Version 1.5.0 #939

tcompa · 2025-04-16T15:19:20Z

Checklist before merging

I added an appropriate entry to CHANGELOG.md

This reverts commit 2e13979.

…-fractal-task-tools Switch to `fractal-task-tools` and deprecate current tools from `fractal-tasks-core`

…v-1-5-branch Also trigger CI for `dev-1.5` target branch

This reverts commit 4a69bd0.

…task-tools-to-0-0-12 Bump fractal-task-tools to 0.0.12

* upgrade to ngio>=0.2 * refactor projection task to use ngio 0.2 * new testing suite ngio based

github-actions · 2025-04-16T15:24:26Z

Coverage report

Click to see where and how coverage changed

File	Statements	Missing	Coverage	Coverage (new stmts)	Lines missing
fractal_tasks_core
__init__.py	$This PR doesn't change the number of statements in fractal_tasks_core/__init__.py, which is 5.$	$This PR doesn't change the number of statements missing coverage in fractal_tasks_core/__init__.py, which is 0.$	$This PR doesn't change the coverage rate in fractal_tasks_core/__init__.py, which is 100% (5/5).$	$In this PR, 1 new statements are added to fractal_tasks_core/__init__.py, 1 of which are covered (100%).$
fractal_tasks_core/ngff
zarr_utils.py	$This PR doesn't change the number of statements in fractal_tasks_core/ngff/zarr_utils.py, which is 61.$	$This PR adds 5 to the number of statements missing coverage in fractal_tasks_core/ngff/zarr_utils.py, taking it from 10 to 15.$	$This PR removes 7.46 percentage points from the coverage rate in fractal_tasks_core/ngff/zarr_utils.py, taking it from 85.07% (51/61) to 77.61% (46/61).$	$This PR does not seem to add statements to fractal_tasks_core/ngff/zarr_utils.py.$
fractal_tasks_core/tasks
_utils.py	$This PR adds 3 to the number of statements in fractal_tasks_core/tasks/_utils.py, taking it from 28 to 31.$	$This PR adds 26 to the number of statements missing coverage in fractal_tasks_core/tasks/_utils.py, taking it from 5 to 31.$	$This PR removes 75.00 percentage points from the coverage rate in fractal_tasks_core/tasks/_utils.py, taking it from 75% (23/28) to 0% (0/31).$	$In this PR, 3 new statements are added to fractal_tasks_core/tasks/_utils.py, 0 of which are covered (0%).$	22-24, 42
apply_registration_to_image.py	$This PR doesn't change the number of statements in fractal_tasks_core/tasks/apply_registration_to_image.py, which is 128.$	$This PR doesn't change the number of statements missing coverage in fractal_tasks_core/tasks/apply_registration_to_image.py, which is 18.$	$This PR doesn't change the coverage rate in fractal_tasks_core/tasks/apply_registration_to_image.py, which is 80.95% (110/128).$	$In this PR, 1 new statements are added to fractal_tasks_core/tasks/apply_registration_to_image.py, 0 of which are covered (0%).$	398
calculate_registration_image_based.py	$This PR doesn't change the number of statements in fractal_tasks_core/tasks/calculate_registration_image_based.py, which is 87.$	$This PR doesn't change the number of statements missing coverage in fractal_tasks_core/tasks/calculate_registration_image_based.py, which is 6.$	$This PR doesn't change the coverage rate in fractal_tasks_core/tasks/calculate_registration_image_based.py, which is 88.78% (81/87).$	$In this PR, 1 new statements are added to fractal_tasks_core/tasks/calculate_registration_image_based.py, 0 of which are covered (0%).$	312
cellpose_segmentation.py	$This PR doesn't change the number of statements in fractal_tasks_core/tasks/cellpose_segmentation.py, which is 183.$	$This PR doesn't change the number of statements missing coverage in fractal_tasks_core/tasks/cellpose_segmentation.py, which is 15.$	$This PR doesn't change the coverage rate in fractal_tasks_core/tasks/cellpose_segmentation.py, which is 87.55% (168/183).$	$In this PR, 1 new statements are added to fractal_tasks_core/tasks/cellpose_segmentation.py, 0 of which are covered (0%).$	612
cellvoyager_to_ome_zarr_compute.py	$This PR doesn't change the number of statements in fractal_tasks_core/tasks/cellvoyager_to_ome_zarr_compute.py, which is 87.$	$This PR doesn't change the number of statements missing coverage in fractal_tasks_core/tasks/cellvoyager_to_ome_zarr_compute.py, which is 4.$	$This PR doesn't change the coverage rate in fractal_tasks_core/tasks/cellvoyager_to_ome_zarr_compute.py, which is 93.45% (83/87).$	$In this PR, 1 new statements are added to fractal_tasks_core/tasks/cellvoyager_to_ome_zarr_compute.py, 0 of which are covered (0%).$	247
cellvoyager_to_ome_zarr_init.py	$This PR doesn't change the number of statements in fractal_tasks_core/tasks/cellvoyager_to_ome_zarr_init.py, which is 167.$	$This PR doesn't change the number of statements missing coverage in fractal_tasks_core/tasks/cellvoyager_to_ome_zarr_init.py, which is 17.$	$This PR doesn't change the coverage rate in fractal_tasks_core/tasks/cellvoyager_to_ome_zarr_init.py, which is 87.78% (150/167).$	$In this PR, 1 new statements are added to fractal_tasks_core/tasks/cellvoyager_to_ome_zarr_init.py, 0 of which are covered (0%).$	485
