Merge master into staging-next

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

@@ -1,11 +1,16 @@
-{ lib
+{ blessed
 , buildPythonPackage
 , fetchPypi
-, pythonOlder
+, lib
+, libcxx
+, libcxxabi
 , llvm
-, typesentry
-, blessed
+, openmp
 , pytest
+, pythonOlder
+, stdenv
+, substituteAll
+, typesentry
 }:
 
 buildPythonPackage rec {
@@ -17,10 +22,25 @@ buildPythonPackage rec {
     sha256 = "1s8z81zffrckvdwrrl0pkjc7gsdvjxw59xgg6ck81dl7gkh5grjk";
   };
 
+  patches = [
+    # Disable the compiler monkey patching, and remove the task that's copying
+    # the native dependencies to the build directory.
+    ./remove-compiler-monkeypatch_disable-native-relocation.patch
+  ] ++ lib.optionals stdenv.isDarwin [
+    # Replace the library auto-detection with hardcoded paths.
+    (substituteAll {
+      src = ./hardcode-library-paths.patch;
+
+      libomp_dylib = "${lib.getLib openmp}/lib/libomp.dylib";
+      libcxx_dylib = "${lib.getLib libcxx}/lib/libc++.1.dylib";
+      libcxxabi_dylib = "${lib.getLib libcxxabi}/lib/libc++abi.dylib";
+    })
+  ];
+
   disabled = pythonOlder "3.5";
 
   propagatedBuildInputs = [ typesentry blessed ];
-  buildInputs = [ llvm ];
+  buildInputs = [ llvm ] ++ lib.optionals stdenv.isDarwin [ openmp ];
   checkInputs = [ pytest ];
 
   LLVM = llvm;

pkgs/development/python-modules/datatable/hardcode-library-paths.patch

@@ -0,0 +1,43 @@
+diff --git a/ci/setup_utils.py b/ci/setup_utils.py
+index 66b385a..6255af0 100644
+--- a/ci/setup_utils.py
++++ b/ci/setup_utils.py
+@@ -600,37 +600,7 @@ def find_linked_dynamic_libraries():
+     them as a list of absolute paths.
+     """
+     with TaskContext("Find the required dynamic libraries") as log:
+-        llvm = get_llvm()
+-        libs = required_link_libraries()
+-        resolved = []
+-        for libname in libs:
+-            if llvm:
+-                fullpath = os.path.join(llvm, "lib", libname)
+-                if os.path.isfile(fullpath):
+-                    resolved.append(fullpath)
+-                    log.info("Library `%s` found at %s" % (libname, fullpath))
+-                    continue
+-                else:
+-                    log.info("%s does not exist" % fullpath)
+-            # Rely on the shell `locate` command to find the dynamic libraries.
+-            proc = subprocess.Popen(["locate", libname], stdout=subprocess.PIPE,
+-                                    stderr=subprocess.PIPE)
+-            stdout, stderr = proc.communicate()
+-            if proc.returncode == 0:
+-                results = stdout.decode().strip().split("\n")
+-                results = [r for r in results if r]
+-                if results:
+-                    results.sort(key=len)
+-                    fullpath = results[0]
+-                    assert os.path.isfile(fullpath), "Invalid path: %r" % (fullpath,)
+-                    resolved.append(fullpath)
+-                    log.info("Library `%s` found at %s" % (libname, fullpath))
+-                    continue
+-                else:
+-                    log.fatal("Cannot locate dynamic library `%s`" % libname)
+-            else:
+-                log.fatal("`locate` command returned the following error:\n%s"
+-                          % stderr.decode())
++        resolved = ["@libomp_dylib@", "@libcxx_dylib@", "@libcxxabi_dylib@"]
+         return resolved
+ 
+ 

pkgs/development/python-modules/datatable/remove-compiler-monkeypatch_disable-native-relocation.patch

@@ -0,0 +1,28 @@
+diff --git a/setup.py b/setup.py
+index 58fc875..8032561 100644
+--- a/setup.py
++++ b/setup.py
+@@ -141,23 +141,6 @@ if cmd in ("build", "bdist_wheel", "build_ext", "install"):
+     extra_link_args = get_extra_link_args()
+     cpp_files = get_c_sources("c")
+ 
+-    with TaskContext("Copy dynamic libraries") as log:
+-        # Copy system libraries into the datatable/lib folder, so that they can
+-        # be packaged with the wheel
+-        libs = find_linked_dynamic_libraries()
+-        for libpath in libs:
+-            trgfile = os.path.join("datatable", "lib",
+-                                   os.path.basename(libpath))
+-            if os.path.exists(trgfile):
+-                log.info("File %s already exists, skipped" % trgfile)
+-            else:
+-                log.info("Copying %s to %s" % (libpath, trgfile))
+-                shutil.copy(libpath, trgfile)
+-
+-    if ismacos():
+-        monkey_patch_compiler()
+-
+-
+ # Create the git version file
+ if cmd in ("build", "sdist", "bdist_wheel", "install"):
+     make_git_version_file(True)

pkgs/development/python-modules/mysql-connector/default.nix

@@ -4,13 +4,13 @@
 
 buildPythonPackage rec {
   pname = "mysql-connector";
-  version = "8.0.16";
+  version = "8.0.17";
 
   src = fetchFromGitHub {
     owner = "mysql";
     repo = "mysql-connector-python";
     rev = version;
-    sha256 = "0yl3fkyws24lc2qrbvn42bqy72aqy8q5v8f0j5zy3mkh9a7wlxdp";
+    sha256 = "1by0g7hrbmb1wj2wh3q9y92mjimck2izh1i4fm1xfbp278p2acbd";
   };
 
   propagatedBuildInputs = [ protobuf ];

