v0.2.5 - Update packages, multi-stage build with standard and buildx,…

… ci / tests

.datalad/.gitattributes

@@ -0,0 +1 @@
+config annex.largefiles=nothing

.datalad/config

@@ -0,0 +1,2 @@
+[datalad "dataset"]
+	id = 94d1fb8d-6eb8-4e5f-993a-3af894400e9e

.devcontainer/devcontainer.json

@@ -5,9 +5,13 @@
         "source=${localWorkspaceFolder},target=/home/coder/work,type=bind,consistency=cached"
     ],
     "updateRemoteUserUID": true,
-    "runArgs": ["--gpus", "all"],
-    "forwardPorts": [3334],
+    "runArgs": ["--gpus", 0],
+    "forwardPorts": [3334, 8888],
     "postCreateCommand": ["/bin/bash"],
+    "containerEnv": {
+        "ENV_NAME": "facsimilab"
+    },
+    "shutdownAction": "none",
     "customizations": {
         "vscode": {
             "extensions": [

.gitattributes

@@ -0,0 +1,3 @@
+* annex.backend=MD5E
+**/.git* annex.largefiles=nothing
+* annex.largefiles=nothing

.gitea/workflows/bleeding-edge.yml

@@ -0,0 +1,74 @@
+name: Bleeding Edge (Gitea)
+
+on:
+  push:
+    branches:
+      - gitea
+      - develop
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  build-test-and-push:
+    runs-on: "ubuntu-latest"
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+        with: 
+          clean: false
+          submodules: true
+
+      - name: Read the image version
+        id: package
+        uses: juliangruber/read-file-action@v1
+        with:
+          path: ./docker/image_version.txt
+
+
+      - name: Matrix Message - Starting Build
+        uses: s3krit/[email protected]
+        with:
+            room_id: ${{ secrets.MATRIX_ROOM_ID }}
+            access_token: ${{ secrets.MATRIX_ACCESS_TOKEN }}
+            message: "Completed FacsimiLab image build for tag ${{ steps.package.outputs.content }}"
+            server: "matrix.drpranavmishra.com"
+
+      - name: Build Docker images
+        run: bash docker/build-all.sh
+
+      - name: Matrix Message - Completed Build
+        uses: s3krit/[email protected]
+        with:
+            room_id: ${{ secrets.MATRIX_ROOM_ID }}
+            access_token: ${{ secrets.MATRIX_ACCESS_TOKEN }}
+            message: "Completed FacsimiLab image build for tag ${{ steps.package.outputs.content }}"
+            server: "matrix.drpranavmishra.com"
+
+
+      - name: Commit changes to git (docker image metadata)
+        uses: devops-infra/action-commit-push@master
+        with:
+          github_token: "${{ secrets.GITHUB_TOKEN }}"
+          # add_timestamp: false
+          commit_prefix: "ci(docker): "
+          commit_message: "Docker images built and pushed [GH Action]"
+          force: false
+          # target_branch:
+
+      - name: Write to workflow job summary
+        run: |
+          build_version=$(cat docker/image_version.txt)
+          builder_header="# $build_version "
+          echo "$builder_header" > testing/results/job_summary.md
+          cat testing/results/job_summary.md >> $GITHUB_STEP_SUMMARY
+
+      - name: Matrix Message - Completed GitHub Action
+        uses: s3krit/[email protected]
+        with:
+            room_id: ${{ secrets.MATRIX_ROOM_ID }}
+            access_token: ${{ secrets.MATRIX_ACCESS_TOKEN }}
+            message: "# Gitea: Completed FacsimiLab build github action for tag ${{ steps.package.outputs.content }}"
+            server: "matrix.drpranavmishra.com"

.gitea/workflows/dev-test-full.yml

@@ -0,0 +1,31 @@
+name: Build Dev Image of FacsimiLab-Full
+
+on:
+  push:
+    paths:
+      - "docker/facsimilab-conda-lock.yml"
+  workflow_dispatch:
+jobs:
+  full-image-devevelopment:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Build Docker images
+        run: bash docker/dev-test-full.sh
+
+      - name: Run Facsmilab-Full:Dev container and execute script
+        run: |
+          docker run --rm -v $(pwd):/home/coder/work --gpus 0  pranavmishra90/facsimilab-full:dev /opt/conda/envs/facsimilab/bin/python testing/full_image.py >> testing/results/full-image.txt
+
+      - name: Push Docker images
+        run: docker push pranavmishra90/facsimilab-full:dev
+
+      - name: Write to workflow job summary
+        run: |
+          build_version=$(cat docker/image_version.txt)
+          builder_header="# $build_version - Development Image"
+          echo "$builder_header" > testing/results/job_summary.md
+          cat testing/results/full-image.txt >> testing/results/job_summary.md
+          cat testing/results/job_summary.md >> $GITHUB_STEP_SUMMARY

