[INFRA] Add GitHub templates and community files #30
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Added: - Issue templates for bug reports, feature requests and docs - Community guidelines (CODE_OF_CONDUCT, CONTRIBUTING) - Security policy - Pull request template All files have been customized for Pkynetics project requirements and contributing guidelines.
WalkthroughThe pull request introduces several new documents and templates to enhance community engagement and contribution processes for the Pkynetics project. Key additions include a Code of Conduct, contributing guidelines, various issue templates (for bugs, documentation, and feature requests), a pull request template, and a security policy. These documents establish clear standards for behavior, streamline contribution submissions, and provide guidance on reporting issues and vulnerabilities. Changes
Sequence Diagram(s)sequenceDiagram
participant Contributor
participant Repository
participant Maintainer
Contributor->>Repository: Submit issue or pull request
Repository->>Maintainer: Notify new submission
Maintainer->>Repository: Review submission
Maintainer->>Contributor: Provide feedback or approval
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Actionable comments posted: 7
🧹 Outside diff range and nitpick comments (12)
.github/ISSUE_TEMPLATE/docs.yaml (2)
1-4: Consider adding more specific documentation labelsWhile the "documentation" label is good for general categorization, consider adding more specific labels to help with issue organization and tracking. For example: "docs/missing", "docs/incorrect", "docs/unclear", etc., matching your dropdown options.
name: Documentation Issue description: Report issues with Pkynetics documentation title: "[Docs]: " -labels: ["documentation"] +labels: ["documentation", "triage-needed"]
37-45: Consider adding pattern validation for documentation locationsTo ensure more consistent and valid locations, consider adding pattern validation for URLs and file paths.
validations: required: true + pattern: ^(https?:\/\/[^\s]+|[^\/\s]+\/[^\s]+|[^:\s]+)$ + pattern-error: "Please provide a valid URL, file path, or section name".github/ISSUE_TEMPLATE/feature.yaml (3)
1-4: Consider enhancing the title format patternThe current title format
"[Feature]: "could be more specific to ensure consistent and searchable feature requests.-title: "[Feature]: " +title: "[Feature Request] <component>: "This format would help categorize features by component and improve searchability.
41-46: Consider using a more generic code exampleThe current example imports a specific module which might not be relevant for all feature requests.
```python # Example usage of your proposed feature: - from pkynetics import model_fitting_methods + from pkynetics import your_module # Replace with relevant module # Your proposed code here ```
56-57: Consider making alternatives section optionalNot all feature requests will have meaningful alternative solutions. Making this section required might discourage simple but valuable feature requests.
validations: - required: true + required: false.github/ISSUE_TEMPLATE/bug.yaml (3)
22-48: Consider adding version format validation.While the placeholder suggests a version format, consider adding a pattern validation to ensure consistent version reporting.
placeholder: "0.2.3" + pattern: "^\\d+\\.\\d+\\.\\d+$" + pattern_error: "Please use semantic versioning format (e.g., 0.2.3)"
64-69: Make the code example template more generic.The current import statement might not be relevant for all bug reports.
```python - # Include a minimal code example that demonstrates the issue - from pkynetics import model_fitting_methods + # Include a minimal, complete code example that demonstrates the issue + from pkynetics import ... - # Your code here + # Code that reproduces the issue
71-73: Fix trailing whitespace in reproduction steps.Remove trailing spaces from the numbered list.
- 1. - 2. - 3. + 1. + 2. + 3.🧰 Tools
🪛 yamllint (1.35.1)
[error] 71-71: trailing spaces
(trailing-spaces)
[error] 72-72: trailing spaces
(trailing-spaces)
[error] 73-73: trailing spaces
(trailing-spaces)
.github/CONTRIBUTING.md (4)
5-5: Fix heading hierarchyThe "Contents" section uses an h3 heading (
###) after an h1 heading. For proper document structure, it should use an h2 heading (##).-### Contents +## Contents🧰 Tools
🪛 Markdownlint (0.35.0)
5-5: Expected: h2; Actual: h3
Heading levels should only increment by one level at a time(MD001, heading-increment)
83-98: Add language specification to commit message templateThe fenced code block for the commit message template should specify a language for proper syntax highlighting.
-``` +```text🧰 Tools
🪛 Markdownlint (0.35.0)
83-83: null
Fenced code blocks should have a language specified(MD040, fenced-code-language)
122-122: Add Oxford comma for clarityAdd an Oxford comma before "and" in the certification statement for better clarity.
-> 1. Your contribution is your original work and you have the right to submit it under the project's license +> 1. Your contribution is your original work, and you have the right to submit it under the project's license🧰 Tools
🪛 LanguageTool
[uncategorized] ~122-~122: Use a comma before ‘and’ if it connects two independent clauses (unless they are closely connected and short).
Context: ... Your contribution is your original work and you have the right to submit it under t...(COMMA_COMPOUND_SENTENCE)
129-129: Consider maintaining consistent toneWhile friendliness is appreciated, consider adjusting the tone to match the professional nature of the rest of the document.
