Aider uses GitPython, which doesn't work with index-version 3 git repos #211

daniel-nimptsch · 2023-08-19T10:29:20Z

When executing aider in an existing repo with R, Python, and Bash scripts, I get this error. When executing aider in a much smaller repo of only Python files, it works without problems. Thank you very much.

Error

aider

Aider v0.12.0
Add .aider* to .gitignore (recommended)? y
Added .aider* to .gitignore
Model: gpt-4
Git repo: .git
Repo-map: universal-ctags using 1024 tokens
Added src/blastn/blastout_to_table/blastout_to_table.R to the chat.
Traceback (most recent call last):
  File "/var/home/soye/.mambaforge/envs/aider-chat/bin/aider", line 8, in <module>
    sys.exit(main())
             ^^^^^^
  File "/var/home/soye/.mambaforge/envs/aider-chat/lib/python3.11/site-packages/aider/main.py", line 479, in main
    coder = Coder.create(
            ^^^^^^^^^^^^^
  File "/var/home/soye/.mambaforge/envs/aider-chat/lib/python3.11/site-packages/aider/coders/base_coder.py", line 84, in create
    return EditBlockCoder(main_model, io, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/var/home/soye/.mambaforge/envs/aider-chat/lib/python3.11/site-packages/aider/coders/editblock_coder.py", line 14, in __init__
    super().__init__(*args, **kwargs)
  File "/var/home/soye/.mambaforge/envs/aider-chat/lib/python3.11/site-packages/aider/coders/base_coder.py", line 206, in __init__
    self.repo.add_new_files(fname for fname in fnames if not Path(fname).is_dir())
  File "/var/home/soye/.mambaforge/envs/aider-chat/lib/python3.11/site-packages/aider/repo.py", line 53, in add_new_files
    cur_files = [Path(fn).resolve() for fn in self.get_tracked_files()]
                                              ^^^^^^^^^^^^^^^^^^^^^^^^
  File "/var/home/soye/.mambaforge/envs/aider-chat/lib/python3.11/site-packages/aider/repo.py", line 181, in get_tracked_files
    staged_files = [path for path, _ in index.entries.keys()]
                                        ^^^^^^^^^^^^^
  File "/var/home/soye/.mambaforge/envs/aider-chat/lib/python3.11/site-packages/gitdb/util.py", line 253, in __getattr__
    self._set_cache_(attr)
  File "/var/home/soye/.mambaforge/envs/aider-chat/lib/python3.11/site-packages/git/index/base.py", line 149, in _set_cache_
    self._deserialize(stream)
  File "/var/home/soye/.mambaforge/envs/aider-chat/lib/python3.11/site-packages/git/index/base.py", line 177, in _deserialize
    self.version, self.entries, self._extension_data, _conten_sha = read_cache(stream)
                                                                    ^^^^^^^^^^^^^^^^^^
  File "/var/home/soye/.mambaforge/envs/aider-chat/lib/python3.11/site-packages/git/index/fun.py", line 245, in read_cache
    version, num_entries = read_header(stream)
                           ^^^^^^^^^^^^^^^^^^^
  File "/var/home/soye/.mambaforge/envs/aider-chat/lib/python3.11/site-packages/git/index/fun.py", line 212, in read_header
    assert version in (1, 2)
           ^^^^^^^^^^^^^^^^^
AssertionError

Details

aider --version

aider 0.12.0

ctags --version

Universal Ctags 6.0.0, Copyright (C) 2015-2022 Universal Ctags Team
Universal Ctags is derived from Exuberant Ctags.
Exuberant Ctags 5.8, Copyright (C) 1996-2009 Darren Hiebert
  Compiled: Aug 13 2023, 02:54:31
  URL: https://ctags.io/
  Output version: 0.0
  Optional compiled features: +wildcards, +regex, +gnulib_regex, +iconv, +option-directory, +xpath, +json, +interactive, +sandbox, +yaml, +packcc, +optscript

The text was updated successfully, but these errors were encountered:

paul-gauthier · 2023-08-19T14:30:29Z

Thanks for trying aider and reporting this issue.

It looks like your git repo may be using a newer index format, which might not be supported by GitPython.

