Merge remote-tracking branch 'origin/release-21.05' into staging-next-21.05

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

@@ -15,7 +15,7 @@ buildPythonPackage rec {
 
   checkPhase = ''
     pushd tests
-    py.test ./.
+    py.test -Wignore::DeprecationWarning ./.
     popd
   '';
 

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

@@ -0,0 +1,19 @@
+{ lib, buildPythonPackage, fetchPypi, locale, pytestCheckHook, click, sortedcontainers, pyyaml }:
+
+buildPythonPackage rec {
+  pname = "cock";
+  version = "0.8.0";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1gwaklvwlyvhz2c07hdmhbnqqmpybssxzzr0399dpjk7dgdqgam3";
+  };
+
+  propagatedBuildInputs = [ click sortedcontainers pyyaml ];
+
+  meta = with lib; {
+    homepage = "https://github.com/pohmelie/cock";
+    description = "Configuration file with click";
+    license = licenses.mit;
+  };
+}

pkgs/development/python-modules/cocotb-bus/default.nix

@@ -0,0 +1,35 @@
+{ lib
+, stdenv
+, buildPythonPackage
+, fetchPypi
+}:
+
+buildPythonPackage rec {
+  pname = "cocotb-bus";
+  version = "0.1.1";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "cc9b0bb00c95061a67f650caf96e3a294bb74ef437124dea456dd9e2a9431854";
+  };
+
+  postPatch = ''
+    # remove circular dependency cocotb from setup.py
+    substituteInPlace setup.py --replace '"cocotb>=1.5.0.dev,<2.0"' ""
+  '';
+
+  # tests require cocotb, disable for now to avoid circular dependency
+  doCheck = false;
+
+  # checkPhase = ''
+  #   export PATH=$out/bin:$PATH
+  #   make test
+  # '';
+
+  meta = with lib; {
+    description = "Pre-packaged testbenching tools and reusable bus interfaces for cocotb";
+    homepage = "https://github.com/cocotb/cocotb-bus";
+    license = licenses.bsd3;
+    maintainers = with maintainers; [ prusnak ];
+  };
+}

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

@@ -1,19 +1,31 @@
-{ lib, stdenv, buildPythonPackage, fetchFromGitHub, setuptools, swig, verilog }:
+{ lib
+, stdenv
+, buildPythonPackage
+, fetchPypi
+, setuptools
+, setuptools-scm
+, cocotb-bus
+, pytest
+, swig
+, verilog
+}:
 
 buildPythonPackage rec {
   pname = "cocotb";
-  version = "1.5.1";
+  version = "1.5.2";
 
-  src = fetchFromGitHub {
-    owner = pname;
-    repo = pname;
-    rev = "v${version}";
-    sha256 = "02bw2i03vd4rcvdk10qdjl2lbvvy81cn9qpr8vzq8cm9h45689mv";
+  # - we need to use the tarball from PyPi
+  #   or the full git checkout (with .git)
+  # - using fetchFromGitHub will cause a build failure,
+  #   because it does not include required metadata
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "9f4f3e6eb9caeb479e98d604770645b57469cd25b39e28df1916ffcd593efbe6";
   };
 
-  propagatedBuildInputs = [
-    setuptools
-  ];
+  nativeBuildInputs = [ setuptools-scm ];
+
+  buildInputs = [ setuptools ];
 
   postPatch = ''
     patchShebangs bin/*.py
@@ -25,16 +37,14 @@ buildPythonPackage rec {
     do
       substituteInPlace $f --replace 'shell which' 'shell command -v'
     done
+
+    # remove circular dependency cocotb-bus from setup.py
+    substituteInPlace setup.py --replace "'cocotb-bus<1.0'" ""
   '';
 
