Merge master into staging-next

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

@@ -6,11 +6,15 @@
 
 buildPythonPackage rec {
   pname = "capstone";
-  version = "3.0.4";
+  version = "3.0.5.post1";
+
+  setupPyBuildFlags = [
+    "--plat-name x86_64-linux"
+  ];
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "945d3b8c3646a1c3914824c416439e2cf2df8969dd722c8979cdcc23b40ad225";
+    sha256 = "3c0f73db9f8392f7048c8a244809f154d7c39f354e2167f6c477630aa517ed04";
   };
 
   patches = [

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

@@ -0,0 +1,27 @@
+{ stdenv, fetchPypi, buildPythonPackage,
+	wrapt, pytest, tox }:
+
+buildPythonPackage rec {
+  pname = "Deprecated";
+  version = "1.2.6";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1hcw9y7dvhwg5flk6wy8aa4kkgpvcqq3q4jd53h54586fp7w85d5";
+  };
+
+  postPatch = ''
+    # odd broken tests, don't appear in GitHub repo
+    rm tests/demo_classic_usage*.py
+  '';
+
+  propagatedBuildInputs = [ wrapt ];
+  checkInputs = [ pytest ];
+  meta = with stdenv.lib; {
+    homepage = "https://github.com/tantale/deprecated";
+    description = "Python @deprecated decorator to deprecate old python classes, functions or methods";
+    platforms = platforms.all;
+    license = licenses.mit;
+    maintainers = with maintainers; [ tilpner ];
+  };
+}

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

@@ -1,6 +1,7 @@
 { stdenv
 , buildPythonPackage
 , fetchPypi
+, requests
 }:
 
 buildPythonPackage rec {
@@ -12,10 +13,15 @@ buildPythonPackage rec {
     sha256 = "f7ce6c06250f694976c3cd4944e3b607b0810b93383839e5b67c7199ce2f0d3d";
   };
 
+  propagatedBuildInputs = [ requests ];
+
   meta = with stdenv.lib; {
     description = "Google Spreadsheets client library";
     homepage = "https://github.com/burnash/gspread";
     license = licenses.mit;
   };
 
+  # No tests included
+  doCheck = false;
+
 }

pkgs/development/python-modules/hocr-tools/default.nix

@@ -0,0 +1,31 @@
+{ buildPythonPackage
+, fetchFromGitHub
+, lxml
+, pillow
+, reportlab
+, stdenv
+}:
+buildPythonPackage rec {
+  pname = "hocr-tools";
+  version = "1.3.0";
+
+  src = fetchFromGitHub {
+    owner = "tmbdev";
+    repo = "${pname}";
+    rev = "v${version}";
+    sha256 = "14f9hkp7pr677085w8iidwd0la9cjzy3pyj3rdg9b03nz9pc0w6p";
+  };
+
+  # hocr-tools uses a test framework that requires internet access
+  doCheck = false;
+
+  propagatedBuildInputs = [ pillow lxml reportlab ];
+
+  meta = with stdenv.lib; {
+    description = "
+Tools for manipulating and evaluating the hOCR format for representing multi-lingual OCR results by embedding them into HTML";
+    homepage = https://github.com/tmbdev/hocr-tools;
+    license = licenses.asl20;
+    maintainers = [ maintainers.kiwi ];
+  };
+}

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

@@ -0,0 +1,21 @@
+{ lib, buildPythonPackage, fetchPypi }:
+
+buildPythonPackage rec {
+  pname = "kconfiglib";
+  version = "10.36.0";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1qhy4vv1rpgx4r1la14symxv3cpz7klqakn1rqdagwyaqp667g9b";
+  };
+
+  # doesnt work out of the box but might be possible
+  doCheck = false;
+
+  meta = with lib; {
+    description = "A flexible Python 2/3 Kconfig implementation and library";
+    homepage = https://github.com/ulfalizer/Kconfiglib;
+    license = licenses.isc;
+    maintainers = with maintainers; [ teto ];
+  };
+}

