From 0c69a1c392d425b93b059065ac4a648dd3c9b9b2 Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Mon, 6 Sep 2021 18:10:01 +0200
Subject: [PATCH 01/32] update test data for PRs

as slash command

and trigger run-all-tool-test only from issues
---
 .github/workflows/pr.yaml    | 44 +++++++++++++++++++++++++++++++++++-
 .github/workflows/slash.yaml | 14 ++++++++++--
 2 files changed, 55 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml
index d44cd5fa4fe..c5d756b7ec2 100644
--- a/.github/workflows/pr.yaml
+++ b/.github/workflows/pr.yaml
@@ -1,5 +1,9 @@
 name: Galaxy Tool Linting and Tests for push and PR
-on: [push, pull_request]
+on:
+  push
+  pull_request
+  repository_dispatch:
+    types: [update-test-data-command]
 env:
   GALAXY_FORK: galaxyproject
   GALAXY_BRANCH: release_21.05
@@ -21,10 +25,27 @@ jobs:
       tool-list: ${{ steps.discover.outputs.tool-list }}
       chunk-count: ${{ steps.discover.outputs.chunk-count }}
       chunk-list: ${{ steps.discover.outputs.chunk-list }}
+      output-test-data: ${{ steps.output-test-data.outputs.output-test-data }}
     strategy:
       matrix:
         python-version: ['3.7']
     steps:
+    - name: Add reaction
+      if: ${{ github.event.client_payload.slash_command.command == 'run-all-tool-tests' }}
+      uses: peter-evans/create-or-update-comment@v1
+      with:
+        token: ${{ secrets.PAT }}
+        repository: ${{ github.event.client_payload.github.payload.repository.full_name }}
+        comment-id: ${{ github.event.client_payload.github.payload.comment.id }}
+        reaction-type: hooray
+    - name: Set update-test-data for slash commands
+      id: update-test-data
+      run: |
+        if [ -n "${{ github.event.client_payload.slash_command.command}}" ]; then
+          echo "::set-output name=update-test-data::true"
+        else
+          echo "::set-output name=update-test-data::false"
+        fi
     - name: Print github context properties
       run: |
         echo 'event: ${{ github.event_name }}'
@@ -70,6 +91,7 @@ jobs:
         galaxy-branch: ${{ env.GALAXY_BRANCH }}
         max-chunks: ${{ env.MAX_CHUNKS }}
         python-version: ${{ matrix.python-version }}
+        update-test-data: ${{ steps.update-test-data.outputs.update-test-data }}
     - name: Show commit range
       run: echo '${{ steps.discover.outputs.commit-range }}'
     - name: Show repository list
@@ -262,6 +284,7 @@ jobs:
         galaxy-branch: ${{ env.GALAXY_BRANCH }}
         chunk: ${{ matrix.chunk }}
         chunk-count: ${{ needs.setup.outputs.chunk-count }}
+        update-test-data: ${{ needs.setup.outputs.update-test-date }}
     - uses: actions/upload-artifact@v2
       with:
         name: 'Tool test output ${{ matrix.chunk }}'
@@ -353,6 +376,25 @@ jobs:
     if: ${{ always() && github.ref != 'refs/heads/master' && github.ref != 'refs/heads/main' }}
     runs-on: ubuntu-latest
     steps:
+    - name: Create URL to the run output
+      if: ${{ github.event.client_payload.slash_command.command == 'run-all-tool-tests' }}
+      id: vars
+      run: echo "::set-output name=run-url::https://github.com/$GITHUB_REPOSITORY/actions/runs/$GITHUB_RUN_ID"
+    - name: Create comment
+      if: ${{ github.event.client_payload.slash_command.command == 'run-all-tool-tests' }}
+      uses: peter-evans/create-or-update-comment@v1
+      with:
+        token: ${{ secrets.PAT }}
+        repository: ${{ github.event.client_payload.github.payload.repository.full_name }}
+        issue-number: ${{ github.event.client_payload.github.payload.issue.number }}
+        body: |
+          Summary:
+
+          ${{ steps.combine.outputs.statistics }}
+
+          [Find all tool test results here][1]
+
+          [1]: ${{ steps.vars.outputs.run-url }}
     - name: Check tool lint status
       if: ${{ needs.lint.result != 'success' && needs.flake8.result != 'skipped' }}
       run: exit 1
diff --git a/.github/workflows/slash.yaml b/.github/workflows/slash.yaml
index 664d53916cd..6e8cec9b131 100644
--- a/.github/workflows/slash.yaml
+++ b/.github/workflows/slash.yaml
@@ -11,5 +11,15 @@ jobs:
         uses: peter-evans/slash-command-dispatch@v2
         with:
           token: ${{ secrets.PAT }}
-          commands: |
-            run-all-tool-tests
+          config: >
+            [
+              {
+                "command": "run-all-tool-tests",
+                "issue_type": "issue"
+              }
+              {
+                "command": "update-test-data",
+                "permission": "write",
+                "issue_type": "pull-request"
+              }
+            ]

From 00b1b8daa424eda190ce9c9ba46c668e95644b95 Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Tue, 7 Sep 2021 16:22:06 +0200
Subject: [PATCH 02/32] try to push

---
 .github/workflows/pr.yaml | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml
index c5d756b7ec2..8e781d432ec 100644
--- a/.github/workflows/pr.yaml
+++ b/.github/workflows/pr.yaml
@@ -285,6 +285,15 @@ jobs:
         chunk: ${{ matrix.chunk }}
         chunk-count: ${{ needs.setup.outputs.chunk-count }}
         update-test-data: ${{ needs.setup.outputs.update-test-date }}
+    - name: Push updated test data
+      if: ${{ needs.setup.outputs.update-test-date }}
+      uses: actions/checkout@v2
+      run: |
+          git config user.name github-actions
+          git config user.email github-actions@github.com
+          git add .
+          git commit -m "update test data"
+          git push 
     - uses: actions/upload-artifact@v2
       with:
         name: 'Tool test output ${{ matrix.chunk }}'

From a6068a0a3be9950109228760b4ad8f0340f5cac9 Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Wed, 8 Sep 2021 09:04:29 +0200
Subject: [PATCH 03/32] slash for bernt-matthias

---
 .github/workflows/slash.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/slash.yaml b/.github/workflows/slash.yaml
index 6e8cec9b131..fd18e1da049 100644
--- a/.github/workflows/slash.yaml
+++ b/.github/workflows/slash.yaml
@@ -7,7 +7,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Slash Command Dispatch
-        if: github.repository_owner == 'galaxyproject'
+        if: github.repository_owner == 'bernt-matthias'
         uses: peter-evans/slash-command-dispatch@v2
         with:
           token: ${{ secrets.PAT }}

From e1d9040677586987f1101e460b2c5aa2140a2a6d Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Wed, 8 Sep 2021 09:05:36 +0200
Subject: [PATCH 04/32] missing comma

