Update Packaging (#102)

AdvancedPhotonSource · Oct 25, 2024 · 56155e7 · 56155e7
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diff --git a/LICENSE b/LICENSE
@@ -1,6 +1,6 @@
-Copyright (c) UChicago Argonne, LLC. All rights reserved.
+Copyright (c) 2024, UChicago Argonne, LLC. All rights reserved.
 
-Copyright UChicago Argonne, LLC. This software was produced
+Copyright 2024. UChicago Argonne, LLC. This software was produced
 under U.S. Government contract DE-AC02-06CH11357 for Argonne National
 Laboratory (ANL), which is operated by UChicago Argonne, LLC for the
 U.S. Department of Energy. The U.S. Government has rights to use,
@@ -29,7 +29,7 @@ conditions are met:
       from this software without specific prior written permission.
 
 THIS SOFTWARE IS PROVIDED BY UChicago Argonne, LLC AND CONTRIBUTORS
-AS IS AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
 LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS
 FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL UChicago
 Argonne, LLC OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,

diff --git a/pyproject.toml b/pyproject.toml
@@ -1,11 +1,34 @@
 [build-system]
-requires = [
-    "setuptools >=46.4.0",
-    "setuptools_scm[toml] >=7",
-    "wheel",
-]
+requires = ["setuptools>=64", "setuptools_scm>=8"]
 build-backend = "setuptools.build_meta"
 
+[project]
+name = "ptychodus"
+description = "Ptychodus is a ptychography data analysis application."
+readme = "README.rst"
+requires-python = ">=3.10"
+license = {file = "LICENSE.txt"}
+dependencies = [
+    "h5py",
+    "matplotlib",
+    "numpy",
+    "psutil",
+    "scikit-image",
+    "scipy",
+    "tifffile",
+    "watchdog",
+]
+dynamic = ["version"]
+
+[project.scripts]
+ptychodus = "ptychodus.__main__:main"
+
+[project.optional-dependencies]
+globus = ["gladier", "gladier-tools"]
+gui = ["PyQt5"]
+ptychonn = ["ptychonn==0.3.*,>=0.3.7"]
+tike = ["tike==0.25.*,>=0.25.3"]
+
 [tool.setuptools_scm]
 
 [tool.mypy]
@@ -33,6 +56,14 @@ ignore_missing_imports = true
 
 [tool.ruff]
 line-length = 100
+target-version = "py310"
 
 [tool.ruff.format]
 quote-style = "single"
+
+[tool.setuptools.package-data]
+"ptychodus" = ["py.typed"]
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
diff --git a/requirements-dev.txt b/requirements-dev.txt
@@ -11,8 +11,8 @@ python>=3.10
 ruff
 scikit-image
 scipy
-setuptools>=46.4.0
-setuptools_scm
+setuptools>=64
+setuptools_scm>=8
 tifffile
 toml
 watchdog

diff --git a/requirements.txt b/requirements.txt
diff --git a/setup.cfg b/setup.cfg
diff --git a/setup.py b/setup.py
diff --git a/ptychodus/__init__.py → src/ptychodus/__init__.py b/ptychodus/__init__.py → src/ptychodus/__init__.py
diff --git a/ptychodus/__main__.py → src/ptychodus/__main__.py b/ptychodus/__main__.py → src/ptychodus/__main__.py
diff --git a/ptychodus/api/__init__.py → src/ptychodus/api/__init__.py b/ptychodus/api/__init__.py → src/ptychodus/api/__init__.py
diff --git a/ptychodus/api/constants.py → src/ptychodus/api/constants.py b/ptychodus/api/constants.py → src/ptychodus/api/constants.py
diff --git a/ptychodus/api/fluorescence.py → src/ptychodus/api/fluorescence.py b/ptychodus/api/fluorescence.py → src/ptychodus/api/fluorescence.py
diff --git a/ptychodus/api/geometry.py → src/ptychodus/api/geometry.py b/ptychodus/api/geometry.py → src/ptychodus/api/geometry.py
diff --git a/ptychodus/api/object.py → src/ptychodus/api/object.py b/ptychodus/api/object.py → src/ptychodus/api/object.py
diff --git a/ptychodus/api/observer.py → src/ptychodus/api/observer.py b/ptychodus/api/observer.py → src/ptychodus/api/observer.py
diff --git a/ptychodus/api/parametric.py → src/ptychodus/api/parametric.py b/ptychodus/api/parametric.py → src/ptychodus/api/parametric.py
diff --git a/ptychodus/api/patterns.py → src/ptychodus/api/patterns.py b/ptychodus/api/patterns.py → src/ptychodus/api/patterns.py
diff --git a/ptychodus/api/plugins.py → src/ptychodus/api/plugins.py b/ptychodus/api/plugins.py → src/ptychodus/api/plugins.py
diff --git a/ptychodus/api/probe.py → src/ptychodus/api/probe.py b/ptychodus/api/probe.py → src/ptychodus/api/probe.py
