Changes pulled from github repo

.github/workflows/Manual_Deployment_to_NIDAP.yml

@@ -0,0 +1,105 @@
+name: Manual Deployment to NIDAP
+run-name: Manual Deployment to NIDAP by ${{ github.actor }} 
+
+on:
+  workflow_dispatch:
+    inputs:
+
+      image_to_use:
+        required: true
+        default: "<Replace with your image>"
+        type: string
+
+      package_to_deploy:
+        required: true
+        type: string
+
+      artifact_rid:
+        required: true
+        default: "<Replace with your artifact RID>"
+        type: string
+
+      token_to_use:
+        required: true
+        type: string
+
+
+jobs:
+  Adding_documentation_files_and_publish_page:
+    runs-on: ubuntu-latest
+    container:
+      image: ${{ inputs.image_to_use }}
+      credentials:
+         username: ${{ github.actor }}
+         password: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - run: echo "Checking in ${{ inputs.image_to_use }}"
+      - uses: actions/checkout@v3
+        with:
+          token: ${{secrets.GITHUB_TOKEN}}
+
+      - name: Continuous Deployment to NIDAP
+        id: nidap-cd
+        run: |
+          export current_wd="/__w/${GITHUB_REPOSITORY#*/}/${GITHUB_REPOSITORY#*/}"
+          cd $current_wd
+
+          export MY_GIT_TOKEN=${{ secrets.GITHUB_TOKEN }}
+          export MY_GIT_USERNAME=${{ github.actor }}
+          export MY_GIT_EMAIL=${{ github.event.pusher.email }}
+          
+          git config --global user.name "$MY_GIT_USERNAME"
+          git config --global user.email "$MY_GIT_EMAIL"
+          git config --global url."https://api:$MY_GIT_TOKEN@github.com/".insteadOf "https://github.com/"
+          git config --global url."https://ssh:$MY_GIT_TOKEN@github.com/".insteadOf "ssh://git@github.com/"
+          git config --global url."https://git:$MY_GIT_TOKEN@github.com/".insteadOf "git@github.com:"
+          
+          git config --global --add safe.directory "$current_wd"
+          
+          git clone https://github.com/${GITHUB_REPOSITORY}.git
+          
+          cd ${GITHUB_REPOSITORY#*/}
+
+          BRANCH_NAME="Conda_Package"
+
+          git checkout $BRANCH_NAME
+
+          echo "########## Git setup complete, moving to deployment... ##########"
+
+          conda install curl
+
+          current_pkg="${{ inputs.package_to_deploy }}"
+          
+          echo "Package to Upload: $current_pkg"
+
+          TOKEN="${{ inputs.token_to_use }}"
+          PACKAGE="$current_pkg"
+          PLATFORM="linux-64" # replace with the package platform (e.g. noarch, linux-64, osx-64)
+          response=$(curl \
+                    -H "Authorization: Bearer $TOKEN" \
+                    -H "Content-Type: application/octet-stream" \
+                    --data-binary "@$PACKAGE" \
+                    -XPUT "https://nidap.nih.gov/artifacts/api/repositories/${{ inputs.artifact_rid }}/contents/release/conda/$PLATFORM/$PACKAGE" \
+                    2>&1)
+
+
+          echo "#########################################################"
+
+          current_datetime="$(date +"%Y-%m-%d %H:%M:%S")"
+
+          # Check if the response contains an error message
+          if echo "$response" | grep -q "errorCode"; then
+            status=$(echo "$response" | grep -o '"errorName":"[^"]*' | awk -F'"' '{print $4}')
+            echo "Error message: $status"
+            echo "<br>Deployment Time: $current_datetime; Deployment Status: $status" >> README.md
+          else
+            status="Success"
+            echo "Update Success!"
+            echo "Package ${{ env.current_pkg }} is now on NIDAP."
+            echo "<br>Deployment Time: $current_datetime; Deployment Status: Success" >> README.md
+          fi
+
+          git commit -a -m "Deployment Performed on $current_datetime with Status: $status."
+
+          git push -f origin $BRANCH_NAME    

.github/workflows/gitflow-R-action.yml

@@ -3,14 +3,21 @@ run-name: ${{ github.actor }} now ${{ github.event_name }} to ${{ github.ref_nam
 
 on:
   push:
-    branches: ['*', '!dev']
+    branches: ['*', '!dev', '!main', '!release_dev', '!Conda_Package', '!github_page']
 
   pull_request:
     types: ['opened', 'closed']
     branches: ['main', 'release*']
 
 jobs:
   Activating_Parser:
-    uses: fnlcr-bids-sdsi/gitflow-R/.github/workflows/parser.yml@SCWorkflow
+    uses: fnlcr-bids-sdsi/gitflow-R/.github/workflows/parser.yml@master
     with:
-      image_to_use: "ghcr.io/nidap-community/single-cell-rna-r4:v1.0"
+      image_to_use: ghcr.io/nidap-community/single-cell-rna-r4:latest
+      package_name: "r-scworkflow"
+      r_version: "4.1.3"
+      artifact_rid_production: "ri.artifacts.main.repository.f36ea39e-b396-46cd-a04a-3c63250273f5"
+      artifact_rid_development: "ri.stemma.main.repository.2172e505-c98f-43d4-881a-47e170aadbe1"
+    secrets:
+      NIDAP_TOKEN_PRODUCTION: ${{ secrets.NIDAP_TOKEN_PRODUCTION }}
+      NIDAP_TOKEN_DEVELOPMENT: ${{ secrets.NIDAP_TOKEN_DEVELOPMENT }}