7. Reading与Coding的交点¶
在我们整个文献处理的流程中，Reading和Coding并不是完全割裂的两个阶段，而是存在大量交集和反馈循环的，尤其是对于 生物医学+AI计算的交叉领域。
文献是理论，代码项目是实践，两者相辅相成。
📌 对于github CLI的科研使用场景，参考GhResearcher，下面的github-export模块是对GhResearcher parse模块固定子命令的简单封装，目前该项目基本定型，后续会依据具体使用需求进行优化与维护
目前暂时提供从pubmed文献元数据中提取github链接的功能模块
❯ paperflow github-export --help
Usage: paperflow github-export [OPTIONS]
Export GitHub links from merged PubMed JSON, validate accessibility, and aggregate `ghresearcher parse <owner/repo>
--view` outputs into one markdown.
╭─ Options ────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ * --input -i TEXT Merged JSON/JSONL file produced by pubmed-merge-json. │
│ [required] │
│ * --output -o TEXT Output markdown file for aggregated ghresearcher parse │
│ results. │
│ [required] │
│ --report TEXT CSV report path for URL audit table. Defaults to │
│ <output>_github_report.csv. │
│ --separator TEXT Separator inserted between repository sections. │
│ [default: <<<PY_PAPERFLOW_REPO_BOUNDARY>>>] │
│ --timeout FLOAT URL request timeout in seconds. [default: 10.0] │
│ --retries INTEGER URL request retries for accessibility checks. │
│ [default: 1] │
│ --sleep FLOAT Sleep seconds between ghresearcher calls. [default: 0.2] │
│ --max-repos INTEGER Optional cap on number of repositories to parse. │
│ --strict-ghresearcher Fail fast when ghresearcher is missing or a parse call │
│ fails. │
│ --overwrite Overwrite output markdown instead of appending. │
│ --include-tree --no-include-tree Include file tree via ghresearcher (default). Use │
│ --no-include-tree to fetch repo info via gh repo view │
│ instead. │
│ [default: include-tree] │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
我们提供了一个输出的统计报告，包含了每个github链接的可访问性检查结果，以及对应的ghresearcher解析状态（成功/失败/跳过）。对于成功解析的链接，我们会将ghresearcher的输出markdown按照文献进行分隔，合并成一个总的markdown文件，方便后续阅读和分析。
输出统计报告有终端查看和csv文件两种形式，csv文件默认命名为<output>_github_report.csv，你也可以通过--report参数自定义命名和路径。
paperflow github-export -i /IDR_all_20260520/analysis/IDR_all_20260520_2026-05-20_18-33-54.json -o /IDR_all_20260520/analysis/method/github_parse_all_20260526.md --report /IDR_all_20260520/analysis/method/github_url_audit_20260526.csv --no-include-tree
Found 66 GitHub URL entries from 109 papers.
[1/44] gh repo view BioComputingUP/AlphaFold-disorder
[2/44] gh repo view BioComputingUP/caid2-reference
[3/44] gh repo view G4REP/G4REPmodel
[4/44] gh repo view GuyAllard/markov_clustering
[5/44] gh repo view HFChenLab/PhantoIDP
[6/44] gh repo view HHJHgithub/MoRFs_MPM
[7/44] gh repo view IDRIDP/IDPFunNet
[8/44] gh repo view JMLab-tifrh/Protein_Ligand_Variational_Autoencoder
[9/44] gh repo view LabWolfrum/Fritze_et_al.2023
[10/44] gh repo view LiZhaoLab/DmelPPI
[11/44] gh repo view ModicLab/smOOPs_project
[12/44] gh repo view amchakra/tosca
[13/44] gh repo view andrewbkleist/chemokine_gpcr_encoding
[14/44] gh repo view benhid/pyMSA
[15/44] gh repo view binhe-lab/E013-Pho4-evolution
[16/44] gh repo view brgenzim/MemDis
[17/44] gh repo view desiro/SClow
[18/44] gh repo view emerson106/SGPPI
[19/44] gh repo view facebookresearch/esm
[20/44] gh repo view feiglab/idpgan_ped
[21/44] gh repo view gcollet/MstatX
[22/44] gh repo view gjoni/mylddt
[23/44] gh repo view holehouse-lab/shephard-data
[24/44] gh repo view idptools/goose
[25/44] gh repo view idptools/sparrow
[26/44] gh repo view ingolia-lab/post-transcriptional-idrs
[27/44] gh repo view isblab/disobind
[28/44] gh repo view jahnl/binding_in_disorder
[29/44] gh repo view julie-forman-kay-lab/IDPConformerGenerator
[30/44] gh repo view melppi/melppi.github.io
[31/44] gh repo view microsoft/LoRA
[32/44] gh repo view mmb-irb/MDDB-workflow
[33/44] gh repo view molML/14-3-3-bindsite
[34/44] gh repo view nadavbra/protein_bert
[35/44] gh repo view naveen-joy-18/Impact-of-Intrinsically-Disordered-Regions-and-Functional-Disorder-Hotspots-in-the-Human-Kinome
[36/44] gh repo view nofundamental/lncRNAnet
[37/44] gh repo view paulrobustelli/Sisk_NTAIL_DeepMSM_2023
[38/44] gh repo view qczhang/icSHAPE
[39/44] gh repo view roneshsharma/MoRFpred-plus
[40/44] gh repo view roneshsharma/Predict-MoRFs
[41/44] gh repo view rwnull/insitu_probe_generator
[42/44] gh repo view ulelab/icount-mini
[43/44] gh repo view ulelab/ultraplex
[44/44] gh repo view wulab-github/IDBSpred
GitHub URL Audit Summary
- total_url_entries: 66
- unique_urls: 61
- accessible_entries: 50
- accessible_ratio: 75.76%
- report: /data2/Project_Paper/IDR_Inter/IDR_all_20260520/analysis/method/github_url_audit_20260526.csv
Repository Export Summary
- selected_repos: 44
- exported: 44
- failed: 0
- output: /data2/Project_Paper/IDR_Inter/IDR_all_20260520/analysis/method/github_parse_all_20260526.md
考虑到部分github仓库的目录树结构比较复杂、繁冗，我们提供了是否跳过解析目录树的选项，--include-tree/--no-include-tree，默认是包含目录树的，如果你觉得目录树信息过于冗余，你可以选择跳过目录树的解析，这样就只会保留仓库的基本信息，而不会展开每个文件的目录结构。
一些未正常提取的github链接可以从报告csv文件中手动修改
修改的结果手动追加到总的markdown文件中