This GitPython issue has some more info and workarounds. You might want to try git update-index --no-skip-worktree based on that issue.

daniel-nimptsch · 2023-08-20T18:42:49Z

I tried git update-index --no-skip-worktree and unfortunately it did not solve the issue. I was able to launch aider in my project by copying it and then removing .git. However, after trying to add a file, it breaks again:

Aider v0.12.0
Model: gpt-4
Git repo: .git
Repo-map: universal-ctags using 1024 tokens
Added pipeline_scripts_dn.R to the chat.
Adding /var/home/soye/Projects/pipeline_scripts_dn_aider/pipeline_scripts_dn.R to git
Use /help to see in-chat commands, run with --help to see cmd line args
Git repo has uncommitted changes.
diff --git a/pipeline_scripts_dn.R b/pipeline_scripts_dn.R
new file mode 100644
index 0000000..e69de29
Traceback (most recent call last):
  File "/var/home/soye/.mambaforge/envs/aider-chat/bin/aider", line 8, in <module>
    sys.exit(main())
             ^^^^^^
  File "/var/home/soye/.mambaforge/envs/aider-chat/lib/python3.11/site-packages/aider/main.py", line 518, in main
    coder.dirty_commit()
  File "/var/home/soye/.mambaforge/envs/aider-chat/lib/python3.11/site-packages/aider/coders/base_coder.py", line 880, in dirty_commit
    self.last_asked_for_commit_time = self.get_last_modified()
                                      ^^^^^^^^^^^^^^^^^^^^^^^^
  File "/var/home/soye/.mambaforge/envs/aider-chat/lib/python3.11/site-packages/aider/coders/base_coder.py", line 722, in get_last_modified
    files = [Path(fn) for fn in self.get_all_abs_files() if Path(fn).exists()]
                                ^^^^^^^^^^^^^^^^^^^^^^^^
  File "/var/home/soye/.mambaforge/envs/aider-chat/lib/python3.11/site-packages/aider/coders/base_coder.py", line 717, in get_all_abs_files
    files = self.get_all_relative_files()
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/var/home/soye/.mambaforge/envs/aider-chat/lib/python3.11/site-packages/aider/coders/base_coder.py", line 710, in get_all_relative_files
    files = self.repo.get_tracked_files()
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/var/home/soye/.mambaforge/envs/aider-chat/lib/python3.11/site-packages/aider/repo.py", line 181, in get_tracked_files
    staged_files = [path for path, _ in index.entries.keys()]
                                        ^^^^^^^^^^^^^
  File "/var/home/soye/.mambaforge/envs/aider-chat/lib/python3.11/site-packages/gitdb/util.py", line 253, in __getattr__
    self._set_cache_(attr)
  File "/var/home/soye/.mambaforge/envs/aider-chat/lib/python3.11/site-packages/git/index/base.py", line 149, in _set_cache_
    self._deserialize(stream)
  File "/var/home/soye/.mambaforge/envs/aider-chat/lib/python3.11/site-packages/git/index/base.py", line 177, in _deserialize
    self.version, self.entries, self._extension_data, _conten_sha = read_cache(stream)
                                                                    ^^^^^^^^^^^^^^^^^^
  File "/var/home/soye/.mambaforge/envs/aider-chat/lib/python3.11/site-packages/git/index/fun.py", line 245, in read_cache
    version, num_entries = read_header(stream)
                           ^^^^^^^^^^^^^^^^^^^
  File "/var/home/soye/.mambaforge/envs/aider-chat/lib/python3.11/site-packages/git/index/fun.py", line 212, in read_header
    assert version in (1, 2)
           ^^^^^^^^^^^^^^^^^
AssertionError

paul-gauthier · 2023-08-23T14:07:34Z

Ok, I am glad to hear you found a good workaround for your git repo.

mi-skam · 2023-11-22T13:01:22Z

He actually, didn't found a workaround :-) Besides I have the same issue

yqrashawn · 2023-11-27T07:38:46Z

Same issue here, @paul-gauthier you might be able to reproduce on your side, the repo is https://github.com/status-im/status-mobile, it's a large repo

Aider v0.18.0

datashaman · 2023-12-15T10:14:09Z

This works for me:

git update-index --index-version=2

dwaltrip · 2024-04-27T04:26:42Z

I'm also hitting this issue (see below), but unfortunately none of the workarounds worked for me. Curiously, I don't seem to be getting it in my other repo.

