From e38ebd737277ba565506d654b0ceecaca0c267e0 Mon Sep 17 00:00:00 2001
From: Abe Levitan <abraham.levitan@psi.ch>
Date: Fri, 24 Oct 2025 15:11:46 +0200
Subject: [PATCH 1/3] Fix a high priority bug with the masking system which was
 introduced in the switch to reconstructors classes

---
 src/cdtools/reconstructors/base.py | 2 +-
 tests/models/test_fancy_ptycho.py  | 4 ++++
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/src/cdtools/reconstructors/base.py b/src/cdtools/reconstructors/base.py
index cf3de8c..1666814 100644
--- a/src/cdtools/reconstructors/base.py
+++ b/src/cdtools/reconstructors/base.py
@@ -190,7 +190,7 @@ 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)
diff --git a/tests/models/test_fancy_ptycho.py b/tests/models/test_fancy_ptycho.py
index 8bc4d87..02893f9 100644
--- a/tests/models/test_fancy_ptycho.py
+++ b/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,

From 008fef6244b7990c8ce5364bf816cc473891a3e5 Mon Sep 17 00:00:00 2001
From: Abe Levitan <abraham.levitan@psi.ch>
Date: Tue, 28 Oct 2025 16:06:21 +0100
Subject: [PATCH 2/3] Add cdtools.__version__ and set it up so that there is a
 single source of truth for the version number. Still not done with
 setuptools_scm, but one step at a time)

---
 setup.py                | 12 +++++++++++-
 src/cdtools/__init__.py |  2 ++
 src/cdtools/_version.py |  1 +
 3 files changed, 14 insertions(+), 1 deletion(-)
 create mode 100644 src/cdtools/_version.py

diff --git a/setup.py b/setup.py
index 4e62c0f..ae710d7 100644
--- a/setup.py
+++ b/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",
diff --git a/src/cdtools/__init__.py b/src/cdtools/__init__.py
index 9132209..19dc4c6 100644
--- a/src/cdtools/__init__.py
+++ b/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
diff --git a/src/cdtools/_version.py b/src/cdtools/_version.py
new file mode 100644
index 0000000..9163035
--- /dev/null
+++ b/src/cdtools/_version.py
@@ -0,0 +1 @@
+__version__ = "0.3.1.dev"

From f79836bfc26225a92075ff1d85e22211436ca758 Mon Sep 17 00:00:00 2001
From: gnzng <damian@guenzing.de>
Date: Wed, 29 Oct 2025 21:40:12 -0700
Subject: [PATCH 3/3] Add tests for version existence and semantic format

---
 tests/test_version.py | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)
 create mode 100644 tests/test_version.py

diff --git a/tests/test_version.py b/tests/test_version.py
new file mode 100644
index 0000000..5b6a778
--- /dev/null
+++ b/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"