spacr 0.1.1__tar.gz → 0.1.6__tar.gz

{spacr-0.1.1/spacr.egg-info → spacr-0.1.6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: spacr
-Version: 0.1.1
+Version: 0.1.6
 Summary: Spatial phenotype analysis of crisp screens (SpaCr)
 Home-page: https://github.com/EinarOlafsson/spacr
 Author: Einar Birnir Olafsson
@@ -9,7 +9,6 @@ Classifier: Programming Language :: Python :: 3
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Operating System :: OS Independent
 License-File: LICENSE
-Requires-Dist: dgl==0.9.1
 Requires-Dist: torch<3.0,>=2.2.1
 Requires-Dist: torchvision<1.0,>=0.17.1
 Requires-Dist: torch-geometric<3.0,>=2.5.1
@@ -40,8 +39,9 @@ Requires-Dist: ttf_opensans>=2020.10.30
 Requires-Dist: customtkinter<6.0,>=5.2.2
 Requires-Dist: biopython<2.0,>=1.80
 Requires-Dist: lxml<6.0,>=5.1.0
+Requires-Dist: huggingface-hub<0.25,>=0.24.0
 Provides-Extra: dev
-Requires-Dist: pytest>=3.9; extra == "dev"
+Requires-Dist: pytest<3.11,>=3.9; extra == "dev"
 Provides-Extra: headless
 Requires-Dist: opencv-python-headless; extra == "headless"
 Provides-Extra: full
@@ -63,7 +63,7 @@ Requires-Dist: opencv-python; extra == "full"
 SpaCr
 =====
 
-Spatial phenotype analysis of CRISPR-Cas9 screens (SpaCr). The spatial organization of organelles and proteins within cells constitutes a key level of functional regulation. In the context of infectious disease, the spatial relationships between host cell structures and intracellular pathogens are critical to understand host clearance mechanisms and how pathogens evade them. SpaCr is a Python-based software package for generating single-cell image data for deep-learning sub-cellular/cellular phenotypic classification from pooled genetic CRISPR-Cas9 screens. SpaCr provides a flexible toolset to extract single-cell images and measurements from high-content cell painting experiments, train deep-learning models to classify cellular/subcellular phenotypes, simulate, and analyze pooled CRISPR-Cas9 imaging screens.
+Spatial phenotype analysis of CRISPR-Cas9 screens (SpaCr). The spatial organization of organelles and proteins within cells constitutes a key level of functional regulation. In the context of infectious disease, the spatial relationships between host cell structures and intracellular pathogens are critical to understanding host clearance mechanisms and how pathogens evade them. SpaCr is a Python-based software package for generating single-cell image data for deep-learning sub-cellular/cellular phenotypic classification from pooled genetic CRISPR-Cas9 screens. SpaCr provides a flexible toolset to extract single-cell images and measurements from high-content cell painting experiments, train deep-learning models to classify cellular/subcellular phenotypes, simulate, and analyze pooled CRISPR-Cas9 imaging screens.
 
 Features
 --------
@@ -72,9 +72,9 @@ Features
 
 -  **Object Measurements:** Measurements for each object including scikit-image-regionprops, intensity percentiles, shannon-entropy, pearsons and manders correlations, homogeneity, and radial distribution. Measurements are saved to a SQL database in object-level tables.
 
--  **Crop Images:** Objects (e.g., cells) can be saved as PNGs from the object area or bounding box area of each object. Object paths are saved in a SQL database that can be annotated and used to train CNNs/Transformer models for classification tasks.
+-  **Crop Images:** Save objects (cells, nuclei, pathogen, cytoplasm) as images. Object image paths are saved in a SQL database.
 
--  **Train CNNs or Transformers:** Train Torch Convolutional Neural Networks (CNNs) or Transformers to classify single object images. Train Torch models with IRM/ERM, checkpointing.
+-  **Train CNNs or Transformers:** Train Torch models to classify single object images.
 
 -  **Manual Annotation:** Supports manual annotation of single-cell images and segmentation to refine training datasets for training CNNs/Transformers or cellpose, respectively.
 
@@ -91,29 +91,20 @@ Features
 Installation
 ------------
 
-Requires Tkinter for graphical user interface features.
+If using Windows, switch to Linux—it's free, open-source, and better.
 