cellvoyager_to_ome_zarr_init_multiplex.py	$This PR doesn't change the number of statements in fractal_tasks_core/tasks/cellvoyager_to_ome_zarr_init_multiplex.py, which is 206.$	$This PR doesn't change the number of statements missing coverage in fractal_tasks_core/tasks/cellvoyager_to_ome_zarr_init_multiplex.py, which is 21.$	$This PR doesn't change the coverage rate in fractal_tasks_core/tasks/cellvoyager_to_ome_zarr_init_multiplex.py, which is 86.15% (185/206).$	$In this PR, 1 new statements are added to fractal_tasks_core/tasks/cellvoyager_to_ome_zarr_init_multiplex.py, 0 of which are covered (0%).$	532
copy_ome_zarr_hcs_plate.py	$This PR removes 34 from the number of statements in fractal_tasks_core/tasks/copy_ome_zarr_hcs_plate.py, taking it from 105 to 71.$	$This PR adds 3 to the number of statements missing coverage in fractal_tasks_core/tasks/copy_ome_zarr_hcs_plate.py, taking it from 2 to 5.$	$This PR removes 5.91 percentage points from the coverage rate in fractal_tasks_core/tasks/copy_ome_zarr_hcs_plate.py, taking it from 97.67% (103/105) to 91.76% (66/71).$	$In this PR, 56 new statements are added to fractal_tasks_core/tasks/copy_ome_zarr_hcs_plate.py, 52 of which are covered (92.85%).$	48-49, 193, 227
find_registration_consensus.py	$This PR doesn't change the number of statements in fractal_tasks_core/tasks/find_registration_consensus.py, which is 47.$	$This PR doesn't change the number of statements missing coverage in fractal_tasks_core/tasks/find_registration_consensus.py, which is 4.$	$This PR doesn't change the coverage rate in fractal_tasks_core/tasks/find_registration_consensus.py, which is 87.3% (43/47).$	$In this PR, 1 new statements are added to fractal_tasks_core/tasks/find_registration_consensus.py, 0 of which are covered (0%).$	168
illumination_correction.py	$This PR doesn't change the number of statements in fractal_tasks_core/tasks/illumination_correction.py, which is 94.$	$This PR doesn't change the number of statements missing coverage in fractal_tasks_core/tasks/illumination_correction.py, which is 7.$	$This PR doesn't change the coverage rate in fractal_tasks_core/tasks/illumination_correction.py, which is 90% (87/94).$	$In this PR, 1 new statements are added to fractal_tasks_core/tasks/illumination_correction.py, 0 of which are covered (0%).$	287
image_based_registration_hcs_init.py	$This PR doesn't change the number of statements in fractal_tasks_core/tasks/image_based_registration_hcs_init.py, which is 21.$	$This PR doesn't change the number of statements missing coverage in fractal_tasks_core/tasks/image_based_registration_hcs_init.py, which is 2.$	$This PR doesn't change the coverage rate in fractal_tasks_core/tasks/image_based_registration_hcs_init.py, which is 90.32% (19/21).$	$In this PR, 1 new statements are added to fractal_tasks_core/tasks/image_based_registration_hcs_init.py, 0 of which are covered (0%).$	93
import_ome_zarr.py	$This PR removes 2 from the number of statements in fractal_tasks_core/tasks/import_ome_zarr.py, taking it from 95 to 93.$	$This PR removes 1 from the number of statements missing coverage in fractal_tasks_core/tasks/import_ome_zarr.py, taking it from 9 to 8.$	$This PR adds 1.22 percentage points to the coverage rate in fractal_tasks_core/tasks/import_ome_zarr.py, taking it from 87.4% (86/95) to 88.61% (85/93).$	$In this PR, 1 new statements are added to fractal_tasks_core/tasks/import_ome_zarr.py, 0 of which are covered (0%).$	295
init_group_by_well_for_multiplexing.py	$This PR doesn't change the number of statements in fractal_tasks_core/tasks/init_group_by_well_for_multiplexing.py, which is 22.$	$This PR doesn't change the number of statements missing coverage in fractal_tasks_core/tasks/init_group_by_well_for_multiplexing.py, which is 3.$	$This PR doesn't change the coverage rate in fractal_tasks_core/tasks/init_group_by_well_for_multiplexing.py, which is 84.37% (19/22).$	$In this PR, 1 new statements are added to fractal_tasks_core/tasks/init_group_by_well_for_multiplexing.py, 0 of which are covered (0%).$	86
napari_workflows_wrapper.py	$This PR doesn't change the number of statements in fractal_tasks_core/tasks/napari_workflows_wrapper.py, which is 235.$	$This PR doesn't change the number of statements missing coverage in fractal_tasks_core/tasks/napari_workflows_wrapper.py, which is 19.$	$This PR doesn't change the coverage rate in fractal_tasks_core/tasks/napari_workflows_wrapper.py, which is 90.39% (216/235).$	$In this PR, 1 new statements are added to fractal_tasks_core/tasks/napari_workflows_wrapper.py, 0 of which are covered (0%).$	633
projection.py	$This PR removes 1 from the number of statements in fractal_tasks_core/tasks/projection.py, taking it from 56 to 55.$	$This PR doesn't change the number of statements missing coverage in fractal_tasks_core/tasks/projection.py, which is 3.$	$This PR adds 0.12 percentage points to the coverage rate in fractal_tasks_core/tasks/projection.py, taking it from 92.18% (53/56) to 92.3% (52/55).$	$In this PR, 22 new statements are added to fractal_tasks_core/tasks/projection.py, 20 of which are covered (90.9%).$	46, 147
Project Total

