Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

JOSS submission #67

Closed
wants to merge 47 commits into from
Closed

JOSS submission #67

wants to merge 47 commits into from

Conversation

adamltyson
Copy link
Member

Hi @FedeClaudi, @vigji,

I've put together a very rough draft of the JOSS submission to get the conversation started. There are guidelines here, and you can see how it compiles here.

@FedeClaudi
Copy link
Contributor

Haven't read through the content, but the format looks good.
Only the footer has something missing:
image

@adamltyson
Copy link
Member Author

Only the footer has something missing:

I'm not sure how we fix that. It may only get fixed with the final submission? You have to fill in a form which may supply those details.

@FedeClaudi
Copy link
Contributor

I've made some edits, but feel free to ignore/include any of it. The only thing I think it's worth changing is this paragram (right under the header statement of need:

Neuroscience is gradually becoming a field reliant on large scale data acquisition, such as whole-brain optical neural recordings [@ahrens:2012], brain-wide connectivity mapping [@Osten:2013] or high-density electrophysiological probes [@jun:2017]. For this reason, custom, computational analysis is now necessary in the majority of neuroscience laboratories, and Python is emerging as the programming language of choice [@muller:2015].

It doesn't really add much, the only relevant part is the fact that python is becoming the most adopted language, but we can mention that elsewhere. I would start talking about atlases, what they are and how useful they are. Then say that the problem of the APIs and justify why we made BG (and we can add a sentence here about why python).

What do you guys think?

@adamltyson
Copy link
Member Author

adamltyson commented Aug 19, 2020 •
edited
Loading

It doesn't really add much, the only relevant part is the fact that python is becoming the most adopted language, but we can mention that elsewhere. I would start talking about atlases, what they are and how useful they are. Then say that the problem of the APIs and justify why we made BG (and we can add a sentence here about why python).

What do you guys think?

Agree, it's waffle. I've removed that paragraph, and slotted in the Python bit into the next paragraph.

@FedeClaudi
Copy link
Contributor

cool, it looks good to me! Is this really all we have to do for submission? Awesome!

@adamltyson
Copy link
Member Author

cool, it looks good to me! Is this really all we have to do for submission? Awesome!

Pretty much, there's just a form to fill in.

Once @vigji has had a chance to take a look (take your time), I'll send it around the senior authors.

@FedeClaudi
Copy link
Contributor

@vigji brainrender is just brainrender, not BrainRender (it used to be like this but now it's just lower case), but thanks for checking it 👍

The other changes also look good.

vigji
vigji reviewed Aug 19, 2020
View reviewed changes
Copy link
Member

@vigji vigji left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

I would also add some reference for the idea of morphing stuff to a common reference (maybe amap, or for zebrafish https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4710481/) if that is fine

@adamltyson
Copy link
Member Author

Looks good to me. @FedeClaudi are you happy to approve this? If so I'll send it round tomorrow.

@vigji
Copy link
Member

vigji commented Aug 19, 2020

I can't preview it (page not found when trying it), is it my browser or I broke something in the md file?

@adamltyson
Copy link
Member Author

I can't preview it (page not found when trying it), is it my browser or I broke something in the md file?

I think the server might have been down. It didn't work for me earlier, but it's working now. I'll send it around later.

@adamltyson adamltyson marked this pull request as ready for review August 20, 2020 08:57
@vigji
Copy link
Member

vigji commented Sep 3, 2020

Good for me now, let me know!

@vigji
Copy link
Member

vigji commented Sep 3, 2020

Perfect! @adamltyson looks good to you?

@adamltyson
Copy link
Member Author

Yep!

