rework the workflow

.gitattributes

@@ -2,4 +2,3 @@
 
 # Auto detect text files and perform LF normalization
 * text=auto
-

.github/CODE_OF_CONDUCT.md

@@ -0,0 +1,58 @@
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We pledge to make our community welcoming, safe, and equitable for all.
+
+We are committed to fostering an environment that respects and promotes the dignity, rights, and contributions of all individuals, regardless of characteristics including race, ethnicity, caste, color, age, physical characteristics, neurodiversity, disability, sex or gender, gender identity or expression, sexual orientation, language, philosophy or religion, national or social origin, socio-economic position, level of education, or other status. The same privileges of participation are extended to everyone who participates in good faith and in accordance with this Covenant.
+
+## Encouraged Behaviors
+
+While acknowledging differences in social norms, we all strive to meet our community’s expectations for positive behavior. We also understand that our words and actions may be interpreted differently than we intend based on culture, background, or native language.
+
+With these considerations in mind, we agree to behave mindfully toward each other and act in ways that center our shared values, including:
+
+1. Respecting the **purpose of our community**, our activities, and our ways of gathering.
+2. Engaging **kindly and honestly** with others.
+3. Respecting **different viewpoints** and experiences.
+4. **Taking responsibility** for our actions and contributions.
+5. Gracefully giving and accepting **constructive feedback**.
+6. Committing to **repairing harm** when it occurs.
+7. Behaving in other ways that promote and sustain the **well-being of our community**.
+
+## Restricted Behaviors
+
+We agree to restrict the following behaviors in our community. Instances, threats, and promotion of these behaviors are violations of this Code of Conduct.
+
+1. **Harassment**. Violating explicitly expressed boundaries or engaging in unnecessary personal attention after any clear request to stop.
+2. **Character attacks**. Making insulting, demeaning, or pejorative comments directed at a community member or group of people.
+3. **Stereotyping or discrimination**. Characterizing anyone’s personality or behavior on the basis of immutable identities or traits.
+4. **Sexualization**. Behaving in a way that would generally be considered inappropriately intimate in the context or purpose of the community.
+5. **Violating confidentiality**. Sharing or acting on someone’s personal or private information without their permission.
+6. **Endangerment**. Causing, encouraging, or threatening violence or other harm toward any person or group.
+7. Behaving in other ways that **threaten the well-being** of our community.
+
+### Other Restrictions
+
+1. **Misleading identity**. Impersonating someone else for any reason, or pretending to be someone else to evade enforcement actions.
+2. **Failing to credit sources**. Not properly crediting the sources of content you contribute.
+3. **Promotional materials**. Sharing marketing or other commercial content in a way that is outside the norms of the community.
+4. **Irresponsible communication**. Failing to responsibly present content which includes, links or describes any other restricted behaviors.
+
+
+## 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.
+
+
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant](http://contributor-covenant.org), version 3.0, available at [https://www.contributor-covenant.org/version/3/0/code_of_conduct/](https://www.contributor-covenant.org/version/3/0/code_of_conduct/)

