Merge master into staging-next

2 files changed, 27 insertions, 92 deletions

diff --git a/pkgs/applications/science/biology/cmtk/default.nix b/pkgs/applications/science/biology/cmtk/default.nix
index 3eef648372555..a131c66454992 100644
--- a/pkgs/applications/science/biology/cmtk/default.nix
+++ b/pkgs/applications/science/biology/cmtk/default.nix
@@ -1,31 +1,47 @@
-{ lib, stdenv, fetchurl, cmake }:
+{ lib
+, stdenv
+, bzip2
+, cmake
+, fetchurl
+, fftw
+, llvmPackages
+, zlib
+}:
 
-stdenv.mkDerivation rec {
+stdenv.mkDerivation (finalAttrs: {
   pname = "cmtk";
-  version = "3.3.1";
+  version = "3.3.2";
 
   src = fetchurl {
     name = "cmtk-source.tar.gz";
-    url = "https://www.nitrc.org/frs/download.php/8198/CMTK-${version}-Source.tar.gz//?i_agree=1&download_now=1";
-    sha256 = "1nmsga9m7vcc4y4a6zl53ra3mwlgjwdgsq1j291awkn7zr1az6qs";
+    url = "https://www.nitrc.org/frs/download.php/13188/CMTK-${finalAttrs.version}-Source.tar.gz//?i_agree=1&download_now=1";
+    hash = "sha256-iE164NCOSOypZLLZfZy9RTyrS+YnY9ECqfb4QhlsMS4=";
   };
 
   nativeBuildInputs = [ cmake ];
 
+  buildInputs = [
+    bzip2
+    fftw
+    zlib
+  ] ++ lib.optionals stdenv.cc.isClang [
+    llvmPackages.openmp
+  ];
+
   env.NIX_CFLAGS_COMPILE = toString [
-    "-std=c++11"
-    (lib.optional stdenv.cc.isClang "-Wno-error=c++11-narrowing")
+    (lib.optionalString stdenv.cc.isGNU "-std=c++11")
+    (lib.optionalString stdenv.cc.isClang "-Wno-error=c++11-narrowing")
+    (lib.optionalString (stdenv.isDarwin && stdenv.isAarch64) "-Dfinite=isfinite")
   ];
 
   meta = with lib; {
-    broken = stdenv.isDarwin;
-    description = "Computational Morphometry Toolkit ";
+    description = "Computational Morphometry Toolkit";
     longDescription = ''A software toolkit for computational morphometry of
       biomedical images, CMTK comprises a set of command line tools and a
       back-end general-purpose library for processing and I/O'';
     maintainers = with maintainers; [ tbenst ];
     platforms = platforms.all;
-    license = licenses.gpl3;
+    license = licenses.gpl3Plus;
     homepage = "https://www.nitrc.org/projects/cmtk/";
   };
-}
+})
diff --git a/pkgs/applications/science/machine-learning/streamlit/default.nix b/pkgs/applications/science/machine-learning/streamlit/default.nix
deleted file mode 100755
index 36b03152f7871..0000000000000
--- a/pkgs/applications/science/machine-learning/streamlit/default.nix
+++ /dev/null
@@ -1,81 +0,0 @@
-{ lib
-, altair
-, blinker
-, buildPythonApplication
-, cachetools
-, click
-, fetchPypi
-, gitpython
-, importlib-metadata
-, jinja2
-, pillow
-, protobuf3
-, pyarrow
-, pydeck
-, pympler
-, requests
-, rich
-, semver
-, setuptools
-, tenacity
-, toml
-, tornado
-, tzlocal
-, validators
-, watchdog
-}:
-
-buildPythonApplication rec {
-  pname = "streamlit";
-  version = "1.24.0";
-  format = "setuptools";
-
-  src = fetchPypi {
-    inherit pname version format;
-    hash = "sha256-NSX6zpTHh5JzPFbWOja0iEUVDjume7UKGa20xZdagiU=";
-  };
-
-  propagatedBuildInputs = [
-    altair
-    blinker
-    cachetools
-    click
-    gitpython
-    importlib-metadata
-    jinja2
-    pillow
-    protobuf3
-    pyarrow
-    pydeck
-    pympler
-    requests
-    rich
-    semver
-    setuptools
-    tenacity
-    toml
-    tornado
-    tzlocal
-    validators
-    watchdog
-  ];
-
-  # pypi package does not include the tests, but cannot be built with fetchFromGitHub
-  doCheck = false;
-
-  pythonImportsCheck = [
-    "streamlit"
-  ];
-
-  postInstall = ''
-    rm $out/bin/streamlit.cmd # remove windows helper
-  '';
-
-  meta = with lib; {
-    homepage = "https://streamlit.io/";
-    changelog = "https://github.com/streamlit/streamlit/releases/tag/${version}";
-    description = "The fastest way to build custom ML tools";
-    maintainers = with maintainers; [ yrashk ];
-    license = licenses.asl20;
-  };
-}