Merge master into staging-next

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

@@ -1,14 +1,19 @@
-{ lib, buildPythonPackage, fetchPypi }:
+{ lib, buildPythonPackage, fetchPypi, python }:
 
 buildPythonPackage rec {
   pname = "bitarray";
-  version = "1.8.1";
+  version = "2.0.1";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "e02f79fba7a470d438eb39017d503498faaf760b17b6b46af1a9de12fd58d311";
+    sha256 = "sha256-7DpPbXEaee0jrqlUFjjTNT3D8IPyk6ExgLFLSC4+Ge8=";
   };
 
+  checkPhase = ''
+    cd $out
+    ${python.interpreter} -c 'import bitarray; bitarray.test()'
+  '';
+
   pythonImportsCheck = [ "bitarray" ];
 
   meta = with lib; {

pkgs/development/python-modules/dask-glm/default.nix

@@ -9,6 +9,7 @@
 , scipy
 , scikitlearn
 , pytest
+, setuptools-scm
 }:
 
 buildPythonPackage rec {
@@ -22,6 +23,7 @@ buildPythonPackage rec {
 
   nativeBuildInputs = [ setuptools-scm ];
   checkInputs = [ pytest ];
+  nativeBuildInputs = [ setuptools-scm ];
   propagatedBuildInputs = [ cloudpickle dask numpy toolz multipledispatch scipy scikitlearn ];
 
   checkPhase = ''

pkgs/development/python-modules/dask-ml/default.nix

@@ -13,6 +13,7 @@
 , multipledispatch
 , packaging
 , distributed
+, setuptools-scm
 }:
 
 buildPythonPackage rec {
@@ -38,6 +39,7 @@ buildPythonPackage rec {
     scipy
     six
     toolz
+    setuptools-scm
   ];
 
   # has non-standard build from source, and pypi doesn't include tests

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

@@ -1,6 +1,7 @@
 { lib
 , bokeh
 , buildPythonPackage
+, fetchpatch
 , fetchFromGitHub
 , fsspec
 , pytestCheckHook
@@ -42,7 +43,7 @@ buildPythonPackage rec {
     distributed
   ];
 
-  doCheck = false;
+  doCheck = true;
 
   checkInputs = [
     pytestCheckHook
@@ -52,6 +53,16 @@ buildPythonPackage rec {
 
   dontUseSetuptoolsCheck = true;
 
+  patches = [
+    # dask dataframe cannot be imported in sandboxed builds
+    # See https://github.com/dask/dask/pull/7601
+    (fetchpatch {
+      url = "https://github.com/dask/dask/commit/9ce5b0d258cecb3ef38fd844135ad1f7ac3cea5f.patch";
+      sha256 = "sha256-1EVRYwAdTSEEH9jp+UOnrijzezZN3iYR6q6ieYJM3kY=";
+      name = "fix-dask-dataframe-imports-in-sandbox.patch";
+    })
+  ];
+
   postPatch = ''
     # versioneer hack to set version of github package
     echo "def get_versions(): return {'dirty': False, 'error': None, 'full-revisionid': None, 'version': '${version}'}" > dask/_version.py
@@ -66,8 +77,13 @@ buildPythonPackage rec {
   disabledTests = [
     "test_annotation_pack_unpack"
     "test_annotations_blockwise_unpack"
+    # this test requires features of python3Packages.psutil that are
+    # blocked in sandboxed-builds
+    "test_auto_blocksize_csv"
   ];
 
+  pythonImportsCheck = [ "dask.dataframe" "dask" "dask.array" ];
+
   meta = with lib; {
     description = "Minimal task scheduling abstraction";
     homepage = "https://dask.org/";

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

@@ -5,34 +5,36 @@
 , pytestCheckHook
 , numpy
 , stdenv
+, aiohttp
+, pytest-vcr
+, requests
 }:
 
 buildPythonPackage rec {
   pname = "fsspec";
-  version = "0.8.3";
+  version = "2021.04.0";
   disabled = pythonOlder "3.5";
 
   src = fetchFromGitHub {
     owner = "intake";
     repo = "filesystem_spec";
     rev = version;
-    sha256 = "0mfy0wxjfwwnp5q2afhhfbampf0fk71wsv512pi9yvrkzzfi1hga";
+    sha256 = "sha256-9072kb1VEQ0xg9hB8yEzJMD2Ttd3UGjBmTuhE+Uya1k=";
   };
 