_{This report was generated by python-coverage-comment-action}

…al-task-tools)

Require ngio 0.2.3

tcompa · 2025-04-23T12:46:03Z

Is there anything here missing or can we merge to main and release (1.5.0a3 or 1.5.0)?

cc @lorenzocerrone @jluethi

jluethi · 2025-04-23T17:11:34Z

I'm not aware of any blockers, 1.5.0a2 worked well in my tests! I'd be in favor of merge to main & 1.5.0 release. If we do hit any unforseen issues, we can fix them in patch releases

Edit: Let's merge the minor projection task update first on renaming the overwrite, then merge :)

tcompa · 2025-04-24T08:39:11Z

I'm merging to main, so that new PRs will have the CI triggered.
I'm not making any new release for now.

tcompa added 30 commits March 13, 2025 16:46

Add dependency on fractal-task-tools

1220bcf

Add a bunch of deprecations

ced325e

Use fractal_task_tools models

48ffd72

Use task-runner wrapper from new package

92b8584

Use fractal_task_tools in test

da38da9

Bump fractal-task-tools

43c7dbe

Fill in metadata in task_list.py

e2fda8d

Bump fractal-task-tools

3abbfce

Merge branch 'main' into 921-switch-to-fractal-task-tools

961ea43

Bump fractal-task-tools

e8305fa

Update method for checking manifest has not changed

c6991ae

BROKEN - intentionally break manifest, to double check GHA

2e13979

Revert "BROKEN - intentionally break manifest, to double check GHA"

c4061e5

This reverts commit 2e13979.