-If you've read these guidelines (thank you!), include the ⚡ lightning emoji at the start of your pull requests and issues. You're awesome! :100: +If you've read these guidelines (thank you!), include the ⚡ lightning emoji at the start of your pull requests and issues. We appreciate your attention to detail. :100:🧰 Tools
🪛 LanguageTool
[style] ~129-~129: Consider using a more formal and expressive alternative to ‘awesome’.
Context: ...f your pull requests and issues. You're awesome! 💯 --- *These contributing guideli...(AWESOME)
[style] ~129-~129: Using many exclamation marks might seem excessive (in this case: 7 exclamation marks for a text that’s 3892 characters long)
Context: ...pull requests and issues. You're awesome! 💯 --- *These contributing guidelin...(EN_EXCESSIVE_EXCLAMATION)
[uncategorized] ~129-~129: Loose punctuation mark.
Context: ...ll requests and issues. You're awesome! 💯 --- *These contributing guidelines...(UNLIKELY_OPENING_PUNCTUATION)
📜 Review details
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Review profile: CHILL
📒 Files selected for processing (8)
.github/CODE_OF_CONDUCT.md(1 hunks).github/CONTRIBUTING.md(1 hunks).github/ISSUE_TEMPLATE/bug.yaml(1 hunks).github/ISSUE_TEMPLATE/config.yaml(1 hunks).github/ISSUE_TEMPLATE/docs.yaml(1 hunks).github/ISSUE_TEMPLATE/feature.yaml(1 hunks).github/PULL_REQUEST_TEMPLATE.md(1 hunks).github/SECURITY.md(1 hunks)
✅ Files skipped from review due to trivial changes (1)
- .github/ISSUE_TEMPLATE/config.yaml
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.github/CODE_OF_CONDUCT.md
[style] ~32-~32: Try using a synonym here to strengthen your wording.
Context: ...ind * Trolling, insulting or derogatory comments, and personal or political attacks * Pu...
(COMMENT_REMARK)
[uncategorized] ~74-~74: You might be missing the article “the” here.
Context: ...rsion/2/1/code_of_conduct.html][v2.1]. Community Impact Guidelines were inspired by [Moz...
(AI_EN_LECTOR_MISSING_DETERMINER_THE)
.github/CONTRIBUTING.md
[grammar] ~9-~9: The verb ‘Help’ is used with an infinitive.
Context: ...etting Help](#thinking-getting-help) - Reporting Issues ...
(ADVISE_VBG)
[uncategorized] ~20-~20: Loose punctuation mark.
Context: ...pace for everyone to participate.** ## ⚖️ Our Standards Please rev...
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[uncategorized] ~28-~28: Loose punctuation mark.
Context: ...s, not questions or debugging help. ## 🐞 Reporting Issues Before [c...
(UNLIKELY_OPENING_PUNCTUATION)
[style] ~69-~69: The word ‘big’ tends to be overused. Consider an alternative.
Context: ... small.** One change per PR - Discuss big changes first - Write clear code over cle...
(BIG_DIFFERENCE)
[uncategorized] ~122-~122: Use a comma before ‘and’ if it connects two independent clauses (unless they are closely connected and short).
Context: ... Your contribution is your original work and you have the right to submit it under t...
(COMMA_COMPOUND_SENTENCE)
[uncategorized] ~123-~123: If this is a compound adjective that modifies the following noun, use a hyphen.
Context: ...d on previous work under an appropriate open source license > 3. The contribution was provi...
(EN_COMPOUND_ADJECTIVE_INTERNAL)
[style] ~129-~129: Consider using a more formal and expressive alternative to ‘awesome’.
Context: ...f your pull requests and issues. You're awesome! 💯 --- *These contributing guideli...
(AWESOME)
[style] ~129-~129: Using many exclamation marks might seem excessive (in this case: 7 exclamation marks for a text that’s 3892 characters long)
Context: ...pull requests and issues. You're awesome! 💯 --- *These contributing guidelin...
(EN_EXCESSIVE_EXCLAMATION)
[uncategorized] ~129-~129: Loose punctuation mark.
Context: ...ll requests and issues. You're awesome! 💯 --- *These contributing guidelines...
(UNLIKELY_OPENING_PUNCTUATION)
.github/PULL_REQUEST_TEMPLATE.md
[style] ~11-~11: Consider using a different verb for a more formal wording.
Context: ...- [ ] Bug fix (non-breaking change that fixes an issue) - [ ] New feature (non-breaki...
(FIX_RESOLVE)
.github/SECURITY.md
[uncategorized] ~4-~4: A comma may be missing after the conjunctive/linking adverb ‘Currently’.
Context: ...Security Policy ## Supported Versions Currently supported versions of Pkynetics with se...
(SENT_START_CONJUNCTIVE_LINKING_ADVERB_COMMA)
[typographical] ~20-~20: Consider wrapping this idiom with two commas if you want to put a strong emphasize on it.
