Prepare the 0.1.0b1 release of kalelinear

.github/CHANGELOG.md

@@ -1,3 +1,33 @@
+# Version 0.1.0b1
+
+#### New Features
+
+* MPCA updated to a new version more compatible with NumPy/scikit-learn workflows, with a memory-efficient implementation and a new `MPCATrainer` pipeline.
+* Added `embed` and `predict` modules to the Kale API.
+* Added a group-specific discriminant analysis (GSDA) example for brain lateralization analysis.
+* Added Sphinx documentation and ReadTheDocs configuration.
+* Added detailed contributing guidelines, a code of conduct, and issue and pull request templates.
+
+#### Code Improvements
+
+* Refactored estimators (ARL, CoIR, manifold learning, GSDA) with a unified base class, consistent variable naming, and improved docstrings.
+* Removed the PyTorch dependency; core methods now run on NumPy only.
+* Updated `setup.py` for default, extras (`full`), and development (`dev`) installation options.
+
+#### Bug Fixes
+
+* Fixed optimization issues in the shared estimator and transformer base classes: the QP Hessian is projected onto the positive-semidefinite cone and generalized eigenproblems are regularized, so solvers such as `osqp` and `scipy` no longer fail on semidefinite inputs.
+
+#### Documentation
+
+* Updated the README, tutorials, and API documentation for the `kalelinear` package.
+
+#### Tests
+
+* Set up the test file structure and strategy.
+* Added tests for the public API, MPCA and `MPCATrainer`, estimators, transformers, and utilities.
+* Added Codecov coverage reporting to the test workflow.
+
 # Version  0.1.0a1
 
 #### New Features

.github/ISSUE_TEMPLATE/bug-report.md

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+---
+name: "\U0001F41B Bug report"
+about: Create a report to help us improve kalelinear
+title: "[Bug]"
+labels: bug
+assignees: ''
+
+---
+
+# Bug
+
+<!-- A clear and concise description of what the bug is. -->
+
+## To reproduce
+
+Steps to reproduce the behavior:
+
+1.
+2.
+3.
+
+Or, code snippet to reproduce the behavior
+
+```python
+# Your code goes here
+# Please make sure it does not require any external dependencies (other than those required by kalelinear!)
+# (We much prefer small snippets rather than links to existing libraries!)
+```
+
+**Stack trace/error message**
+
+```bash
+// Paste the bad output here!
+```
+
+## Expected behavior
+
+<!-- A clear and concise description of what you expected to happen. -->
+
+## Environment
+
+Please fill in the checklist below:
+
+- OS (e.g., Linux):
+- Python version:
+- How you installed kalelinear (`pip`, source):
+- Package versions (e.g., `numpy`, `scipy`, `scikit-learn`, `pandas`, `tensorly`, `cvxopt`, `osqp`):
+- Any other relevant information:
+
+## Additional context
+
+Add any other context about the problem here.

.github/ISSUE_TEMPLATE/documentation.md

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+---
+name: "\U0001F4DA Documentation"
+about: Report an issue related to the kalelinear documentation
+title: "[Docs]"
+labels: documentation
+assignees: ''
+
+---
+
+# Documentation
+
+**Is there documentation missing?**
+<!-- Let us know what modules have missing or incomplete documentation -->
+
+**Is documentation wrong?**
+<!-- Let us know if you find a mistake in the documentation! -->
+
+**Is there a feature that needs some example code?**
+<!-- Let us know if we are missing any example notebooks -->
+
+**Think you know how to fix the docs?** (If so, we would love a pull request from you!)
+
+- Link to the [documentation source](https://github.com/pykale/linear/tree/main/docs/source)

.github/ISSUE_TEMPLATE/feature-request.md

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+---
+name: "\U0001F680 Feature request"
+about: Submit a proposal/request for a new kalelinear feature
+title: "[Feature Request]"
+labels: enhancement
+assignees: ''
+
+---
+
+# 🚀 Feature Request
+
+<!-- A clear and concise description of the feature proposal -->
+
+## Motivation
+
+**Is your feature request related to a problem? Please describe.**
+<!-- A clear and concise description of what the problem is, e.g. I'm always frustrated when [...] -->
+<!-- Please link to any relevant issues or other PRs! -->
+
+## Pitch
+
+**Describe the solution you would like**
+<!-- A clear and concise description of what you want to happen. -->
+
+**Describe alternatives you have considered**
+<!-- A clear and concise description of any alternative solutions or features you have considered. -->
+
+**Are you willing to open a pull request?** (We LOVE contributions!!!)
+
+## Additional context
+
+<!-- Add any other context or screenshots about the feature request here. -->

.github/ISSUE_TEMPLATE/refactor.md

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+---
+name: "\U0001F527 Refactor"
+about: Propose a refactor/speedup/improvement to kalelinear's internals
+title: "[Refactor]"
+labels: refactor
+assignees: ''
+
+---
+
+<!-- A clear and concise description of what you wish to refactor. Please include the following: -->
+
+- <!-- Modules that will be modified -->
+- <!-- Impact on code structure -->
+- <!-- Impact on speed -->
+- <!-- Will this be a breaking change? -->

.github/changelog-ci-config.json

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+{
+  "changelog_type": "pull_request",
+  "header_prefix": "Version",
+  "commit_changelog": true,
+  "comment_changelog": true,
+  "include_unlabeled_changes": true,
+  "unlabeled_group_title": "Other Changes",
+  "pull_request_title_regex": "(?i:release)",
+  "version_regex": "v?[0-9]+[.]+[0-9]+[.]+[0-9]+([ab][0-9]+)?",
+  "exclude_labels": ["dependabot", "bot", "ci"],
+  "group_config": [
+    {
+      "title": "New Features",
+      "labels": ["feature", "enhancement"]
+    },
+    {
+      "title": "Bug Fixes",
+      "labels": ["bug", "bugfix"]
+    },
+    {
+      "title": "Code Improvements",
+      "labels": ["improvements", "refactor", "refactoring"]
+    },
+    {
+      "title": "Documentation",
+      "labels": ["documentation", "docs", "doc"]
+    },
+    {
+      "title": "Tests",
+      "labels": ["tests", "testing", "test"]
+    }
+  ]
+}

.github/pull_request_template.md

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+Fixes #<issue_number>.
+
+### Description
+
+A few sentences describing the changes proposed in this pull request.
+
+### Status
+
+**Ready/Work in progress/Hold**
+
+On the right (delete these after selection):
+
+- Select a reviewer if ready for review. Use the suggested one if unsure.
+- Select at least one appropriate label.
+- Select a project (the next version typically).
+
+### Types of changes
+<!--- Put an `x` in all the boxes that apply, and remove the not applicable items -->
+- [ ] Non-breaking change (fix or new feature that would not break existing functionality).
+- [ ] Breaking change (fix or new feature that would cause existing functionality to change).
+- [ ] New tests added to cover the changes.
+- [ ] In-line docstrings updated and documentation `docs` updated.

.gitignore

@@ -13,6 +13,7 @@ venv/
 *.zip
 *.ckpt
 *.json
+!.github/changelog-ci-config.json
 
 # Distribution / packaging
 build/

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 pykale-group@sheffield.ac.uk. 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