diff --git a/ptychodus/api/product.py → src/ptychodus/api/product.py b/ptychodus/api/product.py → src/ptychodus/api/product.py
diff --git a/ptychodus/api/propagator.py → src/ptychodus/api/propagator.py b/ptychodus/api/propagator.py → src/ptychodus/api/propagator.py
diff --git a/ptychodus/api/reconstructor.py → src/ptychodus/api/reconstructor.py b/ptychodus/api/reconstructor.py → src/ptychodus/api/reconstructor.py
diff --git a/ptychodus/api/scan.py → src/ptychodus/api/scan.py b/ptychodus/api/scan.py → src/ptychodus/api/scan.py
diff --git a/ptychodus/api/settings.py → src/ptychodus/api/settings.py b/ptychodus/api/settings.py → src/ptychodus/api/settings.py
diff --git a/ptychodus/api/tree.py → src/ptychodus/api/tree.py b/ptychodus/api/tree.py → src/ptychodus/api/tree.py
diff --git a/ptychodus/api/typing.py → src/ptychodus/api/typing.py b/ptychodus/api/typing.py → src/ptychodus/api/typing.py
diff --git a/ptychodus/api/visualization.py → src/ptychodus/api/visualization.py b/ptychodus/api/visualization.py → src/ptychodus/api/visualization.py
diff --git a/ptychodus/api/workflow.py → src/ptychodus/api/workflow.py b/ptychodus/api/workflow.py → src/ptychodus/api/workflow.py
diff --git a/ptychodus/controller/__init__.py → src/ptychodus/controller/__init__.py b/ptychodus/controller/__init__.py → src/ptychodus/controller/__init__.py
diff --git a/ptychodus/controller/automation.py → src/ptychodus/controller/automation.py b/ptychodus/controller/automation.py → src/ptychodus/controller/automation.py
diff --git a/ptychodus/controller/core.py → src/ptychodus/controller/core.py b/ptychodus/controller/core.py → src/ptychodus/controller/core.py
diff --git a/ptychodus/controller/data.py → src/ptychodus/controller/data.py b/ptychodus/controller/data.py → src/ptychodus/controller/data.py
diff --git a/ptychodus/controller/image.py → src/ptychodus/controller/image.py b/ptychodus/controller/image.py → src/ptychodus/controller/image.py
diff --git a/ptychodus/controller/memory.py → src/ptychodus/controller/memory.py b/ptychodus/controller/memory.py → src/ptychodus/controller/memory.py
diff --git a/ptychodus/controller/object/__init__.py → src/ptychodus/controller/object/__init__.py b/ptychodus/controller/object/__init__.py → src/ptychodus/controller/object/__init__.py
diff --git a/ptychodus/controller/object/core.py → src/ptychodus/controller/object/core.py b/ptychodus/controller/object/core.py → src/ptychodus/controller/object/core.py
diff --git a/ptychodus/controller/object/editorFactory.py → ...chodus/controller/object/editorFactory.py b/ptychodus/controller/object/editorFactory.py → ...chodus/controller/object/editorFactory.py
diff --git a/ptychodus/controller/object/frc.py → src/ptychodus/controller/object/frc.py b/ptychodus/controller/object/frc.py → src/ptychodus/controller/object/frc.py
diff --git a/ptychodus/controller/object/treeModel.py → src/ptychodus/controller/object/treeModel.py b/ptychodus/controller/object/treeModel.py → src/ptychodus/controller/object/treeModel.py
diff --git a/ptychodus/controller/object/xmcd.py → src/ptychodus/controller/object/xmcd.py b/ptychodus/controller/object/xmcd.py → src/ptychodus/controller/object/xmcd.py
diff --git a/ptychodus/controller/parametric.py → src/ptychodus/controller/parametric.py b/ptychodus/controller/parametric.py → src/ptychodus/controller/parametric.py
diff --git a/ptychodus/controller/patterns/__init__.py → ...ptychodus/controller/patterns/__init__.py b/ptychodus/controller/patterns/__init__.py → ...ptychodus/controller/patterns/__init__.py
diff --git a/ptychodus/controller/patterns/core.py → src/ptychodus/controller/patterns/core.py b/ptychodus/controller/patterns/core.py → src/ptychodus/controller/patterns/core.py
diff --git a/ptychodus/controller/patterns/detector.py → ...ptychodus/controller/patterns/detector.py b/ptychodus/controller/patterns/detector.py → ...ptychodus/controller/patterns/detector.py
diff --git a/ptychodus/controller/patterns/info.py → src/ptychodus/controller/patterns/info.py b/ptychodus/controller/patterns/info.py → src/ptychodus/controller/patterns/info.py
diff --git a/ptychodus/controller/patterns/tree.py → src/ptychodus/controller/patterns/tree.py b/ptychodus/controller/patterns/tree.py → src/ptychodus/controller/patterns/tree.py
