Merge staging-next into staging

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

@@ -11,14 +11,14 @@
 , pillow
 , scikitimage
 , shapely
+, pytest
+, pytest-astropy
 }:
 
 buildPythonPackage rec {
   pname = "aplpy";
   version = "2.0.3";
 
-  doCheck = false; # tests require pytest-astropy
-
   src = fetchPypi {
     pname = "APLpy";
     inherit version;
@@ -28,7 +28,6 @@ buildPythonPackage rec {
   propagatedBuildInputs = [
     numpy
     astropy
-    astropy-helpers
     matplotlib
     reproject
     pyavm
@@ -38,11 +37,21 @@ buildPythonPackage rec {
     shapely
   ];
 
+  nativeBuildInputs = [ astropy-helpers ];
+
+  checkInputs = [ pytest pytest-astropy ];
+
   # Disable automatic update of the astropy-helper module
   postPatch = ''
     substituteInPlace setup.cfg --replace "auto_use = True" "auto_use = False"
   '';
 
+  # Tests must be run in the build directory
+  checkPhase = ''
+    cd build/lib
+    pytest
+  '';
+
   meta = with lib; {
     description = "The Astronomical Plotting Library in Python";
     homepage = http://aplpy.github.io;

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

@@ -3,7 +3,10 @@
 , buildPythonPackage
 , isPy3k
 , numpy
-, pytest }:
+, pytest
+, pytest-astropy
+, astropy-helpers
+}:
 
 buildPythonPackage rec {
   pname = "astropy";
@@ -11,14 +14,30 @@ buildPythonPackage rec {
 
   disabled = !isPy3k; # according to setup.py
 
-  doCheck = false; #Some tests are failing. More importantly setup.py hangs on completion. Needs fixing with a proper shellhook.
-
   src = fetchPypi {
     inherit pname version;
     sha256 = "706c0457789c78285e5464a5a336f5f0b058d646d60f4e5f5ba1f7d5bf424b28";
   };
 
-  propagatedBuildInputs = [ pytest numpy ]; # yes it really has pytest in install_requires
+  nativeBuildInputs = [ astropy-helpers ];
+
+  propagatedBuildInputs = [ numpy pytest ]; # yes it really has pytest in install_requires
+
+  checkInputs = [ pytest pytest-astropy ];
+
+  # Disable automatic update of the astropy-helper module
+  postPatch = ''
+    substituteInPlace setup.cfg --replace "auto_use = True" "auto_use = False"
+  '';
+
+  # Tests must be run from the build directory.  astropy/samp tests
+  # require a network connection, so we ignore them. For some reason
+  # pytest --ignore does not work, so we delete the tests instead.
+  checkPhase = ''
+    cd build/lib.*
+    rm -f astropy/samp/tests/*
+    pytest
+  '';
 
   meta = {
     description = "Astronomy/Astrophysics library for Python";

pkgs/development/python-modules/astroquery/conftest-astropy-3-fix.patch

@@ -0,0 +1,54 @@
+diff -ruN astroquery-0.3.9.orig/astroquery/conftest.py astroquery-0.3.9/astroquery/conftest.py
+--- astroquery-0.3.9.orig/astroquery/conftest.py	2018-11-27 14:51:16.000000000 +0100
++++ astroquery-0.3.9/astroquery/conftest.py	2019-07-23 18:19:17.000000000 +0200
+@@ -5,15 +5,20 @@
+ # by importing them here in conftest.py they are discoverable by py.test
+ # no matter how it is invoked within the source tree.
+ 
+-from astropy.tests.pytest_plugins import (PYTEST_HEADER_MODULES,
+-                                          enable_deprecations_as_exceptions,
+-                                          TESTED_VERSIONS)
++from astropy.version import version as astropy_version
+ 
+-try:
+-    packagename = os.path.basename(os.path.dirname(__file__))
+-    TESTED_VERSIONS[packagename] = version.version
+-except NameError:
+-    pass
++if astropy_version < '3.0':
++    # With older versions of Astropy, we actually need to import the pytest
++    # plugins themselves in order to make them discoverable by pytest.
++    from astropy.tests.pytest_plugins import *
++else:
++    # As of Astropy 3.0, the pytest plugins provided by Astropy are
++    # automatically made available when Astropy is installed. This means it's
++    # not necessary to import them here, but we still need to import global
++    # variables that are used for configuration.
++    from astropy.tests.plugins.display import PYTEST_HEADER_MODULES, TESTED_VERSIONS
++
++from astropy.tests.helper import enable_deprecations_as_exceptions
+ 
+ # Add astropy to test header information and remove unused packages.
+ # Pytest header customisation was introduced in astropy 1.0.
+@@ -36,12 +41,17 @@
+     # The warnings_to_ignore_by_pyver parameter was added in astropy 2.0
+     enable_deprecations_as_exceptions(modules_to_ignore_on_import=['requests'])
+ 
++# add '_testrun' to the version name so that the user-agent indicates that
++# it's being run in a test
++from . import version
++version.version += '_testrun'
++
++
+ # This is to figure out the affiliated package version, rather than
+ # using Astropy's
+-try:
+-    from .version import version
+-except ImportError:
+-    version = 'dev'
++from .version import version, astropy_helpers_version
++
+ 
+ packagename = os.path.basename(os.path.dirname(__file__))
+ TESTED_VERSIONS[packagename] = version
++TESTED_VERSIONS['astropy_helpers'] = astropy_helpers_version