.github/CONTRIBUTING.md

@@ -0,0 +1,42 @@
+# Introduction
+
+Thank you for your interest in contributing to our project! We welcome contributions from the community and appreciate your efforts to help improve our codebase. This document provides guidelines and instructions for contributing to our project.
+
+
+## Installation
+
+To set up the development environment, please follow these steps:
+
+1. Fork the repository:
+   ```bash
+    gh repo fork MatchCake/TorchPfaffian
+   ```
+2. Clone your forked repository:
+   ```bash
+    git clone <your-fork-url>
+    ```
+3. Navigate to the project directory:
+4. Initialize the Virtual Environment using [uv](https://docs.astral.sh/uv/):
+    ```bash
+     uv sync --dev --extra <extra-option>
+    ```
+    - Extra options: See the [README.md](../README.md) for details on extra options for installation.
+5. Set up Pre-commit hooks:
+    ```bash
+     uv run pre-commit install
+    ```
+
+# Guidelines
+
+1. When you whish to contribute, please create a new fork of the repository and create a new branch for your changes.
+2. Make your changes and commit them with clear and descriptive commit messages.
+3. Push your changes to your forked repository.
+4. Create a pull request to the main repository on the `dev` branch, describing the changes you have made and why they are necessary.
+5. Our team will review your pull request and provide feedback. We may ask for changes or improvements before merging your contribution.
+6. Once your contribution is approved, it will be merged into the main repository on the `dev` branch and will eventually be included in the next release.
+7. Please ensure that your code follows the project's coding standards and guidelines, and that it includes appropriate tests and documentation.
+
+
+## Code of Conduct
+
+We expect all contributors to adhere to our code of conduct, which can be found in the [CODE_OF_CONDUCT.md](CODE_OF_CONDUCT.md) file. This code of conduct outlines our expectations for behavior and communication within the community, and we take it seriously to ensure a welcoming and inclusive environment for all contributors.

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -0,0 +1,64 @@
+name: Bug report
+description: File a bug report
+title: '[BUG]'
+labels: "bug :bug:"
+
+body:
+  - type: markdown
+    id: description
+    attributes:
+      value: |
+          ## Before posting a bug report
+          Search existing GitHub issues to make sure the issue does not already exist.
+
+          # Issue description
+          Description of the issue - include code snippets in the Source code section below and screenshots if relevant.
+  - type: textarea
+    id: expected
+    attributes:
+      label: Expected behavior
+      description: |
+        What do you expect to happen?
+    validations:
+      required: true
+  - type: textarea
+    id: actual
+    attributes:
+      label: Actual behavior
+      description: |
+        What actually happens?
+    validations:
+      required: true
+  - type: textarea
+    id: info
+    attributes:
+      label: Additional information
+      description: |
+        Please provide any additional information here that might be necessary to reproduce the issue.
+  - type: textarea
+    id: sourcecode
+    attributes:
+      label: Source code
+      description: Please include a minimal non-working example, or any other code related to the issue.
+      render: shell
+  - type: textarea
+    id: tracebacks
+    attributes:
+      label:  Tracebacks
+      description: Please include the error tracebacks related to the issue here.
+      render: shell
+  - type: textarea
+    id: system
+    attributes:
+      label:  System information
+      description: Please provide informations about you python version and os. The command `python -c "import sys; print(sys.version, sys.platform)"` can be used to get this information. Provide also the output of `pip list` command.
+      render: shell
+    validations:
+      required: true
+  - type: checkboxes
+    id: terms
+    attributes:
+      label: Existing GitHub issues
+      options:
+        - label: I have searched existing GitHub issues to make sure the issue does not already exist.
+          required: true

.github/ISSUE_TEMPLATE/feature_request.yml

@@ -0,0 +1,44 @@
+name: Feature request
+description: Suggest a new feature
+labels: "enhancement :sparkles:"
+
+body:
+  - type: markdown
+    id: description
+    attributes:
+      value: |
+          ## Before posting a feature request
+          Search existing GitHub issues to make sure the issue does not already exist.
+
+          # Feature description
+          Description of the feature request - include code snippets and screenshots here if relevant.
+  - type: textarea
+    id: details
+    attributes:
+      label: Feature details
+      description: |
+        What feature would you like to have?
+    validations:
+      required: true
+  - type: textarea
+    id: implementation
+    attributes:
+      label: Implementation
+      description: |
+        Do you have an idea for how this could be implemented? Please include those details here.
+  - type: dropdown
+    id: urgency
+    attributes:
+      label: How important would you say this feature is?
+      options:
+        - "1: Not important. Would be nice to have."
+        - "2: Somewhat important. Needed this quarter."
+        - "3: Very important! Blocking work."
+    validations:
+      required: true
+  - type: textarea
+    id: info
+    attributes:
+      label: Additional information
+      description: |
+        Please provide any additional information here. Include potential alternative solutions, or workarounds, as well as references, if any.

