Julianus Pfeuffer
Julianus Pfeuffer
E.g. for QC. Similar to our mass trace data structure.
``` /home/jenkins/ws/openms/PR/pyOMSDckr/OpenMS/src/openms/source/METADATA/ExperimentalDesign.cpp: In static member function 'static OpenMS::ExperimentalDesign OpenMS::ExperimentalDesign::fromConsensusMap(const OpenMS::ConsensusMap&)': /home/jenkins/ws/openms/PR/pyOMSDckr/OpenMS/src/openms/source/METADATA/ExperimentalDesign.cpp:155:36: warning: unused variable 'inserted' [-Wunused-variable] const auto& [it, inserted] = samplename_to_sample_mapping.emplace(r.sample_name,samplename_to_sample_mapping.size()); ```
export Constants::UserParam::DC_CHARGE_ADDUCTS to dataframe if available. Or make it configurable. While at it, check for other interesting metavalues that are missing.
Newer appleclang warn for: ``` 13:44:52 BIOCONDA INFO (ERR) In file included from /Users/builder/mambaforge/envs/bioconda/conda-bld/openms-meta_1664364460460/work/src/openms/source/KERNEL/ChromatogramPeak.cpp:36: 13:44:52 BIOCONDA INFO (ERR) In file included from /Users/builder/mambaforge/envs/bioconda/conda-bld/openms-meta_1664364460460/work/src/openms/include/OpenMS/KERNEL/MSSpectrum.h:39: 13:44:52 BIOCONDA INFO (ERR) /Users/builder/mambaforge/envs/bioconda/conda-bld/openms-meta_1664364460460/work/src/openms/include/OpenMS/KERNEL/RangeManager.h:108:14: warning: use...
- [ ] Do not use wildcard imports in our ".py" files or ".pyx" extensions - [ ] Import numpy, pandas etc. as `_np` - [ ] Call our split...
Currently, we use self-written scripts and/or the kind of deprecated GetPrerequisites module. We should use: CMake 3.21: https://cmake.org/cmake/help/git-stage/manual/cmake-generator-expressions.7.html#genex:TARGET_RUNTIME_DLLS and/or CMake 3.16: https://cmake.org/cmake/help/latest/command/file.html#get-runtime-dependencies
I just tried to add a missing header that was not installed but added it in the wrong cmake file. Somehow OpenSwath does not follow our schema of having sources.cmake...
on GCC9 ``` 17:28:27 BIOCONDA INFO (OUT) In file included from /opt/conda/conda-bld/openms-meta_1644422323396/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, 17:28:27 BIOCONDA INFO (OUT) from /opt/conda/conda-bld/openms-meta_1644422323396/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/include/boost/smart_ptr/detail/yield_k.hpp:23, 17:28:27 BIOCONDA INFO (OUT) from /opt/conda/conda-bld/openms-meta_1644422323396/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, 17:28:27 BIOCONDA INFO (OUT) from /opt/conda/conda-bld/openms-meta_1644422323396/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/include/boost/smart_ptr/detail/spinlock.hpp:42,...
similar to here but in the basic SiriusAdapter: https://github.com/OpenMS/OpenMS/blob/ddfbb579815265a7273ac99e59605db66555c662/src/utils/AssayGeneratorMetabo.cpp#L467 We can: - annotate in the original mzML as StringDataArray - write a new annotated mzML with just the IDed MS2...
related to #5619 but probably more than that. Maybe some double packaging, softlinks, the new Qt WebEngine? see https://abibuilder.informatik.uni-tuebingen.de/archive/openms/OpenMSInstaller/release/2.8.0/ Things collected from comments: - split thirdparty and make it optional/external....