dependency cycle

[targos]

• emdb -> ms-spectrum -> emdb
  • add back { "path": "../emdb" } to the tsconfig.json of ms-spectrum when fixed
• mf-parser -> mf-utilities -> mf-parser

[tpoisseau]

https://github.com/acrazing/dpdm

% npx dpdm --no-warning --no-tree circular packages/emdb/src/index.js
✔ [156/156] Analyze done!
• Circular Dependencies
  1) packages/ms-spectrum/lib/src/index.js -> packages/ms-spectrum/lib/src/Spectrum.js -> packages/ms-spectrum/lib/src/getFragmentPeaks.js -> packages/emdb/lib/src/index.js

% find ./packages/*/src -type f -name 'index.*' -depth 1 -print0 | tr '\n' '\0' | xargs -0 -t -n1 npx dpdm --no-warning --no-tree circular
npx dpdm --no-warning --no-tree circular ./packages/atom-sorter/src/index.ts
✔ [1/1] Analyze done!
• Circular Dependencies
  ✅ Congratulations, no circular dependency was found in your project.

npx dpdm --no-warning --no-tree circular ./packages/chemical-elements/src/index.ts
✔ [12/12] Analyze done!
• Circular Dependencies
  ✅ Congratulations, no circular dependency was found in your project.

npx dpdm --no-warning --no-tree circular ./packages/chemical-groups/src/index.js
✔ [4/4] Analyze done!
• Circular Dependencies
  ✅ Congratulations, no circular dependency was found in your project.

npx dpdm --no-warning --no-tree circular ./packages/emdb/src/index.js
✔ [156/156] Analyze done!
• Circular Dependencies
  1) packages/ms-spectrum/lib/src/index.js -> packages/ms-spectrum/lib/src/Spectrum.js -> packages/ms-spectrum/lib/src/getFragmentPeaks.js -> packages/emdb/lib/src/index.js

npx dpdm --no-warning --no-tree circular ./packages/isotopic-distribution/src/index.js
✔ [62/62] Analyze done!
• Circular Dependencies
  ✅ Congratulations, no circular dependency was found in your project.

npx dpdm --no-warning --no-tree circular ./packages/mass-fragmentation/src/index.js
✔ [56/56] Analyze done!
• Circular Dependencies
  ✅ Congratulations, no circular dependency was found in your project.

npx dpdm --no-warning --no-tree circular ./packages/mass-tools/src/index.js
✔ [199/199] Analyze done!
• Circular Dependencies
  1) packages/emdb/lib/src/index.js -> packages/ms-spectrum/lib/src/index.js -> packages/ms-spectrum/lib/src/Spectrum.js -> packages/ms-spectrum/lib/src/getFragmentPeaks.js
  2) packages/emdb/lib/src/index.js -> packages/ms-spectrum/lib/src/index.js -> packages/ms-spectrum/lib/src/jsgraph/index.js -> packages/ms-spectrum/lib/src/jsgraph/getPeaksAnnotation.js

npx dpdm --no-warning --no-tree circular ./packages/mf-finder/src/index.js
✔ [63/63] Analyze done!
• Circular Dependencies
  ✅ Congratulations, no circular dependency was found in your project.

npx dpdm --no-warning --no-tree circular ./packages/mf-from-atomic-ratio/src/index.js
✔ [62/62] Analyze done!
• Circular Dependencies
  ✅ Congratulations, no circular dependency was found in your project.

npx dpdm --no-warning --no-tree circular ./packages/mf-from-ea/src/index.js
✔ [47/47] Analyze done!
• Circular Dependencies
  ✅ Congratulations, no circular dependency was found in your project.

npx dpdm --no-warning --no-tree circular ./packages/mf-from-google-sheet/src/index.js
✔ [62/62] Analyze done!
• Circular Dependencies
  ✅ Congratulations, no circular dependency was found in your project.

npx dpdm --no-warning --no-tree circular ./packages/mf-generator/src/index.js
✔ [60/60] Analyze done!
• Circular Dependencies
  ✅ Congratulations, no circular dependency was found in your project.

