My .gitattributes has this:
.renku/metadata/* merge=zstdmerge
.renku/metadata/**/* merge=zstdmerge
.renku/metadata/** merge=renkumerge
oh I remember zstdmerge was something we tried before we added the renku mergetool. I’d remove those entries and try again.
So are you sure that only the size of the metadata matters? I am trying again, and I see in the tmp-dir, that a full copy of the repo is being created. That is very time consuming, as the repo itself is 150Gb…
Oh now I received an error:
Traceback (most recent call last):
File "[...]/site-packages/renku/infrastructure/git_merger.py", line 82, in merge
local_object = self.merge_objects(local_object, remote_object, base_object)
File "[...]/site-packages/renku/infrastructure/git_merger.py", line 142, in merge_objects
raise errors.MetadataMergeError(
renku.core.errors.MetadataMergeError: Cannot merge BTrees.OOBTree.OOBucket([('/activities/9fd26261aa0041b781c8447727fbcae9', (<BTrees.Length.Length object at 0x2aaafef60040 oid None>, <BTrees.OOBTree.OOTreeSet object at 0x2aaafef4ad40 oid None>)), ('/activities/a027cf3a541e45d18c2879316055a37f', (<BTrees.Length.Length object at 0x2aaafef600b0 oid None>, <BTrees.OOBTree.OOTreeSet object at 0x2aaafef4ae40 oid None>)), ('/activities/a04c74fd3d014a57b8099a36d8570805', (<BTrees.Length.Length object at 0x2aaafef60120 oid None>, <BTrees.OOBTree.OOTreeSet object at 0x2aaafef4af40 oid None>)), ('/activities/a0b1de0cdc854bbb81fa0fc9bd528ef5', (<BTrees.Length.Length object at 0x2aaafef60510 oid None>, <BTrees.OOBTree.OOTreeSet object at 0x2aaabb0d20c0 oid None>)), ('/activities/a1472f98eef84b93bbe617125c8cde0f', (<BTrees.Length.Length object at 0x2aaafef60580 oid None>, <BTrees.OOBTree.OOTreeSet object at 0x2aaabb0d21c0 oid None>)), ('/activities/a1abc38482b64d56bffb2696aef9afd7', (<BTrees.Length.Length object at 0x2aaafef605f0 oid None>, <BTrees.OOBTree.OOTreeSet object at 0x2aaafef4abc0 oid None>)), ('/activities/a1cd8316a1b647bc9bb48386e0fb6549', (<BTrees.Length.Length object at 0x2aaafef60660 oid None>, <BTrees.OOBTree.OOTreeSet object at 0x2aaabb0d2340 oid None>)), ('/activities/a1e960c36663460ead2ae924927c76b1', (<BTrees.Length.Length object at 0x2aaafef606d0 oid None>, <BTrees.OOBTree.OOTreeSet object at 0x2aaabb0d2440 oid None>)), ('/activities/a219fd42eb684cb596e300e21954ee92', (<BTrees.Length.Length object at 0x2aaafef60740 oid None>, <BTrees.OOBTree.OOTreeSet object at 0x2aaabb0d2540 oid None>)), ('/activities/a22af031c795465e930d95db0da40209', (<BTrees.Length.Length object at 0x2aaafef607b0 oid None>, <BTrees.OOBTree.OOTreeSet object at 0x2aaabb0d2640 oid None>)), ('/activities/a23f2b73679f4c64b2567f6eea6329bb', (<BTrees.Length.Length object at 0x2aaafef60820 oid None>, <BTrees.OOBTree.OOTreeSet object at 0x2aaabb0d2740 oid None>)), ('/activities/a244fd83220949b795fee96b0e365abf', (<BTrees.Length.Length object at 0x2aaafef60890 oid None>, <BTrees.OOBTree.OOTreeSet object at 0x2aaabb0d2840 oid None>)), ('/activities/a273aad95894464986a36a6f6c5e5f57', (<BTrees.Length.Length object at 0x2aaafef60900 oid None>, <BTrees.OOBTree.OOTreeSet object at 0x2aaabb0d2940 oid