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View Code? Open in Web Editor NEWPython implementation of calcium imaging analysis pipeline for cardiac myocytes
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calcium-analysis's Issues
Sweep: fix GitHub workflow bug
[Invalid workflow file: .github/workflows/test_workflow.yml#L25](https://github.com/retroam/Calcium-analysis/actions/runs/5286314369/workflow)
You have an error in your yaml syntax on line 25
Sweep: fix GitHub workflow bug
Github workflow not working. Fix issue
Run pytest tests/
/home/runner/work/_temp/06fd0b6f-8015-4e45-9710-fc9055063431.sh: line 1: pytest: command not found
Error: Process completed with exit code 127.
Sweep: create GitHub workflow to run tests before merge
Sweep: Include instructions for running package as a cli
Add instructions on running cli to README
sweep: add typing and docstrings to function
Add typing and docstrings to all functions. do not change the logic of the code
Checklist
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calcium_analysis/analysis.py✅ Commita429be3
• Add typing to all function parameters and return values. • Write comprehensive docstrings for each function.Sandbox Execution Logs
trunk init1/21 ✓⡿ Downloading Trunk 1.16.0... ⡿ Downloading Trunk 1.16.0... ⢿ Downloading Trunk 1.16.0... ⣻ Downloading Trunk 1.16.0... ⣽ Downloading Trunk 1.16.0... ⣾ Downloading Trunk 1.16.0... ⣷ Downloading Trunk 1.16.0... ✔ Downloading Trunk 1.16.0... done ⡿ Verifying Trunk sha256... ✔ Verifying Trunk sha256... done ⡿ Unpacking Trunk... ✔ Unpacking Trunk... done ✔ 13 linters were enabled (.trunk/trunk.yaml) actionlint 1.6.25 (1 github-workflow file) bandit 1.7.5 (13 python files) black 23.9.1 (1 jupyter, 13 python files) checkov 2.4.9 (4 yaml files) git-diff-check (27 files) isort 5.12.0 (13 python files) (created .isort.cfg) markdownlint 0.37.0 (1 markdown file) (created .markdownlint.yaml) osv-scanner 1.4.0 (2 lockfile files) prettier 3.0.3 (1 markdown, 4 yaml files) ruff 0.0.290 (13 python files) (created ruff.toml) trivy 0.45.1 (2 lockfile, 4 yaml files) trufflehog 3.56.1 (27 files) yamllint 1.32.0 (4 yaml files) (created .yamllint.yaml) Next Steps 1. Read documentation Our documentation can be found at https://docs.trunk.io 2. Get help and give feedback Join the Trunk community at https://slack.trunk.io
trunk fmt calcium_analysis/analysis.py2/21 ✓✔ Formatted calcium_analysis/analysis.py Re-checking autofixed files... Checked 1 file ✔ No issues
trunk check --fix calcium_analysis/analysis.py3/21 ❌ (`1`)✔ Auto-fixed calcium_analysis/analysis.py Re-checking autofixed files... ISSUES calcium_analysis/analysis.py:8:5 1:8 high `os` imported but unused ruff/F401 8:5 high Missing argument descriptions in the docstring for `run_analysis`: `image_fld`, `save_fld`, `sd` ruff/D417 Checked 1 file 1 existing issue (1 auto-fixable) ✖ 1 new issue
trunk fmt calcium_analysis/analysis.py4/21 ✓✔ Formatted calcium_analysis/analysis.py Re-checking autofixed files... Checked 1 file ✔ No issues Run trunk upgrade to upgrade 1 linter
trunk check --fix calcium_analysis/analysis.py5/21 ❌ (`1`)✔ Auto-fixed calcium_analysis/analysis.py Re-checking autofixed files... ✔ Auto-fixed calcium_analysis/analysis.py Re-checking autofixed files... ISSUES calcium_analysis/analysis.py:6:5 6:5 high Missing argument descriptions in the docstring for `run_analysis`: `image_fld`, `save_fld`, `sd` ruff/D417 Checked 1 file ✖ 1 new issue
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trunk check --fix calcium_analysis/analysis.py7/21 ❌ (`1`)✔ Auto-fixed calcium_analysis/analysis.py Re-checking autofixed files... ISSUES calcium_analysis/analysis.py:6:5 6:5 high Missing argument descriptions in the docstring for `run_analysis`: `image_fld`, `save_fld`, `sd` ruff/D417 Checked 1 file ✖ 1 new issue
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trunk check --fix calcium_analysis/analysis.py9/21 ❌ (`1`)✔ Auto-fixed calcium_analysis/analysis.py Re-checking autofixed files... ISSUES calcium_analysis/analysis.py:6:5 6:5 high Missing argument descriptions in the docstring for `run_analysis`: `image_fld`, `save_fld`, `sd` ruff/D417 Checked 1 file ✖ 1 new issue
