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ci(dependabot): bump actions/add-to-project from 1.0.2 to 2.0.0 in the actions group#469

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ci(dependabot): bump actions/add-to-project from 1.0.2 to 2.0.0 in the actions group#469
mogres merged 1 commit into
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Bumps the actions group with 1 update: actions/add-to-project.

Updates actions/add-to-project from 1.0.2 to 2.0.0

Release notes

Sourced from actions/add-to-project's releases.

v2

What's Changed

... (truncated)

Commits
  • 5afcf98 Merge pull request #712 from salmanmkc/node24
  • ffed68f Merge main and update action runtime to Node 24
  • 27022a1 Merge pull request #777 from actions/dependabot/npm_and_yarn/types/node-25.5.0
  • cc89d2e Merge pull request #778 from actions/dependabot/npm_and_yarn/globals-17.4.0
  • ef8e6ff Merge pull request #779 from actions/dependabot/npm_and_yarn/eslint-plugin-je...
  • eb406b3 Merge pull request #780 from actions/dependabot/npm_and_yarn/handlebars-4.7.9
  • bb8d4d7 Bump handlebars from 4.7.8 to 4.7.9
  • a6fcf8b Bump eslint-plugin-jest from 29.12.1 to 29.15.1
  • b35f5d3 Bump globals from 17.0.0 to 17.4.0
  • 036fea0 Bump @​types/node from 25.0.3 to 25.5.0
  • Additional commits viewable in compare view

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ci(dependabot): bump actions/add-to-project in the actions group
d4af53b 
Bumps the actions group with 1 update: [actions/add-to-project](https://github.com/actions/add-to-project).


Updates `actions/add-to-project` from 1.0.2 to 2.0.0
- [Release notes](https://github.com/actions/add-to-project/releases)
- [Commits](actions/add-to-project@v1.0.2...v2.0.0)

---
updated-dependencies:
- dependency-name: actions/add-to-project
  dependency-version: 2.0.0
  dependency-type: direct:production
  update-type: version-update:semver-major
  dependency-group: actions
...

Signed-off-by: dependabot[bot] <support@github.com>
@dependabot dependabot Bot added dependencies Pull requests that update a dependency file github_actions Pull requests that update GitHub Actions code labels Jun 1, 2026
@rugeli

rugeli commented Jun 1, 2026

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Packing analysis report

Analysis for packing results located at cellpack/tests/outputs/test_spheres/spheresSST

Ingredient name Encapsulating radius Average number packed
ext_A 25 236.0

Packing image

Packing image

Distance analysis

Expected minimum distance: 50.00
Actual minimum distance: 50.01

Ingredient key Pairwise distance distribution
ext_A Distance distribution ext_A

@mogres mogres merged commit 643fabb into main Jun 8, 2026
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@mogres mogres deleted the dependabot/github_actions/actions-c1bd81b4e7 branch June 8, 2026 16:52
mogres added a commit that referenced this pull request Jun 16, 2026
@mogres @rugeli
@ascibisz @dependabot @github-advanced-security @github-actions @claude
Merge main into cellpack-analysis (#472)
50f7d1c 
* user workflow improvements and config updates  (#411)

* default upload_results to false

* update config file options

* update schema docs

* propose to remove config files from the packing commands but add a section to explain how configs work

* set open_results_in_browser to false since it's dependent on upload_results

* improve loggings

* add a config file for upload results

* correct option default and log level

* update schema

* add aws db to path

* add a layer to detect non-interactive envs for db selection

* fix readme

* add cellpack website url

* remove unnecessary restriction

* update readme

* add screenshots to readme (#413)

* add screenshots to readme

* Quick fix: update bbox value in recipes (#420)

* add randomness_seed to upload and download (#416)

* update bbox value in recipes

* add config option for plot display

* replace result screenshots and update readme

* update docs/index to display images correctly

* Add description field to recipe schema and backend utilities (#430)

* add `description` and `randomness_seed` to top level recipe settings

* add description in example recipes

* add description to download and upload script

* add description field to unit tests

* pr commenting: use native github CLI (#432)

* test github cli

* remove test branch

* Minimal fix: set camera position (#431)

* set camera

* use max dimension

* add checks for pull requests (#434)

* Feature/client upload script (#417)

* add upload script

* add example data and more documentation

* point to correct collection

* return firebase IDs from upload_recipe adn upload_config

* add documentation

* add installation step

* lint fixes

* lint fix

* fix typos

* keep all upload functionality in upload.py, and rename client to studio

* remove accidential line

* update example editable fields to match updates we've done

* add output param

* lint fixes

* small wording fixes

* make config_path optional

* ci(dependabot): bump astral-sh/setup-uv from 4 to 7 (#436)