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

@@ -6,21 +6,42 @@
 , keyring
 , beautifulsoup4
 , html5lib
+, pytest
+, pytest-astropy
+, astropy-helpers
 }:
 
 buildPythonPackage rec {
   pname = "astroquery";
   version = "0.3.9";
 
-  doCheck = false; # Tests require the pytest-astropy package
-
   src = fetchPypi {
     inherit pname version;
     sha256 = "0zw3xp2rfc6h2v569iqsyvzhfnzp7bfjb7jrj61is1hrqw1cqjrb";
   };
 
+  # Fix tests using conftest.py from HEAD in the upstream GitHub
+  # repository.
+  patches = [ ./conftest-astropy-3-fix.patch ];
+
   propagatedBuildInputs = [ astropy requests keyring beautifulsoup4 html5lib ];
 
+  nativeBuildInputs = [ astropy-helpers ];
+
+  checkInputs = [ pytest pytest-astropy ];
+
+  # Disable automatic update of the astropy-helper module
+  postPatch = ''
+    substituteInPlace setup.cfg --replace "auto_use = True" "auto_use = False"
+  '';
+
+  # Tests must be run in the build directory. The tests create files
+  # in $HOME/.astropy so we need to set HOME to $TMPDIR.
+  checkPhase = ''
+    cd build/lib
+    HOME=$TMPDIR pytest
+  '';
+
   meta = with pkgs.lib; {
     description = "Functions and classes to access online data resources";
     homepage = "https://astroquery.readthedocs.io/";

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

@@ -0,0 +1,40 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, uvicorn
+, starlette
+, pydantic
+, python
+, isPy3k
+, which
+}:
+
+buildPythonPackage rec {
+  pname = "fastapi";
+  version = "0.33.0";
+  disabled = !isPy3k;
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1mc8ljfk6xyn2cq725s8hgapp62z5mylzw9akvkhwwz3bh8m5a7f";
+  };
+
+  propagatedBuildInputs = [
+    uvicorn
+    starlette
+    pydantic
+  ];
+
+  patches = [ ./setup.py.patch ];
+
+  checkPhase = ''
+    ${python.interpreter} -c "from fastapi import FastAPI; app = FastAPI()"
+  '';
+
+  meta = with lib; {
+    homepage = "https://github.com/tiangolo/fastapi";
+    description = "FastAPI framework, high performance, easy to learn, fast to code, ready for production";
+    license = licenses.mit;
+    maintainers = with maintainers; [ wd15 ];
+  };
+}

pkgs/development/python-modules/fastapi/setup.py.patch

@@ -0,0 +1,13 @@
+diff --git a/setup.py b/setup.py
+index ccc3d2b..77ce446 100644
+--- a/setup.py
++++ b/setup.py
+@@ -10,7 +10,7 @@ package_data = \
+ {'': ['*']}
+ 
+ install_requires = \
+-['starlette >=0.11.1,<=0.12.0', 'pydantic >=0.30,<=0.30.0']
++['starlette >=0.11.1', 'pydantic >=0.30']
+ 
+ extras_require = \
+ {'all': ['requests',

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

@@ -0,0 +1,51 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, ujson
+, email_validator
+, typing-extensions
+, python
+, isPy3k
+}:
+
+buildPythonPackage rec {
+  pname = "pydantic";
+  version = "0.31";
+  disabled = !isPy3k;
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "0x9xc5hpyrlf05dc4bx9f7v51fahxcahkvh0ij8ibay15nwli53d";
+  };
+
+  propagatedBuildInputs = [
+    ujson
+    email_validator
+    typing-extensions
+  ];
+
+  checkPhase = ''
+    ${python.interpreter} -c """
+from datetime import datetime
+from typing import List
+from pydantic import BaseModel
+
+class User(BaseModel):
+    id: int
+    name = 'John Doe'
+    signup_ts: datetime = None
+    friends: List[int] = []
+
+external_data = {'id': '123', 'signup_ts': '2017-06-01 12:22', 'friends': [1, '2', b'3']}
+user = User(**external_data)
+assert user.id is "123"
+"""
+  '';
+
+  meta = with lib; {
+    homepage = "https://github.com/samuelcolvin/pydantic";
+    description = "Data validation and settings management using Python type hinting";
+    license = licenses.mit;
+    maintainers = with maintainers; [ wd15 ];
+  };
+}