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trunk check --fix calcium_analysis/analysis.py11/21 ❌ (`1`)✔ Auto-fixed calcium_analysis/analysis.py Re-checking autofixed files... ISSUES calcium_analysis/analysis.py:6:5 6:5 high Missing argument descriptions in the docstring for `run_analysis`: `image_fld`, `save_fld`, `sd` ruff/D417 Checked 1 file ✖ 1 new issue
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trunk check --fix calcium_analysis/analysis.py13/21 ❌ (`1`)✔ Auto-fixed calcium_analysis/analysis.py Re-checking autofixed files... ISSUES calcium_analysis/analysis.py:6:5 6:5 high Missing argument descriptions in the docstring for `run_analysis`: `image_fld`, `save_fld`, `sd` ruff/D417 Checked 1 file ✖ 1 new issue
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trunk check --fix calcium_analysis/analysis.py15/21 ❌ (`1`)✔ Auto-fixed calcium_analysis/analysis.py Re-checking autofixed files... ISSUES calcium_analysis/analysis.py:6:5 6:5 high Missing argument descriptions in the docstring for `run_analysis`: `image_fld`, `save_fld`, `sd` ruff/D417 Checked 1 file ✖ 1 new issue
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trunk check --fix calcium_analysis/analysis.py17/21 ❌ (`1`)✔ Auto-fixed calcium_analysis/analysis.py Re-checking autofixed files... ISSUES calcium_analysis/analysis.py:6:5 6:5 high Missing argument descriptions in the docstring for `run_analysis`: `image_fld`, `save_fld`, `sd` ruff/D417 Checked 1 file ✖ 1 new issue
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trunk check --fix calcium_analysis/analysis.py19/21 ❌ (`1`)✔ Auto-fixed calcium_analysis/analysis.py Re-checking autofixed files... ISSUES calcium_analysis/analysis.py:6:5 6:5 high Missing argument descriptions in the docstring for `run_analysis`: `image_fld`, `save_fld`, `sd` ruff/D417 Checked 1 file ✖ 1 new issue
trunk fmt calcium_analysis/analysis.py20/21 ✓✔ Formatted calcium_analysis/analysis.py Re-checking autofixed files... Checked 1 file ✔ No issues
trunk check --fix calcium_analysis/analysis.py21/21 ❌ (`1`)✔ Auto-fixed calcium_analysis/analysis.py Re-checking autofixed files... ISSUES calcium_analysis/analysis.py:6:5 6:5 high Missing argument descriptions in the docstring for `run_analysis`: `image_fld`, `save_fld`, `sd` ruff/D417 Checked 1 file ✖ 1 new issue
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calcium_analysis/cli.py✅ Commitf6d4cf1
• Add typing to all function parameters and return values. • Write comprehensive docstrings for each function.Sandbox Execution Logs
trunk init1/31 ✓⡿ Downloading Trunk 1.16.0... ⡿ Downloading Trunk 1.16.0... ⢿ Downloading Trunk 1.16.0... ⣻ Downloading Trunk 1.16.0... ⣽ Downloading Trunk 1.16.0... ⣾ Downloading Trunk 1.16.0... ⣷ Downloading Trunk 1.16.0... ✔ Downloading Trunk 1.16.0... done ⡿ Verifying Trunk sha256... ✔ Verifying Trunk sha256... done ⡿ Unpacking Trunk... ✔ Unpacking Trunk... done ✔ 13 linters were enabled (.trunk/trunk.yaml) actionlint 1.6.25 (1 github-workflow file) bandit 1.7.5 (13 python files) black 23.9.1 (1 jupyter, 13 python files) checkov 2.4.9 (4 yaml files) git-diff-check (27 files) isort 5.12.0 (13 python files) (created .isort.cfg) markdownlint 0.37.0 (1 markdown file) (created .markdownlint.yaml) osv-scanner 1.4.0 (2 lockfile files) prettier 3.0.3 (1 markdown, 4 yaml files) ruff 0.0.290 (13 python files) (created ruff.toml) trivy 0.45.1 (2 lockfile, 4 yaml files) trufflehog 3.56.1 (27 files) yamllint 1.32.0 (4 yaml files) (created .yamllint.yaml) Next Steps 1. Read documentation Our documentation can be found at https://docs.trunk.io 2. Get help and give feedback Join the Trunk community at https://slack.trunk.io
trunk fmt calcium_analysis/cli.py2/31 ✓✔ Formatted calcium_analysis/cli.py Re-checking autofixed files... ✔ Formatted calcium_analysis/cli.py Re-checking autofixed files... Checked 1 file ✔ No issues