@vigji
Squashed commit of the following:
d2c21a2 
commit aa33d12
Author: Luigi Petrucco <[email protected]>
Date:   Thu Sep 3 13:49:11 2020 +0200

    Added method for shape in um

commit e8c5d51
Author: Luigi Petrucco <[email protected]>
Date:   Wed Sep 2 22:33:21 2020 +0200

    Refactoring atlas generation for automatic update of atlases (#60)

    * Refactoring atlas generation for automatic update of atlases

    * Script for batch running all atlas scripts

    * bugfix for zebrafish atlas generation

    * Merging fixes

    * Lazy loading of secondary references

    * renamed to additional_references

    * bugfix

    * linting

    * Changed secondary to additional references

    * Fixed bug for custom atlas usage

    * StructuresDict repr is now the tree; added  structure id in the tag

    * Removed atlas_gen package, standard orientation is now asr

    * Fixed tests

    * Blacked for good

    * Testing for new class

    * Set back dev deps and markdown description for PyPi

commit e061d8a
Author: Luigi Petrucco <[email protected]>
Date:   Sun Aug 30 12:09:47 2020 +0200

    Update README.md

commit 96e3ade
Author: Luigi Petrucco <[email protected]>
Date:   Sun Aug 30 12:09:33 2020 +0200

    Update README.md

commit c36fda5
Author: Luigi Petrucco <[email protected]>
Date:   Fri Aug 21 14:17:58 2020 +0200

    Bump version: 0.1.0 → 0.1.1

commit 2c41b18
Author: Luigi Petrucco <[email protected]>
Date:   Fri Aug 21 14:17:30 2020 +0200

    Added changelog file and config for bumpversion (#71)

    * Added changelog file and config for bumpversion

    * Update CHANGELOG.md

    * Update __init__.py

commit 6ea8195
Author: Luigi Petrucco <[email protected]>
Date:   Fri Aug 21 12:18:11 2020 +0200

    Fixed bug for hemisphere orientation (#70)
@vigji
black fix
d408893
@vigji
Merge branch 'master' into joss
eb4680f 
# Conflicts:
#	bg_atlasapi/core.py
#	bg_atlasapi/utils.py
@vigji
Merge branch 'master' into joss
2acdae5 
# Conflicts:
#	bg_atlasapi/utils.py
@adamltyson adamltyson marked this pull request as draft September 3, 2020 16:53
@adamltyson
Copy link
Member Author

I converted to draft, so we (I) don't accidentally merge into master.

FedeClaudi and others added 12 commits September 13, 2020 19:19
@FedeClaudi
Update paper.bib
dbe6a38
@vigji
Squashed commit of the following:
818edf5 
commit 2d8c121
Author: Luigi Petrucco <[email protected]>
Date:   Thu Sep 24 22:15:15 2020 +0200

    Test bugfix

commit 31ae172
Author: Federico Claudi <[email protected]>
Date:   Sun Sep 13 20:23:04 2020 +0100

    Added # Contributing

commit b2b2d9e
Author: Oren Amsalem <[email protected]>
Date:   Thu Sep 3 23:16:35 2020 +0300

    Version 0.2.0 does not work with bg-space 0.3.0 (#75)

    I don't know exactly what is the minimum version of bg-space so I set it to above 0.5.0.
    This is important for people who upgrade.
@vigji
Merge remote-tracking branch 'origin/master' into joss
140f2f3 
# Conflicts:
#	requirements.txt
@vigji
acknowledges section
e00e8c6
@adamltyson
Update Acknowledgments
adb242c
@vigji
Updated affiliations
6be9e1b
@adamltyson
Update affiliations
c8ead54
@adamltyson
update references
8e19c74
@vigji
Merge branch 'master' into joss
9dd28b5
@vigji
removed additional pyinspect
950f3e1
@vigji
Merge branch 'master' into joss
0e3b2c6
@adamltyson
fix typo
b1a95d6
@adamltyson
Copy link
Member Author

I guess we can close this PR now?

@vigji
Copy link
Member

vigji commented Oct 6, 2020

guess so yes!

@adamltyson
Copy link
Member Author

Closing now the paper is published.