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

@@ -0,0 +1,73 @@
+{ attrs
+, buildPythonPackage
+, defusedxml
+, fetchPypi
+, hypothesis
+, isPy3k
+, lxml
+, pillow
+, pybind11
+, pytest
+, pytest-helpers-namespace
+, pytest-timeout
+, pytest_xdist
+, pytestrunner
+, python-xmp-toolkit
+, python3
+, qpdf
+, setuptools-scm-git-archive
+, setuptools_scm
+, stdenv
+}:
+
+buildPythonPackage rec {
+  pname = "pikepdf";
+  version = "1.1.0";
+  disabled = ! isPy3k;
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "14b36r6h3088z2sxp2pqvm171js53hz53mwm1g52iadignjnp0my";
+  };
+
+  buildInputs = [
+    pybind11
+    qpdf
+  ];
+
+  nativeBuildInputs = [
+    setuptools-scm-git-archive
+    setuptools_scm
+  ];
+
+  checkInputs = [
+    attrs
+    hypothesis
+    pillow
+    pytest
+    pytest-helpers-namespace
+    pytest-timeout
+    pytest_xdist
+    pytestrunner
+    python-xmp-toolkit
+  ];
+
+  propagatedBuildInputs = [ defusedxml lxml ];
+
+  postPatch = ''
+    substituteInPlace requirements/test.txt \
+       --replace "pytest >= 3.6.0, < 4.1.0" "pytest >= 4.2.1, < 5"
+  '';
+
+  preBuild = ''
+    HOME=$TMPDIR
+  '';
+
+  meta = with stdenv.lib; {
+    homepage = "https://github.com/pikepdf/pikepdf";
+    description = "Read and write PDFs with Python, powered by qpdf";
+    license = licenses.mpl20;
+    maintainers = [ maintainers.kiwi ];
+  };
+}
+

pkgs/development/python-modules/pre-commit/default.nix

@@ -0,0 +1,47 @@
+{ lib, fetchPypi, buildPythonApplication, pythonOlder
+, aspy-yaml
+, cached-property
+, cfgv
+, futures
+, identify
+, importlib-metadata
+, importlib-resources
+, nodeenv
+, six
+, toml
+, virtualenv
+}:
+
+buildPythonApplication rec {
+  pname = "pre-commit";
+  version = "1.18.1";
+
+  src = fetchPypi {
+    inherit version;
+    pname = "pre_commit";
+    sha256 = "0d9ja186g41kw3gmhbi6xjvaslz6z4xis4qn1q6jabkka6jz4qhp";
+  };
+
+  propagatedBuildInputs = [
+    aspy-yaml
+    cached-property
+    cfgv
+    identify
+    nodeenv
+    six
+    toml
+    virtualenv
+    importlib-metadata
+  ] ++ lib.optional (pythonOlder "3.7") importlib-resources
+    ++ lib.optional (pythonOlder "3.2") futures;
+
+  # slow and impure
+  doCheck = false;
+
+  meta = with lib; {
+    description = "A framework for managing and maintaining multi-language pre-commit hooks";
+    homepage = https://pre-commit.com/;
+    license = licenses.mit;
+    maintainers = with maintainers; [ borisbabic ];
+  };
+}

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

@@ -1,22 +1,20 @@
 { stdenv, fetchFromGitHub
-, buildPythonPackage, python-jose, pyjwt }:
+, buildPythonPackage, python-jose, pyjwt, requests, deprecated, httpretty }:
 
 buildPythonPackage rec {
   pname = "PyGithub";
-  version = "1.36";
+  version = "1.43.8";
 
   src = fetchFromGitHub {
     owner = "PyGithub";
     repo = "PyGithub";
     rev = "v${version}";
-    sha256 = "0yb74f9hg2vdsy766m850hfb1ss17lbgcdvvklm4qf72w12nxc5w";
+    sha256 = "1625v558xga5mwhl9jqmibywy5qafmg1vqrirqz6zfq1la1d22mw";
   };
 
-  postPatch = ''
-    # requires network
-    echo "" > github/tests/Issue142.py
-  '';
-  propagatedBuildInputs = [ python-jose pyjwt ];
+  propagatedBuildInputs = [ python-jose pyjwt requests deprecated httpretty ];
+  doCheck = false;
+
   meta = with stdenv.lib; {
     homepage = https://github.com/PyGithub/PyGithub;
     description = "A Python (2 and 3) library to access the GitHub API v3";

