Merge pull request #57688 from dotlambda/pyyaml-5.1

python.pkgs.pyyaml: 3.13 -> 5.1

11 files changed, 108 insertions, 66 deletions

diff --git a/pkgs/development/python-modules/Nikola/default.nix b/pkgs/development/python-modules/Nikola/default.nix
index 55c6c6ec95f0..06bcde602a7b 100644
--- a/pkgs/development/python-modules/Nikola/default.nix
+++ b/pkgs/development/python-modules/Nikola/default.nix
@@ -19,7 +19,6 @@
 , PyRSS2Gen
 , Logbook
 , blinker
-, setuptools
 , natsort
 , requests
 , piexif
@@ -28,7 +27,6 @@
 , jinja2
 , Babel
 , freezegun
-, pyyaml
 , toml
 , notebook
 , ruamel_yaml
@@ -46,9 +44,11 @@ buildPythonPackage rec {
   checkInputs = [ pytest pytestcov mock glibcLocales freezegun ];
 
   propagatedBuildInputs = [
-    pygments pillow dateutil docutils Mako unidecode lxml Yapsy PyRSS2Gen
-    Logbook blinker setuptools natsort requests piexif markdown phpserialize
-    jinja2 doit Babel pyyaml toml notebook ruamel_yaml
+    # requirements.txt
+    doit pygments pillow dateutil docutils Mako markdown unidecode
+    lxml Yapsy PyRSS2Gen Logbook blinker natsort requests piexif Babel
+    # requirements-extras.txt
+    phpserialize jinja2 toml notebook ruamel_yaml
   ];
 
   src = fetchPypi {
diff --git a/pkgs/development/python-modules/canmatrix/default.nix b/pkgs/development/python-modules/canmatrix/default.nix
index 3e07188986d0..a6c3f485d74b 100644
--- a/pkgs/development/python-modules/canmatrix/default.nix
+++ b/pkgs/development/python-modules/canmatrix/default.nix
@@ -1,40 +1,54 @@
 { lib
 , buildPythonPackage
 , fetchFromGitHub
-, python
+, pythonOlder
+, attrs
+, bitstruct
+, future
+, pathlib2
+, typing
 , lxml
 , xlwt
 , xlrd
 , XlsxWriter
 , pyyaml
-, future }:
+, pytest
+}:
 
 buildPythonPackage rec {
   pname = "canmatrix";
-  version = "0.6";
+  version = "0.7";
 
   # uses fetchFromGitHub as PyPi release misses test/ dir
   src = fetchFromGitHub {
     owner = "ebroecker";
     repo = pname;
     rev = version;
-    sha256 = "1lb0krhchja2jqfsh5lsfgmqcchs1pd38akvc407jfmll96f4yqz";
+    sha256 = "0q8qb282nfgirl8r2i9c8whm3hvr14ig2r42ssgnv2hya971cwjq";
   };
 
+  propagatedBuildInputs = [
+    # required
+    attrs
+    bitstruct
+    future
+    pathlib2
+    # optional
+    lxml
+    xlwt
+    xlrd
+    XlsxWriter
+    pyyaml
+  ] ++ lib.optional (pythonOlder "3.5") typing;
+
+  checkInputs = [
+    pytest
+  ];
+
   checkPhase = ''
-    cd test
-    ${python.interpreter} ./test.py
+    pytest -s src/canmatrix
   '';
 
-  propagatedBuildInputs =
-    [ lxml
-      xlwt
-      xlrd
-      XlsxWriter
-      pyyaml
-      future
-    ];
-
   meta = with lib; {
     homepage = https://github.com/ebroecker/canmatrix;
     description = "Support and convert several CAN (Controller Area Network) database formats .arxml .dbc .dbf .kcd .sym fibex xls(x)";
diff --git a/pkgs/development/python-modules/intake/default.nix b/pkgs/development/python-modules/intake/default.nix
index 4434ea0edc11..2646ee1b9363 100644
--- a/pkgs/development/python-modules/intake/default.nix
+++ b/pkgs/development/python-modules/intake/default.nix
@@ -21,12 +21,12 @@
 
 buildPythonPackage rec {
   pname = "intake";
-  version = "0.4.1";
+  version = "0.4.4";
   disabled = isPy27;
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "f47e53aa764eeadf6adcc667b9817b1ad32496477476da0b982d4fc0744b40ef";
+    sha256 = "3fc1b7c2949c9b4200ecbbfdff17da126981a1d8d95ccb7b7bcca3e3dd849d5e";
   };
 
   checkInputs = [ pytest ];
@@ -47,8 +47,9 @@ buildPythonPackage rec {
   ];
 
   checkPhase = ''
-    # single test assumes python for executable name
-    PATH=$out/bin:$PATH HOME=$(mktemp -d) pytest --ignore=intake/catalog/tests/test_default.py
+    # test_filtered_compressed_cache requires calvert_uk_filter.tar.gz, which is not included in tarball
+    # test_which assumes python for executable name
+    PATH=$out/bin:$PATH HOME=$(mktemp -d) pytest -k "not test_filtered_compressed_cache and not test_which"
   '';
 
   meta = with lib; {
diff --git a/pkgs/development/python-modules/kaptan/default.nix b/pkgs/development/python-modules/kaptan/default.nix
index 35194294e9d1..aada19dd45b2 100644
--- a/pkgs/development/python-modules/kaptan/default.nix
+++ b/pkgs/development/python-modules/kaptan/default.nix
@@ -13,6 +13,12 @@ buildPythonPackage rec {
     sha256 = "8403d6e48200c3f49cb6d6b3dcb5898aa5ab9d820831655bf9a2403e00cd4207";
   };
 
