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Development

Install mamba

Download mamba-forge

Manage pypi package

Check versions on conda

Create mobie-dev env

mamba env create -f easybuild/easybuild_env.yaml

Test within Java on the command line

  1. cd mobie-viewer-fiji
  2. ./install.sh
  3. ./mobie-files -r "/Users/tischer/Documents/mobie/src/test/resources/input/skimage-2d-tiff/" -i "image.tif" -l "segmentation.tif" -t "table.tsv"
  4. ./mobie-hcs

Test within python using a local MoBIE build

  1. mvn install current version (could be a SNAPSHOT)
  2. hardcode this version in __init__.py: e.g., _artifactVersion = '3.2.0-SNAPSHOT' #version("mobie_cmd")

continue as in test locally

Release a new version

Example for version 3.0.10:

mobie-viewer-fiji repo

Within the mobie Java code update the versions in all command line tools, e.g.:

@CommandLine.Command(name = "mobie", mixinStandardHelpOptions = true, version = "3.0.10", description = "Visualise multi-modal big image data, see https://mobie.github.io/")

Use the below lines to make a maven release:

mamba activate mobie-cmd-dev # this activates java 8!
./install.sh  # test the line of code suggested by the script!
git add .; git commit -m "prepare for release"; git push
../scijava-scripts/release-version.sh --skip-version-check --skip-license-update
# if successful this will say
# * [new tag]mobie-viewer-fiji-3.0.10 -> mobie-viewer-fiji-3.0.10

mobie-cmd repo

Within mobie_cmd/__init.py__ ensure that _artifactVersion = version("mobie")

Within setup.py set version to 3.0.10

git add setup.py
git commit -m "Version bump 3.0.10"

test locally

TODO: add test data for mobie hcs TODO: add test data for mobie table

mamba activate mobie-cmd-dev
pip install -e .
mobie --help
mobie project -p "https://github.com/mobie/platybrowser-project"
mobie files -r "/Users/tischer/Documents/mobie/src/test/resources/input/skimage-2d-tiff/" -i "image.tif" -l "segmentation.tif" -t "table.tsv"
mobie hcs
mobie table

deploy to pypi

git tag 3.0.10
git push --tags

Pushing a tag triggers build and deploy to pypi via github actions that are configured in the mobie-cmd repo.

release on conda-forge

deploying to pypi (s.a.) automatically triggers a PR in https://github.com/conda-forge/mobie-feedstock

Troubleshooting

Remove a tag (remote and local):

git push origin --delete 3.0.10
git tag -d 3.0.10