feat(analyses-snapshot-testing): add cli and cleaner opentrons installation (#19068)

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-test

.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:
@@ -191,6 +185,8 @@ jobs:
           body: 'This PR was requested on the PR https://github.com/${{ github.repository }}/pull/${{ github.event.pull_request.number }}'
           branch: 'analyses-snapshot-testing/heal-${{ github.event.pull_request.head.ref }}'
           base: ${{ github.event.pull_request.head.ref }}
+          add-paths: |
+            analyses-snapshot-testing/tests/__snapshots__/analyses_snapshot_test/
 
       - name: Comment on feature PR
         if: always() && steps.create_pull_request.outcome == 'success' && github.event_name == 'pull_request'
@@ -214,3 +210,5 @@ jobs:
           body: 'The edge overnight analyses snapshot test is failing. This PR was opened to alert us to the failure.'
           branch: 'analyses-snapshot-testing/heal-edge'
           base: edge
+          add-paths: |
+            analyses-snapshot-testing/tests/__snapshots__/analyses_snapshot_test/

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
@@ -41,7 +37,13 @@ test-protocol-analysis:
 
 .PHONY: ci-setup
 ci-setup:
-	uv sync --locked --all-extras
+	@echo "Setting up CI environment with editable installs..."
+	@if uv sync --locked --all-extras 2>/dev/null; then \
+		echo "Lockfile is current, using locked dependencies"; \
+	else \
+		echo "Lockfile needs update due to editable installs, syncing without lock"; \
+		uv sync --all-extras; \
+	fi
 
 .PHONY: setup
 setup:
@@ -134,12 +136,6 @@ 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 +194,76 @@ 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

analyses-snapshot-testing/README.md

@@ -5,8 +5,7 @@
 1. Follow the instructions in [DEV_SETUP.md](../DEV_SETUP.md) for javascript
 1. `cd analyses-snapshot-testing`
 1. have uv installed
-1. `make setup install-ot`
-1. Have docker installed and the daemon running
+1. `make setup`
 
 ## Concepts