Merge staging-next into staging

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

@@ -0,0 +1,32 @@
+{ lib, isPy3k, fetchPypi, buildPythonPackage
+, atpublic }:
+
+buildPythonPackage rec {
+  pname = "aiosmtpd";
+  version = "1.2";
+  disabled = !isPy3k;
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1xdfk741pjmz1cm8dsi4n5vq4517i175rm94696m3f7kcgk7xsmp";
+  };
+
+  propagatedBuildInputs = [
+    atpublic
+  ];
+
+  # Tests need network access
+  doCheck = false;
+
+  meta = with lib; {
+    homepage = https://aiosmtpd.readthedocs.io/en/latest/;
+    description = "Asyncio based SMTP server";
+    longDescription = ''
+      This is a server for SMTP and related protocols, similar in utility to the
+      standard library's smtpd.py module, but rewritten to be based on asyncio for
+      Python 3.
+    '';
+    license = licenses.asl20;
+    maintainers = with maintainers; [ eadwu ];
+  };
+}

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

@@ -0,0 +1,38 @@
+{ lib, isPy3k, fetchPypi, fetchpatch, buildPythonPackage
+, uvloop, postgresql }:
+
+buildPythonPackage rec {
+  pname = "asyncpg";
+  version = "0.18.3";
+  disabled = !isPy3k;
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "0rrch478ww6ipmh3617sb2jzwsq4w7pjcck869p35zb0mk5fr9aq";
+  };
+
+  patches = [
+    (fetchpatch {
+      url = "https://github.com/MagicStack/asyncpg/commit/aaeb7076e5acb045880b46155014c0640624797e.patch";
+      sha256 = "0r6g6pvb39vzci8g67mv9rlrvavqvfz6vlv8988wv53bpz1mss3p";
+    })
+  ];
+
+  checkInputs = [
+    uvloop
+    postgresql
+  ];
+
+  meta = with lib; {
+    homepage = https://github.com/MagicStack/asyncpg;
+    description = "An asyncio PosgtreSQL driver";
+    longDescription = ''
+      Asyncpg is a database interface library designed specifically for
+      PostgreSQL and Python/asyncio. asyncpg is an efficient, clean
+      implementation of PostgreSQL server binary protocol for use with Python’s
+      asyncio framework.
+    '';
+    license = licenses.asl20;
+    maintainers = with maintainers; [ eadwu ];
+  };
+}

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

@@ -0,0 +1,38 @@
+{ lib, isPy3k, fetchPypi, buildPythonPackage
+, pytest }:
+
+buildPythonPackage rec {
+  pname = "atpublic";
+  version = "1.0";
+  disabled = !isPy3k;
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "0i3sbxkdlbb4560rrlmwwd5y4ps7k73lp4d8wnmd7ag9k426gjkx";
+  };
+
+  checkInputs = [
+    pytest
+  ];
+
+  checkPhase = ''
+    pytest --pyargs public
+  '';
+
+  meta = with lib; {
+    homepage = https://public.readthedocs.io/en/latest/;
+    description = "A decorator and function which populates a module's __all__ and globals";
+    longDescription = ''
+      This is a very simple decorator and function which populates a module's
+      __all__ and optionally the module globals.
+
+      This provides both a pure-Python implementation and a C implementation. It is
+      proposed that the C implementation be added to builtins_ for Python 3.6.
+
+      This proposal seems to have been rejected, for more information see
+      https://bugs.python.org/issue26632.
+    '';
+    license = licenses.asl20;
+    maintainers = with maintainers; [ eadwu ];
+  };
+}

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

@@ -0,0 +1,48 @@
+{ lib
+, fetchPypi
+, rPackages
+, rWrapper
+, buildPythonPackage
+, biopython
+, numpy
+, scipy
+, pandas
+, matplotlib
+, reportlab
+, pysam
+, future
+, pillow
+, pomegranate
+, pyfaidx
+}:
+
+buildPythonPackage rec {
+  pname = "CNVkit";
+  version = "0.9.6";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1hj8c98s538i0hg5mrz4bw4v07qmcl51rhxq611rj2nglnc9r25y";
+  };
+
+  propagatedBuildInputs = [
+    biopython
+    numpy
+    scipy
+    pandas
+    matplotlib
+    reportlab
+    pyfaidx
+    pysam
+    future
+    pillow
+    pomegranate
+  ];
+
+  meta = with lib; {
+    homepage = "https://cnvkit.readthedocs.io";
+    description = "A Python library and command-line software toolkit to infer and visualize copy number from high-throughput DNA sequencing data";
+    license = licenses.asl20;
+    maintainers = [ maintainers.jbedo ];
+  };
+}

