Release

Create a PR from a branch named Release-<anything> into dev. This PR should copy the latest seed environment of the passed/ subdirectory into released/.

This is currently a very manual process.

Dev Bump

Create a PR from a branch named Prepare-<anything> into dev. This PR should (generally) copy the released seed environment from the last epoch into a new passed/ subdirectory for the new epoch being prepared.

The channels should not be updated to the next epoch immediately, as a valid channel with packages is needed to resolve the DAG. The newly resolved seed env will update the first channel to the correct epoch. This new artifact can then be written to the passed/ directory with a no-ci commit.

This is currently a very manual process.

Overview

Legend:

• rounded = start/end
• diamond = descision
• flag = note or manual action
• double-bar = github action (subworkflow)
• rectangle = a step

Regular Development

This figure shows the high-level interaction between different components.

flowchart TB
 start([Something Changes!])
 d_1{Is it a dependency \nor code change?}
 n_code>The change affects the package first.]
 n_distro>The change effects the distro first.]
 done([Done])

 start --> d_1
 d_1 -->|code| n_code
 n_code --> github_pr

 d_1 -->|dependency| n_distro
 n_distro -->|push commit to main| integration_trial_pre
 integration_trial_fail --> individual_trial_pr
 individual_trial_merge -->|re-run| integration_trial_gha

 integration_trial_upload --> reindex_complex
 reindex_complex --> final_merge
 final_gha --> done

 github_upload --> reindex_simple
 reindex_simple -->|push commit to main| integration_trial_pre

 subgraph github_repo1[Individual Github Repository]
  github_pr["Open Pull Request (main ← {anything})"]
  github_pr_gha[[GHA: ci_pr.yml]]
  github_pr_check{Success?}
  github_pr_fail>Write better code.]
  github_pr_merge[Merge PR]
  github_main_gha[[GHA: ci_main.yml]]
  github_upload[["ci_main.yml: upload build(s)"]]

  github_pr -->|"trigger (doesn't start with ci)"| github_pr_gha
  github_pr_gha --> github_pr_check
  github_pr_check -->|yes| github_pr_merge
  github_pr_check -->|no| github_pr_fail
  github_pr_fail -->|push commit| github_pr_gha
  github_pr_merge --> github_main_gha
  github_main_gha -->|if succeeded| github_upload
 end

 subgraph github_repo2[Individual Github Repository]
  individual_trial_pr["Open Pull Request (ci-{change}-{ver} ← {anything})"]
  individual_trial_gha[[GHA: ci_trial.yml]]
  individual_trial_fail>Write better code.]
  individual_trial_merge[Merge PR]
  individual_trial_check{Sucess?}

  individual_trial_pr -->|"trigger (starts with ci)"| individual_trial_gha
  individual_trial_gha --> individual_trial_check
  individual_trial_check --->|yes| individual_trial_merge
  individual_trial_check -->|no| individual_trial_fail
  individual_trial_fail -->|push commit| individual_trial_gha
 end

 subgraph github_repo3["Individual Github Repositor(ies)"]
  final_merge["Merge branch (main ← ci-{change}-{ver})"]
  final_conflict{"Success?"}
  todo>"Handle manually\n(new version + build from main)"]
  final_gha[["GHA: ci_main.yml (not triggered)"]]

  final_merge --> final_conflict
  final_conflict -->|yes| final_gha
  final_conflict -->|no| todo
 end

 subgraph integration_repo[qiime2/package-integration]
  integration_trial_pre["Update /staged/ for distro"]
  integration_trial_queue[["GHA: distro_queue.yml"]]
  integration_trial_pr["Open Pull Request (main ← ci-{change}-{ver})"]
  integration_trial_gha[[GHA: ci_distro_trial.yml]]
  integration_trial_check{Success?}
  integration_trial_fail>Bask in failure.]
  integration_trial_upload[[ci_distro_trial.yml: upload builds]]

  integration_trial_pre -->|triggers| integration_trial_queue
  integration_trial_queue -->|once concurrency group is free| integration_trial_pr
  integration_trial_pr --> integration_trial_gha
  integration_trial_gha --> integration_trial_check
  integration_trial_check -->|yes| integration_trial_upload
  integration_trial_check -->|no| integration_trial_fail
 end

 subgraph library1[library.qiime2.org]
  reindex_simple["reindex (no patch updates)"]
 end

 subgraph library2[library.qiime2.org]
  reindex_complex["reindex (with packagedata patches)"]
 end

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Distro Release

flowchart TB
  TODO

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Github Actions

Sub-workflows for each github action.

