style: Run pre-commit

Author: edmundmiller

.github/workflows/AWSMegatests.yml

@@ -4,12 +4,12 @@ on:
     branches:
       - master
     paths:
-      - 'pulumi/test_datasets/**/*'
+      - "pulumi/test_datasets/**/*"
   pull_request:
     branches:
       - master
     paths:
-      - 'pulumi/test_datasets/**/*'
+      - "pulumi/test_datasets/**/*"
 
 # These are the environment variables that jobs in the workflow have access to.
 # By defining them here, all jobs/steps will have access to these variables.
@@ -29,7 +29,6 @@ jobs:
     name: Pulumi
     runs-on: ubuntu-latest
     steps:
-
       # Turnstyle is used to prevent multiple push jobs from running at the same time. We
       # limit it to push jobs to allow PR jobs to run concurrently.
       - name: Turnstyle
@@ -64,7 +63,6 @@ jobs:
           stack-name: ${{ env.PULUMI_STACK_NAME }}
           work-dir: ${{ env.PULUMI_WORKING_DIRECTORY }}
 
-
       # If you'd like to run your Pulumi application outside of the official GitHub Action
 
       #- name: Install Pulumi CLI

.github/workflows/repos.yml

@@ -42,7 +42,7 @@ jobs:
 
       - name: Install Python
         uses: actions/setup-python@v5
-        cache: 'pip'
+        cache: "pip"
 
       - run: pip install -r requirements.txt
         working-directory: ${{ env.PULUMI_WORKING_DIRECTORY }}
@@ -61,4 +61,3 @@ jobs:
           command: up
           stack-name: ${{ env.PULUMI_STACK_NAME }}
           work-dir: ${{ env.PULUMI_WORKING_DIRECTORY }}
-

docs/1password.md

@@ -15,6 +15,7 @@ op plugin init pulumi
 ```
 
 This should result in:
+
 ```
 
 Pulumi CLI

pulumi/github/repos/__main__.py

@@ -1,3 +1,2 @@
 #!/usr/bin/env python
 
-import pipelines.testpipeline

pulumi/github/repos/core/modules.py

@@ -1,5 +1,3 @@
-import yaml
-
 import pulumi
 import pulumi_github as github
 

pulumi/github/repos/import_by_hand.py

@@ -1,18 +1,7 @@
 #!/usr/bin/env python
 
-import pulumi
-import pulumi_github as github
-
-import pipelines.denovotranscript
-import pipelines.meerpipe
-import pipelines.pairgenomealign
-import pipelines.phaseimpute
-import pipelines.reportho
 
 # ...
 
-import core.github
-import core.modules
 
 # ...
-import core.website

pulumi/github/repos/pipelines/testpipeline.py

@@ -7,24 +7,23 @@
 
 # Configure 1Password provider with account details
 onepassword_provider = onepassword.Provider(
-    "onepassword-provider",
-    account="nf-core.1password.eu"
+    "onepassword-provider", account="nf-core.1password.eu"
 )
 
 # Fetch GitHub token from 1Password
 # Item ID from the 1Password URL: 4ajrv44kc5lcbboa37fr5oydla
 # Vault ID from the 1Password URL: rdfcz6oy6qxxrc4clu467a7dmm
 github_token_item = onepassword.get_item(
     vault="rdfcz6oy6qxxrc4clu467a7dmm",  # Vault ID from the 1Password URL
-    uuid="4ajrv44kc5lcbboa37fr5oydla",   # Item ID from the 1Password URL
-    opts=pulumi.InvokeOptions(provider=onepassword_provider)
+    uuid="4ajrv44kc5lcbboa37fr5oydla",  # Item ID from the 1Password URL
+    opts=pulumi.InvokeOptions(provider=onepassword_provider),
 )
 
 # Configure GitHub provider with token from 1Password
 github_provider = github.Provider(
     "github-provider",
     token=github_token_item.password,  # The token is stored in the password field
-    owner="nf-core-tf"
+    owner="nf-core-tf",
 )
 
 NAME = "testpipeline"
@@ -81,7 +80,7 @@
     visibility="public",
     topics=TOPICS,  # 'repo_keywords' => 'Minimum keywords set',
     # NOTE: @mirpedrol asked if we could add missing topics without deleting existing ones
-    opts=pulumi.ResourceOptions(provider=github_provider)
+    opts=pulumi.ResourceOptions(provider=github_provider),
 )