From 8bc64afaf1812446b122a37be41bd1661c199404 Mon Sep 17 00:00:00 2001
From: mbruns91 <marianbruns91@gmail.com>
Date: Mon, 17 Jun 2024 11:43:41 +0200
Subject: [PATCH 01/20] create .github/workflows/run_workflow.yml

---
 .github/workflows/run_workflow.yml | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 create mode 100644 .github/workflows/run_workflow.yml

diff --git a/.github/workflows/run_workflow.yml b/.github/workflows/run_workflow.yml
new file mode 100644
index 0000000..e69de29

From cfd80af03c8a0924a36f7227ef7388a4132d3351 Mon Sep 17 00:00:00 2001
From: mbruns91 <marianbruns91@gmail.com>
Date: Mon, 17 Jun 2024 11:54:51 +0200
Subject: [PATCH 02/20] add environment.yml

---
 .github/workflows/run_workflow.yml | 0
 environment.yml                    | 4 ++++
 2 files changed, 4 insertions(+)
 delete mode 100644 .github/workflows/run_workflow.yml
 create mode 100644 environment.yml

diff --git a/.github/workflows/run_workflow.yml b/.github/workflows/run_workflow.yml
deleted file mode 100644
index e69de29..0000000
diff --git a/environment.yml b/environment.yml
new file mode 100644
index 0000000..1f735a7
--- /dev/null
+++ b/environment.yml
@@ -0,0 +1,4 @@
+channels:
+  - conda-forge
+dependencies:
+  - pyiron_workflow

From d5d1cd35b0d5e180feed623e5df5e442a674b723 Mon Sep 17 00:00:00 2001
From: mbruns91 <marianbruns91@gmail.com>
Date: Mon, 17 Jun 2024 11:55:46 +0200
Subject: [PATCH 03/20] create .github/workflows/run_workflow.yml

---
 .github/workflows/run_workflow.yml | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)
 create mode 100644 .github/workflows/run_workflow.yml

diff --git a/.github/workflows/run_workflow.yml b/.github/workflows/run_workflow.yml
new file mode 100644
index 0000000..43d9b44
--- /dev/null
+++ b/.github/workflows/run_workflow.yml
@@ -0,0 +1,26 @@
+name: Run workflow
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    types: [labeled, opened, synchronize, reopened]
+
+jobs:
+  build:
+    if: |
+      github.event_name == 'push' ||
+      ( github.event_name == 'pull_request'  && contains(github.event.pull_request.labels.*.name, 'run_workflow' ))
+      
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+    - uses: conda-incubator/setup-miniconda@v2.2.0
+      with:
+        python-version: "3.11"
+        mamba-version: "*"
+        miniforge-variant: Mambaforge
+        channels: conda-forge
+        channel-priority: strict
+        auto-update-conda: true
+        environment-file: environment.yml

From a49e1a9ef1245c3e60d47b7b9558f8b4b6810d74 Mon Sep 17 00:00:00 2001
From: mbruns91 <marianbruns91@gmail.com>
Date: Mon, 17 Jun 2024 11:57:45 +0200
Subject: [PATCH 04/20] create gitignore (just so that it's there)

---
 .gitignore | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 create mode 100644 .gitignore

diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..e69de29

From 8f08a8cb596d0af5fd1bdc4e223a6889ddd3b201 Mon Sep 17 00:00:00 2001
From: mbruns91 <marianbruns91@gmail.com>
Date: Mon, 17 Jun 2024 12:09:17 +0200
Subject: [PATCH 05/20] let the workflow be executed when the label
 run_workflow is added to a PR

---
 .github/workflows/run_workflow.yml | 17 ++++++-----------
 1 file changed, 6 insertions(+), 11 deletions(-)

diff --git a/.github/workflows/run_workflow.yml b/.github/workflows/run_workflow.yml
index 43d9b44..e4cb7bb 100644
--- a/.github/workflows/run_workflow.yml
+++ b/.github/workflows/run_workflow.yml
@@ -5,22 +5,17 @@ on:
     branches: [ main ]
   pull_request:
     types: [labeled, opened, synchronize, reopened]
+  workflow_call:
 
 jobs:
   build:
     if: |
       github.event_name == 'push' ||
       ( github.event_name == 'pull_request'  && contains(github.event.pull_request.labels.*.name, 'run_workflow' ))
-      
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
-    - uses: conda-incubator/setup-miniconda@v2.2.0
-      with:
-        python-version: "3.11"
-        mamba-version: "*"
-        miniforge-variant: Mambaforge
-        channels: conda-forge
-        channel-priority: strict
-        auto-update-conda: true
-        environment-file: environment.yml
+      - uses: actions/checkout@v4
+      - uses: pyiron/actions/build-notebooks@actions-3.1.0
+        with:
+          python-version: '3.11'
+          env-files: environment.yml

