Save progress for MR move

.github/workflows/pydesigner_build.yml

@@ -1,39 +1,39 @@
-name: Docker Build and Push
+# name: Docker Build and Push
 
-on:
-    push:
-      tags:
-        - '**'
+# on:
+#     push:
+#       tags:
+#         - '**'
 
-jobs:
-  docker:
-    runs-on: ubuntu-latest
-    steps:
-        -
-            name: Checkout
-            uses: actions/checkout@v3
-        -
-            name: Fetch version
-            uses: SebRollen/[email protected]
-            id: version
-            with:
-              file: 'pyproject.toml'
-              field: 'tool.poetry.version'
-        -
-            name: Set up QEMU
-            uses: docker/setup-qemu-action@v3
-        -
-            name: Set up Docker Buildx
-            uses: docker/setup-buildx-action@v3
-        -
-            name: Login to Docker Hub
-            uses: docker/login-action@v3
-            with:
-                username: ${{ secrets.DOCKERHUB_USERNAME }}
-                password: ${{ secrets.DOCKERHUB_TOKEN }}
-        -
-            name: Build and push
-            uses: docker/build-push-action@v5
-            with:
-                push: true
-                tags: dmri/neurodock:latest,dmri/neurodock:${{ steps.version.outputs.value }}
+# jobs:
+#   docker:
+#     runs-on: ubuntu-latest
+#     steps:
+#         -
+#             name: Checkout
+#             uses: actions/checkout@v3
+#         -
+#             name: Fetch version
+#             uses: SebRollen/[email protected]
+#             id: version
+#             with:
+#               file: 'pyproject.toml'
+#               field: 'tool.poetry.version'
+#         -
+#             name: Set up QEMU
+#             uses: docker/setup-qemu-action@v3
+#         -
+#             name: Set up Docker Buildx
+#             uses: docker/setup-buildx-action@v3
+#         -
+#             name: Login to Docker Hub
+#             uses: docker/login-action@v3
+#             with:
+#                 username: ${{ secrets.DOCKERHUB_USERNAME }}
+#                 password: ${{ secrets.DOCKERHUB_TOKEN }}
+#         -
+#             name: Build and push
+#             uses: docker/build-push-action@v5
+#             with:
+#                 push: true
+#                 tags: dmri/neurodock:latest,dmri/neurodock:${{ steps.version.outputs.value }}

.github/workflows/pydesigner_ci.yml

@@ -5,10 +5,24 @@ on:
   push:
     branches: [main]
 
+
 jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
-    - uses: actions/setup-python@v3
-    - uses: pre-commit/[email protected]
+    - name: Checkout
+      uses: actions/checkout@v3
+    - name: Set up Python
+      uses: actions/setup-python@v3
+    - name: Run Pre-Commit
+      uses: pre-commit/[email protected]
+      with:
+        pre-commit_version: latest
+        python_version: 3.8
+        system: true 
+    # - name: Auto-commit changed files
+    #   uses: stefanzweifel/git-auto-commit-action@v5
+    #   with:
+    #     commit_message: "Pre-commit fixes"
+
+

Dockerfile

@@ -14,61 +14,57 @@
 # ==============================================================================
 
 # Load base Ubuntu image
-FROM debian:buster-slim
+FROM python:3.11-bullseye
 
-# Add LABEL Information
-# ARG BUILD_DATE
-# ARG VCS_REF
-
-# Labels.
-LABEL maintainer="Siddhartha Dhiman ([email protected])"
+# Labels
+LABEL maintainer="Siddhartha Dhiman ([email protected])"
 LABEL org.label-schema.schema-version="1.0.0-rc1"
-LABEL org.label-schema.build-date=$BUILD_DATE
 LABEL org.label-schema.name="dmri/pydesigner"
 LABEL org.label-schema.description="A state-of-the-art difusion and kurtosis MRI processing pipeline"
 LABEL org.label-schema.url="https://github.com/m-ama/"
 LABEL org.label-schema.vcs-url="https://github.com/m-ama/NeuroDock.git"
-LABEL org.label-schema.vcs-ref=$VCS_REF
-LABEL org.label-schema.vendor="MAMA"
+LABEL org.label-schema.vendor="MUSC BRIDGE"
 
-ARG DEBIAN_FRONTEND=noninteractive
+# ARG DEBIAN_FRONTEND=noninteractive
 
 # Initial update
-RUN apt-get update && \
+RUN apt update && \
       apt-get install -y \
       apt-utils \
       wget \
       curl \
       nano \
       software-properties-common \
-      python2.7 python-pip \
+      python3 \
       python3-pip \
       jq \
       libblas-dev \
       liblapack-dev \
       libatlas-base-dev \
-      gfortran
-
-# Install MRTRIX3 dependencies
-RUN apt-get install -y --no-install-recommends \
-      clang \
+      gfortran \
       git \
+      g++ \
+      python \
       libeigen3-dev \
       zlib1g-dev \
-      libqt4-opengl-dev \
+      libqt5opengl5-dev \
+      libqt5svg5-dev \
       libgl1-mesa-dev \
       libfftw3-dev \
       libtiff5-dev \
-      libomp-dev
-
-RUN rm /bin/sh && ln -s /bin/bash /bin/sh
+      libpng-dev
 
 # Copy and install PyDesigner
-RUN mkdir -p /tmp/PyDesigner
-ADD . / /tmp/PyDesigner/
-RUN pip3 install /tmp/PyDesigner
-RUN echo "alias python=python3" >> ~/.bashrc && source ~/.bashrc
-RUN echo "alias pip=pip3" >> ~/.bashrc && source ~/.bashrc
+RUN mkdir -p /pydesigner
+COPY /pydesigner /app/pydesigner
+COPY pyproject.toml app/
+RUN ls
+RUN ls -la /app
+WORKDIR /app
+ENV PYTHONPATH=${PYTHONPATH}:${PWD} 
+RUN pip3 install poetry
+RUN poetry config virtualenvs.create false
+RUN poetry install --no-dev
 
 # Install Python dependencies
 RUN pip3 install --upgrade setuptools && \
@@ -104,3 +100,5 @@ ENV PATH=$PATH:/usr/lib/mrtrix3/bin
 # Remove unwanted packages
 RUN apt-get autoremove && apt-get clean
 RUN rm /tmp/fslinstaller.py && rm -r /tmp/PyDesigner
+
+USER bridge