Merge pull request conda-forge#17766 from goanpeca/add-stardist

Add stardist recipe

recipes/stardist/clipper.LICENSE.txt

@@ -0,0 +1,24 @@
+Boost Software License - Version 1.0 - August 17th, 2003
+http://www.boost.org/LICENSE_1_0.txt
+
+Permission is hereby granted, free of charge, to any person or organization
+obtaining a copy of the software and accompanying documentation covered by
+this license (the "Software") to use, reproduce, display, distribute,
+execute, and transmit the Software, and to prepare derivative works of the
+Software, and to permit third-parties to whom the Software is furnished to
+do so, all subject to the following:
+
+The copyright notices in the Software and this entire statement, including
+the above license grant, this restriction and the following disclaimer,
+must be included in all copies of the Software, in whole or in part, and
+all derivative works of the Software, unless such copies or derivative
+works are solely in the form of machine-executable object code generated by
+a source language processor.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE, TITLE AND NON-INFRINGEMENT. IN NO EVENT
+SHALL THE COPYRIGHT HOLDERS OR ANYONE DISTRIBUTING THE SOFTWARE BE LIABLE
+FOR ANY DAMAGES OR OTHER LIABILITY, WHETHER IN CONTRACT, TORT OR OTHERWISE,
+ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.

recipes/stardist/meta.yaml

@@ -0,0 +1,62 @@
+{% set name = "stardist" %}
+{% set version = "0.8.1" %}
+
+package:
+  name: {{ name|lower }}
+  version: {{ version }}
+
+source:
+  url: https://github.com/stardist/stardist/archive/refs/tags/{{ version }}.tar.gz
+  sha256: 3d1049b2a136c44c619a858de9de67ffda96d2c51d07c1fcd8a958e87cc1b7e0
+  patches:
+    - setup.patch  # [osx]
+
+build:
+  script: {{ PYTHON }} -m pip install . -vv
+  number: 0
+
+requirements:
+  build:
+    - {{ compiler('c') }}
+    - {{ compiler('cxx') }}
+    - make
+    - llvm-openmp  # [osx]
+    - libgomp      # [linux]
+  host:
+    - numpy
+    - pip
+    - python
+    - setuptools
+  run:
+    - csbdeep >=0.6.3
+    - numba
+    - python
+    - scikit-image
+    - imageio
+    - {{ pin_compatible('numpy') }}
+
+test:
+  imports:
+    - stardist
+  commands:
+    - pip list
+    # - pip check
+  requires:
+    - pip
+
+about:
+  home: https://github.com/stardist/stardist
+  summary: StarDist
+  license: MIT
+  license_file:
+    - LICENSE.txt
+    - stardist/lib/external/qhull_src/COPYING.txt
+    # - stardist/lib/external/clipper # MISSING in repo!
+    - clipper.LICENSE.txt
+    # - stardist/lib/external/nanoflann # MISSING in repo!
+    - nanoflann.LICENSE.txt
+
+extra:
+  recipe-maintainers:
+    - goanpeca
+    - jaimergp

recipes/stardist/nanoflann.LICENSE.txt

@@ -0,0 +1,28 @@
+Software License Agreement (BSD License)
+
+Copyright 2008-2009  Marius Muja ([email protected]). All rights reserved.
+Copyright 2008-2009  David G. Lowe ([email protected]). All rights reserved.
+Copyright 2011 Jose L. Blanco ([email protected]). All rights reserved.
+
+THE BSD LICENSE
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions
+are met:
+
+1. Redistributions of source code must retain the above copyright
+   notice, this list of conditions and the following disclaimer.
+2. Redistributions in binary form must reproduce the above copyright
+   notice, this list of conditions and the following disclaimer in the
+   documentation and/or other materials provided with the distribution.
+
+THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS OR
+IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
+IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT,
+INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
+NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF
+THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

recipes/stardist/setup.patch

@@ -0,0 +1,37 @@
+--- setup.py	2022-04-06 13:34:29.000000000 +0200
++++ setup.py	2022-04-06 13:36:38.000000000 +0200
+@@ -22,6 +22,24 @@
+         if compiler not in self.openmp_compile_args:
+             compiler = '*'
+
++        ## QHull has a mix of C and C++ source files
++        ## Setuptools will apply the same flags to all files
++        ## GCC warns about passing -std=c++11 for C files
++        ## but Clang errors out
++        ## We need to patch the responsible method to filter
++        ## the passed flags depending on the extension
++
++        # 1. keep a ref to the original _compile method
++        original__compile = self.compiler._compile
++        # 2. create a patched variant for the _compile method
++        def patched__compile(obj, src, ext, cc_args, extra_postargs, pp_opts):
++            # remove c++ specific options for C files
++            if src.endswith('.c'):
++                extra_postargs = [arg for arg in extra_postargs if not arg.startswith("-std")]
++            return original__compile(obj, src, ext, cc_args, extra_postargs, pp_opts)
++        # 3. monkey patch the method
++        self.compiler._compile = patched__compile
++
+         _extra_compile_args = list(ext.extra_compile_args)
+         _extra_link_args    = list(ext.extra_link_args)
+         try:
+@@ -33,6 +51,9 @@
+             ext.extra_compile_args = _extra_compile_args
+             ext.extra_link_args    = _extra_link_args
+             super(build_ext_openmp, self).build_extension(ext)
++        finally:
++            # 4. restore to original, just in case
++            self.compiler._compile = original__compile
+
+
+ #------------------------------------------------------------------------------------