pkgs/development/python-modules/django-csp/default.nix

@@ -0,0 +1,23 @@
+{ stdenv, fetchPypi, buildPythonPackage, django }:
+
+buildPythonPackage rec {
+  pname = "django-csp";
+  version = "3.5";
+
+  src = fetchPypi {
+    inherit version;
+    pname = "django_csp";
+    sha256 = "0ks4zszbjx5lyqlc34pjica8hfcjzw4i5m6pivvnyv8yf0vh4q04";
+  };
+
+  # too complicated to setup - needs a running django instance
+  doCheck = false;
+
+  propagatedBuildInputs = [ django ];
+
+  meta = with stdenv.lib; {
+    description = "Adds Content-Security-Policy headers to Django";
+    homepage = "https://github.com/mozilla/django-csp";
+    license = licenses.bsd3;
+  };
+}

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

@@ -0,0 +1,29 @@
+{ lib, fetchFromGitHub, buildPythonPackage
+, python, isPy3k }:
+
+buildPythonPackage rec {
+  pname = "emailthreads";
+  version = "0.1.0";
+  disabled = !isPy3k;
+
+  # pypi is missing files for tests
+  src = fetchFromGitHub {
+    owner = "emersion";
+    repo = "python-emailthreads";
+    rev = "v${version}";
+    sha256 = "17pfal8kbxhs025apkijqbkppw2lljca8x1cwcx49jv60h05c3cn";
+  };
+
+  PKGVER = version;
+
+  checkPhase = ''
+    ${python.interpreter} -m unittest discover test
+  '';
+
+  meta = with lib; {
+    homepage = https://github.com/emersion/python-emailthreads;
+    description = "Python library to parse and format email threads";
+    license = licenses.mit;
+    maintainers = with maintainers; [ eadwu ];
+  };
+}

pkgs/development/python-modules/flake8-polyfill/default.nix

@@ -0,0 +1,40 @@
+{ lib, fetchPypi, buildPythonPackage
+, flake8
+, mock, pep8, pytest }:
+
+buildPythonPackage rec {
+  pname = "flake8-polyfill";
+  version = "1.0.2";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1nlf1mkqw856vi6782qcglqhaacb23khk9wkcgn55npnjxshhjz4";
+  };
+
+  postPatch = ''
+    # Failed: [pytest] section in setup.cfg files is no longer supported, change to [tool:pytest] instead.
+    substituteInPlace setup.cfg \
+      --replace pytest 'tool:pytest'
+  '';
+
+  propagatedBuildInputs = [
+    flake8
+  ];
+
+  checkInputs = [
+    mock
+    pep8
+    pytest
+  ];
+
+  checkPhase = ''
+    pytest tests
+  '';
+
+  meta = with lib; {
+    homepage = https://gitlab.com/pycqa/flake8-polyfill;
+    description = "Polyfill package for Flake8 plugins";
+    license = licenses.mit;
+    maintainers = with maintainers; [ eadwu ];
+  };
+}

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

@@ -0,0 +1,25 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, jsonschema
+}:
+
+buildPythonPackage rec {
+  pname = "jsonmerge";
+  version = "1.6.1";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "03l2j1lrcwcp7af4x8agxnkib0ndybfrbhn2gi7mnk6gbxfw1aw3";
+  };
+
+  propagatedBuildInputs = [ jsonschema ];
+
+  meta = with lib; {
+    description = "Merge a series of JSON documents";
+    homepage = https://github.com/avian2/jsonmerge;
+    changelog = "https://github.com/avian2/jsonmerge/blob/jsonmerge-${version}/ChangeLog";
+    license = licenses.mit;
+    maintainers = with maintainers; [ emily ];
+  };
+}