---
 .github/workflows/slash.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/slash.yaml b/.github/workflows/slash.yaml
index fd18e1da049..3fd8d83b086 100644
--- a/.github/workflows/slash.yaml
+++ b/.github/workflows/slash.yaml
@@ -16,7 +16,7 @@ jobs:
               {
                 "command": "run-all-tool-tests",
                 "issue_type": "issue"
-              }
+              },
               {
                 "command": "update-test-data",
                 "permission": "write",

From e5c24fe53ea52cc4f309a28013c9702f2ead0347 Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Wed, 8 Sep 2021 09:07:52 +0200
Subject: [PATCH 05/32] PR fix on syntax

---
 .github/workflows/pr.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml
index 8e781d432ec..fdb23c6bfd5 100644
--- a/.github/workflows/pr.yaml
+++ b/.github/workflows/pr.yaml
@@ -1,7 +1,7 @@
 name: Galaxy Tool Linting and Tests for push and PR
 on:
-  push
-  pull_request
+  push:
+  pull_request:
   repository_dispatch:
     types: [update-test-data-command]
 env:

From 5413b6f163289b6851961e47a9f6a6b9d41cf076 Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Wed, 8 Sep 2021 09:09:50 +0200
Subject: [PATCH 06/32] PR fix commit

---
 .github/workflows/pr.yaml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml
index fdb23c6bfd5..bec447fa3a6 100644
--- a/.github/workflows/pr.yaml
+++ b/.github/workflows/pr.yaml
@@ -287,7 +287,6 @@ jobs:
         update-test-data: ${{ needs.setup.outputs.update-test-date }}
     - name: Push updated test data
       if: ${{ needs.setup.outputs.update-test-date }}
-      uses: actions/checkout@v2
       run: |
           git config user.name github-actions
           git config user.email github-actions@github.com

From 046999e079e492dd98737720916bb7356193e664 Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Wed, 8 Sep 2021 09:11:33 +0200
Subject: [PATCH 07/32] PR: temp disable for push and PR

---
 .github/workflows/pr.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml
index bec447fa3a6..458f0fc43ac 100644
--- a/.github/workflows/pr.yaml
+++ b/.github/workflows/pr.yaml
@@ -1,7 +1,7 @@
 name: Galaxy Tool Linting and Tests for push and PR
 on:
-  push:
-  pull_request:
+  # push:
+  # pull_request:
   repository_dispatch:
     types: [update-test-data-command]
 env:

From 49b72016428aa35cff6a263e65614fe59e134782 Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Wed, 8 Sep 2021 09:30:49 +0200
Subject: [PATCH 08/32] debug

---
 .github/workflows/pr.yaml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml
index 458f0fc43ac..41ebef1e418 100644
--- a/.github/workflows/pr.yaml
+++ b/.github/workflows/pr.yaml
@@ -31,7 +31,7 @@ jobs:
         python-version: ['3.7']
     steps:
     - name: Add reaction
-      if: ${{ github.event.client_payload.slash_command.command == 'run-all-tool-tests' }}
+      if: ${{ github.event.client_payload.slash_command.command == 'update-test-data' }}
       uses: peter-evans/create-or-update-comment@v1
       with:
         token: ${{ secrets.PAT }}
@@ -55,6 +55,7 @@ jobs:
         echo 'base_ref: ${{ github.base_ref }}'
         echo 'event.before: ${{ github.event.before }}'
         echo 'event.after: ${{ github.event.after }}'
+        echo 'github.event...: ${{ github.event.client_payload.pull_request }}'
     - name: Determine latest commit in the Galaxy repo
       id: get-galaxy-sha
       run: echo "::set-output name=galaxy-head-sha::$(git ls-remote https://github.com/${{ env.GALAXY_FORK }}/galaxy refs/heads/${{ env.GALAXY_BRANCH }} | cut -f1)"

From 6875b6ffaadf3c24b3f0f479e83a365eb0f00228 Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Wed, 8 Sep 2021 09:32:38 +0200
Subject: [PATCH 09/32] debug

---
 .github/workflows/pr.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml
index 41ebef1e418..0efed07af8d 100644
--- a/.github/workflows/pr.yaml
+++ b/.github/workflows/pr.yaml
@@ -55,7 +55,7 @@ jobs:
         echo 'base_ref: ${{ github.base_ref }}'
         echo 'event.before: ${{ github.event.before }}'
         echo 'event.after: ${{ github.event.after }}'
-        echo 'github.event...: ${{ github.event.client_payload.pull_request }}'
+        echo 'github.event...: ${{ toJson(github.event.client_payload) }}'
     - name: Determine latest commit in the Galaxy repo
       id: get-galaxy-sha
       run: echo "::set-output name=galaxy-head-sha::$(git ls-remote https://github.com/${{ env.GALAXY_FORK }}/galaxy refs/heads/${{ env.GALAXY_BRANCH }} | cut -f1)"

From db0207a68c5c5769fe52dbc341f3e7393a6b5a16 Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Wed, 8 Sep 2021 09:34:23 +0200
Subject: [PATCH 10/32] debug

---
 .github/workflows/pr.yaml | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml
index 0efed07af8d..3a60dca270c 100644
--- a/.github/workflows/pr.yaml
+++ b/.github/workflows/pr.yaml
@@ -56,6 +56,10 @@ jobs:
         echo 'event.before: ${{ github.event.before }}'
         echo 'event.after: ${{ github.event.after }}'
         echo 'github.event...: ${{ toJson(github.event.client_payload) }}'
+    - name: Dump the client payload context
+      env:
+        PAYLOAD_CONTEXT: ${{ toJson(github.event.client_payload) }}
+      run: echo "$PAYLOAD_CONTEXT"
     - name: Determine latest commit in the Galaxy repo
       id: get-galaxy-sha
       run: echo "::set-output name=galaxy-head-sha::$(git ls-remote https://github.com/${{ env.GALAXY_FORK }}/galaxy refs/heads/${{ env.GALAXY_BRANCH }} | cut -f1)"

From fc16bc766134fccca0b6d7ee06c841e86fdbcecf Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Wed, 8 Sep 2021 09:48:22 +0200
Subject: [PATCH 11/32] debug

---
 .github/workflows/pr.yaml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml
index 3a60dca270c..3ed2a0a4e55 100644
--- a/.github/workflows/pr.yaml
+++ b/.github/workflows/pr.yaml
@@ -55,10 +55,9 @@ jobs:
         echo 'base_ref: ${{ github.base_ref }}'
         echo 'event.before: ${{ github.event.before }}'
         echo 'event.after: ${{ github.event.after }}'
-        echo 'github.event...: ${{ toJson(github.event.client_payload) }}'
     - name: Dump the client payload context
       env:
-        PAYLOAD_CONTEXT: ${{ toJson(github.event.client_payload) }}
+        PAYLOAD_CONTEXT: ${{ toJson(github.event.client_payload.pull_request) }}
       run: echo "$PAYLOAD_CONTEXT"
     - name: Determine latest commit in the Galaxy repo
       id: get-galaxy-sha