Context: ...d receive a response within 48 hours. If for some reason you do not, please follow up via email ...
(FOR_WHATEVER_REASON_COMMA)
🪛 Markdownlint (0.35.0)
.github/CODE_OF_CONDUCT.md
63-63: null
Bare URL used
(MD034, no-bare-urls)
.github/CONTRIBUTING.md
5-5: Expected: h2; Actual: h3
Heading levels should only increment by one level at a time
(MD001, heading-increment)
118-118: null
Emphasis used instead of a heading
(MD036, no-emphasis-as-heading)
83-83: null
Fenced code blocks should have a language specified
(MD040, fenced-code-language)
.github/PULL_REQUEST_TEMPLATE.md
1-1: null
Bare URL used
(MD034, no-bare-urls)
🪛 yamllint (1.35.1)
.github/ISSUE_TEMPLATE/bug.yaml
[error] 71-71: trailing spaces
(trailing-spaces)
[error] 72-72: trailing spaces
(trailing-spaces)
[error] 73-73: trailing spaces
(trailing-spaces)
🔇 Additional comments (9)
.github/ISSUE_TEMPLATE/docs.yaml (3)
11-21: LGTM! Good use of required checkboxes
The checkboxes effectively ensure users acknowledge guidelines and check for duplicates.
22-36: LGTM! Well-structured dropdown with comprehensive options
The dropdown provides a good balance of specific categories while maintaining flexibility with the "Other" option.
46-71: LGTM! Well-structured textarea sections
The textarea sections are well organized with appropriate required/optional settings and clear descriptions.
.github/ISSUE_TEMPLATE/feature.yaml (2)
24-32: LGTM! Well-structured problem description section
The problem description section is clear, concise, and includes helpful placeholder text.
59-75: LGTM! Well-structured optional sections
The additional context and implementation sections are well-designed and appropriately marked as optional, allowing for flexible feature request submissions.
.github/ISSUE_TEMPLATE/bug.yaml (2)
1-4: LGTM! Well-structured metadata section.
The template metadata is properly configured with appropriate labels and title format.
93-109: LGTM! Well-structured optional sections.
The error and additional context sections are properly configured with appropriate rendering and optional status.
.github/CONTRIBUTING.md (2)
131-132: LGTM: Proper attribution included
The document properly credits the original author while maintaining transparency about its origins.
34-34: Verify referenced security policy file
The document references a SECURITY.md file. Let's ensure this file exists in the repository.
Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
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Actionable comments posted: 1
🧹 Outside diff range and nitpick comments (2)
.github/CONTRIBUTING.md (2)
5-6: Fix heading hierarchyThe "Contents" section uses an h3 heading (
###) before any h2 headings are used. This breaks the document hierarchy.-### Contents +## Contents🧰 Tools
🪛 Markdownlint (0.35.0)
5-5: Expected: h2; Actual: h3
Heading levels should only increment by one level at a time(MD001, heading-increment)
127-130: Clarify token placement instructionsConsider specifying exactly where in the PR/issue the lightning emoji should be placed (e.g., at the start of the title, description, or first comment).
-If you've read these guidelines (thank you!), include the ⚡ lightning emoji at the start of your pull requests and issues. You're awesome! :100: +If you've read these guidelines (thank you!), include the ⚡ lightning emoji at the start of your pull request or issue title. You're awesome! :100:🧰 Tools
🪛 LanguageTool
[style] ~129-~129: Consider using a more formal and expressive alternative to ‘awesome’.
Context: ...f your pull requests and issues. You're awesome! 💯 --- *These contributing guideli...(AWESOME)
[style] ~129-~129: Using many exclamation marks might seem excessive (in this case: 7 exclamation marks for a text that’s 3892 characters long)
Context: ...pull requests and issues. You're awesome! 💯 --- *These contributing guidelin...(EN_EXCESSIVE_EXCLAMATION)
[uncategorized] ~129-~129: Loose punctuation mark.
Context: ...ll requests and issues. You're awesome! 💯 --- *These contributing guidelines...(UNLIKELY_OPENING_PUNCTUATION)
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (1)
.github/CONTRIBUTING.md(1 hunks)
🧰 Additional context used
🪛 LanguageTool
.github/CONTRIBUTING.md
[grammar] ~9-~9: The verb ‘Help’ is used with an infinitive.
Context: ...etting Help](#thinking-getting-help) - Reporting Issues ...
(ADVISE_VBG)
[uncategorized] ~20-~20: Loose punctuation mark.
Context: ...pace for everyone to participate.** ## ⚖️ Our Standards Please rev...
(UNLIKELY_OPENING_PUNCTUATION)
[uncategorized] ~28-~28: Loose punctuation mark.
Context: ...s, not questions or debugging help. ## 🐞 Reporting Issues Before [c...
(UNLIKELY_OPENING_PUNCTUATION)
[style] ~69-~69: The word ‘big’ tends to be overused. Consider an alternative.