-Ubuntu
-~~~~~~
+Before installing SpaCr on OSX ensure OpenMP is installed::
 
-Before installing SpaCr, ensure Tkinter is installed:
+   brew install libomp
 
-(Tkinter is included with the standard Python installation on macOS, and Windows)
-
-On Linux:
-
-::
+SpaCr GUI requires Tkinter. On Linux, ensure Tkinter is installed. (Tkinter is included with the standard Python installation on macOS and Windows)::
 
    sudo apt-get install python3-tk
 
-Install spacr with pip
-
-::
+Install SpaCr with pip::
 
    pip install spacr
 
-Run spacr GUI:
-
-::
+Run SpaCr GUI::
 
-   gui
+   spacr

{spacr-0.1.1 → spacr-0.1.6}/README.rst

@@ -14,7 +14,7 @@
 SpaCr
 =====
 
-Spatial phenotype analysis of CRISPR-Cas9 screens (SpaCr). The spatial organization of organelles and proteins within cells constitutes a key level of functional regulation. In the context of infectious disease, the spatial relationships between host cell structures and intracellular pathogens are critical to understand host clearance mechanisms and how pathogens evade them. SpaCr is a Python-based software package for generating single-cell image data for deep-learning sub-cellular/cellular phenotypic classification from pooled genetic CRISPR-Cas9 screens. SpaCr provides a flexible toolset to extract single-cell images and measurements from high-content cell painting experiments, train deep-learning models to classify cellular/subcellular phenotypes, simulate, and analyze pooled CRISPR-Cas9 imaging screens.
+Spatial phenotype analysis of CRISPR-Cas9 screens (SpaCr). The spatial organization of organelles and proteins within cells constitutes a key level of functional regulation. In the context of infectious disease, the spatial relationships between host cell structures and intracellular pathogens are critical to understanding host clearance mechanisms and how pathogens evade them. SpaCr is a Python-based software package for generating single-cell image data for deep-learning sub-cellular/cellular phenotypic classification from pooled genetic CRISPR-Cas9 screens. SpaCr provides a flexible toolset to extract single-cell images and measurements from high-content cell painting experiments, train deep-learning models to classify cellular/subcellular phenotypes, simulate, and analyze pooled CRISPR-Cas9 imaging screens.
 
 Features
 --------
@@ -23,9 +23,9 @@ Features
 
 -  **Object Measurements:** Measurements for each object including scikit-image-regionprops, intensity percentiles, shannon-entropy, pearsons and manders correlations, homogeneity, and radial distribution. Measurements are saved to a SQL database in object-level tables.
 
--  **Crop Images:** Objects (e.g., cells) can be saved as PNGs from the object area or bounding box area of each object. Object paths are saved in a SQL database that can be annotated and used to train CNNs/Transformer models for classification tasks.
+-  **Crop Images:** Save objects (cells, nuclei, pathogen, cytoplasm) as images. Object image paths are saved in a SQL database.
 
--  **Train CNNs or Transformers:** Train Torch Convolutional Neural Networks (CNNs) or Transformers to classify single object images. Train Torch models with IRM/ERM, checkpointing.
+-  **Train CNNs or Transformers:** Train Torch models to classify single object images.
 
 -  **Manual Annotation:** Supports manual annotation of single-cell images and segmentation to refine training datasets for training CNNs/Transformers or cellpose, respectively.
 
@@ -42,29 +42,20 @@ Features
 Installation
 ------------
 
-Requires Tkinter for graphical user interface features.
+If using Windows, switch to Linux—it's free, open-source, and better.
 
-Ubuntu
-~~~~~~
+Before installing SpaCr on OSX ensure OpenMP is installed::
 
-Before installing SpaCr, ensure Tkinter is installed:
+   brew install libomp
 
-(Tkinter is included with the standard Python installation on macOS, and Windows)
-
-On Linux:
-
-::
+SpaCr GUI requires Tkinter. On Linux, ensure Tkinter is installed. (Tkinter is included with the standard Python installation on macOS and Windows)::
 
    sudo apt-get install python3-tk
 
-Install spacr with pip
-
-::
+Install SpaCr with pip::
 
    pip install spacr
 
-Run spacr GUI:
-
-::
+Run SpaCr GUI::
 
-   gui
+   spacr

{spacr-0.1.1 → spacr-0.1.6}/setup.py

@@ -10,19 +10,11 @@ def get_cuda_version():
     except (subprocess.CalledProcessError, FileNotFoundError):
         return None
 