From 6e7b51ec5685fa495ffb93c36129814ffc9fe0ff Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Wed, 8 Sep 2021 11:44:25 +0200
Subject: [PATCH 12/32] try to get ref

---
 .github/workflows/pr.yaml | 30 ++++++++++++++++--------------
 1 file changed, 16 insertions(+), 14 deletions(-)

diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml
index 3ed2a0a4e55..abc0f549ff3 100644
--- a/.github/workflows/pr.yaml
+++ b/.github/workflows/pr.yaml
@@ -30,6 +30,19 @@ jobs:
       matrix:
         python-version: ['3.7']
     steps:
+    - name: Print github context properties
+      run: |
+        echo 'event: ${{ github.event_name }}'
+        echo 'sha: ${{ github.sha }}'
+        echo 'ref: ${{ github.ref }}'
+        echo 'head_ref: ${{ github.head_ref }}'
+        echo 'base_ref: ${{ github.base_ref }}'
+        echo 'event.before: ${{ github.event.before }}'
+        echo 'event.after: ${{ github.event.after }}'
+    - name: Dump the client payload context
+      env:
+        PAYLOAD_CONTEXT: ${{ toJson(github.event.client_payload.pull_request["head"]["ref"]) }}
+      run: echo "$PAYLOAD_CONTEXT"
     - name: Add reaction
       if: ${{ github.event.client_payload.slash_command.command == 'update-test-data' }}
       uses: peter-evans/create-or-update-comment@v1
@@ -43,22 +56,11 @@ jobs:
       run: |
         if [ -n "${{ github.event.client_payload.slash_command.command}}" ]; then
           echo "::set-output name=update-test-data::true"
+          echo "::set-output name=ref::${{github.event.client_payload.pull_request["head"]["ref"]}}"
         else
           echo "::set-output name=update-test-data::false"
+          echo "::set-output name=ref::''"
         fi
-    - name: Print github context properties
-      run: |
-        echo 'event: ${{ github.event_name }}'
-        echo 'sha: ${{ github.sha }}'
-        echo 'ref: ${{ github.ref }}'
-        echo 'head_ref: ${{ github.head_ref }}'
-        echo 'base_ref: ${{ github.base_ref }}'
-        echo 'event.before: ${{ github.event.before }}'
-        echo 'event.after: ${{ github.event.after }}'
-    - name: Dump the client payload context
-      env:
-        PAYLOAD_CONTEXT: ${{ toJson(github.event.client_payload.pull_request) }}
-      run: echo "$PAYLOAD_CONTEXT"
     - name: Determine latest commit in the Galaxy repo
       id: get-galaxy-sha
       run: echo "::set-output name=galaxy-head-sha::$(git ls-remote https://github.com/${{ env.GALAXY_FORK }}/galaxy refs/heads/${{ env.GALAXY_BRANCH }} | cut -f1)"
@@ -87,7 +89,7 @@ jobs:
       with:
         fetch-depth: 0
     - name: Fake a Planemo run to update cache and determine commit range, repositories, and chunks
-      uses: galaxyproject/planemo-ci-action@v1
+      uses: bernt-matthias/planemo-ci-action@topic/update-test-data
       id: discover
       with:
         create-cache: ${{ steps.cache-pip.outputs.cache-hit != 'true' || steps.cache-planemo.outputs.cache-hit != 'true' }}

From bfd65ea06cd0fdedd6a0387d2a702acb7e423d6a Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Wed, 8 Sep 2021 11:45:50 +0200
Subject: [PATCH 13/32] try

---
 .github/workflows/pr.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml
index abc0f549ff3..113eb9d8741 100644
--- a/.github/workflows/pr.yaml
+++ b/.github/workflows/pr.yaml
@@ -41,7 +41,7 @@ jobs:
         echo 'event.after: ${{ github.event.after }}'
     - name: Dump the client payload context
       env:
-        PAYLOAD_CONTEXT: ${{ toJson(github.event.client_payload.pull_request["head"]["ref"]) }}
+        PAYLOAD_CONTEXT: ${{ toJson(github.event.client_payload.pull_request.head.ref) }}
       run: echo "$PAYLOAD_CONTEXT"
     - name: Add reaction
       if: ${{ github.event.client_payload.slash_command.command == 'update-test-data' }}
@@ -56,7 +56,7 @@ jobs:
       run: |
         if [ -n "${{ github.event.client_payload.slash_command.command}}" ]; then
           echo "::set-output name=update-test-data::true"
-          echo "::set-output name=ref::${{github.event.client_payload.pull_request["head"]["ref"]}}"
+          echo "::set-output name=ref::${{github.event.client_payload.pull_request.ref}}"
         else
           echo "::set-output name=update-test-data::false"
           echo "::set-output name=ref::''"

From dcd0c84a41e9c2fcca12e2e923c8d3960a83826a Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Wed, 8 Sep 2021 11:48:31 +0200
Subject: [PATCH 14/32] try to use ref

---
 .github/workflows/pr.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml
index 113eb9d8741..a9def0e12ff 100644
--- a/.github/workflows/pr.yaml
+++ b/.github/workflows/pr.yaml
@@ -87,6 +87,7 @@ jobs:
       run: pip install flake8 flake8-import-order
     - uses: actions/checkout@v2
       with:
+        ref: ${{ steps.update-test-data.outputs.ref }}
         fetch-depth: 0
     - name: Fake a Planemo run to update cache and determine commit range, repositories, and chunks
       uses: bernt-matthias/planemo-ci-action@topic/update-test-data

From d7023d60776530888322ce49819916850781bbea Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Wed, 8 Sep 2021 11:56:04 +0200
Subject: [PATCH 15/32] try

---
 .github/workflows/pr.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml
index a9def0e12ff..cb048735fb2 100644
--- a/.github/workflows/pr.yaml
+++ b/.github/workflows/pr.yaml
@@ -56,7 +56,7 @@ jobs:
       run: |
         if [ -n "${{ github.event.client_payload.slash_command.command}}" ]; then
           echo "::set-output name=update-test-data::true"
-          echo "::set-output name=ref::${{github.event.client_payload.pull_request.ref}}"
+          echo "::set-output name=ref::${{github.event.client_payload.pull_request.sha}}"
         else
           echo "::set-output name=update-test-data::false"
           echo "::set-output name=ref::''"

From a7b51d7e6fed611b2449cbf2cff7aa4b23312653 Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Wed, 8 Sep 2021 12:13:53 +0200
Subject: [PATCH 16/32] try