@adamltyson adamltyson closed this Oct 6, 2020
willGraham01 pushed a commit that referenced this pull request Feb 14, 2024
@pre-commit-ci
[pre-commit.ci] pre-commit autoupdate (#67)
d946d4f 
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.0.285 → v0.0.286](astral-sh/ruff-pre-commit@v0.0.285...v0.0.286)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
willGraham01 added a commit that referenced this pull request Feb 23, 2024
@willGraham01 @vigji
@adamltyson @MathieuBo @bkntr @kailynkfields @FedeClaudi @Gubra-ApS @JohannaPerens @yoda-vid @samclothier @JoeZiminski @novafae @dstansby @pre-commit-ci @alessandrofelder @viktorpm
Merge with atlasgen (#199)
e34a84a 
* Initial commit

* Update README.md

* First commit

* gitignore

* Almost at complete atlas autogeneration

* Finalized script for automatic atlas generation

* Added template script for atlas generation

* Template description

* First working version of script for auto deployment

* Fixed metadata link

* Trying to fix windows permission error when deleting folders

* add 50um to allen mouse

* v1.2 for allen mouse

* blacked

* Update requirements

* vtkplotter -> vedo

* Format with black

* Update kim mouse atlas generation

* Improve downsampling

* revert roations

* add kim to main script

* rotate annotation volume for meshes

* add osten mouse atlas

* Added function for creating intermediate hierarchy structures masks

* Fix extract_largest_region and compare_mesh_volume

* reformat with black

* save additional metadata

* consistent syntax for empty dict

* Update docstring

* Add atlas packager metadata

* python 3.8 compatibility

* Add mouse spinal cord atlas

* add WHS SD Rat atlas

* add xmltodict to requirements.txt

* remove structures that are missing from annotation volume

* remove structures that are missing from annotation volume

* Fixed vedo Slicer import issue

* Update mesh_utils.py

* Create azba_zfish.py

* Standardise temporary output directory

* add [allenmouse] extra dependency (#17)

* Allow multiple downloads at once, updated citation

* Mesh cleaning improvements (#15)

* gitignore: added vscode

* gitignore: added vscode

* added rich fancy traceback for easier debugging

* replaced mesh cleaning with decimation

* pre-commit cleanup

* added TEST mode to atlas creation

* added smoothing options to all atlas gen scripts

* removed ratlas.py since outdated and theres a better atlas

* atlas gen update

* added smoothing and decimation to adult zebrafish atlas

Co-authored-by: Luigi Petrucco <[email protected]>

* Update azba_zfish.py

Changing the reference file to be af and the additional references to be topro

* some fixes for mpin atlas

* Fix tiny typo (#22)

* Update README.md

* Add lsfm atlas script (#18)

* Update lsfm mouse atlas script

* 2nd update LSFM mouse atlas script

Co-authored-by: Johanna <[email protected]>
Co-authored-by: Johanna Perens <[email protected]>

* Update requirements.txt

* Add ADMBA 3D developing mouse atlases (#25)

* Add ADMBA 3D developing mouse atlases

Extend the `mouse_e15_5` script by @pr4deepr to build all the atlases in the 3D reconstructed version of the Allen Developing Mouse Brain Atlas series. This build script is essentially the same except for the addition of a data class to configure the atlas parameters, which is implemented for each atlas.

* Fix atlas orientation to LSA

Change the input orientation to LSA to fit the NumPy convention used in BrainGlobe. Add docstrings describing the orientation and resolution assumptions in the configuration data class.

* Update package authors

* Add script for the Princeton mouse brain atlas. (#27)

* Added atlas generation script for the Princeton mouse brain atlas. Modified mesh_utils.py for fix.

* Modified atlas minor version, changed atlas orientation, and removed unnecessary html fetch of region hierarchy.

* Finalised atlas minor version.

Co-authored-by: Sam <[email protected]>

* KimLabDevCCFv001 (neuroinformatics team form) (#31)

* Create KimLabDevCCFv001.py

* Update KimLabDevCCFv001.py

* Update and rename KimLabDevCCFv001.py to KimLabDevCCF.py

* Update KimLabDevCCF.py

* first commit

* updated up to mesh creation, working through VTK type error

* kimlabdevccf working version 1 reference only

* rename atlasgen file

* start adding additional references

* add filenames for additional references

* fix unfinished handling of multi-templates

* update pre-commit black version to fix error with _unicode fun import from click

* tidy and install pre-commit

* fix change of plotter I erronoeusly made when using older python version

* testing kim atlsa with additional references

* Update requirements.txt

* add loguru requirement (at least windows 10)

