adding new local dev support

.devcontainer/Dockerfile

@@ -1,14 +1,14 @@
-# See here for image contents: https://github.com/microsoft/vscode-dev-containers/tree/v0.245.0/containers/python-3/.devcontainer/base.Dockerfile
-
 # [Choice] Python version (use -bullseye variants on local arm64/Apple Silicon): 3, 3.10, 3.9, 3.8, 3.7, 3.6, 3-bullseye, 3.10-bullseye, 3.9-bullseye, 3.8-bullseye, 3.7-bullseye, 3.6-bullseye, 3-buster, 3.10-buster, 3.9-buster, 3.8-buster, 3.7-buster, 3.6-buster
-ARG VARIANT="3.10-bullseye"
+ARG VARIANT=3-bullseye
 FROM mcr.microsoft.com/vscode/devcontainers/python:0-${VARIANT}
 
+ENV PYTHONUNBUFFERED 1
+
 # [Choice] Node.js version: none, lts/*, 16, 14, 12, 10
 ARG NODE_VERSION="none"
 RUN if [ "${NODE_VERSION}" != "none" ]; then su vscode -c "umask 0002 && . /usr/local/share/nvm/nvm.sh && nvm install ${NODE_VERSION} 2>&1"; fi
 
-# [Optional] If your pip requirements rarely change, uncomment this section to add them to the image.
+# [Optional] If your requirements rarely change, uncomment this section to add them to the image.
 # COPY requirements.txt /tmp/pip-tmp/
 # RUN pip3 --disable-pip-version-check --no-cache-dir install -r /tmp/pip-tmp/requirements.txt \
 #    && rm -rf /tmp/pip-tmp
@@ -17,5 +17,5 @@ RUN if [ "${NODE_VERSION}" != "none" ]; then su vscode -c "umask 0002 && . /usr/
 # RUN apt-get update && export DEBIAN_FRONTEND=noninteractive \
 #     && apt-get -y install --no-install-recommends <your-package-list-here>
 
-# [Optional] Uncomment this line to install global node packages.
-# RUN su vscode -c "source /usr/local/share/nvm/nvm.sh && npm install -g <your-package-here>" 2>&1
+
+

.devcontainer/devcontainer.json

@@ -1,19 +1,11 @@
 // For format details, see https://aka.ms/devcontainer.json. For config options, see the README at:
-// https://github.com/microsoft/vscode-dev-containers/tree/v0.245.0/containers/python-3
+// https://github.com/microsoft/vscode-dev-containers/tree/v0.245.0/containers/python-3-postgres
+// Update the VARIANT arg in docker-compose.yml to pick a Python version
 {
-	"name": "Python 3",
-	"build": {
-		"dockerfile": "Dockerfile",
-		"context": "..",
-		"args": { 
-			// Update 'VARIANT' to pick a Python version: 3, 3.10, 3.9, 3.8, 3.7, 3.6
-			// Append -bullseye or -buster to pin to an OS version.
-			// Use -bullseye variants on local on arm64/Apple Silicon.
-			"VARIANT": "3.8",
-			// Options
-			"NODE_VERSION": "lts/*"
-		}
-	},
+	"name": "Python 3 & PostgreSQL",
+	"dockerComposeFile": "docker-compose.yml",
+	"service": "app",
+	"workspaceFolder": "/workspace",
 
 	// Configure tool-specific properties.
 	"customizations": {
@@ -32,7 +24,8 @@
 				"python.linting.mypyPath": "/usr/local/py-utils/bin/mypy",
 				"python.linting.pycodestylePath": "/usr/local/py-utils/bin/pycodestyle",
 				"python.linting.pydocstylePath": "/usr/local/py-utils/bin/pydocstyle",
-				"python.linting.pylintPath": "/usr/local/py-utils/bin/pylint"
+				"python.linting.pylintPath": "/usr/local/py-utils/bin/pylint",
+				"python.testing.pytestPath": "/usr/local/py-utils/bin/pytest"
 			},
 
 			// Add the IDs of extensions you want installed when the container is created.
@@ -44,10 +37,11 @@
 	},
 
 	// Use 'forwardPorts' to make a list of ports inside the container available locally.
-	// "forwardPorts": [],
+	// This can be used to network with other containers or the host.
+	// "forwardPorts": [5000, 5432],
 
 	// Use 'postCreateCommand' to run commands after the container is created.
-	// "postCreateCommand": "pip3 install --user -r requirements.txt",
+	// "postCreateCommand": "pip install --user -r requirements.txt",
 
 	// Comment out to connect as root instead. More info: https://aka.ms/vscode-remote/containers/non-root.
 	"remoteUser": "vscode",