---
 .github/workflows/pr.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml
index cb048735fb2..a390ba6fd01 100644
--- a/.github/workflows/pr.yaml
+++ b/.github/workflows/pr.yaml
@@ -41,7 +41,7 @@ jobs:
         echo 'event.after: ${{ github.event.after }}'
     - name: Dump the client payload context
       env:
-        PAYLOAD_CONTEXT: ${{ toJson(github.event.client_payload.pull_request.head.ref) }}
+        PAYLOAD_CONTEXT: ${{ toJson(github.event.client_payload.pull_request.head.sha) }}
       run: echo "$PAYLOAD_CONTEXT"
     - name: Add reaction
       if: ${{ github.event.client_payload.slash_command.command == 'update-test-data' }}
@@ -56,7 +56,7 @@ jobs:
       run: |
         if [ -n "${{ github.event.client_payload.slash_command.command}}" ]; then
           echo "::set-output name=update-test-data::true"
-          echo "::set-output name=ref::${{github.event.client_payload.pull_request.sha}}"
+          echo "::set-output name=ref::${{github.event.client_payload.pull_request.head.sha}}"
         else
           echo "::set-output name=update-test-data::false"
           echo "::set-output name=ref::''"

From e1d06f5ef230a8633fae30a2a19d03ede17f2c5d Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Wed, 8 Sep 2021 12:28:53 +0200
Subject: [PATCH 17/32] checkout the correct ref in all jobs

---
 .github/workflows/pr.yaml | 15 ++++++++++++---
 1 file changed, 12 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml
index a390ba6fd01..59983171544 100644
--- a/.github/workflows/pr.yaml
+++ b/.github/workflows/pr.yaml
@@ -25,7 +25,8 @@ jobs:
       tool-list: ${{ steps.discover.outputs.tool-list }}
       chunk-count: ${{ steps.discover.outputs.chunk-count }}
       chunk-list: ${{ steps.discover.outputs.chunk-list }}
-      output-test-data: ${{ steps.output-test-data.outputs.output-test-data }}
+      output-test-data: ${{ steps.update-test-data.outputs.output-test-data }}
+      ref: ${{ steps.update-test-data.outputs.ref }}
     strategy:
       matrix:
         python-version: ['3.7']
@@ -43,7 +44,7 @@ jobs:
       env:
         PAYLOAD_CONTEXT: ${{ toJson(github.event.client_payload.pull_request.head.sha) }}
       run: echo "$PAYLOAD_CONTEXT"
-    - name: Add reaction
+    - name: Add reaction to update-test-data slash command
       if: ${{ github.event.client_payload.slash_command.command == 'update-test-data' }}
       uses: peter-evans/create-or-update-comment@v1
       with:
@@ -51,7 +52,10 @@ jobs:
         repository: ${{ github.event.client_payload.github.payload.repository.full_name }}
         comment-id: ${{ github.event.client_payload.github.payload.comment.id }}
         reaction-type: hooray
-    - name: Set update-test-data for slash commands
+    # for running the update-test-data slash command 
+    # - set update-test-data::true and false otherwise
+    # - set ref to the PR latest SHA and '' otherwise (which is the default for the checkout action)
+    - name: Set variables depending on update-test-data for slash commands
       id: update-test-data
       run: |
         if [ -n "${{ github.event.client_payload.slash_command.command}}" ]; then
@@ -124,6 +128,7 @@ jobs:
     # and use it as the current working directory
     - uses: actions/checkout@v2
       with:
+        ref: ${{ needs.setup.outputs.ref }}
         fetch-depth: 1
     - uses: actions/setup-python@v1
       with:
@@ -160,6 +165,7 @@ jobs:
     steps:
     - uses: actions/checkout@v2
       with:
+        ref: ${{ needs.setup.outputs.ref }}
         fetch-depth: 1
     - uses: actions/setup-python@v1
       with:
@@ -192,6 +198,7 @@ jobs:
     steps:
     - uses: actions/checkout@v2
       with:
+        ref: ${{ needs.setup.outputs.ref }}
         fetch-depth: 1
     - uses: r-lib/actions/setup-r@master
       with:
@@ -265,6 +272,7 @@ jobs:
     # and use it as the current working directory
     - uses: actions/checkout@v2
       with:
+        ref: ${{ needs.setup.outputs.ref }}
         fetch-depth: 1
     - uses: actions/setup-python@v1
       with:
@@ -359,6 +367,7 @@ jobs:
     steps:
     - uses: actions/checkout@v2
       with:
+        ref: ${{ needs.setup.outputs.ref }}
         fetch-depth: 1
     - uses: actions/setup-python@v1
       with:

From 18f76b4b65ab53abbf1c63afb39c1f5ac605670f Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Wed, 8 Sep 2021 13:06:41 +0200
Subject: [PATCH 18/32] always use branch of the action

---
 .github/workflows/pr.yaml | 18 ++++++++++++------
 1 file changed, 12 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml
index 59983171544..d392d512839 100644
--- a/.github/workflows/pr.yaml
+++ b/.github/workflows/pr.yaml
@@ -140,7 +140,8 @@ jobs:
         path: ~/.cache/pip
         key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }}
     - name: Planemo lint
-      uses: galaxyproject/planemo-ci-action@v1
+      uses: bernt-matthias/planemo-ci-action@topic/update-test-data
+      # uses: galaxyproject/planemo-ci-action@v1
       id: lint
       with:
         mode: lint
@@ -290,7 +291,8 @@ jobs:
         path: ~/.planemo
         key: planemo_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }}
     - name: Planemo test
-      uses: galaxyproject/planemo-ci-action@v1
+      uses: bernt-matthias/planemo-ci-action@topic/update-test-data
+      # uses: galaxyproject/planemo-ci-action@v1
       id: test
       with:
         mode: test
@@ -340,7 +342,8 @@ jobs:
         path: ~/.cache/pip
         key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }}
     - name: Combine outputs
-      uses: galaxyproject/planemo-ci-action@v1
+      uses: bernt-matthias/planemo-ci-action@topic/update-test-data
+      # uses: galaxyproject/planemo-ci-action@v1
       id: combine
       with:
         mode: combine
@@ -350,7 +353,8 @@ jobs:
         name: 'All tool test results'
         path: upload
     - name: Check outputs
-      uses: galaxyproject/planemo-ci-action@v1
+      uses: bernt-matthias/planemo-ci-action@topic/update-test-data
+      # uses: galaxyproject/planemo-ci-action@v1
       id: check
       with:
         mode: check
@@ -379,7 +383,8 @@ jobs:
         path: ~/.cache/pip
         key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }}
     - name: Deploy on testtoolshed
-      uses: galaxyproject/planemo-ci-action@v1
+      uses: bernt-matthias/planemo-ci-action@topic/update-test-data
+      # uses: galaxyproject/planemo-ci-action@v1
       with:
         mode: deploy
         repository-list: ${{ needs.setup.outputs.repository-list }}
@@ -387,7 +392,8 @@ jobs:
         shed-key: ${{ secrets.TTS_API_KEY }}
       continue-on-error: true
     - name: Deploy on toolshed
-      uses: galaxyproject/planemo-ci-action@v1
+      uses: bernt-matthias/planemo-ci-action@topic/update-test-data
+      # uses: galaxyproject/planemo-ci-action@v1
       with:
         mode: deploy
         repository-list: ${{ needs.setup.outputs.repository-list }}