Bumps [astral-sh/setup-uv](https://github.com/astral-sh/setup-uv) from 4 to 7.
- [Release notes](https://github.com/astral-sh/setup-uv/releases)
- [Commits](astral-sh/setup-uv@v4...v7)

---
updated-dependencies:
- dependency-name: astral-sh/setup-uv
  dependency-version: '7'
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Fix Comment Update job: use gh api instead of gh pr review (#438)

* use gh api instead of gh pr review

* remove backslashes

* trigger workflow to test comment update

* use patch instead of delete

* take2-trigger workflow to test comment update

* use an actual new line to avoid \n being treated as literal chars

* Studio: add recipe and config json to outputs for downloading  (#435)

* add recipe and config to output

* refactor

* path guard

* Potential fix for code scanning alert no. 21: Uncontrolled data used in path expression

Co-authored-by: Copilot Autofix powered by AI <62310815+github-advanced-security[bot]@users.noreply.github.com>

* format

* fix 404 comment

* handle firebase recipe, serialize it before passing to s3

* save recipe data directly to outputs

* remove unused import

* one more unused import

---------

Co-authored-by: Copilot Autofix powered by AI <62310815+github-advanced-security[bot]@users.noreply.github.com>

* ci(dependabot): bump actions/upload-artifact from 4 to 6 (#439)

Bumps [actions/upload-artifact](https://github.com/actions/upload-artifact) from 4 to 6.
- [Release notes](https://github.com/actions/upload-artifact/releases)
- [Commits](actions/upload-artifact@v4...v6)

---
updated-dependencies:
- dependency-name: actions/upload-artifact
  dependency-version: '6'
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Miscellaneous gradient updates (#428)

* Add gradient weights to Environment.py and Gradient.py

* Remove unused import

* Refactor Environment.py and utils.py

This commit refactors the `Environment.py` file by separating the loading of grid, compartment grids, and mesh store into separate loops. It also clears the triangles_tree cache and resets the grid. Additionally, the `load_object_from_pickle` function has been removed from `utils.py` as it is no longer used.

* Ignore venv folders

* Update logging level

* Update `aicsimageio` to `bioio`

- Also update the logging of recipe validation to `debug`

* Suppress logging outputs for lower level functions

* Update logs in `ImageWriter.py`

* Update path preference loading to catch empty json

* Update logging for recipe validation

* sort imports

* Update uv lock

* Allow gradient weights to be specified as a dict while combining

* Add uniform weight map option

* Fix gradient weight scaling for equal weights

* Update scaling to just divide by max value

* Add recipe to test gradients

* Rename scaling method to normalize_by_max_value and update references

* Use uniform weight if `decay_length` is 0

* Linting updates

* Update validation for decay length

* Update validation for multiple gradients

* Add zero decay gradient in test recipe

* ci(dependabot): bump aws-actions/configure-aws-credentials from 4 to 5 (#447)

* ci(dependabot): bump aws-actions/configure-aws-credentials from 4 to 5

Bumps [aws-actions/configure-aws-credentials](https://github.com/aws-actions/configure-aws-credentials) from 4 to 5.
- [Release notes](https://github.com/aws-actions/configure-aws-credentials/releases)
- [Changelog](https://github.com/aws-actions/configure-aws-credentials/blob/main/CHANGELOG.md)
- [Commits](aws-actions/configure-aws-credentials@v4...v5)

---
updated-dependencies:
- dependency-name: aws-actions/configure-aws-credentials
  dependency-version: '5'
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>

* matching the regular pr format

* trigger codeQL

---------

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Ruge Li <rugeli0605@gmail.com>

* ci(dependabot): bump peter-evans/create-pull-request from 7 to 8 (#450)

Bumps [peter-evans/create-pull-request](https://github.com/peter-evans/create-pull-request) from 7 to 8.
- [Release notes](https://github.com/peter-evans/create-pull-request/releases)
- [Commits](peter-evans/create-pull-request@v7...v8)

---
updated-dependencies:
- dependency-name: peter-evans/create-pull-request
  dependency-version: '8'
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Use native gh CLI for requirements actions (#453)

* update UV setup to version 7
* update Dependabot configuration

* remove unnecessary permissions for open-PR job in make-requirements.yml

* Make timestamp unique using the run ID

* Avoid expanding the WORKFLOW_PAT

* ci(dependabot): bump the actions group with 4 updates (#456)

Bumps the actions group with 4 updates: [actions/checkout](https://github.com/actions/checkout), [actions/upload-artifact](https://github.com/actions/upload-artifact), [aws-actions/configure-aws-credentials](https://github.com/aws-actions/configure-aws-credentials) and [actions/download-artifact](https://github.com/actions/download-artifact).