Context: ... small.** One change per PR - Discuss big changes first - Write clear code over cle...
(BIG_DIFFERENCE)
[uncategorized] ~122-~122: Use a comma before ‘and’ if it connects two independent clauses (unless they are closely connected and short).
Context: ... Your contribution is your original work and you have the right to submit it under t...
(COMMA_COMPOUND_SENTENCE)
[uncategorized] ~123-~123: If this is a compound adjective that modifies the following noun, use a hyphen.
Context: ...d on previous work under an appropriate open source license > 3. The contribution was provi...
(EN_COMPOUND_ADJECTIVE_INTERNAL)
[style] ~129-~129: Consider using a more formal and expressive alternative to ‘awesome’.
Context: ...f your pull requests and issues. You're awesome! 💯 --- *These contributing guideli...
(AWESOME)
[style] ~129-~129: Using many exclamation marks might seem excessive (in this case: 7 exclamation marks for a text that’s 3892 characters long)
Context: ...pull requests and issues. You're awesome! 💯 --- *These contributing guidelin...
(EN_EXCESSIVE_EXCLAMATION)
[uncategorized] ~129-~129: Loose punctuation mark.
Context: ...ll requests and issues. You're awesome! 💯 --- *These contributing guidelines...
(UNLIKELY_OPENING_PUNCTUATION)
🪛 Markdownlint (0.35.0)
.github/CONTRIBUTING.md
5-5: Expected: h2; Actual: h3
Heading levels should only increment by one level at a time
(MD001, heading-increment)
118-118: null
Emphasis used instead of a heading
(MD036, no-emphasis-as-heading)
83-83: null
Fenced code blocks should have a language specified
(MD040, fenced-code-language)
🔇 Additional comments (4)
.github/CONTRIBUTING.md (4)
111-114: Development tools configuration needs to be updated
83-97: LGTM! Well-structured commit message template
The commit message template provides clear guidance with practical examples.
🧰 Tools
🪛 Markdownlint (0.35.0)
83-83: null
Fenced code blocks should have a language specified
(MD040, fenced-code-language)
116-126: LGTM! Clear developer certification
The Developer's Certificate of Origin is well-presented and includes all necessary points.
🧰 Tools
🪛 LanguageTool
[uncategorized] ~122-~122: Use a comma before ‘and’ if it connects two independent clauses (unless they are closely connected and short).
Context: ... Your contribution is your original work and you have the right to submit it under t...
(COMMA_COMPOUND_SENTENCE)
[uncategorized] ~123-~123: If this is a compound adjective that modifies the following noun, use a hyphen.
Context: ...d on previous work under an appropriate open source license > 3. The contribution was provi...
(EN_COMPOUND_ADJECTIVE_INTERNAL)
🪛 Markdownlint (0.35.0)
118-118: null
Emphasis used instead of a heading
(MD036, no-emphasis-as-heading)
22-22: Verify referenced document links
The document references several important files. Let's ensure they exist and are accessible.
Also applies to: 26-26, 34-34
✅ Verification successful
All referenced documents are present and accessible
The verification confirms that both CODE_OF_CONDUCT.md and SECURITY.md files exist in the repository. Additionally, documentation configuration is present via docs/conf.py. The links in the contributing guidelines are valid and point to existing resources.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Check for referenced documents
echo "Checking for referenced documents..."
files=("CODE_OF_CONDUCT.md" "SECURITY.md")
for file in "${files[@]}"; do
if [ -f ".github/$file" ] || [ -f "$file" ]; then
echo "✓ Found: $file"
else
echo "✗ Missing: $file"
fi
done
# Verify documentation URL
echo -e "\nChecking for documentation configuration..."
fd -t f "mkdocs.yml|conf.py|_config.yml" docs/
Length of output: 537
Updated relative path to CONTRIBUTING.md in issue templates to use proper GitHub URL
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (5)
.github/ISSUE_TEMPLATE/feature.yaml (3)
9-10: Clarify emoji placement instructionThe instruction about the emoji could be more specific about its placement.
- Please include the ⚡ emoji at the start of your title if you've read our contributing guidelines. + Please include the ⚡ emoji at the start of your title (before "[Feature]") if you've read our contributing guidelines.
24-32: Consider adding character limitsTo encourage concise descriptions, consider adding character limits to the textarea.
validations: required: true + maxLength: 2000
41-46: Make code example more genericThe example import statement assumes a specific package structure. Consider making it more generic to avoid confusion.
```python # Example usage of your proposed feature: - from pkynetics import model_fitting_methods + # Import statement (adjust based on your use case): + # from pkynetics import ... # Your proposed code here ```.github/ISSUE_TEMPLATE/bug.yaml (2)
22-48: Consider enhancing version field descriptions.While the input fields are well-structured, consider the following improvements:
- Specify the minimum supported Python version in the description
- Add version format requirements for Pkynetics (e.g., semantic versioning)
description: What version of Pkynetics are you using? - placeholder: "0.2.3" + placeholder: "x.y.z (e.g., 0.2.3)" description: Which Python version(s) have you tested with? - placeholder: "Python 3.9, 3.10, 3.11" + placeholder: "Python 3.9, 3.10, 3.11 (minimum supported: 3.9)"
58-76: Fix trailing spaces in the numbered list.The numbered list in the reproduction steps contains trailing spaces that should be removed.
