@synsci/cli-darwin-x64 1.1.97 → 1.1.99

package/bin/skills/citation-management/assets/bibtex_template.bib

@@ -1,264 +0,0 @@
-% BibTeX Template File
-% Examples of properly formatted entries for all common types
-
-% =============================================================================
-% JOURNAL ARTICLES
-% =============================================================================
-
-@article{Jumper2021,
-  author  = {Jumper, John and Evans, Richard and Pritzel, Alexander and Green, Tim and Figurnov, Michael and Ronneberger, Olaf and Tunyasuvunakool, Kathryn and Bates, Russ and {\v{Z}}{\'\i}dek, Augustin and Potapenko, Anna and others},
-  title   = {Highly Accurate Protein Structure Prediction with {AlphaFold}},
-  journal = {Nature},
-  year    = {2021},
-  volume  = {596},
-  number  = {7873},
-  pages   = {583--589},
-  doi     = {10.1038/s41586-021-03819-2}
-}
-
-@article{Watson1953,
-  author  = {Watson, James D. and Crick, Francis H. C.},
-  title   = {Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid},
-  journal = {Nature},
-  year    = {1953},
-  volume  = {171},
-  number  = {4356},
-  pages   = {737--738},
-  doi     = {10.1038/171737a0}
-}
-
-@article{Doudna2014,
-  author  = {Doudna, Jennifer A. and Charpentier, Emmanuelle},
-  title   = {The New Frontier of Genome Engineering with {CRISPR-Cas9}},
-  journal = {Science},
-  year    = {2014},
-  volume  = {346},
-  number  = {6213},
-  pages   = {1258096},
-  doi     = {10.1126/science.1258096}
-}
-
-% =============================================================================
-% BOOKS
-% =============================================================================
-
-@book{Kumar2021,
-  author    = {Kumar, Vinay and Abbas, Abul K. and Aster, Jon C.},
-  title     = {Robbins and Cotran Pathologic Basis of Disease},
-  publisher = {Elsevier},
-  year      = {2021},
-  edition   = {10},
-  address   = {Philadelphia, PA},
-  isbn      = {978-0-323-53113-9}
-}
-
-@book{Alberts2014,
-  author    = {Alberts, Bruce and Johnson, Alexander and Lewis, Julian and Morgan, David and Raff, Martin and Roberts, Keith and Walter, Peter},
-  title     = {Molecular Biology of the Cell},
-  publisher = {Garland Science},
-  year      = {2014},
-  edition   = {6},
-  address   = {New York, NY},
-  isbn      = {978-0-815-34432-2}
-}
-
-% Book with editor instead of author
-@book{Sambrook2001,
-  editor    = {Sambrook, Joseph and Russell, David W.},
-  title     = {Molecular Cloning: A Laboratory Manual},
-  publisher = {Cold Spring Harbor Laboratory Press},
-  year      = {2001},
-  edition   = {3},
-  address   = {Cold Spring Harbor, NY},
-  isbn      = {978-0-879-69576-7}
-}
-
-% =============================================================================
-% CONFERENCE PAPERS (PROCEEDINGS)
-% =============================================================================
-
-@inproceedings{Vaswani2017,
-  author    = {Vaswani, Ashish and Shazeer, Noam and Parmar, Niki and Uszkoreit, Jakob and Jones, Llion and Gomez, Aidan N. and Kaiser, {\L}ukasz and Polosukhin, Illia},
-  title     = {Attention is All You Need},
-  booktitle = {Advances in Neural Information Processing Systems 30 (NeurIPS 2017)},
-  year      = {2017},
-  pages     = {5998--6008},
-  address   = {Long Beach, CA},
-  url       = {https://proceedings.neurips.cc/paper/2017/hash/3f5ee243547dee91fbd053c1c4a845aa-Abstract.html}
-}
-
-@inproceedings{He2016,
-  author    = {He, Kaiming and Zhang, Xiangyu and Ren, Shaoqing and Sun, Jian},
-  title     = {Deep Residual Learning for Image Recognition},
-  booktitle = {Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition (CVPR)},
-  year      = {2016},
-  pages     = {770--778},
-  address   = {Las Vegas, NV},
-  doi       = {10.1109/CVPR.2016.90}
-}
-
-% =============================================================================
-% BOOK CHAPTERS
-% =============================================================================
-
-@incollection{Brown2020,
-  author    = {Brown, Peter O. and Botstein, David},
-  title     = {Exploring the New World of the Genome with {DNA} Microarrays},
-  booktitle = {DNA Microarrays: A Molecular Cloning Manual},
