Merge master into staging-next

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

@@ -29,7 +29,9 @@ buildPythonPackage rec {
     cvxopt
     ecos
     multiprocess
+    numpy
     osqp
+    scipy
     scs
     six
   ];
@@ -39,11 +41,11 @@ buildPythonPackage rec {
     nosetests
   '';
 
-  meta = {
+  meta = with lib; {
     description = "A domain-specific language for modeling convex optimization problems in Python.";
     homepage = "https://www.cvxpy.org/";
     downloadPage = "https://github.com/cvxgrp/cvxpy/";
-    license = lib.licenses.asl20;
-    maintainers = with lib.maintainers; [ drewrisinger ];
+    license = licenses.asl20;
+    maintainers = with maintainers; [ drewrisinger ];
   };
 }

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

@@ -1,49 +1,52 @@
 { lib
 , buildPythonPackage
 , fetchFromGitHub
+, aiofiles
 , click
 , click-default-group
+, janus
 , jinja2
 , hupper
 , pint
 , pluggy
-, pytest
+, uvicorn
+# Check Inputs
+, pytestCheckHook
 , pytestrunner
 , pytest-asyncio
 , black
 , aiohttp
 , beautifulsoup4
-, uvicorn
 , asgiref
-, aiofiles
 }:
 
 buildPythonPackage rec {
   pname = "datasette";
-  version = "0.35";
+  version = "0.39";
 
   src = fetchFromGitHub {
     owner = "simonw";
     repo = "datasette";
     rev = version;
-    sha256 = "0v6af7agg27lapz1nbab07595v4hl2x5wm2f03drj81f7pm8y7hc";
+    sha256 = "07d46512bc9sdan9lv39sf1bwlf7vf1bfhcsm825vk7sv7g9kczd";
   };
 
   nativeBuildInputs = [ pytestrunner ];
 
   propagatedBuildInputs = [
+    aiofiles
     click
     click-default-group
+    janus
     jinja2
     hupper
     pint
     pluggy
     uvicorn
-    aiofiles
   ];
 
   checkInputs = [
-    pytest
+    pytestCheckHook
     pytest-asyncio
     aiohttp
     beautifulsoup4
@@ -53,24 +56,32 @@ buildPythonPackage rec {
 
   postConfigure = ''
     substituteInPlace setup.py \
-      --replace "click-default-group==1.2" "click-default-group" \
-      --replace "Sanic==0.7.0" "Sanic" \
-      --replace "hupper==1.0" "hupper" \
-      --replace "pint~=0.8.1" "pint" \
-      --replace "pluggy~=0.12.0" "pint" \
-      --replace "Jinja2==2.10.1" "Jinja2" \
-      --replace "uvicorn~=0.8.4" "uvicorn"
+      --replace "click~=7.1.1" "click" \
+      --replace "click-default-group~=1.2.2" "click-default-group" \
+      --replace "Jinja2~=2.10.3" "Jinja2" \
+      --replace "hupper~=1.9" "hupper" \
+      --replace "pint~=0.9" "pint" \
+      --replace "pluggy~=0.13.0" "pint" \
+      --replace "uvicorn~=0.11" "uvicorn" \
+      --replace "aiofiles~=0.4.0" "aiofiles" \
+      --replace "janus~=0.4.0" "janus" \
+      --replace "PyYAML~=5.3" "PyYAML"
   '';
 
   # many tests require network access
   # test_black fails on darwin
-  checkPhase = ''
-    pytest --ignore tests/test_api.py \
-           --ignore tests/test_csv.py \
-           --ignore tests/test_html.py \
-           --ignore tests/test_black.py \
-           -k 'not facet'
-  '';
+  dontUseSetuptoolsCheck = true;
+  pytestFlagsArray = [
+    "--ignore=tests/test_api.py"
+    "--ignore=tests/test_csv.py"
+    "--ignore=tests/test_html.py"
+    "--ignore=tests/test_docs.py"
+    "--ignore=tests/test_black.py"
+  ];
+  disabledTests = [
+    "facet"
+    "_invalid_database" # checks error message when connecting to invalid database
+  ];
 
   meta = with lib; {
     description = "An instant JSON API for your SQLite databases";