diff --git a/ptychodus/controller/patterns/treeModel.py → ...tychodus/controller/patterns/treeModel.py b/ptychodus/controller/patterns/treeModel.py → ...tychodus/controller/patterns/treeModel.py
diff --git a/ptychodus/controller/patterns/wizard.py → src/ptychodus/controller/patterns/wizard.py b/ptychodus/controller/patterns/wizard.py → src/ptychodus/controller/patterns/wizard.py
diff --git a/ptychodus/controller/probe/__init__.py → src/ptychodus/controller/probe/__init__.py b/ptychodus/controller/probe/__init__.py → src/ptychodus/controller/probe/__init__.py
diff --git a/ptychodus/controller/probe/core.py → src/ptychodus/controller/probe/core.py b/ptychodus/controller/probe/core.py → src/ptychodus/controller/probe/core.py
diff --git a/ptychodus/controller/probe/editorFactory.py → ...ychodus/controller/probe/editorFactory.py b/ptychodus/controller/probe/editorFactory.py → ...ychodus/controller/probe/editorFactory.py
diff --git a/ptychodus/controller/probe/exposure.py → src/ptychodus/controller/probe/exposure.py b/ptychodus/controller/probe/exposure.py → src/ptychodus/controller/probe/exposure.py
diff --git a/ptychodus/controller/probe/fluorescence.py → ...tychodus/controller/probe/fluorescence.py b/ptychodus/controller/probe/fluorescence.py → ...tychodus/controller/probe/fluorescence.py
diff --git a/ptychodus/controller/probe/propagator.py → src/ptychodus/controller/probe/propagator.py b/ptychodus/controller/probe/propagator.py → src/ptychodus/controller/probe/propagator.py
diff --git a/ptychodus/controller/probe/stxm.py → src/ptychodus/controller/probe/stxm.py b/ptychodus/controller/probe/stxm.py → src/ptychodus/controller/probe/stxm.py
diff --git a/ptychodus/controller/probe/treeModel.py → src/ptychodus/controller/probe/treeModel.py b/ptychodus/controller/probe/treeModel.py → src/ptychodus/controller/probe/treeModel.py
diff --git a/ptychodus/controller/probe/zernike.py → src/ptychodus/controller/probe/zernike.py b/ptychodus/controller/probe/zernike.py → src/ptychodus/controller/probe/zernike.py
diff --git a/ptychodus/controller/product/__init__.py → src/ptychodus/controller/product/__init__.py b/ptychodus/controller/product/__init__.py → src/ptychodus/controller/product/__init__.py
diff --git a/ptychodus/controller/product/core.py → src/ptychodus/controller/product/core.py b/ptychodus/controller/product/core.py → src/ptychodus/controller/product/core.py
diff --git a/ptychodus/controller/product/editor.py → src/ptychodus/controller/product/editor.py b/ptychodus/controller/product/editor.py → src/ptychodus/controller/product/editor.py
diff --git a/ptychodus/controller/ptychonn/__init__.py → ...ptychodus/controller/ptychonn/__init__.py b/ptychodus/controller/ptychonn/__init__.py → ...ptychodus/controller/ptychonn/__init__.py
diff --git a/ptychodus/controller/ptychonn/controller.py → ...ychodus/controller/ptychonn/controller.py b/ptychodus/controller/ptychonn/controller.py → ...ychodus/controller/ptychonn/controller.py
diff --git a/ptychodus/controller/ptychonn/factory.py → src/ptychodus/controller/ptychonn/factory.py b/ptychodus/controller/ptychonn/factory.py → src/ptychodus/controller/ptychonn/factory.py
diff --git a/ptychodus/controller/ptychonn/model.py → src/ptychodus/controller/ptychonn/model.py b/ptychodus/controller/ptychonn/model.py → src/ptychodus/controller/ptychonn/model.py
diff --git a/ptychodus/controller/ptychonn/training.py → ...ptychodus/controller/ptychonn/training.py b/ptychodus/controller/ptychonn/training.py → ...ptychodus/controller/ptychonn/training.py
diff --git a/ptychodus/controller/reconstructor.py → src/ptychodus/controller/reconstructor.py b/ptychodus/controller/reconstructor.py → src/ptychodus/controller/reconstructor.py
diff --git a/ptychodus/controller/scan/__init__.py → src/ptychodus/controller/scan/__init__.py b/ptychodus/controller/scan/__init__.py → src/ptychodus/controller/scan/__init__.py
diff --git a/ptychodus/controller/scan/core.py → src/ptychodus/controller/scan/core.py b/ptychodus/controller/scan/core.py → src/ptychodus/controller/scan/core.py
