Initial addition of integration tests #171

will-moore · 2025-04-01T19:28:10Z

WIP - adding more tests...

will-moore · 2025-04-02T19:41:12Z

@jburel @joshmoore Any ideas how I install omero-rois that is needed for running tests. I've tried installing it in .omeroci/app-deps and in .omeroci/app-build but they don't seem to have any effect?

joshmoore · 2025-04-03T08:32:48Z

Since you're running STAGE: cli you need to update scripts starting with cli-*

will-moore · 2025-04-03T08:37:21Z

I'm looking at https://github.com/ome/omero-test-infra?tab=readme-ov-file#hooks and the scripts I see there don't include any that start with cli-.
Maybe that's not a complete list and cli-deps will work? I can try....

will-moore · 2025-04-03T08:54:55Z

Nope, it didn't work. The file was copied over:

copying .omeroci/cli-deps -> omero_cli_zarr-0.1.dev1+g3e6e587/.omeroci

but the test still failed as before:

>       from omero_rois.library import mask_from_binary_image
E       ModuleNotFoundError: No module named 'omero_rois'

At this point it's probably easier for me to copy over the mask_from_binary_image() function that I need and move on!

will-moore · 2025-04-03T09:52:30Z

Green now!
My motivation for this PR was because I realise that #169 and #170 had breaking changes but were still "green" because of the lack of tests.
So it would be good to get this one in ahead of those.

joshmoore · 2025-04-03T11:37:41Z

test/integration/clitest/omero_rois.py

+# with this program; if not, write to the Free Software Foundation, Inc.,
+# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+# Code copied from omero-rois as I could not find a way to install it


This is still the case, despite cli-deps? Should I give it a try?

@joshmoore Yes, please try it. Or just check I've got it right at 55e5624 above (and see the corresponding test failure)

Ok. So I can get to:

test/integration/clitest/test_export.py::TestRender::test_export_zarr PASSED [ 33%] test/integration/clitest/test_export.py::TestRender::test_export_plate PASSED [ 66%] test/integration/clitest/test_export.py::TestRender::test_export_masks PASSED [100%]

with the following:

remove the omero_rois file

add omero_rois in setup.py as a main dependency

The reason that cli-deps didn't help is that https://github.com/ome/omero-test-infra/blob/master/docker#L213-L224 doesn't run "cli deps".

Either in cli-build or py-setup we need a command that installs the test dependencies. (Or we update the cli target to run cli-deps or similar)

OK, thanks for testing.
I was reluctant to add omero_rois as a main dependency when it's only used for setting up tests.
But can do if that's preferable to the copying over the code I needed?

I opened a PR at ome/omero-test-infra#76 to add run cli deps but don't know if that helps immediately?

Probably easiest is to just override one of the py-* commands with whatever would install the additional test requirement.

snoopycrimecop · 2025-04-04T00:46:34Z

Conflicting PR. Removed from build OMERO-plugins-push#377. See the console output for more details.
Possible conflicts:

PR Support export of Fileset:ID #123 will-moore 'Support export of Fileset:ID'
- .isort.cfg
PR Add extinfo command #167 dominikl 'Add extinfo command'
- .isort.cfg
- .pre-commit-config.yaml
PR Use the release/v1 branch for the PyPA action publishing to PyPI #168 will-moore 'Use the release/v1 branch for the PyPA action publishing to PyPI'
- .pre-commit-config.yaml

~~--conflicts~~ Conflict resolved in build OMERO-plugins-push#378. See the console output for more details.

will-moore · 2025-04-16T20:26:52Z

Great, gha has stopped caching yesterday! https://gh.io/gha-cache-sunset
Don't really know how to fix that.

joshmoore · 2025-04-23T09:59:54Z

E ModuleNotFoundError: No module named 'omero_rois'

Did you possible not add the py-setup file to your commit?

will-moore · 2025-04-23T11:02:52Z

@joshmoore - oops! Yes, thanks I missed that.
Since the job is failing here for other reasons, I tried running locally...

