← Back to scan
File as GitHub Issue repo: LernerLab/GuPPy

Push this scan report to LernerLab/GuPPy

Click the green button below to open GitHub’s new-issue form, pre-filled with the report title, summary table, top findings, and an embedded score-card image. No authentication needed — you review on GitHub before submitting. Repobility is credited as the scanner.

Embedded score card image

This image will render at the top of the issue body. Hosted on Repobility, refreshes automatically after re-scans.

Repobility score card

Issue title

Missing import: `io` used but not imported

Curate findings to include

Pick exactly which findings appear in the issue body. By default the top 5 are included. Uncheck noise, check what matters.

Top 5 (default)
Severity Rule Title File:line
CRIT MINED019 [MINED019] Ssti Jinja From String: jinja2.Environment().from_string(user_input) — full RC… src/guppy/orchestration/home.py:74
CRIT MINED107 Missing import: `io` used but not imported src/guppy/testing/scripts/create_mock_n…:342
CRIT MINED107 Missing import: `io` used but not imported src/guppy/testing/scripts/create_mock_n…:254
CRIT MINED107 Missing import: `io` used but not imported src/guppy/testing/scripts/create_mock_n…:348
CRIT MINED107 Missing import: `io` used but not imported src/guppy/extractors/dandi_nwb_recordin…:170
CRIT MINED107 Missing import: `io` used but not imported src/guppy/extractors/nwb_recording_extr…:395
CRIT MINED107 Missing import: `signal` used but not imported src/guppy/analysis/timestamp_correction…:294
CRIT MINED107 Missing import: `signal` used but not imported src/guppy/analysis/control_channel.py:140
CRIT MINED116 Workflow uses `secrets.CODECOV_TOKEN` on a `pull_request` trigger .github/workflows/pr-tests.yml:52
HIGH SEC114 [SEC114] path.join / Path() on user-controlled segment without containment check: filepat… src/guppy/utils/utils.py:34
HIGH MINED021 [MINED021] Path Traversal Os Join: os.path.join(user_dir, filename) where filename can co… src/guppy/frontend/progress.py:8
HIGH SEC029 [SEC029] Server-Side Request Forgery (SSRF) — outbound HTTP from user input: Outbound HTT… src/guppy/extractors/dandi_nwb_recordin…:165
HIGH MINED001 [MINED001] Bare Except Pass: except: pass or except Exception: pass — silently swallows e… src/guppy/extractors/csv_recording_extr…:138
HIGH SEC128 [SEC128] Async function without await — fire-and-forget Promise (AI mistake): Async call … src/guppy/frontend/npm_gui_prompts.py:60
HIGH SEC128 [SEC128] Async function without await — fire-and-forget Promise (AI mistake): Async call … src/guppy/extractors/base_recording_ext…:150
HIGH COMP001 [COMP001] High cognitive complexity: Function `compute_psth` has cognitive complexity 34 … src/guppy/analysis/compute_psth.py:9
HIGH MINED115 Action `dawidd6/action-send-mail` pinned to mutable ref `@v3` .github/workflows/dailies.yml:36
HIGH MINED115 Action `actions/checkout` pinned to mutable ref `@v4` .github/workflows/dailies.yml:15
HIGH MINED115 Action `anthropics/claude-code-action` pinned to mutable ref `@v1` .github/workflows/claude.yml:35
HIGH MINED115 Action `actions/checkout` pinned to mutable ref `@v4` .github/workflows/claude.yml:29
HIGH MINED115 Action `pypa/gh-action-pypi-publish` pinned to mutable ref `@v1.12.4` .github/workflows/auto-publish.yml:34
HIGH MINED115 Action `actions/setup-python` pinned to mutable ref `@v5` .github/workflows/auto-publish.yml:23
HIGH MINED115 Action `actions/checkout` pinned to mutable ref `@v5` .github/workflows/auto-publish.yml:21
HIGH MINED115 Action `tj-actions/changed-files` pinned to mutable ref `@v46.0.1` .github/workflows/assess-file-changes.y…:30
HIGH MINED115 Action `actions/checkout` pinned to mutable ref `@v4` .github/workflows/assess-file-changes.y…:24
HIGH MINED115 Action `codecov/codecov-action` pinned to mutable ref `@v5` .github/workflows/run-tests.yml:83
HIGH MINED115 Action `actions/setup-python` pinned to mutable ref `@v5` .github/workflows/run-tests.yml:55
HIGH MINED115 Action `actions/checkout` pinned to mutable ref `@v5` .github/workflows/run-tests.yml:53
HIGH MINED115 Action `re-actors/alls-green` pinned to mutable ref `@release/v1` .github/workflows/pr-tests.yml:66
HIGH MINED115 Action `actions/checkout` pinned to mutable ref `@v4` .github/workflows/pr-tests.yml:22
HIGH MINED131 pre-commit hook `https://github.com/codespell-project/codespell` pinned to mutable rev `v… .pre-commit-config.yaml:24
HIGH MINED131 pre-commit hook `https://github.com/astral-sh/ruff-pre-commit` pinned to mutable rev `v0.… .pre-commit-config.yaml:17
HIGH MINED131 pre-commit hook `https://github.com/psf/black` pinned to mutable rev `25.1.0` .pre-commit-config.yaml:11
HIGH MINED131 pre-commit hook `https://github.com/pre-commit/pre-commit-hooks` pinned to mutable rev `v… .pre-commit-config.yaml:2
HIGH SEC013 [SEC013] Path Traversal — User Input in File Path: User-controlled input used in file pat… src/guppy/utils/utils.py:34
MED ERR001 [ERR001] Silent Exception Swallowing: Silently swallowing all exceptions hides bugs. Even… src/guppy/extractors/csv_recording_extr…:138
MED MINED111 Bare except continues silently src/guppy/orchestration/home.py:86
MED MINED111 Bare except continues silently src/guppy/extractors/doric_recording_ex…:241
MED MINED111 Bare except continues silently src/guppy/extractors/doric_recording_ex…:83
MED MINED111 Bare except continues silently src/guppy/extractors/npm_recording_extr…:198
MED MINED111 Bare except continues silently src/guppy/extractors/csv_recording_extr…:70
MED MINED111 Bare except continues silently src/guppy/analysis/io_utils.py:46
MED MINED109 Mutable default argument in `write_freq_and_amp_to_csv` (list) src/guppy/analysis/standard_io.py:685
MED MINED109 Mutable default argument in `write_freq_and_amp_to_hdf5` (list) src/guppy/analysis/standard_io.py:657
MED MINED109 Mutable default argument in `write_peak_and_area_to_csv` (list) src/guppy/analysis/standard_io.py:636
MED MINED109 Mutable default argument in `write_peak_and_area_to_hdf5` (list) src/guppy/analysis/standard_io.py:612
MED COMP001 [COMP001] High cognitive complexity: Function `add_control_channel` has cognitive complex… src/guppy/analysis/control_channel.py:20
LOW COMP001 [COMP001] High cognitive complexity: Function `combine_data` has cognitive complexity 14 … src/guppy/analysis/combine_data.py:110
LOW AIC003 Duplicated implementation block across source files src/guppy/testing/scripts/create_mock_n…:253
LOW AIC003 Duplicated implementation block across source files src/guppy/testing/scripts/create_mock_n…:30
LOW AIC003 Duplicated implementation block across source files src/guppy/testing/scripts/create_mock_n…:244
LOW AIC003 Duplicated implementation block across source files src/guppy/orchestration/transients.py:242
LOW AIC003 Duplicated implementation block across source files src/guppy/orchestration/preprocess.py:81
LOW AIC003 Duplicated implementation block across source files src/guppy/extractors/nwb_recording_extr…:51
LOW AIC003 Duplicated implementation block across source files src/guppy/extractors/npm_recording_extr…:163
LOW AIC003 Duplicated implementation block across source files src/guppy/extractors/doric_recording_ex…:450
LOW AIC003 Duplicated implementation block across source files src/guppy/analysis/standard_io.py:398
INFO MINED063 [MINED063] Toctou Os Path Exists: if os.path.exists(p): open(p) — file can be replaced/de… src/guppy/frontend/progress.py:69
INFO MINED050 [MINED050] Stub Only Function: Function declared but body is just pass, return None, rais… src/guppy/extractors/dandi_nwb_recordin…:292
INFO MINED050 [MINED050] Stub Only Function: Function declared but body is just pass, return None, rais… src/guppy/extractors/csv_recording_extr…:139
INFO MINED050 [MINED050] Stub Only Function: Function declared but body is just pass, return None, rais… src/guppy/extractors/base_recording_ext…:63
Reset to top 5 61 findings available (after auto-suppression of test files + won't-fix)