None>)), ('/activities/a31abe19bc4d4225ac36439b02c3b23c', (<BTrees.Length.Length object at 0x2aaafef60970 oid None>, <BTrees.OOBTree.OOTreeSet object at 0x2aaabb0d2a40 oid None>)), ('/activities/a336f690b0d846d79754fa5c28fc78a7', (<BTrees.Length.Length object at 0x2aaafef609e0 oid None>, <BTrees.OOBTree.OOTreeSet object at 0x2aaabb0d2b40 oid None>)), ('/activities/a33a554c5b0b4ba290da1c280fa68686', (<BTrees.Length.Length object at 0x2aaafef60a50 oid None>, <BTrees.OOBTree.OOTreeSet object at 0x2aaabb0d2c40 oid None>)), ('/activities/a36d5bb3dedb4a64bfe72928a146e7b3', (<BTrees.Length.Length object at 0x2aaafef60ac0 oid None>, <BTrees.OOBTree.OOTreeSet object at 0x2aaabb0d2d40 oid None>)), ('/activities/a3a5a21692214d5f9e6d4a88f2ac86e1', (<BTrees.Length.Length object at 0x2aaafef60b30 oid None>, <BTrees.OOBTree.OOTreeSet object at 0x2aaabb0d2e40 oid None>))]) and BTrees.OOBTree.OOBucket([('/activities/9fd26261aa0041b781c8447727fbcae9', (<BTrees.Length.Length object at 0x2aaabb0d7350 oid None>, <BTrees.OOBTree.OOTreeSet object at 0x2aaabb0d95c0 oid None>)), ('/activities/a027cf3a541e45d18c2879316055a37f', (<BTrees.Length.Length object at 0x2aaabb0d73c0 oid None>, <BTrees.OOBTree.OOTreeSet object at 0x2aaabb0d96c0 oid None>)), ('/activities/a03f2068d76d4ffabac9a1ad975c4103', (<BTrees.Length.Length object at 0x2aaabb0d7430 oid None>, <BTrees.OOBTree.OOTreeSet object at 0x2aaabb0d97c0 oid None>)), ('/activities/a04c74fd3d014a57b8099a36d8570805', (<BTrees.Length.Length object at 0x2aaabb0d74a0 oid None>, <BTrees.OOBTree.OOTreeSet object at 0x2aaabb0d98c0 oid None>)), ('/activities/a0b1de0cdc854bbb81fa0fc9bd528ef5', (<BTrees.Length.Length object at 0x2aaabb0d7510 oid None>, <BTrees.OOBTree.OOTreeSet object at 0x2aaabb0d99c0 oid None>)), ('/activities/a141f23836b249c7a55b1d822944edc4', (<BTrees.Length.Length object at 0x2aaabb0d7580 oid None>, <BTrees.OOBTree.OOTreeSet object at 0x2aaabb0d9540 oid None>)), ('/activities/a1472f98eef84b93bbe617125c8cde0f', (<BTrees.Length.Length object at 0x2aaabb0d75f0 oid None>, <BTrees.OOBTree.OOTreeSet object at 0x2aaabb0d94c0 oid None>)), ('/activities/a1abc38482b64d56bffb2696aef9afd7', (<BTrees.Length.Length object at 0x2aaabb0d7660 oid None>, <BTrees.OOBTree.OOTreeSet object at 0x2aaabb0d9bc0 oid None>)), ('/activities/a1cd8316a1b647bc9bb48386e0fb6549', (<BTrees.Length.Length object at 0x2aaabb0d76d0 oid None>, <BTrees.OOBTree.OOTreeSet object at 0x2aaabb0d9d40 oid None>)), ('/activities/a1e960c36663460ead2ae924927c76b1', (<BTrees.Length.Length object at 0x2aaabb0d7740 oid None>, <BTrees.OOBTree.OOTreeSet object at 0x2aaabb0d9e40 oid None>)), ('/activities/a22af031c795465e930d95db0da40209', (<BTrees.Length.Length object at 0x2aaabb0d77b0 oid None>, <BTrees.OOBTree.OOTreeSet object at 0x2aaabb0d9f40 oid None>)), ('/activities/a23f2b73679f4c64b2567f6eea6329bb', (<BTrees.Length.Length object at 0x2aaabb0d7820 oid None>, <BTrees.OOBTree.OOTreeSet object at 0x2aaabb0e00c0 oid None>)), ('/activities/a244fd83220949b795fee96b0e365abf', (<BTrees.Length.Length object at 0x2aaabb0d7890 oid None>, <BTrees.OOBTree.OOTreeSet object at 0x2aaabb0e01c0 oid None>)), ('/activities/a273aad95894464986a36a6f6c5e5f57', (<BTrees.Length.Length