Merge master into staging

8 files changed, 138 insertions, 18 deletions

diff --git a/pkgs/development/python-modules/aiohttp/default.nix b/pkgs/development/python-modules/aiohttp/default.nix
index ff03812f80cc..ec76d840a56b 100644
--- a/pkgs/development/python-modules/aiohttp/default.nix
+++ b/pkgs/development/python-modules/aiohttp/default.nix
@@ -12,6 +12,8 @@
 , gunicorn
 , pytest-mock
 , async_generator
+, pytestrunner
+, pytest-timeout
 }:
 
 buildPythonPackage rec {
@@ -25,11 +27,15 @@ buildPythonPackage rec {
 
   disabled = pythonOlder "3.5";
 
-  checkInputs = [ pytest gunicorn pytest-mock async_generator ];
+  checkInputs = [ pytest gunicorn pytest-mock async_generator pytestrunner pytest-timeout ];
 
   propagatedBuildInputs = [ attrs chardet multidict async-timeout yarl ]
     ++ lib.optional (pythonOlder "3.7") idna-ssl;
 
+
+  # Several test failures. Need to be looked into.
+  doCheck = false;
+
   meta = with lib; {
     description = "Asynchronous HTTP Client/Server for Python and asyncio";
     license = licenses.asl20;
diff --git a/pkgs/development/python-modules/git-annex-adapter/default.nix b/pkgs/development/python-modules/git-annex-adapter/default.nix
index 04fae0db1b7a..6cb6e626f279 100644
--- a/pkgs/development/python-modules/git-annex-adapter/default.nix
+++ b/pkgs/development/python-modules/git-annex-adapter/default.nix
@@ -1,5 +1,6 @@
-{ stdenv, buildPythonPackage, isPy3k, fetchFromGitHub, fetchurl
-, utillinux, pygit2, gitMinimal, git-annex }:
+{ stdenv, buildPythonPackage, isPy3k, fetchFromGitHub, fetchpatch
+, utillinux, pygit2, gitMinimal, git-annex
+}:
 
 buildPythonPackage rec {
   pname = "git-annex-adapter";
@@ -22,10 +23,13 @@ buildPythonPackage rec {
   '';
 
   # TODO: Remove for next version
-  patches = fetchurl {
-    url = "https://github.com/alpernebbi/git-annex-adapter/commit/9f64c4b99cae7b681820c6c7382e1e40489f4d1e.patch";
-    sha256 = "1hbw8651amjskakvs1wv2msd1wryrq0vpryvbispg5267rs8q7hp";
-  };
+  patches = [
+    ./not-a-git-repo-testcase.patch
+    (fetchpatch {
+      url = "https://github.com/alpernebbi/git-annex-adapter/commit/9f64c4b99cae7b681820c6c7382e1e40489f4d1e.patch";
+      sha256 = "0yh66gial6bx7kbl7s7lkzljnkpgvgr8yahqqcq9z76d0w752dir";
+    })
+  ];
 
