celldetective 1.5.0b5__tar.gz → 1.5.0b7__tar.gz

{celldetective-1.5.0b5 → celldetective-1.5.0b7}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: celldetective
-Version: 1.5.0b5
+Version: 1.5.0b7
 Summary: description
 Home-page: http://github.com/remyeltorro/celldetective
 Author: Rémy Torro
@@ -15,11 +15,8 @@ Requires-Dist: sphinx_rtd_theme
 Requires-Dist: sphinx
 Requires-Dist: jinja2
 Requires-Dist: ipykernel
-Requires-Dist: stardist
-Requires-Dist: cellpose<3
 Requires-Dist: scikit-learn
 Requires-Dist: btrack
-Requires-Dist: tensorflow~=2.15.0
 Requires-Dist: napari<0.6.0
 Requires-Dist: tqdm
 Requires-Dist: mahotas
@@ -48,6 +45,15 @@ Requires-Dist: prettyprint
 Requires-Dist: pandas
 Requires-Dist: matplotlib
 Requires-Dist: prettytable
+Requires-Dist: scikit-image
+Requires-Dist: natsort
+Provides-Extra: tensorflow
+Requires-Dist: tensorflow~=2.15.0; extra == "tensorflow"
+Requires-Dist: stardist; extra == "tensorflow"
+Provides-Extra: all
+Requires-Dist: cellpose<3; extra == "all"
+Requires-Dist: stardist; extra == "all"
+Requires-Dist: tensorflow~=2.15.0; extra == "all"
 Dynamic: author
 Dynamic: author-email
 Dynamic: description
@@ -55,6 +61,7 @@ Dynamic: description-content-type
 Dynamic: home-page
 Dynamic: license
 Dynamic: license-file
+Dynamic: provides-extra
 Dynamic: requires-dist
 Dynamic: summary
 
@@ -148,10 +155,12 @@ To use the software, you must install python, *e.g.* through
 
 Celldetective requires a version of Python between 3.9 and 3.11 (included). If your Python version is older or more recent, consider using `conda` to create an environment as described below.
 
-With the proper Python version, Celldetective can be directly installed with `pip`:
+With the proper Python version, Celldetective can be directly installed with `pip`.
+**Important**: By default, `pip install celldetective` will **not** install deep-learning libraries (`tensorflow`, `cellpose`, `stardist`) to allow users to manage their own GPU environment (e.g. `torch`, `cuda`).
 
+If you want the standard full installation (recommended for most users), use:
 ``` bash
-pip install celldetective
+pip install celldetective[all]
 ```
 
 We recommend that you create an environment to use Celldetective, to protect your package versions and fix the Python version *e.g.*
@@ -160,7 +169,7 @@ with `conda`:
 ``` bash
 conda create -n celldetective python=3.11 pyqt
 conda activate celldetective
-pip install celldetective
+pip install celldetective[all]
 ```
 
 Need an update? Simply type the following in the terminal (in your

{celldetective-1.5.0b5 → celldetective-1.5.0b7}/README.md

@@ -88,10 +88,12 @@ To use the software, you must install python, *e.g.* through
 
 Celldetective requires a version of Python between 3.9 and 3.11 (included). If your Python version is older or more recent, consider using `conda` to create an environment as described below.
 
-With the proper Python version, Celldetective can be directly installed with `pip`:
+With the proper Python version, Celldetective can be directly installed with `pip`.
+**Important**: By default, `pip install celldetective` will **not** install deep-learning libraries (`tensorflow`, `cellpose`, `stardist`) to allow users to manage their own GPU environment (e.g. `torch`, `cuda`).
 
+If you want the standard full installation (recommended for most users), use:
 ``` bash
-pip install celldetective
+pip install celldetective[all]
 ```
 
 We recommend that you create an environment to use Celldetective, to protect your package versions and fix the Python version *e.g.*
@@ -100,7 +102,7 @@ with `conda`:
 ``` bash
 conda create -n celldetective python=3.11 pyqt
 conda activate celldetective
-pip install celldetective
+pip install celldetective[all]
 ```
 
 Need an update? Simply type the following in the terminal (in your

celldetective-1.5.0b7/celldetective/_version.py

@@ -0,0 +1 @@
+__version__ = "1.5.0b7"

{celldetective-1.5.0b5 → celldetective-1.5.0b7}/celldetective/gui/viewers/base_viewer.py