object at 0x2aaabb0d7900 oid None>, <BTrees.OOBTree.OOTreeSet object at 0x2aaabb0e02c0 oid None>)), ('/activities/a31abe19bc4d4225ac36439b02c3b23c', (<BTrees.Length.Length object at 0x2aaabb0d7970 oid None>, <BTrees.OOBTree.OOTreeSet object at 0x2aaabb0e03c0 oid None>)), ('/activities/a336f690b0d846d79754fa5c28fc78a7', (<BTrees.Length.Length object at 0x2aaabb0d79e0 oid None>, <BTrees.OOBTree.OOTreeSet object at 0x2aaabb0e04c0 oid None>)), ('/activities/a33a554c5b0b4ba290da1c280fa68686', (<BTrees.Length.Length object at 0x2aaabb0d7a50 oid None>, <BTrees.OOBTree.OOTreeSet object at 0x2aaabb0e05c0 oid None>)), ('/activities/a36d5bb3dedb4a64bfe72928a146e7b3', (<BTrees.Length.Length object at 0x2aaabb0d7ac0 oid None>, <BTrees.OOBTree.OOTreeSet object at 0x2aaabb0e06c0 oid None>)), ('/activities/a392eace8cae4ce5ba03e54e2f0e0358', (<BTrees.Length.Length object at 0x2aaabb0d7b30 oid None>, <BTrees.OOBTree.OOTreeSet object at 0x2aaabb0e07c0 oid None>)), ('/activities/a3a5a21692214d5f9e6d4a88f2ac86e1', (<BTrees.Length.Length object at 0x2aaabb0d7ba0 oid None>, <BTrees.OOBTree.OOTreeSet object at 0x2aaabb0e08c0 oid None>))]): type not supported for automated merge.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "[...]/site-packages/renku/ui/cli/exception_handler.py", line 134, in main
return super().main(*args, **kwargs)
File "[...]/site-packages/renku/ui/cli/exception_handler.py", line 93, in main
return super().main(*args, **kwargs)
File "[...]/site-packages/click/core.py", line 1053, in main
rv = self.invoke(ctx)
File "[...]/site-packages/click/core.py", line 1659, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "[...]/site-packages/click/core.py", line 1659, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "[...]/site-packages/click/core.py", line 1395, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "[...]/site-packages/click/core.py", line 754, in invoke
return __callback(*args, **kwargs)
File "[...]/site-packages/renku/ui/cli/mergetool.py", line 53, in merge
mergetool_command().with_communicator(communicator).build().execute(local=local, remote=remote, base=base)
File "[...]/site-packages/renku/command/command_builder/command.py", line 296, in execute
output = context["click_context"].invoke(self._operation, *args, **kwargs)
File "[...]/site-packages/click/core.py", line 754, in invoke
return __callback(*args, **kwargs)
File "[...]/site-packages/inject/__init__.py", line 342, in injection_wrapper
return sync_func(*args, **kwargs)
File "[...]/site-packages/renku/command/mergetool.py", line 45, in _mergetool
merger.merge(local, remote, base)
File "[...]/site-packages/renku/infrastructure/git_merger.py", line 90, in merge
shutil.rmtree(entry.path)
File "[...]/shutil.py", line 709, in rmtree
onerror(os.lstat, path, sys.exc_info())
File "[...]/shutil.py", line 707, in rmtree
orig_st = os.lstat(path)
FileNotFoundError: [Errno 2] No such file or directory: '/mnt/beegfs/home/int/eva/nijzink/tmpqxnsb_u_'
Could this be due to the patch in git_merger.py? The directory it is referring to actually existed, that’s where I saw the files being created. But now it disappeared.