.github/pull_request_template.md

@@ -0,0 +1,19 @@
+# Description
+
+Please provide a brief description of the changes you are making in this pull request.
+
+------------------------------------------------------------------------------------------------------------
+
+# Checklist
+
+Please complete the following checklist when submitting a PR. The PR will not be reviewed until all items are checked.
+
+- [ ] All new features include a unit test.
+      Make sure that the tests passed and the coverage is
+      sufficient by running
+      `uv run pytest --session-timeout=600`.
+- [ ] All new functions and code are clearly documented.
+- [ ] The code passes all pre-commit hooks.
+      You can do this by running `uvx pre-commit run --all-files`.
+- [ ] The code is type-checked using Mypy.
+      You can do this by running `uv run mypy src tests`.

.github/workflows/build_dist.yml

@@ -4,6 +4,15 @@ on:
   push:
     branches: ["main"]
 
+permissions:
+  contents: write
+  pull-requests: write
+  actions: write
+  checks: write
+  statuses: write
+  issues: write
+  discussions: write
+  id-token: write
 
 jobs:
   Build-Dist:
@@ -12,35 +21,83 @@ jobs:
 
     steps:
     - uses: actions/checkout@v3
-    - name: Set up Python 3.10
+    - name: Set up Python 3.11
       uses: actions/setup-python@v3
       with:
-        python-version: "3.10"
+        python-version: "3.11"
 
+    - name: Install uv
+      uses: astral-sh/setup-uv@v6
+      with:
+        version: "0.9.2"
+        python-version: "3.11"
+        enable-cache: true
     - name: Install dependencies
       run: |
-        python -m pip install --upgrade pip
-        pip install flake8
-        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
-        pip install wheel
-        python -m pip install --upgrade build
+        uv venv .venv
+        uv sync --locked --dev --extra cpu
+
+    - name: Gather new package version
+      id: version
+      uses: anothrNick/github-tag-action@1.61.0
+      env:
+        GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}}
+        WITH_V: false
+        DEFAULT_BUMP: patch
+        DRY_RUN: true
+
+    - name: Bump package version in pyproject.toml
+      run: |
+        uv version ${{steps.version.outputs.new_tag}}
+        uv lock
 
     - name: Build dist
       run: |
-        python -m build
+        uv run python -m build --sdist --wheel --no-isolation --outdir dist/ .
+        uv run twine check dist/*
 
-    - name: Commit
+    - name: Commit updated pyproject.toml
       run: |
-        git add -f dist
         git config --local user.email "action@github.com"
         git config --local user.name "GitHub Action"
-        git commit -m "Update dist"
+        git add pyproject.toml
+        git add uv.lock
+        git diff-index --quiet HEAD || git commit -m "Updating version of pyproject.toml"
 
-    - name: Push
+    - name: Push the new pyproject.toml
       uses: ad-m/github-push-action@master
       with:
         github_token: ${{secrets.GITHUB_TOKEN}}
         branch: main
         force: true
-        directory: dist
 
+    - name: Create Tag
+      id: tag
+      uses: anothrNick/github-tag-action@1.61.0
+      env:
+        GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}}
+        WITH_V: false
+        DEFAULT_BUMP: patch
+        DRY_RUN: false
+
+    - name: Create Release
+      uses: softprops/action-gh-release@v1
+      with:
+        tag_name: ${{ steps.tag.outputs.new_tag }}
+        generate_release_notes: true
+
+    - name: Merge 'main' branch -> 'dev' branch
+      uses: devmasx/merge-branch@master
+      with:
+        type: now
+        from_branch: main
+        target_branch: dev
+        message: "Automatic merge from 'main' into 'dev' [skip actions]"
+        label_name: "gh-actions"
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+
+    - name: Publish distribution to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        skip_existing: true
+        verbose: true