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

@@ -18,9 +18,7 @@ buildPythonPackage rec {
     sha256 = "0bkj1xfp6mnvk1i9hl5awsmwi07q6iwwsjznd7kvrx5m19i6dbnx";
   };
 
-  nativeBuildInputs = [
-    pytestCheckHook
-  ] ++ lib.optional isPy27 mock;
+  nativeBuildInputs = lib.optional isPy27 mock;
 
   propagatedBuildInputs = [
     paramiko
@@ -29,12 +27,15 @@ buildPythonPackage rec {
     websocket_client
   ] ++ lib.optional isPy27 backports_ssl_match_hostname;
 
+  checkInputs = [
+    pytestCheckHook
+  ];
+
   pytestFlagsArray = [ "tests/unit" ];
   # Deselect socket tests on Darwin because it hits the path length limit for a Unix domain socket
   disabledTests = lib.optionals stdenv.isDarwin [ "stream_response" "socket_file" ];
 
-  # skip setuptoolsCheckPhase
-  doCheck = false;
+  dontUseSetuptoolsCheck = true;
 
   meta = with lib; {
     description = "An API client for docker written in Python";

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

@@ -4,10 +4,9 @@
 , cmake
 , future
 , numpy
-  # check inputs
 , scipy
+# check inputs
 , pytestCheckHook
-, mkl
 }:
 
 buildPythonPackage rec {
@@ -23,16 +22,15 @@ buildPythonPackage rec {
   dontUseCmakeConfigure = true;
 
   propagatedBuildInputs = [
-    numpy
     future
+    numpy
+    scipy
   ];
 
-  checkInputs = [ scipy pytestCheckHook mkl ];
   pythonImportsCheck = [ "osqp" ];
-  dontUseSetuptoolsCheck = true;  # running setup.py fails if false
-  preCheck = ''
-    export LD_LIBRARY_PATH=${lib.strings.makeLibraryPath [ mkl ]}:$LD_LIBRARY_PATH;
-  '';
+  checkInputs = [ pytestCheckHook ];
+  dontUseSetuptoolsCheck = true;  # don't run checks twice
+  disabledTests = [ "mkl_" ];
 
   meta = with lib; {
     description = "The Operator Splitting QP Solver";
@@ -44,8 +42,8 @@ buildPythonPackage rec {
       where x in R^n is the optimization variable
     '';
     homepage = "https://osqp.org/";
-    downloadPage = "https://github.com/oxfordcontrol/osqp";
+    downloadPage = "https://github.com/oxfordcontrol/osqp-python/releases";
     license = licenses.asl20;
-    maintainers = with lib.maintainers; [ drewrisinger ];
+    maintainers = with maintainers; [ drewrisinger ];
   };
 }

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

@@ -2,20 +2,40 @@
 , buildPythonPackage
 , fetchPypi
 , isPy27
+, pythonOlder
 , funcsigs
+, setuptools_scm
+# Check Inputs
+, pytestCheckHook
+, numpy
+, matplotlib
+, uncertainties
 }:
 
 buildPythonPackage rec {
   pname = "pint";
-  version = "0.9";
+  version = "0.11";
 
   src = fetchPypi {
     inherit version;
     pname = "Pint";
-    sha256 = "32d8a9a9d63f4f81194c0014b3b742679dce81a26d45127d9810a68a561fe4e2";
+    sha256 = "0kfgnmcs6z9ndhzvwg2xzhpwxgyyagdsdz5dns1jy40fa1q113rh";
   };
 
-  propagatedBuildInputs = lib.optional isPy27 funcsigs;
+  disabled = pythonOlder "3.6";
+
+  propagatedBuildInputs = [
+    setuptools_scm
+  ] ++ lib.optional isPy27 funcsigs;
+
+  # Test suite explicitly requires pytest
+  checkInputs = [
+    pytestCheckHook
+    numpy
+    matplotlib
+    uncertainties
+  ];
+  dontUseSetuptoolsCheck = true;
 
   meta = with lib; {
     description = "Physical quantities module";