* fix VTK type error

* remove path

* remove test code

* update to new download dir

* used to run atlas

* update atlas code for general use

* remove standard tempalte from additional references

* further clean up

* edit to run in single script

* fix False flag used to not run meshes

* get working on UNIX

* use PARALLEL and update atlas name

* update template key STP to stp

Co-authored-by: NovaFae <[email protected]>
Co-authored-by: Adam Tyson <[email protected]>

* Add testing config (#35)

* Add testing config

* Specify branchs for workflow trigger

* Bump pre-commit versions

* Fix cov flag

* Run black on code base

* Clean up requirements

* Move requirements to setup.py

* Fix setup.py black

* Replace brainglobe with NI actions (#37)

* Use pyproject.toml

* Update supported Python metadata

* Clean manifest check

* Remove cibuildwheel config

* Catch warnings during tests (#39)

* Add standard pre-commit config (#40)

* Add standard pre-commit config

* Add automated pre-commit fixes

* Ignore line too long

* Fix branches that CI is run on (#42)

* Update link (#48)

* [pre-commit.ci] pre-commit autoupdate (#49)

updates:
- [github.com/charliermarsh/ruff-pre-commit: v0.0.240 → v0.0.272](astral-sh/ruff-pre-commit@v0.0.240...v0.0.272)
- [github.com/psf/black: 23.1.0 → 23.3.0](psf/black@23.1.0...23.3.0)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* [pre-commit.ci] pre-commit autoupdate (#50)

updates:
- [github.com/charliermarsh/ruff-pre-commit: v0.0.272 → v0.0.275](astral-sh/ruff-pre-commit@v0.0.272...v0.0.275)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* [pre-commit.ci] pre-commit autoupdate (#52)

updates:
- https:/charliermarsh/ruff-pre-commit → https:/astral-sh/ruff-pre-commit
- [github.com/astral-sh/ruff-pre-commit: v0.0.275 → v0.0.276](astral-sh/ruff-pre-commit@v0.0.275...v0.0.276)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* [pre-commit.ci] pre-commit autoupdate (#53)

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.0.276 → v0.0.277](astral-sh/ruff-pre-commit@v0.0.276...v0.0.277)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* [pre-commit.ci] pre-commit autoupdate (#54)

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.0.277 → v0.0.278](astral-sh/ruff-pre-commit@v0.0.277...v0.0.278)
- [github.com/psf/black: 23.3.0 → 23.7.0](psf/black@23.3.0...23.7.0)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* [pre-commit.ci] pre-commit autoupdate (#55)

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.0.278 → v0.0.280](astral-sh/ruff-pre-commit@v0.0.278...v0.0.280)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* [pre-commit.ci] pre-commit autoupdate (#57)

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.0.280 → v0.0.281](astral-sh/ruff-pre-commit@v0.0.280...v0.0.281)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* [pre-commit.ci] pre-commit autoupdate (#59)

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.0.281 → v0.0.282](astral-sh/ruff-pre-commit@v0.0.281...v0.0.282)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* Update to newer vedo API (#58)

* [pre-commit.ci] pre-commit autoupdate (#64)

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.0.282 → v0.0.284](astral-sh/ruff-pre-commit@v0.0.282...v0.0.284)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* scale mesh points before mapping to new anatomical space (#62)

Co-authored-by: Will Graham <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* [pre-commit.ci] pre-commit autoupdate (#66)

* [pre-commit.ci] pre-commit autoupdate

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.0.284 → v0.0.285](astral-sh/ruff-pre-commit@v0.0.284...v0.0.285)

* update type assertion

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Adam Tyson <[email protected]>

* [pre-commit.ci] pre-commit autoupdate (#67)

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.0.285 → v0.0.286](astral-sh/ruff-pre-commit@v0.0.285...v0.0.286)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* Set pre-commit autoupdate frequency to monthly (#68)

* [pre-commit.ci] pre-commit autoupdate (#70)

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.0.286 → v0.0.287](astral-sh/ruff-pre-commit@v0.0.286...v0.0.287)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* [pre-commit.ci] pre-commit autoupdate (#83)