   checkInputs = [
     utillinux # `rev` is needed in tests/test_process.py
@@ -43,6 +47,6 @@ buildPythonPackage rec {
     homepage = https://github.com/alpernebbi/git-annex-adapter;
     description = "Call git-annex commands from Python";
     license = licenses.gpl3Plus;
-    maintainers = with maintainers; [ dotlambda ];
+    maintainers = with maintainers; [ dotlambda ma27 ];
   };
 }
diff --git a/pkgs/development/python-modules/git-annex-adapter/not-a-git-repo-testcase.patch b/pkgs/development/python-modules/git-annex-adapter/not-a-git-repo-testcase.patch
new file mode 100644
index 000000000000..2a386ee3f2f9
--- /dev/null
+++ b/pkgs/development/python-modules/git-annex-adapter/not-a-git-repo-testcase.patch
@@ -0,0 +1,13 @@
+diff --git a/tests/test_process.py b/tests/test_process.py
+index 493fc8f..feb1833 100644
+--- a/tests/test_process.py
++++ b/tests/test_process.py
+@@ -126,7 +126,7 @@ class TestProcessOnEmptyDir(TempDirTestCase):
+         with self.assertRaises(subprocess.CalledProcessError) as cm:
+             runner('status', '-sb')
+         self.assertIn(
+-            "fatal: Not a git repository",
++            "fatal: not a git repository",
+             cm.exception.stderr,
+         )
+ 
diff --git a/pkgs/development/python-modules/jupyterlab_launcher/default.nix b/pkgs/development/python-modules/jupyterlab_launcher/default.nix
index 5bbc36f53dfe..f316fe10563d 100644
--- a/pkgs/development/python-modules/jupyterlab_launcher/default.nix
+++ b/pkgs/development/python-modules/jupyterlab_launcher/default.nix
@@ -1,11 +1,11 @@
 { lib, buildPythonPackage, fetchPypi, jsonschema, notebook }:
 buildPythonPackage rec {
   pname = "jupyterlab_launcher";
-  version = "0.11.0";
+  version = "0.10.5";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "2eea0cc95b312e136e6e5abc64e2e62baaeca493cd32f553c2205f79e01c0423";
+    sha256 = "1v1ir182zm2dl14lqvqjhx2x40wnp0i32n6rldxnm1allfpld1n7";
   };
 
   propagatedBuildInputs = [
diff --git a/pkgs/development/python-modules/monty/default.nix b/pkgs/development/python-modules/monty/default.nix
new file mode 100644
index 000000000000..e53098f6f232
--- /dev/null
+++ b/pkgs/development/python-modules/monty/default.nix
@@ -0,0 +1,38 @@
+{ stdenv, buildPythonPackage, fetchFromGitHub, nose, numpy, six, ruamel_yaml, msgpack-python, coverage, coveralls, pymongo, lsof }:
+
+buildPythonPackage rec {
+  pname = "monty";
+  version = "1.0.2";
+
+  # No tests in Pypi
+  src = fetchFromGitHub {
+    owner = "materialsvirtuallab";
+    repo = pname;
+    rev = "v${version}";
+    sha256 = "0ss70fanavqdpj56yymj06lacgnknb4ap39m2q28v9lz32cs6xdg";
+  };
+
+  propagatedBuildInputs = [ nose numpy six ruamel_yaml msgpack-python coverage coveralls pymongo lsof ];
+  
+  preCheck = ''
+    substituteInPlace tests/test_os.py \
+      --replace 'def test_which(self):' '#' \
+      --replace 'py = which("python")' '#' \
+      --replace 'self.assertEqual(os.path.basename(py), "python")' '#' \
+      --replace 'self.assertEqual("/usr/bin/find", which("/usr/bin/find"))' '#' \
+      --replace 'self.assertIs(which("non_existent_exe"), None)' '#' \
+  '';
+
+  meta = with stdenv.lib; {
+    description = "Serves as a complement to the Python standard library by providing a suite of tools to solve many common problems";
+    longDescription = "
+      Monty implements supplementary useful functions for Python that are not part of the 
+      standard library. Examples include useful utilities like transparent support for zipped files, useful design 
+      patterns such as singleton and cached_class, and many more.
+    ";
+    homepage = https://github.com/materialsvirtuallab/monty;
+    license = licenses.mit;
+    maintainers = with maintainers; [ psyanticy ];
+  };
+}
+
diff --git a/pkgs/development/python-modules/pandas/default.nix b/pkgs/development/python-modules/pandas/default.nix
index ebb06f0f47db..08fdddb73467 100644
--- a/pkgs/development/python-modules/pandas/default.nix
+++ b/pkgs/development/python-modules/pandas/default.nix
@@ -24,8 +24,9 @@
 }:
 
 let
-  inherit (stdenv.lib) optional optionalString concatStringsSep;
+  inherit (stdenv.lib) optional optionals optionalString concatStringsSep;
   inherit (stdenv) isDarwin;
+
 in buildPythonPackage rec {
   pname = "pandas";
   version = "0.23.1";
@@ -67,6 +68,24 @@ in buildPythonPackage rec {
                 "['pandas/src/klib', 'pandas/src', '$cpp_sdk']"
   '';
 
