Merge pull request #148 from henrypinkard/main

Change name to NDStorage
micro-manager · Jun 13, 2024 · 4f310a2 · 4f310a2
2 parents 6f4a5ee + 9ec8a42
commit 4f310a2
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diff --git a/python/ndstorage/__init__.py b/python/ndstorage/__init__.py
@@ -0,0 +1,7 @@
+name = "ndstorage"
+
+from ndstorage.ndstorage_base import NDStorageAPI, WritableNDStorageAPI
+from ndstorage._superclass import Dataset
+from ndstorage.ndtiff_dataset import NDTiffDataset
+from ndstorage.ndram_dataset import NDRAMDataset
+from ndstorage.ndtiff_pyramid_dataset import NDTiffPyramidDataset
diff --git a/python/ndtiff/_superclass.py → python/ndstorage/_superclass.py b/python/ndtiff/_superclass.py → python/ndstorage/_superclass.py
@@ -1,10 +1,10 @@
 import os
-from ndtiff.ndtiff_dataset import NDTiffDataset
-from ndtiff.ndtiff_pyramid_dataset import NDTiffPyramidDataset
-from ndtiff.old_format_version_readers.nd_tiff_v2 import NDTiff_v2_0
-from ndtiff.old_format_version_readers.ndtiff_v1 import NDTiff_v1
+from ndstorage.ndtiff_dataset import NDTiffDataset
+from ndstorage.ndtiff_pyramid_dataset import NDTiffPyramidDataset
+from ndstorage.old_format_version_readers.nd_tiff_v2 import NDTiff_v2_0
+from ndstorage.old_format_version_readers.ndtiff_v1 import NDTiff_v1
 import numpy as np
-from ndtiff.file_io import NDTiffFileIO, BUILTIN_FILE_IO
+from ndstorage.file_io import NDTiffFileIO, BUILTIN_FILE_IO
 
 class Dataset:
     """

diff --git a/python/ndtiff/_version.py → python/ndstorage/_version.py b/python/ndtiff/_version.py → python/ndstorage/_version.py
@@ -1,2 +1,2 @@
-version_info = (3, 1, 0)
+version_info = (0, 1, 0)
 __version__ = ".".join(map(str, version_info))
diff --git a/python/ndtiff/file_io.py → python/ndstorage/file_io.py b/python/ndtiff/file_io.py → python/ndstorage/file_io.py
diff --git a/python/ndtiff/ndram_dataset.py → python/ndstorage/ndram_dataset.py b/python/ndtiff/ndram_dataset.py → python/ndstorage/ndram_dataset.py
@@ -1,7 +1,7 @@
 from typing import List, Dict, Union
 
 import threading
-from ndtiff.ndstorage_base import WritableNDStorageAPI, NDStorageBase
+from ndstorage.ndstorage_base import WritableNDStorageAPI, NDStorageBase
 
 
 class NDRAMDataset(NDStorageBase, WritableNDStorageAPI):

diff --git a/python/ndtiff/ndstorage_base.py → python/ndstorage/ndstorage_base.py b/python/ndtiff/ndstorage_base.py → python/ndstorage/ndstorage_base.py
@@ -18,7 +18,7 @@
 import dask.array as da
 import threading
 
-from ndtiff.ndtiff_file import _POSITION_AXIS, _ROW_AXIS, _COLUMN_AXIS, _Z_AXIS, _TIME_AXIS, _CHANNEL_AXIS
+from ndstorage.ndtiff_file import _POSITION_AXIS, _ROW_AXIS, _COLUMN_AXIS, _Z_AXIS, _TIME_AXIS, _CHANNEL_AXIS
 
 # Standard order of axes when opening data. Data does not need to be acquired in this order -- this is just a convention
 _AXIS_ORDER = {_ROW_AXIS: 7,

diff --git a/python/ndtiff/ndtiff_dataset.py → python/ndstorage/ndtiff_dataset.py b/python/ndtiff/ndtiff_dataset.py → python/ndstorage/ndtiff_dataset.py
@@ -6,14 +6,14 @@
 import warnings
 import re
 