trunk check --fix calcium_analysis/cli.py3/31 ❌ (`1`)✔ Auto-fixed calcium_analysis/cli.py Re-checking autofixed files... ISSUES calcium_analysis/cli.py:10:5 10:5 high Missing argument descriptions in the docstring for `main`: `image_fld`, `save_fld`, `sd` ruff/D417 11:5 high First line of docstring should be in imperative mood: "Main function to run the analysis ruff/D401 pipeline." Checked 1 file ✖ 2 new issues
trunk fmt calcium_analysis/cli.py4/31 ✓✔ Formatted calcium_analysis/cli.py Re-checking autofixed files... ✔ Formatted calcium_analysis/cli.py Re-checking autofixed files... Checked 1 file ✔ No issues
trunk check --fix calcium_analysis/cli.py5/31 ❌ (`1`)✔ Auto-fixed calcium_analysis/cli.py Re-checking autofixed files... ISSUES calcium_analysis/cli.py:10:5 10:5 high Missing argument descriptions in the docstring for `main`: `image_fld`, `save_fld`, `sd` ruff/D417 Checked 1 file ✖ 1 new issue Run trunk upgrade to upgrade 1 linter
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calcium_analysis/data_extraction.py✅ Commit1e88079
• Add typing to all function parameters and return values. • Write comprehensive docstrings for each function.Sandbox Execution Logs
trunk init1/30 ✓⡿ Downloading Trunk 1.16.0... ⡿ Downloading Trunk 1.16.0... ⢿ Downloading Trunk 1.16.0... ⣻ Downloading Trunk 1.16.0... ⣽ Downloading Trunk 1.16.0... ⣾ Downloading Trunk 1.16.0... ⣷ Downloading Trunk 1.16.0... ✔ Downloading Trunk 1.16.0... done ⡿ Verifying Trunk sha256... ✔ Verifying Trunk sha256... done ⡿ Unpacking Trunk... ✔ Unpacking Trunk... done ✔ 13 linters were enabled (.trunk/trunk.yaml) actionlint 1.6.25 (1 github-workflow file) bandit 1.7.5 (13 python files) black 23.9.1 (1 jupyter, 13 python files) checkov 2.4.9 (4 yaml files) git-diff-check (27 files) isort 5.12.0 (13 python files) (created .isort.cfg) markdownlint 0.37.0 (1 markdown file) (created .markdownlint.yaml) osv-scanner 1.4.0 (2 lockfile files) prettier 3.0.3 (1 markdown, 4 yaml files) ruff 0.0.290 (13 python files) (created ruff.toml) trivy 0.45.1 (2 lockfile, 4 yaml files) trufflehog 3.56.1 (27 files) yamllint 1.32.0 (4 yaml files) (created .yamllint.yaml) Next Steps 1. Read documentation Our documentation can be found at https://docs.trunk.io 2. Get help and give feedback Join the Trunk community at https://slack.trunk.io
trunk fmt calcium_analysis/data_extraction.py2/30 ✓✔ Formatted calcium_analysis/data_extraction.py Re-checking autofixed files... ✔ Formatted calcium_analysis/data_extraction.py Re-checking autofixed files... Checked 1 file ✔ No issues
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trunk fmt calcium_analysis/data_extraction.py12/30 ❌ (`1`)✔ Formatted calcium_analysis/data_extraction.py Re-checking autofixed files... FAILURES black calcium_analysis/data_extraction.py .trunk/out/VSX5N.yaml black calcium_analysis/data_extraction.py .trunk/out/6zhcq.yaml NOTICES Some tools failed to run. You can open the details yaml files for more information. Checked 1 file ✖ No issues, 2 failures
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trunk check --fix calcium_analysis/data_extraction.py22/30 ❌ (`1`)✔ Auto-fixed calcium_analysis/data_extraction.py Re-checking autofixed files... ISSUES calcium_analysis/data_extraction.py:7:5 7:5 high Missing argument descriptions in the docstring for `roi_to_data`: `image_file`, `roi_file` ruff/D417 Checked 1 file ✖ 1 new issue
trunk fmt calcium_analysis/data_extraction.py23/30 ✓✔ Formatted calcium_analysis/data_extraction.py Re-checking autofixed files... ✔ Formatted calcium_analysis/data_extraction.py Re-checking autofixed files... Checked 1 file ✔ No issues
trunk check --fix calcium_analysis/data_extraction.py24/30 ❌ (`1`)✔ Auto-fixed calcium_analysis/data_extraction.py Re-checking autofixed files... ISSUES calcium_analysis/data_extraction.py:7:5 7:5 high Missing argument descriptions in the docstring for `roi_to_data`: `image_file`, `roi_file` ruff/D417 Checked 1 file ✖ 1 new issue
trunk fmt calcium_analysis/data_extraction.py25/30 ✓✔ Formatted calcium_analysis/data_extraction.py Re-checking autofixed files... ✔ Formatted calcium_analysis/data_extraction.py Re-checking autofixed files... Checked 1 file ✔ No issues