-  editor    = {Eisen, Michael B. and Brown, Patrick O.},
-  publisher = {Cold Spring Harbor Laboratory Press},
-  year      = {2020},
-  pages     = {1--45},
-  address   = {Cold Spring Harbor, NY}
-}
-
-% =============================================================================
-% PHD THESES / DISSERTATIONS
-% =============================================================================
-
-@phdthesis{Johnson2023,
-  author  = {Johnson, Mary L.},
-  title   = {Novel Approaches to Cancer Immunotherapy Using {CRISPR} Technology},
-  school  = {Stanford University},
-  year    = {2023},
-  type    = {{PhD} dissertation},
-  address = {Stanford, CA}
-}
-
-% =============================================================================
-% MASTER'S THESES
-% =============================================================================
-
-@mastersthesis{Smith2022,
-  author  = {Smith, Robert J.},
-  title   = {Machine Learning Methods for Protein Structure Prediction},
-  school  = {Massachusetts Institute of Technology},
-  year    = {2022},
-  type    = {{Master's} thesis},
-  address = {Cambridge, MA}
-}
-
-% =============================================================================
-% TECHNICAL REPORTS
-% =============================================================================
-
-@techreport{WHO2020,
-  author      = {{World Health Organization}},
-  title       = {Clinical Management of {COVID-19}: Interim Guidance},
-  institution = {World Health Organization},
-  year        = {2020},
-  type        = {Technical Report},
-  number      = {WHO/2019-nCoV/clinical/2020.5},
-  address     = {Geneva, Switzerland}
-}
-
-% =============================================================================
-% PREPRINTS
-% =============================================================================
-
-% bioRxiv preprint
-@misc{Zhang2024preprint,
-  author       = {Zhang, Yi and Chen, Li and Wang, Hui and Liu, Xin},
-  title        = {Novel Therapeutic Targets in {Alzheimer}'s Disease},
-  year         = {2024},
-  howpublished = {bioRxiv},
-  doi          = {10.1101/2024.01.15.575432},
-  note         = {Preprint}
-}
-
-% arXiv preprint
-@misc{Brown2024arxiv,
-  author       = {Brown, Alice and Green, Bob},
-  title        = {Advances in Quantum Computing},
-  year         = {2024},
-  howpublished = {arXiv},
-  note         = {arXiv:2401.12345}
-}
-
-% =============================================================================
-% DATASETS
-% =============================================================================
-
-@misc{AlphaFoldDB2021,
-  author       = {{DeepMind} and {EMBL-EBI}},
-  title        = {{AlphaFold} Protein Structure Database},
-  year         = {2021},
-  howpublished = {Database},
-  url          = {https://alphafold.ebi.ac.uk/},
-  doi          = {10.1093/nar/gkab1061},
-  note         = {Version 4}
-}
-
-% =============================================================================
-% SOFTWARE / CODE
-% =============================================================================
-
-@misc{McKinney2010pandas,
-  author       = {McKinney, Wes},
-  title        = {pandas: A Foundational {Python} Library for Data Analysis and Statistics},
-  year         = {2010},
-  howpublished = {Software},
-  url          = {https://pandas.pydata.org/},
-  note         = {Python Data Analysis Library}
-}
-
-% =============================================================================
-% WEBSITES / ONLINE RESOURCES
-% =============================================================================
-
-@misc{NCBI2024,
-  author       = {{National Center for Biotechnology Information}},
-  title        = {{PubMed}: Database of Biomedical Literature},
-  year         = {2024},
-  howpublished = {Website},
-  url          = {https://pubmed.ncbi.nlm.nih.gov/},
-  note         = {Accessed: 2024-01-15}
-}
-
-% =============================================================================
-% SPECIAL CASES
-% =============================================================================
-
-% Article with organization as author
-@article{NatureEditorial2023,
-  author  = {{Nature Editorial Board}},
