feat(workflows): add configuration for pbmc5k data

MODULE.bazel

@@ -4,7 +4,7 @@ pyrovelocity MODULE
 
 module(
     name = "pyrovelocity",
-    version = "0.4.0b1",
+    version = "0.4.0b2",
     compatibility_level = 1,
 )
 

Makefile

@@ -913,8 +913,8 @@ approve-prs: ## Approve github pull requests from bots: PR_ENTRIES="2-5 10 12-18
 		fi; \
 	done
 
-PREVIOUS_VERSION := 0.3.0
-NEXT_VERSION := 0.4.0b1
+PREVIOUS_VERSION := 0.4.0b1
+NEXT_VERSION := 0.4.0b2
 VERSION_FILES := \
 	pyproject.toml \
 	conda/colab/construct.yaml \

conda/colab/construct.yaml

@@ -1,5 +1,5 @@
 name: pyrovelocity-colab
-version: 0.4.0b1
+version: 0.4.0b2
 
 channels:
   - pytorch

containers/gpu.Dockerfile

@@ -77,7 +77,7 @@ COPY . /root
 # development
 RUN pip install --no-deps -e .
 # distribution
-# RUN pip install pyrovelocity==0.4.0b1
+# RUN pip install pyrovelocity==0.4.0b2
 
 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==0.4.0b1
+# RUN pip install pyrovelocity==0.4.0b2
 
 ARG tag
 ENV FLYTE_INTERNAL_IMAGE $tag

docs/source/notebooks/pyrovelocity_colab_template.ipynb

@@ -70,7 +70,7 @@
         }
       ],
       "source": [
-        "pyrovelocity_version = \"0.4.0b1\"\n",
+        "pyrovelocity_version = \"0.4.0b2\"\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 = "0.4.0b1"
+version = "0.4.0b2"
 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"]

scripts/conda

@@ -3,7 +3,7 @@
 set -euo pipefail
 
 PACKAGE_NAME="pyrovelocity"
-PACKAGE_VERSION="0.4.0b1"
+PACKAGE_VERSION="0.4.0b2"
 CONDA_BUILD_STRING="pyhff70e4c"
 CONDA_BUILD_NUMBER="0"
 # CONDA_CHANNEL_LABEL="pyrovelocity_dev"
@@ -32,7 +32,7 @@ Example:
 
     ./conda \\
     --name pyrovelocity \\
-    --version 0.4.0b1.dev1 \\
+    --version 0.4.0b2.dev1 \\
     --build-string pyhff70e4c \\
     --build-number 0 \\
     --label pyrovelocity_dev
@@ -67,9 +67,9 @@ PACKAGE_SPEC="conda-forge/label/\
 $CONDA_CHANNEL_LABEL::\
 $PACKAGE_NAME=$PACKAGE_VERSION=$CONDA_BUILD_STRING"_"$CONDA_BUILD_NUMBER"
 
-BLUE="\0.4.0b1;34;1m"
+BLUE="\0.4.0b2;34;1m"
 BOLD="\033[1m"
-NO_COLOR="\0.4.0b1m"
+NO_COLOR="\0.4.0b2m"
 if [ "$USE_COLOR" = false ]; then
     BLUE=""
     BOLD=""

src/pyrovelocity/workflows/main_configuration.py

@@ -290,6 +290,49 @@ class CombinedMetricsOutputs(DataClassJSONMixin):
     summarizing_resources_limits=default_resource_limits,
 )
 
+
+pbmc5k_dataset_args = DownloadDatasetInterface(
+    data_set_name="pbmc5k",
+)
+pbmc5k_preprocess_data_args = PreprocessDataInterface(
+    data_set_name=f"{pbmc5k_dataset_args.data_set_name}",
+    adata=f"{pbmc5k_dataset_args.data_external_path}/{pbmc5k_dataset_args.data_set_name}.h5ad",
+    use_obs_subset=SUBSET_OBS,
+    use_vars_subset=SUBSET_VARS,
+    cell_state="celltype",
+)
+pbmc5k_train_model1_args = PyroVelocityTrainInterface(
+    adata=f"{pbmc5k_preprocess_data_args.data_processed_path}/{pbmc5k_dataset_args.data_set_name}_processed.h5ad",
+    data_set_name=f"{pbmc5k_dataset_args.data_set_name}",
+    model_identifier="model1",
+    guide_type="auto_t0_constraint",
+    offset=False,
+    max_epochs=MAX_EPOCHS,
+)
+pbmc5k_train_model2_args = PyroVelocityTrainInterface(
+    adata=f"{pbmc5k_preprocess_data_args.data_processed_path}/{pbmc5k_dataset_args.data_set_name}_processed.h5ad",
+    data_set_name=f"{pbmc5k_dataset_args.data_set_name}",
+    model_identifier="model2",
+    max_epochs=MAX_EPOCHS,
+)
+pbmc5k_postprocess_configuration = PostprocessConfiguration(
+    number_posterior_samples=NUMBER_POSTERIOR_SAMPLES,
+)
+pbmc5k_configuration = WorkflowConfiguration(
+    download_dataset=pbmc5k_dataset_args,
+    preprocess_data=pbmc5k_preprocess_data_args,
+    training_configuration_1=pbmc5k_train_model1_args,
+    training_configuration_2=pbmc5k_train_model2_args,
+    postprocess_configuration=pbmc5k_postprocess_configuration,
+    training_resources_requests=large_training_resource_requests,
+    training_resources_limits=large_training_resource_limits,
+    postprocessing_resources_requests=large_resource_requests,
+    postprocessing_resources_limits=large_resource_limits,
+    summarizing_resources_requests=large_resource_requests,
+    summarizing_resources_limits=large_resource_limits,
+)
+
+
 pbmc68k_dataset_args = DownloadDatasetInterface(
     data_set_name="pbmc68k",
 )

src/pyrovelocity/workflows/main_workflow.py

@@ -1,5 +1,4 @@
 import json
-import os
 from dataclasses import asdict
 from datetime import timedelta
 from pathlib import Path
@@ -56,6 +55,7 @@
     larry_multilineage_configuration,
     larry_neu_configuration,
     pancreas_configuration,
+    pbmc5k_configuration,
     pbmc68k_configuration,
     pons_configuration,
     simulated_configuration,
@@ -568,6 +568,7 @@ def combine_all_metrics(
 def training_workflow(
     simulated_configuration: WorkflowConfiguration = simulated_configuration,
     pancreas_configuration: WorkflowConfiguration = pancreas_configuration,
+    pbmc5k_configuration: WorkflowConfiguration = pbmc5k_configuration,
     pbmc68k_configuration: WorkflowConfiguration = pbmc68k_configuration,
     pons_configuration: WorkflowConfiguration = pons_configuration,
     larry_configuration: WorkflowConfiguration = larry_configuration,
@@ -587,6 +588,7 @@ def training_workflow(
     if not PYROVELOCITY_DATA_SUBSET:
         configurations += [
             (pancreas_configuration, "pancreas"),
+            (pbmc5k_configuration, "pbmc5k"),
             # (pbmc68k_configuration, "pbmc68k"),
             # (pons_configuration, "pons"),
             # (larry_configuration, "larry"),