``` - 1. - 2. - 3. + 1. + 2. + 3.🧰 Tools
🪛 yamllint (1.35.1)
[error] 71-71: trailing spaces
(trailing-spaces)
[error] 72-72: trailing spaces
(trailing-spaces)
[error] 73-73: trailing spaces
(trailing-spaces)
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (3)
.github/ISSUE_TEMPLATE/bug.yaml(1 hunks).github/ISSUE_TEMPLATE/docs.yaml(1 hunks).github/ISSUE_TEMPLATE/feature.yaml(1 hunks)
🚧 Files skipped from review as they are similar to previous changes (1)
- .github/ISSUE_TEMPLATE/docs.yaml
🧰 Additional context used
🪛 yamllint (1.35.1)
.github/ISSUE_TEMPLATE/bug.yaml
[error] 71-71: trailing spaces
(trailing-spaces)
[error] 72-72: trailing spaces
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[error] 73-73: trailing spaces
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🔇 Additional comments (7)
.github/ISSUE_TEMPLATE/feature.yaml (3)
11-23: LGTM! Well-structured guidelines section
The checkboxes effectively ensure users acknowledge key requirements and expectations.
50-58: LGTM! Well-structured alternatives section
Making this section required helps ensure thorough feature proposals.
59-75: LGTM! Good optional sections
The optional sections for additional context and implementation details are well-structured and provide valuable flexibility for contributors.
.github/ISSUE_TEMPLATE/bug.yaml (4)
1-4: LGTM! Well-structured template metadata.
The template metadata is properly configured with appropriate name, description, title prefix, and labels for bug tracking.
8-10: Skip duplicate comment about contributing guidelines link.
A previous review has already addressed this issue.
11-21: LGTM! Well-structured guidelines section.
The checkboxes effectively ensure users acknowledge guidelines and perform due diligence before submitting.
49-109: LGTM! Well-structured bug report sections.
The template provides a comprehensive structure for bug reporting with:
- Clear description field
- Reproduction steps with code example
- Expected vs actual behavior
- Optional error messages and additional context
🧰 Tools
🪛 yamllint (1.35.1)
[error] 71-71: trailing spaces
(trailing-spaces)
[error] 72-72: trailing spaces
(trailing-spaces)
[error] 73-73: trailing spaces
(trailing-spaces)
- Move package to src-layout - Add pyproject.toml with modern build configuration - Add version information in __about__.py - Restructure modules into organized hierarchy
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Actionable comments posted: 3
🧹 Outside diff range and nitpick comments (4)
src/pkynetics/__init__.py (1)
__all__list contains modules and functions that are not properly imported or exposedThe verification reveals several issues with the
__all__list:
Several modules listed in
__all__are neither imported nor exist as standalone files:
data_preprocessingadvanced_methodsmachine_learning_methodsstatistical_analysisparallel_processingutility_functions
smooth_datais defined inmodel_fitting_methods.freeman_carrollbut not properly imported and exposed in__init__.pyTo fix this:
- Remove non-existent modules from
__all__- Import
smooth_datafrommodel_fitting_methods.freeman_carrollif it should be exposed- Or create the missing modules if they are intended to be part of the package
🔗 Analysis chain
Line range hint
14-29: Verify completeness of imports against__all__listThe
__all__list includes several modules that aren't imported in this file:
- data_preprocessing
- advanced_methods
- machine_learning_methods
- statistical_analysis
- parallel_processing
- utility_functions
- smooth_data
Let's verify if these modules exist in the package:
Let me verify the imports in the file to complete the analysis.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Check for the existence of modules listed in __all__ for module in "data_preprocessing" "advanced_methods" "machine_learning_methods" "statistical_analysis" "parallel_processing" "utility_functions"; do echo "Checking for $module..." fd -t f "^${module}.py$" done # Check if smooth_data is defined in any of the imported modules rg "def smooth_data" -t pyLength of output: 1773
Script:
#!/bin/bash # Check imports in __init__.py cat src/pkynetics/__init__.py # Check for potential submodules fd -t d . src/pkynetics/Length of output: 1147
pyproject.toml (3)
1-3: Consider pinning the hatchling versionTo ensure build reproducibility across different environments, consider specifying a version for hatchling.