We essentially do
git worktree add <tmpdir> <reference>
cd <tmpdir>
git sparse-checkout init --cone
git sparse-checkout set .renku/metadata
git checkout
but I wonder if we explicitly need to pass --no-checkout to git worktree add (it has both --checkout and --no-checkout)
Yes the error seems to be due to the patch, you could add ignore_errors=True to shutil.rmtree(entry.path)
Locally, I still receive this error:
Error: Git command failed: Cmd('git') failed due to: exit code(128)
cmdline: git sparse-checkout init --cone
stderr: 'fatal: Unable to create '/media/rnijzink/Elements SE/WAVE/renku_projects/budyko/.git/worktrees/tmpw64a9s7w/info/sparse-checkout.lock': No such file or directory'
Traceback (most recent call last):
File "/home/rnijzink/.local/pipx/venvs/renku/lib/python3.8/site-packages/renku/infrastructure/repository.py", line 1734, in _run_git_command
return getattr(repository.git, command)(*args, **kwargs)
File "/home/rnijzink/.local/pipx/venvs/renku/lib/python3.8/site-packages/git/cmd.py", line 639, in <lambda>
return lambda *args, **kwargs: self._call_process(name, *args, **kwargs)
File "/home/rnijzink/.local/pipx/venvs/renku/lib/python3.8/site-packages/git/cmd.py", line 1184, in _call_process
return self.execute(call, **exec_kwargs)
File "/home/rnijzink/.local/pipx/venvs/renku/lib/python3.8/site-packages/git/cmd.py", line 984, in execute
raise GitCommandError(redacted_command, status, stderr_value, stdout_value)
git.exc.GitCommandError: Cmd('git') failed due to: exit code(128)
cmdline: git sparse-checkout init --cone
stderr: 'fatal: Unable to create '/media/rnijzink/Elements SE/WAVE/renku_projects/budyko/.git/worktrees/tmpw64a9s7w/info/sparse-checkout.lock': No such file or directory'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/home/rnijzink/.local/pipx/venvs/renku/lib/python3.8/site-packages/renku/ui/cli/exception_handler.py", line 93, in main
return super().main(*args, **kwargs)
File "/home/rnijzink/.local/pipx/venvs/renku/lib/python3.8/site-packages/click/core.py", line 1053, in main
rv = self.invoke(ctx)
File "/home/rnijzink/.local/pipx/venvs/renku/lib/python3.8/site-packages/click/core.py", line 1659, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/rnijzink/.local/pipx/venvs/renku/lib/python3.8/site-packages/click/core.py", line 1659, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/rnijzink/.local/pipx/venvs/renku/lib/python3.8/site-packages/click/core.py", line 1395, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home/rnijzink/.local/pipx/venvs/renku/lib/python3.8/site-packages/click/core.py", line 754, in invoke
return __callback(*args, **kwargs)
File "/home/rnijzink/.local/pipx/venvs/renku/lib/python3.8/site-packages/renku/ui/cli/mergetool.py", line 53, in merge
mergetool_command().with_communicator(communicator).build().execute(local=local, remote=remote, base=base)
File "/home/rnijzink/.local/pipx/venvs/renku/lib/python3.8/site-packages/renku/command/command_builder/command.py", line 310, in execute
hook(self, context, result, *args, **kwargs)
File "/home/rnijzink/.local/pipx/venvs/renku/lib/python3.8/site-packages/renku/command/command_builder/command.py", line 246, in _post_hook
raise result.error
File "/home/rnijzink/.local/pipx/venvs/renku/lib/python3.8/site-packages/renku/command/command_builder/command.py", line 296, in execute
output = context["click_context"].invoke(self._operation, *args, **kwargs)
File "/home/rnijzink/.local/pipx/venvs/renku/lib/python3.8/site-packages/click/core.py", line 754, in invoke
return __callback(*args, **kwargs)