+
+  disabledTests = stdenv.lib.concatMapStringsSep " and " (s: "not " + s) ([
+    # since dateutil 0.6.0 the following fails: test_fallback_plural, test_ambiguous_flags, test_ambiguous_compat
+    # was supposed to be solved by https://github.com/dateutil/dateutil/issues/321, but is not the case
+    "test_fallback_plural"
+    "test_ambiguous_flags"
+    "test_ambiguous_compat"
+    # Locale-related
+    "test_names"
+    "test_dt_accessor_datetime_name_accessors"
+    "test_datetime_name_accessors"
+    # Can't import from test folder
+    "test_oo_optimizable"
+  ] ++ optionals isDarwin [
+    "test_locale"
+    "test_clipboard"
+  ]);
+
   checkPhase = ''
     runHook preCheck
   ''
@@ -79,13 +98,7 @@ in buildPythonPackage rec {
     chmod a+x pbcopy pbpaste
     export PATH=$(pwd):$PATH
   '' + ''
-    # since dateutil 0.6.0 the following fails: test_fallback_plural, test_ambiguous_flags, test_ambiguous_compat
-    # was supposed to be solved by https://github.com/dateutil/dateutil/issues/321, but is not the case
-    py.test $out/${python.sitePackages}/pandas --skip-slow --skip-network \
-      -k "not test_fallback_plural and \
-          not test_ambiguous_flags and \
-          not test_ambiguous_compat \
-          ${optionalString isDarwin "and not test_locale and not test_clipboard"}"
+    py.test $out/${python.sitePackages}/pandas --skip-slow --skip-network -k "$disabledTests"
     runHook postCheck
   '';
 
diff --git a/pkgs/development/python-modules/python-periphery/default.nix b/pkgs/development/python-modules/python-periphery/default.nix
new file mode 100644
index 000000000000..b2b103858cce
--- /dev/null
+++ b/pkgs/development/python-modules/python-periphery/default.nix
@@ -0,0 +1,21 @@
+{ lib, buildPythonPackage, fetchPypi }:
+
+buildPythonPackage rec {
+  pname = "python-periphery";
+  version = "1.1.1";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "fe8f351934edce72cd919b4eb070878ebff551db5e21aea61e0f446101f0a79f";
+  };
+
+  # Some tests require physical probing and additional physical setup
+  doCheck = false;
+
+  meta = {
+    homepage = https://github.com/vsergeev/python-periphery;
+    description = "Linux Peripheral I/O (GPIO, LED, PWM, SPI, I2C, MMIO, Serial) with Python 2 & 3";
+    license = lib.licenses.mit;
+    maintainers = with lib.maintainers; [ bandresen ];
+  };
+}
diff --git a/pkgs/development/python-modules/seekpath/default.nix b/pkgs/development/python-modules/seekpath/default.nix
new file mode 100644
index 000000000000..de17e65d2bfb
--- /dev/null
+++ b/pkgs/development/python-modules/seekpath/default.nix
@@ -0,0 +1,25 @@
+{ stdenv, buildPythonPackage, fetchPypi, numpy, future, spglib, glibcLocales }:
+
+buildPythonPackage rec {
+  pname = "seekpath";
+  version = "1.8.1";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "0bdc0400c96952525b1165894807e4bec90aaedb11cfeb27a57414e6091eb026";
+  };  
+
+  LC_ALL = "en_US.utf-8";
+
+  propagatedBuildInputs = [ numpy spglib future ];
+
+  nativeBuildInputs = [ glibcLocales ];
+
+  meta = with stdenv.lib; {
+    description = "A module to obtain and visualize band paths in the Brillouin zone of crystal structures.";
+    homepage = https://github.com/giovannipizzi/seekpath;
+    license = licenses.mit;
+    maintainers = with maintainers; [ psyanticy ];
+  };
+}
+