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

@@ -1,28 +1,22 @@
-{ stdenv
-, buildPythonPackage
-, fetchFromGitHub
-, isPy3k
-, pkgs
-, urlgrabber
-, m2crypto
-, pyyaml
-, lxml
+{ stdenv, buildPythonPackage , fetchFromGitHub
+, bashInteractive , urlgrabber, m2crypto
 }:
 
-buildPythonPackage {
+buildPythonPackage rec {
   pname = "osc";
-  version = "0.163.0-40-gb4b1ec7";
-  disabled = isPy3k;    # urlgrabber doesn't support python-3.x
+  version = "0.165.4";
 
   src = fetchFromGitHub {
     owner = "openSUSE";
     repo = "osc";
-    rev = "b4b1ec7b64d4f9bb42f140754519221b810e232c";
-    sha256 = "01z1b15x9vzhd7j94f6n3g50h5br7lwz86akgic0wpp41zv37jad";
+    rev = version;
+    sha256 = "1f8q65wlgchzwzarwrv6a0p60gw0ykpf4d5s7cks835hyawgcbyl";
   };
 
-  buildInputs = [ pkgs.bashInteractive ]; # needed for bash-completion helper
-  propagatedBuildInputs = [ urlgrabber m2crypto pyyaml lxml ];
+  buildInputs = [ bashInteractive ]; # needed for bash-completion helper
+  propagatedBuildInputs = [ urlgrabber m2crypto ];
+
+  doCheck = false;
 
   postInstall = ''
     ln -s $out/bin/osc-wrapper.py $out/bin/osc

pkgs/development/python-modules/pep8-naming/default.nix

@@ -0,0 +1,23 @@
+{ lib, fetchPypi, buildPythonPackage
+, flake8-polyfill }:
+
+buildPythonPackage rec {
+  pname = "pep8-naming";
+  version = "0.8.2";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1aff4g3i2z08cx7z17nbxbf32ddrnvqlk16h6d8h9s9w5ymivjq1";
+  };
+
+  propagatedBuildInputs = [
+    flake8-polyfill
+  ];
+
+  meta = with lib; {
+    homepage = https://github.com/PyCQA/pep8-naming;
+    description = "Check PEP-8 naming conventions, plugin for flake8";
+    license = licenses.mit;
+    maintainers = with maintainers; [ eadwu ];
+  };
+}

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

@@ -0,0 +1,48 @@
+{ lib, isPy3k, fetchFromGitHub, buildPythonPackage
+, six, enum34, pyasn1, cryptography, singledispatch
+, fetchPypi
+, gpgme, flake8, pytest, pytestcov, pep8-naming, pytest-ordering }:
+
+buildPythonPackage rec {
+  pname = "pgpy";
+  version = "0.5.2";
+
+  src = fetchFromGitHub {
+    owner = "SecurityInnovation";
+    repo = "PGPy";
+    rev = version;
+    sha256 = "1v2b1dyq1sl48d2gw7vn4hv6sasd9ihpzzcq8yvxj9dgfak2y663";
+  };
+
+  propagatedBuildInputs = [
+    six
+    pyasn1
+    cryptography
+    singledispatch
+  ] ++ lib.optional (!isPy3k) enum34;
+
+  checkInputs = [
+    gpgme
+    flake8
+    pytest
+    pytestcov
+    pep8-naming
+    pytest-ordering
+  ];
+
+  checkPhase = ''
+    pytest
+  '';
+
+  meta = with lib; {
+    homepage = https://github.com/SecurityInnovation/PGPy;
+    description = "Pretty Good Privacy for Python 2 and 3";
+    longDescription = ''
+      PGPy is a Python (2 and 3) library for implementing Pretty Good Privacy
+      into Python programs, conforming to the OpenPGP specification per RFC
+      4880.
+    '';
+    license = licenses.bsd3;
+    maintainers = with maintainers; [ eadwu ];
+  };
+}

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

@@ -1,17 +1,17 @@
-{ stdenv, buildPythonPackage, fetchFromGitHub, numpy, scipy, cython, networkx, joblib, nose }:
+{ stdenv, buildPythonPackage, fetchFromGitHub, numpy, scipy, cython, networkx, joblib, nose, pyyaml }:
 
 buildPythonPackage rec {
   pname = "pomegranate";
-  version = "0.8.1";
-  
+  version = "0.11.0";
+
   src = fetchFromGitHub {
     repo = pname;
     owner = "jmschrei";
     rev = "v${version}";
-    sha256 = "085nka5bh88bxbd5vl1azyv9cfpp6grz2ngclc85f9kgccac1djr";
+    sha256 = "0gf7z343ag4g7pfccn1sdap3ihkaxrc9ca75awjhmsa2cyqs66df";
   };
 