File "/home/rnijzink/.local/lib/python3.8/site-packages/inject/__init__.py", line 342, in injection_wrapper
return sync_func(*args, **kwargs)
File "/home/rnijzink/.local/pipx/venvs/renku/lib/python3.8/site-packages/renku/command/mergetool.py", line 45, in _mergetool
merger.merge(local, remote, base)
File "/home/rnijzink/.local/pipx/venvs/renku/lib/python3.8/site-packages/renku/infrastructure/git_merger.py", line 62, in merge
self._setup_worktrees(client)
File "/home/rnijzink/.local/pipx/venvs/renku/lib/python3.8/site-packages/renku/infrastructure/git_merger.py", line 109, in _setup_worktrees
remote_repository.checkout(sparse=[database_path])
File "/home/rnijzink/.local/pipx/venvs/renku/lib/python3.8/site-packages/renku/infrastructure/repository.py", line 241, in checkout
self.run_git_command("sparse-checkout", "init", "--cone")
File "/home/rnijzink/.local/pipx/venvs/renku/lib/python3.8/site-packages/renku/infrastructure/repository.py", line 375, in run_git_command
return _run_git_command(self._repository, command, *args, **kwargs)
File "/home/rnijzink/.local/pipx/venvs/renku/lib/python3.8/site-packages/renku/infrastructure/repository.py", line 1736, in _run_git_command
raise errors.GitCommandError(
renku.core.errors.GitCommandError: Git command failed: Cmd('git') failed due to: exit code(128)
cmdline: git sparse-checkout init --cone
stderr: 'fatal: Unable to create '/media/rnijzink/Elements SE/WAVE/renku_projects/budyko/.git/worktrees/tmpw64a9s7w/info/sparse-checkout.lock': No such file or directory'
Could this also happen due to limit space? Locally I also did not apply the patch, just on the HPC. There I received again this error:
Error: Cannot merge BTrees.OOBTree.OOBucket([('/activities/9fd26261aa0041b781c8447727fbcae9', (<BTrees.Length.Length object at 0x2aaafef840b0 oid None>, <BTrees.OOBTree.OOTreeSet object at 0x2aaafef71d40 oid None>)), ('/activities/a027cf3a541e45d18c2879316055a37f', (<BTrees.Length.Length object at 0x2aaafef84120 oid None>, <BTrees.OOBTree.OOTreeSet object at 0x2aaafef71e40 oid None>)), ('/activities/a04c74fd3d014a57b8099a36d8570805', (<BTrees.Length.Length object at 0x2aaafef84200 oid None>, <BTrees.OOBTree.OOTreeSet object at 0x2aaafef71f40 oid None>)), ('/activities/a0b1de0cdc854bbb81fa0fc9bd528ef5', (<BTrees.Length.Length object at 0x2aaafef845f0 oid None>, <BTrees.OOBTree.OOTreeSet object at 0x2aaabb1380c0 oid None>)), ('/activities/a1472f98eef84b93bbe617125c8cde0f', (<BTrees.Length.Length object at 0x2aaafef84660 oid None>, <BTrees.OOBTree.OOTreeSet object at 0x2aaabb1381c0 oid None>)), ('/activities/a1abc38482b64d56bffb2696aef9afd7', (<BTrees.Length.Length object at 0x2aaafef846d0 oid None>, <BTrees.OOBTree.OOTreeSet object at 0x2aaafef71bc0 oid None>)), ('/activities/a1cd8316a1b647bc9bb48386e0fb6549', (<BTrees.Length.Length object at 0x2aaafef84740 oid None>, <BTrees.OOBTree.OOTreeSet object at 0x2aaabb138340 oid None>)), ('/activities/a1e960c36663460ead2ae924927c76b1', (<BTrees.Length.Length object at 0x2aaafef847b0 oid None>, <BTrees.OOBTree.OOTreeSet object at 0x2aaabb138440 oid None>)), ('/activities/a219fd42eb684cb596e300e21954ee92', (<BTrees.Length.Length object at 0x2aaafef84820 oid None>, <BTrees.OOBTree.OOTreeSet object at 0x2aaabb138540 oid None>)), ('/activities/a22af031c795465e930d95db0da40209', (<BTrees.Length.Length object at 0x2aaafef84890 oid None>, <BTrees.OOBTree.OOTreeSet object at 0x2aaabb138640 oid None>)), ('/activities/a23f2b73679f4c64b2567f6eea6329bb', (<BTrees.Length.Length object at 0x2aaafef84900 oid None>, <BTrees.OOBTree.OOTreeSet object at 0x2aaabb138740 oid None>)), ('/activities/a244fd83220949b795fee96b0e365abf', (<BTrees.Length.Length