template sync failed for a couple of repos

[grst]

The v0.7 template sync failed for some repos, including some that worked before, e.g. pertpy.
The error message in the log is not useful. We should look into this.

2025-12-24T10:02:10.6385201Z                     INFO     INFO: scverse_template_scripts._log:Working on template update for scverse-pertpy                         cruft_prs. py: 495
2025-12-24T10:02:11.1293474Z [12/24/25 10:02:11] INFO     INFO:scverse_template_scripts._log:Creating fork for https://api.github.com/repos/scverse/pertpy         cruft_prs.py:205
2025-12-24T10:02:12.8423343Z [12/24/25 10:02:12] INFO     INFO:scverse_template_scripts._log:Cloning https://github.com/scverse-bot/pertpy.git into                cruft_prs. py:240
2025-12-24T10:02:12.8425800Z                              /tmp/tmpt7gg7plu                                                                                                         
2025-12-24T10:02:14.3093704Z [12/24/25 10:02:14] INFO     INFO:scverse_template_scripts._log:Branch template-update-v2-scverse-pertpy does not exists yet,         cruft_prs.py:260
2025-12-24T10:02:14.3096529Z                              creating it from initial commit                                                                                          
2025-12-24T10:02:14.6665396Z                     INFO     INFO:scverse_template_scripts._log:Getting . cruft.json from the main branch in                           cruft_prs.py:281
2025-12-24T10:02:14.6667969Z                              https://github.com/scverse/pertpy. git                                                                                    
2025-12-24T10:02:14.6695418Z                     INFO     INFO: scverse_template_scripts._log:Successfully read .cruft.json from upstream/main                      cruft_prs.py:286
2025-12-24T10:02:14.6710216Z                     INFO     INFO:scverse_template_scripts._log:Running                                                               cruft_prs.py:332
2025-12-24T10:02:14.6712347Z                              /home/runner/work/_temp/setup-uv-cache/archive-v0/acbjExI52lYKlENMl7J5N/bin/python -m cruft create                       
2025-12-24T10:02:14.6713467Z                              https://github.com/scverse/cookiecutter-scverse --checkout=v0.7.0 --no-input                                            
2025-12-24T10:02:14.6714459Z                              --extra-context-file=/tmp/tmpl7jfffn2/cookiecutter. json                                                                  
2025-12-24T10:02:15.6109496Z [12/24/25 10:02:15] ERROR    ERROR:scverse_template_scripts._log:Error while updating https://github.com/scverse/pertpy               cruft_prs.py:586
2025-12-24T10:02:15.6147681Z                     ERROR    ERROR:scverse_template_scripts._log:Command                                                              cruft_prs.py:587
2025-12-24T10:02:15.6151497Z                              '['/home/runner/work/_temp/setup-uv-cache/archive-v0/acbjExI52lYKlENMl7J5N/bin/python', '-m', 'cruft',                   
2025-12-24T10:02:15.6152881Z                              'create', 'https://github.com/scverse/cookiecutter-scverse', '--checkout=v0.7.0', '--no-input',                          
2025-12-24T10:02:15.6154071Z                              '--extra-context-file=/tmp/tmpl7jfffn2/cookiecutter.json']' returned non-zero exit status 1.                            
2025-12-24T10:02:15.6155433Z                              Traceback (most recent call last):                                                                                       
2025-12-24T10:02:15.6156068Z                                File                                                                                                                   
2025-12-24T10:02:15.6156862Z                              "/home/runner/work/_temp/setup-uv-cache/archive-v0/acbjExI52lYKlENMl7J5N/lib/python3.12/site-packages/sc                 
2025-12-24T10:02:15.6157799Z                              verse_template_scripts/cruft_prs.py", line 583, in main                                                                  
2025-12-24T10:02:15.6158689Z                                  make_pr(con, release, repo_url, log_dir=log_dir, dry_run=dry_run)                                                   
2025-12-24T10:02:15.6159400Z                                File                                                                                                                   
2025-12-24T10:02:15.6160173Z                              "/home/runner/work/_temp/setup-uv-cache/archive-v0/acbjExI52lYKlENMl7J5N/lib/python3.12/site-packages/sc                 
2025-12-24T10:02:15.6161101Z                              verse_template_scripts/cruft_prs. py", line 503, in make_pr                                                               
2025-12-24T10:02:15.6161827Z                                  updated = template_update(                                                                                          
2025-12-24T10:02:15.6162527Z                                             ^^^^^^^^^^^^^^^^                                                                                         
2025-12-24T10:02:15.6163638Z                                File                                                                                                                   
2025-12-24T10:02:15.6164435Z                              "/home/runner/work/_temp/setup-uv-cache/archive-v0/acbjExI52lYKlENMl7J5N/lib/python3.12/site-packages/sc                 
2025-12-24T10:02:15.6165565Z                              verse_template_scripts/cruft_prs. py", line 449, in template_update                                                       
2025-12-24T10:02:15.6166274Z                                  _apply_update(                                                                                                      
2025-12-24T10:02:15.6166795Z                                File                                                                                                                   
2025-12-24T10:02:15.6167555Z                              "/home/runner/work/_temp/setup-uv-cache/archive-v0/acbjExI52lYKlENMl7J5N/lib/python3.12/site-packages/sc                 
2025-12-24T10:02:15.6168476Z                              verse_template_scripts/cruft_prs. py", line 333, in _apply_update                                                         
2025-12-24T10:02:15.6169475Z                                  run(cmd, stdout=log_f, stderr=log_f, check=True, cwd=template_dir)                                                  
2025-12-24T10:02:15.6170419Z                                File "/usr/lib/python3.12/subprocess. py", line 571, in run                                                            
2025-12-24T10:02:15.6171442Z                                  raise CalledProcessError(retcode, process. args,                                                                     
2025-12-24T10:02:15.6172189Z                              subprocess.CalledProcessError: Command                                                                                  
2025-12-24T10:02:15.6173164Z                              '['/home/runner/work/_temp/setup-uv-cache/archive-v0/acbjExI52lYKlENMl7J5N/bin/python', '-m', 'cruft',                   
2025-12-24T10:02:15.6174350Z                              'create', 'https://github.com/scverse/cookiecutter-scverse', '--checkout=v0.7.0', '--no-input',                          
2025-12-24T10:02:15.6175658Z                              '--extra-context-file=/tmp/tmpl7jfffn2/cookiecutter.json']' returned non-zero exit status 1.                            
2025-12-24T10:02:15.6178003Z                     INFO     INFO:scverse_template_scripts._log:Working on template update for scverse-pytometry                      cruft_prs.py:495
2025-12-24T10:02:15.8844883Z                     INFO     INFO:scverse_template_scripts._log:Creating fork for https://api.github.com/repos/scverse/pytometry      cruft_prs.py:205
2025-12-24T10:02:17.0287683Z [12/24/25 10:02:17] INFO     INFO:scverse_template_scripts._log:Cloning https://github.com/scverse-bot/pytometry.git into             cruft_prs.py:240
2025-12-24T10:02:17.0290271Z                              /tmp/tmpzotlwd3m                                                                                                         
2025-12-24T10:02:18.8267333Z [12/24/25 10:02:18] INFO     INFO:scverse_template_scripts._log:Branch template-update-v2-scverse-pytometry already exists, checking  cruft_prs. py:268
2025-12-24T10:02:18.8271020Z                              it out                                                                                                                   
2025-12-24T10:02:19.1715535Z [12/24/25 10:02:19] INFO     INFO:scverse_template_scripts._log:Getting .cruft. json from the main branch in                           cruft_prs.py:281

