Merge master into staging-next

pkgs/development/python-modules/colored-traceback/default.nix

@@ -0,0 +1,29 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, pygments
+}:
+
+buildPythonPackage rec {
+  pname = "colored-traceback";
+  version = "0.3.0";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "sha256-bafOKx2oafa7VMkntBW5VyfEu22ahMRhXqd9mHKRGwU=";
+  };
+
+  buildInputs = [ pygments ];
+
+  # No setuptools tests for the package.
+  doCheck = false;
+
+  pythonImportsCheck = [ "colored_traceback" ];
+
+  meta = with lib; {
+    homepage = "https://github.com/staticshock/colored-traceback.py";
+    description = "Automatically color Python's uncaught exception tracebacks";
+    license = licenses.isc;
+    maintainers = with maintainers; [ pamplemousse ];
+  };
+}

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

@@ -1,38 +1,40 @@
 { lib
-, pkgs
 , buildPythonPackage
 , fetchFromGitHub
-, pytest
+, pytestCheckHook
 }:
 
 buildPythonPackage rec {
-  pname   = "DendroPy";
-  version = "4.4.0";
+  pname = "dendropy";
+  version = "4.5.1";
 
-  # tests are incorrectly packaged in pypi version
   src = fetchFromGitHub {
     owner = "jeetsukumaran";
     repo = pname;
     rev = "v${version}";
-    sha256 = "097hfyv2kaf4x92i4rjx0paw2cncxap48qivv8zxng4z7nhid0x9";
+    sha256 = "sha256-FP0+fJkkFtSysPxoHXjyMgF8pPin7aRyzmHe9bH8LlM=";
   };
 
-  preCheck = ''
-    # Needed for unicode python tests
-    export LC_ALL="en_US.UTF-8"
-    cd tests  # to find the 'support' module
-  '';
+  checkInputs = [
+    pytestCheckHook
+  ];
 
-  checkInputs = [ pytest pkgs.glibcLocales ];
+  disabledTests = [
+    # FileNotFoundError: [Errno 2] No such file or directory: 'paup'
+    "test_basic_split_count_with_incorrect_rootings_raises_error"
+    "test_basic_split_count_with_incorrect_weight_treatment_raises_error"
+    "test_basic_split_counting_under_different_rootings"
+    "test_group1"
+    # AssertionError: 6 != 5
+    "test_by_num_lineages"
+  ];
 
-  checkPhase = ''
-    pytest -k 'not test_dataio_nexml_reader_tree_list and not test_pscores_with'
-  '';
+  pythonImportsCheck = [ "dendropy" ];
 
-  meta = {
+  meta = with lib; {
+    description = "Python library for phylogenetic computing";
     homepage = "https://dendropy.org/";
-    description = "A Python library for phylogenetic computing";
-    maintainers = with lib.maintainers; [ unode ];
-    license = lib.licenses.bsd3;
+    license = licenses.bsd3;
+    maintainers = with maintainers; [ unode ];
   };
 }

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

@@ -1,6 +1,6 @@
 { lib
 , buildPythonPackage
-, fetchPypi
+, fetchFromGitHub
 , gevent
 , nose
 , mock
@@ -12,12 +12,34 @@ buildPythonPackage rec {
   pname = "pika";
   version = "1.2.0";
 
-  src = fetchPypi {
-    inherit pname version;
-    sha256 = "f023d6ac581086b124190cb3dc81dd581a149d216fa4540ac34f9be1e3970b89";
+  src = fetchFromGitHub {
+    owner = "pika";
+    repo = "pika";
+    rev = version;
+    sha256 = "sha256-Wog6Wxa8V/zv/bBrFOigZi6KE5qRf82bf1GK2XwvpDI=";
   };
 
-  checkInputs = [ nose mock twisted tornado gevent ];
+  propagatedBuildInputs = [ gevent tornado twisted ];
+
+  checkInputs = [ nose mock ];
+
+  postPatch = ''
+    # don't stop at first test failure
+    # don't run acceptance tests because they access the network
+    # don't report test coverage
+    substituteInPlace setup.cfg \
+      --replace "stop = 1" "stop = 0" \
+      --replace "tests=tests/unit,tests/acceptance" "tests=tests/unit" \
+      --replace "with-coverage = 1" "with-coverage = 0"
+  '';
+
+  checkPhase = ''
+    runHook preCheck
+
+    PIKA_TEST_TLS=true nosetests
+
+    runHook postCheck
+  '';
 
   meta = with lib; {
     description = "Pure-Python implementation of the AMQP 0-9-1 protocol";

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

@@ -8,6 +8,7 @@
 , pygments
 , ROPGadget
 , capstone
+, colored-traceback
 , paramiko
 , pip
 , psutil
@@ -15,6 +16,7 @@
 , pyserial
 , dateutil
 , requests
+, rpyc
 , tox
 , unicorn
 , intervaltree
@@ -25,12 +27,12 @@ let
   debuggerName = lib.strings.getName debugger;
 in
 buildPythonPackage rec {
-  version = "4.3.1";
+  version = "4.5.0";
   pname = "pwntools";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "12ja913kz8wl4afrmpzxh9fx6j7rcwc2vqzkvfr1fxn42gkqhqf4";
+    sha256 = "sha256-IWHMorSASG/po8ib1whS3xPuoUUlD0tbbWI35DI2SIY=";
   };
 
   postPatch = ''
@@ -55,6 +57,7 @@ buildPythonPackage rec {
     pygments
     ROPGadget
     capstone
+    colored-traceback
     paramiko
     pip
     psutil
@@ -62,6 +65,7 @@ buildPythonPackage rec {
     pyserial
     dateutil
     requests
+    rpyc
     tox
     unicorn
     intervaltree