diff --git a/ptychodus/controller/scan/editorFactory.py → ...tychodus/controller/scan/editorFactory.py b/ptychodus/controller/scan/editorFactory.py → ...tychodus/controller/scan/editorFactory.py
diff --git a/ptychodus/controller/scan/tableModel.py → src/ptychodus/controller/scan/tableModel.py b/ptychodus/controller/scan/tableModel.py → src/ptychodus/controller/scan/tableModel.py
diff --git a/ptychodus/controller/settings.py → src/ptychodus/controller/settings.py b/ptychodus/controller/settings.py → src/ptychodus/controller/settings.py
diff --git a/ptychodus/controller/tike/__init__.py → src/ptychodus/controller/tike/__init__.py b/ptychodus/controller/tike/__init__.py → src/ptychodus/controller/tike/__init__.py
diff --git a/ptychodus/controller/tike/core.py → src/ptychodus/controller/tike/core.py b/ptychodus/controller/tike/core.py → src/ptychodus/controller/tike/core.py
diff --git a/ptychodus/controller/tike/viewControllers.py → ...chodus/controller/tike/viewControllers.py b/ptychodus/controller/tike/viewControllers.py → ...chodus/controller/tike/viewControllers.py
diff --git a/...odus/controller/visualization/__init__.py → ...odus/controller/visualization/__init__.py b/...odus/controller/visualization/__init__.py → ...odus/controller/visualization/__init__.py
diff --git a/...us/controller/visualization/controller.py → ...us/controller/visualization/controller.py b/...us/controller/visualization/controller.py → ...us/controller/visualization/controller.py
diff --git a/...us/controller/visualization/parameters.py → ...us/controller/visualization/parameters.py b/...us/controller/visualization/parameters.py → ...us/controller/visualization/parameters.py
diff --git a/ptychodus/controller/visualization/widget.py → ...chodus/controller/visualization/widget.py b/ptychodus/controller/visualization/widget.py → ...chodus/controller/visualization/widget.py
diff --git a/ptychodus/controller/workflow/__init__.py → ...ptychodus/controller/workflow/__init__.py b/ptychodus/controller/workflow/__init__.py → ...ptychodus/controller/workflow/__init__.py
diff --git a/...odus/controller/workflow/authorization.py → ...odus/controller/workflow/authorization.py b/...odus/controller/workflow/authorization.py → ...odus/controller/workflow/authorization.py
diff --git a/ptychodus/controller/workflow/compute.py → src/ptychodus/controller/workflow/compute.py b/ptychodus/controller/workflow/compute.py → src/ptychodus/controller/workflow/compute.py
diff --git a/ptychodus/controller/workflow/controller.py → ...ychodus/controller/workflow/controller.py b/ptychodus/controller/workflow/controller.py → ...ychodus/controller/workflow/controller.py
diff --git a/ptychodus/controller/workflow/execution.py → ...tychodus/controller/workflow/execution.py b/ptychodus/controller/workflow/execution.py → ...tychodus/controller/workflow/execution.py
diff --git a/ptychodus/controller/workflow/inputData.py → ...tychodus/controller/workflow/inputData.py b/ptychodus/controller/workflow/inputData.py → ...tychodus/controller/workflow/inputData.py
diff --git a/ptychodus/controller/workflow/outputData.py → ...ychodus/controller/workflow/outputData.py b/ptychodus/controller/workflow/outputData.py → ...ychodus/controller/workflow/outputData.py
diff --git a/ptychodus/controller/workflow/status.py → src/ptychodus/controller/workflow/status.py b/ptychodus/controller/workflow/status.py → src/ptychodus/controller/workflow/status.py
diff --git a/ptychodus/controller/workflow/tableModel.py → ...ychodus/controller/workflow/tableModel.py b/ptychodus/controller/workflow/tableModel.py → ...ychodus/controller/workflow/tableModel.py
diff --git a/ptychodus/model/__init__.py → src/ptychodus/model/__init__.py b/ptychodus/model/__init__.py → src/ptychodus/model/__init__.py
diff --git a/ptychodus/model/analysis/__init__.py → src/ptychodus/model/analysis/__init__.py b/ptychodus/model/analysis/__init__.py → src/ptychodus/model/analysis/__init__.py
diff --git a/ptychodus/model/analysis/core.py → src/ptychodus/model/analysis/core.py b/ptychodus/model/analysis/core.py → src/ptychodus/model/analysis/core.py
diff --git a/ptychodus/model/analysis/exposure.py → src/ptychodus/model/analysis/exposure.py b/ptychodus/model/analysis/exposure.py → src/ptychodus/model/analysis/exposure.py