Workarounds tried:

git update-index --index-version=2
git update-index --no-skip-worktree

Error:

$ aider --openai-api-key sk-xxx-...-zzz
Aider v0.30.1
Models: gpt-4-1106-preview with udiff edit format, weak model gpt-3.5-turbo
Traceback (most recent call last):
  File "/Users/danielwaltrip/.local/bin/aider", line 8, in <module>
    sys.exit(main())
             ^^^^^^

  ... (more stack info)

  File "/Users/danielwaltrip/.local/pipx/venvs/aider-chat/lib/python3.12/site-packages/git/index/fun.py", line 210, in read_header
    assert version in (1, 2)
           ^^^^^^^^^^^^^^^^^
AssertionError

P.S. Just wanna say I love the idea of aider. Thanks for making it as well as open sourcing it

dwaltrip · 2024-04-28T22:21:11Z

Update: I was able to fix my issue by updating to the latest version of git (2.44) and running the git update-index --index-version=2 command. Aider is now working fine :)

The latest version of git has the option --show-index-version for update-index. I verified that it was at 3 before and then was successfully changed to 2. Not sure what happened when I tried setting it to 2 with my older version of git (it was the system git provided by macos,git version 2.39.3 (Apple Git-145) in this case).

giodamelio · 2024-05-30T17:56:16Z

For future reference, I don't believe that downgrading your index version is supported. I ended up deleting my index (while the repo was fully checked in and backed up) and running git reset.

Digging into it a little deeper, the issue is because GitPython only supports index version 1 and 2 (relevant code), and since the project is in maintenance mode it seems like there is a decent change that this won't be fixed in near future (though the GitPython maintainer is open to merging feature contributions).

Hopefully the authors successor project GitOxide will be stable and have a Python binding at some point soon.

aantn · 2024-06-16T17:18:42Z

Having the same issue.

paul-gauthier · 2024-06-19T05:00:08Z

Did you try updating the index as described earlier in this issue?

aantn · 2024-06-19T06:30:22Z

Yes, I'm not sure what the issue is:

$ ~/Projects/robusta → git update-index --show-index-version
3

$ ~/Projects/robusta → aider
Traceback (most recent call last):
  File "/opt/homebrew/bin/aider", line 8, in <module>
    sys.exit(main())
             ^^^^^^
  File "/opt/homebrew/lib/python3.11/site-packages/aider/main.py", line 404, in main
    coder.show_announcements()
  File "/opt/homebrew/lib/python3.11/site-packages/aider/coders/base_coder.py", line 356, in show_announcements
    for line in self.get_announcements():
                ^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/homebrew/lib/python3.11/site-packages/aider/coders/base_coder.py", line 159, in get_announcements
    num_files = len(self.repo.get_tracked_files())
                    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/homebrew/lib/python3.11/site-packages/aider/repo.py", line 200, in get_tracked_files
    staged_files = [path for path, _ in index.entries.keys()]
                                        ^^^^^^^^^^^^^
  File "/opt/homebrew/lib/python3.11/site-packages/gitdb/util.py", line 253, in __getattr__
    self._set_cache_(attr)
  File "/opt/homebrew/lib/python3.11/site-packages/git/index/base.py", line 168, in _set_cache_
    self._deserialize(stream)
  File "/opt/homebrew/lib/python3.11/site-packages/git/index/base.py", line 197, in _deserialize
    self.version, self.entries, self._extension_data, _conten_sha = read_cache(stream)
                                                                    ^^^^^^^^^^^^^^^^^^
  File "/opt/homebrew/lib/python3.11/site-packages/git/index/fun.py", line 252, in read_cache
    version, num_entries = read_header(stream)
                           ^^^^^^^^^^^^^^^^^^^
  File "/opt/homebrew/lib/python3.11/site-packages/git/index/fun.py", line 210, in read_header
    assert version in (1, 2)
           ^^^^^^^^^^^^^^^^^
AssertionError

However, I can workaround this with aider --no-git - the git integration is not particularly important to me.

aantn · 2024-06-19T06:31:33Z

I should clarify - I know what the issue is, I just haven't looked into how to fix it!

