fix(lineage_fate_correlation): use cached clone trajectory data

MODULE.bazel

@@ -4,7 +4,7 @@ pyrovelocity MODULE
 
 module(
     name = "pyrovelocity",
-    version = "0.4.0",
+    version = "0.4.1",
     compatibility_level = 1,
 )
 

Makefile

@@ -228,13 +228,32 @@ run-async: ## Run registered workflow (async).
 run-check-image: ## Check workflow image exists.
 	crane ls $(WORKFLOW_IMAGE) | grep "$(GIT_REF)\|$(GIT_SHA)\|$(GIT_SHA_SHORT)"
 
-TEST_DATASET_NAME ?= simulated
+TEST_DATASET_NAMES ?= simulated larry larry_neu larry_mono larry_multilineage
 
-workflow-clean-outputs: ## Clean testing dataset and model outputs. make workflow-clean-outputs TEST_DATASET_NAME=simulated.
-	rm data/external/$(TEST_DATASET_NAME).h5ad || true
-	rm data/processed/$(TEST_DATASET_NAME)_* || true
-	rm -r models/$(TEST_DATASET_NAME)_model* || true
-	rm -r reports/$(TEST_DATASET_NAME)_model* || true
+# Function to clean a single dataset
+define clean-dataset
+	@echo "Cleaning outputs for $(1)..."
+	rm -f data/processed/$(1)_* || true
+	rm -rf models/$(1)_model* || true
+	rm -rf reports/$(1)_model* || true
+
+endef
+
+# Function to print external dataset remove command
+define print-rm-external
+	@echo "  rm -f data/external/$(1).h5ad"
+
+endef
+
+workflow-clean-outputs: ## Clean testing dataset and model outputs. make workflow-clean-outputs TEST_DATASET_NAMES="simulated pancreas"
+	@echo "Cleaning outputs for datasets: $(TEST_DATASET_NAMES)"
+	$(foreach dataset,$(TEST_DATASET_NAMES),$(call clean-dataset,$(dataset)))
+	@echo ""
+	@echo "To remove external datasets, run one of these commands:"
+	$(foreach dataset,$(TEST_DATASET_NAMES),$(call print-rm-external,$(dataset)))
+	@echo ""
+	@echo "Or remove all with:"
+	@echo "  rm -f data/external/{$(shell echo $(TEST_DATASET_NAMES) | tr ' ' ',')}.h5ad"
 
 workflow-clear-cache: ## Clear local cache db from ~/.flyte/local-cache/cache.db.
 	pyflyte local-cache clear
@@ -915,8 +934,8 @@ approve-prs: ## Approve github pull requests from bots: PR_ENTRIES="2-5 10 12-18
 		fi; \
 	done
 
-PREVIOUS_VERSION := 0.4.0b5
-NEXT_VERSION := 0.4.0
+PREVIOUS_VERSION := 0.4.0
+NEXT_VERSION := 0.4.1
 VERSION_FILES := \
 	pyproject.toml \
 	conda/colab/construct.yaml \

conda/colab/construct.yaml

@@ -1,5 +1,5 @@
 name: pyrovelocity-colab
-version: 0.4.0
+version: 0.4.1
 
 channels:
   - pytorch
@@ -89,7 +89,7 @@ specs:
   - brotli-python=1.1.0=py311hfdbb021_2
   - bzip2=1.0.8=h4bc722e_7
   - c-ares=1.34.4=hb9d3cd8_0
-  - ca-certificates=2025.1.31=hbcca054_0
+  - ca-certificates=2025.1.31=hbcca0.4.1
   - cached-property=1.5.2=hd8ed1ab_1
   - cached_property=1.5.2=pyha770c72_1
   - cachetools=5.5.2=pyhd8ed1ab_0
@@ -218,7 +218,7 @@ specs:
   - h2=4.2.0=pyhd8ed1ab_0
   - h5netcdf=1.6.1=pyhd8ed1ab_0
   - h5py=3.13.0=nompi_py311hb639ac4_100
-  - harfbuzz=10.4.0=h76408a6_0
+  - harfbuzz=10.4.1=h76408a6_0
   - hdf5=1.14.3=nompi_h2d575fe_109
   - hicolor-icon-theme=0.17=ha770c72_2
   - hpack=4.1.0=pyhd8ed1ab_0
@@ -294,7 +294,7 @@ specs:
   - libcufile=1.13.1.3=0
   - libcups=2.3.3=h4637d8d_4
   - libcurand=10.3.9.90=0
-  - libcurl=8.12.1=h332b0f4_0
+  - libcurl=8.12.1=h332b0.4.1
   - libcusolver=11.6.1.9=0
   - libcusparse=12.3.1.170=0
   - libdeflate=1.23=h4ddbbb0_0

containers/gpu.Dockerfile

@@ -77,7 +77,7 @@ COPY . /root
 # development
 RUN pip install --no-deps -e .
 # distribution
-# RUN pip install pyrovelocity==0.4.0
+# RUN pip install pyrovelocity==0.4.1
 
 ARG tag
 ENV FLYTE_INTERNAL_IMAGE $tag

containers/pkg.Dockerfile

@@ -34,7 +34,7 @@ COPY . /root
 # development
 RUN pip install --no-deps -e .
 # distribution
-# RUN pip install pyrovelocity==0.4.0
+# RUN pip install pyrovelocity==0.4.1
 
 ARG tag
 ENV FLYTE_INTERNAL_IMAGE $tag

docs/source/notebooks/pyrovelocity_colab_template.ipynb

@@ -70,7 +70,7 @@
         }
       ],
       "source": [
-        "pyrovelocity_version = \"0.4.0\"\n",
+        "pyrovelocity_version = \"0.4.1\"\n",
         "pyrovelocity_colab_script_url = (\n",
         "    \"https://storage.googleapis.com/pyrovelocity/data/scripts/\"\n",
         "    + f\"pyrovelocity-colab-{pyrovelocity_version}-Linux-x86_64.sh\"\n",

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pyrovelocity"
-version = "0.4.0"
+version = "0.4.1"
 packages = [{ include = "pyrovelocity", from = "src" }]
 description = "A multivariate RNA Velocity model to estimate future cell states with uncertainty using probabilistic modeling with pyro."
 authors = ["pyrovelocity team"]