@@ -879,6 +879,14 @@ class StackVisualizer(CelldetectiveWidget):
         # Event handler for closing the widget
         if self.loader_thread:
             self.loader_thread.stop()
+            self.loader_thread = None
         if hasattr(self, "frame_cache") and isinstance(self.frame_cache, OrderedDict):
             self.frame_cache.clear()
         self.canvas.close()
+
+    def __del__(self):
+        try:
+            if hasattr(self, "loader_thread") and self.loader_thread:
+                self.loader_thread.stop()
+        except:
+            pass

{celldetective-1.5.0b5 → celldetective-1.5.0b7}/celldetective/processes/unified_process.py

@@ -122,15 +122,29 @@ class UnifiedBatchProcess(Process):
         signal_model = None
 
         if self.run_signals:
-            from celldetective.utils.event_detection import _prep_event_detection_model
-
             try:
+                from celldetective.utils.event_detection import (
+                    _prep_event_detection_model,
+                )
+
                 logger.info("Loading the event detection model...")
                 self.queue.put({"status": "Loading event detection model..."})
                 model_name = self.signal_args["model_name"]
                 signal_model = _prep_event_detection_model(
                     model_name, use_gpu=self.signal_args.get("gpu", True)
                 )
+            except (ImportError, ModuleNotFoundError) as e:
+                if "tensorflow" in str(e):
+                    logger.warning(
+                        "Tensorflow not found/installed. Signal analysis will be skipped."
+                    )
+                    self.run_signals = False
+                else:
+                    logger.error(
+                        f"Failed to initialize event detection model: {e}",
+                        exc_info=True,
+                    )
+                    self.run_signals = False
             except Exception as e:
                 logger.error(
                     f"Failed to initialize event detection model: {e}", exc_info=True

{celldetective-1.5.0b5 → celldetective-1.5.0b7}/celldetective/utils/cellpose_utils/__init__.py

@@ -104,14 +104,27 @@ def _prep_cellpose_model(
       `diam_labels` are attributes of the model.
     """
 
-    import torch
+    try:
+        import torch
+    except ImportError as e:
+        raise RuntimeError(
+            "Torch is not installed. Please install it to use this feature.\n"
+            "You can install the full package with: pip install celldetective[all]\n"
+        ) from e
 
     if not use_gpu:
         device = torch.device("cpu")
     else:
         device = torch.device("cuda")
 
-    from cellpose.models import CellposeModel
+    try:
+        from cellpose.models import CellposeModel
+    except ImportError as e:
+        raise RuntimeError(
+            "Cellpose is not installed. Please install it to use this feature.\n"
+            "You can install the full package with: pip install celldetective[all]\n"
+            "Or specifically: pip install celldetective[cellpose]"
+        ) from e
 
     try:
         model = CellposeModel(

{celldetective-1.5.0b5 → celldetective-1.5.0b7}/celldetective/utils/downloaders.py

@@ -77,18 +77,39 @@ def download_url_to_file(url, dst, progress=True):
                     Default: True
 
     """
-    file_size = None
     import ssl
+    import time
+    from urllib.error import HTTPError, URLError
 
+    file_size = None
     ssl._create_default_https_context = ssl._create_unverified_context
-    u = urlopen(url)
-    meta = u.info()
-    if hasattr(meta, "getheaders"):
-        content_length = meta.getheaders("Content-Length")
-    else:
-        content_length = meta.get_all("Content-Length")
-    if content_length is not None and len(content_length) > 0:
-        file_size = int(content_length[0])
+
+    # Retry configuration
+    max_retries = 5
+    retry_delay = 10  # Initial delay in seconds
+
+    for attempt in range(max_retries):
+        try:
+            u = urlopen(url)
+            meta = u.info()
+            if hasattr(meta, "getheaders"):
+                content_length = meta.getheaders("Content-Length")
+            else:
+                content_length = meta.get_all("Content-Length")
+            if content_length is not None and len(content_length) > 0:
+                file_size = int(content_length[0])
+            break  # Success
+        except (HTTPError, URLError) as e:
+            if attempt < max_retries - 1:
+                logger.warning(
+                    f"Download check failed: {e}. Retrying in {retry_delay}s..."
+                )
+                time.sleep(retry_delay)
+                retry_delay *= 2  # Exponential backoff
+            else:
+                logger.error(f"Download check failed after {max_retries} attempts: {e}")
+                raise e
+
     # We deliberately save it in a temp file and move it after
     dst = os.path.expanduser(dst)
     dst_dir = os.path.dirname(dst)
@@ -143,14 +164,27 @@ def download_url_to_file(url, dst, progress=True):
                 unit_divisor=1024,
             ) as pbar:
                 while True:
-                    buffer = u.read(8192)  # 8192
-                    if len(buffer) == 0:
-                        break
-                    f.write(buffer)
-                    pbar.update(len(buffer))
+                    try:
+                        buffer = u.read(8192)  # 8192
+                        if len(buffer) == 0:
+                            break
+                        f.write(buffer)
+                        pbar.update(len(buffer))
+                    except (HTTPError, URLError) as e:
+                        # Attempt rudimentary resume-like behavior or just fail?
+                        # Simple retry of read is hard without Range headers on a stream.
+                        # Best to just fail the whole download and rely on outer retry if we wrapped the whole thing.
+                        # For now, let's just let it raise, but really we should wrap the whole download block.
+                        raise e
 