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.0.287 → v0.0.292](astral-sh/ruff-pre-commit@v0.0.287...v0.0.292)
- [github.com/psf/black: 23.7.0 → 23.9.1](psf/black@23.7.0...23.9.1)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* [pre-commit.ci] pre-commit autoupdate (#95)

updates:
- [github.com/pre-commit/pre-commit-hooks: v4.4.0 → v4.5.0](pre-commit/pre-commit-hooks@v4.4.0...v4.5.0)
- [github.com/astral-sh/ruff-pre-commit: v0.0.292 → v0.1.4](astral-sh/ruff-pre-commit@v0.0.292...v0.1.4)
- [github.com/psf/black: 23.9.1 → 23.10.1](psf/black@23.9.1...23.10.1)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* [pre-commit.ci] pre-commit autoupdate (#107)

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.1.4 → v0.1.6](astral-sh/ruff-pre-commit@v0.1.4...v0.1.6)
- [github.com/psf/black: 23.10.1 → 23.11.0](psf/black@23.10.1...23.11.0)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* [pre-commit.ci] pre-commit autoupdate (#109)

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.1.6 → v0.1.9](astral-sh/ruff-pre-commit@v0.1.6...v0.1.9)
- [github.com/psf/black: 23.11.0 → 23.12.1](psf/black@23.11.0...23.12.1)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* draft validation functions (#90)

* draft validation functions

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* run on all atlases, don't crash on assertion error

* fixing atlas path

* Clearer output printing

* tidy up validation script, remove weird test_git

* add dev install, make test structure, initial tests

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* add tests and return for _assert_close()

* add test for validate mesh matches annotation

* fix linting

* update version for actions

* drop py3.8 in tox, run pytest in tox

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* fix copy-paste error in pytest command

* drop py3.8 from gh action workflow file too

* Adding docstrings to validation script

* Making path tests stricter, breaking up long strings, adding diff_tolerance argument to _assert_close function

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* restructuring validate_mesh_matches_image_extents function, adding comments

* testing expected files and  meshes directory separately

* looping through validation functions and parameters to catch individual errors

* removing hard coded path, generalising to all atlases

* adding successful_validations list

* tidying up duplications

* fix recursive bug

* addressing Niko's final comments, cleaning code

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Alessandro Felder <[email protected]>
Co-authored-by: alessandrofelder <[email protected]>

* Structure validation (#110)

* draft validation functions

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* run on all atlases, don't crash on assertion error

* fixing atlas path

* Clearer output printing

* tidy up validation script, remove weird test_git

* add dev install, make test structure, initial tests

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* add tests and return for _assert_close()

* add test for validate mesh matches annotation

* fix linting

* update version for actions

* drop py3.8 in tox, run pytest in tox

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* fix copy-paste error in pytest command

* drop py3.8 from gh action workflow file too

* Adding docstrings to validation script

* wip: draft structure validation function

* Making path tests stricter, breaking up long strings, adding diff_tolerance argument to _assert_close function

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* restructuring validate_mesh_matches_image_extents function, adding comments

* testing expected files and  meshes directory separately

* looping through validation functions and parameters to catch individual errors

* removing hard coded path, generalising to all atlases

* adding successful_validations list

* tidying up duplications

* fix recursive bug

* checkout finished validate_atlases.py from validation branch

* adding validate_mesh_structure_pairs function

* Update bg_atlasgen/validate_atlases.py

Co-authored-by: Alessandro Felder <[email protected]>

* adding assertion to validate_mesh_structure_pairs function

* checking IDs via bg_atlasapi, checking if IDs have mesh files and accesible through the atlas

* Update bg_atlasgen/validate_atlases.py

Co-authored-by: Alessandro Felder <[email protected]>

* passing atlas_name to validate_mesh_structure_pairs function

* addressing Niko's final comments, cleaning code

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Alessandro Felder <[email protected]>
Co-authored-by: alessandrofelder <[email protected]>

* simplify validation function (#113)

* simplify validation function

- all validation functions just take an atlas object
- means we don't need a parameters list
- also simplify output list to be dicts of lists mapping the atlas name to values

