pause workflows

.github/workflows/backup.yaml

@@ -1,30 +1,31 @@
-name: backup
-run-name: backup ${{vars.S3_BUCKET}}/${{vars.S3_FOLDER}} to ${{ vars.ZENODO_URL }}
+# pause until all versions.json have been converted to info.json files
+# name: backup
+# run-name: backup ${{vars.S3_BUCKET}}/${{vars.S3_FOLDER}} to ${{ vars.ZENODO_URL }}
 
-on:
-  workflow_run:
-    workflows: [publish]
-    types: [completed]
-    branches: [main]
-  workflow_dispatch:
+# on:
+#   workflow_run:
+#     workflows: [publish]
+#     types: [completed]
+#     branches: [main]
+#   workflow_dispatch:
 
-concurrency: ${{vars.ZENODO_URL}}
+# concurrency: ${{vars.ZENODO_URL}}
 
-env:
-  S3_HOST: ${{vars.S3_HOST}}
-  S3_BUCKET: ${{vars.S3_BUCKET}}
-  S3_FOLDER: ${{vars.S3_FOLDER}}
-  ZENODO_URL: ${{vars.ZENODO_URL}}
-  S3_ACCESS_KEY_ID: ${{secrets.S3_ACCESS_KEY_ID}}
-  S3_SECRET_ACCESS_KEY: ${{secrets.S3_SECRET_ACCESS_KEY}}
-  ZENODO_API_ACCESS_TOKEN: ${{secrets.ZENODO_API_ACCESS_TOKEN}}
+# env:
+#   S3_HOST: ${{vars.S3_HOST}}
+#   S3_BUCKET: ${{vars.S3_BUCKET}}
+#   S3_FOLDER: ${{vars.S3_FOLDER}}
+#   ZENODO_URL: ${{vars.ZENODO_URL}}
+#   S3_ACCESS_KEY_ID: ${{secrets.S3_ACCESS_KEY_ID}}
+#   S3_SECRET_ACCESS_KEY: ${{secrets.S3_SECRET_ACCESS_KEY}}
+#   ZENODO_API_ACCESS_TOKEN: ${{secrets.ZENODO_API_ACCESS_TOKEN}}
 
-jobs:
-  call:
-    uses: bioimage-io/collection/.github/workflows/backup_call.yaml@main
-    with:
-      S3_HOST: ${{vars.S3_HOST}}
-      S3_BUCKET: ${{vars.S3_BUCKET}}
-      S3_FOLDER: ${{vars.S3_FOLDER}}
-      ZENODO_URL: ${{vars.ZENODO_URL}}
-    secrets: inherit
+# jobs:
+#   call:
+#     uses: bioimage-io/collection/.github/workflows/backup_call.yaml@main
+#     with:
+#       S3_HOST: ${{vars.S3_HOST}}
+#       S3_BUCKET: ${{vars.S3_BUCKET}}
+#       S3_FOLDER: ${{vars.S3_FOLDER}}
+#       ZENODO_URL: ${{vars.ZENODO_URL}}
+#     secrets: inherit

.github/workflows/generate_collection_json.yaml

@@ -1,34 +1,35 @@
-name: generate collection.json
-run-name: generate collection for ${{vars.S3_BUCKET}}/${{vars.S3_FOLDER}}
+# pause
+# name: generate collection.json
+# run-name: generate collection for ${{vars.S3_BUCKET}}/${{vars.S3_FOLDER}}
 
-on:
-  workflow_dispatch:
-  push:
-    branches: [main]
-  workflow_run:
-    workflows: [stage, test bioimageio resource, request changes, publish]
-    types: [completed]
-    branches: [main]
+# on:
+#   workflow_dispatch:
+#   push:
+#     branches: [main]
+#   workflow_run:
+#     workflows: [stage, test bioimageio resource, request changes, publish]
+#     types: [completed]
+#     branches: [main]
 
