[ci skip] Merge PR 33780

Merge PR bioconda#33780, commits were: 
 * Update pyopenms_cmakelist2.patch
 * Update meta.yaml
 * Merge pull request #1 from jpfeuffer/timosachsenberg-patch-1

add patch for hidden symbols
 * Update meta.yaml
 * add patch for hidden symbols
 * Update meta.yaml
 * Delete conda_build_config.yaml
 * Merge branch 'master' into pyopenms2_8_separate
 * Add pip..wow MacOS is really barebones
 * nop
 * Merge branch 'master' into pyopenms2_8_separate
 * add cmakelist patch to fix error in pyopenms 2.8 cmakelist
 * Merge branch 'bioconda:master' into pyopenms2_8_separate
 * Update meta.yaml
 * Add setuptools?
 * Prefer find python by location
 * Specify vindas python executable since on MacOS there is another
 * Xfjshajs
 * ...
 * Test cython import
 * Explicitly specify everything.
 * Add back a separate pyopenms package

recipes/pyopenms/build.sh

@@ -0,0 +1,45 @@
+#!/bin/sh
+
+# useless default include directory that is silently added by the compiler packages "to help"...
+# it is not even added with -isystem https://github.com/AnacondaRecipes/aggregate/blob/master/clang/activate-clang%2B%2B.sh#L87
+USELESS="-I${PREFIX}/include"
+export CXXFLAGS=${CXXFLAGS//${USELESS}/}
+
+# Not sure if those are needed 
+export LIBRARY_PATH=${PREFIX}/lib
+export LD_LIBRARY_PATH=${PREFIX}/lib
+#export DYLD_LIBRARY_PATH=${PREFIX}/lib
+
+mkdir build
+cd build
+
+if [[ $(uname -s) == Darwin ]]; then
+  RPATH='@loader_path/../lib'
+else
+  ORIGIN='$ORIGIN'
+  export ORIGIN
+  RPATH='$${ORIGIN}/../lib'
+fi
+LDFLAGS='-Wl,-rpath,${RPATH}'
+
+cmake ../src/pyOpenMS \
+  -DOPENMS_GIT_SHORT_REFSPEC="release/${PKG_VERSION}" \
+  -DOPENMS_GIT_SHORT_SHA1="b59e0c3" \
+  -DCMAKE_BUILD_TYPE="Release" \
+  -DCMAKE_OSX_SYSROOT=${CONDA_BUILD_SYSROOT} \
+  -DCMAKE_MACOSX_RPATH=ON \
+  -DCMAKE_PREFIX_PATH=${PREFIX} \
+  -DCMAKE_INSTALL_PREFIX=${PREFIX} \
+  -DCMAKE_INSTALL_RPATH=${RPATH} \
+  -DCMAKE_INSTALL_NAME_DIR="@rpath" \
+  -DCMAKE_BUILD_WITH_INSTALL_RPATH=ON \
+  -DCMAKE_BUILD_WITH_INSTALL_NAME_DIR=ON \
+  -DPython_EXECUTABLE=$PYTHON \
+  -DPython_FIND_STRATEGY="LOCATION" \
+  -DNO_DEPENDENCIES=ON
+
+# NO_DEPENDENCIES since conda takes over re-linking etc
+
+# limit parallel jobs to 1 for memory usage since pyopenms has huge cython generated cpp files
+make -j1 pyopenms
+$PYTHON -m pip install ./pyOpenMS/dist/*.whl --ignore-installed --no-deps

