phd-deepread-workflow 0.1.0__tar.gz

phd_deepread_workflow-0.1.0/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#poetry.lock
+
+# pdm
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PhD Deep Read specific
+markdown_output/
+structured_literature_notes/
+generation_prompts/
+canvas_templates/
+logs/
+batch_test_output/
+test_output*
+*.pdf
+!examples/test_paper.pdf
+
+# OS generated files
+.DS_Store
+.DS_Store?
+._*
+.Spotlight-V100
+.Trashes
+ehthumbs.db
+Thumbs.db
+
+# Editor directories and files
+.vscode/
+.idea/
+*.swp
+*.swo
+*~

phd_deepread_workflow-0.1.0/.pre-commit-config.yaml

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+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
+        args: ['--maxkb=5000']
+      - id: check-merge-conflict
+      - id: check-toml
+      - id: check-json
+
+  - repo: https://github.com/psf/black
+    rev: 23.12.1
+    hooks:
+      - id: black
+        args: [--line-length=88]
+
+  - repo: https://github.com/pycqa/isort
+    rev: 5.13.2
+    hooks:
+      - id: isort
+        args: ["--profile", "black"]
+
+  - repo: https://github.com/pycqa/flake8
+    rev: 7.0.0
+    hooks:
+      - id: flake8
+        args: [--max-line-length=88, --extend-ignore=E203,W503]
+        additional_dependencies: [flake8-pyproject]
+
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.8.0
+    hooks:
+      - id: mypy
+        additional_dependencies: [types-PyYAML, types-Pillow]
+        args: [--strict, --ignore-missing-imports]
+
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: v3.0.3
+    hooks:
+      - id: prettier
+        types_or: [markdown, yaml, json]
+        exclude: ^(templates/|examples/)  # Don't format templates
+
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.2.6
+    hooks:
+      - id: codespell
+        args: [--skip=*.pdf,*.png,*.jpg,*.jpeg,*.gif,*.svg,*.ico]
+        exclude_types: [binary]
+
+ci:
+  autofix_commit_msg: 🎨 style: pre-commit fixes
+  autofix_prs: true
+  skip: []
+  submodules: false

phd_deepread_workflow-0.1.0/LICENSE

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+MIT License
+
+Copyright (c) 2024 Helen Insights
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+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.

phd_deepread_workflow-0.1.0/MANIFEST.in

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+include LICENSE
+include README.md
+include requirements.txt
+include requirements-dev.txt
+include install.sh
+include Makefile
+include pyproject.toml
+include .gitignore
+include .pre-commit-config.yaml
+include config/*.yaml
+include templates/*
+include docs/*.md
+include examples/*
+recursive-include scripts *.py *.sh
+recursive-include tests *.py

phd_deepread_workflow-0.1.0/Makefile

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+# PhD Deep Read Workflow Makefile
+
+.PHONY: help install install-dev test test-cov lint format type-check clean setup
+
+# Default target
+help:
+	@echo "PhD Deep Read Workflow - Available targets:"
+	@echo ""
+	@echo "  install     - Install core dependencies"
+	@echo "  install-dev - Install development dependencies"
+	@echo "  test        - Run tests"
+	@echo "  test-cov    - Run tests with coverage report"
+	@echo "  lint        - Run linters (flake8)"
+	@echo "  format      - Format code (black, isort)"
+	@echo "  type-check  - Run type checking (mypy)"
+	@echo "  check       - Run all checks (lint, format, type-check, test)"
+	@echo "  clean       - Clean build artifacts and caches"
+	@echo "  setup       - Full setup (install, install-dev, format)"
+	@echo ""
+
+# Installation
+install:
+	pip install -r requirements.txt
+
+install-dev:
+	pip install -r requirements-dev.txt
+
+# Testing
+test:
+	pytest tests/ -v
+
+test-cov:
+	pytest tests/ --cov=scripts --cov-report=html --cov-report=term
+
+# Code quality
+lint:
+	flake8 scripts/ tests/ --max-line-length=88 --extend-ignore=E203,W503
+
+format:
+	black scripts/ tests/
+	isort scripts/ tests/
+
+type-check:
+	mypy scripts/
+
+check: lint format type-check test
+
+# Setup
+setup: install install-dev format
+	@echo "✅ Setup complete! Next steps:"
+	@echo "   1. Install Tesseract OCR: brew install tesseract (macOS) or sudo apt install tesseract-ocr (Linux)"
+	@echo "   2. Test the workflow: python scripts/extract.py --help"
+
+# Cleanup
+clean:
+	rm -rf .pytest_cache/ .mypy_cache/ .coverage htmlcov/ build/ dist/ *.egg-info/
+	find . -type d -name "__pycache__" -exec rm -rf {} + 2>/dev/null || true
+	find . -type f -name "*.pyc" -delete
+
+# Development shortcuts
+dev: install-dev
+	@echo "Development dependencies installed"
+
+run-test:
+	python -m pytest tests/test_extract.py -v
+
+run-extract:
+	python scripts/extract.py --help
+
+run-generate:
+	python scripts/generate.py --help
+
+run-canvas:
+	python scripts/canvas.py --help
+
+run-verify:
+	python scripts/verify.py --help
+
+# Documentation
+docs-serve:
+	mkdocs serve
+
+docs-build:
+	mkdocs build
+
+# Package building
+build:
+	python -m build
+
+publish-test:
+	twine upload --repository testpypi dist/*
+
+publish:
+	twine upload dist/*