Merge master into staging-next

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

@@ -0,0 +1,37 @@
+{ lib
+, buildPythonPackage
+, fetchFromGitHub
+, numpy
+, scipy
+, pymatgen
+, pytestCheckHook
+}:
+
+buildPythonPackage rec {
+  pname = "castepxbin";
+  version = "0.1.0";
+
+  src = fetchFromGitHub {
+    owner = "zhubonan";
+    repo = "castepxbin";
+    rev = "v${version}";
+    sha256 = "16wnd1mwhl204d1s3har2fhyhyjg86sypg00bj812dxk8zixxszf";
+  };
+
+  propagatedBuildInputs = [
+    numpy
+    scipy
+    pymatgen
+  ];
+
+  checkInputs = [
+    pytestCheckHook
+  ];
+
+  meta = with lib; {
+    description = "A collection of readers for CASTEP binary outputs";
+    homepage = "https://github.com/zhubonan/castepxbin";
+    license = licenses.mit;
+    maintainers = with maintainers; [ dotlambda ];
+  };
+}

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

@@ -1,38 +0,0 @@
-{ lib
-, buildPythonPackage
-, fetchPypi
-, chardet
-, attrs
-, pytestCheckHook
-}:
-buildPythonPackage rec {
-  pname = "debut";
-  version = "0.9.9";
-
-  src = fetchPypi {
-    inherit pname version;
-    sha256 = "a3a71e475295f4cf4292440c9c7303ebca0309d395536d2a7f86a5f4d7465dc1";
-  };
-
-  dontConfigure = true;
-
-  propagatedBuildInputs = [
-    chardet
-    attrs
-  ];
-
-  checkInputs = [
-    pytestCheckHook
-  ];
-
-  pythonImportsCheck = [
-    "debut"
-  ];
-
-  meta = with lib; {
-    description = "Python library to parse Debian deb822-style control and copyright files ";
-    homepage = "https://github.com/nexB/debut";
-    license = with licenses; [ asl20 bsd3 mit ];
-    maintainers = teams.determinatesystems.members;
-  };
-}

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

@@ -10,7 +10,7 @@
 , gsettings-desktop-schemas
 , fetchurl
 , dbus
-, xvfb_run
+, xvfb-run
 , wrapGAppsHook
 # , fetchPypi
 }:
@@ -33,7 +33,7 @@ buildPythonPackage {
     ./nix-support.patch
   ];
 
-  nativeBuildInputs = [ gobject-introspection dbus xvfb_run wrapGAppsHook ]; # for setup hooks
+  nativeBuildInputs = [ gobject-introspection dbus xvfb-run wrapGAppsHook ]; # for setup hooks
   propagatedBuildInputs = [ at-spi2-core gtk3 pygobject3 pyatspi pycairo ];
   strictDeps = false; # issue 56943
 

pkgs/development/python-modules/drf-nested-routers/default.nix

@@ -13,13 +13,13 @@
 
 buildPythonPackage rec {
   pname = "drf-nested-routers";
-  version = "0.92.5";
+  version = "0.93.3";
 
   src = fetchFromGitHub {
     owner = "alanjds";
     repo = "drf-nested-routers";
     rev = "v${version}";
-    sha256 = "1l1jza8xz6xcm3gwxh1k6pc8fs95cq3v751gxj497y1a83d26j8i";
+    sha256 = "1gmw6gwiqzfysx8qn7aan7xgkizxy64db94z30pm3bvn6jxv08si";
   };
 
   propagatedBuildInputs = [ django djangorestframework setuptools ];

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

@@ -1,4 +1,13 @@
-{ lib, stdenv, libusb1, udev, darwin, fetchPypi, buildPythonPackage, cython }:
+{ lib
+, stdenv
+, buildPythonPackage
+, fetchPypi
+, xcbuild
+, cython
+, libusb1
+, udev
+, darwin
+}:
 
 buildPythonPackage rec {
   pname = "hidapi";
@@ -9,18 +18,17 @@ buildPythonPackage rec {
     sha256 = "a1170b18050bc57fae3840a51084e8252fd319c0fc6043d68c8501deb0e25846";
   };
 