recipes/pyopenms/meta.yaml

@@ -0,0 +1,66 @@
+{% set name = "pyopenms" %}
+{% set version = "2.8.0" %}
+package:
+  name: {{ name|lower  }}
+  version: {{ version  }}
+
+source:
+  url: https://abibuilder.informatik.uni-tuebingen.de/archive/openms/OpenMSInstaller/release/{{ version }}/OpenMS-{{ version }}-src.tar.gz
+  sha256: c39e3ccdce5c335d2659cfa9d0bb63555a01ec422757afd90706d3869bf611ac
+  patches:
+    - pyopenms_cmakelist2.patch
+    - pyopenms_cmakelist.patch
+
+build:
+  skip: True  # [py2k]
+  number: 0
+
+requirements:
+  build:
+    - {{ compiler('cxx') }}
+    - make
+    - cmake
+  host:
+    - libopenms {{ version }}
+    - llvm-openmp # [osx]
+    - libsvm
+    - xerces-c
+    - boost-cpp
+    - qt
+    - python {{ python }}
+    - cython >=0.25.2
+    - autowrap >=0.22.6
+    - setuptools
+    - wheel
+    - pip
+    - nose
+    - numpy {{ numpy }}
+    - pandas
+  run: # run_exports in libopenms should take care of the libraries. But it does not because of bugs. So copy everthing again and again
+    - libopenms {{ version }}
+    - llvm-openmp # [osx]
+    - libsvm
+    - xerces-c
+    - boost-cpp
+    - qt
+    - python {{ python }}
+    - numpy {{ numpy }}
+    - pandas
+test:
+  requires:
+    - nose
+  commands:
+    - python -c "import pyopenms; print(pyopenms.__version__)"
+    # We cant use the PYTHON variable since it does not exist on the biocontainer?!
+    # TODO run the test suite
+
+about:
+  home: https://github.com/OpenMS/OpenMS
+  license: BSD
+  license_file: LICENSE
+  summary: python bindings for OpenMS, an open-source software C++ library for LC-MS data management and analyses
+
+extra:
+  identifiers:
+    - biotools:openms
+    - doi:10.1038/nmeth.3959

recipes/pyopenms/pyopenms_cmakelist.patch

@@ -0,0 +1,22 @@
+diff --git a/src/pyOpenMS/CMakeLists.txt b/src/pyOpenMS/CMakeLists.txt
+index 829fe486840..e5094fbfddf 100644
+--- a/src/pyOpenMS/CMakeLists.txt
++++ b/src/pyOpenMS/CMakeLists.txt
+@@ -631,7 +631,7 @@ if ("${PY_NUM_MODULES}" GREATER "1")
+         SUFFIX ${PYTHON_EXT_SUFFIX} # since CMake 3.17 you can add WITH_SOABI to Python_add_library
+         CXX_VISIBILITY_PRESET ${VIS_PRESET}
+         VISIBILITY_INLINES_HIDDEN ${INLINES_HIDDEN}
+-        INSTALL_RPATH ${PY_RPATH}
++        INSTALL_RPATH "${PY_RPATH}"
+         BUILD_WITH_INSTALL_RPATH 1
+         BUILD_WITH_INSTALL_NAME_DIR 1
+         ARCHIVE_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/pyOpenMS/pyopenms"
+@@ -652,7 +652,7 @@ else()
+         SUFFIX ${PYTHON_EXT_SUFFIX} # since CMake 3.17 you can add WITH_SOABI to Python_add_library
+         CXX_VISIBILITY_PRESET ${VIS_PRESET}
+         VISIBILITY_INLINES_HIDDEN ${INLINES_HIDDEN}
+-        INSTALL_RPATH ${PY_RPATH}
++        INSTALL_RPATH "${PY_RPATH}"
+         BUILD_WITH_INSTALL_RPATH 1
+         BUILD_WITH_INSTALL_NAME_DIR 1
+         ARCHIVE_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/pyOpenMS/pyopenms"

recipes/pyopenms/pyopenms_cmakelist2.patch

@@ -0,0 +1,13 @@
+diff --git a/src/pyOpenMS/CMakeLists.txt b/src/pyOpenMS/CMakeLists.txt
+index 2c67628dec..626a2dd149 100644
+--- a/src/pyOpenMS/CMakeLists.txt
++++ b/src/pyOpenMS/CMakeLists.txt
+@@ -604,7 +604,7 @@ if (APPLE)
+  list(APPEND PY_RPATH "@loader_path/")
+ endif()
+
+-if (LINUX) # see https://github.com/cython/cython/issues/3380
++if (LINUX OR APPLE) # see https://github.com/cython/cython/issues/3380
+   set(VIS_PRESET "default")
+   set(INLINES_HIDDEN 0)
+ else()