diff --git a/ptychodus/model/analysis/frc.py → src/ptychodus/model/analysis/frc.py b/ptychodus/model/analysis/frc.py → src/ptychodus/model/analysis/frc.py
diff --git a/...odus/model/analysis/objectInterpolator.py → ...odus/model/analysis/objectInterpolator.py b/...odus/model/analysis/objectInterpolator.py → ...odus/model/analysis/objectInterpolator.py
diff --git a/ptychodus/model/analysis/objectStitcher.py → ...tychodus/model/analysis/objectStitcher.py b/ptychodus/model/analysis/objectStitcher.py → ...tychodus/model/analysis/objectStitcher.py
diff --git a/ptychodus/model/analysis/propagator.py → src/ptychodus/model/analysis/propagator.py b/ptychodus/model/analysis/propagator.py → src/ptychodus/model/analysis/propagator.py
diff --git a/ptychodus/model/analysis/settings.py → src/ptychodus/model/analysis/settings.py b/ptychodus/model/analysis/settings.py → src/ptychodus/model/analysis/settings.py
diff --git a/ptychodus/model/analysis/stxm.py → src/ptychodus/model/analysis/stxm.py b/ptychodus/model/analysis/stxm.py → src/ptychodus/model/analysis/stxm.py
diff --git a/ptychodus/model/analysis/xmcd.py → src/ptychodus/model/analysis/xmcd.py b/ptychodus/model/analysis/xmcd.py → src/ptychodus/model/analysis/xmcd.py
diff --git a/ptychodus/model/automation/__init__.py → src/ptychodus/model/automation/__init__.py b/ptychodus/model/automation/__init__.py → src/ptychodus/model/automation/__init__.py
diff --git a/ptychodus/model/automation/buffer.py → src/ptychodus/model/automation/buffer.py b/ptychodus/model/automation/buffer.py → src/ptychodus/model/automation/buffer.py
diff --git a/ptychodus/model/automation/core.py → src/ptychodus/model/automation/core.py b/ptychodus/model/automation/core.py → src/ptychodus/model/automation/core.py
diff --git a/ptychodus/model/automation/processor.py → src/ptychodus/model/automation/processor.py b/ptychodus/model/automation/processor.py → src/ptychodus/model/automation/processor.py
diff --git a/ptychodus/model/automation/repository.py → src/ptychodus/model/automation/repository.py b/ptychodus/model/automation/repository.py → src/ptychodus/model/automation/repository.py
diff --git a/ptychodus/model/automation/settings.py → src/ptychodus/model/automation/settings.py b/ptychodus/model/automation/settings.py → src/ptychodus/model/automation/settings.py
diff --git a/ptychodus/model/automation/watcher.py → src/ptychodus/model/automation/watcher.py b/ptychodus/model/automation/watcher.py → src/ptychodus/model/automation/watcher.py
diff --git a/ptychodus/model/automation/workflow.py → src/ptychodus/model/automation/workflow.py b/ptychodus/model/automation/workflow.py → src/ptychodus/model/automation/workflow.py
diff --git a/ptychodus/model/core.py → src/ptychodus/model/core.py b/ptychodus/model/core.py → src/ptychodus/model/core.py
diff --git a/ptychodus/model/fluorescence/__init__.py → src/ptychodus/model/fluorescence/__init__.py b/ptychodus/model/fluorescence/__init__.py → src/ptychodus/model/fluorescence/__init__.py
diff --git a/ptychodus/model/fluorescence/core.py → src/ptychodus/model/fluorescence/core.py b/ptychodus/model/fluorescence/core.py → src/ptychodus/model/fluorescence/core.py
diff --git a/ptychodus/model/fluorescence/settings.py → src/ptychodus/model/fluorescence/settings.py b/ptychodus/model/fluorescence/settings.py → src/ptychodus/model/fluorescence/settings.py
diff --git a/ptychodus/model/fluorescence/two_step.py → src/ptychodus/model/fluorescence/two_step.py b/ptychodus/model/fluorescence/two_step.py → src/ptychodus/model/fluorescence/two_step.py
diff --git a/ptychodus/model/fluorescence/vspi.py → src/ptychodus/model/fluorescence/vspi.py b/ptychodus/model/fluorescence/vspi.py → src/ptychodus/model/fluorescence/vspi.py
diff --git a/ptychodus/model/memory.py → src/ptychodus/model/memory.py b/ptychodus/model/memory.py → src/ptychodus/model/memory.py
diff --git a/ptychodus/model/patterns/__init__.py → src/ptychodus/model/patterns/__init__.py b/ptychodus/model/patterns/__init__.py → src/ptychodus/model/patterns/__init__.py
diff --git a/ptychodus/model/patterns/active.py → src/ptychodus/model/patterns/active.py b/ptychodus/model/patterns/active.py → src/ptychodus/model/patterns/active.py
