Moving towards a stable PyPI release

.flake8

@@ -0,0 +1,9 @@
+[flake8]
+max-line-length = 100
+extend-ignore = E203,W503,D100,D104
+per-file-ignores =
+    forte_api.py:D,F401,F841,E501
+    forte_demo.py:D,F401,E501
+    examples/*.py:D,E501
+    tests/*.py:D,F401,F811,F841
+    __init__.py:F401,D415

.github/workflows/ci.yml

@@ -0,0 +1,134 @@
+name: CI
+
+on:
+  push:
+    branches: [ main, develop ]
+  pull_request:
+    branches: [ main, develop ]
+
+jobs:
+  test:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        python-version: ['3.9', '3.10', '3.11', '3.12']
+
+    steps:
+    - uses: actions/checkout@v3
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Cache pip dependencies
+      uses: actions/cache@v3
+      with:
+        path: ~/.cache/pip
+        key: ${{ runner.os }}-pip-${{ hashFiles('**/pyproject.toml') }}
+        restore-keys: |
+          ${{ runner.os }}-pip-
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install -e ".[dev]"
+
+    - name: Lint with flake8
+      run: |
+        # Stop the build if there are Python syntax errors or undefined names
+        flake8 src/forte --count --select=E9,F63,F7,F82 --show-source --statistics
+        # Exit-zero treats all errors as warnings
+        flake8 src/forte --count --exit-zero --max-complexity=10 --max-line-length=100 --statistics
+
+    - name: Format check with black
+      run: |
+        black --check src/forte tests
+
+    - name: Run tests with pytest
+      run: |
+        pytest tests/ -v --cov=forte --cov-report=xml --cov-report=term -m "not slow"
+
+    - name: Upload coverage to Codecov
+      uses: codecov/codecov-action@v3
+      with:
+        file: ./coverage.xml
+        flags: unittests
+        name: codecov-umbrella
+        fail_ci_if_error: false
+
+  integration-tests:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: '3.10'
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install -e ".[dev]"
+
+    - name: Run integration tests
+      run: |
+        pytest tests/ -v -m "integration and not slow"
+
+  build:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: '3.10'
+
+    - name: Install build dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install build twine
+
+    - name: Build package
+      run: python -m build
+
+    - name: Check package with twine
+      run: twine check dist/*
+
+    - name: Upload artifacts
+      uses: actions/upload-artifact@v4
+      with:
+        name: dist
+        path: dist/
+
+  docs:
+    runs-on: ubuntu-latest
+    if: github.event_name == 'push' && (github.ref == 'refs/heads/main' || github.ref == 'refs/heads/develop')
+    permissions:
+      contents: write
+    steps:
+    - uses: actions/checkout@v3
+      with:
+        fetch-depth: 0
+
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: '3.10'
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install -e ".[docs]"
+
+    - name: Configure Git
+      run: |
+        git config user.name "github-actions[bot]"
+        git config user.email "github-actions[bot]@users.noreply.github.com"
+
+    - name: Deploy documentation
+      run: mkdocs gh-deploy --force

.gitignore

@@ -1,6 +1,12 @@
+# Project-specific
 data/*
 embeddings/*
 *.png
+*.jpg
+*.jpeg
+
+# Keep example images if needed
+!docs/images/
 
 # Byte-compiled / optimized / DLL files
 __pycache__/
@@ -149,6 +155,7 @@ venv.bak/
 
 # mkdocs documentation
 /site
+site/
 
 # mypy
 .mypy_cache/
@@ -175,4 +182,4 @@ cython_debug/
 .ruff_cache/
 
 # PyPI configuration file
-.pypirc
+.pypirc

.pre-commit-config.yaml

@@ -0,0 +1,69 @@
+# 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
+        exclude: ^mkdocs\.yml$
+      - id: check-added-large-files
+      - id: check-json
+      - id: check-toml
+      - id: check-merge-conflict
+      - id: check-case-conflict
+      - id: detect-private-key
+      - id: mixed-line-ending
+        args: ['--fix=lf']
+      - id: name-tests-test
+        args: ['--pytest-test-first']
+
+  - repo: https://github.com/psf/black
+    rev: 24.1.1
+    hooks:
+      - id: black
+        language_version: python3.9
+
+  - repo: https://github.com/pycqa/isort
+    rev: 5.13.2
+    hooks:
+      - id: isort
+        name: isort (python)
+
+  - repo: https://github.com/pycqa/flake8
+    rev: 7.0.0
+    hooks:
+      - id: flake8
+        args: ['--max-line-length=100', '--extend-ignore=E203,W503']
+        additional_dependencies: [flake8-docstrings]
+
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.8.0
+    hooks:
+      - id: mypy
+        additional_dependencies: [
+          torch,
+          torchvision,
+          transformers,
+          numpy,
+          scipy,
+          scikit-learn,
+          pillow,
+          tqdm,
+        ]
+        args: [--config-file=pyproject.toml, --ignore-missing-imports]
+
+  - repo: https://github.com/PyCQA/bandit
+    rev: 1.7.6
+    hooks:
+      - id: bandit
+        args: ['-c', 'pyproject.toml']
+        additional_dependencies: ['bandit[toml]']
+
+  - repo: https://github.com/pycqa/pydocstyle
+    rev: 6.3.0
+    hooks:
+      - id: pydocstyle
+        args: ['--convention=google', '--add-ignore=D212']
+        exclude: '^(tests/|examples/|forte_api\.py|forte_demo\.py)'

CHANGELOG.md

@@ -12,4 +12,4 @@
 - Basic evaluation metrics: AUROC, FPR@95TPR, AUPRC, F1
 
 ### Fixed
-- None (initial release)
+- None (initial release)

LICENSE

@@ -18,4 +18,4 @@ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
+SOFTWARE.

MANIFEST.in

@@ -0,0 +1,28 @@
+# Include documentation
+include README.md
+include LICENSE
+include CHANGELOG.md
+
+# Include package configuration
+include pyproject.toml
+include setup.py
+
+# Exclude development and build files
+exclude .gitignore
+exclude .git*
+recursive-exclude * __pycache__
+recursive-exclude * *.py[co]
+recursive-exclude * .DS_Store
+
+# Exclude tests, docs, and examples from distribution
+recursive-exclude tests *
+recursive-exclude docs *
+recursive-exclude examples *
+recursive-exclude env *
+recursive-exclude embeddings *
+recursive-exclude data *
+
+# Exclude build artifacts
+recursive-exclude dist *
+recursive-exclude build *
+recursive-exclude *.egg-info *