anthropics/uplifting-biomolecular-modeling
Code Volume
Analysis scope, overview of main, test, generated, deployment, build, and other code.
Source Code Analysis Scope
Files includes and excluded from analyses
pt
diff
patch
pyi
pkl
in
gitattributes

scoping details...
  • 24 extensions are included in analyses: py, md, json, txt, pt, yml, sh, toml, cu, yaml, h, cc, diff, cuh, gitignore, patch, pyi, cpp, pkl, dockerignore, css, in, ipynb, gitattributes
  • 10 criteria are used to exclude files from analysis:
    • exclude files with path like ".*/(3rd|[Tt]hird)[-_]?[Pp]arty/.*" (Dependencies) (48 files).
    • exclude files with path like ".*/[Vv]endors?/.*" (Dependencies) (56 files).
    • exclude files with path like ".*/docs/.*" (Documentation) (66 files).
    • exclude files with path like ".*/bin/.*" (Binaries for distribution) (87 files).
    • exclude files with path like ".*/git[-]commit[-]trailers[.]txt" (Git history trailers) (1 file).
    • exclude files with path like ".*/git[-]history[.]txt" (Git history) (1 file).
    • exclude files with path like ".*/git[-][a-zA-Z0-9_]+[.]txt" (Git data exports for sokrates analyses) (1 file).
    • exclude files with path like ".*/_sokrates/.*" (Sokrates files) (0 files).
    • exclude files with path like ".*/_sokrates_landscape/.*" (Sokrates landscape files) (0 files).
    • exclude files with path like ".*/sokrates_.*?[.]json" (Sokrates conventions and configurations) (0 files).
Overview of Analyzed Files
Basic stats on analyzed files
Intro
For analysis purposes we separate files in scope into several categories: main, test, generated, deployment and build, and other.
main726274 LOC (66%) 3,636 files
test240456 LOC (22%) 1,731 files
generated0 LOC (0%) 0 files
build and deployment10976 LOC (1%) 173 files
other114970 LOC (10%) 942 files
Main Code
All manually created or maintained source code that defines logic of the product that is run in a production environment.
pt
pyi
in
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py688021 LOC (94%) 3,417 files
cu12123 LOC (1%) 49 files
cuh9800 LOC (1%) 20 files
pt5816 LOC (<1%) 5 files
cc5577 LOC (<1%) 28 files
h1868 LOC (<1%) 37 files
yaml1798 LOC (<1%) 60 files
cpp576 LOC (<1%) 6 files
toml494 LOC (<1%) 2 files
pyi170 LOC (<1%) 10 files
in31 LOC (<1%) 2 files

scope details...
  • The following criteria are used to filter files:
    • files with paths like ".*".
  • 3636 files match defined criteria (726,274 LOC, 100.0% vs. main code):
    • 3,417 py files (688,021 LOC)
    • 49 cu files (12,123 LOC)
    • 20 cuh files (9,800 LOC)
    • 5 pt files (5,816 LOC)
    • 28 cc files (5,577 LOC)
    • 37 h files (1,868 LOC)
    • 60 yaml files (1,798 LOC)
    • 6 cpp files (576 LOC)
    • 2 toml files (494 LOC)
    • 10 pyi files (170 LOC)
    • 2 in files (31 LOC)
Test Code
Used only for testing of the product. Normally not deployed in a production environment.
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py239128 LOC (99%) 1,712 files
yaml1324 LOC (<1%) 18 files
sh4 LOC (<1%) 1 file

scope details...
  • The following criteria are used to filter files:
    • files with paths like ".*/[Tt]ests/.*".
    • files with paths like ".*/test_.*".
    • files with paths like ".*_test[.].*".
    • files with paths like ".*/testing[.].*".
    • files with paths like ".*[-]test[-].*".
    • files with paths like ".*/[Tt]est/.*".
    • files with paths like ".*/[Ss]pecs/.*".
  • 1731 files match defined criteria (240,456 LOC, 33.1% vs. main code):
    • 1,712 py files (239,128 LOC)
    • 18 yaml files (1,324 LOC)
    • 1 sh files (4 LOC)
Build and Deployment Code
Source code used to configure or support build and deployment process.
gitattributes
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sh4946 LOC (45%) 66 files
toml3739 LOC (34%) 58 files
yaml962 LOC (8%) 20 files
gitignore662 LOC (6%) 17 files
py597 LOC (5%) 8 files
dockerignore68 LOC (<1%) 3 files
gitattributes2 LOC (<1%) 1 file

scope details...
  • The following criteria are used to filter files:
    • files with paths like ".*[.]sh".
    • files with paths like ".*/pyproject[.]toml".
    • files with paths like ".*[.]git[a-z]+".
    • files with paths like ".*/[.]gitignore".
    • files with paths like ".*/requirements[a-zA-Z0-9._-]*[.]txt".
    • files with paths like ".*/setup[.]py".
    • files with paths like ".*/[.]github/workflows/.*[.]ya?ml".
    • files with paths like ".*/CMakeLists[.]txt".
    • files with paths like ".*/[.]dockerignore".
    • files with paths like "(.*/)?[.]dockerignore".
    • files with paths like ".*/[.]gitattributes".
  • 173 files match defined criteria (10,976 LOC, 1.5% vs. main code):
    • 66 sh files (4,946 LOC)
    • 58 toml files (3,739 LOC)
    • 20 yaml files (962 LOC)
    • 17 gitignore files (662 LOC)
    • 8 py files (597 LOC)
    • 3 dockerignore files (68 LOC)
    • 1 gitattributes files (2 LOC)
Other Code
diff
patch
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json66455 LOC (57%) 319 files
md23132 LOC (20%) 349 files
txt18100 LOC (15%) 200 files
diff2791 LOC (2%) 27 files
yaml2203 LOC (1%) 30 files
patch1883 LOC (1%) 14 files
py406 LOC (<1%) 3 files