-  propagatedBuildInputs = [ numpy scipy cython networkx joblib ];
+  propagatedBuildInputs = [ numpy scipy cython networkx joblib pyyaml ];
 
   checkInputs = [ nose ];
 
@@ -20,9 +20,5 @@ buildPythonPackage rec {
     homepage = https://github.com/jmschrei/pomegranate;
     license = licenses.mit;
     maintainers = with maintainers; [ rybern ];
-
-    # "pomegranate does not yet work with networkx 2.0"
-    # see https://github.com/jmschrei/pomegranate/issues/209
-    broken = true; 
   };
 }

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

@@ -0,0 +1,24 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, six
+}:
+
+buildPythonPackage rec {
+  pname = "pyfaidx";
+  version = "0.5.5.2";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1akc8hk8rlw7sv07bv1n2r471acvmxwc57gb69frjpcwggf2phls";
+  };
+
+  propagatedBuildInputs = [ six ];
+
+  meta = with lib; {
+    homepage = "https://github.com/mdshw5/pyfaidx";
+    description = "Python classes for indexing, retrieval, and in-place modification of FASTA files using a samtools compatible index";
+    license = licenses.bsd3;
+    maintainers = [ maintainers.jbedo ];
+  };
+}

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

@@ -2,28 +2,15 @@
 
 buildPythonPackage rec {
   pname = "pyslurm";
-  version = "18-08-3";
+  version = "19-05-0";
 
   src = fetchFromGitHub {
     repo = "pyslurm";
     owner = "PySlurm";
     rev = version;
-    sha256 = "1rymx106xa99wd4n44s7jw0w41spg39y1ji4fgn01yk7wjfrdrwg";
+    sha256 = "1lfb4q81y96syz5an1lzscfcvmfvlkf4cfl3i5zllw9r3gbarl2r";
   };
 
-  # Needed for patch below to apply
-  prePatch = ''
-    sed -i -e '/__max_slurm_hex_version__ = "0x1208/c__max_slurm_hex_version__ = "0x120804"' setup.py
-  '';
-
-  patches = [
-    # Implements a less strict slurm version check
-    (fetchpatch {
-      url = "https://github.com/PySlurm/pyslurm/commit/d3703f2d58b5177d29092fe1aae1f7a96da61765.diff";
-      sha256 = "1s41z9bhzhplgg08p1llc3i8zw20r1479s04y0l1vx0ak51b6w0k";
-    })
-  ];
-
   buildInputs = [ cython slurm ];
   setupPyBuildFlags = [ "--slurm-lib=${slurm}/lib" "--slurm-inc=${slurm.dev}/include" ];
 

pkgs/development/python-modules/pytest-ordering/default.nix

@@ -0,0 +1,31 @@
+{ lib, fetchFromGitHub, buildPythonPackage
+, pytest }:
+
+buildPythonPackage rec {
+  pname = "pytest-ordering";
+  version = "unstable-2019-06-19";
+
+  # Pypi lacks tests/
+  # Resolves PytestUnknownMarkWarning from pytest
+  src = fetchFromGitHub {
+    owner = "ftobia";
+    repo = pname;
+    rev = "492697ee26633cc31d329c1ceaa468375ee8ee9c";
+    sha256 = "1xim0kj5g37p1skgvp8gdylpx949krmx60w3pw6j1m1h7sakmddn";
+  };
+
+  checkInputs = [
+    pytest
+  ];
+
+  checkPhase = ''
+    pytest tests
+  '';
+
+  meta = with lib; {
+    homepage = https://github.com/ftobia/pytest-ordering;
+    description = "Pytest plugin to run your tests in a specific order";
+    license = licenses.mit;
+    maintainers = with maintainers; [ eadwu ];
+  };
+}

