cleanup

src/beignet/datasets/__uni_ref_dataset.py

@@ -1,8 +1,10 @@
 import re
+from os import PathLike
 from pathlib import Path
 from typing import Callable
 
 import pooch
+from pooch import Decompress
 
 from beignet.transforms import Transform
 
@@ -12,32 +14,30 @@
 class _UniRefDataset(FASTADataset):
     def __init__(
         self,
-        root: str | Path,
-        name: str,
-        md5: (str, str),
+        url: str,
+        root: str | PathLike | None = None,
+        known_hash: str | None = None,
         *,
         index: bool = True,
-        download: bool = False,
         transform: Callable | Transform | None = None,
         target_transform: Callable | Transform | None = None,
     ) -> None:
         """
         Parameters
         ----------
-        root : str | Path
+        url : str
+            URL to the file that needs to be downloaded. Ideally, the URL
+            should end with a file name (e.g., `uniref50.fasta.gz`).
+
+        root : str | PathLike, optional
             Root directory where the dataset subdirectory exists or, if
             `download` is `True`, the directory where the dataset subdirectory
             will be created and the dataset downloaded.
 
         index : bool, optional
-            If `True`, caches the sequence indicies to disk for faster
+            If `True`, caches the sequence indexes to disk for faster
             re-initialization (default: `True`).
 
-        download : bool, optional
-            If `True`, download the dataset and to the `root` directory
-            (default: `False`). If the dataset is already downloaded, it is
-            not redownloaded.
-
         transform : Callable | Transform, optional
             A `Callable` or `Transform` that that maps a sequence to a
             transformed sequence (default: `None`).
@@ -46,20 +46,24 @@ def __init__(
             A `Callable` or `Transform` that maps a target (a cluster
             identifier) to a transformed target (default: `None`).
         """
-        root = Path(root)
+        if root is None:
+            root = pooch.os_cache("beignet")
+
+        if isinstance(root, str):
+            root = Path(root)
 
-        directory = root / name
+        root = root.resolve()
 
-        path = directory / f"{name}.fasta"
+        name = self.__class__.__name__.replace("Dataset", "")
 
-        if download:
-            pooch.retrieve(
-                f"http://ftp.uniprot.org/pub/databases/uniprot/uniref/{name}/{name}.fasta.gz",
-                md5[1],
-                f"{name}.fasta.gz",
-                root / name,
-                progressbar=True,
-            )
+        path = pooch.retrieve(
+            url,
+            known_hash,
+            f"{name}.fasta.gz",
+            root / name,
+            processor=Decompress(),
+            progressbar=True,
+        )
 
         self._pattern = re.compile(r"^UniRef.+_([A-Z0-9]+)\s.+$")
 

src/beignet/datasets/_uniref100_dataset.py

@@ -11,7 +11,6 @@ def __init__(
         root: str | Path,
         *,
         index: bool = True,
-        download: bool = False,
         transform: Callable | Transform | None = None,
         target_transform: Callable | Transform | None = None,
     ) -> None:
@@ -27,11 +26,6 @@ def __init__(
             If `True`, caches the sequence indicies to disk for faster
             re-initialization (default: `True`).
 
-        download : bool, optional
-            If `True`, download the dataset and to the `root` directory
-            (default: `False`). If the dataset is already downloaded, it is
-            not redownloaded.
-
         transform : Callable, optional
             A `Callable` or `Transform` that that maps a sequence to a
             transformed sequence (default: `None`).
@@ -41,11 +35,10 @@ def __init__(
             identifier) to a transformed target (default: `None`).
         """
         super().__init__(
+            "http://ftp.uniprot.org/pub/databases/uniprot/uniref/uniref100/uniref100.fasta.gz",
             root,
-            "uniref100",
-            "0354240a56f4ca91ff426f8241cfeb7d",
+            "md5:0354240a56f4ca91ff426f8241cfeb7d",
             index=index,
-            download=download,
             transform=transform,
             target_transform=target_transform,
         )

src/beignet/datasets/_uniref50_dataset.py

@@ -1,4 +1,4 @@
-from pathlib import Path
+from os import PathLike
 from typing import Callable
 
 from beignet.transforms import Transform
@@ -9,30 +9,24 @@
 class UniRef50Dataset(_UniRefDataset):
     def __init__(
         self,
-        root: str | Path,
+        root: str | PathLike | None = None,
         *,
         index: bool = True,
-        download: bool = False,
         transform: Callable | Transform | None = None,
         target_transform: Callable | Transform | None = None,
     ) -> None:
         """
         Parameters
         ----------
-        root : str | Path
+        root : str | PathLike, optional
             Root directory where the dataset subdirectory exists or, if
             `download` is `True`, the directory where the dataset subdirectory
             will be created and the dataset downloaded.
 
         index : bool, optional
-            If `True`, caches the sequence indicies to disk for faster
+            If `True`, caches the sequence indexes to disk for faster
             re-initialization (default: `True`).
 
-        download : bool, optional
-            If `True`, download the dataset and to the `root` directory
-            (default: `False`). If the dataset is already downloaded, it is
-            not redownloaded.
-
         transform : Callable, optional
             A `Callable` or `Transform` that that maps a sequence to a
             transformed sequence (default: `None`).
@@ -42,11 +36,10 @@ def __init__(
             identifier) to a transformed target (default: `None`).
         """
         super().__init__(
+            "http://ftp.uniprot.org/pub/databases/uniprot/uniref/uniref50/uniref50.fasta.gz",
             root,
-            "uniref50",
-            "e638c63230d13ad5e2098115b9cb5d8f",
+            "md5:e638c63230d13ad5e2098115b9cb5d8f",
             index=index,
-            download=download,
             transform=transform,
             target_transform=target_transform,
         )

src/beignet/datasets/_uniref90_dataset.py

@@ -27,11 +27,6 @@ def __init__(
             If `True`, caches the sequence indicies to disk for faster
             re-initialization (default: `True`).
 
-        download : bool, optional
-            If `True`, download the dataset and to the `root` directory
-            (default: `False`). If the dataset is already downloaded, it is
-            not redownloaded.
-
         transform : Callable, optional
             A `Callable` or `Transform` that that maps a sequence to a
             transformed sequence (default: `None`).
@@ -41,11 +36,10 @@ def __init__(
             identifier) to a transformed target (default: `None`).
         """
         super().__init__(
+            "http://ftp.uniprot.org/pub/databases/uniprot/uniref/uniref90/uniref90.fasta.gz",
             root,
-            "uniref90",
-            "6161bad4d7506365aee882fd5ff9c833",
+            "md5:6161bad4d7506365aee882fd5ff9c833",
             index=index,
-            download=download,
             transform=transform,
             target_transform=target_transform,
         )