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

@@ -0,0 +1,33 @@
+{ lib
+, buildPythonPackage
+, botocore
+, fetchPypi
+, mock
+, mypy
+, python-dateutil
+, pytest
+, requests
+}:
+
+buildPythonPackage rec {
+  pname = "pynamodb";
+  version = "3.4.1";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1cwgqvpqn59y3zq4wv35m1v4jrh3ih6zbyv30g5nxbw13vddxr92";
+  };
+
+  propagatedBuildInputs = [ python-dateutil botocore ];
+  checkInputs = [ requests mock pytest mypy ];
+
+  meta = with lib; {
+    description = "A Pythonic interface for Amazon’s DynamoDB that supports Python 2 and 3.";
+    longDescription = ''
+      DynamoDB is a great NoSQL service provided by Amazon, but the API is
+      verbose. PynamoDB presents you with a simple, elegant API.
+    '';
+    homepage = "http://jlafon.io/pynamodb.html";
+    license = licenses.mit;
+  };
+}

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

@@ -1,4 +1,4 @@
-{ lib, buildPythonPackage, fetchPypi, python, pkgs, pythonOlder, substituteAll
+{ lib, buildPythonPackage, fetchFromGitHub, python, pkgs, pythonOlder, substituteAll
 , aenum
 , cython
 , pytest
@@ -8,11 +8,13 @@
 
 buildPythonPackage rec {
   pname = "pyproj";
-  version = "2.2.1";
+  version = "2.2.2";
 
-  src = fetchPypi {
-    inherit pname version;
-    sha256 = "0yigcxwmx5cczipf2mpmy2gq1dnl0635yjvjq86ay47j1j5fd2gc";
+  src = fetchFromGitHub {
+    owner = "pyproj4";
+    repo = "pyproj";
+    rev = "v${version}rel";
+    sha256 = "0mb0jczgqh3sma69k7237i38h09gxgmvmddls9hpw4f3131f5ax7";
   };
 
   # force pyproj to use ${pkgs.proj}

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

@@ -1,18 +1,20 @@
-{ fetchPypi, buildPythonPackage }:
+{ lib, fetchPypi, buildPythonPackage }:
+
 buildPythonPackage rec {
   pname = "redis";
-  version = "3.1.0";
+  version = "3.3.4";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "7ba8612bbfd966dea8c62322543fed0095da2834dbd5a7c124afbc617a156aa7";
+    sha256 = "18n6k113izfqsm8yysrw1a5ba6kv0vsgfz6ab5n0k6k65yvr690z";
   };
 
   # tests require a running redis
   doCheck = false;
 
-  meta = {
+  meta = with lib; {
     description = "Python client for Redis key-value store";
     homepage = "https://pypi.python.org/pypi/redis/";
+    license = with licenses; [ mit ];
   };
 }

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

@@ -25,18 +25,16 @@
 
 buildPythonPackage rec {
   pname = "spacy";
-  version = "2.1.6";
+  version = "2.1.7";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1s0a0vir9lg5q8n832kkadbajb4i4zl20zmdg3g20qlp4mcbn25p";
+    sha256 = "0k4kh9jnpdawaqjxwcdi2h01s85s5r338ajgv9kkq59iha4hichh";
   };
 
   prePatch = ''
     substituteInPlace setup.py \
-      --replace "plac<1.0.0,>=0.9.6" "plac>=0.9.6" \
-      --replace "regex==" "regex>=" \
-      --replace "wheel>=0.32.0,<0.33.0" "wheel>=0.32.0"
+      --replace "plac<1.0.0,>=0.9.6" "plac>=0.9.6"
   '';
 
   propagatedBuildInputs = [

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

@@ -30,8 +30,6 @@ buildPythonPackage rec {
     sha256 = "50402545ac92b1a931c2365e341cb35c4ebe5575525f1dcc5265901ff3895a5f";
   };
 
-  disabled = isPy27; # 2.7 requires backports.csv
-
   propagatedBuildInputs = [
     cachetools
     cld2-cffi
@@ -64,5 +62,8 @@ buildPythonPackage rec {
     homepage = "http://textacy.readthedocs.io/";
     license = licenses.asl20;
     maintainers = with maintainers; [ rvl ];
+    # ftfy and jellyfish no longer support python2
+    # latest scikitlearn not supported for this: https://github.com/chartbeat-labs/textacy/issues/260
+    broken = true;
   };
 }

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

@@ -3,11 +3,11 @@
 
 buildPythonPackage rec {
   pname = "zstd";
-  version = "1.4.0.0";
+  version = "1.4.1.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "01prq9rwz1gh42idnj2162w79dzs8gf3ac8pn12lz347w280kjbk";
+    sha256 = "0laxg0pag1bzmqmg4x81jb32412pn98p9zg2b0li035m779nka95";
   };
 
   postPatch = ''