Merge master into staging-next

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

@@ -15,14 +15,14 @@
 
 buildPythonPackage rec {
   pname = "astropy";
-  version = "4.2";
+  version = "4.3.1";
   format = "pyproject";
 
   disabled = !isPy3k; # according to setup.py
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "2c194f8a429b8399de64a413a06881ea49f0525cabaa2d78fc132b9e970adc6a";
+    sha256 = "sha256-LTlRIjtOt/No/K2Mg0DSc3TF2OO2NaY2J1rNs481zVE=";
   };
 
   nativeBuildInputs = [ setuptools-scm astropy-helpers astropy-extension-helpers cython jinja2 ];

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

@@ -1,32 +1,19 @@
-{ lib, stdenv, buildPythonPackage, fetchFromGitHub, fetchpatch, pythonOlder
+{ lib, stdenv, buildPythonPackage, fetchFromGitHub, pythonOlder
 , pandas, shapely, fiona, pyproj
 , pytestCheckHook, Rtree }:
 
 buildPythonPackage rec {
   pname = "geopandas";
-  version = "0.9.0";
+  version = "0.10.2";
   disabled = pythonOlder "3.6";
 
   src = fetchFromGitHub {
     owner = "geopandas";
     repo = "geopandas";
     rev = "v${version}";
-    sha256 = "sha256-58X562OkRzZ4UTNMTwXW4U5czoa5tbSMBCcE90DqbaE=";
+    sha256 = "14azl3gppqn90k8h4hpjilsivj92k6p1jh7mdr6p4grbww1b7sdq";
   };
 
-  patches = [
-    (fetchpatch {
-      name = "skip-pandas-master-fillna-test.patch";
-      url = "https://github.com/geopandas/geopandas/pull/1878.patch";
-      sha256 = "1yw3i4dbhaq7f02n329b9y2cqxbwlz9db81mhgrfc7af3whwysdb";
-    })
-    (fetchpatch {
-      name = "fix-proj4strings-test.patch";
-      url = "https://github.com/geopandas/geopandas/pull/1958.patch";
-      sha256 = "0kzmpq5ry87yvhqr6gnh9p2606b06d3ynzjvw0hpp9fncczpc2yn";
-    })
-  ];
-
   propagatedBuildInputs = [
     pandas
     shapely
@@ -35,6 +22,10 @@ buildPythonPackage rec {
   ];
 
   doCheck = !stdenv.isDarwin;
+  preCheck = ''
+    # Wants to write test files into $HOME.
+    export HOME="$TMPDIR"
+  '';
   checkInputs = [ pytestCheckHook Rtree ];
   disabledTests = [
     # requires network access

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

@@ -7,14 +7,14 @@
 
 buildPythonPackage rec {
   pname = "identify";
-  version = "2.3.1";
+  version = "2.3.3";
 
 
   src = fetchFromGitHub {
     owner = "pre-commit";
     repo = pname;
     rev = "v${version}";
-    sha256 = "sha256-6sErta+YnaXe7lHR3kR7UAoWuaw8He7e3gCML9vWYj8=";
+    sha256 = "sha256-mGTSl/aOPQpqFq5dqVDia/7NofO9Tz0N8nYXU2Pyi0c=";
   };
 
   checkInputs = [

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

@@ -1,4 +1,3 @@
-
 { lib
 , aiohttp
 , async-timeout
@@ -10,14 +9,14 @@
 
 buildPythonPackage rec {
   pname = "millheater";
-  version = "0.8.0";
+  version = "0.8.1";
   disabled = pythonOlder "3.6";
 
   src = fetchFromGitHub {
     owner = "Danielhiversen";
     repo = "pymill";
     rev = version;
-    sha256 = "sha256-PL9qP6SKE8gsBUdfrPf9Fs+vU/lkpOjmkvq3cWw3Uak=";
+    sha256 = "0269lhb6y4c13n6krsl2b66ldvzkd26jlax7bbnkvag2iv7g6hzj";
   };
 
   propagatedBuildInputs = [
@@ -29,7 +28,9 @@ buildPythonPackage rec {
   # Project has no tests
   doCheck = false;
 