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

@@ -1,31 +1,33 @@
-{ buildPythonPackage, lib, fetchPypi
-, isPy3k
+{ lib, buildPythonPackage, fetchFromGitHub
+, pythonOlder
 , requests
 , pytest
+, pre-commit
 }:
 
 buildPythonPackage rec {
   pname = "pylibgen";
-  version = "2.0.1";
+  version = "2.0.2";
+  disabled = pythonOlder "3.6";
 
-  src = fetchPypi {
-    inherit pname version;
-    sha256 = "3c2a82b47cb7225dcf4ecea27081b0185ae4d195499140cdbb9597d914e1ae9e";
+  src = fetchFromGitHub {
+    owner = "joshuarli";
+    repo = pname;
+    rev = "v${version}";
+    sha256 = "1a9vhkgnkiwkicr2s287254mrkpnw9jq5r63q820dp3h74ba4kl1";
   };
 
-  disabled = !isPy3k;
-
   propagatedBuildInputs = [ requests ];
 
-  checkInputs = [ pytest ];
+  checkInputs = [ pytest pre-commit ];
 
-  # no tests in PyPI tarball
+  # literally every tests does a network call
   doCheck = false;
 
-  meta = {
+  meta = with lib; {
     description = "Python interface to Library Genesis";
     homepage = https://pypi.org/project/pylibgen/;
-    license = lib.licenses.mit;
-    maintainers = [ lib.maintainers.nico202 ];
+    license = licenses.mit;
+    maintainers = [ maintainers.nico202 ];
   };
 }

pkgs/development/python-modules/pyprof2calltree/default.nix

@@ -0,0 +1,22 @@
+{ lib, buildPythonPackage, fetchFromGitHub }:
+
+buildPythonPackage rec {
+  pname = "pyprof2calltree";
+  version = "1.4.4";
+
+  # Fetch from GitHub because the PyPi packaged version does not
+  # include all test files.
+  src = fetchFromGitHub {
+    owner = "pwaller";
+    repo = "pyprof2calltree";
+    rev = "v" + version;
+    sha256 = "1vrip41ib7nmkwa8rjny1na1wyp7nvvgvm0h9bd21i262kbm4nqx";
+  };
+
+  meta = with lib; {
+    description = "Help visualize profiling data from cProfile with kcachegrind and qcachegrind";
+    homepage = https://pypi.python.org/pypi/pyprof2calltree/;
+    license = licenses.mit;
+    maintainers = with maintainers; [ sfrijters ];
+  };
+}

pkgs/development/python-modules/pytest-helpers-namespace/default.nix

@@ -0,0 +1,35 @@
+{ buildPythonPackage
+, fetchFromGitHub
+, pytest
+, stdenv
+}:
+
+buildPythonPackage rec {
+  pname = "pytest-helpers-namespace";
+  version = "2019.1.8";
+
+  src = fetchFromGitHub {
+    owner = "saltstack";
+    repo = "${pname}";
+    rev = "v${version}";
+    sha256 = "0z9f25d2wpf3lnqzmmnrlvl5b1f7kqwjjf4nzs9x2bpf91s5zny1";
+  };
+
+  buildInputs = [ pytest ];
+
+  checkInputs = [ pytest ];
+
+  checkPhase = ''
+    pytest
+  '';
+
+  # The tests fail with newest pytest. They passed with pytest_3, which no longer exists
+  doCheck = false;
+
+  meta = with stdenv.lib; {
+    homepage = "https://github.com/saltstack/pytest-helpers-namespace";
+    description = "PyTest Helpers Namespace";
+    license = licenses.asl20;
+    maintainers = [ maintainers.kiwi ];
+  };
+}