Bump fractal-task-tools to 0.0.9 and update manifest

8ca1611

Introduce converter tasks

d4d0258

Update deprecation message

041fe15

Relax version constraint on docstring_parser

8bf4b5a

Relax version constraint on docstring_parser

0f01f56

Drop all zarr_urls=[] for converter tasks from tests

ad8e7ad

Fix one more test

6a0856f

depend on fractal-task-tools 0.10.0

e9dac34

CHANGELOG [skip ci]

e44b380

CHANGELOG [skip ci]

e80cb19

Merge pull request #923 from fractal-analytics-platform/921-switch-to…

ab8d952

…-fractal-task-tools Switch to `fractal-task-tools` and deprecate current tools from `fractal-tasks-core`

bump version 1.4.2 -> 1.5.0a0

31879fb

Also trigger CI for dev-1.5 target branch

8adb681

Merge pull request #925 from fractal-analytics-platform/run-ci-for-de…

1da1e01

…v-1-5-branch Also trigger CI for `dev-1.5` target branch

Drop support for python 3.10

ff81848

CHANGELOG [skip ci]

4d2a676

Update poetry.lock

5a4a07c

tcompa and others added 7 commits April 8, 2025 16:08

Revert "Trigger CI"

efc92f4

This reverts commit 4a69bd0.

CHANGELOG [skip ci]

c4e438c

Merge pull request #933 from fractal-analytics-platform/bump-fractal-…

4df0750

…task-tools-to-0-0-12 Bump fractal-task-tools to 0.0.12

bump version 1.5.0a0 -> 1.5.0a1

59b61a7

Ngio projection task (#937)

b63681d

* upgrade to ngio>=0.2 * refactor projection task to use ngio 0.2 * new testing suite ngio based

bump version 1.5.0a1 -> 1.5.0a2

ee54370

Merge branch 'main' into dev-1.5

49000d3

cleanup helper-tasks from external packages test (now tested in fract…

dd2b916

…al-task-tools)

tcompa mentioned this pull request Apr 17, 2025

Use main branch of fractal-tasks-core for tests fractal-analytics-platform/fractal-task-tools#29

Open

tcompa and others added 16 commits April 23, 2025 08:25

Require ngio>=0.2.3

a1c820a

Update poetry lock

8e07e98

fix conftest fixture

124ab8f

require ngio>=0.2.4

67335be

minor projection simplification

ab843ad

fix pre-commit

5793df7

CHANGELOG

e0d2381

Regenerate poetry.lock with poetry v2

c42d6ac

Merge pull request #943 from fractal-analytics-platform/ngio-023

d98acd0

Require ngio 0.2.3

Update ci_pip.yml

a427f4a

Update ci_poetry.yml

e2ca99d

Update documentation.yaml

ba56f64

Update manifest_external_packages.yml

ab9a99d

Update package.yml

a9b38a7

Consolidate CHANGELOG.md [skip ci]

c693cfa

Update poetry_build.yml

4f227b8

tcompa merged commit bb97f76 into main Apr 24, 2025
16 checks passed

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Version 1.5.0 #939

Version 1.5.0 #939

tcompa commented Apr 16, 2025

github-actions bot commented Apr 16, 2025 •

edited

Loading

tcompa commented Apr 23, 2025

jluethi commented Apr 23, 2025 •

edited

Loading

tcompa commented Apr 24, 2025

Version 1.5.0 #939

Version 1.5.0 #939

Conversation

tcompa commented Apr 16, 2025

Checklist before merging

github-actions bot commented Apr 16, 2025 • edited Loading

Coverage report

tcompa commented Apr 23, 2025

jluethi commented Apr 23, 2025 • edited Loading

tcompa commented Apr 24, 2025

github-actions bot commented Apr 16, 2025 •

edited

Loading

jluethi commented Apr 23, 2025 •

edited

Loading