Merge branch 'master' into improved-paragraph-algorithm

.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,39 @@
+# Pull Request Template for MiADE
+
+## Description
+
+Please include a summary of the change and which issue is fixed. Also, include relevant motivation and context. List any dependencies that are required for this change.
+
+Fixes # (issue)
+
+## Type of change
+
+Please delete options that are not relevant.
+
+- [ ] Bug fix (non-breaking change which fixes an issue)
+- [ ] New feature (non-breaking change which adds functionality)
+- [ ] Breaking change (fix or feature that would cause existing functionality to not work as expected)
+- [ ] This change requires a documentation update
+
+## How Has This Been Tested?
+
+Please describe the tests that you ran to verify your changes. Provide instructions so we can reproduce. Please also list any relevant details for your test configuration.
+
+- [ ] Test A
+- [ ] Test B
+
+## Checklist:
+
+Before submitting your pull request, please review the following checklist:
+
+- [ ] I have performed a self-review of my own code.
+- [ ] I have commented my code, particularly in hard-to-understand areas.
+- [ ] I have made corresponding changes to the documentation.
+- [ ] My changes generate no new warnings.
+- [ ] I have added tests that prove my fix is effective or that my feature works.
+- [ ] New and existing unit tests pass locally with my changes.
+- [ ] Any dependent changes have been merged and published in downstream modules.
+
+## Additional Information:
+
+Any additional information that you would like to provide about the pull request.

.github/workflows/build_documentation.yml

@@ -0,0 +1,21 @@
+name: Build documentation
+
+on:
+  pull_request:
+    branches: [master]
+
+jobs:
+  build:
+    name: Build
+    runs-on: ubuntu-20.04
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v2
+        with:
+          python-version: 3.11
+
+      - name: Build the documentation
+        run: |
+          pip install -r docs-requirements.txt
+          pip install ./
+          mkdocs build

.github/workflows/ci.yml

@@ -20,7 +20,7 @@ jobs:
           python-version: 3.11
       - name: install dependencies
         run: |
-          python -m pip install --upgrade pip==24.0
+          python -m pip install pip==24.0
           pip install pytest
           pip install torch --index-url https://download.pytorch.org/whl/cpu
           pip install ./
@@ -31,8 +31,10 @@ jobs:
           pip install -r requirements.txt
       - name: run pytest
         run: pytest ./tests/*
-      - name: Lint with Ruff
+      - name: Install ruff
+        run: pip install ruff
+      - name: Lint with ruff
         run: |
-          pip install ruff
           ruff --output-format=github .
-        continue-on-error: true
+          ruff check --fix
+        continue-on-error: true

.github/workflows/deploy_documentation.yml

@@ -0,0 +1,30 @@
+name: Publish documentation
+
+on:
+  push:
+    branches:
+      - master
+
+permissions:
+  contents: write
+
+jobs:
+  deploy:
+    runs-on: ubuntu-20.04
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v2
+        with:
+          python-version: 3.11
+      - run: echo "cache_id=$(date --utc '+%V')" >> $GITHUB_ENV
+      - uses: actions/cache@v3
+        with:
+          key: mkdocs-material-${{ env.cache_id }}
+          path: .cache
+          restore-keys: |
+            mkdocs-material-
+      - run: |
+          pip install -r docs-requirements.txt
+          pip install ./
+      - name: Build documentation
+        run: mkdocs gh-deploy --force

.github/workflows/publish.yml

@@ -0,0 +1,53 @@
+name: Publish Python 🐍 distribution 📦 to PyPI
+
+on:
+  release:
+    types:
+      - created
+
+jobs:
+  build:
+    name: Build distribution 📦
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: "3.x"
+    - name: Install pypa/build
+      run: >-
+        python3 -m
+        pip install
+        build
+        --user
+    - name: Build a binary wheel and a source tarball
+      run: python3 -m build
+    - name: Store the distribution packages
+      uses: actions/upload-artifact@v3
+      with:
+        name: python-package-distributions
+        path: dist/
+
+  publish-to-pypi:
+    name: >-
+      Publish Python 🐍 distribution 📦 to PyPI
+    if: startsWith(github.ref, 'refs/tags/')  # only publish to PyPI on tag pushes
+    needs:
+    - build
+    runs-on: ubuntu-latest
+    environment:
+      name: release
+      url: https://pypi.org/p/miade  # Replace <package-name> with your PyPI project name
+    permissions:
+      id-token: write  # IMPORTANT: mandatory for trusted publishing
+    steps:
+    - name: Download all the dists
+      uses: actions/download-artifact@v3
+      with:
+        name: python-package-distributions
+        path: dist/
+    - name: Publish distribution 📦 to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+

.gitignore

@@ -43,6 +43,7 @@ venv.bak/
 *.zip
 src/miade/model_builders/output/
 !src/miade/data/*
+.DS_Store
 
 #testing
 tests/data/

CODE_OF_CONDUCT.md

@@ -0,0 +1,128 @@
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible 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.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the
+  overall community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or
+  advances of any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email
+  address, without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders 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, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official e-mail address,
+posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement at
+[email protected].
+All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series
+of actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or
+permanent ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior,  harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within
+the community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.0, available at
+https://www.contributor-covenant.org/version/2/0/code_of_conduct.html.
+
+Community Impact Guidelines were inspired by [Mozilla's code of conduct
+enforcement ladder](https://github.com/mozilla/diversity).
+
+[homepage]: https://www.contributor-covenant.org
+
+For answers to common questions about this code of conduct, see the FAQ at
+https://www.contributor-covenant.org/faq. Translations are available at
+https://www.contributor-covenant.org/translations.