-from ndtiff.file_io import NDTiffFileIO, BUILTIN_FILE_IO
-from ndtiff.ndtiff_file import SingleNDTiffReader
-from ndtiff.ndtiff_file import _CHANNEL_AXIS
-from ndtiff.ndtiff_index import NDTiffIndexEntry, read_ndtiff_index
+from ndstorage.file_io import NDTiffFileIO, BUILTIN_FILE_IO
+from ndstorage.ndtiff_file import SingleNDTiffReader
+from ndstorage.ndtiff_file import _CHANNEL_AXIS
+from ndstorage.ndtiff_index import NDTiffIndexEntry, read_ndtiff_index
 
-from ndtiff.ndtiff_file import SingleNDTiffWriter, MAJOR_VERSION, MINOR_VERSION
+from ndstorage.ndtiff_file import SingleNDTiffWriter, MAJOR_VERSION, MINOR_VERSION
 
-from ndtiff.ndstorage_base import WritableNDStorageAPI, NDStorageBase
+from ndstorage.ndstorage_base import WritableNDStorageAPI, NDStorageBase
 
 class NDTiffDataset(NDStorageBase, WritableNDStorageAPI):
     """

diff --git a/python/ndtiff/ndtiff_file.py → python/ndstorage/ndtiff_file.py b/python/ndtiff/ndtiff_file.py → python/ndstorage/ndtiff_file.py
@@ -7,8 +7,8 @@
 import warnings
 from collections import OrderedDict
 from io import BytesIO
-from ndtiff.file_io import NDTiffFileIO, BUILTIN_FILE_IO
-from ndtiff.ndtiff_index import NDTiffIndexEntry
+from ndstorage.file_io import NDTiffFileIO, BUILTIN_FILE_IO
+from ndstorage.ndtiff_index import NDTiffIndexEntry
 
 from collections import deque
 from concurrent.futures import ThreadPoolExecutor

diff --git a/python/ndtiff/ndtiff_index.py → python/ndstorage/ndtiff_index.py b/python/ndtiff/ndtiff_index.py → python/ndstorage/ndtiff_index.py
diff --git a/python/ndtiff/ndtiff_pyramid_dataset.py → python/ndstorage/ndtiff_pyramid_dataset.py b/python/ndtiff/ndtiff_pyramid_dataset.py → python/ndstorage/ndtiff_pyramid_dataset.py
@@ -1,8 +1,8 @@
 import os
 import numpy as np
 import threading
-from ndtiff.file_io import NDTiffFileIO, BUILTIN_FILE_IO
-from ndtiff.ndtiff_dataset import NDTiffDataset
+from ndstorage.file_io import NDTiffFileIO, BUILTIN_FILE_IO
+from ndstorage.ndtiff_dataset import NDTiffDataset
 
 class NDTiffPyramidDataset:
     """Class that opens a single NDTiffStorage multi-resolution pyramid dataset"""

diff --git a/...ff/old_format_version_readers/__init__.py → ...ge/old_format_version_readers/__init__.py b/...ff/old_format_version_readers/__init__.py → ...ge/old_format_version_readers/__init__.py
diff --git a/.../old_format_version_readers/nd_tiff_v2.py → .../old_format_version_readers/nd_tiff_v2.py b/.../old_format_version_readers/nd_tiff_v2.py → .../old_format_version_readers/nd_tiff_v2.py
@@ -9,7 +9,7 @@
 import warnings
 import struct
 import threading
-from ndtiff.file_io import NDTiffFileIO, BUILTIN_FILE_IO
+from ndstorage.file_io import NDTiffFileIO, BUILTIN_FILE_IO
 
