lixplore-cli 1.0.0__tar.gz

lixplore_cli-1.0.0/.gitattributes

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+# GitHub linguist configuration
+# Exclude generated files and documentation builds from language statistics
+
+# Documentation build outputs
+site/** linguist-generated
+docs/_build/** linguist-generated
+
+# Python bytecode
+*.pyc linguist-generated
+__pycache__/** linguist-generated
+
+# Mark documentation source as documentation
+docs/**/*.md linguist-documentation
+
+# Ensure Python is detected as primary language
+*.py linguist-detectable

lixplore_cli-1.0.0/.github/workflows/docs.yml

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+name: Deploy Documentation
+
+on:
+  push:
+    branches:
+      - main
+    paths:
+      - 'docs/**'
+      - 'mkdocs.yml'
+      - '.github/workflows/docs.yml'
+
+  workflow_dispatch:
+
+permissions:
+  contents: write
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.x
+
+      - name: Install dependencies
+        run: |
+          pip install mkdocs mkdocs-material
+
+      - name: Deploy documentation
+        run: mkdocs gh-deploy --force

lixplore_cli-1.0.0/.github/workflows/publish.yml

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+name: Publish to PyPI
+
+on:
+  release:
+    types: [published]
+  workflow_dispatch:
+
+jobs:
+  build-and-publish:
+    runs-on: ubuntu-latest
+    env:
+      PYTHONUTF8: '1'
+      PYTHONIOENCODING: 'utf-8'
+    
+    steps:
+    - uses: actions/checkout@v4
+    
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: '3.12'
+    
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install build twine
+    
+    - name: Build package
+      run: python -m build
+    
+    - name: Check package
+      run: twine check dist/*
+    
+    - name: Publish to PyPI
+      env:
+        TWINE_USERNAME: __token__
+        TWINE_PASSWORD: ${{ secrets.PYPI_API_TOKEN }}
+      run: twine upload dist/*

lixplore_cli-1.0.0/.github/workflows/test.yml

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+name: Tests
+
+on:
+  push:
+    branches: [ main, develop ]
+  pull_request:
+    branches: [ main, develop ]
+
+jobs:
+  test:
+    runs-on: ${{ matrix.os }}
+    env:
+      PYTHONUTF8: '1'
+      PYTHONIOENCODING: 'utf-8'
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
+    
+    steps:
+    - uses: actions/checkout@v4
+    
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+        cache: 'pip'
+    
+    - name: Configure Windows UTF-8 console
+      if: runner.os == 'Windows'
+      shell: pwsh
+      run: |
+        chcp 65001
+        $OutputEncoding = [Console]::OutputEncoding = [Text.UTF8Encoding]::new()
+        [Console]::InputEncoding = [Text.UTF8Encoding]::new()
+    
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip setuptools wheel
+        pip install -r requirements.txt
+        pip install -e .
+
+    - name: Test basic functionality
+      run: |
+        lixplore -P -q "test" -m 2
+    
+    - name: Test installation
+      run: |
+        lixplore --help
+        lixplore --examples

lixplore_cli-1.0.0/.gitignore

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+# Python
+__pycache__/
+*.py[cod]
+*$py.class
+*.so
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# Virtual Environment
+venv/
+ENV/
+env/
+.venv
+
+# IDEs
+.vscode/
+.idea/
+*.swp
+*.swo
+*~
+.DS_Store
+
+# Lixplore specific - User generated files
+exports/
+results.json
+.lixplore_cache.json
+.crossref
+.semantischolar
+config.json
+lixplore_annotations_*.*
+
+# Test files and debugging
+tmp_rovodev_*
+*.tmp
+test.py
+test1.py
+test_*.py
+troubleshoot.py
+pub.py
+
+# All markdown files in root directory except README and CHANGELOG
+# Documentation is available at https://pryndor.github.io/Lixplore_cli/
+# Source files in docs/ directory are kept for building documentation site
+/*.md
+!README.md
+!CHANGELOG.md
+
+# Distribution / packaging
+*.whl
+*.tar.gz
+
+# Coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+.pytest_cache/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# Logs
+*.log
+
+# Documentation builds
+docs/_build/
+site/
+
+# OS specific
+Thumbs.db
+
+# Keep structure but ignore contents
+exports/*
+!exports/.gitignore