diff --git a/ptychodus/model/patterns/api.py → src/ptychodus/model/patterns/api.py b/ptychodus/model/patterns/api.py → src/ptychodus/model/patterns/api.py
diff --git a/ptychodus/model/patterns/builder.py → src/ptychodus/model/patterns/builder.py b/ptychodus/model/patterns/builder.py → src/ptychodus/model/patterns/builder.py
diff --git a/ptychodus/model/patterns/core.py → src/ptychodus/model/patterns/core.py b/ptychodus/model/patterns/core.py → src/ptychodus/model/patterns/core.py
diff --git a/ptychodus/model/patterns/detector.py → src/ptychodus/model/patterns/detector.py b/ptychodus/model/patterns/detector.py → src/ptychodus/model/patterns/detector.py
diff --git a/ptychodus/model/patterns/io.py → src/ptychodus/model/patterns/io.py b/ptychodus/model/patterns/io.py → src/ptychodus/model/patterns/io.py
diff --git a/ptychodus/model/patterns/metadata.py → src/ptychodus/model/patterns/metadata.py b/ptychodus/model/patterns/metadata.py → src/ptychodus/model/patterns/metadata.py
diff --git a/ptychodus/model/patterns/patterns.py → src/ptychodus/model/patterns/patterns.py b/ptychodus/model/patterns/patterns.py → src/ptychodus/model/patterns/patterns.py
diff --git a/ptychodus/model/patterns/settings.py → src/ptychodus/model/patterns/settings.py b/ptychodus/model/patterns/settings.py → src/ptychodus/model/patterns/settings.py
diff --git a/ptychodus/model/patterns/sizer.py → src/ptychodus/model/patterns/sizer.py b/ptychodus/model/patterns/sizer.py → src/ptychodus/model/patterns/sizer.py
diff --git a/ptychodus/model/product/__init__.py → src/ptychodus/model/product/__init__.py b/ptychodus/model/product/__init__.py → src/ptychodus/model/product/__init__.py
diff --git a/ptychodus/model/product/api.py → src/ptychodus/model/product/api.py b/ptychodus/model/product/api.py → src/ptychodus/model/product/api.py
diff --git a/ptychodus/model/product/core.py → src/ptychodus/model/product/core.py b/ptychodus/model/product/core.py → src/ptychodus/model/product/core.py
diff --git a/ptychodus/model/product/item.py → src/ptychodus/model/product/item.py b/ptychodus/model/product/item.py → src/ptychodus/model/product/item.py
diff --git a/ptychodus/model/product/metadata.py → src/ptychodus/model/product/metadata.py b/ptychodus/model/product/metadata.py → src/ptychodus/model/product/metadata.py
diff --git a/ptychodus/model/product/metadataFactory.py → ...tychodus/model/product/metadataFactory.py b/ptychodus/model/product/metadataFactory.py → ...tychodus/model/product/metadataFactory.py
diff --git a/ptychodus/model/product/object/__init__.py → ...tychodus/model/product/object/__init__.py b/ptychodus/model/product/object/__init__.py → ...tychodus/model/product/object/__init__.py
diff --git a/ptychodus/model/product/object/builder.py → ...ptychodus/model/product/object/builder.py b/ptychodus/model/product/object/builder.py → ...ptychodus/model/product/object/builder.py
diff --git a/...us/model/product/object/builderFactory.py → ...us/model/product/object/builderFactory.py b/...us/model/product/object/builderFactory.py → ...us/model/product/object/builderFactory.py
diff --git a/ptychodus/model/product/object/item.py → src/ptychodus/model/product/object/item.py b/ptychodus/model/product/object/item.py → src/ptychodus/model/product/object/item.py
diff --git a/...hodus/model/product/object/itemFactory.py → ...hodus/model/product/object/itemFactory.py b/...hodus/model/product/object/itemFactory.py → ...hodus/model/product/object/itemFactory.py
diff --git a/ptychodus/model/product/object/random.py → src/ptychodus/model/product/object/random.py b/ptychodus/model/product/object/random.py → src/ptychodus/model/product/object/random.py
diff --git a/ptychodus/model/product/object/settings.py → ...tychodus/model/product/object/settings.py b/ptychodus/model/product/object/settings.py → ...tychodus/model/product/object/settings.py
diff --git a/ptychodus/model/product/objectRepository.py → ...ychodus/model/product/objectRepository.py b/ptychodus/model/product/objectRepository.py → ...ychodus/model/product/objectRepository.py
diff --git a/ptychodus/model/product/probe/__init__.py → ...ptychodus/model/product/probe/__init__.py b/ptychodus/model/product/probe/__init__.py → ...ptychodus/model/product/probe/__init__.py
