BF Migration - Required Updates

[dgault]

Dependency Repos

• [ ] ome-jai (https://github.com/ome/ome-jai)
• [ ] ome-poi (https://github.com/ome/ome-poi)
• [ ] ome-metakit (https://github.com/ome/ome-metakit)
• [ ] ome-mdbtools (https://github.com/ome/ome-mdbtools)
• [ ] ome-codecs (https://github.com/ome/ome-codecs)
• [ ] ome-common (https://github.com/ome/ome-common-java)
• [ ] ome-model (https://github.com/ome/ome-model)

Downstream Repos

• [ ] bio-formats-documentation (https://github.com/ome/bio-formats-documentation)
• [ ] bio-formats-examples (https://github.com/ome/bio-formats-examples)
• [ ] homebrew (https://github.com/ome/homebrew-alt)
• [ ] bio-formats-fiji (https://github.com/ome/bio-formats-fiji)
• [ ] octave-docker (https://github.com/ome/bio-formats-octave-docker)

Links to downloads

• [ ] Homebrew Formulas
• [ ] Octave-docker (https://github.com/ome/bio-formats-octave-docker/blob/7466de366526ea5bcb57b03bf0f5c975e5423c85/Dockerfile)
• [ ] links in docs (https://github.com/ome/bio-formats-documentation) l- [ ] inks in bftools (https://github.com/ome/bioformats/blob/f9f8f17d5037dab717cb22507ef9b0d591ed9a8d/tools/bf.sh and https://github.com/ome/bioformats/blob/f9f8f17d5037dab717cb22507ef9b0d591ed9a8d/tools/bf.bat)
• [ ] links in model (https://github.com/ome/ome-model/blob/94b8af51f6a41dce733ca3cc42469f63f54c28d2/README.md, https://github.com/ome/ome-model/blob/a4770ed5f3acf5c7e3dc1152615a961801acdac3/docs/sphinx/developers/compression.rst, https://github.com/ome/ome-model/blob/cdf754fb3c52d99332048fd9edc62eb4135e4e4b/docs/sphinx/conf.py)
• [ ] links in common (https://github.com/search?p=11&q=org%3Aome+%22downloads.openmicroscopy%22&type=Code)
• [ ] Data repo config readme (https://github.com/openmicroscopy/data_repo_config/blob/09c612847c7e62b667367031014edd461b138550/README.md)
• [ ] ome-files-cpp (https://github.com/ome/ome-files-cpp)
• [ ] ome-cmake-superbuild (https://github.com/ome/ome-cmake-superbuild)
• [ ] ome-files-performance (https://github.com/ome/ome-files-performance/blob/f7e94825049f99b8751c2c63b8c4631842e46a69/doc/metadata-pixeldata.md)
• [ ] links to datasets in training-repo (https://github.com/ome/training-repos)
• [ ] upgrade checker (https://github.com/ome/bioformats/blob/6f50e4d52c9d96112635fd8b2dde737f31041cf0/components/formats-bsd/src/loci/formats/UpgradeChecker.java)
• [ ] macro functions (https://github.com/ome/bioformats/blob/f9f8f17d5037dab717cb22507ef9b0d591ed9a8d/components/bio-formats-plugins/src/loci/plugins/macro/LociFunctions.java)
• [ ] bio-formats-imagej archived (https://github.com/ome/bio-formats-imagej)

Misc Updates

management tools /playbooks

• [ ] CPP + OME-Files artefacts
• [ ] jxrlib

Potential Issues which need investigating

• [ ] FormatTools.VERSION
• [ ] public sample images
• [ ] restoring data repo
• [ ] broken links in old presentations/papers/release notes

[jburel]

homebrew formula: https://downloads.openmicroscopy.org/bio-formats/6.4.0/artifacts/bioformats-6.4.0.zip This is not currently uploaded via actions

[jburel]

Tested GitHub actions to generate and upload artifacts see https://github.com/jburel/bioformats/releases/tag/v6.6.0-m1

[jburel]

https://github.com/jburel/bioformats/releases/tag/v6.6.0-m2 now have the various zip/jars and also the sha256 so it can be used in the homebrew formula: ignore the version mismatch, this is b/c I have tagged without changing to trigger the GH action

[jburel]

new tag created with shasum and md5 to match what is available under download I have opted not to have a sha1 or md5 per file to reduce the number of attachments

[jburel]

I now build on windows and ubuntu via GH actions. so we can get rid of appveyor and travis files

[jburel]

@dgault https://github.com/jburel/bioformats/releases/tag/v6.6.0-m3 should have what is currently under download.o.org Could you double check? See comment above about sha1 and md5 https://github.com/ome/bioformats/issues/3621#issuecomment-708626796

[jburel]

Now I have example using github actions pushing artifacts to Maven central, for both gradle and maven project

[jburel]

https://ci.openmicroscopy.org/job/BIOFORMATS-DEV-latest-version-bump/ only bumps the version in the pom and sets the value in all the pom.xml by running a python scripts

• STABLE_VERSION in UpgradeChecker.java could be removed.
• the version in the pom.xml could be set using mvn versions:set -DnewVersion=XXXX

The workflow could become:

• set the version using mvn versions:set -DnewVersion=XXXX
• commit the changes
• tag
• push the tag
• GH actions
  • create a release and generate the artifacts with sha1 etc.
  • upload the artifacts to GH
  • push the artifacts to maven central

Remaining open question: docs are combined i.e. not one per component so using javadoc.io is not going to work nicely