-  title   = {The Future of {AI} in Scientific Research},
-  journal = {Nature},
-  year    = {2023},
-  volume  = {615},
-  pages   = {1--2},
-  doi     = {10.1038/d41586-023-00001-1}
-}
-
-% Article with no volume number (some journals)
-@article{OpenAccess2024,
-  author  = {Williams, Sarah and Thomas, Michael},
-  title   = {Open Access Publishing in the 21st Century},
-  journal = {Journal of Scholarly Communication},
-  year    = {2024},
-  pages   = {e123456},
-  doi     = {10.1234/jsc.2024.123456}
-}
-
-% Conference paper with DOI
-@inproceedings{Garcia2023,
-  author    = {Garc{\'i}a-Mart{\'i}nez, Jos{\'e} and M{\"u}ller, Hans},
-  title     = {International Collaboration in Science},
-  booktitle = {Proceedings of the International Conference on Academic Publishing},
-  year      = {2023},
-  pages     = {45--52},
-  doi       = {10.1109/ICAP.2023.123456}
-}
-
-% Article with PMID but no DOI (older papers)
-@article{OldPaper1995,
-  author  = {Anderson, Philip W.},
-  title   = {Through the Glass Lightly},
-  journal = {Science},
-  year    = {1995},
-  volume  = {267},
-  number  = {5204},
-  pages   = {1615--1616},
-  note    = {PMID: 17808148}
-}
-

package/bin/skills/citation-management/assets/citation_checklist.md

@@ -1,386 +0,0 @@
-# Citation Quality Checklist
-
-Use this checklist to ensure your citations are accurate, complete, and properly formatted before final submission.
-
-## Pre-Submission Checklist
-
-### ✓ Metadata Accuracy
-
-- [ ] All author names are correct and properly formatted
-- [ ] Article titles match the actual publication
-- [ ] Journal/conference names are complete (not abbreviated unless required)
-- [ ] Publication years are accurate
-- [ ] Volume and issue numbers are correct
-- [ ] Page ranges are accurate
-
-### ✓ Required Fields
-
-- [ ] All @article entries have: author, title, journal, year
-- [ ] All @book entries have: author/editor, title, publisher, year
-- [ ] All @inproceedings entries have: author, title, booktitle, year
-- [ ] Modern papers (2000+) include DOI when available
-- [ ] All entries have unique citation keys
-
-### ✓ DOI Verification
-
-- [ ] All DOIs are properly formatted (10.XXXX/...)
-- [ ] DOIs resolve correctly to the article
-- [ ] No DOI prefix in the BibTeX field (no "doi:" or "https://doi.org/")
-- [ ] Metadata from CrossRef matches your BibTeX entry
-- [ ] Run: `python scripts/validate_citations.py references.bib --check-dois`
-
-### ✓ Formatting Consistency
-
-- [ ] Page ranges use double hyphen (--) not single (-)
-- [ ] No "pp." prefix in pages field
-- [ ] Author names use "and" separator (not semicolon or ampersand)
-- [ ] Capitalization protected in titles ({AlphaFold}, {CRISPR}, etc.)
-- [ ] Month names use standard abbreviations if included
-- [ ] Citation keys follow consistent format
-
-### ✓ Duplicate Detection
-
-- [ ] No duplicate DOIs in bibliography
-- [ ] No duplicate citation keys
-- [ ] No near-duplicate titles
-- [ ] Preprints updated to published versions when available
-- [ ] Run: `python scripts/validate_citations.py references.bib`
-
-### ✓ Special Characters
-
-- [ ] Accented characters properly formatted (e.g., {\"u} for ü)
-- [ ] Mathematical symbols use LaTeX commands
-- [ ] Chemical formulas properly formatted
-- [ ] No unescaped special characters (%, &, $, #, etc.)
-
-### ✓ BibTeX Syntax
-
-- [ ] All entries have balanced braces {}
-- [ ] Fields separated by commas
-- [ ] No comma after last field in each entry
-- [ ] Valid entry types (@article, @book, etc.)
-- [ ] Run: `python scripts/validate_citations.py references.bib`
-
-### ✓ File Organization
-
-- [ ] Bibliography sorted in logical order (by year, author, or key)
-- [ ] Consistent formatting throughout
-- [ ] No formatting inconsistencies between entries
-- [ ] Run: `python scripts/format_bibtex.py references.bib --sort year`
-
-## Automated Validation
-
-### Step 1: Format and Clean
-
-```bash
-python scripts/format_bibtex.py references.bib \
-  --deduplicate \
-  --sort year \
-  --descending \
-  --output clean_references.bib
-```
-
-**What this does**:
-- Removes duplicates
-- Standardizes formatting
-- Fixes common issues (page ranges, DOI format, etc.)
