shallow clone cannot switch branches #379
Description
Bug description
When a shallow clone is used (now the default after #117), and visited an updated URL with a new branch with an update to pull, pull fails with:
File "/opt/conda/lib/python3.13/site-packages/nbgitpuller/pull.py", line 208, in find_upstream_changed
output = subprocess.check_output([
~~~~~~~~~~~~~~~~~~~~~~~^^
'git', 'diff', '..origin/{}'.format(self.branch_name),
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
'--name-status'
^^^^^^^^^^^^^^^
], cwd=self.repo_dir).decode()
^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.13/subprocess.py", line 472, in check_output
return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
**kwargs).stdout
^^^^^^^^^
File "/opt/conda/lib/python3.13/subprocess.py", line 577, in run
raise CalledProcessError(retcode, process.args,
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['git', 'diff', '..origin/main', '--name-status']' returned non-zero exit status 128.
The actual error from git is:
fatal: ambiguous argument '..origin/main': unknown revision or path not in the working tree.
Use '--' to separate paths from revisions, like this:
'git <command> [<revision>...] -- [<file>...]'
This can be fixed by explicitly fetching the new branch:
git fetch --depth 1 origin "+refs/heads/main:origin/main"
How to reproduce
- make a shallow clone of a repo (e.g. with nbgitpuller default)
- push an update to the repo
- visit nbgitpuller link a second time
- see above error
Actual behaviour
All future visits to nbgitpuller URL fail with:
File "/opt/conda/lib/python3.13/site-packages/nbgitpuller/pull.py", line 208, in find_upstream_changed
output = subprocess.check_output([
~~~~~~~~~~~~~~~~~~~~~~~^^
'git', 'diff', '..origin/{}'.format(self.branch_name),
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
'--name-status'
^^^^^^^^^^^^^^^
], cwd=self.repo_dir).decode()
^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.13/subprocess.py", line 472, in check_output
return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
**kwargs).stdout
^^^^^^^^^
File "/opt/conda/lib/python3.13/subprocess.py", line 577, in run
raise CalledProcessError(retcode, process.args,
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['git', 'diff', '..origin/main', '--name-status']' returned non-zero exit status 128.
reproduce without nbgitpuller
You can reproduce the same steps with just the git commands nbgitpuller uses:
ovyan@jupyter-benjaminrk-gmail-com---f8198f73:/tmp$ git clone --depth 1 --branch behind https://github.com/minrk/cgm-sandbox
Cloning into 'cgm-sandbox'...
remote: Enumerating objects: 29, done.
remote: Counting objects: 100% (29/29), done.
remote: Compressing objects: 100% (28/28), done.
remote: Total 29 (delta 0), reused 24 (delta 0), pack-reused 0 (from 0)
Receiving objects: 100% (29/29), 424.59 KiB | 4.25 MiB/s, done.
jovyan@jupyter-benjaminrk-gmail-com---f8198f73:/tmp$ cd cgm-sandbox/
jovyan@jupyter-benjaminrk-gmail-com---f8198f73:/tmp/cgm-sandbox$ git diff ..origin/main --name-status # fails
fatal: ambiguous argument '..origin/main': unknown revision or path not in the working tree.
Use '--' to separate paths from revisions, like this:
'git <command> [<revision>...] -- [<file>...]'
# explicitly fetch origin/main
jovyan@jupyter-benjaminrk-gmail-com---f8198f73:/tmp/cgm-sandbox$ git fetch --depth 1 origin "+refs/heads/main:origin/main"
remote: Enumerating objects: 11, done.
remote: Counting objects: 100% (11/11), done.
remote: Compressing objects: 100% (3/3), done.
remote: Total 6 (delta 5), reused 4 (delta 3), pack-reused 0 (from 0)
Unpacking objects: 100% (6/6), 1.37 KiB | 469.00 KiB/s, done.
From https://github.com/minrk/cgm-sandbox
* [new branch] main -> origin/main
jovyan@jupyter-benjaminrk-gmail-com---f8198f73:/tmp/cgm-sandbox$ git diff ..origin/main --name-status
M extensions.py
M overlays.py
M viewer.py
M visualize_sample.ipynb
Your personal set up
- OS: ubuntu 24.04
- 2i2c jupyter-health deployment
Full environment
aiohappyeyeballs==2.6.1
aiohttp==3.12.15
aiosignal==1.4.0
alembic==1.16.5
altair==5.5.0
annotated-types==0.7.0
anyio==4.11.0
archspec==0.2.5
argon2-cffi==25.1.0
argon2-cffi-bindings==25.1.0
arrow==1.3.0
asttokens==3.0.0
async_generator==1.10
async-lru==2.0.5
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comm==0.2.3
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pip==25.2
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python-dateutil==2.9.0.post0
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python-json-logger==2.0.7
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requests-toolbelt==1.0.0
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zict==3.0.0
zipp==3.23.0
zope.interface==7.2
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Suggested fix
I think a fix might be that we need to unshallow the clone:
git fetch --unshallow
if the repo's not up-to-date. I'm not sure there's another way to update a shallow clone.