Merge pull request #176 from ACCLAB/v2024.03.29

Merge v2024.03.29 into master branch

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,34 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: bug
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior:
+1.  
+2.  
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Your package version (please complete the following information):**
+ - dabest: [e.g. 2023.3.29]
+ - pandas: 
+ - numpy: 
+ - matplotlib:
+ - seaborn:
+ - scipy:
+
+
+**Additional context**
+Add any other context about the problem here.

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,23 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: enhancement
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Is a dataset available for testing out the functionality**
+If yes, please leave a Google Drive link 
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

.github/workflows/test.yaml → .github/workflows/test-nbdev.yaml

@@ -1,7 +1,7 @@
-name: CI
+name: nbdev_prepare
 on:  [workflow_dispatch, pull_request, push]
 
 jobs:
-  test:
+  test-nbdev:
     runs-on: ubuntu-latest
     steps: [uses: fastai/workflows/nbdev-ci@master]

.github/workflows/test-image.yaml → .github/workflows/test-pytest.yaml

@@ -2,17 +2,17 @@ name: Python pytest
 on: [workflow_dispatch, pull_request, push] 
 
 jobs:
-  test:
+  test-pytest:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v3
       - uses: actions/setup-python@v4
         with:
-          python-version: 3.9
+          python-version: 3.8
           cache: "pip"
           cache-dependency-path: settings.ini
       - name: Run pytest
         run: |
           python -m pip install --upgrade pip
-          pip install .[dev]
-          pytest nbs/tests/
+          pip install -e '.[dev]'
+          pytest nbs/tests/ --mpl --mpl-baseline-path=nbs/tests/mpl_image_tests/baseline_images

CHANGELOG.md

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+# Release notes
+
+<!-- do not remove -->
+
+## v2024.03.29
+
+### New Features
+
+- **Standardized Delta-delta Effect Size**: We added a new metric akin to a Hedges’ g for delta-delta effect size, which allows comparisons between delta-delta effects generated from metrics with different units. 
+
+- **New Paired Proportion Plot**: This feature builds upon the existing proportional analysis capabilities by introducing advanced aesthetics and clearer visualization of changes in proportions between different groups, inspired by the informative nature of Sankey Diagrams. It's particularly useful for studies that require detailed examination of how proportions shift in paired observations.
+
+- **Customizable Swarm Plot**: Enhancements allow for tailored swarm plot aesthetics, notably the adjustment of swarm sides to produce asymmetric swarm plots. This customization enhances data representation, making visual distinctions more pronounced and interpretations clearer.
+
+### Enhancement
+
+- **Miscellaneous Improvements**: This version also encompasses a broad range of miscellaneous enhancements, including bug fixes, Bootstrapping speed improvements, new templates for raising issues, and updated unit tests. These improvements are designed to streamline the user experience, increase the software's stability, and expand its versatility. By addressing user feedback and identified issues, DABEST continues to refine its functionality and reliability.
+
+
+
+## v2023.03.29
+
+### New Features
+- **Repeated measures**: Augments the prior function for plotting (independent) multiple test groups versus a shared control; it can now do the same for repeated-measures experimental designs. Thus, together, these two methods can be used to replace both flavors of the 1-way ANOVA with an estimation analysis.
+
+- **Proportional data**: Generates proportional bar plots, proportional differences, and calculates Cohen’s h. Also enables plotting Sankey diagrams for paired binary data. This is the estimation equivalent to a bar chart with Fischer’s exact test.
+
+- **The ∆∆ plot**: Calculates the delta-delta (∆∆) for 2 × 2 experimental designs and plots the four groups with their relevant effect sizes. This design can be used as a replacement for the 2 × 2 ANOVA.
+
+- **Mini-meta**: Calculates and plots a weighted delta (∆) for meta-analysis of experimental replicates. Useful for summarizing data from multiple replicated experiments, for example by different scientists in the same lab, or the same scientist at different times. When the observed values are known (and share a common metric), this makes meta-analysis available as a routinely accessible tool.

CODE_OF_CONDUCT.md

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+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+In the interest of fostering an open and welcoming environment, we as
+contributors and maintainers pledge to making participation in our project and
+our community a harassment-free experience for everyone, regardless of age, body
+size, disability, ethnicity, sex characteristics, gender identity and expression,
+level of experience, education, socio-economic status, nationality, personal
+appearance, race, religion, or sexual identity and orientation.
+
+## Our Standards
+
+Examples of behavior that contributes to creating a positive environment
+include:
+
+* Using welcoming and inclusive language
+* Being respectful of differing viewpoints and experiences
+* Gracefully accepting constructive criticism
+* Focusing on what is best for the community
+* Showing empathy towards other community members
+
+Examples of unacceptable behavior by participants include:
+
+* The use of sexualized language or imagery and unwelcome sexual attention or
+ advances
+* Trolling, insulting/derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or electronic
+ address, without explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+ professional setting
+
+## Our Responsibilities
+
+Project maintainers are responsible for clarifying the standards of acceptable
+behavior and are expected to take appropriate and fair corrective action in
+response to any instances of unacceptable behavior.
+
+Project maintainers have the right and responsibility to remove, edit, or
+reject comments, commits, code, wiki edits, issues, and other contributions
+that are not aligned to this Code of Conduct, or to ban temporarily or
+permanently any contributor for other behaviors that they deem inappropriate,
+threatening, offensive, or harmful.
+
+## Scope
+
+This Code of Conduct applies both within project spaces and in public spaces
+when an individual is representing the project or its community. Examples of
+representing a project or community include using an official project e-mail
+address, posting via an official social media account, or acting as an appointed
+representative at an online or offline event. Representation of a project may be
+further defined and clarified by project maintainers.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported by contacting the project team at joseshowh@gmail.com. All
+complaints will be reviewed and investigated and will result in a response that
+is deemed necessary and appropriate to the circumstances. The project team is
+obligated to maintain confidentiality with regard to the reporter of an incident.
+Further details of specific enforcement policies may be posted separately.
+
+Project maintainers who do not follow or enforce the Code of Conduct in good
+faith may face temporary or permanent repercussions as determined by other
+members of the project's leadership.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4,
+available at https://www.contributor-covenant.org/version/1/4/code-of-conduct.html
+
+[homepage]: https://www.contributor-covenant.org
+
+For answers to common questions about this code of conduct, see
+https://www.contributor-covenant.org/faq

CONTRIBUTING.md

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+# Contributing to DABEST-Python
+
+
+## Did you find a bug?
+- Ensure the bug was not already reported by searching in [Issues](https://github.com/ACCLAB/DABEST-python/issues). Check that the bug hasn't been addressed in a closed issue.
+
+- If the bug isn't being addressed, open a new issue using the Bug report template. Be sure to fill in the necessary information, and a [minimally reproducible code sample](https://matthewrocklin.com/blog/work/2018/02/28/minimal-bug-reports) demonstrating the expected behavior that is not occurring. 
+
+
+## Did you write a patch that fixes a bug?
+- Open a new GitHub [pull request](https://help.github.com/en/articles/about-pull-requests) (PR for short) with the patch.
+
+- Create the PR into the development branch, which is indicated by `v{latest version number}-dev`.
+
+- Clearly state the problem and solution in the PR description. Include the relevant [issue number](https://guides.github.com/features/issues/) if applicable.
+
+
+## Do you intend to add a new feature or change an existing one?
+- Suggest your change by opening an issue using the Feature request template.
+- If the maintainers and the community are in favour, create a fork and start writing code.
+
+
+DABEST is a community tool for estimation statistics and analysis. We look forward to more robust and more elegant data visualizations from you all!