Merge branch 'main' into prepostprocess

Author: MihinP

.github/workflows/docker.yml

@@ -0,0 +1,53 @@
+#
+name: Docker Build
+
+# Configures this workflow to run every time a change is pushed to the branch called `release`.
+on:
+  push:
+    branches: ['main']
+
+# Defines two custom environment variables for the workflow. These are used for the Container registry domain, and a name for the Docker image that this workflow builds.
+env:
+  REGISTRY: ghcr.io
+  IMAGE_NAME: ${{ github.repository }}
+
+# There is a single job in this workflow. It's configured to run on the latest available version of Ubuntu.
+jobs:
+  build-and-push-image:
+    runs-on: ubuntu-latest
+    # Sets the permissions granted to the `GITHUB_TOKEN` for the actions in this job.
+    permissions:
+      contents: read
+      packages: write
+      attestations: write
+      id-token: write
+      # 
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+        with: 
+          submodules: recursive
+      # Uses the `docker/login-action` action to log in to the Container registry registry using the account and password that will publish the packages. Once published, the packages are scoped to the account defined here.
+      - name: Log in to the Container registry
+        uses: docker/login-action@65b78e6e13532edd9afa3aa52ac7964289d1a9c1
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+      # This step uses [docker/metadata-action](https://github.com/docker/metadata-action#about) to extract tags and labels that will be applied to the specified image. The `id` "meta" allows the output of this step to be referenced in a subsequent step. The `images` value provides the base name for the tags and labels.
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/metadata-action@9ec57ed1fcdbf14dcef7dfbe97b2010124a938b7
+        with:
+          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+      # This step uses the `docker/build-push-action` action to build the image, based on your repository's `Dockerfile`. If the build succeeds, it pushes the image to GitHub Packages.
+      # It uses the `context` parameter to define the build's context as the set of files located in the specified path. For more information, see "[Usage](https://github.com/docker/build-push-action#usage)" in the README of the `docker/build-push-action` repository.
+      # It uses the `tags` and `labels` parameters to tag and label the image with the output from the "meta" step.
+      - name: Build and push Docker image
+        id: push
+        uses: docker/build-push-action@f2a1d5e99d037542a71f64918e516c093c6f3fc4
+        with:
+          context: .
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}

.github/workflows/singularity.yml

@@ -0,0 +1,55 @@
+name: Singularity Build
+on: 
+  push:
+
+    # Edit the branches here if you want to change deploy behavior
+    branches:
+      - main
+
+  # Do the builds on all pull requests (to test them)
+  pull_request: []
+
+jobs:
+  build-test-containers:
+    runs-on: ubuntu-latest
+    strategy:
+      # Keep going on other deployments if anything bloops
+      fail-fast: false
+      matrix:
+        singularity_version:
+          - '3.8.1'
+
+    container:
+      image: quay.io/singularity/singularity:v${{ matrix.singularity_version }}
+      options: --privileged
+
+    steps:
+
+      - name: Check out code for the container builds
+        uses: actions/checkout@v2
+        with:
+          submodules: recursive
+
+      - name: Build Container
+        run: |
+         if [ -f Singularity ]; then
+            sudo -E singularity build container.sif Singularity
+         else
+           echo "Singularity is not found."
+           echo "Present working directory: $PWD"
+           ls
+         fi
+      
+      - name: Set Tag Based on Branch Name
+        run: |
+          # Get the branch name and set it as the tag
+          tag=${GITHUB_REF##*/}-singularity
+          echo "Tag is $tag."
+          echo "tag=$tag" >> $GITHUB_ENV
+
+      - name: Login and Deploy Container
+        if: (github.event_name != 'pull_request')
+        run: |
+            echo ${{ secrets.GITHUB_TOKEN }} | singularity remote login -u ${{ secrets.GHCR_USERNAME }} --password-stdin oras://ghcr.io
+            container_name=$(echo ${GITHUB_REPOSITORY} | tr '[:upper:]' '[:lower:]')
+            singularity push container.sif oras://ghcr.io/${container_name}:${tag}

