Add pathway_analysis workflow
#128
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breakthewall
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Oct 20, 2023
* chore(github): update workflows * chore(github): add CONTRIBUTING * fix(get_sbml_model): rm 'parent' * chore(get_sbml_model): handle errors * fix(get_sbml_model): fix 'requests' version * taxonid (#114) * fix(get_sbml_model): rm 'parent' * chore(get_sbml_model): handle errors * fix(get_sbml_model): fix 'requests' version * chore(github): workflow release * feat(selenzy_wrapper): give taxon ID via a file * chore(selenzy_wrapper): rm comment (#115) * Taxonid (#116) * chore(selenzy_wrapper): rm comment * chore(selenzy-wrapper): rm config * chore(selenzy-wrapper): rename * Taxonid (#117) * chore(selenzy_wrapper): rm comment * chore(selenzy-wrapper): rm config * chore(selenzy-wrapper): rename * chore(selenzy-wrapper): rename * chore(selenzy_wrapper): add test * chore(deps): bump tj-actions/changed-files from 35 to 36 (#120) Bumps [tj-actions/changed-files](https://github.com/tj-actions/changed-files) from 35 to 36. - [Release notes](https://github.com/tj-actions/changed-files/releases) - [Changelog](https://github.com/tj-actions/changed-files/blob/main/HISTORY.md) - [Commits](tj-actions/changed-files@v35...v36) --- updated-dependencies: - dependency-name: tj-actions/changed-files dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * fix(github): workflow syntax * chore: rm config folders (#118) * chore: rm config folders * fix(get_sbml_model): fix taxid md5 * fix(icfree): update test section * fix(rp2biosensor): udpate version, add --cache-dir arg * chore(github): skip `partsgenie` test * fix(github): missing files * fix(github): skip aggregate_results if test is skipped * fix(github): increase timeout * fix(github): skip temporarly `rpbasicdesign` --------- Co-authored-by: Guillaume Gricourt <guipagui@gmail.com> * Workflows `basic_assembly_workflow` (#119) * feat(workflows): add one workflow * fix(tools): update `sbol_converter` commands (#122) * chore(github): fix syntax * Add `pathway_analysis` workflow (#128) * fix(workflows): rm unused files * feat(workflows): add `pathway_analysis` * feat(workflows): add `retrosynthesis` (#129) * rp2biosensor: syntax (#130) * fix(rp2biosensor): add attribute to test tag * feat(workflows): add `biosensor` (#131) * feat(workflows): add `straindesign` (#132) * feat(workflows): add `genetic assembly` (#133) * chore(github): fix syntax * chore(github): update workflows to skip * chore(github): fix artefacts log * Tools: `selenzy_wrapper` (#134) * fix(tools): selenzy_wrapper, update test section * chore(github): workflows, fix workflow call * chore(deps): bump tj-actions/changed-files from 36 to 37 (#135) Bumps [tj-actions/changed-files](https://github.com/tj-actions/changed-files) from 36 to 37. - [Release notes](https://github.com/tj-actions/changed-files/releases) - [Changelog](https://github.com/tj-actions/changed-files/blob/main/HISTORY.md) - [Commits](tj-actions/changed-files@v36...v37) --- updated-dependencies: - dependency-name: tj-actions/changed-files dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * chore(github): merge release workflows * chore(github): fix syntax * doc(sampler): update * fix(tools): sampler, table syntax (#136) * doc(changelog): update * doc(changelog): update * doc(changelog): update * doc(changelog): update * doc(changelog): update * doc(changelog): update * doc(changelog): update * doc(changelog): update * get_sbml_model, enable to load file from history (#137) * feat(tools): get_sbml_model, enable to load file from history * doc(changelog): update * fix load from file * doc(changelog): update * chore(deps): bump actions/checkout from 3 to 4 (#140) Bumps [actions/checkout](https://github.com/actions/checkout) from 3 to 4. - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](actions/checkout@v3...v4) --- updated-dependencies: - dependency-name: actions/checkout dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * doc(changelog): update * doc(changelog): update * doc(changelog): update * feat(tools): get_sbml_model, load file from history (#139) * fix(get_sbml_model.xml): rm weird commands * fix(get_sbml_model.xml): add --bigg * feat: add --biomass-id arg + refactor * feat(tools): get_sbml_model, load file from history (#143) Co-authored-by: Guillaume Gricourt <guipagui@gmail.com> * chore(deps): bump tj-actions/changed-files from 37 to 39 (#142) Bumps [tj-actions/changed-files](https://github.com/tj-actions/changed-files) from 37 to 39. - [Release notes](https://github.com/tj-actions/changed-files/releases) - [Changelog](https://github.com/tj-actions/changed-files/blob/main/HISTORY.md) - [Commits](tj-actions/changed-files@v37...v39) --- updated-dependencies: - dependency-name: tj-actions/changed-files dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Updating dnabot from version 3.1.0 to 4.1.0 (#141) * Updating dnabot from version 3.1.0 to 4.1.0 * fix(tools): dnabot, update test * fix(tools): dnabot, syntax * doc(changelog): update * feat(tools): add `neo4jsbml` (#144) * feat(tools): add `neo4jsbml` * docs(tools): update * doc(changelog): update * doc(changelog): update * Rptools (#146) * feat(rpextractsink): add --standalone arg * chore(rp2paths): update version * chore(rptools): v 6.3.0 --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: guillaume-gricourt <guipagui@gmail.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
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Related to #126