+  # https://github.com/emre/kaptan/pull/151
+  postPatch = ''
+    substituteInPlace requirements/base.txt \
+      --replace "PyYAML>=3.13,<4" "PyYAML>=3.13"
+  '';
+
   propagatedBuildInputs = [ pyyaml ];
 
   # No tests in archive
diff --git a/pkgs/development/python-modules/mt-940/default.nix b/pkgs/development/python-modules/mt-940/default.nix
index 820b4c1696b3..f3965b8a74ae 100644
--- a/pkgs/development/python-modules/mt-940/default.nix
+++ b/pkgs/development/python-modules/mt-940/default.nix
@@ -1,36 +1,27 @@
-{ buildPythonPackage, stdenv, pyyaml, pytest, enum34
-, pytestpep8, pytest-flakes, fetchFromGitHub, isPy3k, lib, glibcLocales
+{ lib, buildPythonPackage, fetchPypi, isPy3k
+, enum34, pyyaml, pytest
 }:
 
 buildPythonPackage rec {
-  version = "4.13.2";
+  version = "4.15.0";
   pname = "mt-940";
 
-  # No tests in PyPI tarball
-  # See https://github.com/WoLpH/mt940/pull/72
-  src = fetchFromGitHub {
-    owner = "WoLpH";
-    repo = "mt940";
-    rev = "v${version}";
-    sha256 = "1lvw3qyv7qhjabcvg55br8x4pnc7hv8xzzaf6wnr8cfjg0q7dzzg";
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "4c1d5c23a9c3fec12a61ce3f61d8be107b4693be4a4b97381eca23f4a4dca8ed";
   };
 
-  postPatch = ''
-    # No coverage report
-    sed -i "/--\(no-\)\?cov/d" pytest.ini
-  '';
-
   propagatedBuildInputs = lib.optional (!isPy3k) enum34;
 
-  checkInputs = [ pyyaml pytestpep8 pytest-flakes pytest ];
+  checkInputs = [ pyyaml pytest ];
 
   checkPhase = ''
     py.test
   '';
 
-  meta = with stdenv.lib; {
+  meta = with lib; {
     description = "A library to parse MT940 files and returns smart Python collections for statistics and manipulation";
-    inherit (src.meta) homepage;
+    homepage = https://github.com/WoLpH/mt940;
     license = licenses.bsd3;
   };
 }
diff --git a/pkgs/development/python-modules/pytoml/default.nix b/pkgs/development/python-modules/pytoml/default.nix
index 91661a1fb510..d65de8123235 100644
--- a/pkgs/development/python-modules/pytoml/default.nix
+++ b/pkgs/development/python-modules/pytoml/default.nix
@@ -1,23 +1,29 @@
 { stdenv
 , buildPythonPackage
-, fetchgit
+, fetchFromGitHub
 , python
+, pytest
 }:
 
 buildPythonPackage rec {
   pname = "pytoml";
-  version = "0.1.14";
+  version = "0.1.20";
+
+  src = fetchFromGitHub {
+    owner = "avakar";
+    repo = "pytoml";
+    rev = "v${version}";
+    fetchSubmodules = true; # ensure test submodule is available
+    sha256 = "02hjq44zhh6z0fsbm3hvz34sav6fic90sjrw8g1pkdvskzzl46mz";
+  };
+
+  checkInputs = [ pytest ];
 
   checkPhase = ''
     ${python.interpreter} test/test.py
+    pytest test
   '';
 
-  # fetchgit used to ensure test submodule is available
-  src = fetchgit {
-    url = "${meta.homepage}.git";
-    rev = "refs/tags/v${version}";
-    sha256 = "1ip71yqxnyi4jhw5x1q7a0za61ndhpfh0vbx08jfv0w4ayng6rgv";
-  };
 
   meta = with stdenv.lib; {
     description = "A TOML parser/writer for Python";
diff --git a/pkgs/development/python-modules/pyyaml/default.nix b/pkgs/development/python-modules/pyyaml/default.nix
index b4732e34c4ef..84dfb549fe1c 100644
--- a/pkgs/development/python-modules/pyyaml/default.nix
+++ b/pkgs/development/python-modules/pyyaml/default.nix
@@ -1,17 +1,22 @@
-{ lib, buildPythonPackage, fetchPypi, libyaml, buildPackages }:
+{ lib, buildPythonPackage, fetchPypi, cython, libyaml, buildPackages }:
 
 buildPythonPackage rec {
   pname = "PyYAML";
-  version = "3.13";
+  version = "5.1";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "3ef3092145e9b70e3ddd2c7ad59bdd0252a94dfe3949721633e41344de00a6bf";
+    sha256 = "436bc774ecf7c103814098159fbb84c2715d25980175292c648f2da143909f95";
   };
 