diff --git a/...dus/model/product/probe/averagePattern.py → ...dus/model/product/probe/averagePattern.py b/...dus/model/product/probe/averagePattern.py → ...dus/model/product/probe/averagePattern.py
diff --git a/ptychodus/model/product/probe/builder.py → src/ptychodus/model/product/probe/builder.py b/ptychodus/model/product/probe/builder.py → src/ptychodus/model/product/probe/builder.py
diff --git a/...dus/model/product/probe/builderFactory.py → ...dus/model/product/probe/builderFactory.py b/...dus/model/product/probe/builderFactory.py → ...dus/model/product/probe/builderFactory.py
diff --git a/ptychodus/model/product/probe/disk.py → src/ptychodus/model/product/probe/disk.py b/ptychodus/model/product/probe/disk.py → src/ptychodus/model/product/probe/disk.py
diff --git a/ptychodus/model/product/probe/fzp.py → src/ptychodus/model/product/probe/fzp.py b/ptychodus/model/product/probe/fzp.py → src/ptychodus/model/product/probe/fzp.py
diff --git a/ptychodus/model/product/probe/item.py → src/ptychodus/model/product/probe/item.py b/ptychodus/model/product/probe/item.py → src/ptychodus/model/product/probe/item.py
diff --git a/ptychodus/model/product/probe/itemFactory.py → ...chodus/model/product/probe/itemFactory.py b/ptychodus/model/product/probe/itemFactory.py → ...chodus/model/product/probe/itemFactory.py
diff --git a/ptychodus/model/product/probe/multimodal.py → ...ychodus/model/product/probe/multimodal.py b/ptychodus/model/product/probe/multimodal.py → ...ychodus/model/product/probe/multimodal.py
diff --git a/ptychodus/model/product/probe/rect.py → src/ptychodus/model/product/probe/rect.py b/ptychodus/model/product/probe/rect.py → src/ptychodus/model/product/probe/rect.py
diff --git a/ptychodus/model/product/probe/settings.py → ...ptychodus/model/product/probe/settings.py b/ptychodus/model/product/probe/settings.py → ...ptychodus/model/product/probe/settings.py
diff --git a/...odus/model/product/probe/superGaussian.py → ...odus/model/product/probe/superGaussian.py b/...odus/model/product/probe/superGaussian.py → ...odus/model/product/probe/superGaussian.py
diff --git a/ptychodus/model/product/probe/zernike.py → src/ptychodus/model/product/probe/zernike.py b/ptychodus/model/product/probe/zernike.py → src/ptychodus/model/product/probe/zernike.py
diff --git a/ptychodus/model/product/probeRepository.py → ...tychodus/model/product/probeRepository.py b/ptychodus/model/product/probeRepository.py → ...tychodus/model/product/probeRepository.py
diff --git a/ptychodus/model/product/productGeometry.py → ...tychodus/model/product/productGeometry.py b/ptychodus/model/product/productGeometry.py → ...tychodus/model/product/productGeometry.py
diff --git a/ptychodus/model/product/productRepository.py → ...chodus/model/product/productRepository.py b/ptychodus/model/product/productRepository.py → ...chodus/model/product/productRepository.py
diff --git a/ptychodus/model/product/productValidator.py → ...ychodus/model/product/productValidator.py b/ptychodus/model/product/productValidator.py → ...ychodus/model/product/productValidator.py
diff --git a/ptychodus/model/product/scan/__init__.py → src/ptychodus/model/product/scan/__init__.py b/ptychodus/model/product/scan/__init__.py → src/ptychodus/model/product/scan/__init__.py
diff --git a/ptychodus/model/product/scan/boundingBox.py → ...ychodus/model/product/scan/boundingBox.py b/ptychodus/model/product/scan/boundingBox.py → ...ychodus/model/product/scan/boundingBox.py
diff --git a/ptychodus/model/product/scan/builder.py → src/ptychodus/model/product/scan/builder.py b/ptychodus/model/product/scan/builder.py → src/ptychodus/model/product/scan/builder.py
diff --git a/...odus/model/product/scan/builderFactory.py → ...odus/model/product/scan/builderFactory.py b/...odus/model/product/scan/builderFactory.py → ...odus/model/product/scan/builderFactory.py
diff --git a/ptychodus/model/product/scan/cartesian.py → ...ptychodus/model/product/scan/cartesian.py b/ptychodus/model/product/scan/cartesian.py → ...ptychodus/model/product/scan/cartesian.py
