Major update, restructuring etc

.github/workflows/ci.yaml

@@ -0,0 +1,136 @@
+# GitHub Actions configuration **EXAMPLE**,
+# MODIFY IT ACCORDING TO YOUR NEEDS!
+# Reference: https://docs.github.com/en/actions
+
+name: ci
+
+on:
+  release:
+    types: [published]
+  push:
+    # Avoid using all the resources/limits available by checking only
+    # relevant branches and tags. Other branches can be checked via PRs.
+    branches: [main]
+    tags: ['v?[0-9]+.[0-9]+.?[0-9]?*']  # Match tags that resemble a version
+  pull_request:  # Run in every PR
+  workflow_dispatch:  # Allow manually triggering the workflow
+  schedule:
+    # Run roughly every 15 days at 00:00 UTC
+    # (useful to check if updates on dependencies break the package)
+    - cron: '0 0 1,16 * *'
+
+permissions:
+  contents: read
+
+concurrency:
+  group: >-
+    ${{ github.workflow }}-${{ github.ref_type }}-
+    ${{ github.event.pull_request.number || github.sha }}
+  cancel-in-progress: true
+
+jobs:
+  prepare:
+    runs-on: ubuntu-latest
+    outputs:
+      wheel-distribution: ${{ steps.wheel-distribution.outputs.path }}
+    steps:
+      - uses: actions/checkout@v4
+        with: {fetch-depth: 0}  # deep clone for setuptools-scm
+      - uses: actions/setup-python@v4
+        id: setup-python
+        with: {python-version: "3.11"}
+      - name: Run static analysis and format checkers
+        run: pipx run pre-commit run --all-files --show-diff-on-failure
+      - name: Build package distribution files
+        run: >-
+          pipx run --python '${{ steps.setup-python.outputs.python-path }}'
+          tox -e clean,build
+      - name: Record the path of wheel distribution
+        id: wheel-distribution
+        run: echo "path=$(ls dist/*.whl)" >> $GITHUB_OUTPUT
+      - name: Store the distribution files for use in other stages
+        # `tests` and `publish` will use the same pre-built distributions,
+        # so we make sure to release the exact same package that was tested
+        uses: actions/upload-artifact@v4
+        with:
+          name: python-distribution-files
+          path: dist/
+          retention-days: 1
+
+  test:
+    needs: prepare
+    strategy:
+      matrix:
+        python:
+        - "3.9"  # oldest Python supported by PSF
+        - "3.11"  # newest Python that is stable
+        platform:
+        - ubuntu-latest
+#        - macos-latest
+        - windows-latest
+    runs-on: ${{ matrix.platform }}
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v4
+        id: setup-python
+        with:
+          python-version: ${{ matrix.python }}
+      - name: Retrieve pre-built distribution files
+        uses: actions/download-artifact@v4
+        with: {name: python-distribution-files, path: dist/}
+      - name: Run tests
+        run: >-
+          pipx run --python '${{ steps.setup-python.outputs.python-path }}'
+          tox --installpkg '${{ needs.prepare.outputs.wheel-distribution }}'
+          -- -rFEx --durations 10 --color yes  # pytest args
+      - name: Generate coverage report
+        run: pipx run coverage[toml] lcov -o coverage.lcov
+      - name: Upload partial coverage report
+        uses: coverallsapp/github-action@master
+        with:
+          path-to-lcov: coverage.lcov
+          github-token: ${{ secrets.github_token }}
+          flag-name: ${{ matrix.platform }} - py${{ matrix.python }}
+          parallel: true
+
+  finalize:
+    needs: test
+    runs-on: ubuntu-latest
+    steps:
+      - name: Finalize coverage report
+        uses: coverallsapp/github-action@master
+        with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          parallel-finished: true
+
+  publish:
+    needs: finalize
+    if: ${{ (github.event_name  == 'push' && contains(github.ref, 'refs/tags/')) || (github.event_name == 'release' && github.event.action == 'published') }}
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v4
+        with: {python-version: "3.11"}
+      - name: Retrieve pre-built distribution files
+        uses: actions/download-artifact@v4
+        with: {name: python-distribution-files, path: dist/}
+      # - name: Publish Package (TEST)
+      #   env:
+      #     # TODO: Set your PYPI_TOKEN as a secret using GitHub UI
+      #     # - https://pypi.org/help/#apitoken
+      #     # - https://docs.github.com/en/actions/security-guides/encrypted-secrets
+      #     TWINE_REPOSITORY: pypi
+      #     TWINE_USERNAME: __token__
+      #     TWINE_PASSWORD: ${{ secrets.PYPI_TEST_TOKEN }}
+      #   run: pipx run tox -e publish
+      - name: Publish Package
+        env:
+          # TODO: Set your PYPI_TOKEN as a secret using GitHub UI
+          # - https://pypi.org/help/#apitoken
+          # - https://docs.github.com/en/actions/security-guides/encrypted-secrets
+          TWINE_REPOSITORY: pypi
+          TWINE_USERNAME: __token__
+          TWINE_PASSWORD: ${{ secrets.PYPI_API_TOKEN }}
+        run: pipx run tox -e publish

.gitignore

@@ -154,4 +154,7 @@ scripts/datasets_path.txt
 env
 nestmodel.egginfo
 Untitled.ipynb
-Untitled1.ipynb
+Untitled*.ipynb
+csvs
+demo/images
+experiments

.pre-commit-config.yaml

@@ -0,0 +1,68 @@
+exclude: '^docs/conf.py'
+
+repos:
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v5.0.0
+  hooks:
+  - id: trailing-whitespace
+  - id: check-added-large-files
+  - id: check-ast
+  - id: check-json
+  - id: check-merge-conflict
+  - id: check-xml
+  - id: check-yaml
+  - id: debug-statements
+  - id: end-of-file-fixer
+  - id: requirements-txt-fixer
+  - id: mixed-line-ending
+    args: ['--fix=auto']  # replace 'auto' with 'lf' to enforce Linux/Mac line endings or 'crlf' for Windows
+
+## If you want to automatically "modernize" your Python code:
+# - repo: https://github.com/asottile/pyupgrade
+#   rev: v3.7.0
+#   hooks:
+#   - id: pyupgrade
+#     args: ['--py37-plus']
+
+## If you want to avoid flake8 errors due to unused vars or imports:
+# - repo: https://github.com/PyCQA/autoflake
+#   rev: v2.1.1
+#   hooks:
+#   - id: autoflake
+#     args: [
+#       --in-place,
+#       --remove-all-unused-imports,
+#       --remove-unused-variables,
+#     ]
+
+# - repo: https://github.com/PyCQA/isort
+#   rev: 5.13.2
+#   hooks:
+#   - id: isort
+
+- repo: https://github.com/psf/black
+  rev: 24.10.0
+  hooks:
+  - id: black
+    language_version: python3
+
+## If like to embrace black styles even in the docs:
+# - repo: https://github.com/asottile/blacken-docs
+#   rev: v1.13.0
+#   hooks:
+#   - id: blacken-docs
+#     additional_dependencies: [black]
+
+- repo: https://github.com/PyCQA/flake8
+  rev: 7.1.1
+  hooks:
+  - id: flake8
+    additional_dependencies: [Flake8-pyproject]
+  ## You can add flake8 plugins via `additional_dependencies`:
+  #  additional_dependencies: [flake8-bugbear]
+
+## Check for misspells in documentation files:
+# - repo: https://github.com/codespell-project/codespell
+#   rev: v2.2.5
+#   hooks:
+#   - id: codespell