 
-concurrency: generate-collection-json
+# concurrency: generate-collection-json
 
-env:
-  S3_HOST: ${{vars.S3_HOST}}
-  S3_BUCKET: ${{vars.S3_BUCKET}}
-  S3_FOLDER: ${{vars.S3_FOLDER}}
-  S3_ACCESS_KEY_ID: ${{secrets.S3_ACCESS_KEY_ID}}
-  S3_SECRET_ACCESS_KEY: ${{secrets.S3_SECRET_ACCESS_KEY}}
+# env:
+#   S3_HOST: ${{vars.S3_HOST}}
+#   S3_BUCKET: ${{vars.S3_BUCKET}}
+#   S3_FOLDER: ${{vars.S3_FOLDER}}
+#   S3_ACCESS_KEY_ID: ${{secrets.S3_ACCESS_KEY_ID}}
+#   S3_SECRET_ACCESS_KEY: ${{secrets.S3_SECRET_ACCESS_KEY}}
 
-jobs:
-  call:
-    strategy:
-      matrix:
-        mode: [staged, published]
-    uses: bioimage-io/collection/.github/workflows/generate_collection_json_call.yaml@main
-    with:
-      mode: ${{matrix.mode}}
-      S3_HOST: ${{vars.S3_HOST}}
-      S3_BUCKET: ${{vars.S3_BUCKET}}
-      S3_FOLDER: ${{vars.S3_FOLDER}}
-    secrets: inherit
+# jobs:
+#   call:
+#     strategy:
+#       matrix:
+#         mode: [staged, published]
+#     uses: bioimage-io/collection/.github/workflows/generate_collection_json_call.yaml@main
+#     with:
+#       mode: ${{matrix.mode}}
+#       S3_HOST: ${{vars.S3_HOST}}
+#       S3_BUCKET: ${{vars.S3_BUCKET}}
+#       S3_FOLDER: ${{vars.S3_FOLDER}}
+#     secrets: inherit

.github/workflows/publish.yaml

@@ -1,40 +1,41 @@
-name: publish
-run-name: publish ${{inputs.resource_id}} staged/${{inputs.stage_number}}
+# pause
+# name: publish
+# run-name: publish ${{inputs.resource_id}} staged/${{inputs.stage_number}}
 
-on:
-  workflow_dispatch:
-    inputs:
-      resource_id:
-        description: "Bioimageio ID of the resource - to be used to access the resource on S3"
-        required: true
-        type: string
-      stage_number:
-        description: stage number to publish
-        required: true
-        type: number
-      reviewer:
-        description: GitHub account name of bioimage.io maintainer accepting this resource version
-        required: false
-        default: 'auto detect'
-        type: string
-      sandbox:
-        description: Publish within sandbox
-        required: false
-        default: false
-        type: boolean
+# on:
+#   workflow_dispatch:
+#     inputs:
+#       resource_id:
+#         description: "Bioimageio ID of the resource - to be used to access the resource on S3"
+#         required: true
+#         type: string
+#       stage_number:
+#         description: stage number to publish
+#         required: true
+#         type: number
+#       reviewer:
+#         description: GitHub account name of bioimage.io maintainer accepting this resource version
+#         required: false
+#         default: 'auto detect'
+#         type: string
+#       sandbox:
+#         description: Publish within sandbox
+#         required: false
+#         default: false
+#         type: boolean
 