-  propagatedBuildInputs =
-    lib.optionals stdenv.isLinux [ libusb1 udev ] ++
-    lib.optionals stdenv.isDarwin (with darwin.apple_sdk.frameworks; [ AppKit CoreFoundation IOKit ]) ++
-    [ cython ];
+  nativeBuildInputs = lib.optionals stdenv.isDarwin [ xcbuild ];
+
+  propagatedBuildInputs = [ cython ]
+    ++ lib.optionals stdenv.isLinux [ libusb1 udev ]
+    ++ lib.optionals stdenv.isDarwin (with darwin.apple_sdk.frameworks; [ AppKit CoreFoundation IOKit ]);
 
   # Fix the USB backend library lookup
   postPatch = lib.optionalString stdenv.isLinux ''
     libusb=${libusb1.dev}/include/libusb-1.0
     test -d $libusb || { echo "ERROR: $libusb doesn't exist, please update/fix this build expression."; exit 1; }
     sed -i -e "s|/usr/include/libusb-1.0|$libusb|" setup.py
-  '' + lib.optionalString stdenv.isDarwin ''
-    substituteInPlace setup.py --replace 'macos_sdk_path =' 'macos_sdk_path = "" #'
   '';
 
   pythonImportsCheck = [ "hid" ];
@@ -30,7 +38,7 @@ buildPythonPackage rec {
     homepage = "https://github.com/trezor/cython-hidapi";
     # license can actually be either bsd3 or gpl3
     # see https://github.com/trezor/cython-hidapi/blob/master/LICENSE-orig.txt
-    license = licenses.bsd3;
+    license = with licenses; [ bsd3 gpl3Only ];
     maintainers = with maintainers; [ np prusnak ];
   };
 }

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

@@ -3,7 +3,7 @@
 , buildPythonPackage
 , python
 , pygobject3
-, xvfb_run
+, xvfb-run
 , gobject-introspection
 , gtk3
 , pythonOlder
@@ -32,7 +32,7 @@ buildPythonPackage rec {
 
   checkPhase = ''
     runHook preCheck
-    ${xvfb_run}/bin/xvfb-run -s '-screen 0 800x600x24' \
+    ${xvfb-run}/bin/xvfb-run -s '-screen 0 800x600x24' \
       ${python.interpreter} nix_run_setup test
     runHook postCheck
   '';

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

@@ -0,0 +1,44 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, pytestCheckHook
+, typer
+, dataclasses
+, smart_open
+, pytest
+, mock
+, google-cloud-storage
+}:
+
+buildPythonPackage rec {
+  pname = "pathy";
+  version = "0.5.2";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "sha256-nb8my/5rkc7thuHnXZHe1Hg8j+sLBlYyJcLHWrrKZ5M=";
+  };
+
+  propagatedBuildInputs = [ smart_open typer google-cloud-storage ];
+
+  postPatch = ''
+    substituteInPlace requirements.txt \
+      --replace "smart-open>=2.2.0,<4.0.0" "smart-open>=2.2.0"
+  '';
+
+  checkInputs = [ pytestCheckHook mock ];
+
+  # Exclude tests that require provider credentials
+  pytestFlagsArray = [
+    "--ignore=pathy/_tests/test_clients.py"
+    "--ignore=pathy/_tests/test_gcs.py"
+    "--ignore=pathy/_tests/test_s3.py"
+  ];
+
+  meta = with lib; {
+    description = "A Path interface for local and cloud bucket storage";
+    homepage = "https://github.com/justindujardin/pathy";
+    license = licenses.asl20;
+    maintainers = with maintainers; [ melling ];
+  };
+}

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

@@ -1,4 +1,5 @@
 { lib
+, stdenv
 , fetchPypi
 , buildPythonPackage
 , Mako
@@ -12,14 +13,18 @@
 , opencl-headers
 , ocl-icd
 , pybind11
+, mesa_drivers
 }:
 
-buildPythonPackage rec {
+let
+  os-specific-buildInputs =
+    if stdenv.isDarwin then [ mesa_drivers.dev ] else [ ocl-icd ];
+in buildPythonPackage rec {
   pname = "pyopencl";
   version = "2021.1.4";
 
   checkInputs = [ pytest ];
-  buildInputs = [ opencl-headers ocl-icd pybind11 ];
+  buildInputs = [ opencl-headers pybind11 ] ++ os-specific-buildInputs;
 
   propagatedBuildInputs = [ numpy cffi pytools decorator appdirs six Mako ];
 

