Refactor: Convert pytorch_connectomics from submodule to downloaded package

- Remove git submodule configuration (.gitmodules)
- Add setup_pytorch_connectomics.sh script to download at commit 20ccfde (v1.0)
- Update Dockerfile to download package instead of copying submodule
- Update start.sh to auto-setup pytorch_connectomics if missing
- Update README.md with new installation instructions
- Add pytorch_connectomics/ to .gitignore to prevent accidental commits

Author: akgohain

.gitignore

@@ -5,6 +5,7 @@
 *.png
 node_modules/
 pytc/
+pytorch_connectomics/
 logs/
 data/
 outputs/

.gitmodules

@@ -1,3 +0,0 @@
-[submodule "pytorch_connectomics"]
-	path = pytorch_connectomics
-	url = https://github.com/zudi-lin/pytorch_connectomics.git

Dockerfile

@@ -1,10 +1,11 @@
 #centOS
 FROM nvidia/cuda:11.1.1-devel-ubi8
 
-# Enable AppStream and install Python 3.9
+# Enable AppStream and install Python 3.9 and git
 RUN yum -y module enable python39 && \
     yum install -y python39-3.9.2 && \
     yum install -y python39-devel-3.9.2 && \
+    yum install -y git && \
     yum clean all && \ 
     (python3.9 --version || echo "Python installation failed" && exit 1)
 
@@ -21,7 +22,11 @@ WORKDIR /app
 # Install dependencies
 RUN pip3 install --no-cache-dir torch==1.9.0 torchvision==0.10.0 cuda-python==11.1.1
 
-COPY ./pytorch_connectomics /app/pytorch_connectomics
+# Download pytorch_connectomics at specific commit (version 1.0)
+RUN git clone https://github.com/zudi-lin/pytorch_connectomics.git /app/pytorch_connectomics && \
+    cd /app/pytorch_connectomics && \
+    git checkout 20ccfde
+
 COPY ./samples_pytc /app/samples_pytc
 COPY ./server_pytc /app/server_pytc
 COPY ./server_api /app/server_api
@@ -35,9 +40,10 @@ WORKDIR /app/server_api
 RUN pip3 install --no-cache-dir -r requirements.txt
 
 WORKDIR /app
-# Copies the startup script, and runs it at CMD
+# Copies the startup scripts, and runs it at CMD
 COPY ./start.sh /app/
-RUN chmod +x start.sh
+COPY ./setup_pytorch_connectomics.sh /app/
+RUN chmod +x start.sh setup_pytorch_connectomics.sh
 
 # Expose ports
 EXPOSE 4242 4243 4244 6006

README.md

@@ -62,8 +62,17 @@ pip install -r requirements.txt
 
 In root folder,
 ```bash
+# The setup script will automatically download pytorch_connectomics at commit 20ccfde (version 1.0)
+./setup_pytorch_connectomics.sh
+cd pytorch_connectomics
+pip install --editable .
+```
+
+Alternatively, you can run this manually:
+```bash
 git clone https://github.com/zudi-lin/pytorch_connectomics.git
 cd pytorch_connectomics
+git checkout 20ccfde
 pip install --editable .
 ```
 

setup_pytorch_connectomics.sh

@@ -0,0 +1,33 @@
+#!/bin/bash
+
+# Setup script for pytorch_connectomics
+# Downloads the repository at commit 20ccfde (version 1.0)
+
+set -e
+
+PYTORCH_CONNECTOMICS_COMMIT="20ccfde"
+REPO_URL="https://github.com/zudi-lin/pytorch_connectomics.git"
+PYTORCH_CONNECTOMICS_DIR="pytorch_connectomics"
+
+echo "Setting up pytorch_connectomics at commit ${PYTORCH_CONNECTOMICS_COMMIT}"
+
+# Remove existing directory if it exists
+if [ -d "${PYTORCH_CONNECTOMICS_DIR}" ]; then
+    echo "Removing existing ${PYTORCH_CONNECTOMICS_DIR} directory"
+    rm -rf "${PYTORCH_CONNECTOMICS_DIR}"
+fi
+
+# Clone the repository
+echo "Cloning pytorch_connectomics repository..."
+git clone "${REPO_URL}" "${PYTORCH_CONNECTOMICS_DIR}"
+
+# Change to the directory and checkout the specific commit
+cd "${PYTORCH_CONNECTOMICS_DIR}"
+echo "Checking out commit ${PYTORCH_CONNECTOMICS_COMMIT}..."
+git checkout "${PYTORCH_CONNECTOMICS_COMMIT}"
+
+# Return to parent directory
+cd ..
+
+echo "pytorch_connectomics setup complete!"
+echo "To install, run: cd ${PYTORCH_CONNECTOMICS_DIR} && pip install --editable ."

start.sh

@@ -1,5 +1,13 @@
 #!/bin/bash
 
+# Setup pytorch_connectomics if not already present
+if [ ! -d "pytorch_connectomics" ]; then
+    echo "Setting up pytorch_connectomics..."
+    ./setup_pytorch_connectomics.sh
+    echo "Installing pytorch_connectomics..."
+    cd pytorch_connectomics && pip3 install --editable . && cd ..
+fi
+
 # Install dependencies in ./server_api
 pip3 install -r server_api/requirements.txt