batoolset 0.1.2__tar.gz → 0.1.5__tar.gz

{batoolset-0.1.2 → batoolset-0.1.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: batoolset
-Version: 0.1.2
+Version: 0.1.5
 Summary: An aggregate of functions I find useful
 Home-page: https://github.com/baigouy/batoolset
 Author: Benoit Aigouy
@@ -37,11 +37,11 @@ Requires-Dist: pyperclip
 Requires-Dist: QtPy>=2.1.0
 Requires-Dist: Deprecated
 Requires-Dist: Requests
-Requires-Dist: python-bioformats
-Requires-Dist: python-javabridge
 Requires-Dist: pyautogui
 Requires-Dist: imagecodecs
-Requires-Dist: zarr
+Provides-Extra: all
+Requires-Dist: python-javabridge; extra == "all"
+Requires-Dist: python-bioformats; extra == "all"
 
 # batoolset
 An aggregate of functions I find useful

{batoolset-0.1.2 → batoolset-0.1.5}/batoolset/images/centralstore.py

@@ -1,7 +1,5 @@
 import os.path
-import traceback
 import gc
-import zarr
 
 # from batoolset.img import Img
 # pb the store should also store metadata  -−> see how I can do that

{batoolset-0.1.2 → batoolset-0.1.5}/batoolset/version.py

@@ -1,10 +1,9 @@
 __MAJOR__ = 0
 __MINOR__ = 1
-__MICRO__ = 2
+__MICRO__ = 5
 __RELEASE__ = ''  # a #b  # https://www.python.org/dev/peps/pep-0440/#public-version-identifiers --> alpha beta, ...
 __VERSION__ = ''.join([str(__MAJOR__), '.', str(__MINOR__), '.', str(__MICRO__)])
-__DESCRIPTION__= """An aggregate of functions I find useful"""
-__URL__='https://github.com/baigouy/batoolset'
-
+__DESCRIPTION__ = """An aggregate of functions I find useful"""
+__URL__ = 'https://github.com/baigouy/batoolset'
 __EMAIL__ = 'benoit.aigouy@gmail.com'
-__AUTHOR__ = 'Benoit Aigouy'
+__AUTHOR__ = 'Benoit Aigouy'

{batoolset-0.1.2 → batoolset-0.1.5}/batoolset.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: batoolset
-Version: 0.1.2
+Version: 0.1.5
 Summary: An aggregate of functions I find useful
 Home-page: https://github.com/baigouy/batoolset
 Author: Benoit Aigouy
@@ -37,11 +37,11 @@ Requires-Dist: pyperclip
 Requires-Dist: QtPy>=2.1.0
 Requires-Dist: Deprecated
 Requires-Dist: Requests
-Requires-Dist: python-bioformats
-Requires-Dist: python-javabridge
 Requires-Dist: pyautogui
 Requires-Dist: imagecodecs
-Requires-Dist: zarr
+Provides-Extra: all
+Requires-Dist: python-javabridge; extra == "all"
+Requires-Dist: python-bioformats; extra == "all"
 
 # batoolset
 An aggregate of functions I find useful

{batoolset-0.1.2 → batoolset-0.1.5}/batoolset.egg-info/SOURCES.txt

@@ -164,6 +164,5 @@ batoolset/utils/loadlist.py
 batoolset/xml/__init__.py
 batoolset/xml/tools.py
 batoolset/zarr/__init__.py
-batoolset/zarr/centralstorezarrstore.py
 batoolset/zip_tools/__init__.py
 batoolset/zip_tools/tools.py

{batoolset-0.1.2 → batoolset-0.1.5}/batoolset.egg-info/requires.txt

@@ -23,8 +23,9 @@ pyperclip
 QtPy>=2.1.0
 Deprecated
 Requests
-python-bioformats
-python-javabridge
 pyautogui
 imagecodecs
-zarr
+
+[all]
+python-javabridge
+python-bioformats

