From 745f1740cd8cb24db67b6287f67827473c7cee6c Mon Sep 17 00:00:00 2001
From: alexPatrie <alexanderpatrie@gmail.com>
Date: Wed, 6 Mar 2024 12:51:05 -0500
Subject: [PATCH] updated for release and docker

---
 .idea/workspace.xml                               | 13 ++++++-------
 Dockerfile => container-assets/Dockerfile         |  6 ++++--
 poetry.lock => container-assets/poetry.lock       |  0
 pyproject.toml => container-assets/pyproject.toml |  0
 scripts/build-container.sh                        |  6 ++++--
 5 files changed, 14 insertions(+), 11 deletions(-)
 rename Dockerfile => container-assets/Dockerfile (91%)
 rename poetry.lock => container-assets/poetry.lock (100%)
 rename pyproject.toml => container-assets/pyproject.toml (100%)

diff --git a/.idea/workspace.xml b/.idea/workspace.xml
index ae744f6b9..6ce6cf9e7 100644
--- a/.idea/workspace.xml
+++ b/.idea/workspace.xml
@@ -6,11 +6,10 @@
   <component name="ChangeListManager">
     <list default="true" id="f0b09f0c-19d0-4b22-b7e9-7eb0e3893827" name="Changes" comment="">
       <change beforePath="$PROJECT_DIR$/.idea/workspace.xml" beforeDir="false" afterPath="$PROJECT_DIR$/.idea/workspace.xml" afterDir="false" />
-      <change beforePath="$PROJECT_DIR$/Dockerfile" beforeDir="false" afterPath="$PROJECT_DIR$/Dockerfile" afterDir="false" />
-      <change beforePath="$PROJECT_DIR$/poetry.lock" beforeDir="false" afterPath="$PROJECT_DIR$/poetry.lock" afterDir="false" />
-      <change beforePath="$PROJECT_DIR$/pyproject.toml" beforeDir="false" afterPath="$PROJECT_DIR$/pyproject.toml" afterDir="false" />
-      <change beforePath="$PROJECT_DIR$/scripts/run-container.sh" beforeDir="false" afterPath="$PROJECT_DIR$/scripts/run-container.sh" afterDir="false" />
-      <change beforePath="$PROJECT_DIR$/setup.py" beforeDir="false" afterPath="$PROJECT_DIR$/setup.py" afterDir="false" />
+      <change beforePath="$PROJECT_DIR$/Dockerfile" beforeDir="false" afterPath="$PROJECT_DIR$/container-assets/Dockerfile" afterDir="false" />
+      <change beforePath="$PROJECT_DIR$/poetry.lock" beforeDir="false" afterPath="$PROJECT_DIR$/container-assets/poetry.lock" afterDir="false" />
+      <change beforePath="$PROJECT_DIR$/pyproject.toml" beforeDir="false" afterPath="$PROJECT_DIR$/container-assets/pyproject.toml" afterDir="false" />
+      <change beforePath="$PROJECT_DIR$/scripts/build-container.sh" beforeDir="false" afterPath="$PROJECT_DIR$/scripts/build-container.sh" afterDir="false" />
     </list>
     <option name="SHOW_DIALOG" value="false" />
     <option name="HIGHLIGHT_CONFLICTS" value="true" />
@@ -66,11 +65,11 @@
       <recent name="$PROJECT_DIR$/scripts" />
     </key>
     <key name="MoveFile.RECENT_KEYS">
+      <recent name="$PROJECT_DIR$/container-assets" />
       <recent name="$PROJECT_DIR$/biosimulator_processes/steps" />
       <recent name="$PROJECT_DIR$/biosimulator_processes/processes" />
       <recent name="$PROJECT_DIR$/biosimulator_processes" />
       <recent name="$PROJECT_DIR$/builder" />
-      <recent name="$PROJECT_DIR$/composer-api/composer_api" />
     </key>
   </component>
   <component name="RunManager" selected="Python.biosimulator-processes-process">
@@ -160,7 +159,7 @@
       <workItem from="1709575179051" duration="10177000" />
       <workItem from="1709645971220" duration="5986000" />
       <workItem from="1709654330514" duration="14028000" />
-      <workItem from="1709740597728" duration="5022000" />
+      <workItem from="1709740597728" duration="5473000" />
     </task>
     <servers />
   </component>
diff --git a/Dockerfile b/container-assets/Dockerfile
similarity index 91%
rename from Dockerfile
rename to container-assets/Dockerfile
index 270932c24..f945d1e16 100644
--- a/Dockerfile
+++ b/container-assets/Dockerfile
@@ -10,14 +10,16 @@ ENV DEBIAN_FRONTEND=noninteractive
     # STORAGE_GCS_CREDENTIALS_FILE="/app/secret/gcs_credentials.json" \
     # STORAGE_LOCAL_CACHE_DIR="/app/scratch"
 
+RUN cd ..
+
 WORKDIR /app
 
 # copy and make dirs
 # COPY ./biosimulator_processes /app/biosimulator_processes
-COPY ./notebooks /app/notebooks
+COPY ../notebooks /app/notebooks
 
 # copy files
-COPY ./pyproject.toml ./poetry.lock ./data ./scripts/trust-notebooks.sh /app/
+COPY ./container-assets/pyproject.toml ./container-assets/poetry.lock ./data ./scripts/trust-notebooks.sh /app/
 # COPY ./scripts/xvfb-startup.sh /xvfb-startup.sh
 
 VOLUME /app/data
diff --git a/poetry.lock b/container-assets/poetry.lock
similarity index 100%
rename from poetry.lock
rename to container-assets/poetry.lock
diff --git a/pyproject.toml b/container-assets/pyproject.toml
similarity index 100%
rename from pyproject.toml
rename to container-assets/pyproject.toml
diff --git a/scripts/build-container.sh b/scripts/build-container.sh
index 0de4c5c8a..4f3085587 100755
--- a/scripts/build-container.sh
+++ b/scripts/build-container.sh
@@ -15,8 +15,10 @@ docker buildx inspect --bootstrap
 
 set -e
 
-docker build --platform linux/amd64 \
-    -t ghcr.io/biosimulators/biosimulator-processes:"${version}" .
+docker build \
+  --platform linux/amd64 \
+  --file container-assets/Dockerfile \
+  -t ghcr.io/biosimulators/biosimulator-processes:"${version}" .
 
 if [ "${run}" == "-r" ]; then
   ./scripts/run-container.sh "${version}"