object at 0x2aaafef84970 oid None>, <BTrees.OOBTree.OOTreeSet object at 0x2aaabb138840 oid None>)), ('/activities/a273aad95894464986a36a6f6c5e5f57', (<BTrees.Length.Length object at 0x2aaafef849e0 oid None>, <BTrees.OOBTree.OOTreeSet object at 0x2aaabb138940 oid None>)), ('/activities/a31abe19bc4d4225ac36439b02c3b23c', (<BTrees.Length.Length object at 0x2aaafef84a50 oid None>, <BTrees.OOBTree.OOTreeSet object at 0x2aaabb138a40 oid None>)), ('/activities/a336f690b0d846d79754fa5c28fc78a7', (<BTrees.Length.Length object at 0x2aaafef84ac0 oid None>, <BTrees.OOBTree.OOTreeSet object at 0x2aaabb138b40 oid None>)), ('/activities/a33a554c5b0b4ba290da1c280fa68686', (<BTrees.Length.Length object at 0x2aaafef84b30 oid None>, <BTrees.OOBTree.OOTreeSet object at 0x2aaabb138c40 oid None>)), ('/activities/a36d5bb3dedb4a64bfe72928a146e7b3', (<BTrees.Length.Length object at 0x2aaafef84ba0 oid None>, <BTrees.OOBTree.OOTreeSet object at 0x2aaabb138d40 oid None>)), ('/activities/a3a5a21692214d5f9e6d4a88f2ac86e1', (<BTrees.Length.Length object at 0x2aaafef84c10 oid None>, <BTrees.OOBTree.OOTreeSet object at 0x2aaabb138e40 oid None>))]) and BTrees.OOBTree.OOBucket([('/activities/9fd26261aa0041b781c8447727fbcae9', (<BTrees.Length.Length object at 0x2aaabb13e430 oid None>, <BTrees.OOBTree.OOTreeSet object at 0x2aaabb1405c0 oid None>)), ('/activities/a027cf3a541e45d18c2879316055a37f', (<BTrees.Length.Length object at 0x2aaabb13e4a0 oid None>, <BTrees.OOBTree.OOTreeSet object at 0x2aaabb1406c0 oid None>)), ('/activities/a03f2068d76d4ffabac9a1ad975c4103', (<BTrees.Length.Length object at 0x2aaabb13e510 oid None>, <BTrees.OOBTree.OOTreeSet object at 0x2aaabb1407c0 oid None>)), ('/activities/a04c74fd3d014a57b8099a36d8570805', (<BTrees.Length.Length object at 0x2aaabb13e580 oid None>, <BTrees.OOBTree.OOTreeSet object at 0x2aaabb1408c0 oid None>)), ('/activities/a0b1de0cdc854bbb81fa0fc9bd528ef5', (<BTrees.Length.Length object at 0x2aaabb13e5f0 oid None>, <BTrees.OOBTree.OOTreeSet object at 0x2aaabb1409c0 oid None>)), ('/activities/a141f23836b249c7a55b1d822944edc4', (<BTrees.Length.Length object at 0x2aaabb13e660 oid None>, <BTrees.OOBTree.OOTreeSet object at 0x2aaabb140540 oid None>)), ('/activities/a1472f98eef84b93bbe617125c8cde0f', (<BTrees.Length.Length object at 0x2aaabb13e6d0 oid None>, <BTrees.OOBTree.OOTreeSet object at 0x2aaabb1404c0 oid None>)), ('/activities/a1abc38482b64d56bffb2696aef9afd7', (<BTrees.Length.Length object at 0x2aaabb13e740 oid None>, <BTrees.OOBTree.OOTreeSet object at 0x2aaabb140bc0 oid None>)), ('/activities/a1cd8316a1b647bc9bb48386e0fb6549', (<BTrees.Length.Length object at 0x2aaabb13e7b0 oid None>, <BTrees.OOBTree.OOTreeSet object at 0x2aaabb140d40 oid None>)), ('/activities/a1e960c36663460ead2ae924927c76b1', (<BTrees.Length.Length object at 0x2aaabb13e820 oid None>, <BTrees.OOBTree.OOTreeSet object at 0x2aaabb140e40 oid None>)), ('/activities/a22af031c795465e930d95db0da40209', (<BTrees.Length.Length object at 0x2aaabb13e890 oid None>, <BTrees.OOBTree.OOTreeSet object at 0x2aaabb140f40 oid None>)), ('/activities/a23f2b73679f4c64b2567f6eea6329bb', (<BTrees.Length.Length object at 0x2aaabb13e900 oid None>, <BTrees.OOBTree.OOTreeSet object at 0x2aaabb1470c0 oid None>)), ('/activities/a244fd83220949b795fee96b0e365abf', (<BTrees.Length.Length object at 0x2aaabb13e970 oid None>, <BTrees.OOBTree.OOTreeSet object at 0x2aaabb1471c0 oid None>)), ('/activities/a273aad95894464986a36a6f6c5e5f57', (<BTrees.Length.Length object at 0x2aaabb13e9e0 oid None>, <BTrees.OOBTree.OOTreeSet object at 0x2aaabb1472c0 oid