-- Sorts by year (newest first)
-
-### Step 2: Validate
-
-```bash
-python scripts/validate_citations.py clean_references.bib \
-  --check-dois \
-  --report validation_report.json \
-  --verbose
-```
-
-**What this does**:
-- Checks required fields
-- Verifies DOIs resolve
-- Detects duplicates
-- Validates syntax
-- Generates detailed report
-
-### Step 3: Review Report
-
-```bash
-cat validation_report.json
-```
-
-**Address any**:
-- **Errors**: Must fix (missing fields, broken DOIs, syntax errors)
-- **Warnings**: Should fix (missing recommended fields, formatting issues)
-- **Duplicates**: Remove or consolidate
-
-### Step 4: Final Check
-
-```bash
-python scripts/validate_citations.py clean_references.bib --verbose
-```
-
-**Goal**: Zero errors, minimal warnings
-
-## Manual Review Checklist
-
-### Critical Citations (Top 10-20 Most Important)
-
-For your most important citations, manually verify:
-
-- [ ] Visit DOI link and confirm it's the correct article
-- [ ] Check author names against the actual publication
-- [ ] Verify year matches publication date
-- [ ] Confirm journal/conference name is correct
-- [ ] Check that volume/pages match
-
-### Common Issues to Watch For
-
-**Missing Information**:
-- [ ] No DOI for papers published after 2000
-- [ ] Missing volume or page numbers for journal articles
-- [ ] Missing publisher for books
-- [ ] Missing conference location for proceedings
-
-**Formatting Errors**:
-- [ ] Single hyphen in page ranges (123-145 → 123--145)
-- [ ] Ampersands in author lists (Smith & Jones → Smith and Jones)
-- [ ] Unprotected acronyms in titles (DNA → {DNA})
-- [ ] DOI includes URL prefix (https://doi.org/10.xxx → 10.xxx)
-
-**Metadata Mismatches**:
-- [ ] Author names differ from publication
-- [ ] Year is online-first instead of print publication
-- [ ] Journal name abbreviated when it should be full
-- [ ] Volume/issue numbers swapped
-
-**Duplicates**:
-- [ ] Same paper cited with different citation keys
-- [ ] Preprint and published version both cited
-- [ ] Conference paper and journal version both cited
-
-## Field-Specific Checks
-
-### Biomedical Sciences
-
-- [ ] PubMed Central ID (PMCID) included when available
-- [ ] MeSH terms appropriate (if using)
-- [ ] Clinical trial registration number included (if applicable)
-- [ ] All references to treatments/drugs accurately cited
-
-### Computer Science
-
-- [ ] arXiv ID included for preprints
-- [ ] Conference proceedings properly cited (not just "NeurIPS")
-- [ ] Software/dataset citations include version numbers
-- [ ] GitHub links stable and permanent
-
-### General Sciences
-
-- [ ] Data availability statements properly cited
-- [ ] Retracted papers identified and removed
-- [ ] Preprints checked for published versions
-- [ ] Supplementary materials referenced if critical
-
-## Final Pre-Submission Steps
-
-### 1 Week Before Submission
-
-- [ ] Run full validation with DOI checking
-- [ ] Fix all errors and critical warnings
-- [ ] Manually verify top 10-20 most important citations
-- [ ] Check for any retracted papers
-
-### 3 Days Before Submission
-
-- [ ] Re-run validation after any manual edits
-- [ ] Ensure all in-text citations have corresponding bibliography entries
-- [ ] Ensure all bibliography entries are cited in text
-- [ ] Check citation style matches journal requirements
-
-### 1 Day Before Submission
-
-- [ ] Final validation check
-- [ ] LaTeX compilation successful with no warnings
-- [ ] PDF renders all citations correctly
-- [ ] Bibliography appears in correct format
-- [ ] No placeholder citations (Smith et al. XXXX)
-
-### Submission Day
-
-- [ ] One final validation run
-- [ ] No last-minute edits without re-validation
-- [ ] Bibliography file included in submission package
-- [ ] Figures/tables referenced in text match bibliography
-
-## Quality Metrics
-
-### Excellent Bibliography