From 81bd1e04ad029d10741fa570d3de6688f93bff62 Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Wed, 8 Sep 2021 13:19:56 +0200
Subject: [PATCH 19/32] try ref instead of sha

---
 .github/workflows/pr.yaml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml
index d392d512839..fac9b259577 100644
--- a/.github/workflows/pr.yaml
+++ b/.github/workflows/pr.yaml
@@ -42,7 +42,7 @@ jobs:
         echo 'event.after: ${{ github.event.after }}'
     - name: Dump the client payload context
       env:
-        PAYLOAD_CONTEXT: ${{ toJson(github.event.client_payload.pull_request.head.sha) }}
+        PAYLOAD_CONTEXT: ${{ toJson(github.event.client_payload.pull_request.head.ref) }}
       run: echo "$PAYLOAD_CONTEXT"
     - name: Add reaction to update-test-data slash command
       if: ${{ github.event.client_payload.slash_command.command == 'update-test-data' }}
@@ -60,7 +60,7 @@ jobs:
       run: |
         if [ -n "${{ github.event.client_payload.slash_command.command}}" ]; then
           echo "::set-output name=update-test-data::true"
-          echo "::set-output name=ref::${{github.event.client_payload.pull_request.head.sha}}"
+          echo "::set-output name=ref::${{github.event.client_payload.pull_request.head.ref}}"
         else
           echo "::set-output name=update-test-data::false"
           echo "::set-output name=ref::''"
@@ -303,7 +303,7 @@ jobs:
         chunk-count: ${{ needs.setup.outputs.chunk-count }}
         update-test-data: ${{ needs.setup.outputs.update-test-date }}
     - name: Push updated test data
-      if: ${{ needs.setup.outputs.update-test-date }}
+      if: ${{ needs.setup.outputs.update-test-data }}
       run: |
           git config user.name github-actions
           git config user.email github-actions@github.com

From 8e0cf316c464c871c9ca416d9ee79521f43d55e0 Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Wed, 8 Sep 2021 13:29:23 +0200
Subject: [PATCH 20/32] only push if changed

---
 .github/workflows/pr.yaml | 14 ++++++++------
 1 file changed, 8 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml
index fac9b259577..f9bb0f23bf0 100644
--- a/.github/workflows/pr.yaml
+++ b/.github/workflows/pr.yaml
@@ -42,7 +42,7 @@ jobs:
         echo 'event.after: ${{ github.event.after }}'
     - name: Dump the client payload context
       env:
-        PAYLOAD_CONTEXT: ${{ toJson(github.event.client_payload.pull_request.head.ref) }}
+        PAYLOAD_CONTEXT: ${{ toJson(github.event.client_payload.pull_request) }}
       run: echo "$PAYLOAD_CONTEXT"
     - name: Add reaction to update-test-data slash command
       if: ${{ github.event.client_payload.slash_command.command == 'update-test-data' }}
@@ -305,11 +305,13 @@ jobs:
     - name: Push updated test data
       if: ${{ needs.setup.outputs.update-test-data }}
       run: |
-          git config user.name github-actions
-          git config user.email github-actions@github.com
-          git add .
-          git commit -m "update test data"
-          git push 
+          if git diff --exit-code; then
+            git config user.name github-actions
+            git config user.email github-actions@github.com
+            git add .
+            git commit -m "update test data"
+            git push 
+          fi
     - uses: actions/upload-artifact@v2
       with:
         name: 'Tool test output ${{ matrix.chunk }}'

From 48db873883f8f3cc067b42118e37eb15e90016c5 Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Wed, 8 Sep 2021 13:53:21 +0200
Subject: [PATCH 21/32] checkout from fork for dispactch event

---
 .github/workflows/pr.yaml | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml
index f9bb0f23bf0..fae0833bb00 100644
--- a/.github/workflows/pr.yaml
+++ b/.github/workflows/pr.yaml
@@ -26,6 +26,7 @@ jobs:
       chunk-count: ${{ steps.discover.outputs.chunk-count }}
       chunk-list: ${{ steps.discover.outputs.chunk-list }}
       output-test-data: ${{ steps.update-test-data.outputs.output-test-data }}
+      repository: ${{ steps.update-test-data.outputs.repository }}
       ref: ${{ steps.update-test-data.outputs.ref }}
     strategy:
       matrix:
@@ -60,9 +61,11 @@ jobs:
       run: |
         if [ -n "${{ github.event.client_payload.slash_command.command}}" ]; then
           echo "::set-output name=update-test-data::true"
+          echo "::set-output name=repository::${{github.event.client_payload.pull_request.head.repo.full_name}}"
           echo "::set-output name=ref::${{github.event.client_payload.pull_request.head.ref}}"
         else
           echo "::set-output name=update-test-data::false"
+          echo "::set-output name=repository::''"
           echo "::set-output name=ref::''"
         fi
     - name: Determine latest commit in the Galaxy repo
@@ -91,6 +94,7 @@ jobs:
       run: pip install flake8 flake8-import-order
     - uses: actions/checkout@v2
       with:
+        ref: ${{ steps.update-test-data.outputs.repository }}
         ref: ${{ steps.update-test-data.outputs.ref }}
         fetch-depth: 0
     - name: Fake a Planemo run to update cache and determine commit range, repositories, and chunks
@@ -128,6 +132,7 @@ jobs:
     # and use it as the current working directory
     - uses: actions/checkout@v2
       with:
+        ref: ${{ needs.setup.outputs.repository }}
         ref: ${{ needs.setup.outputs.ref }}
         fetch-depth: 1
     - uses: actions/setup-python@v1
@@ -166,6 +171,7 @@ jobs:
     steps:
     - uses: actions/checkout@v2
       with:
+        ref: ${{ needs.setup.outputs.repository }}
         ref: ${{ needs.setup.outputs.ref }}
         fetch-depth: 1
     - uses: actions/setup-python@v1
@@ -199,6 +205,7 @@ jobs:
     steps:
     - uses: actions/checkout@v2
       with:
+        ref: ${{ needs.setup.outputs.repository }}
         ref: ${{ needs.setup.outputs.ref }}
         fetch-depth: 1
     - uses: r-lib/actions/setup-r@master
@@ -273,6 +280,7 @@ jobs:
     # and use it as the current working directory
     - uses: actions/checkout@v2
       with:
+        ref: ${{ needs.setup.outputs.repository }}
         ref: ${{ needs.setup.outputs.ref }}
         fetch-depth: 1
     - uses: actions/setup-python@v1
@@ -373,6 +381,7 @@ jobs:
     steps:
     - uses: actions/checkout@v2
       with:
+        ref: ${{ needs.setup.outputs.repository }}
         ref: ${{ needs.setup.outputs.ref }}
         fetch-depth: 1
     - uses: actions/setup-python@v1

From 531d711a595e0175be23431f0562ebb7cb8e6cff Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Wed, 8 Sep 2021 13:55:48 +0200
Subject: [PATCH 22/32] fix

