build: move pooch to dependencies decorator (#3118)

Co-authored-by: Lumberbot (aka Jack) <[email protected]>
Co-authored-by: Martin Kim <[email protected]>
Co-authored-by: Can Ergen <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Justin Hong <[email protected]>
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Co-authored-by: ori-kron-wis <[email protected]>
Co-authored-by: Yishen Miao <[email protected]>
Co-authored-by: Ramon Viñas <[email protected]>
Co-authored-by: Martin Kim <[email protected]>
Co-authored-by: Ethan Weinberger <[email protected]>
Co-authored-by: Ethan Weinberger <[email protected]>
Co-authored-by: access <[email protected]>

src/scvi/data/_built_in_data/_dataset_10x.py

@@ -8,6 +8,7 @@
 
 from scvi import settings
 from scvi.data._download import _download
+from scvi.utils import dependencies
 
 logger = logging.getLogger(__name__)
 
@@ -74,6 +75,7 @@
 }
 
 
+@dependencies("scanpy")
 def _load_dataset_10x(
     dataset_name: str = None,
     filename: str = None,
@@ -83,10 +85,7 @@ def _load_dataset_10x(
     remove_extracted_data: bool = False,
     **scanpy_read_10x_kwargs,
 ):
-    try:
-        import scanpy
-    except ImportError as err:
-        raise ImportError("Please install scanpy -- `pip install scanpy`") from err
+    import scanpy
 
     # form data url and filename unless manual override
     if dataset_name is not None:

src/scvi/data/_built_in_data/_loom.py

@@ -1,19 +1,23 @@
 import logging
 import os
 
-import pooch
 from anndata import AnnData, read_h5ad
 
+from scvi.utils import dependencies
+
 logger = logging.getLogger(__name__)
 
 
+@dependencies("pooch")
 def _load_retina(save_path: str = "data/") -> AnnData:
     """Loads retina dataset.
 
     The dataset of bipolar cells contains after their original pipeline for filtering 27,499 cells
     and 13,166 genes coming from two batches. We use the cluster annotation from 15 cell-types from
     the author. We also extract their normalized data with Combat and use it for benchmarking.
     """
+    import pooch
+
     save_path = os.path.abspath(save_path)
     adata = read_h5ad(
         pooch.retrieve(
@@ -27,11 +31,14 @@ def _load_retina(save_path: str = "data/") -> AnnData:
     return adata
 
 
+@dependencies("pooch")
 def _load_prefrontalcortex_starmap(save_path: str = "data/") -> AnnData:
     """Loads a starMAP dataset from the mouse pre-frontal cortex :cite:p:`Wang18`.
 
     Contains 3,704 cells and 166 genes.
     """
+    import pooch
+
     save_path = os.path.abspath(save_path)
     adata = read_h5ad(
         pooch.retrieve(
@@ -45,7 +52,10 @@ def _load_prefrontalcortex_starmap(save_path: str = "data/") -> AnnData:
     return adata
 
 
+@dependencies("pooch")
 def _load_frontalcortex_dropseq(save_path: str = "data/") -> AnnData:
+    import pooch
+
     save_path = os.path.abspath(save_path)
     adata = read_h5ad(
         pooch.retrieve(
@@ -62,6 +72,7 @@ def _load_frontalcortex_dropseq(save_path: str = "data/") -> AnnData:
     return adata
 
 
+@dependencies("pooch")
 def _load_annotation_simulation(name: str, save_path: str = "data/") -> AnnData:
     """Simulated datasets for scANVI tutorials.
 
@@ -75,6 +86,8 @@ def _load_annotation_simulation(name: str, save_path: str = "data/") -> AnnData:
     save_path
         Location for saving the dataset.
     """
+    import pooch
+
     if name == "1":
         fileid = "51086192"
         known_hash = "5d604adce93b3034885646605c2e9a72f5ccf8163caffb2930485f93a9fcb3a3"

src/scvi/data/_built_in_data/_smfish.py

@@ -3,7 +3,8 @@
 
 import anndata
 import pandas as pd
-import pooch
+
+from scvi.utils import dependencies
 
 logger = logging.getLogger(__name__)
 
@@ -41,7 +42,10 @@
 }
 
 
+@dependencies("pooch")
 def _load_smfish(save_path: str = "data/", use_high_level_cluster=True) -> anndata.AnnData:
+    import pooch
+
     save_path = os.path.abspath(save_path)
     adata = anndata.read_h5ad(
         pooch.retrieve(