├── .gitignore ├── LICENSE ├── README.md └── computational-reproducibility-pmc ├── analyses ├── Index.ipynb ├── N1.Repository.ipynb ├── N1.Skip.Notebook.ipynb ├── N10.Markdown.ipynb ├── N2.Notebook.ipynb ├── N3.Cell.ipynb ├── N4.Features.ipynb ├── N5.Modules.ipynb ├── N6.AST.ipynb ├── N7.Name.ipynb ├── N8.Execution.ipynb ├── PMC1.GeneralInfo.ipynb ├── PMC2.ProgrammingLanguages.ipynb ├── PMC3.ReproducibilityStudy.ipynb ├── PMC4.DecayRate.ipynb ├── PMC5.AnalysisResearchField.ipynb ├── PMC6.MetricsCorrelation.ipynb ├── PMC7.ExceptionAnalysis.ipynb ├── analysis_helpers.py ├── analysis_helpers_executions.py ├── requirements.txt └── variables.dat ├── archaeology ├── config.py ├── consts.py ├── db.py ├── e0_clear_nonzip.py ├── e1_clone_removed.py ├── e2_delete_unlinked_files.py ├── e3_extract_cell_again.py ├── e4_find_missing_files.py ├── e5_unzip_repositories.py ├── e6_fix_ast_others.py ├── empty.py ├── execution_rules.py ├── load_repository.py ├── main.py ├── main_download.py ├── main_with_crawler.py ├── main_without_crawler.py ├── p0_local_possibility.py ├── p1_notebook_aggregate.py ├── p2_sha1_exercises.py ├── pid.py ├── r0_article_db.py ├── r0_main.py ├── r0_publications.py ├── r1_article_metadata.py ├── r1_run_pipeline.py ├── r2_article_repository.py ├── r3_github_api.py ├── r4_pycodestyle_check.py ├── r5_pmid_mesh.py ├── requirements.txt ├── run_notebook.py ├── runjob.py ├── s0_repository_crawler.py ├── s1_notebooks_and_cells.py ├── s2_requirement_files.py ├── s3_compress.py ├── s4_markdown_features.py ├── s5_extract_files.py ├── s6_cell_features.py ├── s7_execute_repositories.py ├── s8_execute_cellorder.py ├── setup.py ├── test_connection.py └── utils.py └── conda-setup.sh /.gitignore: -------------------------------------------------------------------------------- 1 | */.ipynb_checkpoints/ 2 | */__pycache__/ 3 | -------------------------------------------------------------------------------- /LICENSE: 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