-  pythonImportsCheck = [ "mill" ];
+  pythonImportsCheck = [
+    "mill"
+  ];
 
   meta = with lib; {
     description = "Python library for Mill heater devices";

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

@@ -1,19 +1,24 @@
 { lib
+, aiofiles
+, aioftp
+, aiohttp
 , buildPythonPackage
 , fetchPypi
-, tqdm
-, aiohttp
-, pytest
-, setuptools-scm
+, pytest-asyncio
 , pytest-localserver
 , pytest-socket
-, pytest-asyncio
-, aioftp
+, pytestCheckHook
+, pythonOlder
+, setuptools-scm
+, tqdm
 }:
 
 buildPythonPackage rec {
   pname = "parfive";
   version = "1.5.0";
+  format = "setuptools";
+
+  disabled = pythonOlder "3.7";
 
   src = fetchPypi {
     inherit pname version;
@@ -25,27 +30,34 @@ buildPythonPackage rec {
   ];
 
   propagatedBuildInputs = [
-    tqdm
-    aiohttp
     aioftp
+    aiohttp
+    tqdm
   ];
 
   checkInputs = [
-    pytest
+    aiofiles
+    pytest-asyncio
     pytest-localserver
     pytest-socket
-    pytest-asyncio
+    pytestCheckHook
   ];
 
-  checkPhase = ''
-    # these two tests require network connection
-    pytest parfive -k "not test_ftp and not test_ftp_http"
-  '';
+  disabledTests = [
+    # Requires network access
+    "test_ftp"
+    "test_ftp_pasv_command"
+    "test_ftp_http"
+  ];
+
+  pythonImportsCheck = [
+    "parfive"
+  ];
 
   meta = with lib; {
     description = "A HTTP and FTP parallel file downloader";
     homepage = "https://parfive.readthedocs.io/";
     license = licenses.mit;
-    maintainers = [ maintainers.costrouc ];
+    maintainers = with maintainers; [ costrouc ];
   };
 }

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

@@ -2,6 +2,7 @@
 , buildPythonPackage
 , fetchPypi
 , isPy3k
+, setuptools-scm
 , liberfa
 , packaging
 , numpy
@@ -10,17 +11,25 @@
 buildPythonPackage rec {
   pname = "pyerfa";
   format = "pyproject";
-  version = "1.7.1.1";
+  version = "2.0.0";
 
   doCheck = false;
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "09i2qcsvxd3q04a5yaf6fwzg79paaslpksinan9d8smj7viql15i";
+    sha256 = "sha256-+QQjHhpXD5REDgYUB5lZCJUQf5QoR7UqdTzoHJYJFi0=";
   };
 
-  nativeBuildInputs = [ packaging ];
-  propagatedBuildInputs = [ liberfa numpy ];
+  nativeBuildInputs = [
+    packaging
+    setuptools-scm
+  ];
+
+  propagatedBuildInputs = [
+    liberfa
+    numpy
+  ];
+
   preBuild = ''
     export PYERFA_USE_SYSTEM_LIBERFA=1
   '';

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

@@ -17,7 +17,7 @@
 buildPythonPackage rec {
   pname = "pytest-astropy";
   version = "0.9.0";
-  disabled = pythonOlder "3.6";
+  disabled = pythonOlder "3.7";
 
   src = fetchPypi {
     inherit pname version;
@@ -43,11 +43,8 @@ buildPythonPackage rec {
     pytest-remotedata
   ];
 