trunk check --fix calcium_analysis/data_extraction.py26/30 ❌ (`1`)✔ Auto-fixed calcium_analysis/data_extraction.py Re-checking autofixed files... ISSUES calcium_analysis/data_extraction.py:7:5 7:5 high Missing argument descriptions in the docstring for `roi_to_data`: `image_file`, `roi_file` ruff/D417 Checked 1 file ✖ 1 new issue
trunk fmt calcium_analysis/data_extraction.py27/30 ✓✔ Formatted calcium_analysis/data_extraction.py Re-checking autofixed files... ✔ Formatted calcium_analysis/data_extraction.py Re-checking autofixed files... Checked 1 file ✔ No issues
trunk check --fix calcium_analysis/data_extraction.py28/30 ❌ (`1`)✔ Auto-fixed calcium_analysis/data_extraction.py Re-checking autofixed files... ISSUES calcium_analysis/data_extraction.py:7:5 7:5 high Missing argument descriptions in the docstring for `roi_to_data`: `image_file`, `roi_file` ruff/D417 Checked 1 file ✖ 1 new issue
trunk fmt calcium_analysis/data_extraction.py29/30 ✓✔ Formatted calcium_analysis/data_extraction.py Re-checking autofixed files... ✔ Formatted calcium_analysis/data_extraction.py Re-checking autofixed files... Checked 1 file ✔ No issues
trunk check --fix calcium_analysis/data_extraction.py30/30 ❌ (`1`)✔ Auto-fixed calcium_analysis/data_extraction.py Re-checking autofixed files... ISSUES calcium_analysis/data_extraction.py:7:5 7:5 high Missing argument descriptions in the docstring for `roi_to_data`: `image_file`, `roi_file` ruff/D417 Checked 1 file ✖ 1 new issue
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calcium_analysis/image_processing.py✅ Commit5c1cb0e
• Add typing to all function parameters and return values. • Write comprehensive docstrings for each function.Sandbox Execution Logs
trunk init1/26 ✓⡿ Downloading Trunk 1.16.0... ⡿ Downloading Trunk 1.16.0... ⢿ Downloading Trunk 1.16.0... ⣻ Downloading Trunk 1.16.0... ⣽ Downloading Trunk 1.16.0... ⣾ Downloading Trunk 1.16.0... ⣷ Downloading Trunk 1.16.0... ✔ Downloading Trunk 1.16.0... done ⡿ Verifying Trunk sha256... ✔ Verifying Trunk sha256... done ⡿ Unpacking Trunk... ✔ Unpacking Trunk... done ✔ 13 linters were enabled (.trunk/trunk.yaml) actionlint 1.6.25 (1 github-workflow file) bandit 1.7.5 (13 python files) black 23.9.1 (1 jupyter, 13 python files) checkov 2.4.9 (4 yaml files) git-diff-check (27 files) isort 5.12.0 (13 python files) (created .isort.cfg) markdownlint 0.37.0 (1 markdown file) (created .markdownlint.yaml) osv-scanner 1.4.0 (2 lockfile files) prettier 3.0.3 (1 markdown, 4 yaml files) ruff 0.0.290 (13 python files) (created ruff.toml) trivy 0.45.1 (2 lockfile, 4 yaml files) trufflehog 3.56.1 (27 files) yamllint 1.32.0 (4 yaml files) (created .yamllint.yaml) Next Steps 1. Read documentation Our documentation can be found at https://docs.trunk.io 2. Get help and give feedback Join the Trunk community at https://slack.trunk.io
trunk fmt calcium_analysis/image_processing.py2/26 ✓✔ Formatted calcium_analysis/image_processing.py Re-checking autofixed files... ✔ Formatted calcium_analysis/image_processing.py Re-checking autofixed files... Checked 1 file ✔ No issues
trunk check --fix calcium_analysis/image_processing.py3/26 ❌ (`1`)✔ Auto-fixed calcium_analysis/image_processing.py Re-checking autofixed files... ISSUES calcium_analysis/image_processing.py:2:0 2:0 low Using xml.etree.ElementTree to parse untrusted XML data is known to be vulnerable to XML bandit/B405 attacks. Replace xml.etree.ElementTree with the equivalent defusedxml pac... .trunk/out/iJW.txt 10:5 high Missing argument description in the docstring for `load_image`: `image_path` ruff/D417 10:36 high Undefined name `Tuple` ruff/F821 10:54 high Undefined name `Dict` ruff/F821 10:64 high Undefined name `Any` ruff/F821 29:5 high Missing argument descriptions in the docstring for `image_to_stack`: `image_fldr`, ruff/D417 `save_fldr` 54:9 high Ambiguous variable name: `I` ruff/E741 56:0 medium Using xml.etree.ElementTree.fromstring to parse untrusted XML data is known to be bandit/B314 vulnerable to XML attacks. Replace xml.etree.ElementTree.fromstring with its def... .trunk/out/evl.txt Checked 1 file 2 existing issues ✖ 6 new issues