None>)), ('/activities/a31abe19bc4d4225ac36439b02c3b23c', (<BTrees.Length.Length object at 0x2aaabb13ea50 oid None>, <BTrees.OOBTree.OOTreeSet object at 0x2aaabb1473c0 oid None>)), ('/activities/a336f690b0d846d79754fa5c28fc78a7', (<BTrees.Length.Length object at 0x2aaabb13eac0 oid None>, <BTrees.OOBTree.OOTreeSet object at 0x2aaabb1474c0 oid None>)), ('/activities/a33a554c5b0b4ba290da1c280fa68686', (<BTrees.Length.Length object at 0x2aaabb13eb30 oid None>, <BTrees.OOBTree.OOTreeSet object at 0x2aaabb1475c0 oid None>)), ('/activities/a36d5bb3dedb4a64bfe72928a146e7b3', (<BTrees.Length.Length object at 0x2aaabb13eba0 oid None>, <BTrees.OOBTree.OOTreeSet object at 0x2aaabb1476c0 oid None>)), ('/activities/a392eace8cae4ce5ba03e54e2f0e0358', (<BTrees.Length.Length object at 0x2aaabb13ec10 oid None>, <BTrees.OOBTree.OOTreeSet object at 0x2aaabb1477c0 oid None>)), ('/activities/a3a5a21692214d5f9e6d4a88f2ac86e1', (<BTrees.Length.Length object at 0x2aaabb13ec80 oid None>, <BTrees.OOBTree.OOTreeSet object at 0x2aaabb1478c0 oid None>))]): type not supported for automated merge.
That second does look like a proper bug, I’ll look into creating a fix for that tomorrow (along with the other issues we saw). Should be an easy fix.
I’m not sure about the sparse checkout, as that is a git error. It might be space related. I couldn’t find a lot of information on it online (As few people use worktrees and even fewer still use them with sparse checkouts).
I’ll see if I can clone budyko and reproduce your issues (are the branches you want to merge pushed to the repo? which branches?)
Okay, thanks for looking into it! I am trying to merge this branch into master:
I’ve create a bugfix PR in fix(cli): fix mergetool not working with OOBuckets by Panaetius · Pull Request #3023 · SwissDataScienceCenter/renku-python · GitHub
The merge seems to work fine with that:
$ GIT_LFS_SKIP_SMUDGE=1 git merge origin/branch2merge
Auto-merging .renku/metadata/0b/cd/0bcd3976cee945a58954c0a5f217e72cbe8228c3209a44da8d27933e288300e7
Auto-merging .renku/metadata/0f/c2/0fc2abcdb1294b68a62a02772abe15602350c66939c1401e9bb0c92aedf11c59
Auto-merging .renku/metadata/15/af/15af29a4720449e6b27de6dd579e2c40cba4a4ec64124d8593bca2fd37ce4620
Auto-merging .renku/metadata/22/52/22525eacfd9e4eb0b8e0918f8a6203fdf88cc9391be04fc5a815b2e6b9a43514
Auto-merging .renku/metadata/37/ec/37ec949f4bd94f96b1e7f091992392e3b22bedee7f67488d9f1731c6bd127ff3
Auto-merging .renku/metadata/3d/8a/3d8a9a20d5f44c5796e06c3449b536e62512c0f1c7ff45b9a40f39239c742f36
Auto-merging .renku/metadata/3d/c1/3dc110667510484db41b2f949a9f02e2c08b416d13184085a450d4752f52d753
Auto-merging .renku/metadata/42/11/4211f3d7cc9d41b48ee1ffcb3db01d9da0f89f658cbd435897be785f6e06beb3
Auto-merging .renku/metadata/66/06/6606b9c4f5ff44fdbdb1716160409d8e3aa120853eda4fb3a561e4a3303f51a3
Auto-merging .renku/metadata/71/65/71659686d21b44d4915a321eb41b92b0fbdfe349f20045a3ae19e37cb1be8f4b
Auto-merging .renku/metadata/97/bf/97bfdedbbca84c44a9a25a513c9590c6516aef72c0134502bb404f95f4f59657
Auto-merging .renku/metadata/af/01/af01ab06536147bb850efa4374a0838e556d6ee9347b4826942ee2b7864ea0ad
Auto-merging .renku/metadata/b5/83/b5837197730f4e51bd2da7835b214e85151bdee77c7b4e47afe1aa3aaad886de
Auto-merging .renku/metadata/d2/52/d25283c3f49b4a84acd25d834ffd7971d31976aa1add4087a7a6348f8e3bcd20
Auto-merging .renku/metadata/d6/82/d682c7c562a04f8a80f98b940ebe532b7f7960f9a4154addb4f4d58928339b3d
CONFLICT (modify/delete): data/VOM/HowardSprings/sce_prec04/delz_hourly.txt deleted in HEAD and modified in origin/branch2merge. Version origin/branch2merge of data/VOM/HowardSprings/sce_prec04/delz_hourly.txt left in tree.