-  # pytest-astropy is a meta package and has no tests
-  #doCheck = false;
-  checkPhase = ''
-    # 'doCheck = false;' still invokes the pytestCheckPhase which makes the build fail
-  '';
+  # pytest-astropy is a meta package that only propagates requirements
+  doCheck = false;
 
   meta = with lib; {
     description = "Meta-package containing dependencies for testing";

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

@@ -1,6 +1,7 @@
 { lib
 , fetchPypi
 , buildPythonPackage
+, setuptools-scm
 , astropy
 , pytestCheckHook
 , pytest-doctestplus
@@ -17,6 +18,10 @@ buildPythonPackage rec {
     sha256 = "e34902d91713ccab9f450b9d3e82317e292cf46a30bd42f9ad3c9a0519fcddcd";
   };
 
+  nativeBuildInputs = [
+    setuptools-scm
+  ];
+
   propagatedBuildInputs = [ astropy ];
 
   checkInputs = [ pytestCheckHook pytest-doctestplus scipy ];

pkgs/development/python-modules/subprocess-tee/default.nix

@@ -24,6 +24,11 @@ buildPythonPackage rec {
     enrich
   ];
 
+  disabledTests = [
+    # cyclic dependency on `molecule` (see https://github.com/pycontribs/subprocess-tee/issues/50)
+    "test_molecule"
+  ];
+
   pythonImportsCheck = [
     "subprocess_tee"
   ];

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

@@ -31,12 +31,12 @@
 
 buildPythonPackage rec {
   pname = "sunpy";
-  version = "3.0.2";
+  version = "3.1.0";
   disabled = pythonOlder "3.6";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "5dcd2c5cbf2f419da00abde00798d067b515c2f082ce63f4fbe1de47682c1c41";
+    sha256 = "sha256-0DF+/lQpsQKO5omBKJAe3gBjQ6QQb50IdRSacIRL/JA=";
   };
 
   nativeBuildInputs = [
@@ -86,6 +86,20 @@ buildPythonPackage rec {
   disabledTestPaths = [
     "sunpy/io/special/asdf/schemas/sunpy.org/sunpy/coordinates/frames/helioprojective-1.0.0.yaml"
     "sunpy/io/special/asdf/schemas/sunpy.org/sunpy/coordinates/frames/heliocentric-1.0.0.yaml"
+    # requires mpl-animators package
+    "sunpy/map/tests/test_compositemap.py"
+    "sunpy/map/tests/test_mapbase.py"
+    "sunpy/map/tests/test_mapsequence.py"
+    "sunpy/map/tests/test_plotting.py"
+    "sunpy/map/tests/test_reproject_to.py"
+    "sunpy/net/tests/test_helioviewer.py"
+    "sunpy/timeseries/tests/test_timeseriesbase.py"
+    "sunpy/visualization/animator/tests/test_basefuncanimator.py"
+    "sunpy/visualization/animator/tests/test_mapsequenceanimator.py"
+    "sunpy/visualization/animator/tests/test_wcs.py"
+    "sunpy/visualization/colormaps/tests/test_cm.py"
+    # requires cdflib package
+    "sunpy/timeseries/tests/test_timeseries_factory.py"
   ];
 
   pytestFlagsArray = [

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

@@ -23,6 +23,11 @@ buildPythonPackage rec {
   };
 
   checkInputs = [ pytestCheckHook numpy scipy ];
+  disabledTests = [
+    # accepts a limited set of cpu models based on project
+    # developers' hardware
+    "test_architecture"
+  ];
 
   meta = with lib; {
     homepage = "https://github.com/joblib/threadpoolctl";

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

@@ -1,10 +1,13 @@
-{ lib, buildPythonPackage, fetchFromGitHub
+{ lib
+, buildPythonPackage
+, fetchFromGitHub
 , packaging
-, fetchurl, python }:
+, python
+}:
 
 buildPythonPackage rec {
   pname = "vcver";
-  version = "0.2.10";
+  version = "0.2.12";
 
   src = fetchFromGitHub {
     owner = "toumorokoshi";