-  checkInputs = [ swig verilog ];
+  checkInputs = [ cocotb-bus pytest swig verilog ];
 
   checkPhase = ''
-    # test expected failures actually pass because of a fix in our icarus version
-    # https://github.com/cocotb/cocotb/issues/1952
-    substituteInPlace tests/test_cases/test_discovery/test_discovery.py \
-      --replace 'def access_single_bit' $'def foo(x): pass\ndef foo'
-
     export PATH=$out/bin:$PATH
     make test
   '';

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

@@ -5,19 +5,21 @@
 , setuptools-scm
 , toml
 , importlib-metadata
+, cssselect
+, lxml
 , mock
 , pytestCheckHook
 }:
 
 buildPythonPackage rec {
   pname = "cssutils";
-  version = "2.2.0";
+  version = "2.3.0";
 
   disabled = pythonOlder "3.6";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "5bef59f6b59bdccbea8e36cb292d2be1b6be1b485fc4a9f5886616f19eb31aaf";
+    sha256 = "sha256-stOxYEfKroLlxZADaTW6+htiHPRcLziIWvS+SDjw/QA=";
   };
 
   nativeBuildInputs = [
@@ -30,6 +32,8 @@ buildPythonPackage rec {
   ];
 
   checkInputs = [
+    cssselect
+    lxml
     mock
     pytestCheckHook
   ];
@@ -38,6 +42,12 @@ buildPythonPackage rec {
     # access network
     "test_parseUrl"
     "encutils"
+    "website.logging"
+  ] ++ lib.optionals (pythonOlder "3.9") [
+    # AttributeError: module 'importlib.resources' has no attribute 'files'
+    "test_parseFile"
+    "test_parseString"
+    "test_combine"
   ];
 
   pythonImportsCheck = [ "cssutils" ];

pkgs/development/python-modules/drf-jwt/default.nix

@@ -3,18 +3,17 @@
 , fetchFromGitHub
 , pyjwt
 , djangorestframework
-, pytestCheckHook
 }:
 
 buildPythonPackage rec {
   pname = "drf-jwt";
-  version = "1.19.0";
+  version = "1.19.1";
 
   src = fetchFromGitHub {
     owner = "Styria-Digital";
     repo = "django-rest-framework-jwt";
     rev = version;
-    sha256 = "012rmm25w5gvkzi4lyyhn47y1n6g68q9gasga2mkv9i6mn8n4kp7";
+    sha256 = "sha256-++8rFXVsA5WMTt+aC4di3Rpa0BAW285/qM087i9uQ0g=";
   };
 
   propagatedBuildInputs = [

pkgs/development/python-modules/google-api-python-client/default.nix

@@ -4,11 +4,11 @@
 
 buildPythonPackage rec {
   pname = "google-api-python-client";
-  version = "2.0.2";
+  version = "2.6.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "04c0c8m4c7lzqv0m3jm0zks9wjcv1myas80rxswvi36wn376qs28";
+    sha256 = "1s1q1nw05925ryvnycq4bmqrxc14cicdl1j4l9xvyis26cjg71va";
   };
 
   # No tests included in archive

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

@@ -40,6 +40,8 @@ buildPythonPackage rec {
     "test_mem_vec_diff_clusters"
     "test_all_points_mem_vec_diff_clusters"
     "test_approx_predict_diff_clusters"
+    # another flaky test https://github.com/scikit-learn-contrib/hdbscan/issues/421
+    "test_hdbscan_boruvka_balltree_matches"
   ];
 
   meta = with lib; {

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

@@ -77,6 +77,8 @@ buildPythonPackage rec {
     "test_delete"
   ];
 
+  __darwinAllowLocalNetworking = true;
+
   meta = with lib; {
     description = "The backend—i.e. core services, APIs, and REST endpoints—to Jupyter web applications.";
     homepage = "https://github.com/jupyter-server/jupyter_server";

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

@@ -41,6 +41,8 @@ buildPythonPackage rec {
     "test_get_language_pack"
   ];
 