-
-- ✓ 100% of entries have DOIs (for modern papers)
-- ✓ Zero validation errors
-- ✓ Zero missing required fields
-- ✓ Zero broken DOIs
-- ✓ Zero duplicates
-- ✓ Consistent formatting throughout
-- ✓ All citations manually spot-checked
-
-### Acceptable Bibliography
-
-- ✓ 90%+ of modern entries have DOIs
-- ✓ Zero high-severity errors
-- ✓ Minor warnings only (e.g., missing recommended fields)
-- ✓ Key citations manually verified
-- ✓ Compilation succeeds without errors
-
-### Needs Improvement
-
-- ✗ Missing DOIs for recent papers
-- ✗ High-severity validation errors
-- ✗ Broken or incorrect DOIs
-- ✗ Duplicate entries
-- ✗ Inconsistent formatting
-- ✗ Compilation warnings or errors
-
-## Emergency Fixes
-
-If you discover issues at the last minute:
-
-### Broken DOI
-
-```bash
-# Find correct DOI
-# Option 1: Search CrossRef
-# https://www.crossref.org/
-
-# Option 2: Search on publisher website
-# Option 3: Google Scholar
-
-# Re-extract metadata
-python scripts/extract_metadata.py --doi CORRECT_DOI
-```
-
-### Missing Information
-
-```bash
-# Extract from DOI
-python scripts/extract_metadata.py --doi 10.xxxx/yyyy
-
-# Or from PMID (biomedical)
-python scripts/extract_metadata.py --pmid 12345678
-
-# Or from arXiv
-python scripts/extract_metadata.py --arxiv 2103.12345
-```
-
-### Duplicate Entries
-
-```bash
-# Auto-remove duplicates
-python scripts/format_bibtex.py references.bib \
-  --deduplicate \
-  --output fixed_references.bib
-```
-
-### Formatting Errors
-
-```bash
-# Auto-fix common issues
-python scripts/format_bibtex.py references.bib \
-  --output fixed_references.bib
-
-# Then validate
-python scripts/validate_citations.py fixed_references.bib
-```
-
-## Long-Term Best Practices
-
-### During Research
-
-- [ ] Add citations to bibliography file as you find them
-- [ ] Extract metadata immediately using DOI
-- [ ] Validate after every 10-20 additions
-- [ ] Keep bibliography file under version control
-
-### During Writing
-
-- [ ] Cite as you write
-- [ ] Use consistent citation keys
-- [ ] Don't delay adding references
-- [ ] Validate weekly
-
-### Before Submission
-
-- [ ] Allow 2-3 days for citation cleanup
-- [ ] Don't wait until the last day
-- [ ] Automate what you can
-- [ ] Manually verify critical citations
-
-## Tool Quick Reference
-
-### Extract Metadata
-
-```bash
-# From DOI
-python scripts/doi_to_bibtex.py 10.1038/nature12345
-
-# From multiple sources
-python scripts/extract_metadata.py \
-  --doi 10.1038/nature12345 \
-  --pmid 12345678 \
-  --arxiv 2103.12345 \
-  --output references.bib
-```
-
-### Validate
-
-```bash
-# Basic validation
-python scripts/validate_citations.py references.bib
-
-# With DOI checking (slow but thorough)
-python scripts/validate_citations.py references.bib --check-dois
-
-# Generate report
-python scripts/validate_citations.py references.bib \
-  --report validation.json \
-  --verbose
-```
-
-### Format and Clean
-
-```bash
-# Format and fix issues
-python scripts/format_bibtex.py references.bib
-
-# Remove duplicates and sort
-python scripts/format_bibtex.py references.bib \
-  --deduplicate \
-  --sort year \
-  --descending \
-  --output clean_refs.bib
-```
-
-## Summary
-
-**Minimum Requirements**:
-1. Run `format_bibtex.py --deduplicate`
-2. Run `validate_citations.py`
-3. Fix all errors
-4. Compile successfully
-
-**Recommended**:
-1. Format, deduplicate, and sort
-2. Validate with `--check-dois`
-3. Fix all errors and warnings
-4. Manually verify top citations
-5. Re-validate after fixes
-
-**Best Practice**:
-1. Validate throughout research process
-2. Use automated tools consistently
-3. Keep bibliography clean and organized
-4. Document any special cases
-5. Final validation 1-3 days before submission
-
-**Remember**: Citation errors reflect poorly on your scholarship. Taking time to ensure accuracy is worthwhile!
-