From 0906b630d2da0fae122e6322162b1c82560954e8 Mon Sep 17 00:00:00 2001
From: mbruns91 <marianbruns91@gmail.com>
Date: Mon, 17 Jun 2024 12:16:02 +0200
Subject: [PATCH 06/20] adjust path to env file

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

diff --git a/.github/workflows/run_workflow.yml b/.github/workflows/run_workflow.yml
index e4cb7bb..208479d 100644
--- a/.github/workflows/run_workflow.yml
+++ b/.github/workflows/run_workflow.yml
@@ -18,4 +18,4 @@ jobs:
       - uses: pyiron/actions/build-notebooks@actions-3.1.0
         with:
           python-version: '3.11'
-          env-files: environment.yml
+          env-files: ./environment.yml

From 3dac0da861b360746c140deb6695f1a69330b6e3 Mon Sep 17 00:00:00 2001
From: mbruns91 <marianbruns91@gmail.com>
Date: Mon, 17 Jun 2024 12:22:09 +0200
Subject: [PATCH 07/20] ???

---
 .ci_support/environment.yml | 4 ++++
 1 file changed, 4 insertions(+)
 create mode 100644 .ci_support/environment.yml

diff --git a/.ci_support/environment.yml b/.ci_support/environment.yml
new file mode 100644
index 0000000..1f735a7
--- /dev/null
+++ b/.ci_support/environment.yml
@@ -0,0 +1,4 @@
+channels:
+  - conda-forge
+dependencies:
+  - pyiron_workflow

From f1e6233637864d667cb164d0d16a1fb85b24294f Mon Sep 17 00:00:00 2001
From: mbruns91 <marianbruns91@gmail.com>
Date: Mon, 17 Jun 2024 12:22:58 +0200
Subject: [PATCH 08/20] forgot to change this in the gh-workflow file

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

diff --git a/.github/workflows/run_workflow.yml b/.github/workflows/run_workflow.yml
index 208479d..c1cc662 100644
--- a/.github/workflows/run_workflow.yml
+++ b/.github/workflows/run_workflow.yml
@@ -18,4 +18,4 @@ jobs:
       - uses: pyiron/actions/build-notebooks@actions-3.1.0
         with:
           python-version: '3.11'
-          env-files: ./environment.yml
+          env-files: .ci_support/environment.yml

From 0b9ea6ea01b7e4d435d08cc4cf6dd067ff5bd0cc Mon Sep 17 00:00:00 2001
From: mbruns91 <marianbruns91@gmail.com>
Date: Mon, 17 Jun 2024 12:33:22 +0200
Subject: [PATCH 09/20] update pyiron/actions release

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

diff --git a/.github/workflows/run_workflow.yml b/.github/workflows/run_workflow.yml
index c1cc662..97c6ddb 100644
--- a/.github/workflows/run_workflow.yml
+++ b/.github/workflows/run_workflow.yml
@@ -15,7 +15,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-      - uses: pyiron/actions/build-notebooks@actions-3.1.0
+      - uses: pyiron/actions/build-notebooks@actions-3.2.0
         with:
           python-version: '3.11'
-          env-files: .ci_support/environment.yml
+          env-files: environment.yml

From fa7cfc08eb8484392cdd18e18dc10cfbdfdd98f2 Mon Sep 17 00:00:00 2001
From: mbruns91 <marianbruns91@gmail.com>
Date: Mon, 17 Jun 2024 12:37:04 +0200
Subject: [PATCH 10/20] remove environment.yml form root dir; located now in
 .ci_support/

---
 environment.yml | 4 ----
 1 file changed, 4 deletions(-)
 delete mode 100644 environment.yml

diff --git a/environment.yml b/environment.yml
deleted file mode 100644
index 1f735a7..0000000
--- a/environment.yml
+++ /dev/null
@@ -1,4 +0,0 @@
-channels:
-  - conda-forge
-dependencies:
-  - pyiron_workflow

From efd2d54f9b2808ca3da8c3297285c5c874772257 Mon Sep 17 00:00:00 2001
From: mbruns91 <marianbruns91@gmail.com>
Date: Mon, 17 Jun 2024 12:37:41 +0200
Subject: [PATCH 11/20] account for this in the action

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

diff --git a/.github/workflows/run_workflow.yml b/.github/workflows/run_workflow.yml
index 97c6ddb..2cfbc19 100644
--- a/.github/workflows/run_workflow.yml
+++ b/.github/workflows/run_workflow.yml
@@ -18,4 +18,4 @@ jobs:
       - uses: pyiron/actions/build-notebooks@actions-3.2.0
         with:
           python-version: '3.11'
-          env-files: environment.yml
+          env-files: .ci_support/environment.yml

