Merge pull request #46 from zacharyburnett/deprecate/copy_arrays

replace usages of ``copy_arrays`` with ``memmap``

Author: braingram

CHANGES.rst

@@ -1,7 +1,7 @@
 0.1.0 (unreleased)
 ------------------
 
--
+- replace usages of ``copy_arrays`` with ``memmap`` [#46]
 
 0.0.4 (2024-06-28)
 ------------------

asdf_zarr/tests/test_zarr.py

@@ -26,13 +26,13 @@ def create_zarray(shape=None, chunks=None, dtype="f8", store=None, chunk_store=N
     return arr
 
 
-@pytest.mark.parametrize("copy_arrays", [True, False])
+@pytest.mark.parametrize("memmap", [True, False])
 @pytest.mark.parametrize("lazy_load", [True, False])
 @pytest.mark.parametrize("compression", ["input", "zlib"])
 @pytest.mark.parametrize("store_type", [DirectoryStore, KVStore, MemoryStore, NestedDirectoryStore, TempStore])
 @pytest.mark.parametrize("to_internal", [True, False])
 @pytest.mark.parametrize("meta_store", [True, False])
-def test_write_to(tmp_path, copy_arrays, lazy_load, compression, store_type, to_internal, meta_store):
+def test_write_to(tmp_path, memmap, lazy_load, compression, store_type, to_internal, meta_store):
     if store_type in (DirectoryStore, NestedDirectoryStore):
         store1 = store_type(tmp_path / "zarr_array_1")
         store2 = store_type(tmp_path / "zarr_array_2")
@@ -66,7 +66,7 @@ def test_write_to(tmp_path, copy_arrays, lazy_load, compression, store_type, to_
     af = asdf.AsdfFile(tree)
     af.write_to(fn, all_array_compression=compression)
 
-    with asdf.open(fn, mode="r", copy_arrays=copy_arrays, lazy_load=lazy_load) as af:
+    with asdf.open(fn, mode="r", memmap=memmap, lazy_load=lazy_load) as af:
         for n, a in (("arr1", arr1), ("arr2", arr2)):
             assert isinstance(af[n], zarr.core.Array)
             if to_internal or store_type in (KVStore, MemoryStore, TempStore):
@@ -76,10 +76,10 @@ def test_write_to(tmp_path, copy_arrays, lazy_load, compression, store_type, to_
             assert numpy.allclose(af[n], a)
 
 
-@pytest.mark.parametrize("copy_arrays", [True, False])
+@pytest.mark.parametrize("memmap", [True, False])
 @pytest.mark.parametrize("lazy_load", [True, False])
 @pytest.mark.parametrize("with_update", [True, False])
-def test_modify(tmp_path, with_update, copy_arrays, lazy_load):
+def test_modify(tmp_path, with_update, memmap, lazy_load):
     # make a file
     store = DirectoryStore(tmp_path / "zarr_array")
     arr = create_zarray(store=store)
@@ -89,7 +89,7 @@ def test_modify(tmp_path, with_update, copy_arrays, lazy_load):
     af.write_to(fn)
 
     # open the file, modify the array
-    with asdf.open(fn, mode="rw", copy_arrays=copy_arrays, lazy_load=lazy_load) as af:
+    with asdf.open(fn, mode="rw", memmap=memmap, lazy_load=lazy_load) as af:
         assert af["arr"][0, 0] != 42
         af["arr"][0, 0] = 42
         # now modify
@@ -100,7 +100,7 @@ def test_modify(tmp_path, with_update, copy_arrays, lazy_load):
             af.update()
 
     # reopen the file, check for the modification
-    with asdf.open(fn, mode="rw", copy_arrays=copy_arrays, lazy_load=lazy_load) as af:
+    with asdf.open(fn, mode="rw", memmap=memmap, lazy_load=lazy_load) as af:
         assert af["arr"][0, 0] == 42
 
 

notebooks/ASDF_array_storage_intro.ipynb

@@ -623,7 +623,7 @@
     "\n",
     "For local files, asdf will memory map arrays allowing the operating system to read only the portion of the array that is requested.\n",
     "\n",
-    "Note that array memory mapping can be disabled by setting the keyword argument `copy_arrays` to `True` in `asdf.open`."
+    "Note that array memory mapping can be disabled by setting the keyword argument `memmap` to `False` in `asdf.open`."
    ]
   },
   {
@@ -641,15 +641,15 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "With default copy_arrays=False\n",
+      "With default memmap=True\n",
       "\tarray 0 base array type = <class 'numpy.memmap'>\n"
      ]
     }
    ],
    "source": [
     "# open our example file with memory mapping (enabled by default)\n",
     "with asdf.open(example_fn) as af:\n",
-    "    print(\"With default copy_arrays=False\") \n",
+    "    print(\"With default memmap=True\") \n",
     "    # the array data has a base array that is of type numpy.memmap\n",
     "    print(f\"\\tarray 0 base array type = {type(af['array0'].base)}\")"
    ]
@@ -669,15 +669,15 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "With copy_arrays=True\n",
+      "With memmap=False\n",
       "\tarray 0 base array type = <class 'numpy.ndarray'>\n"
      ]
     }
    ],
    "source": [
     "# open our example file with memory mapping disabled\n",
-    "with asdf.open(example_fn, copy_arrays=True) as af:\n",
-    "    print(\"With copy_arrays=True\")\n",
+    "with asdf.open(example_fn, memmap=False) as af:\n",
+    "    print(\"With memmap=False\")\n",
     "    print(f\"\\tarray 0 base array type = {type(af['array0'].base)}\")"
    ]
   },

pyproject.toml

@@ -19,7 +19,7 @@ dynamic = [
   'version',
 ]
 dependencies = [
-  "asdf >= 3.0.0",
+  "asdf >= 3.1.0",
   "zarr >= 2.14, < 3.0.0",
   "fsspec",
 ]