.gitea/workflows/python-packages.yml

@@ -0,0 +1,97 @@
+name: Check Python Packages
+
+on:
+  # push:
+  #   branches:
+  #     - gitea
+  #     - develop
+  #     - main
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  build-test-and-push:
+    runs-on: "ubuntu-latest"
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Read the image version
+        id: package
+        uses: juliangruber/read-file-action@v1
+        with:
+          path: ./docker/image_version.txt
+
+      - name: Workspace variable
+        run: echo "$GITHUB_WORKSPACE"
+
+      - name: List workspace
+        run: |
+          echo "Workspace ${{ github.workspace }}"
+          echo "PWD: $(pwd)"
+          find /workspace -type d -name '.git' -prune -o -type f -print
+
+
+
+      - name: Pull Docker image
+        run: |
+          echo "Pulling image pranavmishra90/facsimilab-full:${{ steps.package.outputs.content }}"
+          docker pull pranavmishra90/facsimilab-full:${{ steps.package.outputs.content }}
+
+      - name: List contents of main image
+        run: |
+              docker run --rm --user 0:0 --volumes-from=${{ env.JOB_CONTAINER_NAME }} -v $(pwd):/home/coder/work -e ENV_NAME=base  pranavmishra90/facsimilab-main:dev cp -r ${{ github.workspace }} /home/coder/work && find /home/coder -type d -name '.git' -prune -o -type f -print
+
+      # - name: Main Image
+      #   run: |
+      #         docker run --rm -v $(pwd):/home/coder/work -e ENV_NAME=base  pranavmishra90/facsimilab-main:dev  /opt/conda/bin/python /home/coder/work/testing/main_image.py | tee output.txt
+
+
+      # - name: Full Image
+      #   run: |
+      #         docker run --rm -v $(pwd):/home/coder/work -e ENV_NAME=facsimilab  pranavmishra90/facsimilab-full:dev  /opt/conda/envs/facsimilab/bin/python /home/coder/work/testing/full_image.py | tee output.txt
+
+      # - name: Main Image
+      #   uses: addnab/docker-run-action@v3
+      #   env:
+      #     WORKSPACE_DIR: ${{ github.workspace }}
+      #     GITHUB_WORKSPACE: ${{ github.workspace }}
+      #   with:
+      #     image: pranavmishra90/facsimilab-main:${{ steps.package.outputs.content }}
+      #     options: --rm --user 1000:1000 --volumes-from=${{ env.JOB_CONTAINER_NAME }} --entrypoint ${{ github.workspace }}
+      #     run: |
+      #       cp -r ${{ github.workspace }} /home/coder/work
+      #       cd ${{ github.workspace }} && pwd && ls -lahgR .
+      #       echo "----------------------------------------------------"
+      #       cd /home/coder/work/facsimilab-platform && pwd && ls -lahgR .
+      #       /opt/conda/bin/python ${{ github.workspace }}/testing/main_image.py > testing/results/main-image.txt 
+
+      # - name: Full Image
+      #   uses: addnab/docker-run-action@v3
+      #   env:
+      #     WORKSPACE_DIR: ${{ github.workspace }}
+      #     GITHUB_WORKSPACE: ${{ github.workspace }}
+      #   with:
+      #     image: pranavmishra90/facsimilab-full:${{ steps.package.outputs.content }}
+      #     options: --rm --user 1000:1000 --volumes-from=${{ env.JOB_CONTAINER_NAME }} --entrypoint ${{ github.workspace }}
+      #     run: |
+      #       cp -r ${{ github.workspace }} /home/coder/work
+      #       cd ${{ github.workspace }} && pwd && ls -lahgR .
+      #       echo "----------------------------------------------------"
+      #       cd /home/coder/work/facsimilab-platform && pwd && ls -lahgR .
+      #       /opt/conda/bin/python ${{ github.workspace }}/testing/full_image.py > testing/results/full-image.txt 
+
+
+      - name: Write to workflow job summary
+        run: |
+          build_version=$(cat docker/image_version.txt)
+          builder_header="# $build_version "
+          echo "$builder_header" > testing/results/job_summary.md
+          cat "## Main Image" >> testing/results/job_summary.md
+          cat "   " >> testing/results/job_summary.md
+          cat testing/results/job_summary.md >> $GITHUB_STEP_SUMMARY
+    # cat testing/results/main-image.txt >> testing/results/job_summary.md
+    # cat testing/results/full-image.txt >> testing/results/job_summary.md

