Merge pull request #3 from biosimulators/main

feat: merge second version changes

.gitignore

@@ -19,3 +19,4 @@ __pycache__
 submit-biosimulators-container.sh
 .vagrant
 ._vagrant
+.THIS-IS-FOR-CONTAINER-DEV-ONLY

README.md

@@ -19,7 +19,7 @@ There are two primary methods of interaction with `biosimulator-processes`:
 
    3. Run the image, ensuring that the running of the container is platform-agnostic:
 
-            docker run --platform linux/amd64 -it -p 8888:8888 ghcr.io/biosimulators/biosimulator-processes:latest 
+            docker run --platform linux/amd64 -it -p 8888:8888 ghcr.io/biosimulators/biosimulator-processes:latest
 
    As an alternative, there is a helper script that does this and more. To use this script:
 

pyproject.toml

@@ -20,6 +20,7 @@ cobra = "*"
 tellurium = "*"
 smoldyn = "*"
 bigraph-viz = "^0.0.31"
+python-libsbml = "^5.20.2"
 
 [tool.poetry.group.dev.dependencies]
 pytest = "*"

scripts/build-container.sh

@@ -0,0 +1,16 @@
+#!/bin/bash
+
+version="$1"
+
+set -e
+
+if [ "${version}" == "" ]; then
+  echo "Please enter the version you would like to build as a runtime arg. Exiting."
+  exit 1
+fi
+
+yes | docker system prune
+docker buildx create --name biosimbuilder --use
+docker buildx inspect --bootstrap
+docker buildx build --platform linux/amd64 \
+    -t ghcr.io/biosimulators/biosimulator-processes:"${version}" .

scripts/docker-pipeline.sh

@@ -0,0 +1,34 @@
+#!/bin/bash
+
+
+version="$1"
+
+run="$2"
+
+if [ "${version}" == "" ]; then
+  echo "You must pass the container version you wish to run as an argument to this script. Exiting."
+  exit 1
+fi
+
+
+if [ "${version}" == "${current}" ]; then
+  echo "This version already exists on GHCR. Exiting."
+  exit 1
+fi
+
+echo "Enter your Github User-Name: "
+read -r usr_name
+
+if docker login ghcr.io -u "${usr_name}"; then
+  echo "Successfully logged in to GHCR!"
+else
+  echo "Could not validate credentials."
+  exit 1
+fi
+
+./scripts/build-container.sh "${version}" \
+  && ./scripts/release-container.sh "${version}" \
+
+if [ "${run}" == "-r" ]; then
+  ./scripts/run-container.sh "${version}"
+fi

scripts/release-container.sh

@@ -0,0 +1,38 @@
+#!/bin/bash
+
+
+version="$1"
+
+# PLEASE UPDATE THE LATEST VERSION HERE BEFORE RUNNING. CURRENT: 0.0.2
+current="0.0.2"
+
+set -e
+
+if [ "${version}" == "" ]; then
+  echo "You must pass the container version you wish to release as an argument to this script. Exiting."
+  exit 1
+fi
+
+if [ "${version}" == "${current}" ]; then
+  echo "This version already exists on GHCR. Exiting."
+  exit 1
+fi
+
+echo "Enter your Github User-Name: "
+read -r usr_name
+
+if docker login ghcr.io -u "${usr_name}"; then
+  echo "Successfully logged in to GHCR!"
+else
+  echo "Could not validate credentials."
+  exit 1
+fi
+
+yes | docker system prune
+docker buildx create --name biosimbuilder --use
+docker buildx inspect --bootstrap
+docker buildx build --platform linux/amd64 \
+    -t ghcr.io/biosimulators/biosimulator-processes:"${version}" . \
+    --push
+docker tag ghcr.io/biosimulators/biosimulator-processes:"${version}" ghcr.io/biosimulators/biosimulator-processes:latest
+docker push ghcr.io/biosimulators/biosimulator-processes:latest

scripts/run-container.sh

@@ -0,0 +1,10 @@
+#!/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 run --platform linux/amd64 -it -p 8888:8888 ghcr.io/biosimulators/biosimulator-processes:"${version}"