[build-system] -requires = ["hatchling"] +requires = ["hatchling~=1.18.0"] build-backend = "hatchling.build"
43-52: Enhance development dependenciesConsider adding more development tools and using stricter version constraints:
dev = [ - "pytest>=6.2.0", - "pytest-cov>=4.1.0", - "black>=23.0.0", - "isort>=5.0.0", - "mypy>=1.0.0", - "sphinx>=4.0.0", - "sphinx-rtd-theme>=1.0.0", + "pytest~=7.4.0", + "pytest-cov~=4.1.0", + "black~=23.9.0", + "isort~=5.12.0", + "mypy~=1.5.0", + "sphinx~=7.2.0", + "sphinx-rtd-theme~=1.3.0", + "ruff~=0.0.291", # Fast Python linter + "pre-commit~=3.4.0", # Git hooks manager + "pip-audit~=2.6.1", # Dependency security checker ]
97-100: Consider enhancing pytest configurationThe current configuration is good, but consider adding these useful pytest options:
[tool.pytest.ini_options] -addopts = "--cov=pkynetics --cov-report=term --cov-report=xml" +addopts = """ + --cov=pkynetics + --cov-report=term + --cov-report=xml + --cov-report=html + --cov-fail-under=80 + -v + --durations=10 + """ testpaths = ["tests"] python_files = "test_*.py"
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Configuration used: CodeRabbit UI
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⛔ Files ignored due to path filters (2)
src/pkynetics/data/sample_dsc_data.csvis excluded by!**/*.csvsrc/pkynetics/data/sample_tga_data.csvis excluded by!**/*.csv
📒 Files selected for processing (26)
examples/coats_redfern_method_example.py(1 hunks)examples/custom_importer_example.py(1 hunks)examples/freeman_carroll_method_example.py(1 hunks)examples/friedman_method_example.py(1 hunks)examples/horowitz_metzger_method_example.py(1 hunks)examples/importer_examples.py(1 hunks)examples/jmak_method_example.py(1 hunks)examples/kas_method_example.py(1 hunks)examples/kissinger_method_example.py(1 hunks)examples/ofw_method_example.py(1 hunks)examples/synthetic_data_example.py(1 hunks)pyproject.toml(1 hunks)setup.py(0 hunks)src/pkynetics/__about__.py(1 hunks)src/pkynetics/__init__.py(1 hunks)src/pkynetics/result_visualization/kinetic_plot.py(1 hunks)src/pkynetics/result_visualization/model_specific_plots.py(0 hunks)tests/test_custom_importer.py(1 hunks)tests/test_freeman_carroll_method.py(1 hunks)tests/test_friedman_method.py(1 hunks)tests/test_horowitz_metzger_method.py(1 hunks)tests/test_importers.py(1 hunks)tests/test_jmak_method.py(1 hunks)tests/test_kas_method.py(1 hunks)tests/test_kissinger_method.py(1 hunks)tests/test_ofw_method.py(1 hunks)
💤 Files with no reviewable changes (2)
- setup.py
- src/pkynetics/result_visualization/model_specific_plots.py
✅ Files skipped from review due to trivial changes (20)
- examples/coats_redfern_method_example.py
- examples/custom_importer_example.py
- examples/freeman_carroll_method_example.py
- examples/friedman_method_example.py
- examples/horowitz_metzger_method_example.py
- examples/jmak_method_example.py
- examples/kas_method_example.py
- examples/ofw_method_example.py
- examples/synthetic_data_example.py
- src/pkynetics/about.py
- src/pkynetics/result_visualization/kinetic_plot.py
- tests/test_custom_importer.py
- tests/test_freeman_carroll_method.py
- tests/test_friedman_method.py
- tests/test_horowitz_metzger_method.py
- tests/test_importers.py
- tests/test_jmak_method.py
- tests/test_kas_method.py
- tests/test_kissinger_method.py
- tests/test_ofw_method.py
🔇 Additional comments (6)
src/pkynetics/__init__.py (1)
9-9:
Reconsider the use of src. prefix in import statements
The current absolute imports using the src. prefix might cause issues:
- This pattern typically indicates the package is being imported from outside its installed location
- It could break when the package is installed via pip, as
srcwon't be in the Python path
Consider one of these alternatives:
-from src.pkynetics import data_import, model_fitting_methods, model_free_methods, result_visualization
-from src.pkynetics.data_import import tga_importer, dsc_importer
-from src.pkynetics.model_fitting_methods import kissinger_methodOption 1 (Recommended) - Use relative imports:
+from . import data_import, model_fitting_methods, model_free_methods, result_visualization
+from .data_import import tga_importer, dsc_importer
+from .model_fitting_methods import kissinger_methodOption 2 - Use absolute imports without 'src':
+from pkynetics import data_import, model_fitting_methods, model_free_methods, result_visualization
+from pkynetics.data_import import tga_importer, dsc_importer
+from pkynetics.model_fitting_methods import kissinger_methodLet's verify the package structure and installation:
Also applies to: 11-12
examples/importer_examples.py (2)
4-4: Question: Is this change related to the PR objectives?