trunk fmt calcium_analysis/image_processing.py4/26 ❌ (`1`)✔ Formatted calcium_analysis/image_processing.py Re-checking autofixed files... FAILURES black calcium_analysis/image_processing.py .trunk/out/9O3nc.yaml black calcium_analysis/image_processing.py .trunk/out/jG9Dd.yaml NOTICES Some tools failed to run. You can open the details yaml files for more information. Checked 1 file ✖ No issues, 2 failures Run trunk upgrade to upgrade 1 linter
trunk fmt calcium_analysis/image_processing.py5/26 ❌ (`1`)✔ Formatted calcium_analysis/image_processing.py Re-checking autofixed files... FAILURES black calcium_analysis/image_processing.py .trunk/out/9hkFG.yaml black calcium_analysis/image_processing.py .trunk/out/z0ZrP.yaml NOTICES Some tools failed to run. You can open the details yaml files for more information. Checked 1 file ✖ No issues, 2 failures
trunk fmt calcium_analysis/image_processing.py6/26 ❌ (`1`)✔ Formatted calcium_analysis/image_processing.py Re-checking autofixed files... FAILURES black calcium_analysis/image_processing.py .trunk/out/iQj92.yaml black calcium_analysis/image_processing.py .trunk/out/qtsDl.yaml NOTICES Some tools failed to run. You can open the details yaml files for more information. Checked 1 file ✖ No issues, 2 failures
trunk fmt calcium_analysis/image_processing.py7/26 ✓✔ Formatted calcium_analysis/image_processing.py Re-checking autofixed files... ✔ Formatted calcium_analysis/image_processing.py Re-checking autofixed files... Checked 1 file ✔ No issues
trunk check --fix calcium_analysis/image_processing.py8/26 ❌ (`1`)✔ Auto-fixed calcium_analysis/image_processing.py Re-checking autofixed files... ISSUES calcium_analysis/image_processing.py:10:5 5:45 high `defusedxml.ElementTree.parse` imported but unused ruff/F401 10:5 high Missing argument description in the docstring for `load_image`: `image_path` ruff/D417 29:5 high Missing argument descriptions in the docstring for `image_to_stack`: `image_fldr`, `save_fldr` ruff/D417 Checked 1 file 1 existing issue (1 auto-fixable) ✖ 2 new issues
trunk fmt calcium_analysis/image_processing.py9/26 ✓✔ Formatted calcium_analysis/image_processing.py Re-checking autofixed files... ✔ Formatted calcium_analysis/image_processing.py Re-checking autofixed files... Checked 1 file ✔ No issues
trunk check --fix calcium_analysis/image_processing.py10/26 ❌ (`1`)✔ Auto-fixed calcium_analysis/image_processing.py Re-checking autofixed files... ISSUES calcium_analysis/image_processing.py:10:5 4:19 high `imageio` imported but unused ruff/F401 10:5 high Missing argument description in the docstring for `load_image`: `image_path` ruff/D417 29:5 high Missing argument descriptions in the docstring for `image_to_stack`: `image_fldr`, `save_fldr` ruff/D417 Checked 1 file 1 existing issue (1 auto-fixable) ✖ 2 new issues
trunk fmt calcium_analysis/image_processing.py11/26 ❌ (`1`)✔ Formatted calcium_analysis/image_processing.py Re-checking autofixed files... FAILURES black calcium_analysis/image_processing.py .trunk/out/ZtGdb.yaml black calcium_analysis/image_processing.py .trunk/out/OUOOs.yaml NOTICES Some tools failed to run. You can open the details yaml files for more information. Checked 1 file ✖ No issues, 2 failures
trunk fmt calcium_analysis/image_processing.py12/26 ✓✔ Formatted calcium_analysis/image_processing.py Re-checking autofixed files... ✔ Formatted calcium_analysis/image_processing.py Re-checking autofixed files... Checked 1 file ✔ No issues
trunk check --fix calcium_analysis/image_processing.py13/26 ❌ (`1`)✔ Auto-fixed calcium_analysis/image_processing.py Re-checking autofixed files... ISSUES calcium_analysis/image_processing.py:9:5 9:5 high Missing argument description in the docstring for `load_image`: `image_path` ruff/D417 28:5 high Missing argument descriptions in the docstring for `image_to_stack`: `image_fldr`, `save_fldr` ruff/D417 29:5 high First line of docstring should be in imperative mood: "This function will load each tif image in ruff/D401 the image folder, concatenate them into a single numpy array," 29:5 high First word of the docstring should not be "This" ruff/D404 Checked 1 file ✖ 4 new issues
