Merge pull request #30762 from mayflower/jupyter-update

Update jupyter and enable a few tests

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

@@ -0,0 +1,38 @@
+{ lib
+, python
+, buildPythonPackage
+, fetchPypi
+, ipython
+, traitlets
+, glibcLocales
+, mock
+, pytest
+}:
+
+buildPythonPackage rec {
+  pname = "jupyter_core";
+  version = "4.3.0";
+  name = "${pname}-${version}";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "a96b129e1641425bf057c3d46f4f44adce747a7d60107e8ad771045c36514d40";
+  };
+
+  buildInputs = [ pytest mock glibcLocales ];
+  propagatedBuildInputs = [ ipython traitlets ];
+
+  patches = [ ./tests_respect_pythonpath.patch ];
+
+  checkPhase = ''
+    mkdir tmp
+    HOME=tmp TMPDIR=tmp LC_ALL=en_US.utf8 py.test
+  '';
+
+  meta = with lib; {
+    description = "Jupyter core package. A base package on which Jupyter projects rely";
+    homepage = http://jupyter.org/;
+    license = licenses.bsd3;
+    maintainers = with maintainers; [ fridh globin ];
+  };
+}

pkgs/development/python-modules/jupyter_core/tests_respect_pythonpath.patch

@@ -0,0 +1,24 @@
+--- a/jupyter_core/tests/test_command.py	2016-09-13 15:22:49.000000000 +0200
++++ b/jupyter_core/tests/test_command.py	2017-10-23 12:49:27.489527705 +0200
+@@ -113,7 +113,10 @@
+     witness = a.join(witness_cmd)
+     witness.write('#!%s\n%s\n' % (sys.executable, 'print("WITNESS ME")'))
+     witness.chmod(0o700)
+-    out = check_output([sys.executable, str(jupyter), 'witness'], env={'PATH': ''})
++    out = check_output(
++        [sys.executable, str(jupyter), 'witness'],
++        env={'PATH': '', 'PYTHONPATH': os.environ['PYTHONPATH']}
++    )
+     assert b'WITNESS' in out
+ 
+ 
+@@ -136,5 +139,8 @@
+     witness_b.write('#!%s\n%s\n' % (sys.executable, 'print("WITNESS B")'))
+     witness_b.chmod(0o700)
+ 
+-    out = check_output([sys.executable, str(jupyter), 'witness'], env={'PATH': str(b)})
++    out = check_output(
++        [sys.executable, str(jupyter), 'witness'],
++        env={'PATH': str(b), 'PYTHONPATH': os.environ['PYTHONPATH']}
++    )
+     assert b'WITNESS A' in out

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

@@ -0,0 +1,24 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, nose
+}:
+
+buildPythonPackage rec {
+  pname = "mistune";
+  version = "0.7.4";
+  name = "${pname}-${version}";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "0byj9jg9ly7karf5sb1aqcw7avaim9sxl8ws7yw7p1fibjgsy5w5";
+  };
+
+  buildInputs = [ nose ];
+
+  meta = with lib; {
+    description = "The fastest markdown parser in pure Python";
+    homepage = https://github.com/lepture/mistune;
+    license = licenses.bsd3;
+  };
+}

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

@@ -3,6 +3,7 @@
 , fetchPypi
 , pytest
 , nose
+, glibcLocales
 , entrypoints
 , bleach
 , mistune
@@ -21,15 +22,15 @@
 
 buildPythonPackage rec {
   pname = "nbconvert";
-  version = "5.2.1";
+  version = "5.3.1";
   name = "${pname}-${version}";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "9ed68ec7fe90a8672b43795b29ea91cc75ea355c83debc83ebd12171521ec274";
+    sha256 = "1f9dkvpx186xjm4xab0qbph588mncp4vqk3fmxrsnqs43mks9c8j";
   };
 
-  checkInputs = [ nose pytest ];
+  checkInputs = [ nose pytest glibcLocales ];
 
   propagatedBuildInputs = [
     entrypoints bleach mistune jinja2 pygments traitlets testpath
@@ -37,16 +38,14 @@ buildPythonPackage rec {
   ];
 
   checkPhase = ''
-    nosetests -v
+    mkdir tmp
+    LC_ALL=en_US.utf8 HOME=`realpath tmp` py.test -v
   '';
 
-  # PermissionError. Likely due to being in a chroot
-  doCheck = false;
-
   meta = {
     description = "Converting Jupyter Notebooks";
     homepage = http://jupyter.org/;
     license = lib.licenses.bsd3;
-    maintainers = with lib.maintainers; [ fridh ];
+    maintainers = with lib.maintainers; [ fridh globin ];
   };
 }

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

@@ -19,18 +19,21 @@ buildPythonPackage rec {
     inherit pname version;
     sha256 = "f7494ef0df60766b7cabe0a3651556345a963b74dbc16bc7c18479041170d402";
   };
-  LC_ALL="en_US.UTF-8";
+
+  LC_ALL="en_US.utf8";
 
   checkInputs = [ pytest glibcLocales ];
   propagatedBuildInputs = [ ipython_genutils traitlets testpath jsonschema jupyter_core ];
 
-  # Failing tests and permission issues
+  preCheck = ''
-  doCheck = false;
+    mkdir tmp
+    export HOME=tmp
+  '';
 
   meta = {
     description = "The Jupyter Notebook format";
     homepage = http://jupyter.org/;
     license = lib.licenses.bsd3;
-    maintainers = with lib.maintainers; [ fridh ];
+    maintainers = with lib.maintainers; [ fridh globin ];
   };
 }

