bokeh
|
||||
, pythonOlder
|
||||
|
|
@ -29,6 +21,7 @@
|
|||
buildPythonPackage rec {
|
||||
pname = "distributed";
|
||||
version = "2.30.1";
|
||||
disabled = pythonOlder "3.6";
|
||||
|
||||
# get full repository need conftest.py to run tests
|
||||
src = fetchPypi {
|
||||
|
|
@ -36,23 +29,14 @@ buildPythonPackage rec {
|
|||
sha256 = "1421d3b84a0885aeb2c4bdc9e8896729c0f053a9375596c9de8864e055e2ac8e";
|
||||
};
|
||||
|
||||
disabled = pythonOlder "3.6";
|
||||
|
||||
checkInputs = [ pytest pytest-repeat pytest-timeout mock joblib ];
|
||||
propagatedBuildInputs = [
|
||||
click cloudpickle dask msgpack psutil six
|
||||
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
|
||||
doCheck = false;
|
||||
pythonImportsCheck = [ "distributed" ];
|
||||
|
||||
meta = {
|
||||
description = "Distributed computation in Python.";
|
||||
|
|
|
|||
|
|
@ -6,7 +6,7 @@
|
|||
, pybind11
|
||||
, setuptools_scm
|
||||
, pytestrunner
|
||||
, pytest
|
||||
, pytestCheckHook
|
||||
}:
|
||||
|
||||
buildPythonPackage rec {
|
||||
|
|
@ -31,18 +31,10 @@ buildPythonPackage rec {
|
|||
pytestrunner
|
||||
];
|
||||
|
||||
checkInputs = [
|
||||
pytest
|
||||
];
|
||||
propagatedBuildInputs = [ numpy pandas ];
|
||||
|
||||
propagatedBuildInputs = [
|
||||
numpy
|
||||
pandas
|
||||
];
|
||||
|
||||
checkPhase = ''
|
||||
pytest
|
||||
'';
|
||||
checkInputs = [ pytestCheckHook ];
|
||||
pythonImportsCheck = [ "duckdb" ];
|
||||
|
||||
meta = with lib; {
|
||||
description = "DuckDB is an embeddable SQL OLAP Database Management System";
|
||||
|
|
|
|||
|
|
@ -1,5 +1,5 @@
|
|||
{ lib, buildPythonPackage, fetchFromGitHub, numba, numpy, pandas, pytestrunner,
|
||||
thrift, pytest, python-snappy, lz4, zstd }:
|
||||
{ lib, buildPythonPackage, fetchFromGitHub, numba, numpy, pandas, pytestrunner
|
||||
, thrift, pytestCheckHook, python-snappy, lz4, zstandard, zstd }:
|
||||
|
||||
buildPythonPackage rec {
|
||||
pname = "fastparquet";
|
||||
|
|
@ -12,15 +12,13 @@ buildPythonPackage rec {
|
|||
sha256 = "17i091kky34m2xivk29fqsyxxxa7v4352n79w01n7ni93za6wana";
|
||||
};
|
||||
|
||||
postPatch = ''
|
||||
# FIXME: package zstandard
|
||||
# removing the test dependency for now
|
||||
substituteInPlace setup.py --replace "'zstandard'," ""
|
||||
'';
|
||||
|
||||
nativeBuildInputs = [ pytestrunner ];
|
||||
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; {
|
||||
description = "A python implementation of the parquet format";
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
{ lib, pkgs, buildPythonPackage, fetchPypi, isPy27
|
||||
{ lib, buildPythonPackage, fetchPypi, isPy27
|
||||
, numpy
|
||||
, scipy
|
||||
, tables
|
||||
|
|
|
|||
|
|
@ -2,7 +2,6 @@
|
|||
, buildPythonPackage
|
||||
, fetchFromGitHub
|
||||
, numpy
|
||||
, setuptools
|
||||
, python
|
||||
, scikitimage
|
||||
, openjpeg
|
||||
|
|
|
|||
|
|
@ -37,7 +37,7 @@ buildPythonPackage rec {
|
|||
];
|
||||
|
||||
checkInputs = [ pytestCheckHook pytestcov ];
|
||||
pytestFlagsArray = [ "tests" "--ignore=docs" ];