[Zethson]

including some that worked before, e.g. pertpy.

That's because I had "MIT" instead of "MIT license".

[grst]

Using license terms not in the prespecified list also seems to be the reason for a couple of other repos I checked. The failure comes from cruft, so it is outside our control.

In principle I think it should work for users to change the license to whatever they want and still receive template updates.

Possible solutions:

• Add all OSI-compliant licenses to the list. Then it still wouldn't work for non-open source licenses (like e.g. polyform non-commercial used by theislab/cellflow). It also wouldn't have saved pertpy where the license was MIT, but not the correct identifier has been used.
• Replace cruft with something else. It's anyway not actively maintained anymore. We also don't rely on it for template sync anymore, we just use it to instantiate the template. any cookiecutter implementation would do.

Probably the latter is preferable. @Zethson @flying-sheep are you aware of an actively and sustainably maintained cookiecutter implementation that we could use? I think the original cookiecutter is dead, too?

[grst]

While replacing cruft may be a good change by itself, it wouldn't solve the problem at hand unless the new tool provided an option to ignore the prespecified options in the template's cookiecutter.json.

So I think the solution is actually to download a temporary copy of the template and change the cookiecutter.json such that all "choice" fields (i.e. JSON lists) are replaced with a freetext field.

[Zethson]

I think the original cookiecutter is dead, too?

Not really actively worked on anymore but it kind of works.

I guess https://github.com/copier-org/copier is of interest. However, it uses different configuration file names so it wouldn't be a smooth transition.