Deprecate worker watcher

Makefile

@@ -62,9 +62,8 @@ help:
 export DOCKER_ORG_NAME := nadeemlab
 export DOCKER_REPO_PREFIX := spt
 export DOCKER_SCAN_SUGGEST:=false
-SUBMODULES := apiserver graphs ondemand db workflow watcher
-TESTABLE_SUBMODULES := apiserver graphs ondemand db workflow
-DOCKERIZED_SUBMODULES := apiserver db ondemand watcher
+SUBMODULES := apiserver graphs ondemand db workflow
+DOCKERIZED_SUBMODULES := apiserver db ondemand
 
 DOCKERFILES := $(foreach submodule,$(DOCKERIZED_SUBMODULES),${BUILD_LOCATION}/$(submodule)/Dockerfile)
 
@@ -73,9 +72,9 @@ _UNPUSHABLES := db
 PUSHABLE_SUBMODULES := $(filter-out ${_UNPUSHABLES},$(DOCKERIZED_SUBMODULES))
 DOCKER_PUSH_TARGETS := $(foreach submodule,$(PUSHABLE_SUBMODULES),docker-push-${PACKAGE_NAME}/$(submodule))
 DOCKER_PUSH_DEV_TARGETS := $(foreach submodule,$(DOCKERIZED_SUBMODULES),docker-push-dev-${PACKAGE_NAME}/$(submodule))
-MODULE_TEST_TARGETS := $(foreach submodule,$(TESTABLE_SUBMODULES),module-test-$(submodule))
-UNIT_TEST_TARGETS := $(foreach submodule,$(TESTABLE_SUBMODULES),unit-test-$(submodule))
-SINGLETON_TEST_TARGETS := $(foreach submodule,$(TESTABLE_SUBMODULES),singleton-test-$(submodule))
+MODULE_TEST_TARGETS := $(foreach submodule,$(SUBMODULES),module-test-$(submodule))
+UNIT_TEST_TARGETS := $(foreach submodule,$(SUBMODULES),unit-test-$(submodule))
+SINGLETON_TEST_TARGETS := $(foreach submodule,$(SUBMODULES),singleton-test-$(submodule))
 DLI := force-rebuild-data-loaded-image
 
 # Define PHONY targets
@@ -411,7 +410,7 @@ clean-files:
 >@rm -f .initial_time.txt
 >@rm -f ${BUILD_LOCATION}/*/.initiation_message_size
 >@rm -f ${BUILD_LOCATION}/*/.current_time.txt
->@for submodule in ${TESTABLE_SUBMODULES} ; do \
+>@for submodule in ${SUBMODULES} ; do \
         submodule_directory=${BUILD_LOCATION}/$$submodule ; \
         ${MAKE} SHELL=$(SHELL) --no-print-directory -C $$submodule_directory clean ; \
         rm -rf $$submodule_directory/docker.built ; \

build/apiserver/Makefile

@@ -23,8 +23,7 @@ setup-testing:
      spt-apiserver-testing \
      spt-db---testing-only \
      spt-ondemand--testing \
-     spt-ondemand-testing2 \
-     spt-watcher---testing ; \
+     spt-ondemand-testing2 ; \
     echo "$$?" > status_code
 >@bash ${BUILD_SCRIPTS_LOCATION_ABSOLUTE}/print_docker_logs.sh
 >@${MESSAGE} end "Setup env." "Env not setup."

build/apiserver/compose.yaml

@@ -33,17 +33,6 @@ services:
       SINGLE_CELL_DATABASE_PASSWORD: postgres
     pull_policy: never
 
