k-dominik / mobie-cmd

Development

Install mamba

Download mamba-forge

Manage pypi packages

• https://pypi.org/

Create mobie-dev env

mamba create -y -n mobie-dev -c conda-forge openjdk=8 jgo pip maven blosc

Test within Java on the command line

1. cd to the main folder of 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"

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")

continue as in test locally

Release a new version

This is not needed for local testing.

Example for version 3.0.11:

mobie-viewer-fiji repo

Within the mobie Java code change the versions here:

@CommandLine.Command(name = "mobie", mixinStandardHelpOptions = true, version = "3.0.11", description = "Visualise multi-modal big image data, see https://mobie.github.io/")

Use the below lines to make a maven release:

mamba activate mobie-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

Go to setup.py and change the version to 3.0.10

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

test locally

mamba activate mobie-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"

deploy

git tag 3.0.10
git push --tags

Troubleshooting

Remove a tag (remote and local):

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