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

@@ -1,22 +1,35 @@
-{ stdenv, fetchFromGitHub
-, buildPythonPackage, python-jose, pyjwt, requests, deprecated, httpretty }:
+{ stdenv
+, buildPythonPackage
+, cryptography
+, deprecated
+, fetchFromGitHub
+, httpretty
+, isPy3k
+, parameterized
+, pyjwt
+, pytestCheckHook
+, requests }:
 
 buildPythonPackage rec {
   pname = "PyGithub";
-  version = "1.45";
+  version = "1.47";
+  disabled = !isPy3k;
 
   src = fetchFromGitHub {
     owner = "PyGithub";
     repo = "PyGithub";
     rev = "v${version}";
-    sha256 = "1aiyqwdxpcr7yzz7aqmmjn1g2ajs5bpbln4sax5zw19dqi6qgp9z";
+    sha256 = "0zvp1gib2lryw698vxkbdv40n3lsmdlhwp7vdcg41dqqa5nfryhn";
   };
 
-  propagatedBuildInputs = [ python-jose pyjwt requests deprecated httpretty ];
+  checkInputs = [ httpretty parameterized pytestCheckHook ];
+  propagatedBuildInputs = [ cryptography deprecated pyjwt requests ];
+
+  # Test suite makes REST calls against github.com
   doCheck = false;
 
   meta = with stdenv.lib; {
-    homepage = https://github.com/PyGithub/PyGithub;
+    homepage = "https://github.com/PyGithub/PyGithub";
     description = "A Python (2 and 3) library to access the GitHub API v3";
     platforms = platforms.all;
     license = licenses.gpl3;

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

@@ -6,16 +6,17 @@
 , libuv
 , psutil
 , isPy27
-, pythonAtLeast
 , CoreServices
 , ApplicationServices
+# Check Inputs
+, pytestCheckHook
+# , pytest-asyncio
 }:
 
 buildPythonPackage rec {
   pname = "uvloop";
   version = "0.14.0";
-  # python 3.8 hangs on tests, assuming it's subtly broken with race condition
-  disabled = isPy27 || pythonAtLeast "3.8";
+  disabled = isPy27;
 
   src = fetchPypi {
     inherit pname version;
@@ -28,20 +29,44 @@ buildPythonPackage rec {
     libuv
   ] ++ lib.optionals stdenv.isDarwin [ CoreServices ApplicationServices ];
 
-  postPatch = ''
-    # Removing code linting tests, which we don't care about
-    rm tests/test_sourcecode.py
-  '';
+  pythonImportsCheck = [
+    "uvloop"
+    "uvloop.loop"
+  ];
 
-  checkInputs = [ pyopenssl psutil ];
+  dontUseSetuptoolsCheck = true;
+  checkInputs = [ pytestCheckHook pyopenssl psutil ];
+
+  pytestFlagsArray = [
+    # from pytest.ini, these are NECESSARY to prevent failures
+    "--capture=no"
+    "--assert=plain"
+    "--tb=native"
+    # ignore code linting tests
+    "--ignore=tests/test_sourcecode.py"
+  ];
+
+  disabledTests = [
+    "test_sock_cancel_add_reader_race"  # asyncio version of test is supposed to be skipped but skip doesn't happen. uvloop version runs fine
+  ];
+
+  # force using installed/compiled uvloop vs source by moving tests to temp dir
+  preCheck = ''
+    export TEST_DIR=$(mktemp -d)
+    cp -r tests $TEST_DIR
+    pushd $TEST_DIR
+  '';
+  postCheck = ''
+    popd
+  '';
 
   # Some of the tests use localhost networking.
   __darwinAllowLocalNetworking = true;
 
   meta = with lib; {
     description = "Fast implementation of asyncio event loop on top of libuv";
-    homepage = https://github.com/MagicStack/uvloop;
+    homepage = "https://github.com/MagicStack/uvloop";
     license = licenses.mit;
-    maintainers = [ maintainers.costrouc ];
+    maintainers = with maintainers; [ costrouc ];
   };
 }