- another advantage of this is that it simplifies mocking of atlas functions in the tests

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Fix bug found in code review

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* [pre-commit.ci] pre-commit autoupdate (#117)

* [pre-commit.ci] pre-commit autoupdate

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.1.9 → v0.2.0](astral-sh/ruff-pre-commit@v0.1.9...v0.2.0)
- [github.com/psf/black: 23.12.1 → 24.1.1](psf/black@23.12.1...24.1.1)

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* Add manifest to ci (#118)

* Add manifest to CI

* Standardise tox.ini into pyproject

* printing data frames with validation function information (#115)

* first test functions for validate_mesh_structure_pairs

* storing atlases and successful/failed validation functions in a data frame

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* restoring test_validation.py to the original merged version. Chages are implemented on another branch

* validate_atlases.py: going back to the version on main, appending only the name of the successful and failed functions (not the function object) to lists in validate_atlases function

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* populating dictionaries in for loop, writing JSON files

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* saving JSON files to ~/.brainglobe/atlases/validation

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* printing where to find the result files

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Update bg_atlasgen/validate_atlases.py

Co-authored-by: Alessandro Felder <[email protected]>

* Update bg_atlasgen/validate_atlases.py

removing unused variables

Co-authored-by: Alessandro Felder <[email protected]>

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* saving only one JSON file with all the information

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* uncommenting test functions

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Alessandro Felder <[email protected]>

* bg-atlasapi -> brainglobe-atlasapi

* bg_atlasapi -> brainglobe_atlasapi, package restructure

* Move tests for API into separate subfolder

* Revert "bg_atlasapi -> brainglobe_atlasapi, package restructure"

This reverts commit 120c3b2.

* bg_atlasapi -> brainglobe_atlasapi, package restructure

* Update manifest

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Pre-commit pass

* fixing small bug: validation_functions function argument as variable instead of all_validation_functions (#119)

* Bump NIU action versions

* Move conftest back to top-level directory

* Refactor atlasgen into a submodule

* pre-commit pass

* test functions for validate_mesh_structure_pairs (#114)

* first test functions for validate_mesh_structure_pairs

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* adding docstring

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* writing docstrings to explain the behaviour of the test functions

* validate_atlases.py: updated validate_mesh_structure_pairs function, test_validation.py: updated tests

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* spliting validate_mesh_structure_pairs function, checking mesh files and structures separately

* writing tests for catch_missing_mesh_files and catch_missing_structures validation functions

* creating an atlas with a missing structure to test catch_missing_structures function

* Update tests/test_unit/test_validation.py

Co-authored-by: Alessandro Felder <[email protected]>

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Alessandro Felder <[email protected]>

* Revert "Prepare for merge and rename (#198)"

This reverts commit 9d5317d.

* Update pyproject.toml

Co-authored-by: Alessandro Felder <[email protected]>

---------

Co-authored-by: Luigi Petrucco <[email protected]>
Co-authored-by: Adam Tyson <[email protected]>
Co-authored-by: Mathieu <[email protected]>
Co-authored-by: Adam Tyson <[email protected]>
Co-authored-by: Ben Kantor <[email protected]>
Co-authored-by: Kailyn Fields <[email protected]>
Co-authored-by: Federico Claudi <[email protected]>
Co-authored-by: Gubra-ApS <[email protected]>
Co-authored-by: Johanna <[email protected]>
Co-authored-by: Johanna Perens <[email protected]>
Co-authored-by: David Young <[email protected]>
Co-authored-by: Sam Clothier <[email protected]>
Co-authored-by: Sam <[email protected]>
Co-authored-by: Joe Ziminski <[email protected]>
Co-authored-by: NovaFae <[email protected]>
Co-authored-by: David Stansby <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Alessandro Felder <[email protected]>
Co-authored-by: viktorpm <[email protected]>
Co-authored-by: alessandrofelder <[email protected]>
@adamltyson adamltyson deleted the joss branch July 22, 2024 10:23
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@vigji vigji vigji left review comments

@FedeClaudi FedeClaudi FedeClaudi approved these changes

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
3 participants
@adamltyson @FedeClaudi @vigji