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

@@ -2,6 +2,7 @@
 , buildPythonPackage
 , isPy3k
 , fetchPypi
+, setuptools_scm
 , requests
 , lxml
 , beautifulsoup4
@@ -9,13 +10,13 @@
 
 buildPythonPackage rec {
   pname = "snscrape";
-  version = "0.2.0";
+  version = "0.3.0";
 
   disabled = !isPy3k;
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "02mlpzkvpl2mv30cknq6ngw02y7gj2614qikq25ncrpg5vb903d9";
+    sha256 = "1f3lyq06l8s4kcsmwbxcwcxnv6mvz9c3zj70np8vnx149p3zi983";
   };
 
   # There are no tests; make sure the executable works.
@@ -24,6 +25,7 @@ buildPythonPackage rec {
     snscrape --help
   '';
 
+  nativeBuildInputs = [ setuptools_scm ];
   propagatedBuildInputs = [ requests lxml beautifulsoup4 ];
 
   meta = with lib; {

pkgs/development/python-modules/sqlalchemy-utils/default.nix

@@ -0,0 +1,50 @@
+{ lib, fetchPypi, buildPythonPackage
+, six, sqlalchemy
+, mock, pytz, isort, flake8, jinja2, pg8000, pyodbc, pytest, pymysql, dateutil
+, docutils, flexmock, psycopg2, pygments }:
+
+buildPythonPackage rec {
+  pname = "sqlalchemy-utils";
+  version = "0.34.0";
+
+  src = fetchPypi {
+    inherit version;
+    pname = "SQLAlchemy-Utils";
+    sha256 = "0rlixs084isgxsvvpz96njqzikvg8x021sgjp4yj71jpd8blvg8f";
+  };
+
+  propagatedBuildInputs = [
+    six
+    sqlalchemy
+  ];
+
+  # Attempts to access localhost and there's also no database access
+  doCheck = false;
+  checkInputs = [
+    mock
+    pytz
+    isort
+    flake8
+    jinja2
+    pg8000
+    pyodbc
+    pytest
+    pymysql
+    dateutil
+    docutils
+    flexmock
+    psycopg2
+    pygments
+  ];
+
+  checkPhase = ''
+    pytest tests
+  '';
+
+  meta = with lib; {
+    homepage = https://github.com/kvesteri/sqlalchemy-utils;
+    description = "Various utility functions and datatypes for SQLAlchemy";
+    license = licenses.bsd3;
+    maintainers = with maintainers; [ eadwu ];
+  };
+}

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

@@ -1,17 +1,15 @@
-{ stdenv, buildPythonPackage, fetchPypi, pycurl, isPy3k }:
+{ stdenv, buildPythonPackage, fetchPypi, pycurl, six }:
 
 buildPythonPackage rec {
   pname = "urlgrabber";
-  version = "3.10.2";
-
-  disabled = isPy3k;
+  version = "4.0.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "0w1h7hlsq406bxfy2pn4i9bd003bwl0q9b7p03z3g6yl0d21ddq5";
+    sha256 = "0fazs574fgixd525cn2dh027f4qf0c0gbwcfyfkhc6fkblfa1ibr";
   };
 
-  propagatedBuildInputs = [ pycurl ];
+  propagatedBuildInputs = [ pycurl six ];
 
   meta = with stdenv.lib; {
     homepage = http://urlgrabber.baseurl.org;
@@ -20,4 +18,3 @@ buildPythonPackage rec {
     maintainers = with maintainers; [ qknight ];
   };
 }
-

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

@@ -1,37 +0,0 @@
-{ lib
-, buildPythonPackage
-, fetchPypi
-, beautifulsoup4
-, requests
-, python
-}:
-
-buildPythonPackage rec {
-  pname = "wikipedia";
-  version = "1.4.0";
-
-  src = fetchPypi {
-    inherit pname version;
-    sha256 = "db0fad1829fdd441b1852306e9856398204dc0786d2996dd2e0c8bb8e26133b2";
-  };
-
-  propagatedBuildInputs = [
-    beautifulsoup4
-    requests
-  ];
-
-  checkPhase = ''
-    runHook preCheck
-
-    ${python.interpreter} -m unittest discover tests/ '*test.py'
-
-    runHook postCheck
-  '';
-
-  meta = with lib; {
-    description = "Wikipedia API for Python";
-    homepage = https://github.com/goldsmith/Wikipedia;
-    license = licenses.mit;
-    maintainers = [ maintainers.worldofpeace ];
-  };
-}