lixplore_cli-1.0.0/.python-version

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+lixplore-env

lixplore_cli-1.0.0/CHANGELOG.md

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+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [2.0.0] - 2024-12-24
+
+### Added - Major Export Enhancement Update
+
+**New Export Features:**
+- **Citation Style Export** - Export formatted citations in APA, MLA, Chicago, IEEE styles (`-C`)
+- **Batch Export** - Export to multiple formats simultaneously (`-X csv,ris,bibtex`)
+- **Export Field Filtering** - Select specific fields to export (`--export-fields title authors year doi`)
+- **Metadata Enrichment** - Enrich results using CrossRef, PubMed, arXiv APIs (`--enrich`)
+- **DOI Resolution** - Automatically validate and find missing DOIs (integrated with enrichment)
+- **Export Templates** - Use predefined templates for journals (`--template nature`)
+- **Export Compression** - Auto-compress exports to ZIP (`--zip`)
+- **Export Profiles** - Save and reuse export configurations (`--save-profile`, `--load-profile`)
+- **Enhanced Deduplication** - Advanced strategies with metadata merging (`-D strict --dedup-merge`)
+
+**New CLI Flags:**
+- `-C, --citation STYLE` - Export as formatted citations (apa|mla|chicago|ieee)
+- `-X FORMAT[,FORMAT...]` - Batch export to multiple formats (comma-separated)
+- `--export-fields FIELD [FIELD ...]` - Select specific fields to export
+- `--enrich [API ...]` - Enrich metadata (crossref|pubmed|arxiv|all)
+- `--template NAME` - Use predefined export template (nature|science|ieee)
+- `--zip` - Compress exported files to ZIP
+- `--save-profile NAME` - Save current export settings as profile
+- `--load-profile NAME` - Load saved export profile
+- `--list-profiles` - List all saved profiles
+- `--delete-profile NAME` - Delete saved profile
+- `--list-templates` - List all available templates
+- `-D [STRATEGY]` - Enhanced deduplication (auto|strict|loose|doi_only|title_only)
+- `--dedup-threshold FLOAT` - Title similarity threshold (0.0-1.0, default: 0.85)
+- `--dedup-keep STRATEGY` - Which duplicate to keep (first|most_complete|prefer_doi)
+- `--dedup-merge` - Merge metadata from duplicates
+
+**New Modules:**
+- `lixplore/utils/citations.py` - Citation formatting engine
+- `lixplore/utils/enrichment.py` - Metadata enrichment and DOI resolution
+- `lixplore/utils/profiles.py` - Profile management
+- `lixplore/utils/template_engine.py` - Template processing
+- `lixplore/templates/` - Built-in templates (nature, science, ieee)
+
+**New Export Features:**
+- `exports/citations/` - Citation format exports folder
+- `~/.lixplore/profiles.json` - User profiles storage
+- `~/.lixplore/templates/` - User custom templates folder
+
+### Changed
+- `-D, --deduplicate` now accepts optional strategy parameter
+- `-X, --export` now supports comma-separated format list for batch export
+- Enhanced deduplication with configurable strategies and metadata merging
+- Improved field filtering across all export formats
+
+### Removed
+- `-Z, --zotero` flag (replaced by RIS export which works with Zotero)
+- Stub Zotero integration function (use `-X ris` instead)
+
+### Fixed
+- Deduplication now properly handles metadata completeness scoring
+- Export field filtering now validates field names
+- Better handling of missing metadata fields
+
+## [1.0.0] - 2024-12-19
+
+### Added
+- Multi-source search across 5 academic databases (PubMed, arXiv, Crossref, DOAJ, EuropePMC)
+- Boolean operator support (AND, OR, NOT, parentheses)
+- 8 export formats (CSV, Excel, JSON, BibTeX, RIS, EndNote XML, EndNote Tagged, XML)
+- Smart selection patterns (odd, even, ranges, first:N, last:N, top:N)
+- Sorting options (relevant, newest, oldest, journal, author)
+- Review feature - view articles in separate terminal windows
+- Deduplication across multiple sources
+- Organized export folders by format type
+- Date range filtering
+- Author and DOI search
+- Complete documentation (man page, help, examples, TLDR)
+- Cross-platform support (Linux, macOS, Windows)
+
+### Features
+- `-P, --pubmed` - Search PubMed
+- `-C, --crossref` - Search Crossref
+- `-J, --doaj` - Search DOAJ
+- `-E, --europepmc` - Search EuropePMC
+- `-x, --arxiv` - Search arXiv
+- `-A, --all` - Search all sources
+- `-s, --sources` - Combined source selection
+- `-q, --query` - Search query with Boolean operators
+- `-au, --author` - Search by author
+- `-DOI, --doi` - Search by DOI
+- `-m, --max_results` - Maximum results (default: 10)
+- `-d, --date` - Date range filter
+- `-D, --deduplicate` - Remove duplicates
+- `--sort` - Sort results (relevant, newest, oldest, journal, author)
+- `-a, --abstract` - Show abstracts
+- `-N, --number` - View details in console
+- `-R, --review` - Review in separate terminal
+- `-st, --stat` - Get statistics
+- `-X, --export` - Export format
+- `-o, --output` - Custom output filename
+- `-S, --select` - Smart selection
+- `-H, --history` - Show search history
+- `--examples` - Show quick examples
+- `-h, --help` - Show help message
+
+### Documentation
+- Comprehensive README with examples
+- Professional Unix man page
+- Quick examples (TLDR-style)
+- Complete help system
+- API documentation
+
+### Package Distribution
+- PyPI package support
+- Cross-platform compatibility (Linux, macOS, Windows)
+- Python 3.7+ support
+- Modern packaging with pyproject.toml
+- GitHub Actions for CI/CD
+- Automated testing across platforms
+
+## [Unreleased]
+
+### Planned Features
+- PDF download support
+- Citation network visualization
+- Bookmarking system
+- Search profiles
+- Web interface
+- Batch processing from file
+
+---
+
+For more details, see the [README](README.md).

lixplore_cli-1.0.0/LICENSE

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+MIT License
+
+Copyright (c) 2024 Lixplore Contributors
+
+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.

lixplore_cli-1.0.0/MANIFEST.in

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+# Include documentation
+include README.md
+include LICENSE
+include requirements.txt
+include CHANGELOG.md
+
+# Include documentation files
+recursive-include docs *.md *.1
+
+# Exclude unnecessary files
+global-exclude __pycache__
+global-exclude *.py[co]
+global-exclude .DS_Store
+global-exclude *.so
+
+# Exclude test files
+prune tests
+prune exports
+
+# Exclude cache and temp files
+exclude .lixplore_cache.json
+exclude results.json
+exclude .crossref
+exclude .semantischolar