# Toolkit fixes for CSV, Shell, Workspace, Gemini, GitHub, Local File System and PubMed

> Agno's CsvTools, ShellTools and Workspace honor an explicit zero, GeminiTools returns real video bytes, GithubTools fixes Enterprise branch links and non-ASCII files, LocalFileSystemTools uses UTF-8, and PubmedTools keeps titles for short abstracts.

- Published: 2026-10-01
- Author: hfg369
- Categories: Changelog
- Canonical: https://www.agno.com/blog/toolkit-fixes-for-csv-shell-workspace-gemini-github-local-file-system-and-pubmed
- Markdown: https://www.agno.com/blog/toolkit-fixes-for-csv-shell-workspace-gemini-github-local-file-system-and-pubmed.md

Agno's `CsvTools`, `ShellTools`, `Workspace`, `GeminiTools`, `GithubTools`, `LocalFileSystemTools` and `PubmedTools` each got a fix for a value they dropped, ignored or mangled. The outputs below come from running the previous release and this one, with the Gemini, GitHub and PubMed APIs stubbed.

### `CsvTools` honors `row_limit=0`

`CsvTools.read_csv_file` picked its limit with `row_limit or self.row_limit`, so an explicit `0` fell back to the toolkit's limit, or to every row when none was set. A `0` now returns no rows, and an omitted `row_limit` still uses the toolkit's setting:

```python
CsvTools(csvs=[path]).read_csv_file("people", row_limit=0)
# Before: '[{"name": "Alice", "city": "Paris"}, {"name": "Bob", "city": "Rome"}]'
# Now:    '[]'
```

### `ShellTools` and `Workspace` honor `tail=0`

`ShellTools.run_shell_command`, `agno.utils.shell.run_shell_command`, and `Workspace.run_command` and `arun_command` cut output with `[-tail:]`. For `tail=0` that slice is `[-0:]`, the whole list. All four now return an empty string, on success and on the `Workspace` error path:

```python
ShellTools().run_shell_command(["printf", "one\\ntwo\\nthree"], tail=0)
# Before: 'one\ntwo\nthree'
# Now:    ''
```

### `GeminiTools.generate_video` returns raw video bytes

`generate_video` built its `Video` artifact from the base64 text of the video. `Video.content` holds raw bytes, so anything that saved or uploaded the artifact got base64 text. It now stores the bytes from Gemini, like `generate_image` and the other video toolkits do, and the cookbook writes `video.content` straight to a file. The first bytes of `video.content` for an MP4:

```text
Before: b'AAAAGGZ0eXBtcDQy'
Now:    b'\x00\x00\x00\x18ftypmp42'
```

### `GithubTools` fixes branch links and non-ASCII files

`GithubTools.create_branch` built its link by rewriting the Git ref API URL, which only works on github.com. It now builds the link from the repository's web URL and escapes the branch name. `get_file_content` counted every non-ASCII character as a binary signal, so a file with more than 200 of them in its first 1000 characters came back as a binary file. It now counts only NUL and control characters. For a GitHub Enterprise repository and a Chinese README:

```text
Before: url     https://github.example.com/api/v3/repos/acme/app/tree/feature/agent
        content 'Binary file (content not displayed)'
Now:    url     https://github.example.com/acme/app/tree/feature/agent
        content '# 智能体平台\n\n这是一个用于构建、运行和管理智...'
```

### `LocalFileSystemTools` reads and writes UTF-8

`LocalFileSystemTools.write_file` and `read_file` used the locale's encoding. On a host set to cp1252, GBK or Latin-1, writing non-ASCII text failed and reading a UTF-8 file returned garbled text. Both now use UTF-8. Under a Latin-1 locale:

```text
Before: write 'Grüße aus Zürich, 東京' -> Error: Failed to write file: 'latin-1' codec can't encode characters in position 18-19
        read  'café 東京'              -> 'café æ\x9d±äº¬'
Now:    write 'Grüße aus Zürich, 東京' -> Successfully wrote file to: .../note.txt
        read  'café 東京'              -> 'café 東京'
```

### `PubmedTools` keeps metadata for short abstracts

`PubmedTools.search_pubmed` applied its 200-character check to the whole result string, so an abstract of 200 characters or fewer, or no abstract at all, came back without `Title` and `Published`. The check now only decides whether to cut the summary:

```text
Before: Summary: We test tool calling in 1B to 8B models.
Now:    Title: Tool use in small language models
        Published: 2026-03-02
        Summary: We test tool calling in 1B to 8B models.
```

See the [cookbook](https://github.com/agno-agi/agno/blob/main/cookbook/91_tools/models/gemini_video_generation.py), and learn more about the [CSV](https://docs.agno.com/tools/toolkits/database/csv), [Shell](https://docs.agno.com/tools/toolkits/local/shell), [Workspace](https://docs.agno.com/tools/toolkits/local/workspace), [Gemini](https://docs.agno.com/tools/toolkits/models/gemini), [GitHub](https://docs.agno.com/tools/toolkits/others/github), [Local File System](https://docs.agno.com/tools/toolkits/local/local-file-system) and [PubMed](https://docs.agno.com/tools/toolkits/search/pubmed) toolkits in the documentation.