[ci skip] Merge PR 39736

Merge PR bioconda#39736, commits were: 
 * recreate deleted files
 * revert pyopenms. has to be in a separate PR
 * revert simplifying config. apparently bioconda-build does NOT FOLLOW the official conda specification!
 * remove nightly specifics and simply config
 * try with matplotlib-base
 * try without matplotlib version
 * Apply suggestions from code review
 * adding matplotlib
 * Update conda_build_config.yaml
 * Update conda_build_config.yaml
 * Update conda_build_config.yaml
 * Update conda_build_config.yaml
 * move pyopenms config file into proper recipe
 * remove bumpershot
 * remove crux from meta.yaml
 * [UPDATE] (py)openms to 3.0 nightly

recipes/openms-meta/build.sh

@@ -1,8 +1,5 @@
 #!/bin/sh
 
-# Download URLs have changed!
-sed -i.bak "s/informatik/cs/g" contrib/macros.cmake
-
 # 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${PREFIX}/include"
@@ -13,31 +10,23 @@ export LIBRARY_PATH=${PREFIX}/lib
 export LD_LIBRARY_PATH=${PREFIX}/lib
 #export DYLD_LIBRARY_PATH=${PREFIX}/lib
 
-mkdir contrib-build
-cd contrib-build
-## By default WM is built and linked statically such that it does not
-## introduce a dependency that needs to be exported
-cmake -DBUILD_TYPE=WILDMAGIC ../contrib
-cd ..
-
-#sed -i.bak "s/CMAKE_INSTALL_NAME_DIR/FOO/g" CMakeLists.txt
-
 mkdir build
 cd build
 
-
 if [[ $(uname -s) == Darwin ]]; then
   RPATH='@loader_path/../lib'
 else
   ORIGIN='$ORIGIN'
   export ORIGIN
   RPATH='$${ORIGIN}/../lib'
 fi
+
+# not sure if needed. CMake should take care of that.
 LDFLAGS='-Wl,-rpath,${RPATH}'
 
 cmake .. \
   -DOPENMS_GIT_SHORT_REFSPEC="release/${PKG_VERSION}" \
-  -DOPENMS_GIT_SHORT_SHA1="b59e0c3" \
+  -DOPENMS_GIT_SHORT_SHA1="d36094e" \
   -DOPENMS_CONTRIB_LIBS="$SRC_DIR/contrib-build" \
   -DCMAKE_BUILD_TYPE="Release" \
   -DCMAKE_OSX_SYSROOT=${CONDA_BUILD_SYSROOT} \

recipes/openms-meta/meta.yaml

@@ -1,18 +1,15 @@
 {% set name = "OpenMS" %}
-{% set version = "2.8.0" %}
+{% set version = "2.9.0" %}
 package:
   name: {{ name|lower  }}-meta
   version: {{ version  }}
 
 source:
   url: https://abibuilder.cs.uni-tuebingen.de/archive/openms/OpenMSInstaller/release/{{ version }}/OpenMS-{{ version }}-src.tar.gz
-  sha256: c39e3ccdce5c335d2659cfa9d0bb63555a01ec422757afd90706d3869bf611ac
-  # patch should be removed in 2.9 https://github.com/OpenMS/OpenMS/pull/6122
-  patches:
-    - sirius-2.8.0.patch
+  sha256: d2e80ac3000516bb046a13db9aa862d3cc961bad43446f7b09f672e6362afefe
 
 build:
-  number: 4
+  number: 0
 
 # Try this when building with GUI
 #extra:
@@ -33,13 +30,11 @@ requirements:
       - xerces-c
       - boost-cpp
       - eigen >=3.3.2
-      - glpk
       - hdf5 >=1.10
       - bzip2
       - qt
       - libsvm
       - coinmp
-      - sqlite
 
 test:
   commands:
@@ -63,27 +58,23 @@ outputs:
           - xerces-c
           - boost-cpp
           - eigen >=3.3.2
-          - glpk
           - hdf5 >=1.10
           - bzip2
           - qt
           - libsvm
           - coinmp
-          - sqlite
     build:
       run_exports:
           - {{ pin_compatible('llvm-openmp', max_pin='x.x') }} # [osx]
           - {{ pin_compatible('zlib', max_pin='x.x') }}
           - {{ pin_compatible('xerces-c', max_pin='x.x') }}
           - {{ pin_compatible('boost-cpp', max_pin='x.x') }}
           - {{ pin_compatible('eigen', max_pin='x.x') }}
-          - {{ pin_compatible('glpk', max_pin='x.x') }}
           - {{ pin_compatible('hdf5', max_pin='x.x') }}
           - {{ pin_compatible('bzip2', max_pin='x.x') }}
           - {{ pin_compatible('qt', max_pin='x.x') }}
           - {{ pin_compatible('libsvm', max_pin='x.x') }}
           - {{ pin_compatible('coinmp', max_pin='x.x') }}
-          - {{ pin_compatible('sqlite', max_pin='x.x') }}
           - libopenms {{ version }}
 
   - name: openms
@@ -105,27 +96,23 @@ outputs:
         - xerces-c
         - boost-cpp
         - eigen >=3.3.2
-        - glpk
         - hdf5 >=1.10
         - bzip2
         - qt
         - libsvm
         - coinmp
-        - sqlite
       run:
         - {{ pin_subpackage('libopenms', exact=True) }}
         - {{ pin_compatible('llvm-openmp', max_pin='x.x') }} # [osx]
         - {{ pin_compatible('zlib', max_pin='x.x') }}
         - {{ pin_compatible('xerces-c', max_pin='x.x') }}
         - {{ pin_compatible('boost-cpp', max_pin='x.x') }}
         - {{ pin_compatible('eigen', max_pin='x.x') }}
-        - {{ pin_compatible('glpk', max_pin='x.x') }}
         - {{ pin_compatible('hdf5', max_pin='x.x') }}
         - {{ pin_compatible('bzip2', max_pin='x.x') }}
         - {{ pin_compatible('qt', max_pin='x.x') }}
         - {{ pin_compatible('libsvm', max_pin='x.x') }}
         - {{ pin_compatible('coinmp', max_pin='x.x') }}
-        - {{ pin_compatible('sqlite', max_pin='x.x') }}
     test:
       commands:
         - OPENMS_DATA_PATH=${PREFIX}/share/OpenMS/ ${PREFIX}/bin/OpenMSInfo
@@ -139,9 +126,7 @@ outputs:
     requirements:
      run:
        - {{ pin_subpackage('openms', exact=True) }}
-       - bumbershoot ==3_0_21142_0e4f4a4
        - comet-ms ==2019015
-       - crux-toolkit ==3.2
        - fido ==1.0
        - luciphor2 ==2020_04_03
        - msgf_plus ==2021.03.22
@@ -156,7 +141,6 @@ outputs:
      # Test copied from openms output to make sure a test environment for this output is created.
      commands:
        - OPENMS_DATA_PATH=${PREFIX}/share/OpenMS/ ${PREFIX}/bin/OpenMSInfo
-       - sirius --help
 
 about:
   home: https://github.com/OpenMS/OpenMS