Merge pull request #53 from WEHI-ResearchComputing/feature/gradio-gui

Feature/gradio gui

Author: MihinP

.github/workflows/deploy.yml

@@ -0,0 +1,41 @@
+name: Deploy to GitHub Pages
+
+on:
+  push:
+    branches:
+      - main
+
+permissions:
+  contents: write
+
+defaults:
+  run:
+    working-directory: docs
+
+jobs:
+  deploy:
+    name: Deploy to GitHub Pages
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - uses: actions/setup-node@v4
+        with:
+          node-version: 20
+          cache: npm
+          cache-dependency-path: docs/package-lock.json
+
+      - name: Install dependencies
+        run: npm ci
+
+      - name: Build website
+        run: npm run build
+
+      - name: Deploy to GitHub Pages
+        uses: peaceiris/actions-gh-pages@v4
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: docs/build
+          commit_message: "Deploy website"

.github/workflows/singularity.yml

@@ -8,43 +8,42 @@ jobs:
   build-test-containers:
     runs-on: ubuntu-latest
     strategy:
-      # Keep going on other deployments if anything bloops
       fail-fast: false
       matrix:
+        # Must match an existing tag on quay.io/singularity/singularity (full semver, e.g. 4.1.0 not 4.0).
         singularity_version:
-          - '3.8.1'
+          - '4.1.0'
 
     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
+        uses: actions/checkout@v4
         with:
           submodules: recursive
 
-      - name: Build Container
+      - name: Verify Singularity definition exists
         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
-      
+          if [ ! -f Singularity ]; then
+            echo "Singularity definition file not found in $(pwd)"
+            ls -la
+            exit 1
+          fi
+
+      - name: Build Container
+        run: sudo -E singularity build container.sif Singularity
+
       - name: Set Tag Based on Branch Name
         run: |
-          # Get the branch name and set it as the tag
           tag=${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}
+          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}

.github/workflows/test-deploy.yml

@@ -0,0 +1,31 @@
+name: Test deployment
+
+on:
+  pull_request:
+    branches:
+      - main
+
+defaults:
+  run:
+    working-directory: docs
+
+jobs:
+  test-deploy:
+    name: Test deployment
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - uses: actions/setup-node@v4
+        with:
+          node-version: 20
+          cache: npm
+          cache-dependency-path: docs/package-lock.json
+
+      - name: Install dependencies
+        run: npm ci
+
+      - name: Test build website
+        run: npm run build

.gitignore

@@ -164,3 +164,9 @@ cython_debug/
 
 # DynamicDet run files
 runs
+gui/.venv/
+partinet-env/
+
+# Container images and scratch shell scripts
+*.sif
+*.sh

Dockerfile

@@ -8,4 +8,4 @@ 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 v1.0.1
+LABEL VERSION v1.1.0

README.md

@@ -17,6 +17,7 @@ Use our pretrained model at [Model Weights](https://huggingface.co/MihinP/PartiN
 - Seamless integration with cryoSPARC and RELION workflows
 - Confidence-based particle filtering
 - Visual detection validation
+- Browser GUI (`partinet gui`) with optional Slurm job submission
 
 ## Prerequisites
 
@@ -112,6 +113,7 @@ Available commands:
 - `denoise`: Clean input micrographs
 - `detect`: Identify particles
 - `star`: Generate STAR files
+- `gui`: Launch the Gradio GUI (local or Slurm execution)
 - `train`: Train custom models
 
 

Singularity

@@ -18,4 +18,4 @@ from: python:3.9.19-slim-bookworm
 %labels
   AUTHORS Mihin Perera, Edward Yang, Julie Iskander
   MAINTAINERS Mihin Perera, Edward Yang, Julie Iskander
-  VERSION v1.0.1
+  VERSION v1.1.0

docs/docs/getting-started.md

@@ -6,6 +6,14 @@ sidebar_position: 3
 
 This guide walks you through your first PartiNet analysis using the three-stage pipeline. We'll process cryo-EM micrographs from start to finish.
 
+:::tip New to PartiNet?
+The **[GUI](gui.md)** is the easiest way to get started — no command-line experience needed. Launch it with `partinet gui` and run all three stages from your browser.
+
+![PartiNet GUI overview](/img/gui_overview.png)
+
+The CLI walkthrough below is for users who prefer scripting, are working in containers, or need to run PartiNet on an HPC cluster.
+:::
+
 ## Prerequisites
 
 Before starting, ensure you have:
@@ -24,27 +32,29 @@ project_directory/
 │   ├── micrograph1.mrc
 │   ├── micrograph2.mrc
 │   └── ...
-├── denoised/                  # Created by denoise stage
-│   ├── micrograph1.mrc
-│   ├── micrograph2.mrc
+├── denoised/                  # Created by denoise stage (default: .png)
+│   ├── micrograph1.png
+│   ├── micrograph2.png
 │   └── ...
 ├── exp/                       # Created by detect stage
 │   ├── labels/               # Detection coordinates (YOLO format)
 │   │   ├── micrograph1.txt
 │   │   ├── micrograph2.txt
 │   │   └── ...
-│   ├── micrograph1.png    # Micrographs with detections drawn
-│   ├── micrograph2.
+│   ├── micrograph1.png       # Micrographs with detections drawn
+│   ├── micrograph2.png
 │   └── ...
 └── partinet_particles.star   # CryoSPARC-style STAR file (created by star stage)
 ```
 
 **Pipeline Flow:**
 1. **Input** → `motion_corrected/` (your micrographs)
-2. **Stage 1** → `denoised/` (cleaned micrographs)
+2. **Stage 1** → `denoised/` (cleaned micrographs, PNG by default)
 3. **Stage 2** → `exp*/` (detections + visualizations)
 4. **Stage 3** → `*.star` (final particle coordinates)
 
+See [Detect — skip denoise](stages/detect.md#skip-denoise-raw-mrc) if picking directly on raw MRC without denoising.
+
 ## Stage 1: Denoise
 
 The first stage removes noise from your micrographs and improves signal-to-noise ratios:
@@ -53,8 +63,8 @@ The first stage removes noise from your micrographs and improves signal-to-noise
 
 ```shell title="Local Installation"
 partinet denoise \
-    --source /data/my_project/motion_corrected \
-    --project /data/my_project
+    --source /data/partinet_picking/motion_corrected \
+    --project /data/partinet_picking
 ```
 
 </div>
@@ -100,9 +110,9 @@ The final stage converts detections to STAR format and applies confidence filter
 
 ```shell title="Local Installation"
 partinet star \
-    --labels /data/my_project/exp/labels \
-    --images /data/my_project/denoised \
-    --output /data/my_project/partinet_particles.star \
+    --labels /data/partinet_picking/exp/labels \
+    --images /data/partinet_picking/denoised \
+    --output /data/partinet_picking/partinet_particles.star \
     --conf 0.1
 ```
 
@@ -118,7 +128,7 @@ partinet star \
 After running all three stages, you'll have:
 
 1. **Denoised micrographs** (`denoised/`) - Cleaned input for particle detection
-2. **Detection visualizations** (`exp/*.mrc`) - Micrographs with particle boxes drawn
+2. **Detection visualizations** (`exp/*.png`) - Micrographs with particle boxes drawn
 3. **Detection coordinates** (`exp/labels/*.txt`) - Raw detection data
 4. **STAR file** (`*.star`) - Final particle coordinates ready for downstream processing