npx dpdm --no-warning --no-tree circular ./packages/mf-global/src/index.js
✔ [155/155] Analyze done!
• Circular Dependencies
  1) packages/emdb/lib/src/index.js -> packages/ms-spectrum/lib/src/index.js -> packages/ms-spectrum/lib/src/Spectrum.js -> packages/ms-spectrum/lib/src/getFragmentPeaks.js
  2) packages/emdb/lib/src/index.js -> packages/ms-spectrum/lib/src/index.js -> packages/ms-spectrum/lib/src/jsgraph/index.js -> packages/ms-spectrum/lib/src/jsgraph/getPeaksAnnotation.js

npx dpdm --no-warning --no-tree circular ./packages/mf-matcher/src/index.js
✔ [58/58] Analyze done!
• Circular Dependencies
  ✅ Congratulations, no circular dependency was found in your project.

npx dpdm --no-warning --no-tree circular ./packages/mf-parser/src/index.ts
✔ [49/49] Analyze done!
• Circular Dependencies
  ✅ Congratulations, no circular dependency was found in your project.

npx dpdm --no-warning --no-tree circular ./packages/mf-utilities/src/index.ts
✔ [54/54] Analyze done!
• Circular Dependencies
  ✅ Congratulations, no circular dependency was found in your project.

npx dpdm --no-warning --no-tree circular ./packages/mfs-deconvolution/src/index.js
✔ [74/74] Analyze done!
• Circular Dependencies
  ✅ Congratulations, no circular dependency was found in your project.

npx dpdm --no-warning --no-tree circular ./packages/ms-report/src/index.js
✔ [90/90] Analyze done!
• Circular Dependencies
  ✅ Congratulations, no circular dependency was found in your project.

npx dpdm --no-warning --no-tree circular ./packages/ms-spectrum/src/index.js
✔ [152/152] Analyze done!
• Circular Dependencies
  1) packages/emdb/lib/src/index.js -> packages/ms-spectrum/lib/src/index.js -> packages/ms-spectrum/lib/src/Spectrum.js -> packages/ms-spectrum/lib/src/getFragmentPeaks.js
  2) packages/emdb/lib/src/index.js -> packages/ms-spectrum/lib/src/index.js -> packages/ms-spectrum/lib/src/jsgraph/index.js -> packages/ms-spectrum/lib/src/jsgraph/getPeaksAnnotation.js

npx dpdm --no-warning --no-tree circular ./packages/nucleotide/src/index.js
✔ [64/64] Analyze done!
• Circular Dependencies
  ✅ Congratulations, no circular dependency was found in your project.

npx dpdm --no-warning --no-tree circular ./packages/number-treemap/src/index.js
✔ [2/2] Analyze done!
• Circular Dependencies
  ✅ Congratulations, no circular dependency was found in your project.

npx dpdm --no-warning --no-tree circular ./packages/octochemdb/src/index.js
✔ [172/172] Analyze done!
• Circular Dependencies
  1) packages/ms-spectrum/lib/src/index.js -> packages/ms-spectrum/lib/src/Spectrum.js -> packages/ms-spectrum/lib/src/getFragmentPeaks.js -> packages/emdb/lib/src/index.js

npx dpdm --no-warning --no-tree circular ./packages/peptide/src/index.js
✔ [64/64] Analyze done!
• Circular Dependencies
  ✅ Congratulations, no circular dependency was found in your project.

[tpoisseau]

So it seems we need to solve this last circular deps between emdb and ms-spectrum

[tpoisseau]

Is it OK if I move packages/emdb/src/from/fromMonoisotopicMass.js to packages/ms-spectrum/src/fromMonoisotopicMass ?

ms-spectrum depend on emdb only to do emdb.fromMonoisotopicMass

emdb depend on ms-spectrum to do experimentalSpectrum.normedY(), this.experimentalSpectrum = new Spectrum(data, { threshold }), get experimentalSpectrum.dataandexperimentalSpectrum.sumY()`

I can keep fromMonoisotopicMass in EMDB prototype, but calling ms-spectrum#fromMonoisotopicMass.
Like that, emdb depend on ms-spectrum but ms-spectrum do not depend on emdb

[targos]

@lpatiny wdyt?

[lpatiny]

Yes seems ok to me as long as the API does not change and all the tests continue to pass (you will need somehow to duplicate some tests to test fromMonoisotopicMass in ms-spectrum and in emdb)