From a5268ba556d500d766e744def93ef36bf8894849 Mon Sep 17 00:00:00 2001 From: Julianus Pfeuffer Date: Mon, 6 Mar 2023 20:01:17 +0100 Subject: [PATCH] [ci skip] Merge PR 39736 Merge PR #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 | 17 +++------------- recipes/openms-meta/conda_build_config.yaml | 6 ------ recipes/openms-meta/install_pyopenms.sh | 16 --------------- recipes/openms-meta/meta.yaml | 22 +++------------------ recipes/openms-meta/sirius-2.8.0.patch | 14 ------------- 5 files changed, 6 insertions(+), 69 deletions(-) delete mode 100644 recipes/openms-meta/conda_build_config.yaml delete mode 100644 recipes/openms-meta/install_pyopenms.sh delete mode 100644 recipes/openms-meta/sirius-2.8.0.patch diff --git a/recipes/openms-meta/build.sh b/recipes/openms-meta/build.sh index ee17156a80835..3ab476e843b98 100644 --- a/recipes/openms-meta/build.sh +++ b/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${PREFIX}/include" @@ -13,19 +10,9 @@ export LIBRARY_PATH=${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 @@ -33,11 +20,13 @@ else 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} \ diff --git a/recipes/openms-meta/conda_build_config.yaml b/recipes/openms-meta/conda_build_config.yaml deleted file mode 100644 index 97c661b4ab474..0000000000000 --- a/recipes/openms-meta/conda_build_config.yaml +++ /dev/null @@ -1,6 +0,0 @@ -python: - - 3.9.* *_cpython -python_impl: - - cpython -numpy: - - 1.19.* \ No newline at end of file diff --git a/recipes/openms-meta/install_pyopenms.sh b/recipes/openms-meta/install_pyopenms.sh deleted file mode 100644 index 488b8e60ebdb8..0000000000000 --- a/recipes/openms-meta/install_pyopenms.sh +++ /dev/null @@ -1,16 +0,0 @@ -#!/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 -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 -m pip install . --ignore-installed --no-deps -popd -popd diff --git a/recipes/openms-meta/meta.yaml b/recipes/openms-meta/meta.yaml index 2176b24d33ee3..681e193451f8d 100644 --- a/recipes/openms-meta/meta.yaml +++ b/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: @@ -63,13 +58,11 @@ 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] @@ -77,13 +70,11 @@ outputs: - {{ 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 @@ -105,13 +96,11 @@ 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] @@ -119,13 +108,11 @@ outputs: - {{ 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 diff --git a/recipes/openms-meta/sirius-2.8.0.patch b/recipes/openms-meta/sirius-2.8.0.patch deleted file mode 100644 index 1f05e9a539039..0000000000000 --- a/recipes/openms-meta/sirius-2.8.0.patch +++ /dev/null @@ -1,14 +0,0 @@ -diff -ruN OpenMS-2.8.0-org/src/openms/source/ANALYSIS/ID/SiriusAdapterAlgorithm.cpp OpenMS-2.8.0/src/openms/source/ANALYSIS/ID/SiriusAdapterAlgorithm.cpp ---- OpenMS-2.8.0-org/src/openms/source/ANALYSIS/ID/SiriusAdapterAlgorithm.cpp 2022-05-17 10:03:33.295974032 +0200 -+++ OpenMS-2.8.0/src/openms/source/ANALYSIS/ID/SiriusAdapterAlgorithm.cpp 2022-05-17 10:05:40.491967708 +0200 -@@ -564,10 +564,6 @@ - // the actual process - QProcess qp; - QString executable_qstring = SiriusAdapterAlgorithm::determineSiriusExecutable(executable).toQString(); -- QString wd = File::path(executable).toQString(); -- qp.setWorkingDirectory(wd); //since library paths are relative to sirius executable path -- //since library paths are relative to sirius executable path -- qp.setWorkingDirectory(File::path(executable).toQString()); - qp.start(executable_qstring, command_line); // does automatic escaping etc... start - - std::stringstream ss;