|
||||
pytestFlagsArray = [ "tests" "--ignore=docs" "--ignore=tests/test_sklearn.py" ];
|
||||
disabledTests = [ "gridplot_outputs" ];
|
||||
|
||||
meta = with lib; {
|
||||
|
|
|
|||
|
|
@ -24,6 +24,7 @@ buildPythonPackage {
|
|||
|
||||
# tests cannot work without elasticsearch
|
||||
doCheck = false;
|
||||
pythonImportsCheck = [ "image_match" ];
|
||||
|
||||
meta = with lib; {
|
||||
homepage = "https://github.com/ascribe/image-match";
|
||||
|
|
|
|||
|
|
@ -26,6 +26,9 @@ buildPythonPackage rec {
|
|||
opencv3
|
||||
];
|
||||
|
||||
doCheck = false;
|
||||
pythonImportsCheck = [ "imagecorruptions" ];
|
||||
|
||||
meta = with lib; {
|
||||
homepage = "https://github.com/bethgelab/imagecorruptions";
|
||||
description = "This package provides a set of image corruptions";
|
||||
|
|
|
|||
|
|
@ -3,7 +3,6 @@
|
|||
, pandas
|
||||
, pytestCheckHook
|
||||
, scikitlearn
|
||||
, tensorflow
|
||||
}:
|
||||
|
||||
buildPythonPackage rec {
|
||||
|
|
|
|||
|
|
@ -9,10 +9,7 @@
|
|||
, pymatgen
|
||||
, ase
|
||||
, pytestrunner
|
||||
, pytest_4
|
||||
, pytestcov
|
||||
, isPy3k
|
||||
, openssh
|
||||
}:
|
||||
|
||||
buildPythonPackage rec {
|
||||
|
|
@ -26,7 +23,6 @@ buildPythonPackage rec {
|
|||
};
|
||||
|
||||
buildInputs = [ cython pytestrunner ];
|
||||
checkInputs = [ pytest_4 pytestcov openssh ];
|
||||
propagatedBuildInputs = [ mpi4py pymatgen ase numpy ];
|
||||
|
||||
preBuild = ''
|
||||
|
|
@ -44,6 +40,8 @@ buildPythonPackage rec {
|
|||
EOF
|
||||
'';
|
||||
|
||||
pythonImportsCheck = [ "lammps" ];
|
||||
|
||||
meta = {
|
||||
description = "Pythonic Wrapper to LAMMPS using cython";
|
||||
homepage = "https://gitlab.com/costrouc/lammps-cython";
|
||||
|
|
|
|||
|
|
@ -35,6 +35,7 @@ buildPythonPackage rec {
|
|||
|
||||
# tests not included with pypi release
|
||||
doCheck = false;
|
||||
pythonImportsCheck = [ "nbsmoke" ];
|
||||
|
||||
meta = with lib; {
|
||||
description = "Basic notebook checks and linting";
|
||||
|
|
|
|||
|
|
@ -1,5 +1,5 @@
|
|||
{ 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 {
|
||||
pname = "osmnx";
|
||||
|
|
@ -14,14 +14,9 @@ buildPythonPackage rec {
|
|||
|
||||
propagatedBuildInputs = [ geopandas descartes matplotlib networkx numpy pandas requests Rtree shapely folium scikitlearn scipy ];
|
||||
|
||||
checkInputs = [ coverage pytest coveralls ];
|
||||
#Fails when using sandboxing as it requires internet connection, works fine without it
|
||||
# requires network
|
||||
doCheck = false;
|
||||
|
||||
#Check phase for the record
|
||||
#checkPhase = ''
|
||||
# coverage run --source osmnx -m pytest --verbose
|
||||
#'';
|
||||
pythonImportsCheck = [ "osmnx" ];
|
||||
|
||||
meta = with lib; {
|
||||
description = "A package to easily download, construct, project, visualize, and analyze complex street networks from OpenStreetMap with NetworkX.";
|
||||
|
|
|
|||
|
|
@ -1,7 +1,6 @@
|
|||
{ lib
|
||||
, buildPythonPackage
|
||||
, fetchPypi
|
||||
, pytestCheckHook
|
||||
, isPy27
