updated builders

Dockerfile

@@ -1,24 +1,24 @@
 # TODO: Use a more specific tag instead of latest for reproducibility
 FROM ubuntu:latest
 
-ENV DEBIAN_FRONTEND=noninteractive \
-    XVFB_RES="1920x1080x24" \
-    XVFB_ARGS="" \
-    PATH="/app/.venv/bin:$PATH" \
-    CONFIG_ENV_FILE="/app/config/config.env" \
-    SECRET_ENV_FILE="/app/secret/secret.env" \
-    STORAGE_GCS_CREDENTIALS_FILE="/app/secret/gcs_credentials.json" \
-    STORAGE_LOCAL_CACHE_DIR="/app/scratch"
+ENV DEBIAN_FRONTEND=noninteractive
+    # XVFB_RES="1920x1080x24" \
+    # XVFB_ARGS="" \
+    # PATH="/app/.venv/bin:$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 and make dirs
-COPY ./biosimulator_processes /app/biosimulator_processes
+# COPY ./biosimulator_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
+# COPY ./scripts/xvfb-startup.sh /xvfb-startup.sh
 
 VOLUME /app/data
 
@@ -43,20 +43,19 @@ RUN apt-get update && apt-get install -y --no-install-recommends \
     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 run pip install psutil \
     && poetry update \
     && poetry install \
     && chmod +x ./trust-notebooks.sh \
     && ./trust-notebooks.sh \
-    && rm ./trust-notebooks.sh
+    && rm ./trust-notebooks.sh \
+    && apt-get install --reinstall -y ca-certificates python3-pip \
+    && apt-get clean \
+    && apt-get autoclean
 
-CMD ["poetry", "run", "jupyter", "lab", "--port=8888", "--no-browser", "--allow-root"]
+# CMD ["poetry", "run", "jupyter", "lab", "--port=8888", "--no-browser", "--allow-root"]
 
 
 # PLEASE NOTE: We do not need to add a USER in the Dockerfile as Singularity will handle

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "biosimulator-processes"
-version = "0.0.17"
+version = "0.0.18"
 description = "Core implementations of process-bigraph.composite.Process aligning with BioSimulators simulator tools."
 authors = ["Alex Patrie <[email protected]>"]
 readme = "README.md"

scripts/exec-docker.sh

@@ -0,0 +1,12 @@
+#!/bin/bash
+
+version="$1"
+
+if [ "${version}" == "" ]; then
+  echo "Please enter the version you would like to run as a runtime arg. Exiting."
+  exit 1
+fi
+
+docker exec \
+  -it biosimulator-processes-container \
+  sh -c "poetry run jupyter lab --ip=0.0.0.0 --port=8888 --no-browser --allow-root"

scripts/run-container.sh

@@ -7,4 +7,9 @@ if [ "${version}" == "" ]; then
   exit 1
 fi
 
-docker run --platform linux/amd64 -it -p 8888:8888 ghcr.io/biosimulators/biosimulator-processes:"${version}"
+docker run -d \
+  --platform linux/amd64 \
+  -p 8888:8888 \
+  --name biosimulator-processes-container \
+  ghcr.io/biosimulators/biosimulator-processes:"${version}" \
+  sh -c "poetry run jupyter lab --ip=0.0.0.0 --port=8888 --no-browser --allow-root"

setup.py

@@ -2,7 +2,7 @@
 from setuptools import setup, find_packages
 
 
-__version__ = "0.0.17"
+__version__ = "0.0.18"
 
 with open("README.md", "r") as readme:
     description = readme.read()
@@ -43,7 +43,7 @@
     python_requires=">=3.10",
     install_requires=[
         "bigraph-schema",
-        "process-bigraph",
+        # "process-bigraph",
         "bigraph-builder",
         "numpy",
         "pytest>=6.2.5",