Merge branch 'master' into multigpu

setup.py

@@ -1,11 +1,21 @@
 import setuptools
+import os
+import re
 
 with open("README.md", "r") as fh:
     long_description = fh.read()
 
+# read version from src/cdtools/_version.py
+version_file = os.path.join("src/cdtools", "_version.py")
+with open(version_file) as f:
+    version_match = re.search(r"^__version__ = ['\"]([^'\"]*)['\"]", f.read(), re.M)
+if not version_match:
+    raise RuntimeError("Unable to find version string.")
+version = version_match.group(1)
+    
 setuptools.setup(
     name="cdtools-py",
-    version="0.3.0",
+    version=version,
     python_requires='>3.8', # recommended minimum version for pytorch 2.3.0
     author="Abe Levitan",
     author_email="abraham.levitan@psi.ch",

src/cdtools/__init__.py

@@ -6,6 +6,8 @@ warnings.filterwarnings("ignore",
 
 __all__ = ['tools', 'datasets', 'models', 'reconstructors']
 
+from ._version import __version__
+
 from cdtools import tools
 from cdtools import datasets
 from cdtools import models

src/cdtools/_version.py

@@ -0,0 +1 @@
+__version__ = "0.3.1.dev"

src/cdtools/reconstructors/base.py

@@ -243,7 +243,7 @@ class Reconstructor:
                     sim_patterns = self.model.forward(*inp)
 
                     # Calculate the loss
-                    if hasattr(self, 'mask'):
+                    if hasattr(self.model, 'mask'):
                         loss = self.model.loss(pats,
                                                sim_patterns,
                                                mask=self.model.mask)

tests/models/test_fancy_ptycho.py

@@ -52,6 +52,10 @@ def test_lab_ptycho(lab_ptycho_cxi, reconstruction_device, show_plot):
     print('\nTesting performance on the standard transmission ptycho dataset')
     dataset = cdtools.datasets.Ptycho2DDataset.from_cxi(lab_ptycho_cxi)
 
+    # Test the masking system
+    dataset.mask[110:115,65:70] = 0
+    dataset.patterns[...,~dataset.mask] = t.max(dataset.patterns)
+    
     model = cdtools.models.FancyPtycho.from_dataset(
         dataset,
         n_modes=3,

tests/test_version.py

@@ -0,0 +1,18 @@
+from cdtools import __version__
+import re
+
+
+def test_version_exists():
+    """Test that version is defined and not empty."""
+    assert __version__
+    assert isinstance(__version__, str)
+    assert len(__version__) > 0
+
+
+def test_version_format():
+    """Test that version follows semantic versioning format."""
+    # Basic semantic versioning pattern (X.Y.Z with optional pre-release)
+    pattern = r"^\d+\.\d+\.\d+(?:[-.]?(?:alpha|beta|rc|dev)\d*)?$"
+    assert re.match(
+        pattern, __version__
+    ), f"Version '{__version__}' doesn't follow semantic versioning"