While the import path change appears to be a good structural improvement, it seems unrelated to the PR's stated objective of adding GitHub templates and community files. Consider:
- Moving this change to a separate PR focused on code organization
- Updating the PR description to include these structural changes
4-4: Verify the new import path structure across the project
The import path has been updated to use the full package path src.pkynetics.data_import. Let's verify this change is consistent across the project.
✅ Verification successful
Let me verify the package structure further to ensure the import path changes are valid.
Let me check one final thing to verify the location of these importers.
Import path changes are correctly structured and consistent
The import path changes reflect the proper package structure:
- The package has a correct hierarchical structure with proper
__init__.pyfiles - Both
tga_importeranddsc_importerfunctions exist in their respective modules undersrc/pkynetics/data_import/ - The new import pattern is consistently used across example files and main package imports
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Check for any remaining old import paths and verify the new structure
# Check for any remaining old imports
echo "Checking for old import paths..."
rg "from data_import import" -l
# Verify the new import structure exists
echo "Verifying new package structure..."
fd -t f "data_import.py" src/pkynetics/
# Check for consistency in other example files
echo "Checking other example files..."
rg "from src\.pkynetics\.data_import import" examples/
Length of output: 541
Script:
#!/bin/bash
# Check if the package structure is properly set up
echo "Checking package structure..."
fd -t f "__init__.py" src/pkynetics/
# Check the content of data_import.py to verify the imported functions exist
echo "Searching for imported functions in the codebase..."
ast-grep --pattern 'def tga_importer($$$)'
ast-grep --pattern 'def dsc_importer($$$)'
# Check if there are any other import patterns that might need updating
echo "Checking for other import patterns..."
rg "import.*data_import" -g "!examples/*"
Length of output: 811
Script:
#!/bin/bash
# Check the content of data_import directory for the importers
echo "Checking data_import directory contents..."
fd . src/pkynetics/data_import/
# Look for importer definitions in data_import directory
echo "Searching for importer definitions..."
rg "def (tga_importer|dsc_importer)" src/pkynetics/data_import/
Length of output: 704
examples/kissinger_method_example.py (2)
Line range hint 1-70: Excellent example implementation!
While not part of the changes, it's worth noting that this example file demonstrates excellent practices:
- Clear structure and documentation
- Proper error analysis and confidence intervals
- Reproducible results with fixed random seed
- Informative visualization with results overlay
3-3: LGTM! Import path updated to reflect new package structure.
The import statement has been updated to use the new module structure under src.pkynetics, which improves the project's organization.
Let's verify the consistency of import paths across other example files:
✅ Verification successful
Import paths are consistently updated across all example files
The verification shows that all example files in the codebase have been properly updated to use the new import structure src.pkynetics.model_fitting_methods. No instances of the old import pattern model_fitting_methods were found, confirming the changes are consistent.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Check if all example files use the new import structure consistently
# Search for any remaining old import patterns in example files
echo "Checking for old import patterns:"
rg "from model_fitting_methods\." "examples/"
# Verify new import pattern usage
echo -e "\nVerifying new import pattern usage:"
rg "from src\.pkynetics\.model_fitting_methods" "examples/"
Length of output: 889
pyproject.toml (1)
70-95: LGTM! Excellent code quality tool configuration
The configuration demonstrates best practices:
- Black and isort settings are aligned (same line length, black profile)
- Strict mypy settings for better type safety
- Appropriate overrides for third-party packages
| [project.urls] | ||
| Homepage = "https://github.com/PPeitsch/pkynetics" | ||
| Documentation = "https://pkynetics.readthedocs.io/" | ||
| Repository = "https://github.com/PPeitsch/pkynetics.git" | ||
| "Bug Tracker" = "https://github.com/PPeitsch/pkynetics/issues" | ||
| Changelog = "https://github.com/PPeitsch/pkynetics/blob/main/CHANGELOG.md" |
There was a problem hiding this comment.
💡 Codebase verification
Update changelog URL to point to the correct file
The changelog is located at docs/changelog.rst, not at CHANGELOG.md. While all other URLs are valid and accessible, and main is confirmed as the default branch, the changelog URL needs to be updated to:
Changelog = "https://github.com/PPeitsch/pkynetics/blob/main/docs/changelog.rst"
🔗 Analysis chain
Verify URL accessibility and branch references
Please verify:
- The documentation URL is active or will be set up
- The changelog path exists in the repository
- The main branch is indeed the default branch (not master)
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Check if URLs are accessible and valid
for url in \
"https://github.com/PPeitsch/pkynetics" \
"https://pkynetics.readthedocs.io/" \
"https://github.com/PPeitsch/pkynetics.git" \
"https://github.com/PPeitsch/pkynetics/blob/main/CHANGELOG.md"; do
echo "Checking $url..."
curl -sL -w "%{http_code}\n" "$url" -o /dev/null
done
# Check default branch
gh api repos/PPeitsch/pkynetics | jq .default_branch
Length of output: 1694
Script:
#!/bin/bash
# Let's check if CHANGELOG.md exists in the repository, possibly with a different case
fd -i changelog.md
# Also check if there's any changelog file with a different extension
fd -i changelog
Length of output: 57
| [tool.hatch.version] | ||
| path = "src/pkynetics/__about__.py" | ||
|
|
||
| [tool.hatch.build.hooks.version] | ||
| path = "src/pkynetics/_version.py" | ||
|
|
||
| [tool.hatch.build.targets.wheel] | ||
| packages = ["src/pkynetics"] |
There was a problem hiding this comment.
