Branch Management

[mbaudis]

This discussion should be used to reflect the current branches and their purposes.

Core branches

main

develop

website-docs

This branch is used to maintain the website at http://docs.genomebeacons.org. The relevant files consists of anything under /docs as well as the configuration file (/mkdocs.yaml) and the workflow file for processing the pages under /.github/workflows/mk-beacon-docs.yaml.

The main branch is updated from website-docs during version updates.

Changes to the Markdown files in the /docs directory (and its children) will initiate the processing of the workflow file; updating of the website than may take some minutes.

gh-pages

The gh-pages branch is generated from the /docs directory through its mkdocs workflow and contains the website itself. Do not edit

Topic branches

[costero-e]

main branch is the branch used for production, it reflects the last version that beacon v2 has reached by accomplishing the milestones that ga4gh has set for the beacon to be considered as a new version. It can only be committed by a PR from the develop branch and exceptionally by some hotfixes to correct errors spotted after its official deployment.
develop branch is the branch used for development, it reflects the current state of the progress of development. It can be modified by all the PR from the feature branches that have been finished (this means that must include all the merges from the subfeature branches) and the PR must reach a consensus to be finally accepted

[mbaudis]

@costero-e @laurenfromont I have moved the topic to a dedicated documentation page, including @costero-e 's additions. This is now visible at http://docs.genomebeacons.org/code-organization/ .

However, I want to keep this discussion open for more details including topic branches (some of which then can go to the documentation, too).

[costero-e]

good idea @mbaudis ! now we will need to write a description for topic branches

[costero-e]

Repository and Branch Organization

The development of Beacon code and documentation happens in the beacon-v2 repository.

Core branches

main

The main branch is the branch used for production, it reflects the last version that beacon v2 has reached by accomplishing the milestones that ga4gh has set for the beacon to be considered as a new version. It can only be committed by a PR from the develop branch and exceptionally by some hotfixes to correct errors spotted after its official deployment.

develop

The develop branch is the branch used for development, it reflects the current state of the progress of development. It can be modified by all the PR from the feature branches that have been finished (this means that must include all the merges from the subfeature branches) and the PR must reach a consensus to be finally accepted.

website-docs

This branch is used to maintain the website at https://docs.genomebeacons.org. The relevant files consists of anything under /docs as well as the configuration file (/mkdocs.yaml) and the workflow file for processing the pages under /.github/workflows/mk-beacon-docs.yaml.

Changes to the Markdown files in the /docs directory (and its children) will initiate the processing of the workflow file; updating of the website than may take some minutes.

gh-pages

The gh-pages branch is generated from the /docs directory through its mkdocs workflow and contains the website itself. Do not edit

Hotfix branches

These are the branches that are meant to fix some bugs that break the specifications and need an urgent fix. The branches are directly deployed towards the main branch.

entry-type-definitions-cleanup

This branch aims to redefine the wording of the entry types in a way that makes more clear what are the entry types. As the old definitions could mislead to some confusions, this is a sensible change that is needed to directly affect the current modification.

Current status:Waiting for PR to be accepted.

hotfix_filteringTermsResults

As the beaconFilteringTermsResults.json "type" property of the FilteringTerm is ambiguous, this branch has the objective to fix this and make filtering terms object to be operative and ready to point to the filtering terms type.

Current status:Waiting for PR to be accepted.

schema-urgent-fixes

• some of the instances of the schema were missing attributes and other aspects that are required to make a beacon work. This is mandatory to be urgently fixed and this is the purpose of this branch deployment
• content merges after dev team review w/ leads +1

inline-documentation-updates ([link](https://github.com/ga4gh-beacon/beacon-v2/tree/inline-documentation-updates

))

• branch for continuous improvements of the inline documentation (format, examples, wording, typos...) which do not affect the code per se (but the schema documents, in contrast to website-docs)
• occasional content merges after dev team review

Feature and subfeature branches

The feature branches are the branches that bring a lot of changes together to change some specific part of the specifications. They can be composed by different subfeature branches that commit to them or just have one single working branch. The feature branches commit to the develop branch as they are the changes that will lead beacon to be upgraded to a new version. The subfeature branches commit to their parent feature branch, as they are a microchange of all the aspects that have to change in a new feature that is being developed. The branches are named as the main purpose of them, so it is made very clear what is the working area of them and the subfeature branches add the name of the feature branch they belong as a prefix followed by an underscore. The list of these feature branches with their subfeature branches is the one shown next:

clean-up

clean-up_sticky_modified_files

Current status:Last commit by @jrambla.

clean-up_renaming_entity_to_entry_type

Current status:Added in framework-refactor-entry-type-definitions branch by @mbaudis and waiting for a PR to be accepted.

clean-up_decouple-model-framework-refs

Current status:Last commit by @mbaudis.

clean-up_move-CURIE-to-beaconCommonComponents

Current status:This branch has not had any commit.

clean-up_de-snakify-token-names

Current status:This branch has not had any commit.

clean-up_refactor-analysys-pipeline-info

Current status:Last commit by @mbaudis.

resultsets

resultsets_remove-requirement-results-resultsCount

Current status:Last commit by @mbaudis.

requestParameters

requestParameters_genomicVariations-fix

Current status:Last commit by @mbaudis.

requestParameters_list-parameters-with-comma

Current status:This branch has not had any commit.

phenopackets

phenopackets_standards-alignment

Current status:Last commit by @mbaudis.

network

network_aggregator-and-networks-support

Current status:This branch has not had any commit.

network_meta-add-aggregator-flag

Current status:Last commit by @mbaudis.

anyOf

anyOf_filteringTerms

Current status:This branch has not had any commit.

genomicVariations

Current status:Waiting for PR to be accepted.

received-filters

Current status:Waiting for PR to be accepted.

response-meta-add-warnings

Current status:Waiting for PR to be accepted.

framework-refactor-entry-type-definitions

Current status:Waiting for PR to be accepted.

==TBD==

[costero-e]

I have updated the website-docs branch with the current information of the work and the current status of every branch in our repository. I think this can help to know what is happening in every branch and what we need to do in order to close them. Most of the work is pending the PR approval. The next step will be to define the milestones and the achievements we make by developing and adding the new features into the beacon specs.

[mbaudis]

👏