Merge branch 'main' into flux_jsr_check

.github/workflows/cont_int.yml

@@ -1,6 +1,6 @@
 name: CI
 
-on: 
+on:
     pull_request:
         branches:
             - main
@@ -27,7 +27,7 @@ jobs:
             haskell: true
             large-packages: true
             swap-storage: true
-        
+
         - name: Cache RMG
           id: cache-rmg
           uses: actions/cache@v2
@@ -64,7 +64,7 @@ jobs:
             path: RMG-database
             ref: main
             fetch-depth: 1
-        
+
         - name: Cache ARC
           id: cache-arc
           uses: actions/cache@v2
@@ -91,9 +91,8 @@ jobs:
             key:
                 ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('environment.yml') }}-t3
 
-
         - name: Setup RMG-Py Env
-          uses: conda-incubator/setup-miniconda@v2
+          uses: conda-incubator/setup-miniconda@v3.0.1
           with:
               miniforge-variant: Mambaforge
               miniforge-version: latest
@@ -108,7 +107,7 @@ jobs:
               conda-${{ runner.os }}--${{ runner.arch }}-rmgpyenv-${{ env.CACHE_NUMBER}}
           env:
             # Increase this value to reset cache if etc/example-environment.yml has not changed
-            CACHE_NUMBER: 1
+            CACHE_NUMBER: 3
           id: cache-rmgpy-env
         - name: Update environment
           run: mamba env update -n rmg_env -f RMG-Py/environment.yml
@@ -164,7 +163,7 @@ jobs:
             mamba install -c conda-forge pytest-cov
 
         - name: Run T3 Tests
-          shell: bash -el {0} 
+          shell: bash -el {0}
           run: |
             source ~/.bashrc
             conda activate t3_env

.github/workflows/docker_build.yml

@@ -4,26 +4,34 @@ name: Docker Image Build and Push
 #https://docs.github.com/en/actions/reference/workflow-syntax-for-github-actions#permissions
 
 
+
 on:
   schedule:
     - cron: "0 0 */7 * *" # every 7 days
   push:
     branches:
       - main
+    paths:
+      - "Dockerfile"
+      - "devtools/Dockerfile_rmgpy"
+      - ".github/workflows/docker_build.yml"
   pull_request:
-    types: [opened, synchronize, reopened]
     branches:
       - main
     paths:
-      - "./Dockerfile"
+      - "Dockerfile"
+      - "devtools/Dockerfile_rmgpy"
+      - ".github/workflows/docker_build.yml"
+    types: [opened, synchronize, reopened, ready_for_review]
+  #workflow_dispatch: # Add this line to enable manual trigger
 
 permissions:
   contents: read
   pull-requests: write
 
 jobs:
   ci-check:
-    if: github.event_name == 'pull_request'
+    if: github.event_name == 'pull_request' || (github.event_name == 'push' && github.ref != 'refs/heads/main')
     runs-on: ubuntu-latest
     steps:
       - name: Free Disk Space (Ubuntu)
@@ -42,28 +50,15 @@ jobs:
           swap-storage: false
       - name: Checkout
         uses: actions/[email protected]
-      # Add steps for CI checks of the Dockerfile
-      - name: Login to Docker Hub
-        uses: docker/[email protected]
-        with:
-          username: ${{ secrets.DOCKERHUB_USERNAME }}
-          password: ${{ secrets.DOCKERHUB_TOKEN }}
       - name: Set up Docker Buildx
         uses: docker/[email protected]
-      - name: Build RMG-Py
-        uses: docker/[email protected]
-        with:
-          context: .
-          file: ./devtools/Dockerfile_rmgpy
-          push: false
-          tags: ${{ secrets.DOCKERHUB_USERNAME }}/rmgpy:latest
-      - name: Build T3
-        uses: docker/[email protected]
+      # Add steps for CI checks of the Dockerfile
+      - name: Build Docker Image (No Push)
+        uses: docker/[email protected]
         with:
           context: .
           file: ./Dockerfile
           push: false
-          tags: ${{ secrets.DOCKERHUB_USERNAME }}/thetandemtool-t3:latest
 
   build-and-push:
     if: github.event_name == 'push' && github.ref == 'refs/heads/main'

Dockerfile

@@ -1,38 +1,12 @@
 # Using the a base image of rmgpy:latest from DockerHub - Not the official version but a custom version that is smaller in size
-FROM --platform=linux/amd64 laxzal/rmgpy:latest
+FROM --platform=linux/amd64 laxzal/arc:latest
 