+  __darwinAllowLocalNetworking = true;
+
   meta = with lib; {
     description = "JupyterLab Server";
     homepage = "https://jupyter.org";

pkgs/development/python-modules/mat2/default.nix

@@ -3,6 +3,7 @@
 , python
 , pythonOlder
 , fetchFromGitLab
+, fetchpatch
 , substituteAll
 , bubblewrap
 , exiftool
@@ -49,6 +50,12 @@ buildPythonPackage rec {
     ./executable-name.patch
     # hardcode path to mat2 executable
     ./tests.patch
+    # remove for next release
+    (fetchpatch {
+      name = "fix-tests-ffmpeg-4.4.patch";
+      url = "https://0xacab.org/jvoisin/mat2/-/commit/c9be50f968212b01f8d8ad85e59e19c3e67d8578.patch";
+      sha256 = "0895dkv6575ps3drdfnli15cggx27n9irjx0axigrm4ql4ma0648";
+    })
   ];
 
   postPatch = ''

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

@@ -1,16 +1,21 @@
-{ lib, stdenv, fetchPypi, writeText, python, buildPythonPackage, isPy3k, pycairo, backports_functools_lru_cache
-, which, cycler, dateutil, nose, numpy, pyparsing, sphinx, tornado, kiwisolver
+{ lib, stdenv, fetchPypi, writeText, buildPythonPackage, isPy3k, pycairo
+, which, cycler, dateutil, numpy, pyparsing, sphinx, tornado, kiwisolver
 , freetype, qhull, libpng, pkg-config, mock, pytz, pygobject3, gobject-introspection
 , certifi, pillow
 , enableGhostscript ? true, ghostscript, gtk3
 , enableGtk3 ? false, cairo
 # darwin has its own "MacOSX" backend
-, enableTk ? !stdenv.isDarwin, tcl, tk, tkinter, libX11
+, enableTk ? !stdenv.isDarwin, tcl, tk, tkinter
 , enableQt ? false, pyqt5
+# required for headless detection
+, libX11, wayland
 , Cocoa
-, pythonOlder
 }:
 
+let
+  interactive = enableTk || enableGtk3 || enableQt;
+in
+
 buildPythonPackage rec {
   version = "3.4.1";
   pname = "matplotlib";
@@ -62,8 +67,14 @@ buildPythonPackage rec {
     let
       tcl_tk_cache = ''"${tk}/lib", "${tcl}/lib", "${lib.strings.substring 0 3 tk.version}"'';
     in
-    lib.optionalString enableTk
-      "sed -i '/self.tcl_tk_cache = None/s|None|${tcl_tk_cache}|' setupext.py";
+    lib.optionalString enableTk ''
+      sed -i '/self.tcl_tk_cache = None/s|None|${tcl_tk_cache}|' setupext.py
+    '' + lib.optionalString (stdenv.isLinux && interactive) ''
+      # fix paths to libraries in dlopen calls (headless detection)
+      substituteInPlace src/_c_internal_utils.c \
+        --replace libX11.so.6 ${libX11}/lib/libX11.so.6 \
+        --replace libwayland-client.so.0 ${wayland}/lib/libwayland-client.so.0
+    '';
 
   # Matplotlib needs to be built against a specific version of freetype in
   # order for all of the tests to pass.
@@ -72,6 +83,7 @@ buildPythonPackage rec {
   meta = with lib; {
     description = "Python plotting library, making publication quality plots";
     homepage    = "https://matplotlib.org/";
+    license     = with licenses; [ psfl bsd0 ];
     maintainers = with maintainers; [ lovek323 veprbl ];
   };
 

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

@@ -28,6 +28,8 @@ buildPythonPackage rec {
     pytest-tornasync
   ];
 
+  __darwinAllowLocalNetworking = true;
+
   meta = with lib; {
     description = "Jupyter lab environment notebook server extension.";
     license = with licenses; [ bsd3 ];

