Merge pull request #4 from biosimulators/main

updating process constructor configurations

.gitignore

@@ -20,3 +20,4 @@ submit-biosimulators-container.sh
 .vagrant
 ._vagrant
 .THIS-IS-FOR-CONTAINER-DEV-ONLY
+buildDockerImage.yml

Dockerfile

@@ -1,60 +1,64 @@
+# TODO: Use a more specific tag instead of latest for reproducibility
 FROM ubuntu:latest
 
-ENV DEBIAN_FRONTEND=noninteractive
+ENV DEBIAN_FRONTEND=noninteractive \
+    XVFB_RES="1920x1080x24" \
+    XVFB_ARGS="" \
+    PATH="/app/.venv/bin:$PATH" \
+    CONFIG_ENV_FILE="/app/config/config.env" \
+    SECRET_ENV_FILE="/app/secret/secret.env" \
+    STORAGE_GCS_CREDENTIALS_FILE="/app/secret/gcs_credentials.json" \
+    STORAGE_LOCAL_CACHE_DIR="/app/scratch"
 
 WORKDIR /app
 
-COPY . /app
+# copy and make dirs
+COPY ./biosimulator_processes/processes /app/biosimulator_processes
+COPY ./notebooks /app/notebooks
+
+# copy files
+COPY ./pyproject.toml ./poetry.lock ./data ./scripts/trust-notebooks.sh /app/
+COPY ./scripts/xvfb-startup.sh /xvfb-startup.sh
 
 RUN apt-get update && apt-get install -y --no-install-recommends \
-    python3 \
-    python3-pip \
-    build-essential \
-    libncurses5 \
-    cmake \
-    make \
-    libx11-dev \
-    libc6-dev \
-    libx11-6 \
-    libc6 \
-    gcc \
+    python3.10  \
+    python3-pip  \
+    build-essential  \
+    libncurses5  \
+    cmake  \
+    make  \
+    libx11-dev  \
+    libc6-dev  \
+    libx11-6  \
+    libc6  \
+    gcc  \
     swig \
-    pkg-config \
-    curl \
-    tar \
-    libgl1-mesa-glx \
-    libice6 \
-    libpython3.10 \
-    wget \
-    && rm -rf /var/lib/apt/lists/*
-
-# RUN apt-get update && apt-get install -y python3-pip
-
-RUN apt-get -y update \
-    \
-    && apt-get install --no-install-recommends -y \
-        xvfb \
-    && mkdir /tmp/.X11-unix \
-    && chmod 1777 /tmp/.X11-unix \
-    \
-    && rm -rf /var/lib/apt/lists/*
-
-COPY scripts/xvfb-startup.sh /xvfb-startup.sh
-
-ENV XVFB_RES="1920x1080x24" \
-    XVFB_ARGS=""
-
-RUN pip install --upgrade pip \
-    && pip install poetry
+    pkg-config  \
+    curl  \
+    tar  \
+    libgl1-mesa-glx  \
+    libice6  \
+    libpython3.10  \
+    wget  \
+    xvfb \
+    && mkdir /tmp/.X11-unix  \
+    && chmod 1777 /tmp/.X11-unix  \
+    && rm -rf /var/lib/apt/lists/* \
+    && pip install --upgrade pip && pip install poetry \
+    && poetry config virtualenvs.in-project true \
+    && poetry install \
+    && chmod +x ./trust-notebooks.sh \
+    && ./trust-notebooks.sh \
+    && rm ./trust-notebooks.sh
 
-# Add Poetry to PATH
-ENV PATH="/root/.local/bin:${PATH}"
+VOLUME /app/data
 
-# RUN poetry config virtualenvs.create false
+CMD ["poetry", "run", "jupyter", "lab", "--ip=0.0.0.0", "--port=8888", "--no-browser", "--allow-root"]
 
-RUN poetry run pip install --upgrade pip \
-    && poetry run pip install python-libnuml --use-pep517 \
-    && poetry install
 
-ENTRYPOINT ["poetry", "run", "jupyter", "lab", "--ip=0.0.0.0", "--port=8888", "--no-browser", "--allow-root"]
+# PLEASE NOTE: We do not need to add a USER in the Dockerfile as Singularity will handle
+ # such logic in conversion on the HPC.
 
+# type imports
+# dist
+# param scan demo/location

README.md

@@ -176,3 +176,9 @@ A simplified view of the above script:
          >> workflow.run(10)
          >> results = workflow.gather_results()
          >> print(f'RESULTS: {pf(results)}')
+
+
+### A NOTE FOR DEVELOPERS:
+This tooling implements version control for dynamically-created composite containers through
+`poetry`. The version control for content on the Python Package Index is performed by 
+`setup.py`.

biosimulator_processes/__init__.py

@@ -22,3 +22,9 @@
         print(f"{class_name} registered successfully.")
     except ImportError as e:
         print(f"{class_name} not available. Error: {e}")
+
+
+from biosimulator_processes.copasi_process import CopasiProcess
+from biosimulator_processes.smoldyn_process import SmoldynProcess
+from biosimulator_processes.cobra_process import CobraProcess
+from biosimulator_processes.tellurium_process import TelluriumProcess

biosimulator_processes/container-assets/Dockerfile-base

@@ -0,0 +1,72 @@
+FROM ubuntu:latest
+
+ENV DEBIAN_FRONTEND=noninteractive
+
+WORKDIR /app
+
+COPY ./biosimulator_processes /app
+
+# COPY ./scripts /app
+
+# RUN rm -r /app/composer-api
+
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    python3 \
+    python3-pip \
+    build-essential \
+    libncurses5 \
+    cmake \
+    make \
+    libx11-dev \
+    libc6-dev \
+    libx11-6 \
+    libc6 \
+    gcc \
+    swig \
+    pkg-config \
+    curl \
+    tar \
+    libgl1-mesa-glx \
+    libice6 \
+    libpython3.10 \
+    wget \
+    && rm -rf /var/lib/apt/lists/*
+
+RUN apt-get -y update \
+    && apt-get install --no-install-recommends -y \
+        xvfb \
+    && mkdir /tmp/.X11-unix \
+    && chmod 1777 /tmp/.X11-unix \
+    && rm -rf /var/lib/apt/lists/*
+
+COPY ./scripts/xvfb-startup.sh /xvfb-startup.sh
+
+# RUN rm -r ./scripts
+
+ENV XVFB_RES="1920x1080x24" \
+    XVFB_ARGS=""
+
+# RUN pip install --upgrade pip \
+#     && pip install poetry
+
+# RUN poetry config virtualenvs.in-project true
+
+# Add Poetry to PATH
+# ENV PATH="/root/.local/bin:${PATH}"
+
+# RUN poetry run pip install --upgrade pip \
+#     && poetry run pip install python-libnuml --use-pep517 \
+#     && poetry install
+
+# activate poetry virtualenv
+# ENV PATH="/app/.venv/bin:$PATH"
+# ENV CONFIG_ENV_FILE="/app/config/config.env"
+# ENV SECRET_ENV_FILE="/app/secret/secret.env"
+# ENV STORAGE_GCS_CREDENTIALS_FILE="/app/secret/gcs_credentials.json"
+# ENV STORAGE_LOCAL_CACHE_DIR="/app/scratch"
+#
+# # activate the poetry virtualenv each new non-interative shell
+# RUN echo "source /app/.venv/bin/activate" >> /etc/bash.bashrc
+
+RUN pip install --upgrade pip && pip install jupyterlab
+# ENTRYPOINT ["poetry", "run", "jupyter", "lab", "--ip=0.0.0.0", "--port=8888", "--no-browser", "--allow-root"]