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ome / omero-figure

An OMERO.web app for creating Figures from images in OMERO
http://figure.openmicroscopy.org
GNU Affero General Public License v3.0
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update README #515

Closed will-moore closed 9 months ago

will-moore commented 1 year ago

Issues with Docker-based dev instructions at https://forum.image.sc/t/omero-figure-dev-install-with-docker-fails/86022 prompted me to tidy them (fix formatting) and add the option of local install.

NB: However, as noted on that issue, the instructions won't work because openmicroscopy/omero-web-standalone:latest Docker image is still python 3.6, which forces Django 3.2 to be installed, which is incompatible (in development mode) with https://github.com/ome/omero-web/pull/480 which was included in omero-web 5.22.0.

Can try to use older omero-web in Dockerfile...

FROM openmicroscopy/omero-web-standalone:5.21.0

imagesc-bot commented 1 year ago

This pull request has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/omero-figure-dev-install-with-docker-fails/86022/5

snoopycrimecop commented 1 year ago

Conflicting PR. Removed from build OMERO-plugins-push#47. See the console output for more details. Possible conflicts:

--conflicts

snoopycrimecop commented 1 year ago

Conflicting PR. Removed from build OMERO-plugins-push#49. See the console output for more details. Possible conflicts:

--conflicts Conflict resolved in build OMERO-plugins-push#252. See the console output for more details.

will-moore commented 11 months ago

@jburel - I can't seem to reproduce the original error reported above, so I've reverted the Dockerfile change (maybe the omero-web-standalone got updated already)? Otherwise, just updates to the README...

jburel commented 11 months ago

@will-moore I have merged the omeroweb-docker so it is now running Python 3.9

will-moore commented 11 months ago

Hmm - OK, now I'm confused....

The error you're seeing is what's described in the PR description above. And I worked around it at the time with FROM openmicroscopy/omero-web-standalone:5.21.0

But then I removed that change (to try and check the error again) and didn't see an error (maybe the Docker Image was cached and removing the change had no effect).

And now @jburel comment https://github.com/ome/omero-figure/pull/515#issuecomment-1847914977 implies that we don't need the workaround any more as the omero-web standalone docker is now up-to-date (python 3.9)??

jburel commented 11 months ago

I have merged the omero-web-docker PR but not tagged the repository so the new docker image is not available on dockerhub. I was waiting for the next release of omero-web We could do a tag if it is urgent

will-moore commented 11 months ago

I have reverted to use FROM openmicroscopy/omero-web-standalone:5.21.0 which should fix that error until omero-web-standalone is updated.

pwalczysko commented 11 months ago

I have reverted to use FROM openmicroscopy/omero-web-standalone:5.21.0 which should fix that error until omero-web-standalone is updated.

But some problem is then detected when following the workflow in the browser, see https://github.com/ome/omero-figure/pull/515/files#r1426873071 (not claiming that it was not there before, just that the README does somehow not work as written)

pwalczysko commented 11 months ago

Failed checks.

@will-moore could you maybe read my suggestions in the text and accept or reformulate, then commit and we can read afresh on Monday ? I do not see any probs anymore with the workflow (although the failed checks are worrying) - it is just about formulating the README.

pwalczysko commented 11 months ago

The failing checks are connected to flake8 install imho https://github.com/ome/omero-figure/actions/runs/7264947038/job/19793566993 - the attempt to fix them by upgrading the testing framework in https://github.com/ome/omero-figure/pull/535 have failed - the flake8 error persists. Any ideas please @joshmoore @khaledk2 ?

jburel commented 11 months ago

@pwalczysko The requirements in omero-test-infra will need to be updated see https://github.com/ome/omero-test-infra/blob/master/requirements.txt. That also means that omero-figure will need to be adjusted. Possibly some new flake8 failure e.g. usage of parameter like l is not permitted anymore Some Javascripts failure might occur too.

I will not recommend to upgrade omero-test-infra before the break since many repositories will be affected (including external repo like ezomero)

One option will be to work from a personal branch to get omero-figure green via the omero_plugin.yml

pwalczysko commented 11 months ago

One option will be to work from a personal branch to get omero-figure green via the omero_plugin.yml

Meaning pointing inside omero_plugin.yml to a personal branch on the https://github.com/ome/omero-test-infra/blob/master/requirements.txt repo ? We discussed on Standup and will sort this out in the New Year.

will-moore commented 11 months ago

@jburel @pwalczysko Thanks for your help. Added all your commits here - Tests of Figure export script are failing - don't know why just now, but will look again in the New Year!

jburel commented 10 months ago

@will-moore could you remove the commit not related to the README update? The commits related to the upgrade to test-infra are included in #537

will-moore commented 10 months ago

@jburel Done. Just the README and DockerFile changed now.

jburel commented 10 months ago

The latest docker image has now been updated to Rocky Linux 9 so Python version will now be 3.10

will-moore commented 9 months ago

Decided that we don't want to keep supporting Docker for omero-web development. Takes too much testing (as above) and maintenance.