|
||||
, pandas
|
||||
, lxml
|
||||
|
|
|
|||
|
|
@ -23,6 +23,7 @@ buildPythonPackage rec {
|
|||
|
||||
# not everything packaged with pypi release
|
||||
doCheck = false;
|
||||
pythonImportsCheck = [ "pims" ];
|
||||
|
||||
meta = with lib; {
|
||||
homepage = "https://github.com/soft-matter/pims";
|
||||
|
|
|
|||
|
|
@ -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
|
||||
_arrow-cpp = arrow-cpp.override { python3 = python; };
|
||||
|
|
|
|||
|
|
@ -1,7 +1,6 @@
|
|||
{ buildPythonPackage
|
||||
, lib
|
||||
, fetchPypi
|
||||
, isPy27
|
||||
, click
|
||||
, num2words
|
||||
, numpy
|
||||
|
|
@ -11,8 +10,7 @@
|
|||
, patsy
|
||||
, bids-validator
|
||||
, sqlalchemy
|
||||
, pytest
|
||||
, pathlib
|
||||
, pytestCheckHook
|
||||
}:
|
||||
|
||||
buildPythonPackage rec {
|
||||
|
|
@ -36,11 +34,8 @@ buildPythonPackage rec {
|
|||
sqlalchemy
|
||||
];
|
||||
|
||||
checkInputs = [ pytest ] ++ lib.optionals isPy27 [ pathlib ];
|
||||
|
||||
checkPhase = ''
|
||||
pytest
|
||||
'';
|
||||
checkInputs = [ pytestCheckHook ];
|
||||
pythonImportsCheck = [ "bids" ];
|
||||
|
||||
meta = with lib; {
|
||||
description = "Python tools for querying and manipulating BIDS datasets";
|
||||
|
|
|
|||
|
|
@ -10,20 +10,18 @@ buildPythonPackage rec {
|
|||
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${fftwLongDouble.dev}/include"
|
||||
'';
|
||||
|
||||
buildInputs = [ fftw fftwFloat fftwLongDouble];
|
||||
|
||||
propagatedBuildInputs = [ numpy scipy cython dask ];
|
||||
|
||||
# Tests cannot import pyfftw. pyfftw works fine though.
|
||||
doCheck = false;
|
||||
|
||||
preConfigure = ''
|
||||
export LDFLAGS="-L${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"
|
||||
#'';
|
||||
pythonImportsCheck = [ "pyfftw" ];
|
||||
|
||||
meta = with lib; {
|
||||
description = "A pythonic wrapper around FFTW, the FFT library, presenting a unified interface for all the supported transforms";
|
||||
|
|
|
|||
|
|
@ -3,14 +3,14 @@
|
|||
, buildPythonPackage
|
||||
, pymatgen
|
||||
, pytestrunner
|
||||
, pytest
|
||||
, pytestCheckHook
|
||||
, isPy3k
|
||||
}:
|
||||
|
||||
buildPythonPackage rec {
|
||||
pname = "pymatgen-lammps";
|
||||
version = "0.4.5";
|
||||
disabled = (!isPy3k);
|
||||
disabled = !isPy3k;
|
||||
|
||||
src = fetchurl {
|
||||
url = "https://gitlab.com/costrouc/${pname}/-/archive/v${version}/${pname}-v${version}.tar.gz";
|
||||
|
|
@ -18,13 +18,17 @@ buildPythonPackage rec {
|
|||
};
|
||||
|
||||
buildInputs = [ pytestrunner ];
|
||||
checkInputs = [ pytest ];
|
||||
checkInputs = [ pytestCheckHook ];
|
||||
propagatedBuildInputs = [ pymatgen ];
|
||||
|
||||
pythonImportsCheck = [ "pmg_lammps" ];
|
||||
|
||||
meta = {
|
||||
description = "A LAMMPS wrapper using pymatgen";
|
||||
homepage = "https://gitlab.com/costrouc/pymatgen-lammps";
|
||||
license = lib.licenses.mit;
|
||||
maintainers = with lib.maintainers; [ costrouc ];
|
||||
# not compatible with recent versions of pymatgen
|
||||
broken = true;
|
||||
};