trunk fmt calcium_analysis/image_processing.py14/26 ✓✔ Formatted calcium_analysis/image_processing.py Re-checking autofixed files... ✔ Formatted calcium_analysis/image_processing.py Re-checking autofixed files... Checked 1 file ✔ No issues
trunk check --fix calcium_analysis/image_processing.py15/26 ❌ (`1`)✔ Auto-fixed calcium_analysis/image_processing.py Re-checking autofixed files... ISSUES calcium_analysis/image_processing.py:9:5 9:5 high Missing argument description in the docstring for `load_image`: `image_path` ruff/D417 28:5 high Missing argument descriptions in the docstring for `image_to_stack`: `image_fldr`, `save_fldr` ruff/D417 Checked 1 file ✖ 2 new issues
trunk fmt calcium_analysis/image_processing.py16/26 ✓✔ Formatted calcium_analysis/image_processing.py Re-checking autofixed files... ✔ Formatted calcium_analysis/image_processing.py Re-checking autofixed files... Checked 1 file ✔ No issues
trunk check --fix calcium_analysis/image_processing.py17/26 ❌ (`1`)✔ Auto-fixed calcium_analysis/image_processing.py Re-checking autofixed files... ISSUES calcium_analysis/image_processing.py:9:5 9:5 high Missing argument description in the docstring for `load_image`: `image_path` ruff/D417 28:5 high Missing argument descriptions in the docstring for `image_to_stack`: `image_fldr`, `save_fldr` ruff/D417 Checked 1 file ✖ 2 new issues
trunk fmt calcium_analysis/image_processing.py18/26 ✓✔ Formatted calcium_analysis/image_processing.py Re-checking autofixed files... ✔ Formatted calcium_analysis/image_processing.py Re-checking autofixed files... Checked 1 file ✔ No issues
trunk check --fix calcium_analysis/image_processing.py19/26 ❌ (`1`)✔ Auto-fixed calcium_analysis/image_processing.py Re-checking autofixed files... ISSUES calcium_analysis/image_processing.py:9:5 9:5 high Missing argument description in the docstring for `load_image`: `image_path` ruff/D417 28:5 high Missing argument descriptions in the docstring for `image_to_stack`: `image_fldr`, `save_fldr` ruff/D417 Checked 1 file ✖ 2 new issues
trunk fmt calcium_analysis/image_processing.py20/26 ✓✔ Formatted calcium_analysis/image_processing.py Re-checking autofixed files... ✔ Formatted calcium_analysis/image_processing.py Re-checking autofixed files... Checked 1 file ✔ No issues
trunk check --fix calcium_analysis/image_processing.py21/26 ❌ (`1`)✔ Auto-fixed calcium_analysis/image_processing.py Re-checking autofixed files... ✔ Auto-fixed calcium_analysis/image_processing.py Re-checking autofixed files... ISSUES calcium_analysis/image_processing.py:9:5 9:5 high Missing argument description in the docstring for `load_image`: `image_path` ruff/D417 28:5 high Missing argument descriptions in the docstring for `image_to_stack`: `image_fldr`, `save_fldr` ruff/D417 Checked 1 file ✖ 2 new issues
trunk fmt calcium_analysis/image_processing.py22/26 ✓✔ Formatted calcium_analysis/image_processing.py Re-checking autofixed files... ✔ Formatted calcium_analysis/image_processing.py Re-checking autofixed files... Checked 1 file ✔ No issues
trunk check --fix calcium_analysis/image_processing.py23/26 ❌ (`1`)✔ Auto-fixed calcium_analysis/image_processing.py Re-checking autofixed files... ✔ Auto-fixed calcium_analysis/image_processing.py Re-checking autofixed files... ✔ Auto-fixed calcium_analysis/image_processing.py Re-checking autofixed files... ISSUES calcium_analysis/image_processing.py:9:5 9:5 high Missing argument description in the docstring for `load_image`: `image_path` ruff/D417 28:5 high Missing argument descriptions in the docstring for `image_to_stack`: `image_fldr`, `save_fldr` ruff/D417 Checked 1 file ✖ 2 new issues
trunk fmt calcium_analysis/image_processing.py24/26 ❌ (`1`)✔ Formatted calcium_analysis/image_processing.py Re-checking autofixed files... FAILURES black calcium_analysis/image_processing.py .trunk/out/4rhv9.yaml black calcium_analysis/image_processing.py .trunk/out/UuxlJ.yaml NOTICES Some tools failed to run. You can open the details yaml files for more information. Checked 1 file ✖ No issues, 2 failures
trunk fmt calcium_analysis/image_processing.py25/26 ✓✔ Formatted calcium_analysis/image_processing.py Re-checking autofixed files... ✔ Formatted calcium_analysis/image_processing.py Re-checking autofixed files... Checked 1 file ✔ No issues