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

@@ -1,18 +1,20 @@
 { lib
 , buildPythonPackage
 , fetchPypi
+, fetchpatch
 , pyparsing
 , numpy
 , cython
 , astropy
+, astropy-helpers
+, pytest
+, pytest-astropy
 }:
 
 buildPythonPackage rec {
   pname = "pyregion";
   version = "2.0";
 
-  doCheck = false; # tests require pytest-astropy
-
   src = fetchPypi {
     inherit pname version;
     sha256 = "a8ac5f764b53ec332f6bc43f6f2193ca13e8b7d5a3fb2e20ced6b2ea42a9d094";
@@ -25,6 +27,30 @@ buildPythonPackage rec {
     astropy
   ];
 
+  # Upstream patch needed for the test to pass
+  patches = [
+    (fetchpatch {
+      name = "conftest-astropy-3-fix.patch";
+      url = "https://github.com/astropy/pyregion/pull/136.patch";
+      sha256 = "13yxjxiqnhjy9gh24hvv6pnwx7qic2mcx3ccr1igjrc3f881d59m";
+	  })
+	];
+
+  nativeBuildInputs = [ astropy-helpers ];
+
+  checkInputs = [ pytest pytest-astropy ];
+
+  # Disable automatic update of the astropy-helper module
+  postPatch = ''
+    substituteInPlace setup.cfg --replace "auto_use = True" "auto_use = False"
+  '';
+
+  # Tests must be run in the build directory
+  checkPhase = ''
+    cd build/lib.*
+    pytest
+  '';
+
   meta = with lib; {
     description = "Python parser for ds9 region files";
     homepage = https://github.com/astropy/pyregion;

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

@@ -22,14 +22,10 @@ buildPythonPackage rec {
     pytest
   ];
 
-  checkInputs = [
-    pytest
-    astropy
-  ];
-
-  checkPhase = ''
-    pytest
-  '';
+  # The tests requires astropy, which itself requires
+  # pytest-arraydiff. This causes an infinite recursion if the tests
+  # are enabled.
+  doCheck = false;
 
   meta = with lib; {
     description = "Pytest plugin to help with comparing array output from tests";

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

@@ -1,14 +1,17 @@
 { lib
 , fetchPypi
 , buildPythonPackage
-, astropy }:
+, astropy
+, pytest
+, pytest-astropy
+, astropy-helpers
+, scipy
+}:
 
 buildPythonPackage rec {
   pname = "radio_beam";
   version = "0.3.1";
 
-  doCheck = false; # the tests requires several pytest plugins that are not in nixpkgs
-
   src = fetchPypi {
     inherit pname version;
     sha256 = "1wgd9dyz3pcc9ighkclb6qfyshwbg35s57lz6k62jhcxpvp8r5zb";
@@ -16,6 +19,21 @@ buildPythonPackage rec {
 
   propagatedBuildInputs = [ astropy ];
 
+  nativeBuildInputs = [ astropy-helpers ];
+
+  # Disable automatic update of the astropy-helper module
+  postPatch = ''
+    substituteInPlace setup.cfg --replace "auto_use = True" "auto_use = False"
+  '';
+
+  checkInputs = [ pytest pytest-astropy scipy ];
+
+  # Tests must be run in the build directory
+  checkPhase = ''
+    cd build/lib
+    pytest
+  '';
+
   meta = {
     description = "Tools for Beam IO and Manipulation";
     homepage = http://radio-astro-tools.github.io;

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

@@ -0,0 +1,24 @@
+{ stdenv, fetchPypi, buildPythonPackage, click, redis }:
+
+buildPythonPackage rec {
+  pname = "rq";
+  version = "1.1.0";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1fs03g1n1l8k03zwhkhckhsrnnsm3645sqby2nwh5gfij2kcc9sg";
+  };
+
+  # test require a running redis rerver, which is something we can't do yet
+  doCheck = false;
+
+  propagatedBuildInputs = [ click redis ];
+
+  meta = with stdenv.lib; {
+    description = "A simple, lightweight library for creating background jobs, and processing them";
+    homepage = "https://github.com/nvie/rq/";
+    maintainers = with maintainers; [ mrmebelman ];
+    license = licenses.bsd2;
+  };
+}
+