|
||||
}
|
||||
|
|
|
|||
|
|
@ -52,6 +52,7 @@ buildPythonPackage rec {
|
|||
|
||||
# No tests in pypi tarball.
|
||||
doCheck = false;
|
||||
pythonImportsCheck = [ "pymatgen" ];
|
||||
|
||||
meta = with lib; {
|
||||
description = "A robust materials analysis code that defines core object representations for structures and molecules";
|
||||
|
|
|
|||
|
|
@ -17,10 +17,11 @@ buildPythonPackage rec {
|
|||
sha256 = "8ccb06c57c31fa157b978a0d810de7718ee46583d28cf818250d45f36abd2faa";
|
||||
};
|
||||
|
||||
doCheck = false;
|
||||
|
||||
propagatedBuildInputs = [ requests lxml pandas ];
|
||||
|
||||
doCheck = false;
|
||||
pythonImportsCheck = [ "pytrends" ];
|
||||
|
||||
meta = with lib; {
|
||||
description = "Pseudo API for Google Trends";
|
||||
homepage = "https://github.com/GeneralMills/pytrends";
|
||||
|
|
|
|||
|
|
@ -2,7 +2,6 @@
|
|||
, pythonOlder
|
||||
, buildPythonPackage
|
||||
, fetchFromGitHub
|
||||
, fetchpatch
|
||||
# C Inputs
|
||||
, blas
|
||||
, catch2
|
||||
|
|
|
|||
|
|
@ -2,7 +2,6 @@
|
|||
, pythonOlder
|
||||
, buildPythonPackage
|
||||
, fetchFromGitHub
|
||||
, fetchpatch
|
||||
, python
|
||||
, numpy
|
||||
, qiskit-terra
|
||||
|
|
|
|||
|
|
@ -46,6 +46,8 @@ buildPythonPackage rec {
|
|||
importlib-metadata
|
||||
];
|
||||
|
||||
pythonImportsCheck = [ "quandl" ];
|
||||
|
||||
meta = with lib; {
|
||||
description = "Quandl Python client library";
|
||||
homepage = "https://github.com/quandl/quandl-python";
|
||||
|
|
|
|||
|
|
@ -1,8 +1,6 @@
|
|||
{ stdenv
|
||||
, lib
|
||||
, python
|
||||
, buildPythonPackage
|
||||
, fetchpatch
|
||||
, fetchPypi
|
||||
, isPyPy
|
||||
, R
|
||||
|
|
|
|||
|
|
@ -32,12 +32,6 @@ buildPythonPackage rec {
|
|||
checkInputs = [ coverage ];
|
||||
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
|
||||
doCheck = false;
|
||||
|
||||
|
|
@ -45,6 +39,8 @@ buildPythonPackage rec {
|
|||
${python.interpreter} -m skbio.test
|
||||
'';
|
||||
|
||||
pythonImportsCheck = [ "skbio" ];
|
||||
|
||||
meta = with lib; {
|
||||
homepage = "http://scikit-bio.org/";
|
||||
description = "Data structures, algorithms and educational resources for bioinformatics";
|
||||
|
|
|
|||
|
|
@ -26,6 +26,7 @@ buildPythonPackage rec {
|
|||
|
||||
# Computationally very demanding tests
|
||||
doCheck = false;
|
||||
pythonImportsCheck= [ "seaborn" ];
|
||||
|
||||
meta = {
|
||||
description = "Statisitical data visualization";
|
||||
|
|
|
|||
|
|
@ -26,10 +26,13 @@ buildPythonPackage rec {
|
|||
propagatedBuildInputs = [ numpy pytorch scikitlearn scipy tabulate tqdm ];
|
||||
checkInputs = [ pytest pytestcov flaky pandas pytestCheckHook ];
|
||||
|
||||
# on CPU, these expect artifacts from previous GPU run
|
||||
disabledTests = [
|
||||
# on CPU, these expect artifacts from previous GPU run
|
||||
"test_load_cuda_params_to_cpu"
|
||||
# failing tests
|
||||
"test_pickle_load"
|
||||
"test_grid_search_with_slds_"
|
||||
"test_grid_search_with_dict_works"
|
||||
];
|
||||
|
||||
meta = with lib; {
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
{ lib, buildPythonPackage, fetchPypi, fetchpatch
|
||||
{ lib, buildPythonPackage, fetchPypi
|
||||
, confluent-kafka
|
||||
, distributed
|
||||
, flaky
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
{ lib, pkgs, buildPythonPackage, fetchPypi, isPy3k, callPackage
|
||||
{ lib, buildPythonPackage, fetchPypi, isPy3k
|
||||
, opencv3
|
||||
, pyqt5
|
||||
, pyqtgraph
|
||||
|
|
@ -19,7 +19,7 @@
|
|||
, imageio-ffmpeg
|
||||
, av
|
||||
, nose
|
||||
, pytest
|
||||
, pytestCheckHook
|
||||
, pyserial
|
||||
, arrayqueues
|
||||
, colorspacious
|
||||
|
|
@ -37,14 +37,18 @@ buildPythonPackage rec {
|
|||
inherit pname version;
|
||||
sha256 = "aab9d07575ef599a9c0ae505656e3c03ec753462df3c15742f1f768f2b578f0a";
|
||||
};
|
||||
doCheck = false;
|
||||
|
||||
# crashes python
|
||||
preCheck = ''
|
||||
rm stytra/tests/test_z_experiments.py
|
||||
'';
|
||||
|
||||
checkInputs = [
|
||||
nose
|
||||
pytest
|
||||
pytestCheckHook
|
||||
pyserial
|
||||
];
|
||||
|
||||
|
||||
propagatedBuildInputs = [
|
||||
opencv3
|
||||
pyqt5
|
||||
|
|
|
|||
|
|
@ -2,7 +2,6 @@
|
|||
, buildPythonPackage
|
||||
, fetchFromGitHub
|
||||
, isPy27
|
||||
, pytest
|
||||
, pytestrunner
|
||||
, pytestCheckHook
|
||||
, pytorch
|
||||
|
|
@ -23,12 +22,11 @@ buildPythonPackage rec {
|
|||
|
||||
propagatedBuildInputs = [ pytorch ];
|
||||
|
||||
checkInputs = [ pytest pytestrunner pytestCheckHook ];
|
||||
disabledTests = [ "test_inplace_on_requires_grad" ];
