Package only bioformats_package.jar

[rleigh-codelibre]

Fetch the current versioned jar, and drop the version to recreate the unversioned jar.

Check the versioned bio-formats-matlab zip has the same contents as the unversioned bfmatlab.zip from downloads.openmicroscopy.org. Without this commit, it packs up all transitive dependencies.

Check that it works with matlab.

[rleigh-codelibre]

Green in https://web-proxy.openmicroscopy.org/east-ci/job/BIOFORMATS-merge/34/ -- zip can be downloaded from the workspace (bio-formats-matlab/target)

[joshmoore]

Does this mean that there's no longer a formal dependency between this repo and the upstream one?

[rleigh-codelibre]

There is, in that the maven-dependency-plugin is pulling in the jar. But it's not a <dependency>, since this type of package-level dependency pulls in all the transitive dependencies which aren't needed for simple bundling of the uberjar in the zip.

[rleigh-codelibre]

@joshmoore Please could we merge this in so I can rebase ome/bioformats#2989 for this new repository?

[joshmoore]

Quick feedback from background investigation: https://stackoverflow.com/a/7556707/56887 suggests that wildcard exclusions are supported. joshmoore@b674423 seems to only download:

maven@9852f05838a2:/tmp/build$ ls -ltra ~/.m2/repository/ome/
total 20
drwxr-xr-x  3 maven maven 4096 Mar 23 13:13 bio-formats_plugins
drwxr-xr-x  3 maven maven 4096 Mar 23 13:13 pom-bio-formats
drwxr-xr-x  3 maven maven 4096 Mar 23 13:13 bio-formats-tools

Tested via this Dockerfile:

FROM maven
RUN useradd -ms /bin/bash maven
USER maven
RUN git clone -b package-bioformats-package-jar git://github.com/rleigh-codelibre/bio-formats-matlab /tmp/build
WORKDIR /tmp/build
RUN git remote add josh git://github.com/joshmoore/bio-formats-matlab
RUN git fetch josh
RUN git merge --ff-only josh/package-bioformats-package-jar

[rleigh-codelibre]

@joshmoore Thanks, this is useful to know. However, what we are doing here is packaging, and <dependencies> is not really the appropriate mechanism for that. We are aggregating several files and bundling them together, and that's not what <dependencies> is intended for. This is one of the intended uses of the dependency plugin--fetching file dependencies which are not for building or testing. We are using the maven dependency plugin in bio-formats-documentation to do almost exactly the same thing--fetching the examples and formats source code; the only difference is we unpack the contents into the target rather than leave the jar as is. There's very little difference to what we do here.

<dependencies> have a scope of compile, test, runtime etc. And none of these are appropriate or applicable to what we are doing here.

[joshmoore]

Under the assumption that we'll likely be moving this repository away from maven (to gradle?), let's go ahead and get your strategy merged and then we can reevaluate in the next round.