         f.close()
         shutil.move(f.name, dst)
+    except Exception as e:
+        f.close()
+        remove_file_if_exists(f.name)
+        # If we failed during download reading (after open), we should probably retry the whole function from start
+        # but that requires significant refactoring. Given the error was 504 on open, the retry block above handles it.
+        raise e
     finally:
         f.close()
         remove_file_if_exists(f.name)

{celldetective-1.5.0b5 → celldetective-1.5.0b7}/celldetective/utils/stardist_utils/__init__.py

@@ -43,7 +43,13 @@ def _prep_stardist_model(
     - GPU support depends on the availability of compatible hardware and software setup.
     """
 
-    from stardist.models import StarDist2D
+    try:
+        from stardist.models import StarDist2D
+    except ImportError as e:
+        raise RuntimeError(
+            "StarDist is not installed. Please install it to use this feature.\n"
+            "You can install the full package with: pip install celldetective[all]"
+        ) from e
 
     model = StarDist2D(None, name=model_name, basedir=path)
     model.config.use_gpu = use_gpu

{celldetective-1.5.0b5 → celldetective-1.5.0b7}/celldetective.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: celldetective
-Version: 1.5.0b5
+Version: 1.5.0b7
 Summary: description
 Home-page: http://github.com/remyeltorro/celldetective
 Author: Rémy Torro
@@ -15,11 +15,8 @@ Requires-Dist: sphinx_rtd_theme
 Requires-Dist: sphinx
 Requires-Dist: jinja2
 Requires-Dist: ipykernel
-Requires-Dist: stardist
-Requires-Dist: cellpose<3
 Requires-Dist: scikit-learn
 Requires-Dist: btrack
-Requires-Dist: tensorflow~=2.15.0
 Requires-Dist: napari<0.6.0
 Requires-Dist: tqdm
 Requires-Dist: mahotas
@@ -48,6 +45,15 @@ Requires-Dist: prettyprint
 Requires-Dist: pandas
 Requires-Dist: matplotlib
 Requires-Dist: prettytable
+Requires-Dist: scikit-image
+Requires-Dist: natsort
+Provides-Extra: tensorflow
+Requires-Dist: tensorflow~=2.15.0; extra == "tensorflow"
+Requires-Dist: stardist; extra == "tensorflow"
+Provides-Extra: all
+Requires-Dist: cellpose<3; extra == "all"
+Requires-Dist: stardist; extra == "all"
+Requires-Dist: tensorflow~=2.15.0; extra == "all"
 Dynamic: author
 Dynamic: author-email
 Dynamic: description
@@ -55,6 +61,7 @@ Dynamic: description-content-type
 Dynamic: home-page
 Dynamic: license
 Dynamic: license-file
+Dynamic: provides-extra
 Dynamic: requires-dist
 Dynamic: summary
 
@@ -148,10 +155,12 @@ To use the software, you must install python, *e.g.* through
 
 Celldetective requires a version of Python between 3.9 and 3.11 (included). If your Python version is older or more recent, consider using `conda` to create an environment as described below.
 
-With the proper Python version, Celldetective can be directly installed with `pip`:
+With the proper Python version, Celldetective can be directly installed with `pip`.
+**Important**: By default, `pip install celldetective` will **not** install deep-learning libraries (`tensorflow`, `cellpose`, `stardist`) to allow users to manage their own GPU environment (e.g. `torch`, `cuda`).
 