{batoolset-0.1.2 → batoolset-0.1.5}/setup.py

@@ -48,11 +48,16 @@ setuptools.setup(
         "QtPy>=2.1.0",
         "Deprecated",
         "Requests",
-        "python-bioformats",
-        "python-javabridge",
+        # "python-bioformats",
+        # "python-javabridge",
         "pyautogui",
         "imagecodecs",
-        "zarr",
+        # "zarr",
+    ],
+    extras_require={'all': [
+        "python-javabridge",
+        "python-bioformats",
     ],
+    },
     python_requires='>=3.7, <3.11' # from 04/05/23 colab is using python 3.10.11
 )

batoolset-0.1.2/batoolset/zarr/centralstorezarrstore.py

@@ -1,108 +0,0 @@
-import traceback
-import gc
-import zarr
-
-# from batoolset.img import Img
-# pb the store should also store metadata  -−> see how I can do that
-
-__DEBUG__ = True
-
-class ImageCentralStoreZarr:
-    store = None
-
-    @classmethod
-    def init(cls, folder_path=None):
-        try:
-            if folder_path is None:
-                # Create a Zarr store in memory
-                zarr_store = zarr.MemoryStore()
-            else:
-                zarr_store = zarr.DirectoryStore(folder_path)  # just a single line is sufficient to handle the stuff
-            zarr_root = zarr.group(store=zarr_store)
-            cls.store = zarr_root
-        except:
-            traceback.print_exc()
-            print('Error zarr store could not be created')
-
-    @classmethod
-    def set_store(cls, store):
-        if __DEBUG__:
-            print('setting store', cls.store)
-        # Set the central store (zarr store)
-        if isinstance(store, str):
-            cls.store = zarr.open(store, mode='a')
-        else:
-            cls.store = store
-
-    @classmethod
-    def get_store(cls):
-        if __DEBUG__:
-            print('getting store', cls.store)
-        return cls.store
-
-    @classmethod
-    def append(cls, image_id, data):
-        # Save the image data to the central store
-        if cls.store is not None:
-            if data is not None:
-                cls.store[image_id] = data
-            else:
-                try:
-                    if __DEBUG__:
-                        print('deleting image store entry because None')
-                    del cls.store[image_id]
-                except:
-                    pass
-            if __DEBUG__:
-                print(f"Image {image_id} added to central store.")
-
-            if hasattr(data, 'metadata'):
-                cls.store.attrs[image_id] = data.metadata
-            else:
-                cls.store.attrs[image_id] = None  # just in case there was already a metadata attribute --> make sure to have this
-        # else:
-        #     if __DEBUG__:
-        #         print("Central store is not set.")
-
-    @classmethod
-    def load(cls, image_id):
-        if False:
-            # shall I do gc
-            # Check if central store is available and if the image exists in the store
-            # gc.collect()
-            # Print the number of objects that were garbage collected
-            print(f"{gc.collect():,} objects were garbage collected")
-        if cls.store is not None:
-            if image_id in cls.store:
-                img = cls.store[image_id][:]
-                metadata = cls.store.attrs.get(image_id, None)
-                if __DEBUG__:
-                    print(f"Image {image_id} loaded from central store.")
-                return metadata,img
-            else:
-                metadata, img = cls.reload(image_id)
-                return metadata, img
-
-        if __DEBUG__:
-            print('No store found --> skipping loading from store for', image_id)
-        return None, None
-
-    # maybe put a relaod where the image is necessarily reloaded -−> force an update of the image from source file
-    @classmethod
-    def reload(cls, image_id):
-        from batoolset.img import Img
-        if __DEBUG__:
-            print('Img called for file', image_id)
-        img = Img(image_id,
-                  prefer_store_if_available=False)  # pb will this launch an infinite loop -−> maybe so make sure to prevent reload form it
-        metadata = None
-        if hasattr(img, 'metadata'):
-            metadata = img.metadata
-        # add image to the store
-        cls.append(image_id, img)
-        del img
-
-        img = cls.store[image_id] # then we reload it from the store in order not to duplicate it # MEGA TODO -−> check
-        metadata = cls.store.attrs.get(image_id, None)
-
-        return metadata, img