💡 Codebase verification
Update version file configuration in pyproject.toml
The configuration needs adjustment:
__about__.pyexists and is correctly configured_version.pyis missing but configured as a build hook path- Package structure is properly defined with all necessary modules included in the wheel build
Recommendations:
- Remove or update the
[tool.hatch.build.hooks.version]section as_version.pydoesn't exist - Current wheel package configuration correctly includes all modules
🔗 Analysis chain
Verify package paths and version files
Please ensure that:
- The version file paths exist in the project structure
- All necessary packages are included in the wheel build
The first verification showed that __about__.py exists but didn't show _version.py. Let's verify if _version.py exists and check the Python modules structure to ensure all packages are properly included in the wheel build configuration.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Check if version files exist
fd -t f "__about__.py|_version.py" src/pkynetics
# Check package structure
fd -t d . src/pkynetics
Length of output: 287
Script:
#!/bin/bash
# Check if _version.py exists (it might be generated during build)
ls -la src/pkynetics/_version.py 2>/dev/null || echo "File not found: _version.py"
# Check for Python modules in the directories
fd -e py -t f . src/pkynetics/
Length of output: 1198
| dependencies = [ | ||
| "numpy~=1.24.3", | ||
| "matplotlib~=3.7.5", | ||
| "pandas~=2.0.3", | ||
| "scipy~=1.10.1", | ||
| "statsmodels~=0.14.1", | ||
| "scikit-learn>=0.24.0", | ||
| "seaborn>=0.11.0", | ||
| ] |
There was a problem hiding this comment.
💡 Codebase verification
🛠️ Refactor suggestion
Update dependencies to address security vulnerabilities and maintain consistency
Several critical security and version concerns require attention:
-
scikit-learn (current: >=0.24.0):
- Has critical vulnerability in <=0.23.0
- Has high severity DoS in >=0.23.2, <1.0.1
- Has moderate data leakage in <1.5.0
- Latest version is 1.5.2
-
scipy (current: ~=1.10.1):
- Has withdrawn vulnerabilities patched in 1.8.0 and 1.10.0
- Latest version is 1.14.1
-
numpy (current: ~=1.24.3):
- All known vulnerabilities are patched in current version
- Latest version is 2.1.3
Recommended updates:
dependencies = [
- "numpy~=1.24.3",
- "matplotlib~=3.7.5",
- "pandas~=2.0.3",
- "scipy~=1.10.1",
- "statsmodels~=0.14.1",
- "scikit-learn>=0.24.0",
- "seaborn>=0.11.0",
+ "numpy~=2.1.3",
+ "matplotlib~=3.9.2",
+ "pandas~=2.2.3",
+ "scipy~=1.14.1",
+ "statsmodels~=0.14.4",
+ "scikit-learn~=1.5.2",
+ "seaborn~=0.13.2",
]🔗 Analysis chain
Review dependency versions for security and compatibility
There are several concerns with the current dependency specifications:
- Inconsistent version pinning strategy (mix of ~= and >=)
- Some dependencies are using older versions that might have security vulnerabilities
- scikit-learn and seaborn versions are quite old
Consider updating to more recent versions and using consistent version pinning:
dependencies = [
- "numpy~=1.24.3",
- "matplotlib~=3.7.5",
- "pandas~=2.0.3",
- "scipy~=1.10.1",
- "statsmodels~=0.14.1",
- "scikit-learn>=0.24.0",
- "seaborn>=0.11.0",
+ "numpy~=1.26.0",
+ "matplotlib~=3.8.0",
+ "pandas~=2.1.0",
+ "scipy~=1.11.0",
+ "statsmodels~=0.14.0",
+ "scikit-learn~=1.3.0",
+ "seaborn~=0.13.0",
]🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Check PyPI for latest versions and potential security advisories
for package in numpy matplotlib pandas scipy statsmodels scikit-learn seaborn; do
echo "Checking $package..."
curl -s "https://pypi.org/pypi/$package/json" | jq -r '.info.version'
# Check for security advisories
gh api graphql -f query="{
securityVulnerabilities(first: 5, ecosystem: PIP, package: \"$package\") {
nodes {
advisory {
summary
severity
publishedAt
}
vulnerableVersionRange
firstPatchedVersion {
identifier
}
}
}
}"
done
Length of output: 6242
Added:
All files have been customized for Pkynetics project requirements and contributing guidelines.
Summary by CodeRabbit
Release Notes
New Features
Documentation
pyproject.tomlfile for project metadata and dependencies.