…g up protein pool exchange and proteomics integrated, adjusting 'percUsage' accordingly.

…g up protein pool exchange and proteomics integrated, adjusting 'percUsage' accordingly.

- use fluxes from usageData
- give protein pool in usageReport instead of printing to command window

 Update ProtPool Calculation by Including usage_prot_ Reaction Fluxes

* fix: loadDatabases error when uniprot dl fails

* chore: updateDocumentation

* chore: update Actions dependency

and trying to fix an issue: https://stackoverflow.com/questions/70435286/resource-not-accessible-by-integration-on-github-post-repos-owner-repo-ac

* fix: calculateFfactor read header in paxDB.tsv

sometimes, the first # in the file is missed

* chore: updateGECKOdoc

* fix: runDLKcat parse full paths

* fix: applyKcatConstraints if all kcat are zero

* fix: getStandardKcat also if enzyme is missing

* feat: removeStandardKcat new function

* chore: RAVEN release 2.9.1 as dependency

* fix: calculateFfactor can take protData input

* feat: constrainEnzConcs keep prot pool draw

addresses #375

* fix: updateProtPool obsolete

* doc: update full_ecModel for prot_usage rxns

* fix: enzymeUsage correct mention of output units

solves #376

* doc: updateGECKOdoc

* doc: update README.md with protocol change

* fix: README.md link

* Revert "Merge pull request #372 from HossFir/update-reportEnzymeUsage"

This reverts commit cc8e449, reversing
changes made to 883b40d.

* fix: reportEnzymeUsage gives total protein usage