CONFLICT (modify/delete): data/VOM/HowardSprings/sce_prec04/results_daily.txt deleted in HEAD and modified in origin/branch2merge. Version origin/branch2merge of data/VOM/HowardSprings/sce_prec04/results_daily.txt left in tree.
CONFLICT (modify/delete): data/VOM/HowardSprings/sce_prec04/results_hourly.txt deleted in HEAD and modified in origin/branch2merge. Version origin/branch2merge of data/VOM/HowardSprings/sce_prec04/results_hourly.txt left in tree.
CONFLICT (modify/delete): data/VOM/HowardSprings/sce_prec04/results_yearly.txt deleted in HEAD and modified in origin/branch2merge. Version origin/branch2merge of data/VOM/HowardSprings/sce_prec04/results_yearly.txt left in tree.
CONFLICT (modify/delete): data/VOM/HowardSprings/sce_prec04/rsurf_daily.txt deleted in HEAD and modified in origin/branch2merge. Version origin/branch2merge of data/VOM/HowardSprings/sce_prec04/rsurf_daily.txt left in tree.
CONFLICT (modify/delete): data/VOM/HowardSprings/sce_prec04/ruptkt_hourly.txt deleted in HEAD and modified in origin/branch2merge. Version origin/branch2merge of data/VOM/HowardSprings/sce_prec04/ruptkt_hourly.txt left in tree.
CONFLICT (modify/delete): data/VOM/HowardSprings/sce_prec04/sce_bestpars.txt deleted in HEAD and modified in origin/branch2merge. Version origin/branch2merge of data/VOM/HowardSprings/sce_prec04/sce_bestpars.txt left in tree.
CONFLICT (modify/delete): data/VOM/HowardSprings/sce_prec04/sce_lastbest.txt deleted in HEAD and modified in origin/branch2merge. Version origin/branch2merge of data/VOM/HowardSprings/sce_prec04/sce_lastbest.txt left in tree.
CONFLICT (modify/delete): data/VOM/HowardSprings/sce_prec04/sce_lastloop.txt deleted in HEAD and modified in origin/branch2merge. Version origin/branch2merge of data/VOM/HowardSprings/sce_prec04/sce_lastloop.txt left in tree.
CONFLICT (modify/delete): data/VOM/HowardSprings/sce_prec04/sce_out.txt deleted in HEAD and modified in origin/branch2merge. Version origin/branch2merge of data/VOM/HowardSprings/sce_prec04/sce_out.txt left in tree.
CONFLICT (modify/delete): data/VOM/HowardSprings/sce_prec04/sce_progress.txt deleted in HEAD and modified in origin/branch2merge. Version origin/branch2merge of data/VOM/HowardSprings/sce_prec04/sce_progress.txt left in tree.
CONFLICT (modify/delete): data/VOM/HowardSprings/sce_prec04/su_hourly.txt deleted in HEAD and modified in origin/branch2merge. Version origin/branch2merge of data/VOM/HowardSprings/sce_prec04/su_hourly.txt left in tree.
CONFLICT (modify/delete): work/VOM/HowardSprings/input_prec04/dailyweather.prn deleted in HEAD and modified in origin/branch2merge. Version origin/branch2merge of work/VOM/HowardSprings/input_prec04/dailyweather.prn left in tree.
CONFLICT (modify/delete): work/VOM/HowardSprings/input_prec04/soilprofile.par deleted in HEAD and modified in origin/branch2merge. Version origin/branch2merge of work/VOM/HowardSprings/input_prec04/soilprofile.par left in tree.
Automatic merge failed; fix conflicts and then commit the result.
All the conflicts are in data files, not in metadata.
Okay thank you! The files in conflict are actually the new files as a results of model runs of the HPC (so will keep those). Can I use this bugfix already or do I have to wait until the PR is included?
You can use the branch, there’s no new breaking changes in the branch/develop and the fix itself doesn’t pose any risk, either.