batoolset 0.1.0__tar.gz → 0.1.1__tar.gz

{batoolset-0.1.0 → batoolset-0.1.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: batoolset
-Version: 0.1.0
+Version: 0.1.1
 Summary: An aggregate of functions I find useful
 Home-page: https://github.com/baigouy/batoolset
 Author: Benoit Aigouy
@@ -15,7 +15,7 @@ License-File: LICENSE
 Requires-Dist: czifile
 Requires-Dist: Markdown
 Requires-Dist: matplotlib>=3.5.2
-Requires-Dist: numpy
+Requires-Dist: numpy<1.26.4
 Requires-Dist: Pillow>=8.1.2
 Requires-Dist: PyQt6
 Requires-Dist: read-lif
@@ -40,6 +40,7 @@ Requires-Dist: Requests
 Requires-Dist: python-bioformats
 Requires-Dist: python-javabridge
 Requires-Dist: pyautogui
+Requires-Dist: imagecodecs
 
 # batoolset
 An aggregate of functions I find useful

{batoolset-0.1.0 → batoolset-0.1.1}/batoolset/img.py

@@ -49,13 +49,15 @@ normalization_ranges = [[0, 1], [-1, 1]]
 def start_JVM():
     # NB BELOW IS MANDATORY TO HAVE SUPPORT FOR BIOFORMATS --> start_JVM SHOULD BE CALLED ONLY ONCE PER INSTANCE AND stop_JVM SHOULD BE CALLED ON LEAVE!
     try:
+        # raise Exception('test error') # force error
         # Start the JVM when the application launches
         import javabridge
         import bioformats
 
         javabridge.start_vm(class_path=bioformats.JARS, run_headless=True, max_heap_size='1G')
     except:
-        pass
+        traceback.print_exc()
+        logger.error('Could not instantiate javabridge bioformats will not work')
 
 def stop_JVM():
     try:
@@ -71,7 +73,8 @@ def guess_dimensions(img):
 
     if hasattr(img, 'metadata'):
         if 'dimensions' in img.metadata:
-            return img.metadata['dimensions']
+            if isinstance(img.metadata['dimensions'],str):
+                return img.metadata['dimensions']
 
     if len(img.shape) == 2:
         return 'hw'
@@ -5094,6 +5097,13 @@ class ImageReader:
 
 
 if __name__ == '__main__':
+    if True:
+        from batoolset.tools.logger import TA_logger
+
+
+        print('bob')
+        sys.exit(0)
+
 
     if True:
         # tst = Img('/media/teamPrudhomme/EqpPrudhomme2/Vani/RNAi/Transvection_WT/Het/RNAi_het_20240312/26296_het_F1.tif')

{batoolset-0.1.0 → batoolset-0.1.1}/batoolset/version.py

@@ -1,6 +1,6 @@
 __MAJOR__ = 0
 __MINOR__ = 1
-__MICRO__ = 0
+__MICRO__ = 1
 __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"""

{batoolset-0.1.0 → batoolset-0.1.1}/batoolset.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: batoolset
-Version: 0.1.0
+Version: 0.1.1
 Summary: An aggregate of functions I find useful
 Home-page: https://github.com/baigouy/batoolset
 Author: Benoit Aigouy
@@ -15,7 +15,7 @@ License-File: LICENSE
 Requires-Dist: czifile
 Requires-Dist: Markdown
 Requires-Dist: matplotlib>=3.5.2
-Requires-Dist: numpy
+Requires-Dist: numpy<1.26.4
 Requires-Dist: Pillow>=8.1.2
 Requires-Dist: PyQt6
 Requires-Dist: read-lif
@@ -40,6 +40,7 @@ Requires-Dist: Requests
 Requires-Dist: python-bioformats
 Requires-Dist: python-javabridge
 Requires-Dist: pyautogui
+Requires-Dist: imagecodecs
 
 # batoolset
 An aggregate of functions I find useful

{batoolset-0.1.0 → batoolset-0.1.1}/batoolset.egg-info/requires.txt

@@ -1,7 +1,7 @@
 czifile
 Markdown
 matplotlib>=3.5.2
-numpy
+numpy<1.26.4
 Pillow>=8.1.2
 PyQt6
 read-lif
@@ -26,3 +26,4 @@ Requests
 python-bioformats
 python-javabridge
 pyautogui
+imagecodecs

{batoolset-0.1.0 → batoolset-0.1.1}/setup.py

@@ -26,7 +26,7 @@ setuptools.setup(
         "czifile",
         "Markdown",
         "matplotlib>=3.5.2",
-        "numpy",
+        "numpy<1.26.4", # <1.26.4 for compat with javabridge
         "Pillow>=8.1.2",
         "PyQt6",
         "read-lif",
@@ -51,6 +51,7 @@ setuptools.setup(
         "python-bioformats",
         "python-javabridge",
         "pyautogui",
+        "imagecodecs",
     ],
     python_requires='>=3.7, <3.11' # from 04/05/23 colab is using python 3.10.11
 )