Updates `actions/checkout` from 4 to 6
- [Release notes](https://github.com/actions/checkout/releases)
- [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md)
- [Commits](actions/checkout@v4...v6)

Updates `actions/upload-artifact` from 6 to 7
- [Release notes](https://github.com/actions/upload-artifact/releases)
- [Commits](actions/upload-artifact@v6...v7)

Updates `aws-actions/configure-aws-credentials` from 5 to 6
- [Release notes](https://github.com/aws-actions/configure-aws-credentials/releases)
- [Changelog](https://github.com/aws-actions/configure-aws-credentials/blob/main/CHANGELOG.md)
- [Commits](aws-actions/configure-aws-credentials@v5...v6)

Updates `actions/download-artifact` from 6 to 8
- [Release notes](https://github.com/actions/download-artifact/releases)
- [Commits](actions/download-artifact@v6...v8)

---
updated-dependencies:
- dependency-name: actions/checkout
  dependency-version: '6'
  dependency-type: direct:production
  update-type: version-update:semver-major
  dependency-group: actions
- dependency-name: actions/upload-artifact
  dependency-version: '7'
  dependency-type: direct:production
  update-type: version-update:semver-major
  dependency-group: actions
- dependency-name: aws-actions/configure-aws-credentials
  dependency-version: '6'
  dependency-type: direct:production
  update-type: version-update:semver-major
  dependency-group: actions
- dependency-name: actions/download-artifact
  dependency-version: '8'
  dependency-type: direct:production
  update-type: version-update:semver-major
  dependency-group: actions
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Upgrading dependencies (#457)

* Upgrading dependencies

* Update black target version

* Formatting via `uv run black cellpack`

* Updating requirements.txt after change to `uv.lock` was pushed to `main` (#458)

Co-authored-by: github-actions[bot] <github-actions[bot]@users.noreply.github.com>

* Server should Accept Recipe JSON  (#419)

* add upload script

* add example data and more documentation

* point to correct collection

* have server accept recipe as json object in body of request

* update documentation

* remove accidential dockerfile changes

* rename param json_recipe

* remove file that shouldn't be in this PR

* remove accidential file

* lint fixes

* refactor to try to improve clarity of json recipe vs file path

* lint fixes

* lint fix

* minimize changeset

* minimize changeset

* simplify changeset

* code cleanup

* minimize changeset

* remove trailing comma

* Feature/firebase lookup (#445)

* remove os fetch for job_id

* use dedup_hash instead of job id

* proposal: get hash from recipe loader

* renaming and add TODOs

* format

* rename param to hash

* remove unused validate param and doc strings in pack

* simplify get_ dedup_hash

* refactor job_status update

* cleanup

* fix upload_job_status to handle awshandler

* pass dedup_pash to env for fetching across files

* add tests

* format1

* format test

* Only upload simularium file once (#446)

* proposal: get hash from recipe loader

* simplify get_ dedup_hash

* only post simularium results file once for server job runs

* update code for rebase

* code cleanup

---------

Co-authored-by: Ruge Li <rugeli0605@gmail.com>

* Maint/firebase collection cleanup (#448)

* remove local metadata writes for auto-pop feature

* remove cleanup firebase workflow

* remove cleanup firebase code

* 1. make doc url a constant 2.remove unused param

* handle both recipe_path and json body requests (#449)

* change error message body

* lint fixes

* add more checks when attempting to read json body

* add upload script

* add example data and more documentation

* point to correct collection

* have server accept recipe as json object in body of request

* update documentation

* remove accidential dockerfile changes

* rename param json_recipe

* remove file that shouldn't be in this PR

* remove accidential file

* lint fixes

* refactor to try to improve clarity of json recipe vs file path

* lint fixes

* lint fix

* minimize changeset

* minimize changeset

* simplify changeset

* code cleanup

* minimize changeset

* remove trailing comma

* Feature/firebase lookup (#445)

* remove os fetch for job_id

* use dedup_hash instead of job id

* proposal: get hash from recipe loader

* renaming and add TODOs

* format

* rename param to hash

* remove unused validate param and doc strings in pack

* simplify get_ dedup_hash

* refactor job_status update

* cleanup

* fix upload_job_status to handle awshandler

* pass dedup_pash to env for fetching across files

* add tests

* format1

* format test

* Only upload simularium file once (#446)

* proposal: get hash from recipe loader

* simplify get_ dedup_hash

* only post simularium results file once for server job runs

* update code for rebase

* code cleanup

---------

Co-authored-by: Ruge Li <rugeli0605@gmail.com>

* Maint/firebase collection cleanup (#448)

* remove local metadata writes for auto-pop feature

* remove cleanup firebase workflow

* remove cleanup firebase code

* 1. make doc url a constant 2.remove unused param

* handle both recipe_path and json body requests (#449)