 USER rmguser
 
 # Installing ARC
 # Change directory to Code
 WORKDIR /home/rmguser/Code
 
-# Clone main branch ARC repository from GitHub and set as working directory
-RUN git clone -b main https://github.com/ReactionMechanismGenerator/ARC.git
-WORKDIR /home/rmguser/Code/ARC
-
-# Set environment variables for the Docker run and container
-ENV PYTHONPATH="${PYTHONPATH}:/home/rmguser/Code/ARC"
-ENV PYTHONPATH="${PYTHONPATH}:/home/rmguser/Code/AutoTST"
-ENV PYTHONPATH="${PYTHONPATH}:/home/rmguser/Code/TS-GCN"
-ENV PATH /home/rmguser/Code/ARC:$PATH
-
-# Install ARC Environment
-RUN micromamba create -y -f environment.yml && \
-    micromamba clean --all -f -y && \
-    rm -rf /home/rmguser/.cache/yarn \
-    rm -rf /home/rmguser/.cache/pip &&\
-    rm -rf /home/rmguser/.cache/pip && \
-    find -name '*.a' -delete && \
-    find -name '*.pyc' -delete && \
-    find -name '__pycache__' -type d -exec rm -rf '{}' '+' && \
-    find /opt/conda/envs/arc_env/lib/python3.7/site-packages/scipy -name 'tests' -type d -exec rm -rf '{}' '+' && \
-    find /opt/conda/envs/arc_env/lib/python3.7/site-packages/numpy -name 'tests' -type d -exec rm -rf '{}' '+' && \
-    find /opt/conda/envs/arc_env/lib/python3.7/site-packages/pandas -name 'tests' -type d -exec rm -rf '{}' '+' && \
-    find /opt/conda/envs/arc_env/lib/python3.7/site-packages -name '*.pyx' -delete && \
-    rm -rf /opt/conda/envs/arc_env/lib/python3.7/site-packages/uvloop/loop.c &&\
-    make clean
-
 # Install T3
 
 # Change directory to Code
@@ -54,21 +28,20 @@ RUN micromamba create -y -f environment.yml && \
     find /opt/conda/envs/t3_env/lib/python3.7/site-packages -name '*.pyx' -delete \
     && find /opt/conda/ -follow -type f -name '*.a' -delete \
     && find /opt/conda/ -follow -type f -name '*.pyc' -delete \
-    && find /opt/conda/ -follow -type f -name '*.js.map' -delete 
+    && find /opt/conda/ -follow -type f -name '*.js.map' -delete
 
 # Add alias to bashrc - rmge to activate the environment
 # These commands are not necessary for the Docker image to run, but they are useful for the user
-RUN echo "alias arce='micromamba activate arc_env'" >> ~/.bashrc \
-    && echo "export PYTHONPATH=/home/rmguser/Code/ARC:$PYTHONPATH" >> ~/.bashrc \
-    && echo "export PYTHONPATH=\"${PYTHONPATH}:/home/rmguser/Code/AutoTST\"" >> ~/.bashrc \
-    && echo "alias arc='python /home/rmguser/Code/ARC/ARC.py input.yml'" >> ~/.bashrc \
-    && echo "export PYTHONPATH=\"${PYTHONPATH}:/home/rmguser/Code/TS-GCN\"" >> ~/.bashrc \
-    && echo "alias deact='micromamba deactivate'" >> ~/.bashrc \
-    && echo "export arc_path='/home/rmguser/Code/ARC/'" >> ~/.bashrc \
+RUN echo "export arc_path='/home/rmguser/Code/ARC/'" >> ~/.bashrc \
     && echo "export t3_path='/home/rmguser/Code/T3/'" >> ~/.bashrc \
-    && echo "alias arccode='cd \$arc_path'" >> ~/.bashrc \
     && echo "alias t3code='cd \$t3_path'" >> ~/.bashrc \
     && echo "alias t3e='micromamba activate t3_env'" >> ~/.bashrc \
-    && echo "alias t3='python /home/rmguser/Code/T3/T3.py input.yml'" >> ~/.bashrc 
+    && echo "alias t3='python /home/rmguser/Code/T3/T3.py input.yml'" >> ~/.bashrc
+
+# Set the wrapper script as the entrypoint
+ENTRYPOINT ["/home/rmguser/entrywrapper.sh"]
 
-SHELL ["/bin/bash", "-c"]
+# Activate the T3 environment
+WORKDIR /home/rmguser/
+ARG MAMBA_DOCKERFILE_ACTIVATE=1
+ENV ENV_NAME=t3_env

README.md

@@ -3,7 +3,7 @@
 </p>
 
 # The Tandem Tool (T3) for automated chemical kinetic model development
-
+[![Docker Image Build and Push](https://github.com/ReactionMechanismGenerator/T3/actions/workflows/docker_build.yml/badge.svg?branch=main)](https://github.com/ReactionMechanismGenerator/T3/actions/workflows/docker_build.yml)
 ![Release](https://img.shields.io/badge/version-0.1.0-blue.svg)
 ![Build Status](https://github.com/ReactionMechanismGenerator/T3/actions/workflows/cont_int.yml/badge.svg)
 [![codecov](https://codecov.io/gh/ReactionMechanismGenerator/T3/branch/main/graph/badge.svg)](https://codecov.io/gh/ReactionMechanismGenerator/T3)

devtools/Dockerfile_rmgpy

@@ -87,6 +87,7 @@ RUN make \
 # Install RMS
 # The extra arguments are required to install PyCall and RMS in this Dockerfile. Will not work without them.
 # Final command is to compile the RMS during Docker build - This will reduce the time it takes to run RMS for the first time
+ENV JULIA_CPU_TARGET="x86-64,haswell,skylake,broadwell,znver1,znver2,znver3,cascadelake,icelake-client,cooperlake,generic,native"
 RUN touch /opt/conda/envs/rmg_env/condarc-julia.yml
 RUN CONDA_JL_CONDA_EXE=/bin/micromamba julia -e 'ENV["CONDA_JL_CONDA_EXE"]="/opt/conda/envs/rmg_env/bin/conda";using Pkg;Pkg.add(PackageSpec(name="PyCall", rev="master")); Pkg.build("PyCall"); Pkg.add(PackageSpec(name="ReactionMechanismSimulator", rev="main"))' \
     && python -c "import julia; julia.install(); import diffeqpy; diffeqpy.install()" \