Individual Repository

Github actions for individual plugins or repositories.

ci_pr.yml

Test a pull request (in the usual way)

flowchart TB
  TODO

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ci_main.yml

Test (and build) a commit pushed to main

flowchart TB
  TODO

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ci_trial.yml

Test a PR in the context of an existing trial from package-integration

flowchart TB
  start(["A PR exists from (ci-{change}-{ver} ← {anything})"])
  collect["Download partial environment from \n package-integration (ci-{change}-{ver}) \n (Includes patched repodata from trial)"]
  setup["Setup local channels and environment"]
  build["Build package"]
  test["Test built package"]

  start --> collect
  collect --> setup
  setup --> build
  build --> test

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Package Integration

Github workflows for creating distributions

distro_queue.yml

Prevents too many GHA runners from being used by arbitrarily many distros

flowchart TB
  start([A distro's /staged/ changes])
  alt_start([A timer has elapsed])
  busy{"Is there a running job\nin QUEUE\nconcurrency group?"}
  replace>"GHA queues this action\n(replacing/canceling any pending job)"]
  workflow_start["Generate diff of each distro"]
  integration_trial_pr["Open Pull Request (main ← ci-{change}-{ver})"]
  random["Pick a random diff"]
  done([Done])

  start & alt_start --> busy
  busy -->|yes| replace
  busy -->|no| workflow_start
  replace -->|once free| workflow_start
  workflow_start --> random
  random --> integration_trial_pr
  integration_trial_pr --> done

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ci_distro_trial.yml

Produce a new configuration for a distribution

flowchart TB
  start(["A commit exists in a ci-{change}-{ver} branch"])
  busy{"Is there a running job\nin QUEUE\nconcurrency group?"}
  replace>"GHA queues this action\n(replacing/canceling any pending job)"]
  workflow_start["Create DAG of changes"]
  workflow_report["Create report of Trial plan"]
  workflow_matrix["Create matrix generations"]
  done([Done])

  start  --> busy
  busy -->|yes| replace
  busy -->|no| workflow_start
  replace -->|once free| workflow_start
  workflow_start --> workflow_report

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Process and necessary steps/scripts for ci_distro_trial.yml workflow

flowchart TB
  start(["conda_build_config.yml"])
  alt_start(["$REF(ish)"])
  find_diff["1. find_diff.py"]
  pkg_diffs>"[PKG1, PKG2, etc...]"]
  make_dag["2. make_dag.py"]
  job_sum(["GHA Job Summary"])
  pkg_diff_vers>"{ 'PKG1 version': [...], 'PKG2 version': [...] }"]
  make_channel["3. make_channel.py"]
  channel_dir1>"local/conda/channel"]
  patch_channel["4. patch_channel.py"]
  os_paths>"{osx: path/to/patch, linux: path/to/patch}"]
  channel_dir2>"local/conda/channel"]
  render_meta["render_metapackage"]
  install["install"]
  test["test"]
  publish(["publish"])

  start --> find_diff
  alt_start --> find_diff
  find_diff -->|list of pkgs changed in a given distro| pkg_diffs
  pkg_diffs --> make_dag
  start --> make_dag
  make_dag -->|mermaid diagram with pkg deps to update| job_sum
  make_dag --> pkg_diff_vers
  start --> make_channel
  make_channel -->|create local conda channel| channel_dir1
  pkg_diff_vers --> patch_channel
  channel_dir1 --> patch_channel
  patch_channel --> os_paths
  patch_channel -->|creates repodata_patch.json file| channel_dir2
  channel_dir2 --> render_meta
  render_meta --> install
  install --> test
  test --> publish
  os_paths --> publish

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