Checked-out omero-test-infra into .omeroci/.omero then

$ .omero/docker cli
...

waiting on port: #28
waiting on port: #29
waiting on port: #30
Sleeping for 30
Login attempt 1 failed. Trying again in 2 seconds
Login attempt 2 failed. Trying again in 3 seconds
Login attempt 3 failed. Trying again in 4 seconds
Login attempt 4 failed. Trying again in 5 seconds
Login attempt 5 failed. Trying again in 6 seconds
travis_fold:end:wait-on-login
+ TARGET=/.omeroci
+++ dirname -- /infra/py-common
++ cd -P -- /infra
++ pwd -P
+ dir=/infra
+ cd /.omeroci
+ pip install --upgrade build
Collecting build
  Downloading build-1.2.2.post1-py3-none-any.whl (22 kB)
Requirement already satisfied: importlib-metadata>=4.6 in /opt/omero/server/venv3/lib/python3.9/site-packages (from build) (8.6.1)
Collecting tomli>=1.1.0
  Downloading tomli-2.2.1-py3-none-any.whl (14 kB)
Collecting pyproject_hooks
  Downloading pyproject_hooks-1.2.0-py3-none-any.whl (10 kB)
Requirement already satisfied: packaging>=19.1 in /opt/omero/server/venv3/lib/python3.9/site-packages (from build) (24.2)
Requirement already satisfied: zipp>=3.20 in /opt/omero/server/venv3/lib/python3.9/site-packages (from importlib-metadata>=4.6->build) (3.21.0)
Installing collected packages: tomli, pyproject-hooks, build
Successfully installed build-1.2.2.post1 pyproject-hooks-1.2.0 tomli-2.2.1
WARNING: You are using pip version 21.3.1; however, version 25.0.1 is available.
You should consider upgrading via the '/opt/omero/server/venv3/bin/python3 -m pip install --upgrade pip' command.
+ pip install --upgrade -r /infra/requirements.txt
Collecting flake8
  Downloading flake8-7.2.0-py2.py3-none-any.whl (57 kB)
...
...
Collecting distlib<1,>=0.3.7
  Downloading distlib-0.3.9-py2.py3-none-any.whl (468 kB)
Collecting webencodings
  Downloading webencodings-0.5.1-py2.py3-none-any.whl (11 kB)
Using legacy 'setup.py install' for restructuredtext-lint, since package 'wheel' is not installed.
Installing collected packages: webencodings, pygments, pyflakes, pycodestyle, pluggy, platformdirs, mccabe, iniconfig, filelock, exceptiongroup, docutils, distlib, bleach, virtualenv, readme-renderer, pytest, nodeenv, identify, flake8, cfgv, restview, restructuredtext-lint, pytest-mock, pytest-django, pre-commit, pep8-naming, attrs
    Running setup.py install for restructuredtext-lint: started
    Running setup.py install for restructuredtext-lint: finished with status 'done'
Successfully installed attrs-25.3.0 bleach-6.2.0 cfgv-3.4.0 distlib-0.3.9 docutils-0.21.2 exceptiongroup-1.2.2 filelock-3.18.0 flake8-7.2.0 identify-2.6.10 iniconfig-2.1.0 mccabe-0.7.0 nodeenv-1.9.1 pep8-naming-0.14.1 platformdirs-4.3.7 pluggy-1.5.0 pre-commit-4.2.0 pycodestyle-2.13.0 pyflakes-3.3.2 pygments-2.19.1 pytest-8.3.5 pytest-django-4.11.1 pytest-mock-3.14.0 readme-renderer-36.0 restructuredtext-lint-1.4.0 restview-3.0.2 virtualenv-20.30.0 webencodings-0.5.1
WARNING: You are using pip version 21.3.1; however, version 25.0.1 is available.
You should consider upgrading via the '/opt/omero/server/venv3/bin/python3 -m pip install --upgrade pip' command.
+ TARGET=/.omeroci
+ git config --global --add safe.directory /.omeroci
+ cd /.omeroci
+ '[' -f .pre-commit-config.yaml ']'
+ flake8 -v .
flake8.checker            MainProcess    679 INFO     Making checkers
flake8.main.application   MainProcess    698 INFO     Finished running
flake8.main.application   MainProcess    698 INFO     Reporting errors
flake8.main.application   MainProcess    699 INFO     Found a total of 0 violations and reported 0
+ '[' -f README.rst ']'
+ rst-lint README.md
Path "README.md" not found as a file nor directory
[+] Running 4/3
 ⠿ Container omeroci-db-1     Removed                                                                                                                0.8s
 ⠿ Container omeroci-web-1    Removed                                                                                                                0.7s
 ⠿ Container omeroci-omero-1  Removed                                                                                                                0.8s
 ⠿ Network omeroci_default    Removed

