Merge branch 'main' of https://github.com/bioimage-io/bioengine

bioimage-io · Mar 13, 2024 · b41c770 · b41c770
2 parents c6deb57 + db6eac0
commit b41c770
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Showing 8 changed files with 114 additions and 11 deletions.
diff --git a/.github/workflows/build-conda.yml b/.github/workflows/build-conda.yml
@@ -6,6 +6,7 @@ on:
       - main
     paths:
       - 'environments/*.yml'
+  workflow_dispatch:
 
 jobs:
   build-and-upload:
@@ -26,21 +27,21 @@ jobs:
       - name: Discover Environments
         id: discover
         run: |
-          echo "envs=$(ls environments/*.yml | xargs -n 1 basename)" >> $GITHUB_ENV
+          echo "envs=$(ls environments/*.yml | xargs -n 1 basename | tr '\n' ' ')" >> $GITHUB_ENV
 
       - name: Create, Pack, and Upload Environments
         env:
           AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
           AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
-          AWS_S3_BUCKET_NAME: ${{ secrets.AWS_S3_BUCKET_NAME }}
-          AWS_S3_ENDPOINT: ${{ secrets.AWS_S3_ENDPOINT }}
+          AWS_S3_BUCKET_NAME: "bioimage.io"
+          AWS_S3_ENDPOINT: "https://uk1s3.embassy.ebi.ac.uk"
           AWS_EC2_METADATA_DISABLED: "true" # https://github.com/aws/aws-cli/issues/5262#issuecomment-705832151
           PYTHONNOUSERSITE: "True"
         run: |
           # copy manifest to s3
-          aws s3 --endpoint-url $AWS_S3_ENDPOINT cp hypha-services-manifest.yaml s3://$AWS_S3_BUCKET_NAME/hypha-services-manifest.yaml
-          # copy the services folder to s3
-          aws s3 --endpoint-url $AWS_S3_ENDPOINT cp --recursive  services s3://$AWS_S3_BUCKET_NAME/services
+          # aws s3 --endpoint-url $AWS_S3_ENDPOINT cp hypha-services-manifest.yaml s3://$AWS_S3_BUCKET_NAME/hypha-services-manifest.yaml
+          # copy the apps folder to s3
+          aws s3 --endpoint-url $AWS_S3_ENDPOINT cp --recursive apps s3://$AWS_S3_BUCKET_NAME/apps
           for env_file in $envs; do
             env_name="${env_file%.*}"
             echo "Processing $env_name"
@@ -52,4 +53,4 @@ jobs:
             conda env remove -n $env_name
             rm $env_name.tar.gz
           done
-          
+          
diff --git a/.github/workflows/build-container.yml b/.github/workflows/build-container.yml
@@ -6,6 +6,7 @@ on:
       - main
     paths:
       - 'environments/**/Dockerfile'
+  workflow_dispatch:
 
 env:
   REGISTRY: ghcr.io

diff --git a/docs/img/bioengine-icon.svg b/docs/img/bioengine-icon.svg
diff --git a/docs/img/bioengine-logo-black-acc.svg b/docs/img/bioengine-logo-black-acc.svg
diff --git a/docs/img/bioengine-logo-black.svg b/docs/img/bioengine-logo-black.svg
diff --git a/docs/img/bioengine-logo-gray.svg b/docs/img/bioengine-logo-gray.svg
diff --git a/docs/img/bioengine-logo-white.svg b/docs/img/bioengine-logo-white.svg
diff --git a/environments/pyimagej-py310.yml b/environments/pyimagej-py310.yml
@@ -9,3 +9,4 @@ dependencies:
   - pip
   - pip:
     - imjoy-rpc
+
-Original file line number
+Diff line change
@@ Expand Up / @@ -6,6 +6,7 @@ on: @@
           - main
         paths:
           - 'environments/**/Dockerfile'
+      workflow_dispatch:
     env:
       REGISTRY: ghcr.io
@@ Expand Down @@
Original file line number	Diff line number	Diff line change
Expand Up		@@ -9,3 +9,4 @@ dependencies:
		- pip
		- pip:
		- imjoy-rpc