working on new docker files

Dockerfile

@@ -1,24 +1,9 @@
 # -------------------------------------------------------------------------------------
 # Container to serve FastAPI backend api from sbmlutils
 # -------------------------------------------------------------------------------------
-# https://fastapi.tiangolo.com/deployment/docker/
-# see https://github.com/tiangolo/uvicorn-gunicorn-docker for env variables
+FROM python:3.12
 
-# build image
-#   docker build -t myimage .
-
-# start container
-#  docker run -d --name mycontainer -p 80:80 -e MODULE_NAME="sbmlutils.report.api" -e VARIABLE_NAME="api" myimage
-#  docker run -d --name mycontainer -p 80:80 myimage
-# -------------------------------------------------------------------------------------
-FROM tiangolo/uvicorn-gunicorn-fastapi:python3.11
-
-# Caching of python requirements
-# COPY ./requirements.txt /code/requirements.txt
-# CMD pip install --requirement /code/requirements.txt
-
-# Adds application code to the image
-# COPY . /code
+# Add application code to the image
 COPY ./src /code/src
 COPY ./setup.cfg /code/setup.cfg
 COPY ./setup.py /code/setup.py
@@ -31,13 +16,9 @@ WORKDIR /code
 # Install sbmlutils
 RUN pip install -e . --no-cache-dir --upgrade
 
-ENV MODULE_NAME="sbmlutils.report.api"
-ENV VARIABLE_NAME="api"
-ENV PORT="1444"
+#ENV MODULE_NAME="sbmlutils.report.api"
+#ENV VARIABLE_NAME="api"
+#ENV PORT="1444"
 
-# EXPOSE 80
 EXPOSE 1444
-
-# Run the start script, it will check for an /app/prestart.sh script (e.g. for migrations)
-# And then will start Gunicorn with Uvicorn
-CMD ["/start.sh"]
+CMD ["uvicorn", "sbmlutils.report.api:api", "--host", "0.0.0.0", "--port", "1444"]

Dockerfile_old

@@ -0,0 +1,43 @@
+# -------------------------------------------------------------------------------------
+# Container to serve FastAPI backend api from sbmlutils
+# -------------------------------------------------------------------------------------
+# https://fastapi.tiangolo.com/deployment/docker/
+# see https://github.com/tiangolo/uvicorn-gunicorn-docker for env variables
+
+# build image
+#   docker build -t myimage .
+
+# start container
+#  docker run -d --name mycontainer -p 80:80 -e MODULE_NAME="sbmlutils.report.api" -e VARIABLE_NAME="api" myimage
+#  docker run -d --name mycontainer -p 80:80 myimage
+# -------------------------------------------------------------------------------------
+FROM tiangolo/uvicorn-gunicorn-fastapi:python3.11
+
+# Caching of python requirements
+# COPY ./requirements.txt /code/requirements.txt
+# CMD pip install --requirement /code/requirements.txt
+
+# Adds application code to the image
+# COPY . /code
+COPY ./src /code/src
+COPY ./setup.cfg /code/setup.cfg
+COPY ./setup.py /code/setup.py
+COPY ./README.rst /code/README.rst
+COPY ./MANIFEST.in /code/MANIFEST.in
+COPY ./LICENSE /code/LICENSE
+
+WORKDIR /code
+
+# Install sbmlutils
+RUN pip install -e . --no-cache-dir --upgrade
+
+ENV MODULE_NAME="sbmlutils.report.api"
+ENV VARIABLE_NAME="api"
+ENV PORT="1444"
+
+# EXPOSE 80
+EXPOSE 1444
+
+# Run the start script, it will check for an /app/prestart.sh script (e.g. for migrations)
+# And then will start Gunicorn with Uvicorn
+CMD ["/start.sh"]

deploy.md

@@ -43,7 +43,3 @@ Pull latest changes
 ```
 ./deploy.sh
 ```
-
-
-
-

docker-compose-develop.yml

@@ -3,13 +3,12 @@
 # -----------------------------------------------------------------------------
 #
 # build containers
-#   docker-compose -f docker-compose-develop.yml build --no-cache
-#   docker-compose -f docker-compose-develop.yml build
+#   docker compose -f docker-compose-develop.yml build --no-cache
+#   docker compose -f docker-compose-develop.yml build
 # serve containers
-#   docker-compose -f docker-compose-develop.yml up --detach
-#   docker-compose -f docker-compose-develop.yml up
+#   docker compose -f docker-compose-develop.yml up --detach
+#   docker compose -f docker-compose-develop.yml up
 # -----------------------------------------------------------------------------
-
 version: '3'
 
 volumes:
@@ -29,7 +28,7 @@ services:
       - "80"
     ports:
       - "1444:80"
-    command: ["/start.sh"]
+    # command: ["/start.sh"]
 
   frontend:
     restart: always

misc/xpp/xpp_models.py

@@ -142,7 +142,6 @@ def simulate(sbml_file):
 
 if __name__ == "__main__":
 
-
     # download and unzip all sbml files
     # ode_all = get_models(download=True)
 

setup.cfg

@@ -60,19 +60,21 @@ install_requires =
 	numpy>=1.26.4
 	python-libsbml>=5.20.4
 	antimony>=2.15.0
-
 	scipy>=1.14
 	pandas>=2.2.0
+    tabulate>=0.9.0
 	pint>=0.24.3
-	tabulate>=0.9.0
-	beautifulsoup4>=4.12.3
+
 	markdown-it-py>=3.0.0
 	openpyxl>=3.1.5
 	xmlschema>=3.3.2
-    uvicorn>=0.30.6
 	matplotlib>=3.9
 	py4cytoscape>=1.9.0
-	libroadrunner>=1.26.4
+	libroadrunner>=1.27.0
+
+    uvicorn>=0.30.6
+    fastapi>=0.112.0
+	python-multipart>=0.0.9
 tests_require =
 	tox>=3.24.3
 	pytest>=7.0.1
@@ -90,9 +92,6 @@ test = pytest
 where = src
 
 [options.extras_require]
-sbml4humans =
-	fastapi>=0.112.0
-	python-multipart>=0.0.9
 development =
 	pip-tools>=7.4.1
 	black>=24.8.0
@@ -104,6 +103,7 @@ development =
 	mypy>=1.4.1
 	pytest>=7.4.0
 	pytest-cov>=4.1.0
+	beautifulsoup4>=4.12.3
 docs =
 	sphinx>=3.4.3
 	ipykernel>=5.4.3