-concurrency: ${{inputs.resource_id}}
+# concurrency: ${{inputs.resource_id}}
 
-jobs:
-  call:
-    uses: bioimage-io/collection/.github/workflows/publish_call.yaml@main
-    with:
-      resource_id: ${{inputs.resource_id}}
-      stage_number: ${{fromJson(inputs.stage_number)}}  # wo 'fromJson' the number is given as string, see https://github.com/orgs/community/discussions/67182
-      reviewer: ${{inputs.reviewer == 'auto detect' && format('github|{0}', github.actor_id) || inputs.reviewer}}
-      S3_HOST: ${{vars.S3_HOST}}
-      S3_BUCKET: ${{vars.S3_BUCKET}}
-      S3_FOLDER: ${{inputs.sandbox && vars.S3_SANDBOX_FOLDER || vars.S3_FOLDER}}
-      REVIEWERS: ${{vars.REVIEWERS}}
+# jobs:
+#   call:
+#     uses: bioimage-io/collection/.github/workflows/publish_call.yaml@main
+#     with:
+#       resource_id: ${{inputs.resource_id}}
+#       stage_number: ${{fromJson(inputs.stage_number)}}  # wo 'fromJson' the number is given as string, see https://github.com/orgs/community/discussions/67182
+#       reviewer: ${{inputs.reviewer == 'auto detect' && format('github|{0}', github.actor_id) || inputs.reviewer}}
+#       S3_HOST: ${{vars.S3_HOST}}
+#       S3_BUCKET: ${{vars.S3_BUCKET}}
+#       S3_FOLDER: ${{inputs.sandbox && vars.S3_SANDBOX_FOLDER || vars.S3_FOLDER}}
+#       REVIEWERS: ${{vars.REVIEWERS}}
 
-    secrets: inherit
+#     secrets: inherit

.github/workflows/request_changes.yaml

@@ -1,40 +1,41 @@
-name: request changes
-run-name: request changes for ${{inputs.resource_id}} staged/${{inputs.stage_number}}
+# pause
+# name: request changes
+# run-name: request changes for ${{inputs.resource_id}} staged/${{inputs.stage_number}}
 
-on:
-  workflow_dispatch:
-    inputs:
-      resource_id:
-        description: "Bioimageio ID of the resource - to be used to access the resource on S3"
-        required: true
-        type: string
-      stage_number:
-        description: stage number
-        required: true
-        type: number
-      reviewer:
-        description: GitHub account name of bioimage.io maintainer requesting changes
-        required: false
-        default: 'auto detect'
-        type: string
-      reason:
-        description: Why are changes required? What needs changing?
-        required: true
-        type: string
+# on:
+#   workflow_dispatch:
+#     inputs:
+#       resource_id:
+#         description: "Bioimageio ID of the resource - to be used to access the resource on S3"
+#         required: true
+#         type: string
+#       stage_number:
+#         description: stage number
+#         required: true
+#         type: number
+#       reviewer:
+#         description: GitHub account name of bioimage.io maintainer requesting changes
+#         required: false
+#         default: 'auto detect'
+#         type: string
+#       reason:
+#         description: Why are changes required? What needs changing?
+#         required: true
+#         type: string
 
-concurrency: ${{inputs.resource_id}}
+# concurrency: ${{inputs.resource_id}}
 
-jobs:
-  call:
-    uses: bioimage-io/collection/.github/workflows/request_changes_call.yaml@main
-    with:
-      resource_id: ${{inputs.resource_id}}
-      stage_number: ${{fromJson(inputs.stage_number)}}  # wo 'fromJson' the number is given as string, see https://github.com/orgs/community/discussions/67182
-      reviewer: ${{inputs.reviewer == 'auto detect' && format('github|{0}', github.actor_id) || inputs.reviewer}}
-      reason: ${{inputs.reason}}
-      S3_HOST: ${{vars.S3_HOST}}
-      S3_BUCKET: ${{vars.S3_BUCKET}}
-      S3_FOLDER: ${{vars.S3_FOLDER}}
-      ZENODO_URL: ${{vars.ZENODO_URL}}
-      REVIEWERS: ${{vars.REVIEWERS}}
-    secrets: inherit
+# jobs:
+#   call:
+#     uses: bioimage-io/collection/.github/workflows/request_changes_call.yaml@main
+#     with:
+#       resource_id: ${{inputs.resource_id}}
+#       stage_number: ${{fromJson(inputs.stage_number)}}  # wo 'fromJson' the number is given as string, see https://github.com/orgs/community/discussions/67182
+#       reviewer: ${{inputs.reviewer == 'auto detect' && format('github|{0}', github.actor_id) || inputs.reviewer}}
+#       reason: ${{inputs.reason}}
+#       S3_HOST: ${{vars.S3_HOST}}
+#       S3_BUCKET: ${{vars.S3_BUCKET}}
+#       S3_FOLDER: ${{vars.S3_FOLDER}}
+#       ZENODO_URL: ${{vars.ZENODO_URL}}
+#       REVIEWERS: ${{vars.REVIEWERS}}
+#     secrets: inherit