* change error message body

* lint fixes

* add more checks when attempting to read json body

* let recipe loader check the input and key stripping

* Update cellpack/autopack/writers/__init__.py

Co-authored-by: Saurabh Mogre <saurabh.mogre@alleninstitute.org>

* use `isinstance` for AWSHandler, and misc

* update aws tests

* initialize dedup_hash

* add in-line comment

* temp solution: use requirement.txt

---------

Co-authored-by: Ruge Li <91452427+rugeli@users.noreply.github.com>
Co-authored-by: Ruge Li <rugeli0605@gmail.com>
Co-authored-by: Saurabh Mogre <saurabh.mogre@alleninstitute.org>

* ci(dependabot): bump the actions group across 1 directory with 4 updates (#466)

Bumps the actions group with 4 updates in the / directory: [actions/configure-pages](https://github.com/actions/configure-pages), [actions/upload-pages-artifact](https://github.com/actions/upload-pages-artifact), [actions/deploy-pages](https://github.com/actions/deploy-pages) and [codecov/codecov-action](https://github.com/codecov/codecov-action).


Updates `actions/configure-pages` from 5 to 6
- [Release notes](https://github.com/actions/configure-pages/releases)
- [Commits](actions/configure-pages@v5...v6)

Updates `actions/upload-pages-artifact` from 4 to 5
- [Release notes](https://github.com/actions/upload-pages-artifact/releases)
- [Commits](actions/upload-pages-artifact@v4...v5)

Updates `actions/deploy-pages` from 4 to 5
- [Release notes](https://github.com/actions/deploy-pages/releases)
- [Commits](actions/deploy-pages@v4...v5)

Updates `codecov/codecov-action` from 5 to 6
- [Release notes](https://github.com/codecov/codecov-action/releases)
- [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md)
- [Commits](codecov/codecov-action@v5...v6)

---
updated-dependencies:
- dependency-name: actions/configure-pages
  dependency-version: '6'
  dependency-type: direct:production
  update-type: version-update:semver-major
  dependency-group: actions
- dependency-name: actions/upload-pages-artifact
  dependency-version: '5'
  dependency-type: direct:production
  update-type: version-update:semver-major
  dependency-group: actions
- dependency-name: actions/deploy-pages
  dependency-version: '5'
  dependency-type: direct:production
  update-type: version-update:semver-major
  dependency-group: actions
- dependency-name: codecov/codecov-action
  dependency-version: '6'
  dependency-type: direct:production
  update-type: version-update:semver-major
  dependency-group: actions
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Test updates: stabler debup hash and cli integration coverage (#462)

* normalize data order before hashing and tests

* test pack cli

* refactor test file: use tmp_path instead of writing to a working dir

* cleanup

* formatting

* add recipe fixture

* Remove Support for Recipe URL Param (#464)

* we only support recipe as JSON body now, remove support for reading recipe file path from URL

* update documentation to use new communication protocol and strip out references to AWS batch

* remove unused import

* Maint/deprecate requirements txt (#467)

* remove requirements.txt related code

* update pyproject.toml

* generate new uv file

* update pip install for dockerfile

* use uv sync

* move server dep list under dependency-groups

* update docker

* fix path and use uv sync

* add pydantic to pyproject toml

* update lock file

* Feature/v2 bloodplasma (#471)

* update migration script and validation

* add v2 blood plasma recipe

* ci(dependabot): bump actions/add-to-project in the actions group (#469)

Bumps the actions group with 1 update: [actions/add-to-project](https://github.com/actions/add-to-project).


Updates `actions/add-to-project` from 1.0.2 to 2.0.0
- [Release notes](https://github.com/actions/add-to-project/releases)
- [Commits](actions/add-to-project@v1.0.2...v2.0.0)

---
updated-dependencies:
- dependency-name: actions/add-to-project
  dependency-version: 2.0.0
  dependency-type: direct:production
  update-type: version-update:semver-major
  dependency-group: actions
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* fix KeyError: 'weight_mode' when packing v2.1 recipes with under-specified gradients (#470)

* Add recipe and config to test gradient mixing in peroxisome data

* normalize grad in early process

* add tests

---------

Co-authored-by: mogres <saurabh.mogre@alleninstitute.org>

* pack: log resolved cellpack package path at DEBUG level

Adds a DEBUG-level log of which cellpack package pack.py imported
(autopack path), so it is easy to confirm whether a run used an
installed/pinned cellpack vs a checked-out branch when debugging.
Kept at DEBUG so normal packing output is unchanged.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

---------

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: Ruge Li <91452427+rugeli@users.noreply.github.com>
Co-authored-by: Alli <111383930+ascibisz@users.noreply.github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Copilot Autofix powered by AI <62310815+github-advanced-security[bot]@users.noreply.github.com>
Co-authored-by: Ruge Li <rugeli0605@gmail.com>
Co-authored-by: github-actions[bot] <github-actions[bot]@users.noreply.github.com>
Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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