.devcontainer/docker-compose.yml

@@ -0,0 +1,46 @@
+version: '3.8'
+
+services:
+  app:
+    container_name: dev-env
+    build:
+      context: ..
+      dockerfile: .devcontainer/Dockerfile
+      args:
+        # Update 'VARIANT' to pick a version of Python: 3, 3.10, 3.9, 3.8, 3.7, 3.6
+        # Append -bullseye or -buster to pin to an OS version.
+        # Use -bullseye variants on local arm64/Apple Silicon.
+        VARIANT: "3.8"
+        # Optional Node.js version to install
+        NODE_VERSION: "lts/*"
+
+    volumes:
+      - ..:/workspace:cached
+
+    # Overrides default command so things don't shut down after the process ends.
+    command: sleep infinity
+
+    # Runs app on the same network as the database container, allows "forwardPorts" in devcontainer.json function.
+    network_mode: service:db
+    # Uncomment the next line to use a non-root user for all processes.
+    # user: vscode
+
+    env_file:
+      - ../.dev.env
+
+    # Use "forwardPorts" in **devcontainer.json** to forward an app port locally.
+    # (Adding the "ports" property to this file will not forward from a Codespace.)
+
+  db:
+    image: postgres:latest
+    container_name: dev-db
+    restart: unless-stopped
+    volumes:
+      - postgresql:/var/lib/postgresql/data
+    env_file:
+      - ../.dev-db.env
+    # Add "forwardPorts": ["5432"] to **devcontainer.json** to forward PostgreSQL locally.
+    # (Adding the "ports" property to this file will not forward from a Codespace.
+
+volumes:
+  postgresql:

.gitignore

@@ -1,7 +1,10 @@
-chp_db_fixture.json.gz
-#deployment-script
-deployment-script
+# env files for development
+.dev-db.env
+.dev.env
+
+# data files for development
 chp.sql
+chp_db_fixture.json.gz
 
 #SSH Keys
 id_rsa*
@@ -135,3 +138,4 @@ dmypy.json
 
 # Pyre type checker
 .pyre/
+/Dockerfile.dev-db

Dockerfile.new

@@ -0,0 +1,38 @@
+################
+# venv builder #
+################
+FROM python:3.8.3 as venv_builder
+
+COPY requirements.txt .
+RUN python3 -m venv /opt/venv
+RUN /opt/venv/bin/pip install -r requirements.txt
+
+###########
+# CHP API #
+###########
+FROM python:3.8.3-slim as chp-api
+
+# set environment variables
+ENV PYTHONDONTWRITEBYTECODE 1
+ENV PYTHONUNBUFFERED 1
+ENV TZ=America/New_York
+ENV SERVER_DIR=/chp_api/
+ENV VIRTUAL_ENV_PATH=/opt/venv
+
+# copy venv from venv builder image
+COPY --from=venv_builder ${VIRTUAL_ENV_PATH} ${VIRTUAL_ENV_PATH}
+
+# copy project
+COPY ./chp_api $SERVER_DIR
+
+# copy entry point
+COPY ./entrypoint.sh ${SERVER_DIR}
+
+# enter app directory
+WORKDIR $SERVER_DIR
+
+# Enable venv
+ENV PATH="/opt/venv/bin:$PATH"
+# run server
+# ENTRYPOINT ["./entrypoint.sh"]
+CMD ["python", "manage.py", "runserver"]

docker-compose.yml

@@ -0,0 +1,25 @@
+version: '3.8'
+
+services:
+  api:
+    build: 
+      context: .
+      dockerfile: Dockerfile
+    container_name: chp-api
+    command: python manage.py runserver 0.0.0.0:8000
+    volumes:
+      - static_volume:/chp_api/staticfiles
+    expose:
+      - 80
+    env_file:
+      - ./.dev.env
+  db:
+    image: postgres:latest
+    restart: unless-stopped
+    volumes:
+      - ../chp.sql:/var/lib/postgresql/data
+    env_file:
+      - .dev-db.env
+
+volumes:
+  static_volume:

requirements-dev.txt

@@ -1,6 +1,6 @@
-chp_learn @ git+https://github.com/di2ag/chp_learn.git@master
-chp_utils @ git+https://github.com/di2ag/chp_utils.git@master
-trapi_model @ git+https://github.com/di2ag/trapi_model.git@master
-chp_look_up @ git+https://github.com/di2ag/chp_look_up.git@master
-gene-specificity @ git+https://github.com/di2ag/gene-specificity.git@master
+chp_learn @ git+https://github.com/di2ag/chp_learn.git@master
+chp_utils @ git+https://github.com/di2ag/chp_utils.git@master
+trapi_model @ git+https://github.com/di2ag/trapi_model.git@master
+chp_look_up @ git+https://github.com/di2ag/chp_look_up.git@master
+gene-specificity @ git+https://github.com/di2ag/gene-specificity.git@master
 reasoner-validator @ git+https://github.com/di2ag/reasoner-validator.git@master