Startup quickfixes

[samuelbray32]

Description

Fixes #1264

• Add kachery-cloud as a dependency since no longer comes with sortingview

dj config setup tutorial

• pull variables to top of cell so harder for users to miss
• First connect to data base with initial admin-given password
• Ensure saves global (common thing users miss

Checklist:

• N If this PR should be accompanied by a release, I have updated the CITATION.cff
• N If this PR edits table definitions, I have included an alter snippet for release notes.
• N If this PR makes changes to position, I ran the relevant tests locally.
• If this PR makes user-facing changes, I have added/edited docs/notebooks to reflect the changes
• I have updated the CHANGELOG.md with PR number and description.

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Pull Request Overview

This PR addresses startup issues for new users by adding the missing kachery-cloud dependency and improving the database configuration tutorial workflow.

• Added kachery-cloud as an explicit dependency across all environment files
• Refactored the database setup tutorial to pull configuration variables to the top for better visibility
• Fixed return type consistency in AnalysisNwbfile.get_abs_path method

Reviewed Changes

Copilot reviewed 9 out of 9 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
pyproject.toml	Added kachery-cloud to project dependencies
environment.yml, environment_dlc.yml, environment_moseq_cpu.yml, environment_moseq_gpu.yml	Added kachery-cloud to pip dependencies in all environment files
notebooks/00_Setup.ipynb, notebooks/py_scripts/00_Setup.py	Restructured database setup tutorial to clarify configuration steps and ensure global config is saved
src/spyglass/common/common_nwbfile.py	Changed return type from Path to str for consistency
CHANGELOG.md	Added changelog entries for the dependency addition and return type fix

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[edeno]

Line #17.            "database.host": "lmf-db.cin.ucsf.edu",

Do we want this to be specific to our database?

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[samuelbray32]

Ah, sorry. this should be the database_host value defined above

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Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 71.24%. Comparing base (85b1415) to head (06a1675).

Additional details and impacted files

@@           Coverage Diff           @@
##           master    #1430   +/-   ##
=======================================
  Coverage   71.24%   71.24%           
=======================================
  Files         114      114           
  Lines       13248    13248           
=======================================
  Hits         9438     9438           
  Misses       3810     3810           

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[CBroz1]

Given the migration to globally saved config, we could delete the chdir lines across all notebooks, to avoid carrying the vestige

I might also add a 'common error' section to 01_Concepts.ipynb along the lines of "Prompted for your username when you thought you saved your config? Find your settings with:"

print(dj.config) # Usually ./dj_local_conf.json or ~/.datajoint_config.json

"To manually connect without a config..."

dj.conn(user="youruser", password="yourpass", host="yourhost")

"If you think you may be having connection issues, try the above or contact admin to reset your password"

Could be this pr, could be an issue to resolve in the next

[CBroz1]

I would remove this line, let it use the default, global

[CBroz1]

Does this need to be in yaml and toml files? As an imported package, my thought would be to only list here in toml and let the yaml's - . handle installing for the conda env

[CBroz1]

Because save_dj_config should do this already, yeah? I might change this too a check-exists.

Suggested change

	dj.config.save_global()
	dj.config.save_local()
	your_config = Path.home() / '.datajoint_config.json'
	print(f"Config exists: {your_config.exists()}"

[CBroz1]

Suggested change

	- Add explicit `kachery-cloud` dependency #1430
	- Add explicit `kachery-cloud` dependency #1430
	- Default ton globally saved config #1430