pkgs/development/python-modules/simple-salesforce/default.nix

@@ -0,0 +1,51 @@
+{ lib
+, fetchFromGitHub
+, buildPythonPackage
+, requests
+, pyopenssl
+, cryptography
+, idna
+, mock
+, isPy27
+, nose
+, pytz
+, responses
+}:
+
+buildPythonPackage rec {
+  pname = "simple-salesforce";
+  version = "0.74.3";
+
+  src = fetchFromGitHub {
+    owner = pname;
+    repo = pname;
+    rev = "v${version}";
+    sha256 = "1n960xgrnmv20l31nm0im7pb4nfa83bmx4x4clqrh2jkpzq3ric0";
+  };
+
+  propagatedBuildInputs = [
+    requests
+    pyopenssl
+    cryptography
+    idna
+  ];
+
+  checkInputs = [
+    nose
+    pytz
+    responses
+  ] ++ lib.optionals isPy27 [ mock ];
+
+  postPatch = ''
+    substituteInPlace setup.py \
+      --replace "mock==1.0.1" "mock"
+  '';
+
+  meta = with lib; {
+    description = "A very simple Salesforce.com REST API client for Python";
+    homepage = https://github.com/simple-salesforce/simple-salesforce;
+    license = licenses.asl20;
+    maintainers = with maintainers; [ costrouc ];
+  };
+
+}

pkgs/development/python-modules/spectral-cube/default.nix

@@ -3,20 +3,36 @@
 , buildPythonPackage
 , astropy
 , radio_beam
-, pytest }:
+, pytest
+, pytest-astropy
+, astropy-helpers
+}:
 
 buildPythonPackage rec {
   pname = "spectral-cube";
   version = "0.4.4";
 
-  doCheck = false; # the tests requires several pytest plugins that are not in nixpkgs
-
   src = fetchPypi {
     inherit pname version;
     sha256 = "9051ede204b1e25b6358b5e0e573b624ec0e208c24eb03a7ed4925b745c93b5e";
   };
 
-  propagatedBuildInputs = [ astropy radio_beam pytest ];
+  propagatedBuildInputs = [ astropy radio_beam ];
+
+  nativeBuildInputs = [ astropy-helpers ];
+
+  checkInputs = [ pytest pytest-astropy ];
+
+  # Disable automatic update of the astropy-helper module
+  postPatch = ''
+    substituteInPlace setup.cfg --replace "auto_use = True" "auto_use = False"
+  '';
+
+  # Tests must be run in the build directory
+  checkPhase = ''
+    cd build/lib
+    pytest
+  '';
 
   meta = {
     description = "Library for reading and analyzing astrophysical spectral data cubes";

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

@@ -0,0 +1,51 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, aiofiles
+, graphene
+, itsdangerous
+, jinja2
+, pyyaml
+, requests
+, ujson
+, pytest
+, python
+, uvicorn
+, isPy27
+}:
+
+buildPythonPackage rec {
+  pname = "starlette";
+  version = "0.12.4";
+  disabled = isPy27;
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1m7qf4g5dn7n36406zbqsag71nmwp2dz91yxpplm7h7wiw2xxw93";
+  };
+
+  propagatedBuildInputs = [
+    aiofiles
+    graphene
+    itsdangerous
+    jinja2
+    pyyaml
+    requests
+    ujson
+    uvicorn
+  ];
+
+  checkPhase = ''
+    ${python.interpreter} -c """
+from starlette.applications import Starlette
+app = Starlette(debug=True)
+"""
+  '';
+
+  meta = with lib; {
+    homepage = https://www.starlette.io/;
+    description = "The little ASGI framework that shines";
+    license = licenses.bsd3;
+    maintainers = with maintainers; [ wd15 ];
+  };
+}

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

@@ -0,0 +1,44 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, click
+, h11
+, httptools
+, uvloop
+, websockets
+, wsproto
+, isPy27
+}:
+
+buildPythonPackage rec {
+  pname = "uvicorn";
+  version = "0.8.4";
+  disabled = isPy27;
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1l8rfm30inx9pma893i7sby9h7y910k58841zqaajksn563b882k";
+  };
+
+  propagatedBuildInputs = [
+    click
+    h11
+    httptools
+    uvloop
+    websockets
+    wsproto
+  ];
+
+  checkPhase = ''
+    $out/bin/uvicorn --help
+  '';
+
+  patches = [ ./setup.patch ];
+
+  meta = with lib; {
+    homepage = https://www.uvicorn.org/;
+    description = "The lightning-fast ASGI server";
+    license = licenses.bsd3;
+    maintainers = with maintainers; [ wd15 ];
+  };
+}

pkgs/development/python-modules/uvicorn/setup.patch

@@ -0,0 +1,13 @@
+diff --git a/setup.py b/setup.py
+index 802cda4..561abf4 100755
+--- a/setup.py
++++ b/setup.py
+@@ -42,7 +42,7 @@ env_marker = (
+ 
+ requirements = [
+     "click==7.*",
+-    "h11==0.8.*",
++    "h11",
+     "websockets==7.*",
+     "httptools==0.0.13 ;" + env_marker,
+     "uvloop==0.12.* ;" + env_marker,