bump luciphor to 2.1

[bernt-matthias]

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[bernt-matthias]

ping @oliveralka

do you think we java requirements are OK this way?

just realized how bad the versioning is now. somehow I chose the date as version. seems impossible to switch to the correct version (2.1) since this is smaller (?) than the date 2019

[oliveralka]

I think the java requirements are alright - tested with java8 and java13 on MacOS 10.15.13.

Version wise, the only difference is that the 2.1 is using maven, which allows the use of luciphor2 with higher java versions. It seems that the base version of LuciPhor does not have changed directly... (Version: 1.2014Oct10)

Edit: There was an update around 2018-06-28, which allowed the use of different precision values for mz and int in the mzML e.g. 64bit m/z and 32bit int, but it seems that the version number was not changed internally.

conda install -c bioconda luciphor2=2020_04_03

Should work - I guess!

[bernt-matthias]

@BiocondaBot please fetch artifacts

[BiocondaBot]

Package(s) built on CircleCI are ready for inspection:

Arch	Package	Repodata
noarch	luciphor2-2020_04_03-0.tar.bz2	repodata.json

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You may also use conda to install these:

• For packages on noarch:

conda install -c https://102620-42372094-gh.circle-artifacts.com/0/tmp/artifacts/packages <package name>

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Docker image(s) built:

Package	Tag	Install with docker
luciphor2	2020_04_03--0	show curl "https://102620-42372094-gh.circle-artifacts.com/0/tmp/artifacts/images/luciphor2%3A2020_04_03--0.tar.gz" | gzip -dc | docker load

[bernt-matthias]

OK. Maybe we should have a round of testing:

conda create --override-channels -c https://102620-42372094-gh.circle-artifacts.com/0/tmp/artifacts/packages -c conda-forge -c bioconda -n luciphor2.1 luciphor2

I can test on Linux. Do you have a command / test data in mind?

[oliveralka]

I uploaded some data here:

https://drive.google.com/drive/folders/1Po15DJpuzZVXcHx7VIPNWJC3LvyiJ3hi?usp=sharing

Unfortunately, we do not have anything smaller, since there might be a bug when we reindex the attributes in the mzML, which might clash with the java mzML parser used in luciphor2. We are not sure yet.

[oliveralka]

Works for me (LuciPhor2.1 - using the environment above):

MacOS 10.15.4
conda 4.8.2
openjdk 11.0.1 2018-10-16 LTS 

[bernt-matthias]

Work. But I get a few warnings in the beginning:

JarClassLoader: Warning: module-info.class in lib/jaxb-runtime-2.3.1.jar is hidden by lib/jaxb-api-2.3.1.jar (with different bytecode)
JarClassLoader: Warning: module-info.class in lib/txw2-2.3.1.jar is hidden by lib/jaxb-api-2.3.1.jar (with different bytecode)
JarClassLoader: Warning: module-info.class in lib/istack-commons-runtime-3.0.7.jar is hidden by lib/jaxb-api-2.3.1.jar (with different bytecode)
JarClassLoader: Warning: module-info.class in lib/stax-ex-1.8.jar is hidden by lib/jaxb-api-2.3.1.jar (with different bytecode)
JarClassLoader: Warning: module-info.class in lib/FastInfoset-1.2.15.jar is hidden by lib/jaxb-api-2.3.1.jar (with different bytecode)

[oliveralka]

Yes, I saw them as well, but that is probably due to the maven fix - not sure.
@chhh Is that ok?

[chhh]

@oliveralka This is ok, what this says is one dependency library is "shadowed" by another. That would only (possibly) be a problem in case someone was consuming this as a library from Java JDK 9+ and even then most likely not. But this is just an application, not a library, so it's ok. As long as you don't mind the warnings.

[bernt-matthias]

Wonderful, then lets go ahead

[bernt-matthias]

@BiocondaBot please add label

[bernt-matthias]

@BiocondaBot please merge

[BiocondaBot]

I will attempt to upload artifacts and merge this PR. This may take some time, please have patience.