---
 .github/workflows/pr.yaml | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml
index fae0833bb00..cf792f144ab 100644
--- a/.github/workflows/pr.yaml
+++ b/.github/workflows/pr.yaml
@@ -94,7 +94,7 @@ jobs:
       run: pip install flake8 flake8-import-order
     - uses: actions/checkout@v2
       with:
-        ref: ${{ steps.update-test-data.outputs.repository }}
+        repository: ${{ steps.update-test-data.outputs.repository }}
         ref: ${{ steps.update-test-data.outputs.ref }}
         fetch-depth: 0
     - name: Fake a Planemo run to update cache and determine commit range, repositories, and chunks
@@ -132,7 +132,7 @@ jobs:
     # and use it as the current working directory
     - uses: actions/checkout@v2
       with:
-        ref: ${{ needs.setup.outputs.repository }}
+        repository: ${{ needs.setup.outputs.repository }}
         ref: ${{ needs.setup.outputs.ref }}
         fetch-depth: 1
     - uses: actions/setup-python@v1
@@ -171,7 +171,7 @@ jobs:
     steps:
     - uses: actions/checkout@v2
       with:
-        ref: ${{ needs.setup.outputs.repository }}
+        repository: ${{ needs.setup.outputs.repository }}
         ref: ${{ needs.setup.outputs.ref }}
         fetch-depth: 1
     - uses: actions/setup-python@v1
@@ -205,7 +205,7 @@ jobs:
     steps:
     - uses: actions/checkout@v2
       with:
-        ref: ${{ needs.setup.outputs.repository }}
+        repository: ${{ needs.setup.outputs.repository }}
         ref: ${{ needs.setup.outputs.ref }}
         fetch-depth: 1
     - uses: r-lib/actions/setup-r@master
@@ -280,7 +280,7 @@ jobs:
     # and use it as the current working directory
     - uses: actions/checkout@v2
       with:
-        ref: ${{ needs.setup.outputs.repository }}
+        repository: ${{ needs.setup.outputs.repository }}
         ref: ${{ needs.setup.outputs.ref }}
         fetch-depth: 1
     - uses: actions/setup-python@v1
@@ -381,7 +381,7 @@ jobs:
     steps:
     - uses: actions/checkout@v2
       with:
-        ref: ${{ needs.setup.outputs.repository }}
+        repository: ${{ needs.setup.outputs.repository }}
         ref: ${{ needs.setup.outputs.ref }}
         fetch-depth: 1
     - uses: actions/setup-python@v1

From 2fd0bd85f6ddd7532de4eef8279839fd4ed93dcb Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Wed, 8 Sep 2021 14:08:11 +0200
Subject: [PATCH 23/32] fix variable name

---
 .github/workflows/pr.yaml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml
index cf792f144ab..fe8dc5103ab 100644
--- a/.github/workflows/pr.yaml
+++ b/.github/workflows/pr.yaml
@@ -25,7 +25,7 @@ jobs:
       tool-list: ${{ steps.discover.outputs.tool-list }}
       chunk-count: ${{ steps.discover.outputs.chunk-count }}
       chunk-list: ${{ steps.discover.outputs.chunk-list }}
-      output-test-data: ${{ steps.update-test-data.outputs.output-test-data }}
+      update-test-data: ${{ steps.update-test-data.outputs.update-test-data }}
       repository: ${{ steps.update-test-data.outputs.repository }}
       ref: ${{ steps.update-test-data.outputs.ref }}
     strategy:
@@ -55,7 +55,7 @@ jobs:
         reaction-type: hooray
     # for running the update-test-data slash command 
     # - set update-test-data::true and false otherwise
-    # - set ref to the PR latest SHA and '' otherwise (which is the default for the checkout action)
+    # - set repository / ref to the PR fork name / latest SHA and '' otherwise (which is the default for the checkout action)
     - name: Set variables depending on update-test-data for slash commands
       id: update-test-data
       run: |
@@ -309,7 +309,7 @@ jobs:
         galaxy-branch: ${{ env.GALAXY_BRANCH }}
         chunk: ${{ matrix.chunk }}
         chunk-count: ${{ needs.setup.outputs.chunk-count }}
-        update-test-data: ${{ needs.setup.outputs.update-test-date }}
+        update-test-data: ${{ needs.setup.outputs.update-test-data }}
     - name: Push updated test data
       if: ${{ needs.setup.outputs.update-test-data }}
       run: |

From 13aaf3712bdb19961bfb1536768ea9ad3e4c485e Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Wed, 8 Sep 2021 14:25:46 +0200
Subject: [PATCH 24/32] try to commit only if modifying changes are piresent

add resonse comment
---
 .github/workflows/pr.yaml | 29 ++++++++++++++++++++++++-----
 1 file changed, 24 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml
index fe8dc5103ab..19106dc6f60 100644
--- a/.github/workflows/pr.yaml
+++ b/.github/workflows/pr.yaml
@@ -25,7 +25,7 @@ jobs:
       tool-list: ${{ steps.discover.outputs.tool-list }}
       chunk-count: ${{ steps.discover.outputs.chunk-count }}
       chunk-list: ${{ steps.discover.outputs.chunk-list }}
-      update-test-data: ${{ steps.update-test-data.outputs.update-test-data }}
+      output-test-data: ${{ steps.update-test-data.outputs.output-test-data }}
       repository: ${{ steps.update-test-data.outputs.repository }}
       ref: ${{ steps.update-test-data.outputs.ref }}
     strategy:
@@ -309,17 +309,36 @@ jobs:
         galaxy-branch: ${{ env.GALAXY_BRANCH }}
         chunk: ${{ matrix.chunk }}
         chunk-count: ${{ needs.setup.outputs.chunk-count }}
-        update-test-data: ${{ needs.setup.outputs.update-test-data }}
+        update-test-data: ${{ needs.setup.outputs.update-test-date }}
     - name: Push updated test data
+      id: push-updated-test-data
       if: ${{ needs.setup.outputs.update-test-data }}
       run: |
-          if git diff --exit-code; then
+          if git diff --diff-filter=M --exit-code; then
             git config user.name github-actions
             git config user.email github-actions@github.com
-            git add .
-            git commit -m "update test data"
+            git commit -m "update test data" .
             git push 
           fi
+    - name: Create URL to the run output
+      if: ${{ github.event.client_payload.slash_command.command == 'run-all-tool-tests' }}
+      id: vars
+      run: echo "::set-output name=run-url::https://github.com/$GITHUB_REPOSITORY/actions/runs/$GITHUB_RUN_ID"
+    - name: Create comment
+      if: ${{ github.event.client_payload.slash_command.command == 'update-test-data' }}
+      uses: peter-evans/create-or-update-comment@v1
+      with:
+        token: ${{ secrets.PAT }}
+        repository: ${{ github.event.client_payload.github.payload.repository.full_name }}
+        issue-number: ${{ github.event.client_payload.github.payload.issue.number }}
+        body: |
+          Summary:
+
+          ${{ toJson(steps.push-updated-test-data.outputs) }}
+
+          [Find all tool test results here][1]
+
+          [1]: ${{ steps.vars.outputs.run-url }}
     - uses: actions/upload-artifact@v2
       with:
         name: 'Tool test output ${{ matrix.chunk }}'