-  nativeBuildInputs = [ buildPackages.stdenv.cc ];
+  # force regeneration using Cython
+  postPatch = ''
+    rm ext/_yaml.c
+  '';
 
-  propagatedBuildInputs = [ libyaml ];
+  nativeBuildInputs = [ cython buildPackages.stdenv.cc ];
+
+  buildInputs = [ libyaml ];
 
   meta = with lib; {
     description = "The next generation YAML parser and emitter for Python";
diff --git a/pkgs/development/tools/build-managers/conan/default.nix b/pkgs/development/tools/build-managers/conan/default.nix
index 8ae56834702b..ed7babf49332 100644
--- a/pkgs/development/tools/build-managers/conan/default.nix
+++ b/pkgs/development/tools/build-managers/conan/default.nix
@@ -37,6 +37,13 @@ let newPython = python3.override {
         sha256 = "c0abe3218b86533cca287e7057a37481883c07acef7814b70583406938214cc8";
       };
     });
+    pyyaml = super.pyyaml.overridePythonAttrs (oldAttrs: rec {
+      version = "3.13";
+      src = oldAttrs.src.override {
+        inherit version;
+        sha256 = "3ef3092145e9b70e3ddd2c7ad59bdd0252a94dfe3949721633e41344de00a6bf";
+      };
+    });
   };
 };
 
diff --git a/pkgs/development/tools/remarshal/default.nix b/pkgs/development/tools/remarshal/default.nix
index 6632d0626339..10bfd0c2f2d0 100644
--- a/pkgs/development/tools/remarshal/default.nix
+++ b/pkgs/development/tools/remarshal/default.nix
@@ -2,13 +2,11 @@
 
 python3Packages.buildPythonApplication rec {
   pname = "remarshal";
-  version = "0.8.0";
+  version = "0.9.1";
 
-  src = fetchFromGitHub {
-    owner  = "dbohdan";
-    repo   = "remarshal";
-    rev    = "v${version}";
-    sha256 = "192r1mfd5yj6kg6fqmkjngdlgn25g5rkvm0p6xaflpvavnhvhnsj";
+  src = python3Packages.fetchPypi {
+    inherit pname version;
+    sha256 = "564ffe9cbde85bd28a9c184b90c764abd2003abd6101a30802262198b5c7fc40";
   };
 
   propagatedBuildInputs = with python3Packages; [
diff --git a/pkgs/tools/admin/awscli/default.nix b/pkgs/tools/admin/awscli/default.nix
index c36b6d2fbd65..e09833869d67 100644
--- a/pkgs/tools/admin/awscli/default.nix
+++ b/pkgs/tools/admin/awscli/default.nix
@@ -21,6 +21,13 @@ let
           sha256 = "48eb22f4f8461b1df5734a074b57042430fb06e1d61bd1e11b078c0fe6d7a1f1";
         };
       });
+      pyyaml = super.pyyaml.overridePythonAttrs (oldAttrs: rec {
+        version = "3.13";
+        src = oldAttrs.src.override {
+          inherit version;
+          sha256 = "3ef3092145e9b70e3ddd2c7ad59bdd0252a94dfe3949721633e41344de00a6bf";
+        };
+      });
     };
   };
 
diff --git a/pkgs/tools/misc/pubs/default.nix b/pkgs/tools/misc/pubs/default.nix
index fcf67870e878..4e840957ce32 100644
--- a/pkgs/tools/misc/pubs/default.nix
+++ b/pkgs/tools/misc/pubs/default.nix
@@ -11,11 +11,18 @@ python3Packages.buildPythonApplication rec {
     sha256 = "16zwdqfbmlla6906g3a57a4nj8wnl11fq78r20qms717bzv211j0";
   };
 
-  # Fix for bibtexparser 1.1.0
-  patches = fetchpatch {
-    url = https://github.com/pubs/pubs/pull/185/commits/e58ae98b93b8364a07fd5f5f452ba88ad332c948.patch;
-    sha256 = "1n7zrk119v395jj8wqg8wlymc9l9pq3v752yy3kam9kflc0aashp";
-  };
+  patches = [
+    # Fix for bibtexparser 1.1.0
+    (fetchpatch {
+      url = https://github.com/pubs/pubs/pull/185/commits/e58ae98b93b8364a07fd5f5f452ba88ad332c948.patch;
+      sha256 = "1n7zrk119v395jj8wqg8wlymc9l9pq3v752yy3kam9kflc0aashp";
+    })
+    # Fix test broken by PyYAML 5.1
+    (fetchpatch {
+      url = https://github.com/pubs/pubs/pull/194/commits/c3cb713ae76528eeeaaeb948fe319a76ab3934d8.patch;
+      sha256 = "05as418m7wzs65839bb91b2jrs8l68z8ldcjcd9cn4b9fcgsf3rk";
+    })
+  ];
 
   propagatedBuildInputs = with python3Packages; [
     argcomplete dateutil configobj feedparser bibtexparser pyyaml requests six beautifulsoup4