+If you want the standard full installation (recommended for most users), use:
 ``` bash
-pip install celldetective
+pip install celldetective[all]
 ```
 
 We recommend that you create an environment to use Celldetective, to protect your package versions and fix the Python version *e.g.*
@@ -160,7 +169,7 @@ with `conda`:
 ``` bash
 conda create -n celldetective python=3.11 pyqt
 conda activate celldetective
-pip install celldetective
+pip install celldetective[all]
 ```
 
 Need an update? Simply type the following in the terminal (in your

{celldetective-1.5.0b5 → celldetective-1.5.0b7}/celldetective.egg-info/SOURCES.txt

@@ -184,6 +184,7 @@ tests/test_io.py
 tests/test_measure.py
 tests/test_neighborhood.py
 tests/test_notebooks.py
+tests/test_partial_install.py
 tests/test_preprocessing.py
 tests/test_segmentation.py
 tests/test_signals.py

{celldetective-1.5.0b5 → celldetective-1.5.0b7}/celldetective.egg-info/requires.txt

@@ -5,11 +5,8 @@ sphinx_rtd_theme
 sphinx
 jinja2
 ipykernel
-stardist
-cellpose<3
 scikit-learn
 btrack
-tensorflow~=2.15.0
 napari<0.6.0
 tqdm
 mahotas
@@ -38,3 +35,14 @@ prettyprint
 pandas
 matplotlib
 prettytable
+scikit-image
+natsort
+
+[all]
+cellpose<3
+stardist
+tensorflow~=2.15.0
+
+[tensorflow]
+tensorflow~=2.15.0
+stardist

{celldetective-1.5.0b5 → celldetective-1.5.0b7}/setup.py

@@ -70,5 +70,10 @@ setup(
         "console_scripts": ["celldetective = celldetective.__main__:main"],
     },
     install_requires=requirements,
+    extras_require={
+        "tensorflow": ["tensorflow~=2.15.0", "stardist"],
+        #"process": ["cellpose<3", "stardist", "tensorflow~=2.15.0"],
+        "all": ["cellpose<3", "stardist", "tensorflow~=2.15.0"],
+    },
     # dependency_links = links
 )

celldetective-1.5.0b7/tests/test_partial_install.py

@@ -0,0 +1,75 @@
+import unittest
+from unittest.mock import MagicMock, patch
+import sys
+import importlib
+
+
+class TestPartialValidation(unittest.TestCase):
+
+    def test_imports_without_extras(self):
+        """Test that main modules can be imported even if optional extras are missing."""
+        # This test assumes the environment MIGHT have them, so we must mock them as missing
+        # to ensure the code handles it.
+
+        with patch.dict(
+            sys.modules,
+            {
+                "tensorflow": None,
+                "torch": None,
+                "stardist": None,
+                "cellpose": None,
+                "cellpose.models": None,
+                "stardist.models": None,
+            },
+        ):
+            # Force reload of celldetective.segmentation to test its imports
+            try:
+                import celldetective.segmentation
+
+                importlib.reload(celldetective.segmentation)
+            except ImportError as e:
+                self.fail(
+                    f"Could not import celldetective.segmentation without extras: {e}"
+                )
+            except Exception as e:
+                self.fail(f"Unexpected error importing celldetective.segmentation: {e}")
+
+    def test_graceful_failure_stardist(self):
+        """Test that calling stardist functions raises RuntimeError if missing."""
+        with patch.dict(sys.modules, {"stardist": None, "stardist.models": None}):
+            # We need to reload the util module to pick up the missing module
+            import celldetective.utils.stardist_utils
+
+            importlib.reload(celldetective.utils.stardist_utils)
+
+            from celldetective.utils.stardist_utils import _prep_stardist_model
+
+            with self.assertRaises(RuntimeError) as cm:
+                _prep_stardist_model("fake_model", "fake_path")
+
+            self.assertIn("StarDist is not installed", str(cm.exception))
+
+    def test_graceful_failure_cellpose(self):
+        """Test that calling cellpose functions raises RuntimeError if missing."""
+        with patch.dict(
+            sys.modules, {"cellpose": None, "cellpose.models": None, "torch": None}
+        ):
+            import celldetective.utils.cellpose_utils
+
+            importlib.reload(celldetective.utils.cellpose_utils)
+
+            from celldetective.utils.cellpose_utils import _prep_cellpose_model
+
+            with self.assertRaises(RuntimeError) as cm:
+                _prep_cellpose_model("fake_model", "fake_path")
+
+            # Message check might correspond to torch or cellpose depending on which import hits first
+            # Our code checks torch first.
+            self.assertTrue(
+                "Torch is not installed" in str(cm.exception)
+                or "Cellpose is not installed" in str(cm.exception)
+            )
+
+
+if __name__ == "__main__":
+    unittest.main()

celldetective-1.5.0b5/celldetective/_version.py

@@ -1 +0,0 @@
-__version__ = "1.5.0b5"