Openms 2.8 (#33351)

* adapt nightlies to 2.8 dev cycle

* fix patch for new code

* remove all patches. not needed anymore

* change boost finding and enable debug for it

* was it the comments???

* bump autowrap

* Add dependencies to libopenms again. Problems after install

* Bump build number to check

* Added back all dependencies to openms bins as well

* try to separate openms and pyopenms

* cleanp

* contrib path?

* braces

* parent

* use SRCDIR

* hardcode openms version

* change version

* add conda config to ignore py2 and have same compiler

* use new cmake install components for installing

* need cmake to run cmake install

* add some more deps to pyopensm

* use no_dependencies in pyopenms

* remove . before dev version

* remove . before dev version

* add equals to version dep?

* well specify without ninja variable

* forgot to install

* Update meta.yaml

* Path to wheel

* Update build.sh

* remove newlines

* cleanup

* switch from nightly to release

* reset build number and limit builds

* forgot to save

* remove pyopenms since bioconda cannot figure out dependencies

* do not specify versions of pinned packages?

I thought I would do the ridiculously slow solver a favor.. but conda is just full of bugs

* add gplots, see  #32788

recipes/openms-meta/build.sh

@@ -33,9 +33,9 @@ fi
 LDFLAGS='-Wl,-rpath,${RPATH}'
 
 cmake .. \
-  -DOPENMS_CONTRIB_LIBS='../../contrib-build' \
   -DOPENMS_GIT_SHORT_REFSPEC="release/${PKG_VERSION}" \
-  -DOPENMS_GIT_SHORT_SHA1="9110e58" \
+  -DOPENMS_GIT_SHORT_SHA1="b59e0c3" \
+  -DOPENMS_CONTRIB_LIBS="$SRC_DIR/contrib-build" \
   -DCMAKE_BUILD_TYPE="Release" \
   -DCMAKE_OSX_SYSROOT=${CONDA_BUILD_SYSROOT} \
   -DCMAKE_MACOSX_RPATH=ON \
@@ -53,8 +53,7 @@ cmake .. \
   -DBoost_ARCHITECTURE="-x64" \
   -DBUILD_EXAMPLES=OFF
 
-make -j${CPU_COUNT} OpenMS TOPP UTILS
-# The subpackages will do that (unfortunately "make install" installs everything right away)
-# Another option would be to install somewhere into the build dir (to use the existent install commands)
-# and then copy the relevant parts to the prefix. See CMAKE_INSTALL_PREFIX.
+# limit concurrent build jobs due to memory usage on CI
+make -j4 OpenMS TOPP UTILS
+# The subpackages will do the installing of the parts
 #make install

recipes/openms-meta/conda_build_config.yaml

@@ -1,9 +1,6 @@
 python:
   - 3.9.*  *_cpython
-  - 3.8.*  *_cpython
 python_impl:
   - cpython
-c_compiler_version:            # [linux]
-  - 11                                      # [linux]
-cxx_compiler_version:         # [linux]
-  - 11                                      # [linux]
+numpy:
+  - 1.19.*

recipes/openms-meta/install_pyopenms.sh

@@ -1,17 +1,16 @@
 #!/bin/bash
 # TODO actually it would be better if we could adapt our MANIFEST.in
 # to not package the openms libs and dependencies again. Same for share.
-
 pushd build
-cmake -DPYOPENMS=ON -DPY_NUM_THREADS=1 -DPY_NUM_MODULES=12 .
+cmake -DPYOPENMS=ON -DNO_DEPENDENCIES=ON . #-DPY_NUM_THREADS=1 -DPY_NUM_MODULES=12 .
 # Unfortunately if we would call make, it thinks that OpenMS lib is not built since the build folder
 # might have been copied, so it rebuilds. Skip this by using setup.py directly.
 # TODO check that it actually uses the prebuilt libOpenMS from the prefix.
 #make -j${CPU_COUNT} pyopenms
 pushd pyOpenMS
 $PYTHON create_cpp_extension.py
 # try to separate the extension building from the rest. Let's hope pip install is smart enough to not do it again.
-$PYTHON setup.py build_ext -j 1 --single-threaded
+$PYTHON setup.py build_ext #-j 1 --single-threaded
 $PYTHON -m pip install . --ignore-installed --no-deps
 popd
 popd