.github/workflows/bleeding-edge.yml

@@ -0,0 +1,97 @@
+name: Bleeding Edge
+
+on:
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  build-test-and-push:
+    runs-on: [self-hosted, linux, x64]
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+        with: 
+          clean: false
+          submodules: true
+
+      - name: Read the image version
+        id: package
+        uses: juliangruber/read-file-action@v1
+        with:
+          path: ./docker/image_version.txt
+
+      - name: Login to Docker Hub
+        uses: docker/login-action@v3
+        with:
+          username: pranavmishra90
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+
+
+      - name: Matrix Message - Starting Build
+        uses: s3krit/[email protected]
+        with:
+            room_id: ${{ secrets.MATRIX_ROOM_ID }}
+            access_token: ${{ secrets.MATRIX_ACCESS_TOKEN }}
+            message: "Starting FacsimiLab image build for tag ${{ steps.package.outputs.content }} <br><br> ${{ github.workflow }}-${{ github.ref }}"
+            server: "matrix.drpranavmishra.com"
+
+      - name: Build Docker images
+        run: bash docker/build-all.sh
+
+      - name: Matrix Message - Completed Build
+        uses: s3krit/[email protected]
+        with:
+            room_id: ${{ secrets.MATRIX_ROOM_ID }}
+            access_token: ${{ secrets.MATRIX_ACCESS_TOKEN }}
+            message: "# Completed FacsimiLab image build for tag ${{ steps.package.outputs.content }}"
+            server: "matrix.drpranavmishra.com"
+
+      - name: Run Facsmilab-Main container and execute script
+        run: |
+          docker pull pranavmishra90/facsimilab-main:${{ steps.package.outputs.content }}
+          docker run --rm -v ${{ GITHUB_WORKSPACE }}:/home/coder/work  -v ~/.gitconfig:/home/coder/.gitconfig -e ENV_NAME=base  pranavmishra90/facsimilab-main:${{ steps.package.outputs.content }} /opt/conda/bin/python testing/main_image.py > testing/results/main-image.txt
+          
+
+      - name: Run Facsmilab-Full container and execute script
+        run: |
+          docker pull pranavmishra90/facsimilab-full:${{ steps.package.outputs.content }}
+          docker run --rm -v ${{ GITHUB_WORKSPACE }}:/home/coder/work --gpus 0 -e ENV_NAME=facsimilab  pranavmishra90/facsimilab-full:${{ steps.package.outputs.content }} /opt/conda/envs/facsimilab/bin/python testing/full_image.py > testing/results/full-image.txt
+
+      # docker run --rm -v $(pwd):/home/coder/work --gpus 0 -e ENV_NAME=facsimilab  pranavmishra90/facsimilab-full:dev /opt/conda/envs/facsimilab/bin/python testing/full_image.py > testing/results/full-image.txt
+
+      - name: Push Docker images
+        run: bash docker/push-all.sh
+
+      - name: Commit changes to git (docker image metadata)
+        uses: devops-infra/action-commit-push@master
+        with:
+          github_token: "${{ secrets.GITHUB_TOKEN }}"
+          # add_timestamp: false
+          commit_prefix: "ci(docker): "
+          commit_message: "Docker images built and pushed [GH Action]"
+          force: false
+          # target_branch:
+
+      - name: Write to workflow job summary
+        run: |
+          build_version=$(cat docker/image_version.txt)
+          builder_header="# $build_version "
+          echo "$builder_header" > testing/results/job_summary.md
+          echo "## Main Image" >> testing/results/job_summary.md
+          echo "   " >> testing/results/job_summary.md
+          cat testing/results/main-image.txt >> testing/results/job_summary.md
+          cat testing/results/full-image.txt >> testing/results/job_summary.md
+          cat testing/results/job_summary.md >> $GITHUB_STEP_SUMMARY
+  # # notify-completed:
+  # #   runs-on: ubuntu-latest
+  #   steps:
+      - name: Matrix Message - Completed GitHub Action
+        uses: s3krit/[email protected]
+        with:
+            room_id: ${{ secrets.MATRIX_ROOM_ID }}
+            access_token: ${{ secrets.MATRIX_ACCESS_TOKEN }}
+            message: "Completed FacsimiLab build github action for tag ${{ steps.package.outputs.content }}"
+            server: "matrix.drpranavmishra.com"