From f0e50924df8326bd1033e6731c284bc1402b29d1 Mon Sep 17 00:00:00 2001
From: mbruns91 <marianbruns91@gmail.com>
Date: Mon, 17 Jun 2024 12:57:20 +0200
Subject: [PATCH 12/20] use another action

---
 .github/workflows/run_workflow.yml | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/run_workflow.yml b/.github/workflows/run_workflow.yml
index 2cfbc19..e32c922 100644
--- a/.github/workflows/run_workflow.yml
+++ b/.github/workflows/run_workflow.yml
@@ -8,14 +8,22 @@ on:
   workflow_call:
 
 jobs:
-  build:
+  run_workflow:
     if: |
       github.event_name == 'push' ||
       ( github.event_name == 'pull_request'  && contains(github.event.pull_request.labels.*.name, 'run_workflow' ))
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-      - uses: pyiron/actions/build-notebooks@actions-3.2.0
+      - name: Setup environment
+        uses: pyiron/actions/cached-miniforge@actions-3.2.0
         with:
           python-version: '3.11'
           env-files: .ci_support/environment.yml
+          use-cache: 'true'
+          miniforge-channels: conda-forge
+          pip-install-versioneer: 'false'
+          no-build-isolation: 'false'
+      - name: Execute notebook
+        shell: bash -l {0}
+        run: jupyter nbconvert --execute --to notebook workflow.ipynb

From b023189cb4602c65c3fd82d8a1a7763fabf4ffae Mon Sep 17 00:00:00 2001
From: mbruns91 <marianbruns91@gmail.com>
Date: Mon, 17 Jun 2024 13:04:48 +0200
Subject: [PATCH 13/20] no local code to be pip-installed

---
 .github/workflows/run_workflow.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/run_workflow.yml b/.github/workflows/run_workflow.yml
index e32c922..37b9af1 100644
--- a/.github/workflows/run_workflow.yml
+++ b/.github/workflows/run_workflow.yml
@@ -20,6 +20,7 @@ jobs:
         with:
           python-version: '3.11'
           env-files: .ci_support/environment.yml
+          local-code-directory: ''
           use-cache: 'true'
           miniforge-channels: conda-forge
           pip-install-versioneer: 'false'

From 1cc4d8f4f788651ea06eff9700910e7283a2c97a Mon Sep 17 00:00:00 2001
From: mbruns91 <marianbruns91@gmail.com>
Date: Mon, 17 Jun 2024 13:28:56 +0200
Subject: [PATCH 14/20] install jupyter from within the gh-workflow def

---
 .github/workflows/run_workflow.yml | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/run_workflow.yml b/.github/workflows/run_workflow.yml
index 37b9af1..fa32d1b 100644
--- a/.github/workflows/run_workflow.yml
+++ b/.github/workflows/run_workflow.yml
@@ -6,7 +6,7 @@ on:
   pull_request:
     types: [labeled, opened, synchronize, reopened]
   workflow_call:
-
+    
 jobs:
   run_workflow:
     if: |
@@ -25,6 +25,9 @@ jobs:
           miniforge-channels: conda-forge
           pip-install-versioneer: 'false'
           no-build-isolation: 'false'
-      - name: Execute notebook
+      - name: Add jupyter
+        shell: bash -l {0}
+        run: mamba install -n my-env jupyter
+      - name: Execute workflow
         shell: bash -l {0}
         run: jupyter nbconvert --execute --to notebook workflow.ipynb

From 26e00d909a3db4b8901b4fd27f521ac1aacae056 Mon Sep 17 00:00:00 2001
From: mbruns91 <marianbruns91@gmail.com>
Date: Mon, 17 Jun 2024 13:36:48 +0200
Subject: [PATCH 15/20] explicitly specify the kernel to be used

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

diff --git a/.github/workflows/run_workflow.yml b/.github/workflows/run_workflow.yml
index fa32d1b..891d115 100644
--- a/.github/workflows/run_workflow.yml
+++ b/.github/workflows/run_workflow.yml
@@ -30,4 +30,4 @@ jobs:
         run: mamba install -n my-env jupyter
       - name: Execute workflow
         shell: bash -l {0}
-        run: jupyter nbconvert --execute --to notebook workflow.ipynb
+        run: jupyter nbconvert --ExecutePreprocessor.kernel_name=python3 --execute --to notebook workflow.ipynb

From 9e251661e898b9747ff30fac1e987ea85eb180c4 Mon Sep 17 00:00:00 2001
From: mbruns91 <marianbruns91@gmail.com>
Date: Mon, 17 Jun 2024 13:45:17 +0200
Subject: [PATCH 16/20] testing: make a trivial change to a node

---
 nodes/time.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nodes/time.py b/nodes/time.py
index 8aa303f..587ad11 100644
--- a/nodes/time.py
+++ b/nodes/time.py
@@ -2,4 +2,4 @@
 
 @Workflow.wrap.as_function_node("travel_time")
 def get_time(distance: float, speed: float) -> float:
-    return 10.
+    return 42.