trunk check --fix calcium_analysis/image_processing.py26/26 ❌ (`1`)✔ Auto-fixed calcium_analysis/image_processing.py Re-checking autofixed files... ISSUES calcium_analysis/image_processing.py:9:5 9:5 high Missing argument description in the docstring for `load_image`: `image_path` ruff/D417 28:5 high Missing argument descriptions in the docstring for `image_to_stack`: `image_fldr`, `save_fldr` ruff/D417 Checked 1 file ✖ 2 new issues
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calcium_analysis/image_segmentation.py✅ Commitbec88ee
• Add typing to all function parameters and return values. • Write comprehensive docstrings for each function.Sandbox Execution Logs
trunk init1/11 ✓⡿ Downloading Trunk 1.16.0... ⡿ Downloading Trunk 1.16.0... ⢿ Downloading Trunk 1.16.0... ⣻ Downloading Trunk 1.16.0... ⣽ Downloading Trunk 1.16.0... ⣾ Downloading Trunk 1.16.0... ⣷ Downloading Trunk 1.16.0... ✔ Downloading Trunk 1.16.0... done ⡿ Verifying Trunk sha256... ✔ Verifying Trunk sha256... done ⡿ Unpacking Trunk... ✔ Unpacking Trunk... done ✔ 13 linters were enabled (.trunk/trunk.yaml) actionlint 1.6.25 (1 github-workflow file) bandit 1.7.5 (13 python files) black 23.9.1 (1 jupyter, 13 python files) checkov 2.4.9 (4 yaml files) git-diff-check (27 files) isort 5.12.0 (13 python files) (created .isort.cfg) markdownlint 0.37.0 (1 markdown file) (created .markdownlint.yaml) osv-scanner 1.4.0 (2 lockfile files) prettier 3.0.3 (1 markdown, 4 yaml files) ruff 0.0.290 (13 python files) (created ruff.toml) trivy 0.45.1 (2 lockfile, 4 yaml files) trufflehog 3.56.1 (27 files) yamllint 1.32.0 (4 yaml files) (created .yamllint.yaml) Next Steps 1. Read documentation Our documentation can be found at https://docs.trunk.io 2. Get help and give feedback Join the Trunk community at https://slack.trunk.io
trunk fmt calcium_analysis/image_segmentation.py2/11 ✓✔ Formatted calcium_analysis/image_segmentation.py Re-checking autofixed files... ✔ Formatted calcium_analysis/image_segmentation.py Re-checking autofixed files... Checked 1 file ✔ No issues
trunk check --fix calcium_analysis/image_segmentation.py3/11 ❌ (`1`)✔ Auto-fixed calcium_analysis/image_segmentation.py Re-checking autofixed files... ISSUES calcium_analysis/image_segmentation.py:8:5 8:5 high Missing argument descriptions in the docstring for `stack_to_roi`: `image_path`, `sd` ruff/D417 Checked 1 file ✖ 1 new issue
trunk fmt calcium_analysis/image_segmentation.py4/11 ✓✔ Formatted calcium_analysis/image_segmentation.py Re-checking autofixed files... ✔ Formatted calcium_analysis/image_segmentation.py Re-checking autofixed files... Checked 1 file ✔ No issues
trunk check --fix calcium_analysis/image_segmentation.py5/11 ❌ (`1`)✔ Auto-fixed calcium_analysis/image_segmentation.py Re-checking autofixed files... ISSUES calcium_analysis/image_segmentation.py:8:5 8:5 high Missing argument descriptions in the docstring for `stack_to_roi`: `image_path`, `sd` ruff/D417 Checked 1 file ✖ 1 new issue Run trunk upgrade to upgrade 1 linter
trunk fmt calcium_analysis/image_segmentation.py6/11 ✓✔ Formatted calcium_analysis/image_segmentation.py Re-checking autofixed files... ✔ Formatted calcium_analysis/image_segmentation.py Re-checking autofixed files... Checked 1 file ✔ No issues
trunk check --fix calcium_analysis/image_segmentation.py7/11 ❌ (`1`)✔ Auto-fixed calcium_analysis/image_segmentation.py Re-checking autofixed files... ISSUES calcium_analysis/image_segmentation.py:8:5 8:5 high Missing argument descriptions in the docstring for `stack_to_roi`: `image_path`, `sd` ruff/D417 Checked 1 file ✖ 1 new issue
trunk fmt calcium_analysis/image_segmentation.py8/11 ✓✔ Formatted calcium_analysis/image_segmentation.py Re-checking autofixed files... ✔ Formatted calcium_analysis/image_segmentation.py Re-checking autofixed files... Checked 1 file ✔ No issues
trunk check --fix calcium_analysis/image_segmentation.py9/11 ❌ (`1`)✔ Auto-fixed calcium_analysis/image_segmentation.py Re-checking autofixed files... ISSUES calcium_analysis/image_segmentation.py:8:5 8:5 high Missing argument descriptions in the docstring for `stack_to_roi`: `image_path`, `sd` ruff/D417 Checked 1 file ✖ 1 new issue