.github/workflows/retest_all.yaml

@@ -1,49 +1,50 @@
-name: retest all bioimageio resources adding to their logs
-
-on:
-  workflow_dispatch:
-    inputs:
-      sandbox:
-        description: use sandbox
-        required: false
-        default: true
-        type: boolean
-
-concurrency: retest
-
-jobs:
-  setup:
-    runs-on: ubuntu-latest
-    outputs:
-      matrix: ${{steps.get_matrix.outputs.matrix}}
-
-    steps:
-      - run: wget ${{vars.S3_HOST}}/${{vars.S3_BUCKET}}/${{inputs.sandbox && vars.S3_SANDBOX_FOLDER || vars.S3_FOLDER}}/collection.json
-      - shell: python
-        id: get_matrix
-        run: |
-          import json, os
-
-          with open("collection.json") as f:
-            collection = json.load(f)
-
-          published = [{"id": entry["id"], "v": entry["version_number"]} for entry in collection["collection"]]
-          matrix = {"include": published}
-          with open(os.environ["GITHUB_OUTPUT"], "a") as f:
-            print(f"matrix={matrix}", file=f)
-
-  test:
-    needs: setup
-    strategy:
-      matrix: ${{fromJson(needs.setup.outputs.matrix)}}
-    uses: bioimage-io/collection/.github/workflows/test_call.yaml@main
-    with:
-      resource_id: ${{matrix.id}}
-      version: ${{matrix.v}}
-      conclude: 'no'
-      S3_HOST: ${{vars.S3_HOST}}
-      S3_BUCKET: ${{vars.S3_BUCKET}}
-      S3_FOLDER: ${{inputs.sandbox && vars.S3_SANDBOX_FOLDER || vars.S3_FOLDER}}
-    secrets: inherit
-
-# TODO: call emailer
+# pause
+# name: retest all bioimageio resources adding to their logs
+
+# on:
+#   workflow_dispatch:
+#     inputs:
+#       sandbox:
+#         description: use sandbox
+#         required: false
+#         default: true
+#         type: boolean
+
+# concurrency: retest
+
+# jobs:
+#   setup:
+#     runs-on: ubuntu-latest
+#     outputs:
+#       matrix: ${{steps.get_matrix.outputs.matrix}}
+
+#     steps:
+#       - run: wget ${{vars.S3_HOST}}/${{vars.S3_BUCKET}}/${{inputs.sandbox && vars.S3_SANDBOX_FOLDER || vars.S3_FOLDER}}/collection.json
+#       - shell: python
+#         id: get_matrix
+#         run: |
+#           import json, os
+
+#           with open("collection.json") as f:
+#             collection = json.load(f)
+
+#           published = [{"id": entry["id"], "v": entry["version_number"]} for entry in collection["collection"]]
+#           matrix = {"include": published}
+#           with open(os.environ["GITHUB_OUTPUT"], "a") as f:
+#             print(f"matrix={matrix}", file=f)
+
+#   test:
+#     needs: setup
+#     strategy:
+#       matrix: ${{fromJson(needs.setup.outputs.matrix)}}
+#     uses: bioimage-io/collection/.github/workflows/test_call.yaml@main
+#     with:
+#       resource_id: ${{matrix.id}}
+#       version: ${{matrix.v}}
+#       conclude: 'no'
+#       S3_HOST: ${{vars.S3_HOST}}
+#       S3_BUCKET: ${{vars.S3_BUCKET}}
+#       S3_FOLDER: ${{inputs.sandbox && vars.S3_SANDBOX_FOLDER || vars.S3_FOLDER}}
+#     secrets: inherit
+
+# # TODO: call emailer