From e6df18893370f1c14aaee1a1a51ed6dfc3e91152 Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Wed, 8 Sep 2021 14:43:01 +0200
Subject: [PATCH 25/32] typos

---
 .github/workflows/pr.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml
index 19106dc6f60..71169f53aea 100644
--- a/.github/workflows/pr.yaml
+++ b/.github/workflows/pr.yaml
@@ -25,7 +25,7 @@ jobs:
       tool-list: ${{ steps.discover.outputs.tool-list }}
       chunk-count: ${{ steps.discover.outputs.chunk-count }}
       chunk-list: ${{ steps.discover.outputs.chunk-list }}
-      output-test-data: ${{ steps.update-test-data.outputs.output-test-data }}
+      update-test-data: ${{ steps.update-test-data.outputs.update-test-data }}
       repository: ${{ steps.update-test-data.outputs.repository }}
       ref: ${{ steps.update-test-data.outputs.ref }}
     strategy:
@@ -309,7 +309,7 @@ jobs:
         galaxy-branch: ${{ env.GALAXY_BRANCH }}
         chunk: ${{ matrix.chunk }}
         chunk-count: ${{ needs.setup.outputs.chunk-count }}
-        update-test-data: ${{ needs.setup.outputs.update-test-date }}
+        update-test-data: ${{ needs.setup.outputs.update-test-data }}
     - name: Push updated test data
       id: push-updated-test-data
       if: ${{ needs.setup.outputs.update-test-data }}

From d613b1e462eed0c6452a397ebd23c5c05a52300a Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Wed, 8 Sep 2021 15:18:30 +0200
Subject: [PATCH 26/32] mod git diff

---
 .github/workflows/pr.yaml | 16 +++++++++-------
 1 file changed, 9 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml
index 71169f53aea..a4c88a59b21 100644
--- a/.github/workflows/pr.yaml
+++ b/.github/workflows/pr.yaml
@@ -311,17 +311,21 @@ jobs:
         chunk-count: ${{ needs.setup.outputs.chunk-count }}
         update-test-data: ${{ needs.setup.outputs.update-test-data }}
     - name: Push updated test data
-      id: push-updated-test-data
       if: ${{ needs.setup.outputs.update-test-data }}
+      id: push-updated-test-data
       run: |
-          if git diff --diff-filter=M --exit-code; then
+          set -x
+          if git diff HEAD^..HEAD --diff-filter=M --exit-code; then
             git config user.name github-actions
             git config user.email github-actions@github.com
             git commit -m "update test data" .
-            git push 
+            git push
+            echo "::set-output name=number-of-changed-files::$(git diff HEAD^..HEAD --name-only | wc -l)"
+          else
+            echo "::set-output name=number-of-changed-files::0"
           fi
     - name: Create URL to the run output
-      if: ${{ github.event.client_payload.slash_command.command == 'run-all-tool-tests' }}
+      if: ${{ github.event.client_payload.slash_command.command == 'update-test-data' }}
       id: vars
       run: echo "::set-output name=run-url::https://github.com/$GITHUB_REPOSITORY/actions/runs/$GITHUB_RUN_ID"
     - name: Create comment
@@ -332,9 +336,7 @@ jobs:
         repository: ${{ github.event.client_payload.github.payload.repository.full_name }}
         issue-number: ${{ github.event.client_payload.github.payload.issue.number }}
         body: |
-          Summary:
-
-          ${{ toJson(steps.push-updated-test-data.outputs) }}
+          Summary: ${{ steps.push-updated-test-data.outputs.number-of-changed-files }} files changed
 
           [Find all tool test results here][1]
 

From 7da299497fbfa8d170d2c2f37bc33756f6d8435b Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Wed, 8 Sep 2021 15:49:38 +0200
Subject: [PATCH 27/32] revert diff chnage

---
 .github/workflows/pr.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml
index a4c88a59b21..0c36f83d764 100644
--- a/.github/workflows/pr.yaml
+++ b/.github/workflows/pr.yaml
@@ -315,7 +315,7 @@ jobs:
       id: push-updated-test-data
       run: |
           set -x
-          if git diff HEAD^..HEAD --diff-filter=M --exit-code; then
+          if git diff --diff-filter=M --exit-code; then
             git config user.name github-actions
             git config user.email github-actions@github.com
             git commit -m "update test data" .

From 8a70250a7476055fc3307a13d031826da772cde8 Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Wed, 8 Sep 2021 17:17:16 +0200
Subject: [PATCH 28/32] fix if

---
 .github/workflows/pr.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml
index 0c36f83d764..a53909cf0e9 100644
--- a/.github/workflows/pr.yaml
+++ b/.github/workflows/pr.yaml
@@ -315,7 +315,7 @@ jobs:
       id: push-updated-test-data
       run: |
           set -x
-          if git diff --diff-filter=M --exit-code; then
+          if ! git diff --diff-filter=M --exit-code >& /dev/null; then
             git config user.name github-actions
             git config user.email github-actions@github.com
             git commit -m "update test data" .

From 0f420382c0701f4fca8925dbc8a957356e8f2ecf Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Wed, 8 Sep 2021 17:40:20 +0200
Subject: [PATCH 29/32] reenable push and pr

---
 .github/workflows/pr.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml
index a53909cf0e9..c9a8ac56c4c 100644
--- a/.github/workflows/pr.yaml
+++ b/.github/workflows/pr.yaml
@@ -1,7 +1,7 @@
 name: Galaxy Tool Linting and Tests for push and PR
 on:
-  # push:
-  # pull_request:
+  push:
+  pull_request:
   repository_dispatch:
     types: [update-test-data-command]
 env:

From 34a22485783285130a8a92eba1c1fcaa201d8cb1 Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Wed, 8 Sep 2021 21:44:50 +0200
Subject: [PATCH 30/32] try to fix empty string

---
 .github/workflows/pr.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml
index c9a8ac56c4c..6a632d6b374 100644
--- a/.github/workflows/pr.yaml
+++ b/.github/workflows/pr.yaml
@@ -65,8 +65,8 @@ jobs:
           echo "::set-output name=ref::${{github.event.client_payload.pull_request.head.ref}}"
         else
           echo "::set-output name=update-test-data::false"
-          echo "::set-output name=repository::''"
-          echo "::set-output name=ref::''"
+          echo "::set-output name=repository::"
+          echo "::set-output name=ref::"
         fi
     - name: Determine latest commit in the Galaxy repo
       id: get-galaxy-sha

From 8717c96ca681f091638d0cd3b70fd7b8816de9a6 Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Wed, 8 Sep 2021 22:15:02 +0200
Subject: [PATCH 31/32] do not run linters for dispatch actions

