Merge staging-next into staging

pkgs/development/python-modules/apache-airflow/default.nix

@@ -52,13 +52,16 @@
 , typing
 , nose
 , python
-, isPy3k
+, pythonOlder
+, pythonAtLeast
 }:
 
 buildPythonPackage rec {
   pname = "apache-airflow";
   version = "1.10.5";
-  disabled = (!isPy3k);
+  # Upstream does not yet support python 3.8
+  # https://github.com/apache/airflow/issues/8674
+  disabled = pythonOlder "3.5" || pythonAtLeast "3.8";
 
   src = fetchFromGitHub rec {
     owner = "apache";
@@ -189,6 +192,6 @@ buildPythonPackage rec {
     description = "Programmatically author, schedule and monitor data pipelines";
     homepage = "http://airflow.apache.org/";
     license = licenses.asl20;
-    maintainers = with maintainers; [ costrouc ingenieroariel ];
+    maintainers = with maintainers; [ bhipple costrouc ingenieroariel ];
   };
 }

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

@@ -2,6 +2,7 @@
 , buildPythonPackage
 , isPy27
 , fetchFromGitHub
+, fetchpatch
 , pytest
 , unittest2
 , future
@@ -27,6 +28,13 @@ buildPythonPackage rec {
     
   };
 
+  patches = [
+    (fetchpatch {
+      url = "https://github.com/MIC-DKFZ/batchgenerators/pull/59.patch";
+      sha256 = "171b3dm40yn0wi91m9s2nq3j565s1w39jpdf1mvc03rn75i8vdp0";
+    })
+  ];
+
   propagatedBuildInputs = [
     future numpy pillow scipy scikitlearn scikitimage threadpoolctl
   ];

pkgs/development/python-modules/django-versatileimagefield/default.nix

@@ -4,6 +4,7 @@
 , django
 , python
 , pillow
+, python_magic
 }:
 
 buildPythonPackage rec {
@@ -14,7 +15,7 @@ buildPythonPackage rec {
     inherit pname version;
     sha256 = "8322ee9d7bf5ffa5360990320d2cc2efc7017feff35422636d49f625721edf82";
   };
-  propagatedBuildInputs = [ pillow ];
+  propagatedBuildInputs = [ pillow python_magic ];
 
   checkInputs = [ django ];
 

pkgs/development/python-modules/google-api-python-client/default.nix

@@ -4,11 +4,11 @@
 
 buildPythonPackage rec {
   pname = "google-api-python-client";
-  version = "1.8.4";
+  version = "1.9.1";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "06csvbpdv3kl806nqvh5hpag86wpafp1q9r07m7kc1fw3xhi5qmv";
+    sha256 = "0nfqf62g3l7ij779ind41p800ahdjijkhqx8nq6y029p98672c52";
   };
 
   # No tests included in archive

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

@@ -1,14 +1,16 @@
 { lib, buildPythonPackage, fetchPypi, pythonOlder, isPy27
-, google_auth, protobuf, googleapis_common_protos, requests, setuptools, grpcio, mock }:
+, google_auth, protobuf, googleapis_common_protos, requests, setuptools, grpcio
+, mock
+}:
 
 buildPythonPackage rec {
   pname = "google-api-core";
-  version = "1.16.0";
+  version = "1.17.0";
   disabled = isPy27; # google namespace no longer works on python2
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1qh30ji399gngv2j1czzvi3h0mgx3lfdx2n8qp8vii7ihyh65scj";
+    sha256 = "12fn05x2fdhqmcaspjkkny2lh66hnnl0xf6pz3idxhlx8w5jl274";
   };
 
   propagatedBuildInputs = [
@@ -27,8 +29,13 @@ buildPythonPackage rec {
   ];
 
   meta = with lib; {
-    description = "This library is not meant to stand-alone. Instead it defines common helpers used by all Google API clients.";
-    homepage = "https://github.com/GoogleCloudPlatform/google-cloud-python";
+    description = "Core Library for Google Client Libraries";
+    longDescription = ''
+      This library is not meant to stand-alone. Instead it defines common
+      helpers used by all Google API clients.
+    '';
+    homepage = "https://github.com/googleapis/python-api-core";
+    changelog = "https://github.com/googleapis/python-api-core/blob/v${version}/CHANGELOG.md";
     license = licenses.asl20;
     maintainers = with maintainers; [ ];
   };