$ git update-index --index-version=2
$ git update-index --show-index-version
3

grass29 · 2024-07-22T11:54:17Z

No skip worktree works for me, but this isn't a solution, as I have to keep certain files silenced, so they do not keep popping up in Source Control changes.

Is there a better workaround?

rehno-lindeque · 2024-09-10T19:10:08Z

Just to mention, this also happens when you've used git add --intent-to-add. (just git reset or git add --update or whatnot)

See this comment.

fry69 · 2024-09-11T03:43:45Z

Since this was new to me and the official documentation about git index versions is quite dense, I asked Sonnet-3.5 and ChatGPT for clarification, with ChatGPT producing a much better answer in this case (may be helpful for others, hopefully):

--- AI slop start ---

Git index versions (2, 3, and 4) represent different formats of the index file (also known as the staging area) that Git uses to track the state of your working directory between commits. Here's an explanation of the key points regarding when the index version changes, the default version, and how certain Git features might force an index upgrade.

1. Default Git Index Version

Version 2 is the default index version used by Git. This is the version that most tools, like GitPython, typically interact with.
Version 3 and Version 4 were introduced to support new features, but Git only upgrades the index version when certain features are used that require these newer formats.

2. Index Upgrades via Git Features

Git will upgrade the index version under specific circumstances, often related to optimizations or special features that require newer formats.

Version 3 introduced:
- Path compression in the index (optimized storage for file paths).
- Version 3 is not widely used, and its adoption has been limited.
Version 4 introduced:
- Cache tree extensions: These are optimizations for handling large repositories, particularly with submodules or large numbers of files.
- Support for SHA-256 hash algorithm: This could be relevant for future cryptographic algorithm changes.
- Sparse index: For large repositories, this feature makes Git operations faster by only loading part of the working directory's index into memory.

Git does not automatically upgrade the index unless you explicitly use features that require a newer version. For example, working with very large repositories or using experimental features (like the SHA-256 transition) may force an upgrade to version 4.

3. How Git Index Version Is Set

You can set the index version manually by running:
```
git update-index --index-version=<2|3|4>
```
However, Git will automatically upgrade the index if you use features that require a higher version, as mentioned above.

4. Ensuring Compatibility with GitPython

Since GitPython only supports version 2, the safest approach is to:

Avoid features that require newer index versions (particularly in large repositories with features like cache tree extensions).
Regularly check the index version with:
```
git ls-files --debug | grep index
```
If needed, you can manually downgrade the index version back to version 2 using the following command:
```
git update-index --index-version=2
```

Conclusion

If you're using basic Git features (commits, branches, diffs, etc.), the index will likely stay at version 2. However, advanced features like sparse checkouts, experimental SHA-256 support, or very large repositories may trigger an automatic upgrade to version 4. As long as you avoid these scenarios, the repository should remain compatible with tools that use GitPython.

--- AI slop end ---

iryryb · 2024-11-17T00:01:08Z

Dear community,
I have just encountered same problem while working on a project.
First, some words about what triggered it. I used git update-index --skip-worktree command, and it switched index version from 2 to 3.

Explicitly commanding git to change version:

git update-index --index-version 2 --verbose

responded with

index-version: was 3, set to 2

However, just next call of git update-index --show-index-version printed 3.

Then I decided to roll back my action and applied git update-index --no-skip-worktree command. To my surprise, git update-index --show-index-version now showed 2 (!) without any action from my side without explicitly changing the version.

For better precision, my git version is 2.47.0, working on Mac OS X Sequia 15.1 24B83 and installed via homebrew. On other environments it might not be relevant but as far as this is homebrew git, I think it should work.

The fix is reproducible reliably and should help you. Just try to find the actual reason (your action) what led to switching the version of git index. OF course, --no-skip-worktree is far not the only thing which might lead to this.

quasar-pankaj · 2024-12-04T09:21:16Z

I am also facing the same problem when working with git repositories created by Qt Creator. I am using aider 0.66.0. But I have faced no problems in repos created by others.

klochowicz · 2025-01-02T07:03:11Z

@fry69's AI slop turned out to be helpful to resolve the issue in my case:

However, Git will automatically upgrade the index if you use features that require a higher version, as mentioned above.