Issue body (markdown)

## Code-quality scan: `LernerLab/GuPPy`

**Score: 88/100 (A-)**  ·  115 findings  ·  scanned 2026-06-05 17:54 UTC  ·  36,517 LOC

| Severity | Count |
|---|---|
| CRITICAL | 9 |
| HIGH | 26 |
| MEDIUM | 12 |
| LOW | 10 |

📊 [Full filterable report](https://repobility.com/scan/6afc82b8-5e88-4ea6-a648-91134ab73397/)  ·  ![scorecard](https://repobility.com/scan/6afc82b8-5e88-4ea6-a648-91134ab73397/report.png?v=1780682046-s2)

### Top findings

1. **CRITICAL** `MINED019` — Ssti Jinja From String
   `src/guppy/orchestration/home.py:74` · CWE-94 · ✓ Repobility
2. **CRITICAL** `MINED107` — Missing import: `io` used but not imported
   `src/guppy/testing/scripts/create_mock_nwbfile_ndx_fiber_photometry_v0_2_ndx_events_v0_2.py:342` · ✓ Repobility
3. **CRITICAL** `MINED107` — Missing import: `io` used but not imported
   `src/guppy/testing/scripts/create_mock_nwbfile_ndx_fiber_photometry_v0_1_ndx_events_v0_2.py:254` · ✓ Repobility
4. **CRITICAL** `MINED107` — Missing import: `io` used but not imported
   `src/guppy/testing/scripts/create_mock_nwbfile_ndx_fiber_photometry_v0_2_ndx_events_v0_4.py:348` · ✓ Repobility
5. **CRITICAL** `MINED107` — Missing import: `io` used but not imported
   `src/guppy/extractors/dandi_nwb_recording_extractor.py:170` · ✓ Repobility

---

_Filed automatically. Close this issue if not useful — we won't refile. Full report: https://repobility.com/scan/6afc82b8-5e88-4ea6-a648-91134ab73397/_
Megaproject â high spam risk
Could not determine 'LernerLab/GuPPy' star count (GitHub API rate-limited or unreachable). When in doubt about repo size, prefer opening a focused PR or a discussion rather than an issue.
Already filed
69/117 findings (59%) on this scan are already flagged as test-file, won't-fix, or suppressed. The scan is too noisy to file as a single issue. Curate down to specific actionable findings, or address the FP source first.
I read the warnings â override Cancel

The button opens GitHubâs new-issue page in a new tab. You will see the title + body pre-filled â review, edit if you want, then click GitHubâs "Submit new issue" button. Repobility never posts anything on your behalf.

For real security findings on big repos: use the project's SECURITY.md or private advisory flow instead of a public issue.