scope details...
  • The following criteria are used to filter files:
    • files with paths like ".*[.]md".
    • files with paths like ".*/README[.][a-z0-9]+".
    • files with paths like ".*[.]txt".
    • files with paths like ".*[.]json".
    • files with paths like ".*/[Ee]xamples/.*".
    • files with paths like ".*/LICENSE[.][a-z0-9]+".
    • files with paths like ".*/vendor/.*".
    • files with paths like ".*[.]diff".
    • files with paths like ".*[.]patch".
  • 942 files match defined criteria (114,970 LOC, 15.8% vs. main code):
    • 319 json files (66,455 LOC)
    • 349 md files (23,132 LOC)
    • 200 txt files (18,100 LOC)
    • 27 diff files (2,791 LOC)
    • 30 yaml files (2,203 LOC)
    • 14 patch files (1,883 LOC)
    • 3 py files (406 LOC)
About This Analysis
learn more about scopes (main, test, generated, build, other)...

  • The main category contains all manually created source code files that are being used in the production.
  • Files in the main category are used as input for other analyses: logical decomposition, concerns, duplication, file size, unit size, and conditional complexity.
  • Test source code files are used only for testing of the product. These files are normally not deployed to production.
  • Build and deployment source code files are used to configure or support build and deployment process.
  • Generated source code files are automatically generated files that have not been manually changed after generation.
  • While a source code folder may contain a number of files, we are primarily interested in the source code files that are being written and maintained by developers.
  • Files containing binaries, documentation, or third-party libraries, for instance, are excluded from analysis. The exception are third-party libraries that have been changed by developers.

learn more about used code analyzers...
  • *.py files are analyzed with PythonAnalyzer:
    • All basic standard analyses supported (source code overview, duplication, file size, concerns, findings, metrics, controls)
    • Advanced code cleaning (empty lines and comments removed for LOC calculations, additional cleaning for duplication calculations)
    • Unit size analysis
    • Conditional complexity analysis
    • Basic heuristic dependency analysis
  • *.cu files are analyzed with DefaultLanguageAnalyzer:
    • All basic standard analyses supported (source code overview, duplication, file size, concerns, findings, metrics, controls)
    • Basic code cleaning (empty lines removed for LOC calculations and duplication calculations)
    • No unit size analysis
    • No conditional complexity analysis
    • No dependency analysis
  • *.cuh files are analyzed with DefaultLanguageAnalyzer:
    • All basic standard analyses supported (source code overview, duplication, file size, concerns, findings, metrics, controls)
    • Basic code cleaning (empty lines removed for LOC calculations and duplication calculations)
    • No unit size analysis
    • No conditional complexity analysis
    • No dependency analysis
  • *.pt files are analyzed with XmlAnalyzer:
    • All basic standard analyses supported (source code overview, duplication, file size, concerns, findings, metrics, controls)
    • Advanced code cleaning (empty lines and comments removed for LOC calculations, additional cleaning for duplication calculations)
    • No unit size analysis
    • No conditional complexity analysis
    • No dependency analysis
  • *.cc files are analyzed with CppAnalyzer:
    • All basic standard analyses supported (source code overview, duplication, file size, concerns, findings, metrics, controls)
    • Advanced code cleaning (empty lines and comments removed for LOC calculations, additional cleaning for duplication calculations)
    • Unit size analysis
    • Conditional complexity analysis
    • Advanced heuristic dependency analysis
  • *.h files are analyzed with CppAnalyzer:
    • All basic standard analyses supported (source code overview, duplication, file size, concerns, findings, metrics, controls)
    • Advanced code cleaning (empty lines and comments removed for LOC calculations, additional cleaning for duplication calculations)
    • Unit size analysis
    • Conditional complexity analysis
    • Advanced heuristic dependency analysis
  • *.yaml files are analyzed with YamlAnalyzer:
    • All basic standard analyses supported (source code overview, duplication, file size, concerns, findings, metrics, controls)
    • Advanced code cleaning (empty lines and comments removed for LOC calculations, additional cleaning for duplication calculations)
    • No unit size analysis
    • No conditional complexity analysis
    • No dependency analysis
  • *.cpp files are analyzed with CppAnalyzer:
    • All basic standard analyses supported (source code overview, duplication, file size, concerns, findings, metrics, controls)
    • Advanced code cleaning (empty lines and comments removed for LOC calculations, additional cleaning for duplication calculations)
    • Unit size analysis
    • Conditional complexity analysis
    • Advanced heuristic dependency analysis
  • *.toml files are analyzed with DefaultLanguageAnalyzer:
    • All basic standard analyses supported (source code overview, duplication, file size, concerns, findings, metrics, controls)
    • Basic code cleaning (empty lines removed for LOC calculations and duplication calculations)
    • No unit size analysis
    • No conditional complexity analysis
    • No dependency analysis
  • *.pyi files are analyzed with PythonAnalyzer:
    • All basic standard analyses supported (source code overview, duplication, file size, concerns, findings, metrics, controls)
    • Advanced code cleaning (empty lines and comments removed for LOC calculations, additional cleaning for duplication calculations)
    • Unit size analysis
    • Conditional complexity analysis
    • Basic heuristic dependency analysis
  • *.in files are analyzed with RustAnalyzer:
    • All basic standard analyses supported (source code overview, duplication, file size, concerns, findings, metrics, controls)
    • Advanced code cleaning (empty lines and comments removed for LOC calculations, additional cleaning for duplication calculations)
    • Unit size analysis
    • Conditional complexity analysis
    • No dependency analysis