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

@@ -17,11 +17,11 @@
 
 buildPythonPackage rec {
   pname = "google-auth";
-  version = "1.11.3";
+  version = "1.16.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "05av4clwv7kdk1v55ibcv8aim6dwfg1mi4wy0vv91fr6wq3205zc";
+    sha256 = "1xd7fi7vhqbbkvwjg5fgj8bkbfjwxx4f2bb0zsnj8wci46qk4dqv";
   };
 
   propagatedBuildInputs = [ six pyasn1-modules cachetools rsa setuptools ];
@@ -43,8 +43,14 @@ buildPythonPackage rec {
   '';
 
   meta = with stdenv.lib; {
-    description = "This library simplifies using Google’s various server-to-server authentication mechanisms to access Google APIs.";
-    homepage = "https://google-auth.readthedocs.io/en/latest/";
+    description = "Google Auth Python Library";
+    longDescription = ''
+      This library simplifies using Google’s various server-to-server
+      authentication mechanisms to access Google APIs.
+    '';
+    homepage = "https://github.com/googleapis/google-auth-library-python";
+    changelog = "https://github.com/googleapis/google-auth-library-python/blob/v${version}/CHANGELOG.md";
+    # Documentation: https://googleapis.dev/python/google-auth/latest/index.html
     license = licenses.asl20;
     maintainers = with maintainers; [ ];
   };

pkgs/development/python-modules/pillow/6.nix

@@ -0,0 +1,82 @@
+{ stdenv, buildPythonPackage, fetchPypi, isPyPy
+, olefile
+, freetype, libjpeg, zlib, libtiff, libwebp, tcl, lcms2, tk, libX11
+, openjpeg, libimagequant
+, pytest, pytestrunner, pyroma, numpy
+}:
+
+buildPythonPackage rec {
+  pname = "Pillow";
+  version = "6.2.2";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "0l5rv8jkdrb5q846v60v03mcq64yrhklidjkgwv6s1pda71g17yv";
+  };
+
+  # Disable imagefont tests, because they don't work well with infinality:
+  # https://github.com/python-pillow/Pillow/issues/1259
+  postPatch = ''
+    rm Tests/test_imagefont.py
+  '';
+
+  checkPhase = ''
+    runHook preCheck
+    python -m pytest -v -x -W always
+    runHook postCheck
+  '';
+
+  propagatedBuildInputs = [ olefile ];
+
+  checkInputs = [ pytest pytestrunner pyroma numpy ];
+
+  buildInputs = [
+    freetype libjpeg openjpeg libimagequant zlib libtiff libwebp tcl lcms2 ]
+    ++ stdenv.lib.optionals (isPyPy) [ tk libX11 ];
+
+  # NOTE: we use LCMS_ROOT as WEBP root since there is not other setting for webp.
+  # NOTE: The Pillow install script will, by default, add paths like /usr/lib
+  # and /usr/include to the search paths. This can break things when building
+  # on a non-NixOS system that has some libraries installed that are not
+  # installed in Nix (for example, Arch Linux has jpeg2000 but Nix doesn't
+  # build Pillow with this support). We patch the `disable_platform_guessing`
+  # setting here, instead of passing the `--disable-platform-guessing`
+  # command-line option, since the command-line option doesn't work when we run
+  # tests.
+  preConfigure = let
+    libinclude' = pkg: ''"${pkg.out}/lib", "${pkg.out}/include"'';
+    libinclude = pkg: ''"${pkg.out}/lib", "${pkg.dev}/include"'';
+  in ''
+    sed -i "setup.py" \
+        -e 's|^FREETYPE_ROOT =.*$|FREETYPE_ROOT = ${libinclude freetype}|g ;
+            s|^JPEG_ROOT =.*$|JPEG_ROOT = ${libinclude libjpeg}|g ;
+            s|^JPEG2K_ROOT =.*$|JPEG2K_ROOT = ${libinclude openjpeg}|g ;
+            s|^IMAGEQUANT_ROOT =.*$|IMAGEQUANT_ROOT = ${libinclude' libimagequant}|g ;
+            s|^ZLIB_ROOT =.*$|ZLIB_ROOT = ${libinclude zlib}|g ;
+            s|^LCMS_ROOT =.*$|LCMS_ROOT = ${libinclude lcms2}|g ;
+            s|^TIFF_ROOT =.*$|TIFF_ROOT = ${libinclude libtiff}|g ;
+            s|^TCL_ROOT=.*$|TCL_ROOT = ${libinclude' tcl}|g ;
+            s|self\.disable_platform_guessing = None|self.disable_platform_guessing = True|g ;'
+    export LDFLAGS="-L${libwebp}/lib"
+    export CFLAGS="-I${libwebp}/include"
+  ''
+  # Remove impurities
+  + stdenv.lib.optionalString stdenv.isDarwin ''
+    substituteInPlace setup.py \
+      --replace '"/Library/Frameworks",' "" \
+      --replace '"/System/Library/Frameworks"' ""
+  '';
+
+  meta = with stdenv.lib; {
+    homepage = "https://python-pillow.github.io/";
+    description = "Fork of The Python Imaging Library (PIL)";
+    longDescription = ''
+      The Python Imaging Library (PIL) adds image processing
+      capabilities to your Python interpreter.  This library
+      supports many file formats, and provides powerful image
+      processing and graphics capabilities.
+    '';
+    license = "http://www.pythonware.com/products/pil/license.htm";
+    maintainers = with maintainers; [ goibhniu prikhi ];
+  };
+}