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

@@ -1,5 +1,5 @@
 { lib, buildPythonPackage, fetchFromGitHub
-, pillow, xlib, six, xvfb_run, sphinx }:
+, pillow, xlib, six, xvfb-run, sphinx }:
 
 buildPythonPackage rec {
   pname = "pystray";
@@ -14,7 +14,7 @@ buildPythonPackage rec {
 
   nativeBuildInputs = [ sphinx ];
   propagatedBuildInputs = [ pillow xlib six ];
-  checkInputs = [ xvfb_run ];
+  checkInputs = [ xvfb-run ];
 
   checkPhase = ''
     rm tests/icon_tests.py # test needs user input

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

@@ -6,7 +6,7 @@
 , pytest
 , pythonOlder
 , qt5
-, xvfb_run
+, xvfb-run
 }:
 
 buildPythonPackage rec {
@@ -31,7 +31,7 @@ buildPythonPackage rec {
 
   checkInputs = [
     pytest
-    xvfb_run
+    xvfb-run
   ];
 
   checkPhase = ''

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

@@ -7,6 +7,7 @@
 , blis
 , catalogue
 , cymem
+, jinja2
 , jsonschema
 , murmurhash
 , numpy
@@ -16,8 +17,12 @@
 , requests
 , setuptools
 , srsly
+, spacy-legacy
 , thinc
 , wasabi
+, packaging
+, pathy
+, pydantic
 }:
 
 buildPythonPackage rec {
@@ -33,6 +38,7 @@ buildPythonPackage rec {
     blis
     catalogue
     cymem
+    jinja2
     jsonschema
     murmurhash
     numpy
@@ -41,8 +47,12 @@ buildPythonPackage rec {
     requests
     setuptools
     srsly
+    spacy-legacy
     thinc
     wasabi
+    packaging
+    pathy
+    pydantic
   ] ++ lib.optional (pythonOlder "3.4") pathlib;
 
   checkInputs = [
@@ -60,7 +70,8 @@ buildPythonPackage rec {
       --replace "catalogue>=0.0.7,<1.1.0" "catalogue>=0.0.7,<3.0" \
       --replace "plac>=0.9.6,<1.2.0" "plac>=0.9.6,<2.0" \
       --replace "srsly>=1.0.2,<1.1.0" "srsly>=1.0.2,<3.0" \
-      --replace "thinc>=7.4.1,<7.5.0" "thinc>=7.4.1,<8"
+      --replace "thinc>=7.4.1,<7.5.0" "thinc>=7.4.1,<8" \
+      --replace "pydantic>=1.7.1,<1.8.0" "pydantic>=1.7.1,<1.8.3"
   '';
 
   pythonImportsCheck = [ "spacy" ];

pkgs/development/python-modules/spacy/legacy.nix

@@ -0,0 +1,26 @@
+{ lib
+, fetchPypi
+, buildPythonPackage
+, pytestCheckHook
+}:
+
+buildPythonPackage rec {
+  pname = "spacy-legacy";
+  version = "3.0.5";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "sha256-Uy94rjFllSj622RTzd6UJaQmIniCw4gpeq/X57QcIpA=";
+  };
+
+  # checkInputs = [ pytestCheckHook spacy ];
+  doCheck = false;
+  pythonImportsCheck = [ "spacy_legacy" ];
+
+  meta = with lib; {
+    description = "A Path interface for local and cloud bucket storage";
+    homepage = "https://github.com/justindujardin/pathy";
+    license = licenses.asl20;
+    maintainers = with maintainers; [ melling ];
+  };
+}

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

@@ -1,37 +1,44 @@
-{ lib, buildPythonPackage, fetchFromGitHub, isPy27
+{ lib, buildPythonPackage, fetchFromGitHub
+, pythonOlder
 , h5py
 , matplotlib
 , numpy
 , phonopy
 , pymatgen
-, pytest
 , scipy
 , seekpath
 , spglib
+, castepxbin
+, pytestCheckHook
 }:
 
 buildPythonPackage rec {
   pname = "sumo";
-  version = "2.2.1";
+  version = "2.2.4";
+
+  disabled = pythonOlder "3.6";
 
   # No tests in Pypi tarball
   src = fetchFromGitHub {
     owner = "SMTG-UCL";
     repo = "sumo";
     rev = "v${version}";
-    sha256 = "0r88f5w33h9b0mv7shlqc4przwvas5ycgndvl91wqjnm3b2s3ix0";
+    sha256 = "051353gsxmh4qnabshfnc00mmzdbh1fgk1xdfnsfgcnijxgw25bb";
   };
 