-cuda_version = get_cuda_version()
-
-if cuda_version:
-    dgl_dependency = f'dgl-cu{cuda_version}==0.9.1'  # Specify the version of DGL compatible with your setup
-else:
-    dgl_dependency = 'dgl==0.9.1'  # Fallback to CPU version if no CUDA is detected
-
 # Ensure you have read the README.rst content into a variable, e.g., `long_description`
 with open("README.rst", "r", encoding="utf-8") as fh:
     long_description = fh.read()
 
 dependencies = [
-    dgl_dependency,
     'torch>=2.2.1,<3.0',
     'torchvision>=0.17.1,<1.0',
     'torch-geometric>=2.5.1,<3.0',
@@ -52,12 +44,13 @@ dependencies = [
     'ttf_opensans>=2020.10.30',
     'customtkinter>=5.2.2,<6.0', 
     'biopython>=1.80,<2.0',
-    'lxml>=5.1.0,<6.0'
+    'lxml>=5.1.0,<6.0',
+    'huggingface-hub>=0.24.0,<0.25'
 ]
 
 setup(
     name="spacr",
-    version="0.1.01",
+    version="0.1.6",
     author="Einar Birnir Olafsson",
     author_email="olafsson@med.umich.com",
     description="Spatial phenotype analysis of crisp screens (SpaCr)",
@@ -69,18 +62,17 @@ setup(
     install_requires=dependencies,
     entry_points={
         'console_scripts': [
-            'mask=spacr.gui_mask_app:gui_mask',
-            'measure=spacr.gui_measure_app:gui_measure',
-            'make_masks=spacr.mask_app:gui_make_masks',
-            'annotate=spacr.annotate_app:gui_annotation',
-            'classify=spacr.gui_classify_app:gui_classify',
-            'sim=spacr.gui_sim_app:gui_sim',
-            'gui=spacr.gui:gui_app',
-            'gui2=spacr.gui_2:gui_app',
+            'mask=spacr.app_mask:start_mask_app',
+            'measure=spacr.app_measure:start_measure_app',
+            'make_masks=spacr.app_make_masks:gui_make_masks',
+            'annotate=spacr.app_annotate:gui_annotate',
+            'classify=spacr.app_classify:start_classify_app',
+            'sim=spacr.app_sim:gui_sim',
+            'spacr=spacr.gui:gui_app',
         ],
     },
     extras_require={
-        'dev': ['pytest>=3.9'],
+        'dev': ['pytest>=3.9,<3.11'],
         'headless': ['opencv-python-headless'],
         'full': ['opencv-python'],
     },
@@ -89,4 +81,32 @@ setup(
         "License :: OSI Approved :: MIT License",
         "Operating System :: OS Independent",
     ]
-)
+)
+
+cuda_version = get_cuda_version()
+
+if cuda_version:
+    dgl = f'dgl-cu{cuda_version}==0.9.1'
+else:
+    dgl = 'dgl==0.9.1'  # Fallback to CPU version if no CUDA is detected
+try:
+    subprocess.run(['pip', 'install', dgl], check=True)
+except subprocess.CalledProcessError:
+    subprocess.run(['pip', 'install', 'dgl'], check=True)
+
+deps = ['pyqtgraph>=0.13.7,<0.14',
+        'pyqt6>=6.7.1,<6.8',
+        'pyqt6.sip',
+        'qtpy>=2.4.1,<2.5',
+        'superqt>=0.6.7,<0.7',
+        'pyqtgraph',
+        'pyqt6',
+        'pyqt6.sip',
+        'qtpy',
+        'superqt']
+
+for dep in deps:
+    try:
+        subprocess.run(['pip', 'install', dep], check=True)
+    except subprocess.CalledProcessError:
+        pass

{spacr-0.1.1 → spacr-0.1.6}/spacr/__init__.py

@@ -12,13 +12,18 @@ from . import sim
 from . import sequencing
 from . import timelapse
 from . import deep_spacr
-from . import annotate_app
-from . import annotate_app_v2
+from . import app_annotate
 from . import gui_utils
-from . import mask_app
-from . import gui_mask_app
-from . import gui_measure_app
-from . import gui_classify_app
+from . import gui_elements
+from . import gui_core
+from . import gui_run
+from . import gui_wrappers
+from . import app_make_masks
+from . import app_mask
+from . import app_measure
+from . import app_classify
+from . import app_sequencing
+from . import app_umap
 from . import logger
 
 
@@ -33,13 +38,15 @@ __all__ = [
     "sequencing"
     "timelapse",
     "deep_spacr",
-    "annotate_app",
-    "annotate_app_v2",
+    "app_annotate",
     "gui_utils",
-    "mask_app",
-    "gui_mask_app",
-    "gui_measure_app",
-    "gui_classify_app",
+    "app_make_masks",
+    "app_make_masks_v2",
+    "app_mask",
+    "app_measure",
+    "app_classify",
+    "app_sequencing",
+    "app_umap",
     "logger"
 ]