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

@@ -1,32 +1,37 @@
 { stdenv, buildPythonPackage, fetchPypi, isPyPy
 , olefile
 , freetype, libjpeg, zlib, libtiff, libwebp, tcl, lcms2, tk, libX11
-, pytestrunner
-, pytest
+, openjpeg, libimagequant
+, pyroma, numpy, pytestCheckHook
+, isPy3k
 }:
+
 buildPythonPackage rec {
   pname = "Pillow";
-  version = "6.2.2";
+  version = "7.1.2";
+
+  disabled = !isPy3k;
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "db9ff0c251ed066d367f53b64827cc9e18ccea001b986d08c265e53625dab950";
+    sha256 = "1pdh1zzdwxilvsjg6rnl4q810pc2p2y16q6lx9gzzihb25h9kd50";
   };
 
-  doCheck = !stdenv.isDarwin && !isPyPy;
-
   # Disable imagefont tests, because they don't work well with infinality:
   # https://github.com/python-pillow/Pillow/issues/1259
   postPatch = ''
     rm Tests/test_imagefont.py
   '';
 
+  # Disable darwin tests which require executables: `iconutil` and `screencapture`
+  disabledTests = stdenv.lib.optionals stdenv.isDarwin [ "test_save" "test_grab" "test_grabclipboard" ];
+
   propagatedBuildInputs = [ olefile ];
 
-  checkInputs = [ pytest pytestrunner ];
+  checkInputs = [ pytestCheckHook pyroma numpy ];
 
   buildInputs = [
-    freetype libjpeg zlib libtiff libwebp tcl lcms2 ]
+    freetype libjpeg openjpeg libimagequant zlib libtiff libwebp tcl lcms2 ]
     ++ stdenv.lib.optionals (isPyPy) [ tk libX11 ];
 
   # NOTE: we use LCMS_ROOT as WEBP root since there is not other setting for webp.
@@ -45,6 +50,8 @@ buildPythonPackage rec {
     sed -i "setup.py" \
         -e 's|^FREETYPE_ROOT =.*$|FREETYPE_ROOT = ${libinclude freetype}|g ;
             s|^JPEG_ROOT =.*$|JPEG_ROOT = ${libinclude libjpeg}|g ;
+            s|^JPEG2K_ROOT =.*$|JPEG2K_ROOT = ${libinclude openjpeg}|g ;
+            s|^IMAGEQUANT_ROOT =.*$|IMAGEQUANT_ROOT = ${libinclude' libimagequant}|g ;
             s|^ZLIB_ROOT =.*$|ZLIB_ROOT = ${libinclude zlib}|g ;
             s|^LCMS_ROOT =.*$|LCMS_ROOT = ${libinclude lcms2}|g ;
             s|^TIFF_ROOT =.*$|TIFF_ROOT = ${libinclude libtiff}|g ;
@@ -61,8 +68,8 @@ buildPythonPackage rec {
   '';
 
   meta = with stdenv.lib; {
-    homepage = "https://python-pillow.github.io/";
-    description = "Fork of The Python Imaging Library (PIL)";
+    homepage = "https://python-pillow.org/";
+    description = "The friendly PIL fork (Python Imaging Library)";
     longDescription = ''
       The Python Imaging Library (PIL) adds image processing
       capabilities to your Python interpreter.  This library

pkgs/development/python-modules/py4j/default.nix

@@ -7,7 +7,6 @@ buildPythonPackage rec {
 
   src = fetchPypi {
     inherit pname version;
-    extension= "zip";
     sha256 = "36ec57f43ff8ced260a18aa9a4e46c3500a730cac8860e259cbaa546c2b9db2f";
   };
 

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

@@ -1,11 +1,11 @@
 { stdenv, buildPythonPackage, fetchPypi, mupdf, swig }:
 buildPythonPackage rec {
   pname = "PyMuPDF";
-  version = "1.16.18";
+  version = "1.17.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "0gpcmmcjgwc6x4rn6nm3akiijdkpa9nahsw2x8a0i7z7kzj4firk";
+    sha256 = "0de92a8fb65db6e661594cc5865a340a2daac3cb9bb58e030820769ece1343c1";
   };
 
   patchPhase = ''

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

@@ -4,6 +4,7 @@
 buildPythonPackage rec {
   pname = "shellingham";
   version = "1.3.2";
+  format = "pyproject";
 
   src = fetchPypi {
     inherit pname version;

pkgs/development/python-modules/toggl-cli/default.nix

@@ -1,13 +1,26 @@
-{ stdenv, buildPythonPackage, fetchPypi, twine, pbr, click, click-completion, validate-email,
-pendulum, ptable, requests, inquirer, pythonOlder, pytest, pytestcov, pytest-mock, faker, factory_boy,
-setuptools }:
+{ stdenv, buildPythonPackage, fetchPypi, pythonAtLeast, pythonOlder
+, click
+, click-completion
+, factory_boy
+, faker
+, inquirer
+, pbr
+, pendulum
+, ptable
+, pytest
+, pytestcov
+, pytest-mock
+, requests
+, setuptools
+, twine
+, validate-email
+}:
 
 
 buildPythonPackage rec {
   pname = "toggl-cli";
   version = "2.1.0";
-
-  disabled = pythonOlder "3.5";
+  disabled = pythonOlder "3.5" || pythonAtLeast "3.8";
 
   src = fetchPypi {
     pname = "togglCli";