analysis cli and simplified opentrons install

Author: y3rsh

.github/workflows/analyses-snapshot-lint.yaml

@@ -35,3 +35,6 @@ jobs:
       - name: ruff-check
         working-directory: ./analyses-snapshot-testing
         run: make ruff-check
+      - name: unit tests
+        working-directory: ./analyses-snapshot-testing
+        run: make unit-tests

.github/workflows/analyses-snapshot-test.yaml

@@ -105,9 +105,6 @@ jobs:
       - name: Sync the project
         working-directory: ./analyses-snapshot-testing
         run: make ci-setup
-      - name: Install Opentrons
-        working-directory: ./analyses-snapshot-testing
-        run: make install-ot
       - uses: actions/download-artifact@v4
         with:
           name: chunks
@@ -145,9 +142,6 @@ jobs:
       - name: Sync the project
         working-directory: ./analyses-snapshot-testing
         run: make ci-setup
-      - name: Install Opentrons
-        working-directory: ./analyses-snapshot-testing
-        run: make install-ot
       - name: Download All Analysis Results
         uses: actions/download-artifact@v4
         with:

analyses-snapshot-testing/.gitignore

@@ -1,6 +1,10 @@
 .env
 results
+analysis_results/**/*
 analysis_results/*.json
+!analysis_results/.keepme
+temp_sample_protocols/**/*
+temp_single_protocol/**/*
 files/protocols/generated_protocols/*
 !files/protocols/generated_protocols/.keepme
 chunks/*.json

analyses-snapshot-testing/Makefile

@@ -27,10 +27,6 @@ format:
 	@echo "Formatting the readme with yarn prettier"
 	$(MAKE) format-readme
 
-.PHONY: test-ci
-test-ci:
-	$uv run python -m pytest -m "emulated_alpha"
-
 .PHONY: audit
 audit:
 	uv run python -m automation.audit_snapshots
@@ -134,12 +130,6 @@ CHUNK ?= chunk_0.json
 analyze-chunk:
 	uv run python -m automation.analyze_from_chunk --chunk $(CHUNK)
 
-.PHONY: install-ot
-install-ot:
-	@echo "Installing the opentrons package from the local codebase"
-	uv pip install -e ../shared-data
-	uv pip install -e ../api
-
 .PHONY: create-pl-protocols
 create-pl-protocols:
 	uv run python -m automation.data.create_pl_protocols
@@ -198,3 +188,76 @@ build-opentrons-analysis-%:
 .PHONY: unit-test
 unit-test:
 	uv run python -m pytest -m "unit" -vv
+
+# CLI analysis targets
+OUTPUT_DIR ?= analysis_results
+PROTOCOLS_DIR ?= files/protocols
+LABWARE_DIR ?= files/labware
+TEMP_SINGLE_DIR ?= temp_single_protocol
+TEMP_SAMPLE_DIR ?= temp_sample_protocols
+CLI_MODULE ?= automation.protocol_analysis_cli
+
+SINGLE_OUTPUT_SUBDIR ?= single
+SAMPLE_OUTPUT_SUBDIR ?= sample
+SAMPLE_PATTERN ?= *Simple*
+SAMPLE_LIMIT ?= 5
+
+.PHONY: cli-dry-run
+cli-dry-run: cli-clean
+	@echo "Running Protocol Analysis CLI in dry-run mode"
+	@echo "Protocols directory: $(PROTOCOLS_DIR)"
+	@echo "Output directory: $(OUTPUT_DIR)"
+	uv run python -m $(CLI_MODULE) \
+		--protocols-dir $(PROTOCOLS_DIR) \
+		--output-dir $(OUTPUT_DIR) \
+		--labware-dir $(LABWARE_DIR) \
+		--dry-run
+
+.PHONY: cli-analyze-single
+cli-analyze-single: cli-clean
+ifndef PROTOCOL
+	@echo "Error: PROTOCOL variable must be set"
+	@echo "Usage: make cli-analyze-single PROTOCOL=$(PROTOCOLS_DIR)/your_protocol.py"
+	@exit 1
+endif
+	@echo "Running Protocol Analysis CLI on single protocol: $(PROTOCOL)"
+	@mkdir -p $(TEMP_SINGLE_DIR)
+	@cp $(PROTOCOL) $(TEMP_SINGLE_DIR)/
+	uv run python -m $(CLI_MODULE) \
+		--protocols-dir $(TEMP_SINGLE_DIR) \
+		--output-dir $(OUTPUT_DIR)/$(SINGLE_OUTPUT_SUBDIR) \
+		--labware-dir $(LABWARE_DIR) \
+		--verbose
+	@rm -rf $(TEMP_SINGLE_DIR)
+
+.PHONY: cli-analyze-sample
+cli-analyze-sample: cli-clean
+	@echo "Running Protocol Analysis CLI on a small sample of protocols"
+	@mkdir -p $(TEMP_SAMPLE_DIR)
+	@find $(PROTOCOLS_DIR) -name "$(SAMPLE_PATTERN)" -type f \( -name "*.py" -o -name "*.json" \) | head -$(SAMPLE_LIMIT) | xargs -I {} cp {} $(TEMP_SAMPLE_DIR)/
+	@echo "Found $$(ls $(TEMP_SAMPLE_DIR)/ | wc -l) sample protocols"
+	uv run python -m $(CLI_MODULE) \
+		--protocols-dir $(TEMP_SAMPLE_DIR) \
+		--output-dir $(OUTPUT_DIR)/$(SAMPLE_OUTPUT_SUBDIR) \
+		--labware-dir $(LABWARE_DIR) \
+		--verbose
+	@rm -rf $(TEMP_SAMPLE_DIR)
+
+.PHONY: cli-clean
+cli-clean:
+	@echo "Cleaning CLI analysis results"
+	@if [ -d "$(OUTPUT_DIR)" ]; then \
+		find $(OUTPUT_DIR) -name "*.json" -delete; \
+		find $(OUTPUT_DIR) -type d -empty -not -path $(OUTPUT_DIR) -delete; \
+		echo "Cleaned analysis JSON files from $(OUTPUT_DIR) (keeping .keep-me files)"; \
+	else \
+		echo "No $(OUTPUT_DIR) directory found"; \
+	fi
+	@rm -rf $(TEMP_SAMPLE_DIR) $(TEMP_SINGLE_DIR)
+	@echo "Cleaned temporary directories"
+
+# Interactive CLI target
+.PHONY: cli-interactive
+cli-interactive: cli-clean
+	@echo "Starting interactive protocol analysis CLI..."
+	uv run python -m $(CLI_MODULE) --interactive