 _POSITION_AXIS = "position"
 _ROW_AXIS = "row"

diff --git a/...f/old_format_version_readers/ndtiff_v1.py → ...e/old_format_version_readers/ndtiff_v1.py b/...f/old_format_version_readers/ndtiff_v1.py → ...e/old_format_version_readers/ndtiff_v1.py
@@ -8,7 +8,7 @@
 import dask.array as da
 import warnings
 import struct
-from ndtiff.file_io import NDTiffFileIO, BUILTIN_FILE_IO
+from ndstorage.file_io import NDTiffFileIO, BUILTIN_FILE_IO
 
 class _MultipageTiffReader:
     # Class corresponsing to a single multipage tiff file in a Micro-Magellan dataset. Pass the full path of the TIFF to

diff --git a/python/ndtiff/test/__init__.py → python/ndstorage/test/__init__.py b/python/ndtiff/test/__init__.py → python/ndstorage/test/__init__.py
diff --git a/python/ndtiff/test/conftest.py → python/ndstorage/test/conftest.py b/python/ndtiff/test/conftest.py → python/ndstorage/test/conftest.py
diff --git a/python/ndtiff/test/data_loading_test.py → python/ndstorage/test/data_loading_test.py b/python/ndtiff/test/data_loading_test.py → python/ndstorage/test/data_loading_test.py
@@ -1,5 +1,5 @@
 import numpy as np
-from ndtiff import Dataset
+from ndstorage import Dataset
 import os
 
 

diff --git a/python/ndtiff/test/test_custom_io.py → python/ndstorage/test/test_custom_io.py b/python/ndtiff/test/test_custom_io.py → python/ndstorage/test/test_custom_io.py
@@ -1,5 +1,5 @@
 import numpy as np
-from ndtiff import Dataset, file_io
+from ndstorage import Dataset, file_io
 import os
 import pytest
 from typing import List

diff --git a/python/ndtiff/test/write_speed_test.py → python/ndstorage/test/write_speed_test.py b/python/ndtiff/test/write_speed_test.py → python/ndstorage/test/write_speed_test.py
@@ -1,8 +1,8 @@
 # import numpy as np
 # import os
 # import shutil
-# from ndtiff.ndtiff_file import SingleNDTiffWriter, SingleNDTiffReader
-# from ndtiff.ndtiff_dataset import NDTiffDataset
+# from ndstorage.ndtiff_file import SingleNDTiffWriter, SingleNDTiffReader
+# from ndstorage.ndtiff_dataset import NDTiffDataset
 # import pytest
 # import time
 # from tqdm import tqdm

diff --git a/python/ndtiff/test/writing_test.py → python/ndstorage/test/writing_test.py b/python/ndtiff/test/writing_test.py → python/ndstorage/test/writing_test.py
@@ -1,9 +1,9 @@
 import numpy as np
 import os
 import shutil
-from ndtiff.ndtiff_file import SingleNDTiffWriter, SingleNDTiffReader
-from ndtiff.ndtiff_dataset import NDTiffDataset
-from ndtiff.ndram_dataset import NDRAMDataset
+from ndstorage.ndtiff_file import SingleNDTiffWriter, SingleNDTiffReader
+from ndstorage.ndtiff_dataset import NDTiffDataset
+from ndstorage.ndram_dataset import NDRAMDataset
 import pytest
 
 @pytest.fixture(scope="function")

diff --git a/python/ndtiff/__init__.py b/python/ndtiff/__init__.py
diff --git a/python/setup.py b/python/setup.py
@@ -5,7 +5,7 @@
     long_description = fh.read()
 
 # extract version
-path = path.realpath("ndtiff/_version.py")
+path = path.realpath("ndstorage/_version.py")
 version_ns = {}
 with open(path, encoding="utf8") as f:
     exec(f.read(), {}, version_ns)
@@ -15,14 +15,14 @@
     requirements = f.read().splitlines()
 
 setuptools.setup(
-    name="ndtiff",
+    name="ndstorage",
     version=version,
     author="Henry Pinkard",
     author_email="[email protected]",
-    description="Python libraries for NDTiff datasets",
+    description="Python libraries for N-dimensional datasets, including NDTiff",
     long_description=long_description,
     long_description_content_type="text/markdown",
-    url="https://github.com/micro-manager/NDTiffStorage",
+    url="https://github.com/micro-manager/NDStorage",
     packages=setuptools.find_packages(),
     install_requires=requirements,
     python_requires=">=3.6",