-  testing-watcher:
-    image: nadeemlab/spt-watcher
-    container_name: spt-watcher---testing
-    networks:
-      - isolated_temporary_test
-    environment:
-      SINGLE_CELL_DATABASE_HOST: spt-db---testing-only
-      SINGLE_CELL_DATABASE_USER: postgres
-      SINGLE_CELL_DATABASE_PASSWORD: postgres
-    pull_policy: never
-
   testing-api-server:
     image: nadeemlab/spt-apiserver
     container_name: spt-apiserver-testing

build/build_scripts/poll_container_readiness.sh

@@ -3,7 +3,6 @@ declare -A expectedmessages
 expectedmessages[spt-apiserver-testing]="Uvicorn running on"
 expectedmessages[spt-ondemand--testing]="Listening on queue_activity channel"
 expectedmessages[spt-ondemand-testing2]="Listening on queue_activity channel"
-expectedmessages[spt-watcher---testing]="Watching workers"
 expectedmessages[spt-db---testing-only]="database system is ready to accept connections"
 expectedmessages[spt--workflow-testing]="workflow container is ready to work"
 expectedmessages[temporary-spt-db-preloading]="database system is ready to accept connections"

build/build_scripts/record_docker_logs.sh

@@ -12,6 +12,5 @@ unbuffer docker compose logs --since="$nowtime" -f testing-database > dlogs.db.t
 unbuffer docker compose logs --since="$nowtime" -f testing-api-server > dlogs.api.txt &
 unbuffer docker compose logs --since="$nowtime" -f testing-fast-counts-server > dlogs.od.txt &
 unbuffer docker compose logs --since="$nowtime" -f testing-fast-counts-server2 > dlogs.od2.txt &
-unbuffer docker compose logs --since="$nowtime" -f testing-watcher > dlogs.ww.txt &
 
 tail -f /dev/null

build/ondemand/Makefile

@@ -21,7 +21,6 @@ setup-testing:
 >@docker compose up -d && \
     bash ${BUILD_SCRIPTS_LOCATION_ABSOLUTE}/poll_container_readiness.sh \
      spt-ondemand--testing \
-     spt-watcher---testing \
      spt-db---testing-only ; \
     echo "$$?" > status_code
 >@if [[ $$(cat status_code) -gt 0 ]]; then echo "Printing docker compose logs in case of error:"; docker compose logs; echo ""; docker network ls; echo ""; docker container ls; fi;

build/ondemand/compose.yaml

@@ -10,17 +10,6 @@ services:
       SINGLE_CELL_DATABASE_PASSWORD: postgres
     pull_policy: never
 
-  testing-watcher:
-    image: nadeemlab/spt-watcher
-    container_name: spt-watcher---testing
-    networks:
-      - isolated_temporary_test
-    environment:
-      SINGLE_CELL_DATABASE_HOST: spt-db---testing-only
-      SINGLE_CELL_DATABASE_USER: postgres
-      SINGLE_CELL_DATABASE_PASSWORD: postgres
-    pull_policy: never
-
   testing-database:
     image: nadeemlab/spt-db-preloaded-1and2
     container_name: spt-db---testing-only

pyproject.toml.unversioned

@@ -65,7 +65,6 @@ ondemand = [
     "pydantic==2.7.2",
     "squidpy==1.5.0",
 ]
-watcher = []
 workflow = [
     "matplotlib==3.9.0",
     "umap-learn==0.5.6",
@@ -130,8 +129,6 @@ packages = [
     "spatialprofilingtoolbox.db.exchange_data_formats",
     "spatialprofilingtoolbox.db.scripts",
     "spatialprofilingtoolbox.db.data_model",
-    "spatialprofilingtoolbox.watcher",
-    "spatialprofilingtoolbox.watcher.scripts",
     "spatialprofilingtoolbox.workflow",
     "spatialprofilingtoolbox.workflow.scripts",
     "spatialprofilingtoolbox.workflow.component_interfaces",
@@ -147,9 +144,6 @@ packages = [
 
 [tool.setuptools.package-data]
 "spatialprofilingtoolbox.entry_point" = ["spt-completion.sh.jinja"]
-"spatialprofilingtoolbox.watcher.scripts" = [
-    "start.py"
-]
 "spatialprofilingtoolbox.workflow.scripts" = [
     "aggregate_core_results.py",
     "core_job.py",