fix: can't pass env to compose up, use env vars

Author: dshemetov

.github/workflows/ci.yaml

@@ -56,12 +56,6 @@ jobs:
           ln -s repos/delphi/delphi-epidata/dev/local/pyproject.toml repos/
           ln -s repos/delphi/delphi-epidata/dev/local/setup.cfg repos/
 
-      - name: Build docker images
-        run: |
-          make db
-          make web
-          make redis
-
       - name: Run tests
         run: |
           make test

dev/local/Makefile

@@ -65,9 +65,6 @@ NOW:=$(shell date "+%Y-%m-%d")
 LOG_WEB:=delphi_web_epidata_$(NOW).log
 LOG_DB:=delphi_database_epidata_$(NOW).log
 LOG_REDIS:=delphi_redis_instance_$(NOW).log
-WEB_CONTAINER_ID:=$(shell docker ps -q --filter 'name=delphi_web_epidata')
-DATABASE_CONTAINER_ID:=$(shell docker ps -q --filter 'name=delphi_database_epidata')
-REDIS_CONTAINER_ID:=$(shell docker ps -q --filter 'name=delphi_redis')
 
 M1=
 ifeq ($(shell uname -smp), Darwin arm64 arm)
@@ -82,9 +79,7 @@ db:
 
 .PHONY=web
 web:
-	@docker compose up delphi_web_epidata $(M1) \
-		--env "SQLALCHEMY_DATABASE_URI=$(sqlalchemy_uri)" \
-		--detach
+	@SQLALCHEMY_DATABASE_URI=$(sqlalchemy_uri) docker compose up delphi_web_epidata $(M1) --detach
 	@docker logs -f delphi_web_epidata >$(LOG_WEB) 2>&1 &
 
 .PHONY=redis
@@ -94,15 +89,17 @@ redis:
 
 .PHONY=test
 test:
-	@docker compose run delphi_web_python $(M1) python -m pytest --import-mode importlib $(pdb) $(test) | tee test_output_$(NOW).log
+	@SQLALCHEMY_DATABASE_URI=$(sqlalchemy_uri) docker compose run delphi_web_python $(M1) \
+		python -m pytest --import-mode importlib $(pdb) $(test) | tee test_output_$(NOW).log
 
 .PHONY=r-test
 r-test:
-	@docker compose run delphi_web_python $(M1) Rscript repos/delphi/delphi-epidata/integrations/client/test_delphi_epidata.R | tee r-test_output_$(NOW).log
+	@SQLALCHEMY_DATABASE_URI=$(sqlalchemy_uri) docker compose run delphi_web_python $(M1) \
+		Rscript repos/delphi/delphi-epidata/integrations/client/test_delphi_epidata.R | tee r-test_output_$(NOW).log
 
 .PHONY=bash
 bash:
-	@docker compose run delphi_web_python $(M1) bash
+	@SQLALCHEMY_DATABASE_URI=$(sqlalchemy_uri) docker compose run delphi_web_python $(M1) bash
 
 .PHONY=sql
 sql:

dev/local/docker-compose.yaml

@@ -27,7 +27,7 @@ services:
       dockerfile: ./devops/Dockerfile
     environment:
       MODULE_NAME: delphi.epidata.server.main
-      SQLALCHEMY_DATABASE_URI: mysql+mysqldb://user:pass@delphi_database_epidata:3306/epidata
+      SQLALCHEMY_DATABASE_URI: ${SQLALCHEMY_DATABASE_URI:-mysql+mysqldb://user:pass@delphi_database_epidata:3306/epidata}
       FLASK_SECRET: abc
       FLASK_PREFIX: /epidata
       LOG_DEBUG: "1"
@@ -68,7 +68,7 @@ services:
       context: .
       dockerfile: repos/delphi/delphi-epidata/dev/docker/python/Dockerfile
     environment:
-      SQLALCHEMY_DATABASE_URI: mysql+mysqldb://user:pass@delphi_database_epidata:3306/epidata
+      SQLALCHEMY_DATABASE_URI: ${SQLALCHEMY_DATABASE_URI:-mysql+mysqldb://user:pass@delphi_database_epidata:3306/epidata}
       FLASK_SECRET: abc
     volumes:
       - type: bind