Not sure that the tests actually ran, or if they did, what the results were?

joshmoore · 2025-04-23T12:36:38Z

Pushed a fix of py-setup; tests are passing locally.

joshmoore · 2025-04-23T12:50:41Z

Green!

will-moore · 2025-04-23T14:03:49Z

Wow, thanks @joshmoore!

Any feedback on the tests themselves, or can we just get them in and go from there?

There's one fix in the code was for exporting masks -> labels when theC is set on a mask - now theC is ignored (instead of exporting labels that have a sizeC > 1.

Also this PR fixes handling of output path with $ omero zarr masks Image:1 --output path as used in the test (previously --output was being ignored here)

joshmoore

Barring the one minor catch, I'd say let's get these in. Then we can build on top of them, e.g., as we move towards OME-Zarr 0.5 😄

joshmoore · 2025-04-23T14:10:10Z

setup.py

    url="https://github.com/ome/omero-cli-zarr/",
    setup_requires=["setuptools_scm==7.1.0"],
    use_scm_version={"write_to": "src/omero_zarr/_version.py"},
+    tests_require=["omero-py>=5.18.0", "pytest", "omero-rois"],


Oops. I think we wanted to omit this omero-rois, right?

I'm happy to remove it. Could remove the whole line as it's not being used? Unless it's useful to someone running the tests locally to know that omero-rois is required?

Good point. Let's leave it for local development. We can always review later. 👍

will-moore added 2 commits April 1, 2025 20:27

Initial addition of integration tests

2ef0a1d

lint fixes

a01052a

will-moore force-pushed the integration_tests branch from ba6fd8e to a01052a Compare April 1, 2025 20:56

will-moore added 6 commits April 1, 2025 22:14

Fix assertion

3ec76c7

Test export checks that zarr json is written as expected

656969b

Add test export plate

a1161ca

Add test export labels

d301a43

Add .omeroci/app-deps to install omero-rois for tests

7f9e6f1

Rename .omeroci/app-deps -> .omeroci/app-build

6266696

will-moore added 2 commits April 3, 2025 09:38

Rename .omeroci/app-build -> .omeroci/cli-deps

96b3be0

chmod +x .omeroci/cli-deps

55e5624

will-moore added 4 commits April 3, 2025 10:07

Add omero-rois to test deps

e23dcbb

Copy over code from omero_rois

988e13b

Fix --output argument for masks export

4877927

Fix export of masks that have a theC value

101b0e1

will-moore marked this pull request as ready for review April 3, 2025 09:47

will-moore mentioned this pull request Apr 3, 2025

Zarr export tests #102

Closed

will-moore requested a review from joshmoore April 3, 2025 09:52

joshmoore reviewed Apr 3, 2025

View reviewed changes

will-moore mentioned this pull request Apr 16, 2025

Run cli deps ome/omero-test-infra#76

Closed

Use .omeroci/py-setup to install omero_rois

276d16d

Add missing .omeroci/py-setup

c161a6a

joshmoore added 2 commits April 23, 2025 14:10

Update py-setup

8874951

Update py-setup to invoke parent

1c0613b

Remove precommit.yml (maintenance mode)

541d92a

joshmoore reviewed Apr 23, 2025

View reviewed changes

will-moore merged commit 5b2ca82 into ome:master Apr 24, 2025
2 checks passed

will-moore deleted the integration_tests branch April 24, 2025 12:49

will-moore mentioned this pull request Jun 19, 2025

Use zarr v3 and updated ome-zarr-py #172

Open

Initial addition of integration tests #171

Initial addition of integration tests #171

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