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

@@ -7,7 +7,7 @@
 
 buildPythonPackage rec {
   pname = "pyrituals";
-  version = "0.0.2";
+  version = "0.0.3";
   format = "pyproject";
   disabled = pythonOlder "3.8";
 
@@ -15,7 +15,7 @@ buildPythonPackage rec {
     owner = "milanmeu";
     repo = pname;
     rev = version;
-    sha256 = "0hrwhk3kpvdg78fgnvhmnnh3wprdv10j8jqjm4ly64chr8cdi6f2";
+    sha256 = "sha256-oAxQRGP6GxiidnGshSJZEh2RD3XsZ/7kFGwcqaYaBnM=";
   };
 
   propagatedBuildInputs = [ aiohttp ];

pkgs/development/python-modules/scikit-learn/default.nix

@@ -66,10 +66,30 @@ buildPythonPackage rec {
 
   doCheck = !stdenv.isAarch64;
 
-  # Skip test_feature_importance_regression - does web fetch
-  disabledTests = [ "test_feature_importance_regression" ];
+  disabledTests = [
+    # Skip test_feature_importance_regression - does web fetch
+    "test_feature_importance_regression"
 
-  pytestFlagsArray = [ "-n" "$NIX_BUILD_CORES" "--pyargs" "sklearn" ];
+    # failing on macos
+    "check_regressors_train"
+    "check_classifiers_train"
+    "xfail_ignored_in_check_estimator"
+  ];
+
+  pytestFlagsArray = [
+    # verbose build outputs needed to debug hard-to-reproduce hydra failures
+    "-v"
+    "--pyargs" "sklearn"
+
+    # NuSVC memmap tests causes segmentation faults in certain environments
+    # (e.g. Hydra Darwin machines) related to a long-standing joblib issue
+    # (https://github.com/joblib/joblib/issues/563). See also:
+    # https://github.com/scikit-learn/scikit-learn/issues/17582
+    # Since we are overriding '-k' we need to include the 'disabledTests' from above manually.
+    "-k" "'not (NuSVC and memmap) ${toString (lib.forEach disabledTests (t: "and not ${t}"))}'"
+
+    "-n" "$NIX_BUILD_CORES"
+  ];
 
   preCheck = ''
     cd $TMPDIR
@@ -89,6 +109,6 @@ buildPythonPackage rec {
       "https://scikit-learn.org/stable/whats_new/v${major}.${minor}.html#version-${dashVer}";
     homepage = "https://scikit-learn.org";
     license = licenses.bsd3;
-    maintainers = with maintainers; [ ];
+    maintainers = with maintainers; [ davhau ];
   };
 }

pkgs/development/python-modules/smhi-pkg/default.nix

@@ -8,13 +8,13 @@
 
 buildPythonPackage rec {
   pname = "smhi-pkg";
-  version = "1.0.14";
+  version = "1.0.15";
 
   src = fetchFromGitHub {
     owner = "joysoftware";
     repo = "pypi_smhi";
     rev = version;
-    sha256 = "186xwrg3hvr0hszq2kxvygd241q2sp11gfk6mwj9z4zqywwfcbn3";
+    sha256 = "sha256-tBNmfn2hBkS36B9zKDP+TgqeumbgzBVDiJ5L54RaSc8=";
   };
 
   propagatedBuildInputs = [

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

@@ -1,4 +1,5 @@
-{ buildPythonPackage
+{ lib
+, buildPythonPackage
 , pytestCheckHook
 , cmake
 , scipy
@@ -56,6 +57,11 @@ buildPythonPackage {
   disabledTests = [
     "test_cli_binary_classification"
     "test_model_compatibility"
+  ] ++ lib.optionals stdenv.isDarwin [
+    # fails to connect to the com.apple.fonts daemon in sandboxed mode
+    "test_plotting"
+    "test_sklearn_plotting"
   ];
 
+  __darwinAllowLocalNetworking = true;
 }