-  checkInputs = [
-    pytestCheckHook
-    numpy
-  ];
+  checkInputs = [ pytestCheckHook numpy pytest-vcr ];
+
+  __darwinAllowLocalNetworking = true;
+
+  propagatedBuildInputs = [ aiohttp requests ];
 
   disabledTests = [
     # Test assumes user name is part of $HOME
     # AssertionError: assert 'nixbld' in '/homeless-shelter/foo/bar'
     "test_strip_protocol_expanduser"
-    # flaky: works locally but fails on hydra
-    # as it uses the install dir for tests instead of a temp dir
-    # resolved in https://github.com/intake/filesystem_spec/issues/432 and
-    # can be enabled again from version 0.8.4
-    "test_pathobject"
+    # test accesses this remote ftp server:
+    # https://ftp.fau.de/debian-cd/current/amd64/log/success
+    "test_find"
   ] ++ lib.optionals (stdenv.isDarwin) [
     # works locally on APFS, fails on hydra with AssertionError comparing timestamps
     # darwin hydra builder uses HFS+ and has only one second timestamp resolution

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

@@ -0,0 +1,37 @@
+{ buildPythonPackage, fetchFromGitHub, lib, pytestCheckHook, google-auth
+, google-auth-oauthlib, requests, decorator, fsspec, ujson, aiohttp, crcmod
+, pytest-vcr, vcrpy }:
+
+buildPythonPackage rec {
+  pname = "gcsfs";
+  version = "2021.04.0";
+
+  # github sources needed for test data
+  src = fetchFromGitHub {
+    owner = "dask";
+    repo = pname;
+    rev = version;
+    sha256 = "sha256-OA43DaQue7R5d6SzfKThEQFEwJndjLfznu1LMubs5fs=";
+  };
+
+  propagatedBuildInputs = [
+    google-auth
+    google-auth-oauthlib
+    requests
+    decorator
+    fsspec
+    aiohttp
+    ujson
+    crcmod
+  ];
+
+  checkInputs = [ pytestCheckHook pytest-vcr vcrpy ];
+  pythonImportsCheck = [ "gcsfs" ];
+
+  meta = with lib; {
+    description = "Convenient Filesystem interface over GCS";
+    homepage = "https://github.com/dask/gcsfs";
+    license = licenses.bsd3;
+    maintainers = [ maintainers.nbren12 ];
+  };
+}

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

@@ -0,0 +1,27 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, pythonOlder
+}:
+
+buildPythonPackage rec {
+  pname = "nclib";
+  version = "1.0.0";
+  disabled = pythonOlder "3.5";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "0kf8x30lrwhijab586i54g70s3sxvm2945al48zj27grj0pagh7g";
+  };
+
+  # Project has no tests
+  doCheck = false;
+  pythonImportsCheck = [ "nclib" ];
+
+  meta = with lib; {
+    description = "Python module that provides netcat features";
+    homepage = "https://nclib.readthedocs.io/";
+    license = with licenses; [ mit ];
+    maintainers = with maintainers; [ fab ];
+  };
+}

pkgs/development/python-modules/sphinx-serve/default.nix

@@ -0,0 +1,25 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+}:
+
+buildPythonPackage rec {
+  pname = "sphinx-serve";
+  version = "1.0.1";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "8d90f6595114108500b1f935d3f4d07bf5192783c67ce83f944ef289099669c9";
+  };
+
+  doCheck = false; # No tests
+
+  pythonImportsCheck = [ "sphinx_serve" ];
+
+  meta = with lib; {
+    description = "Spawns a simple HTTP server to preview your sphinx documents";
+    homepage = "https://github.com/tlatsas/sphinx-serve";
+    maintainers = with maintainers; [ FlorianFranzen ];
+    license = licenses.mit;
+  };
+}

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

@@ -2,32 +2,22 @@
 , stdenv
 , buildPythonPackage
 , fetchPypi
-, fetchpatch
 , argh
 , pathtools
 , pyyaml
-, pytest-cov
 , pytestCheckHook
 , CoreServices
 }:
 
 buildPythonPackage rec {
   pname = "watchdog";
-  version = "2.0.2";
+  version = "2.0.3";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "sha256-Uy/t2ZPnVVRnH6o2zQTFgM7T+uCEJUp3mvu9iq8AVms=";
+    sha256 = "sha256-QojTqYQyTbSS5XqhaWZiOKJXjwr1oIFoVSZgj7n2vWE=";
   };
 
-  patches = [
-    (fetchpatch {
-      # Fix test flakiness on Apple Silicon, remove after upgrade to 2.0.6.
-      url = "https://github.com/gorakhargosh/watchdog/commit/331fd7c2c819663be39bc146e78ce67553f265fa.patch";
-      sha256 = "sha256-pLkZmbPN3qRNHs53OP0HIyDxqYCPPo6yOcBLD3aO2YE=";
-    })
-  ];
-
   buildInputs = lib.optionals stdenv.isDarwin [ CoreServices ];
 
   propagatedBuildInputs = [
@@ -37,10 +27,15 @@ buildPythonPackage rec {
   ];
 
   checkInputs = [
-    pytest-cov
     pytestCheckHook
   ];
 
+  postPatch = ''
+    substituteInPlace setup.cfg \
+      --replace "--cov=watchdog" "" \
+      --replace "--cov-report=term-missing" ""
+  '';
+
   pythonImportsCheck = [ "watchdog" ];
 
   meta = with lib; {