.gitignore

@@ -161,3 +161,6 @@ cython_debug/
 *.out
 .vscode/settings.json
 */core.*
+
+# DynamicDet run files
+runs

.gitmodules

@@ -0,0 +1,11 @@
+FROM python:3.9.19-slim-bookworm
+
+COPY pyproject.toml /opt/PartiNet/pyproject.toml
+COPY partinet /opt/PartiNet/partinet
+
+RUN apt-get update && apt-get install libglib2.0-0 libxext6 libx11-6 -y && rm -rf /var/cache/apt/archives /var/lib/apt/lists/* && apt-get clean
+RUN python -m pip install --no-cache-dir --no-cache /opt/PartiNet
+
+LABEL AUTHORS Mihin Perera, Edward Yang, Julie Iskander
+LABEL MAINTAINERS Mihin Perera, Edward Yang, Julie Iskander
+LABEL VERSION v0.1.1

Dockerfile

@@ -47,6 +47,7 @@ Options:
 Commands:
   detect
   preprocess
+  test
   train
 ```
 
@@ -264,3 +265,62 @@ Options:
 ```
 
 TODO: more details...
+
+## Testing
+
+```bash
+partinet test --help
+```
+```
+Usage: partinet test [OPTIONS]
+
+Options:
+  --backbone-detector [yolov7|yolov7-w6|yolov7x]
+                                  The choice of backbone to be used.
+                                  [default: yolov7]
+  --weight TEXT                   model.pt path(s)  [required]
+  --data TEXT                     data.yaml path  [default: data/coco.yaml]
+  --batch-size INTEGER            total batch size for all GPUs  [default: 1]
+  --img-size INTEGER              validation image size (pixels)  [default:
+                                  640]
+  --conf-thres FLOAT              object confidence threshold  [default:
+                                  0.001]
+  --iou-thres FLOAT               IOU threshold for NMS  [default: 0.65]
+  --task [train|val|test]         train, val, test, speed or study  [default:
+                                  test]
+  --device TEXT                   cuda device, i.e. 0 or 0,1,2,3 or cpu
+  --single-cls                    train multi-class data as single-class
+  --augment                       augmented inference
+  --verbose                       report mAP by class
+  --save-txt                      save results to *.txt
+  --save-hybrid                   save label+prediction hybrid results to
+                                  *.txt
+  --save-conf                     save confidences in --save-txt labels
+  --save-json                     save a cocoapi-compatible JSON results file
+  --project TEXT                  save to project/name  [default: runs/test]
+  --name TEXT                     save to project/name  [default: exp]
+  --exist-ok                      existing project/name ok, do not increment
+  --v5-metric                     assume maximum recall as 1.0 in AP
+                                  calculation
+  --dy-thres FLOAT                dynamic thres  [default: 0.5]
+  --save-results                  save results
+  --help                          Show this message and exit.
+```
+
+TODO: more details...
+
+## Get the container
+
+Replace `partinet <subcommand> <args>` with one of the below:
+
+### Docker
+
+```bash
+docker run ghcr.io/wehi-researchcomputing/partinet:latest <subcommand> <args>
+```
+
+### Singularity/Apptainer
+
+```bash
+singularity run oras://ghcr.io/wehi-researchcomputing/partinet:latest <subcommand> <args>
+```

README.md

@@ -0,0 +1,21 @@
+bootstrap: docker
+from: python:3.9.19-slim-bookworm
+
+%files
+  . /opt/PartiNet
+
+%post
+  # install system dependencies
+  apt-get update
+  apt-get install libglib2.0-0 libxext6 libx11-6 -y
+
+  # cleanup apt package index
+  rm -rf /var/cache/apt/archives /var/lib/apt/lists/*
+  apt-get clean
+
+  python -m pip install --no-cache-dir /opt/PartiNet
+
+%labels
+  AUTHORS Mihin Perera, Edward Yang, Julie Iskander
+  MAINTAINERS Mihin Perera, Edward Yang, Julie Iskander
+  VERSION v0.1.1