trunk fmt calcium_analysis/image_segmentation.py10/11 ✓✔ Formatted calcium_analysis/image_segmentation.py Re-checking autofixed files... ✔ Formatted calcium_analysis/image_segmentation.py Re-checking autofixed files... Checked 1 file ✔ No issues
trunk check --fix calcium_analysis/image_segmentation.py11/11 ❌ (`1`)✔ Auto-fixed calcium_analysis/image_segmentation.py Re-checking autofixed files... ISSUES calcium_analysis/image_segmentation.py:8:5 8:5 high Missing argument descriptions in the docstring for `stack_to_roi`: `image_path`, `sd` ruff/D417 Checked 1 file ✖ 1 new issue
Sweep: Write Unit Tests
sweep: fix bugs in CI test workflow
fix the following bug:
Run pytest tests/
============================= test session starts ==============================
platform linux -- Python 3.[1](https://github.com/retroam/Calcium-analysis/actions/runs/5561099006/job/15064197256#step:5:1)1.4, pytest-[7](https://github.com/retroam/Calcium-analysis/actions/runs/5561099006/job/15064197256#step:5:8).4.0, pluggy-1.2.0
rootdir: /home/runner/work/Calcium-analysis/Calcium-analysis
collected 0 items / 3 errors
==================================== ERRORS ====================================
________________ ERROR collecting tests/test_data_extraction.py ________________
ImportError while importing test module '/home/runner/work/Calcium-analysis/Calcium-analysis/tests/test_data_extraction.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/opt/hostedtoolcache/Python/3.[11](https://github.com/retroam/Calcium-analysis/actions/runs/5561099006/job/15064197256#step:5:12).4/x64/lib/python3.11/importlib/__init__.py:[12](https://github.com/retroam/Calcium-analysis/actions/runs/5561099006/job/15064197256#step:5:13)6: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
tests/test_data_extraction.py:3: in <module>
from calcium_analysis.data_extraction import roi_to_data
E ModuleNotFoundError: No module named 'calcium_analysis'
_______________ ERROR collecting tests/test_image_processing.py ________________
ImportError while importing test module '/home/runner/work/Calcium-analysis/Calcium-analysis/tests/test_image_processing.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/opt/hostedtoolcache/Python/3.11.4/x64/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
tests/test_image_processing.py:1: in <module>
import coverage
E ModuleNotFoundError: No module named 'coverage'
______________ ERROR collecting tests/test_image_segmentation.py _______________
ImportError while importing test module '/home/runner/work/Calcium-analysis/Calcium-analysis/tests/test_image_segmentation.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/opt/hostedtoolcache/Python/3.11.4/x64/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
tests/test_image_segmentation.py:3: in <module>
from calcium_analysis.image_segmentation import stack_to_roi
E ModuleNotFoundError: No module named 'calcium_analysis'
=========================== short test summary info ============================
ERROR tests/test_data_extraction.py
ERROR tests/test_image_processing.py
ERROR tests/test_image_segmentation.py
!!!!!!!!!!!!!!!!!!! Interrupted: 3 errors during collection !!!!!!!!!!!!!!!!!!!!
============================== 3 errors in 0.[22](https://github.com/retroam/Calcium-analysis/actions/runs/5561099006/job/15064197256#step:5:23)s ===============================
Error: Process completed with exit code 2.
Sweep: add code test coverage badge to readme
Add test code coverage badge to README
Sweep: refactor codebase to modern Python standards
Sweep: Modify CLI to use the click python package
Use the click python package: https://github.com/pallets/click
Sweep: fix GitHub workflow bug
Bug:
/home/runner/work/_temp/06fd0b6f-8015-4e45-9710-fc9055063431.sh: line 1: pytest: command not found
Error: Process completed with exit code 127.
Sweep: Turn app into a cli tool
Sweep: modify README to provide instructions on using the package
Focus on files in:Calcium-analysis/calcium_analysis
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