From f7a804a7d0227da2f6e4b2871a3943d43072c9b4 Mon Sep 17 00:00:00 2001
From: mbruns91 <marianbruns91@gmail.com>
Date: Mon, 17 Jun 2024 13:59:24 +0200
Subject: [PATCH 17/20] papermill instead of jupyter nbconvert

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

diff --git a/.github/workflows/run_workflow.yml b/.github/workflows/run_workflow.yml
index 891d115..939b5ee 100644
--- a/.github/workflows/run_workflow.yml
+++ b/.github/workflows/run_workflow.yml
@@ -27,7 +27,7 @@ jobs:
           no-build-isolation: 'false'
       - name: Add jupyter
         shell: bash -l {0}
-        run: mamba install -n my-env jupyter
+        run: mamba install -n my-env papermill
       - name: Execute workflow
         shell: bash -l {0}
-        run: jupyter nbconvert --ExecutePreprocessor.kernel_name=python3 --execute --to notebook workflow.ipynb
+        run: papermill workflow.ipynb workflow-out.ipynb

From 49f6aeb5b0a4a2b21858ab6bae6ce0eaad66b853 Mon Sep 17 00:00:00 2001
From: mbruns91 <marianbruns91@gmail.com>
Date: Mon, 17 Jun 2024 14:01:40 +0200
Subject: [PATCH 18/20] rename corresponding section in the action def; specify
 kernel name

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

diff --git a/.github/workflows/run_workflow.yml b/.github/workflows/run_workflow.yml
index 939b5ee..75f793b 100644
--- a/.github/workflows/run_workflow.yml
+++ b/.github/workflows/run_workflow.yml
@@ -25,9 +25,9 @@ jobs:
           miniforge-channels: conda-forge
           pip-install-versioneer: 'false'
           no-build-isolation: 'false'
-      - name: Add jupyter
+      - name: Add papermill
         shell: bash -l {0}
         run: mamba install -n my-env papermill
       - name: Execute workflow
         shell: bash -l {0}
-        run: papermill workflow.ipynb workflow-out.ipynb
+        run: papermill workflow.ipynb workflow-out.ipynb -k python3

From 69a74f9fee709f483df8696146e03fcfdf25fa18 Mon Sep 17 00:00:00 2001
From: mbruns91 <marianbruns91@gmail.com>
Date: Mon, 17 Jun 2024 14:11:51 +0200
Subject: [PATCH 19/20] upload the updated notebook as artifact

---
 .github/workflows/run_workflow.yml | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/.github/workflows/run_workflow.yml b/.github/workflows/run_workflow.yml
index 75f793b..1473137 100644
--- a/.github/workflows/run_workflow.yml
+++ b/.github/workflows/run_workflow.yml
@@ -31,3 +31,8 @@ jobs:
       - name: Execute workflow
         shell: bash -l {0}
         run: papermill workflow.ipynb workflow-out.ipynb -k python3
+      - name: Upload updated notebook as artifact
+        uses: actions/upload-artifact@v4
+        with:
+          name: workflow-out.ipynb
+          path: ./workflow-out.ipynb

From eb6b6602b552974c1a9ca15d8c559d2f0d5bde55 Mon Sep 17 00:00:00 2001
From: mbruns91 <marianbruns91@gmail.com>
Date: Mon, 17 Jun 2024 14:58:50 +0200
Subject: [PATCH 20/20] update README.md

---
 README.md | 17 ++++++++---------
 1 file changed, 8 insertions(+), 9 deletions(-)

diff --git a/README.md b/README.md
index 2b91c3c..1399409 100644
--- a/README.md
+++ b/README.md
@@ -1,11 +1,10 @@
 # graphathon
 
-Playground for collaborative environment in order to create a workflow in parallel by distributing nodes (i.e. tasks) to different people.
-
-## Basic idea
-
-1. Create a workflow in a large group, with empty nodes with only inputs and outputs defined
-2. Distribute the nodes to different people
-3. As people finish their tasks, they push the nodes to the repository, where CI takes care of the workflow execution
-
-More will follow...
+A template repository for setting up an environment where nodes for a workflow using `pyiron_workflow` can be developed by different people in parallel.
+
+Usage goes like so:
+- the team sets up a dummy workflow using placeholder-vwersions of the involved nodes
+- the team creates a repository using *this* repo as a template (especially anything located in `.github/` and `.ci_support/`)
+- each dev opens a branch + PR for her work
+- as soon as the `run_workflow` label is added to the PR, each push triggers workflow execution via actions.
+- the updated notebook is uploaded as a github action artifact (Actions -> select CI run -> Artifacts). Download, unzip and view locally.