delete unnecesary print commands and edited docker-publish.yml

.github/workflows/docker-publish.yml

@@ -1,15 +1,19 @@
-name: publish docker container for macsima2mc.py
+name: Docker
 
 # This workflow uses actions that are not certified by GitHub.
 # They are provided by a third-party and are governed by
 # separate terms of service, privacy policy, and support
 # documentation.
 
 on: [push]
-  #release:
-   # types: published
-  #pull_request:
-   # branches: [ "main" ]
+#  schedule:
+#    - cron: '1 * * * *'
+#  push:
+#    branches: [ "main" ]
+    # Publish semver tags as releases.
+#    tags: [ 'v*.*.*' ]
+#  pull_request:
+#    branches: [ "main" ]
 
 env:
   # Use docker.io for Docker Hub if empty
@@ -30,29 +34,28 @@ jobs:
       id-token: write
 
     steps:
-      - name: Set up QEMU
-        uses: docker/setup-qemu-action@v2
-
       - name: Checkout repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       # Install the cosign tool except on PR
       # https://github.com/sigstore/cosign-installer
       - name: Install cosign
         if: github.event_name != 'pull_request'
-        uses: sigstore/cosign-installer@f3c664df7af409cb4873aa5068053ba9d61a57b6 #v2.6.0
+        uses: sigstore/cosign-installer@v3.5.0 #v3.1.1
         with:
-          cosign-release: 'v1.11.0'
-
-      # Workaround: https://github.com/docker/build-push-action/issues/461
-      - name: Setup Docker buildx
-        uses: docker/setup-buildx-action@79abd3f86f79a9d68a23c75a09a9a85889262adf
+          cosign-release: 'v2.2.4'
+
+      # Set up BuildKit Docker container builder to be able to build
+      # multi-platform images and export cache
+      # https://github.com/docker/setup-buildx-action
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@f95db51fddba0c2d1ec667646a06c2ce06100226 # v3.0.0
 
       # Login against a Docker registry except on PR
       # https://github.com/docker/login-action
       - name: Log into registry ${{ env.REGISTRY }}
         if: github.event_name != 'pull_request'
-        uses: docker/login-action@28218f9b04b4f3f62068d7b6ce6ca5b26e35336c
+        uses: docker/login-action@343f7c4344506bcbf9b4de18042ae17996df046d # v3.0.0
         with:
           registry: ${{ env.REGISTRY }}
           username: ${{ github.actor }}
@@ -62,24 +65,35 @@ jobs:
       # https://github.com/docker/metadata-action
       - name: Extract Docker metadata
         id: meta
-        uses: docker/metadata-action@98669ae865ea3cffbcbaa878cf57c20bbf1c6c38
+        uses: docker/metadata-action@96383f45573cb7f253c731d3b3ab81c87ef81934 # v5.0.0
         with:
           images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
-
-      - name: Get the tag name
-        run: echo "TAG=${GITHUB_REF/refs\/tags\//}" >> $GITHUB_ENV
-
-      - name: Set up QEMU
-        uses: docker/setup-qemu-action@v2
-
+
       # Build and push Docker image with Buildx (don't push on PR)
       # https://github.com/docker/build-push-action
       - name: Build and push Docker image
         id: build-and-push
-        uses: docker/build-push-action@ac9327eae2b366085ac7f6a2d02df8aa8ead720a
+        uses: docker/build-push-action@0565240e2d4ab88bba5387d719585280857ece09 # v5.0.0
         with:
           context: .
           platforms: linux/amd64,linux/arm64
           push: ${{ github.event_name != 'pull_request' }}
           tags: ${{ steps.meta.outputs.tags }}
-          labels: ${{ steps.meta.outputs.labels }}
+          labels: ${{ steps.meta.outputs.labels }}
+          cache-from: type=gha
+          cache-to: type=gha,mode=max
+
+      # Sign the resulting Docker image digest except on PRs.
+      # This will only write to the public Rekor transparency log when the Docker
+      # repository is public to avoid leaking data.  If you would like to publish
+      # transparency data even for private images, pass --force to cosign below.
+      # https://github.com/sigstore/cosign
+      - name: Sign the published Docker image
+        if: ${{ github.event_name != 'pull_request' }}
+        env:
+          # https://docs.github.com/en/actions/security-guides/security-hardening-for-github-actions#using-an-intermediate-environment-variable
+          TAGS: ${{ steps.meta.outputs.tags }}
+          DIGEST: ${{ steps.build-and-push.outputs.digest }}
+        # This step uses the identity token to provision an ephemeral certificate
+        # against the sigstore community Fulcio instance.
+        run: echo "${TAGS}" | xargs -I {} cosign sign --yes {}@${DIGEST}

macsima2mc_v2.py

@@ -243,7 +243,6 @@ def create_ome(img_info,xy_tile_positions_units,img_path):
         pixel_size=1000*pixel_size
         #pixel_units='um'
     no_of_tiles=len(xy_tile_positions_units)
-    print(img_info)
     tifff.tiffcomment(img_path,'')
     #--Generate tiff_data_blocks--#
     tiff_block=[]
@@ -591,10 +590,8 @@ def main():
 
 
     for e in exp:
-        print(e)
         if extract_bleach:
             for key,value in out_ant.items():
-                print(key,':',value)
             df1=pd.DataFrame(out_ant).groupby('exposure_level').get_group(e)
             df2=pd.DataFrame(out_ble).groupby('exposure_level').get_group(e)
             df=pd.concat([df1,df2],ignore_index=True)