---
 .github/workflows/pr.yaml | 47 +++++++++++++--------------------------
 1 file changed, 15 insertions(+), 32 deletions(-)

diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml
index 6a632d6b374..3af6f0b34da 100644
--- a/.github/workflows/pr.yaml
+++ b/.github/workflows/pr.yaml
@@ -121,7 +121,7 @@ jobs:
   lint:
     name: Lint tool-list
     needs: setup
-    if: ${{ needs.setup.outputs.repository-list != '' || needs.setup.outputs.tool-list != '' }}
+    if: ${{ github.event_name != 'repository-dispatch' && (needs.setup.outputs.repository-list != '' || needs.setup.outputs.tool-list != '') }}
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
@@ -162,7 +162,7 @@ jobs:
   flake8:
     name: Lint Python scripts
     needs: setup
-    if: ${{ needs.setup.outputs.repository-list != '' }}
+    if: ${{ github.event_name != 'repository-dispatch' && needs.setup.outputs.repository-list != '' }}
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
@@ -196,7 +196,7 @@ jobs:
   lintr:
     name: Lint R scripts
     needs: setup
-    if: ${{ needs.setup.outputs.repository-list != '' }}
+    if: ${{ github.event_name != 'repository-dispatch' && needs.setup.outputs.repository-list != '' }}
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
@@ -310,6 +310,12 @@ jobs:
         chunk: ${{ matrix.chunk }}
         chunk-count: ${{ needs.setup.outputs.chunk-count }}
         update-test-data: ${{ needs.setup.outputs.update-test-data }}
+    - uses: actions/upload-artifact@v2
+      with:
+        name: 'Tool test output ${{ matrix.chunk }}'
+        path: upload
+    # push updated test data
+    # - if no test data was updated then create a note (otherwise the commit should be sufficient)
     - name: Push updated test data
       if: ${{ needs.setup.outputs.update-test-data }}
       id: push-updated-test-data
@@ -325,26 +331,22 @@ jobs:
             echo "::set-output name=number-of-changed-files::0"
           fi
     - name: Create URL to the run output
-      if: ${{ github.event.client_payload.slash_command.command == 'update-test-data' }}
+      if: ${{ github.event.client_payload.slash_command.command == 'update-test-data' && steps.push-updated-test-data.outputs.number-of-changed-files != 0 }}
       id: vars
       run: echo "::set-output name=run-url::https://github.com/$GITHUB_REPOSITORY/actions/runs/$GITHUB_RUN_ID"
     - name: Create comment
-      if: ${{ github.event.client_payload.slash_command.command == 'update-test-data' }}
+      if: ${{ github.event.client_payload.slash_command.command == 'update-test-data' && steps.push-updated-test-data.outputs.number-of-changed-files != 0 }}
       uses: peter-evans/create-or-update-comment@v1
       with:
         token: ${{ secrets.PAT }}
         repository: ${{ github.event.client_payload.github.payload.repository.full_name }}
         issue-number: ${{ github.event.client_payload.github.payload.issue.number }}
         body: |
-          Summary: ${{ steps.push-updated-test-data.outputs.number-of-changed-files }} files changed
+          No test data was updated
 
           [Find all tool test results here][1]
 
           [1]: ${{ steps.vars.outputs.run-url }}
-    - uses: actions/upload-artifact@v2
-      with:
-        name: 'Tool test output ${{ matrix.chunk }}'
-        path: upload
 
   # - combine the results of the test chunks (which will never fail due
   #   to `|| true`) and create a global test report as json and html which
@@ -354,7 +356,7 @@ jobs:
   combine_outputs:
     name: Combine chunked test results
     needs: [setup, test]
-    if: ${{ needs.setup.outputs.repository-list != '' }}
+    if: ${{ github.event_name != 'repository-dispatch' && needs.setup.outputs.repository-list != '' }}
     runs-on: ubuntu-latest
     strategy:
       matrix:
@@ -394,7 +396,7 @@ jobs:
   deploy:
     name: Deploy
     needs: [setup, lint, flake8, lintr, combine_outputs]
-    if: ${{ (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/main' ) && github.repository_owner == 'galaxyproject' }}
+    if: ${{ github.event_name != 'repository-dispatch' && (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/main' ) && github.repository_owner == 'galaxyproject' }}
     runs-on: ubuntu-latest
     strategy:
       matrix:
@@ -435,28 +437,9 @@ jobs:
   determine-success:
     name: Check workflow success
     needs: [setup, lint, flake8, lintr, combine_outputs]
-    if: ${{ always() && github.ref != 'refs/heads/master' && github.ref != 'refs/heads/main' }}
+    if: ${{ always() && github.event_name != 'repository-dispatch' && github.ref != 'refs/heads/master' && github.ref != 'refs/heads/main' }}
     runs-on: ubuntu-latest
     steps:
-    - name: Create URL to the run output
-      if: ${{ github.event.client_payload.slash_command.command == 'run-all-tool-tests' }}
-      id: vars
-      run: echo "::set-output name=run-url::https://github.com/$GITHUB_REPOSITORY/actions/runs/$GITHUB_RUN_ID"
-    - name: Create comment
-      if: ${{ github.event.client_payload.slash_command.command == 'run-all-tool-tests' }}
-      uses: peter-evans/create-or-update-comment@v1
-      with:
-        token: ${{ secrets.PAT }}
-        repository: ${{ github.event.client_payload.github.payload.repository.full_name }}
-        issue-number: ${{ github.event.client_payload.github.payload.issue.number }}
-        body: |
-          Summary:
-
-          ${{ steps.combine.outputs.statistics }}
-
-          [Find all tool test results here][1]
-
-          [1]: ${{ steps.vars.outputs.run-url }}
     - name: Check tool lint status
       if: ${{ needs.lint.result != 'success' && needs.flake8.result != 'skipped' }}
       run: exit 1

From 9789f9d387b97cf696840b697df9e7a294498b6b Mon Sep 17 00:00:00 2001
From: Simon Bray <32272674+simonbray@users.noreply.github.com>
Date: Wed, 8 Sep 2021 18:06:42 +0200
Subject: [PATCH 32/32] test changing test data

---
 tools/abricate/test-data/output_noresults.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/abricate/test-data/output_noresults.txt b/tools/abricate/test-data/output_noresults.txt
index 9423b576eb1..2698470473b 100644
--- a/tools/abricate/test-data/output_noresults.txt
+++ b/tools/abricate/test-data/output_noresults.txt
@@ -1 +1 @@
-#FILE	SEQUENCE	START	END	STRAND	GENE	COVERAGE	COVERAGE_MAP	GAPS	%COVERAGE	%IDENTITY	DATABASE	ACCESSION	PRODUCT	RESISTANCE
+#FILE	SEQUENCE	START	END	STRAND	GENE	COVERAGE	COVERAGE_MAP	GAPS	%COVERAGE	%IDENTITY	DATABASE	ACCESSION