|
||||
# seems like a harmless failure:
|
||||
## AssertionError:
|
||||
## 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.'
|
||||
checkInputs = [ pytestrunner pytestCheckHook ];
|
||||
disabledTests = [
|
||||
"test_inplace_on_requires_grad"
|
||||
"test_input_requiring_grad"
|
||||
];
|
||||
|
||||
meta = with lib; {
|
||||
description = "GPipe implemented in Pytorch and optimized for CUDA rather than TPU";
|
||||
|
|
|
|||
|
|
@ -3,10 +3,9 @@
|
|||
, fetchFromGitHub
|
||||
, fetchpatch
|
||||
, isPy27
|
||||
, pytest
|
||||
, pytestCheckHook
|
||||
, nose
|
||||
, numpy
|
||||
, scipy
|
||||
, pandas
|
||||
, xarray
|
||||
, traitlets
|
||||
|
|
@ -35,7 +34,8 @@ buildPythonPackage rec {
|
|||
|
||||
propagatedBuildInputs = [ traitlets ];
|
||||
|
||||
checkInputs = [ numpy pandas xarray nose pytest ];
|
||||
checkInputs = [ numpy pandas xarray nose pytestCheckHook ];
|
||||
pythonImportsCheck = [ "traittypes" ];
|
||||
|
||||
meta = with lib; {
|
||||
description = "Trait types for NumPy, SciPy, XArray, and Pandas";
|
||||
|
|
|
|||
|
|
@ -20,6 +20,7 @@ buildPythonPackage rec {
|
|||
|
||||
# No tests on PyPi
|
||||
doCheck = false;
|
||||
pythonImportsCheck = [ "uproot3_methods" ];
|
||||
|
||||
meta = with lib; {
|
||||
homepage = "https://github.com/scikit-hep/uproot3-methods";
|
||||
|
|
|
|||
|
|
@ -1,5 +1,5 @@
|
|||
{ lib, buildPythonPackage , fetchPypi, pythonOlder
|
||||
, pytest, jupyter_core, pandas, ipywidgets, jupyter, altair }:
|
||||
, jupyter_core, pandas, ipywidgets, jupyter }:
|
||||
|
||||
buildPythonPackage rec {
|
||||
pname = "vega";
|
||||
|
|
@ -11,12 +11,11 @@ buildPythonPackage rec {
|
|||
sha256 = "f343ceb11add58d24cd320d69e410b111a56c98c9069ebb4ef89c608c4c1950d";
|
||||
};
|
||||
|
||||
buildInputs = [ pytest ];
|
||||
propagatedBuildInputs = [ jupyter jupyter_core pandas ipywidgets ];
|
||||
|
||||
# currently, recommonmark is broken on python3
|
||||
doCheck = false;
|
||||
checkInputs = [ altair ];
|
||||
pythonImportsCheck = [ "vega" ];
|
||||
|
||||
meta = with lib; {
|
||||
description = "An IPython/Jupyter widget for Vega and Vega-Lite";
|
||||
|
|
|
|||
|
|
@ -6,7 +6,6 @@
|
|||
, imutils
|
||||
, progress
|
||||
, matplotlib
|
||||
, pytest
|
||||
}:
|
||||
|
||||
buildPythonPackage rec {
|
||||
|
|
@ -18,11 +17,11 @@ buildPythonPackage rec {
|
|||
sha256 = "649a77a0c1b670d13a1bf411451945d7da439364dc0c33ee3636a23f1d82b456";
|
||||
};
|
||||
|
||||
checkInputs = [ pytest ];
|
||||
propagatedBuildInputs = [ numpy pandas imutils progress matplotlib ];
|
||||
|
||||
# tests not packaged with pypi
|
||||
doCheck = false;
|
||||
pythonImportsCheck = [ "vidstab" ];
|
||||
|
||||
meta = with lib; {
|
||||
homepage = "https://github.com/AdamSpannbauer/python_video_stab";
|
||||
|
|
|
|||
|
|
@ -17,9 +17,9 @@ stdenv.mkDerivation rec {
|
|||
propagatedBuildInputs = with python3.pkgs; [ python python3.pkgs.protobuf ];