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

@@ -0,0 +1,31 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, isPy3k
+, nose
+}:
+
+buildPythonPackage rec {
+  pname = "nose_warnings_filters";
+  version = "0.1.5";
+  name = "${pname}-${version}";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "17dvfqfy2fm7a5cmiffw2dc3064kpx72fn5mlw01skm2rhn5nv25";
+  };
+
+  disabled = !isPy3k;
+
+  propagatedBuildInputs = [ nose ];
+
+  checkPhase = ''
+    nosetests -v
+  '';
+
+  meta = {
+    description = "Allow injecting warning filters during nosetest";
+    homepage = https://github.com/Carreau/nose_warnings_filters;
+    license = lib.licenses.mit;
+  };
+}

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

@@ -2,8 +2,9 @@
 , buildPythonPackage
 , fetchPypi
 , nose
+, nose_warnings_filters
 , glibcLocales
-, isPy27
+, isPy3k
 , mock
 , jinja2
 , tornado
@@ -21,32 +22,39 @@
 
 buildPythonPackage rec {
   pname = "notebook";
-  version = "5.0.0";
+  version = "5.2.0";
   name = "${pname}-${version}";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1cea3bbbd03c8e5842a1403347a8cc8134486b3ce081a2e5b1952a00ea66ed54";
+    sha256 = "1sh3jkkmjzv17c3r8ii3kfhpxi6dkjk846b2lfy71g9qwqdcvbvz";
   };
 
-  LC_ALL = "en_US.UTF-8";
+  LC_ALL = "en_US.utf8";
 
-  buildInputs = [nose glibcLocales]  ++ lib.optionals isPy27 [mock];
+  buildInputs = [ nose glibcLocales ]
+    ++ (if isPy3k then [ nose_warnings_filters ] else [ mock ]);
 
-  propagatedBuildInputs = [jinja2 tornado ipython_genutils traitlets jupyter_core
+  propagatedBuildInputs = [
-    jupyter_client nbformat nbconvert ipykernel terminado requests pexpect ];
+    jinja2 tornado ipython_genutils traitlets jupyter_core
+    jupyter_client nbformat nbconvert ipykernel terminado requests pexpect
+  ];
 
+  # disable warning_filters
+  preCheck = lib.optionalString (!isPy3k) ''
+    echo "" > setup.cfg
+    cat setup.cfg
+  '';
   checkPhase = ''
-    nosetests -v
+    runHook preCheck
+    mkdir tmp
+    HOME=tmp nosetests -v
   '';
 
-  # Certain tests fail due to being in a chroot.
-  # PermissionError
-  doCheck = false;
   meta = {
     description = "The Jupyter HTML notebook is a web-based notebook environment for interactive computing";
     homepage = http://jupyter.org/;
     license = lib.licenses.bsd3;
-    maintainers = with lib.maintainers; [ fridh ];
+    maintainers = with lib.maintainers; [ fridh globin ];
   };
 }

pkgs/top-level/python-packages.nix

@@ -10798,32 +10798,7 @@ in {
 
   jupyter_client = callPackage ../development/python-modules/jupyter_client { };
 
-  jupyter_core = buildPythonPackage rec {
+  jupyter_core = callPackage ../development/python-modules/jupyter_core { };
-    version = "4.3.0";
-    name = "jupyter_core-${version}";
-
-    src = pkgs.fetchurl {
-      url = "mirror://pypi/j/jupyter_core/${name}.tar.gz";
-      sha256 = "a96b129e1641425bf057c3d46f4f44adce747a7d60107e8ad771045c36514d40";
-    };
-
-    buildInputs = with self; [ pytest mock ];
-    propagatedBuildInputs = with self; [ ipython traitlets];
-
-    checkPhase = ''
-      py.test
-    '';
-
-    # Several tests fail due to being in a chroot
-    doCheck = false;
-
-    meta = {
-      description = "Jupyter core package. A base package on which Jupyter projects rely";
-      homepage = http://jupyter.org/;
-      license = licenses.bsd3;
-      maintainers = with maintainers; [ fridh ];
-    };
-  };
 
   jsonpath_rw = buildPythonPackage rec {
     name = "jsonpath-rw-${version}";
@@ -11902,23 +11877,7 @@ in {
     };
   };
 
-  mistune = buildPythonPackage rec {
+  mistune = callPackage ../development/python-modules/mistune { };
-    version = "0.7.1";
-    name = "mistune-${version}";
-
-    src = pkgs.fetchurl {
-      url = "mirror://pypi/m/mistune/${name}.tar.gz";
-      sha256 = "6076dedf768348927d991f4371e5a799c6a0158b16091df08ee85ee231d929a7";
-    };
-
-    buildInputs = with self; [nose];
-
-    meta = {
-      description = "The fastest markdown parser in pure Python";
-      homepage = https://github.com/lepture/mistune;
-      license = licenses.bsd3;
-    };
-  };
 
   brotlipy = buildPythonPackage rec {
     name = "brotlipy-${version}";
@@ -13151,6 +13110,8 @@ in {
     buildInputs = with self; [ nose ];
   };
 
+  nose_warnings_filters = callPackage ../development/python-modules/nose_warnings_filters { };
+
   notebook = callPackage ../development/python-modules/notebook { };
 
   notify = pkgs.stdenv.mkDerivation (rec {