pkgs/development/python-modules/python-xmp-toolkit/default.nix

@@ -0,0 +1,44 @@
+{ buildPythonPackage
+, exempi
+, fetchFromGitHub
+, mock
+, pythonOlder
+, pytz
+, stdenv
+}:
+
+buildPythonPackage rec {
+  pname = "python-xmp-toolkit";
+  version = "2.0.2";
+
+  # PyPi has version 2.0.1; the tests fail
+  # There are commits for a 2.0.2 release that was never published
+  # Not to github, not to PyPi
+  # This is the latest commit from Jun 29, 2017 (as of Mar 13, 2019)
+  # It includes the commits for the unreleased version 2.0.2 and more
+  # Tests pass with this version
+  src = fetchFromGitHub {
+    owner = "python-xmp-toolkit";
+    repo = "python-xmp-toolkit";
+    rev = "5692bdf8dac3581a0d5fb3c5aeb29be0ab6a54fc";
+    sha256 = "16bylcm183ilzp7mrpdzw0pzp6csv9v5v247914qsv2abg0hgl5y";
+  };
+
+  buildInputs = [ exempi ];
+
+  checkInputs = stdenv.lib.optionals (pythonOlder "3.3") [ mock ];
+
+  propagatedBuildInputs = [ pytz ];
+
+  postPatch = ''
+    substituteInPlace libxmp/exempi.py \
+      --replace "ctypes.util.find_library('exempi')" "'${exempi}/lib/libexempi${stdenv.hostPlatform.extensions.sharedLibrary}'"
+  '';
+
+  meta = with stdenv.lib; {
+    homepage = https://github.com/python-xmp-toolkit/python-xmp-toolkit;
+    description = "Python XMP Toolkit for working with metadata";
+    license = licenses.bsd3;
+    maintainers = [ maintainers.kiwi ];
+  };
+}

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

@@ -0,0 +1,53 @@
+{ gevent
+, buildPythonPackage
+, fetchFromGitHub
+, hostname
+, pytest
+, python
+, stdenv
+}:
+
+buildPythonPackage rec {
+  pname = "ruffus";
+  version = "2.8.1";
+
+  src = fetchFromGitHub {
+    owner = "cgat-developers";
+    repo = "${pname}";
+    rev = "v${version}";
+    sha256 = "1gyabqafq4s2sy0prh3k1m8859shzjmfxr7fimx10liflvki96a9";
+  };
+
+  propagatedBuildInputs = [ gevent ];
+
+  postPatch = ''
+    sed -i -e 's|/bin/bash|${stdenv.shell}|'          ruffus/test/Makefile
+    sed -i -e 's|\tpytest|\t${pytest}/bin/pytest|'    ruffus/test/Makefile
+    sed -i -e 's|\tpython|\t${python.interpreter}|'   ruffus/test/Makefile
+    sed -i -e 's|/usr/bin/env bash|${stdenv.shell}|'  ruffus/test/run_all_unit_tests.cmd
+    sed -i -e 's|python3|${python.interpreter}|'      ruffus/test/run_all_unit_tests3.cmd
+    sed -i -e 's|python %s|${python.interpreter} %s|' ruffus/test/test_drmaa_wrapper_run_job_locally.py
+  '';
+
+  makefile = "ruffus/test/Makefile";
+
+  checkInputs = [
+    gevent
+    hostname
+    pytest
+  ];
+
+  checkPhase = ''
+    export HOME=$TMPDIR
+    cd ruffus/test
+    make all PYTEST_OPTIONS="-q --disable-warnings"
+  '';
+
+  meta = with stdenv.lib; {
+    description = "Light-weight Python Computational Pipeline Management";
+    homepage = http://www.ruffus.org.uk;
+    license = licenses.mit;
+    maintainers = [ maintainers.kiwi ];
+  };
+}
+

pkgs/development/python-modules/unittest-data-provider/default.nix

@@ -0,0 +1,21 @@
+{ buildPythonPackage
+, lib
+, fetchPypi
+}:
+
+buildPythonPackage rec {
+  version = "1.0.1";
+  pname = "unittest-data-provider";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1gn2ka4vqpayx4cpbp8712agqjh3wdpk9smdxnp709ccc2v7zg46";
+  };
+
+  meta = with lib; {
+    description = "PHPUnit-like @dataprovider decorator for unittest";
+    homepage = https://github.com/yourlabs/unittest-data-provider;
+    license = licenses.mit;
+    maintainers = with maintainers; [ jonringer ];
+  };
+}