-  propagatedBuildInputs = [ numpy scipy spglib pymatgen h5py matplotlib seekpath phonopy ];
+  propagatedBuildInputs = [
+    spglib
+    numpy
+    scipy
+    h5py
+    pymatgen
+    phonopy
+    matplotlib
+    seekpath
+    castepxbin
+  ];
 
-  checkInputs = [ pytest ];
-
-  checkPhase = ''
-    pytest .
-  '';
-
-  # tests have type annotations, can only run on 3.5+
-  doCheck = (!isPy27);
+  checkInputs = [ pytestCheckHook ];
 
   meta = with lib; {
     description = "Toolkit for plotting and analysis of ab initio solid-state calculation data";

pkgs/development/python-modules/tern/0001-Replace-debut-with-debian-inspector.patch

@@ -0,0 +1,40 @@
+From d944d8fa6cb6d1667f3e4c4e0cff4c4b2a7c0a30 Mon Sep 17 00:00:00 2001
+From: Cole Helbling <cole.e.helbling@outlook.com>
+Date: Fri, 7 May 2021 11:00:46 -0700
+Subject: [PATCH] Replace `debut` with `debian-inspector`
+
+---
+ requirements.in        | 2 +-
+ tern/analyze/common.py | 4 ++--
+ 2 files changed, 3 insertions(+), 3 deletions(-)
+
+diff --git a/requirements.in b/requirements.in
+index edd90ab..5135841 100644
+--- a/requirements.in
++++ b/requirements.in
+@@ -12,6 +12,6 @@ requests
+ stevedore
+ pbr
+ dockerfile-parse
+-debut
++debian-inspector
+ regex
+ GitPython
+diff --git a/tern/analyze/common.py b/tern/analyze/common.py
+index 6962404..0f5e77d 100644
+--- a/tern/analyze/common.py
++++ b/tern/analyze/common.py
+@@ -19,8 +19,8 @@ from tern.utils import cache
+ from tern.utils import constants
+ from tern.utils import general
+ from tern.utils import rootfs
+-from debut import debcon
+-from debut import copyright as debut_copyright
++from debian_inspector import debcon
++from debian_inspector import copyright as debut_copyright
+ 
+ # global logger
+ logger = logging.getLogger(constants.logger_name)
+-- 
+2.31.1
+

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

@@ -7,7 +7,7 @@
 , requests
 , stevedore
 , pbr
-, debut
+, debian-inspector
 , regex
 , GitPython
 , prettytable
@@ -22,6 +22,14 @@ buildPythonPackage rec {
     sha256 = "606c62944991b2cbcccf3f5353be693305d6d7d318c3865b9ecca49dbeab2727";
   };
 
+  patches = [
+    # debut was renamed to debian-inspector
+    # https://github.com/tern-tools/tern/pull/962
+    # NOTE: Has to be in-tree because the upstream patch doesn't apply cleanly
+    # to the PyPi source.
+    ./0001-Replace-debut-with-debian-inspector.patch
+  ];
+
   preBuild = ''
     cp requirements.{in,txt}
   '';
@@ -36,7 +44,7 @@ buildPythonPackage rec {
     dockerfile-parse
     requests
     stevedore
-    debut
+    debian-inspector
     regex
     GitPython
     prettytable

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

@@ -1,4 +1,4 @@
-{ lib, buildPythonPackage, fetchPypi, isPy3k, python3, xvfb_run
+{ lib, buildPythonPackage, fetchPypi, isPy3k, python3, xvfb-run
 , wrapGAppsHook, gobject-introspection, pygobject3, graphviz, gtk3, numpy }:
 
 buildPythonPackage rec {
@@ -13,7 +13,7 @@ buildPythonPackage rec {
   disabled = !isPy3k;
   nativeBuildInputs = [ wrapGAppsHook ];
   propagatedBuildInputs = [ gobject-introspection pygobject3 graphviz gtk3 numpy ];
-  checkInputs = [ xvfb_run ];
+  checkInputs = [ xvfb-run ];
 
   checkPhase = ''
     xvfb-run -s '-screen 0 800x600x24' ${python3.interpreter} nix_run_setup test