I was using sparse-checkout, which made downgrading the index impossible. after disabling it, downgrading index worked smoothly. :). hope it helps someone!

lockmeister · 2025-01-02T09:37:19Z

@paul-gauthier @daniel-nimptsch
I had the same problem but was able to fix it by running:

git gc --prune=now # Garbage collection, cleaned up 23,686 objects

git repack -ad # Repacked objects, optimizing repository storage

I had this problem when running aider in a very large repo.

I had previously had a problem
Unable to list files in git repo: index out of range Is your git repo corrupted? Unable to read git repository, it may be corrupt? index out of range

which was fixed by the prune and repack; and when I later encountered the Aider only works with git repos with version number 1 or 2. problem, the same fix worked for me.

thiswillbeyourgithub · 2025-01-03T08:04:37Z

Not sure this is related but for one of my repo i have a submodule called bvae and aider shows me Repo-map can't include /[path]/QuestEA/utils/bvae Has it been deleted from the file system but not from git?. It seemed to be hanging so I ctrl+c once then up arrow key and alt+enter to retry the previous line and it worked as usual.

ParetoOptimalDev · 2025-01-13T16:19:06Z

FYI using nix flake update --commit-lock-file or any nix commands upgrades your git repo index version to 3.

I got aider to add a nix flake to my project, ran nix commands, and encountered this bug. I later found out that nix was what upgraded the git repo index version.

paul-gauthier added the bug Something isn't working label Aug 19, 2023

paul-gauthier closed this as completed Aug 23, 2023

paul-gauthier reopened this Jun 16, 2024

paul-gauthier changed the title ~~AssertionError when executing aider on an existing repo~~ Aider uses GitPython which can't work with index-version 3 git repos Jun 20, 2024

paul-gauthier changed the title ~~Aider uses GitPython which can't work with index-version 3 git repos~~ Aider uses GitPython, which doesn't work with index-version 3 git repos Jun 20, 2024

paul-gauthier mentioned this issue Jun 21, 2024

Using the aider open large git repository #702

Closed

lmmx mentioned this issue Jul 29, 2024

Consider switching from GitPython to another package #292

Open

paul-gauthier mentioned this issue Aug 5, 2024

AssertionError #991

Closed

paul-gauthier mentioned this issue Aug 30, 2024

Uncaught AssertionError in fun.py line 210 #1241

Closed

kenny-kvibe mentioned this issue Nov 22, 2024

GIT ASSERT ERROR - Uncaught AssertionError in fun.py line 210 #2428

Closed

aleloi mentioned this issue Jan 10, 2025

Uncaught AssertionError in fun.py line 210 #2819

Closed

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Aider uses GitPython, which doesn't work with index-version 3 git repos #211

Aider uses GitPython, which doesn't work with index-version 3 git repos #211

daniel-nimptsch commented Aug 19, 2023 •

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Aider uses GitPython, which doesn't work with index-version 3 git repos #211

Aider uses GitPython, which doesn't work with index-version 3 git repos #211

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daniel-nimptsch commented Aug 19, 2023 • edited Loading

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paul-gauthier commented Aug 19, 2023

daniel-nimptsch commented Aug 20, 2023 • edited Loading

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mi-skam commented Nov 22, 2023

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giodamelio commented May 30, 2024

aantn commented Jun 16, 2024

paul-gauthier commented Jun 19, 2024

aantn commented Jun 19, 2024

aantn commented Jun 19, 2024

grass29 commented Jul 22, 2024

rehno-lindeque commented Sep 10, 2024

fry69 commented Sep 11, 2024

1. Default Git Index Version

2. Index Upgrades via Git Features

3. How Git Index Version Is Set

4. Ensuring Compatibility with GitPython

Conclusion

iryryb commented Nov 17, 2024 • edited Loading

quasar-pankaj commented Dec 4, 2024 • edited Loading

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lockmeister commented Jan 2, 2025 • edited Loading

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