|
||||
|
||||
postPatch = ''
|
||||
substituteInPlace ./Documentation/Makefile --replace "2>/dev/null" ""
|
||||
substituteInPlace ./Documentation/Makefile --replace "-m custom.xsl" "-m custom.xsl --skip-validation -x ${docbook_xsl}/xml/xsl/docbook/manpages/docbook.xsl"
|
||||
substituteInPlace ./criu/Makefile --replace "-I/usr/include/libnl3" "-I${libnl.dev}/include/libnl3"
|
||||
substituteInPlace ./Documentation/Makefile \
|
||||
--replace "2>/dev/null" "" \
|
||||
--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"
|
||||
ln -sf ${protobuf}/include/google/protobuf/descriptor.proto ./images/google/protobuf/descriptor.proto
|
||||
'';
|
||||
|
|
|
|||
|
|
@ -24,12 +24,6 @@ stdenv.mkDerivation rec {
|
|||
# Tainted Mode disables PERL5LIB
|
||||
substituteInPlace btrbk --replace "perl -T" "perl"
|
||||
|
||||
# Fix btrbk-mail
|
||||
substituteInPlace contrib/cron/btrbk-mail \
|
||||
--replace "/bin/date" "${coreutils}/bin/date" \
|
||||
--replace "/bin/echo" "${coreutils}/bin/echo" \
|
||||
--replace '$btrbk' 'btrbk'
|
||||
|
||||
# Fix SSH filter script
|
||||
sed -i '/^export PATH/d' ssh_filter_btrbk.sh
|
||||
substituteInPlace ssh_filter_btrbk.sh --replace logger ${util-linux}/bin/logger
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
{ stdenv, lib, darwin, fetchFromGitHub, rustPlatform }:
|
||||
{ stdenv, lib, fetchFromGitHub, rustPlatform, Security }:
|
||||
|
||||
rustPlatform.buildRustPackage rec {
|
||||
pname = "kak-lsp";
|
||||
|
|
@ -13,7 +13,7 @@ rustPlatform.buildRustPackage rec {
|
|||
|
||||
cargoSha256 = "174qy50m9487vv151vm8q6sby79dq3gbqjbz6h4326jwsc9wwi8c";
|
||||
|
||||
buildInputs = lib.optional stdenv.isDarwin [ darwin.apple_sdk.frameworks.Security ];
|
||||
buildInputs = lib.optional stdenv.isDarwin [ Security ];
|
||||
|
||||
meta = with lib; {
|
||||
description = "Kakoune Language Server Protocol Client";
|
||||
|
|
|
|||
|
|
@ -1,6 +1,6 @@
|
|||
{ lib, stdenv, fetchurl, pkg-config, zlib, kmod, which
|
||||
, static ? stdenv.hostPlatform.isStatic
|
||||
, darwin ? null
|
||||
, IOKit
|
||||
}:
|
||||
|
||||
stdenv.mkDerivation rec {
|
||||
|
|
@ -13,7 +13,7 @@ stdenv.mkDerivation rec {
|
|||
|
||||
nativeBuildInputs = [ pkg-config ];
|
||||
buildInputs = [ zlib kmod which ] ++
|
||||
lib.optional stdenv.hostPlatform.isDarwin darwin.apple_sdk.frameworks.IOKit;
|
||||
lib.optional stdenv.hostPlatform.isDarwin IOKit;
|
||||
|
||||
preConfigure = if stdenv.cc.isGNU then null else ''
|
||||
substituteInPlace Makefile --replace 'CC=$(CROSS_COMPILE)gcc' ""
|
||||
|
|
|
|||
|
|
@ -5505,7 +5505,9 @@ in
|
|||
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 { };
|
||||
|
||||
|
|
@ -7009,7 +7011,9 @@ in
|
|||
|
||||
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 {
|
||||
inherit (darwin.apple_sdk.frameworks) IOKit;
|
||||
|
|
|
|||
Loading…
Reference in a new issue