Initial commit

.github/ISSUE_TEMPLATE/bug_report.md

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+---
+name: Bug Report
+about: Use to report a bug
+title: ''
+labels: bug
+assignees: ''
+---
+
+## Bug Report
+
+### Description
+
+Provide a brief overview of the bug encountered. Describe the behavior observed when the bug occurs and explain the behavior expected when the bug is not present.
+
+### Reproducibility
+
+- [ ] The bug is reproducible.
+- [ ] The bug is intermittent.
+- [ ] The bug occurs only under specific conditions.
+
+#### Steps to Reproduce
+
+1. List the steps to reproduce the bug.
+2. Be as detailed as possible to help with replication.
+
+#### Screenshots / Error Messages (if applicable)
+
+Insert any relevant screenshots or error messages related to the bug.
+
+#### Environment
+
+- **Operating System**: [e.g., Windows 10, macOS, Linux]
+- **Browser (if applicable)**: [e.g., Google Chrome, Firefox, Safari]
+- **Application Version/Commit**: [e.g., v1.2.3, Git commit hash]
+- **Additional Environment Details**: [e.g., hardware specifications, network conditions]
+
+### Additional Context
+
+Provide any additional context or information about the bug.
+
+### Possible Fix
+
+If you have suggestions for a fix, please describe them here.

.github/ISSUE_TEMPLATE/feature_request.md

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+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: ''
+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.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

.github/ISSUE_TEMPLATE/peer_review.md

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+---
+name: Peer Review
+about: Use to submit a peer review
+title: ''
+labels: review
+assignees: ''
+---
+
+## Peer Review for Reproducibility Checks
+
+### Review Checklist
+
+Please review the following aspects related to reproducibility checks:
+
+- [ ] **Environment Setup**:
+  - [ ] Were detailed instructions provided for setting up the development environment?
+  - [ ] Are all necessary dependencies and libraries clearly documented?
+- [ ] **Data Preparation**:
+  - [ ] Are source data files and preprocessing steps clearly documented?
+  - [ ] Are scripts or commands for data transformation included and well-documented?
+- [ ] **Code Execution**:
+  - [ ] Were clear instructions provided for running the code?
+  - [ ] Does the code execute without errors and produce expected outputs?
+- [ ] **Configuration Management**:
+  - [ ] Is version control information (e.g., Git commit hash) included for reproducibility?
+  - [ ] Are any configuration files or parameters used properly documented?
+- [ ] **Results Verification**:
+  - [ ] Are output results (e.g., metrics, visualizations) included and matched with expected outcomes?
+  - [ ] Have any discrepancies between expected and actual results been identified and explained?
+- [ ] **Documentation**:
+  - [ ] Is there a detailed README or documentation explaining the experiment setup and execution process?
+  - [ ] Are code comments and documentation clear and informative?
+- [ ] **External Dependencies**:
+  - [ ] Are any external data sources or APIs used accessible and well-documented?
+  - [ ] Are external libraries or packages properly cited and versioned for reproducibility?
+- [ ] **Validation**:
+  - [ ] Can an independent reviewer replicate the experiment using the provided instructions?
+  - [ ] Are the results consistent across different environments or platforms?
+
+### Additional Comments
+
+Include any additional comments, concerns, or suggestions related to reproducibility.

.github/dependabot.yml

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+version: 2
+updates:
+  - package-ecosystem: "pip"
+    directory: "/"
+    schedule:
+      interval: "weekly"

.github/workflows/gh-pages.yml

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+name: Publish to GitHub Pages
+
+on:
+  push:
+    branches:
+      - main
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+          cache: "pip"
+      - name: Dependencies
+        run: |
+          if [ -f docs/requirements.txt ]; then pip install -r docs/requirements.txt; fi
+          if [ -f pyproject.toml ]; then pip install ".[docs]"; fi
+      - name: Build Jupyter Book
+        run: |
+          jupyter-book build . --config docs/_config.yml --toc docs/_toc.yml
+      - name: Deploy
+        uses: peaceiris/actions-gh-pages@v3
+        if: github.ref == 'refs/heads/main' && job.status == 'success'
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: ./_build/html
+          enable_jekyll: false

.pre-commit-config.yaml

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+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
+      - id: check-added-large-files
+      - id: check-ast
+      - id: check-json
+      - id: detect-aws-credentials
+        args: [--allow-missing-credentials]
+      - id: detect-private-key
+  - repo: https://github.com/igorshubovych/markdownlint-cli
+    rev: v0.39.0
+    hooks:
+      - id: markdownlint
+        name: Markdownlint
+        files: \.(md|mdown|markdown)$
+        args: [
+            "--disable=MD013", # line-length
+            "--disable=MD033", # no-inline-html
+          ]
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.2.6
+    hooks:
+      - id: codespell
+        name: codespell
+        description: Checks for common misspellings in text files
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.3.3
+    hooks:
+      - id: ruff
+        types_or: [python, pyi, jupyter]
+        args: [--fix]
+      - id: ruff-format
+        types_or: [python, pyi, jupyter]