diff --git a/ptychodus/model/product/scan/concentric.py → ...tychodus/model/product/scan/concentric.py b/ptychodus/model/product/scan/concentric.py → ...tychodus/model/product/scan/concentric.py
diff --git a/ptychodus/model/product/scan/item.py → src/ptychodus/model/product/scan/item.py b/ptychodus/model/product/scan/item.py → src/ptychodus/model/product/scan/item.py
diff --git a/ptychodus/model/product/scan/itemFactory.py → ...ychodus/model/product/scan/itemFactory.py b/ptychodus/model/product/scan/itemFactory.py → ...ychodus/model/product/scan/itemFactory.py
diff --git a/ptychodus/model/product/scan/lissajous.py → ...ptychodus/model/product/scan/lissajous.py b/ptychodus/model/product/scan/lissajous.py → ...ptychodus/model/product/scan/lissajous.py
diff --git a/ptychodus/model/product/scan/settings.py → src/ptychodus/model/product/scan/settings.py b/ptychodus/model/product/scan/settings.py → src/ptychodus/model/product/scan/settings.py
diff --git a/ptychodus/model/product/scan/spiral.py → src/ptychodus/model/product/scan/spiral.py b/ptychodus/model/product/scan/spiral.py → src/ptychodus/model/product/scan/spiral.py
diff --git a/ptychodus/model/product/scan/streaming.py → ...ptychodus/model/product/scan/streaming.py b/ptychodus/model/product/scan/streaming.py → ...ptychodus/model/product/scan/streaming.py
diff --git a/ptychodus/model/product/scan/transform.py → ...ptychodus/model/product/scan/transform.py b/ptychodus/model/product/scan/transform.py → ...ptychodus/model/product/scan/transform.py
diff --git a/ptychodus/model/product/scanRepository.py → ...ptychodus/model/product/scanRepository.py b/ptychodus/model/product/scanRepository.py → ...ptychodus/model/product/scanRepository.py
diff --git a/ptychodus/model/ptychonn/__init__.py → src/ptychodus/model/ptychonn/__init__.py b/ptychodus/model/ptychonn/__init__.py → src/ptychodus/model/ptychonn/__init__.py
diff --git a/ptychodus/model/ptychonn/buffers.py → src/ptychodus/model/ptychonn/buffers.py b/ptychodus/model/ptychonn/buffers.py → src/ptychodus/model/ptychonn/buffers.py
diff --git a/ptychodus/model/ptychonn/common.py → src/ptychodus/model/ptychonn/common.py b/ptychodus/model/ptychonn/common.py → src/ptychodus/model/ptychonn/common.py
diff --git a/ptychodus/model/ptychonn/core.py → src/ptychodus/model/ptychonn/core.py b/ptychodus/model/ptychonn/core.py → src/ptychodus/model/ptychonn/core.py
diff --git a/ptychodus/model/ptychonn/model.py → src/ptychodus/model/ptychonn/model.py b/ptychodus/model/ptychonn/model.py → src/ptychodus/model/ptychonn/model.py
diff --git a/ptychodus/model/ptychonn/reconstructor.py → ...ptychodus/model/ptychonn/reconstructor.py b/ptychodus/model/ptychonn/reconstructor.py → ...ptychodus/model/ptychonn/reconstructor.py
diff --git a/ptychodus/model/ptychonn/settings.py → src/ptychodus/model/ptychonn/settings.py b/ptychodus/model/ptychonn/settings.py → src/ptychodus/model/ptychonn/settings.py
diff --git a/ptychodus/model/reconstructor/__init__.py → ...ptychodus/model/reconstructor/__init__.py b/ptychodus/model/reconstructor/__init__.py → ...ptychodus/model/reconstructor/__init__.py
diff --git a/ptychodus/model/reconstructor/api.py → src/ptychodus/model/reconstructor/api.py b/ptychodus/model/reconstructor/api.py → src/ptychodus/model/reconstructor/api.py
diff --git a/ptychodus/model/reconstructor/core.py → src/ptychodus/model/reconstructor/core.py b/ptychodus/model/reconstructor/core.py → src/ptychodus/model/reconstructor/core.py
diff --git a/ptychodus/model/reconstructor/matcher.py → src/ptychodus/model/reconstructor/matcher.py b/ptychodus/model/reconstructor/matcher.py → src/ptychodus/model/reconstructor/matcher.py
diff --git a/ptychodus/model/reconstructor/presenter.py → ...tychodus/model/reconstructor/presenter.py b/ptychodus/model/reconstructor/presenter.py → ...tychodus/model/reconstructor/presenter.py
diff --git a/ptychodus/model/reconstructor/settings.py → ...ptychodus/model/reconstructor/settings.py b/ptychodus/model/reconstructor/settings.py → ...ptychodus/model/reconstructor/settings.py
diff --git a/ptychodus/model/tike/__init__.py → src/ptychodus/model/tike/__init__.py b/ptychodus/model/tike/__init__.py → src/ptychodus/model/tike/__init__.py
diff --git a/ptychodus/model/tike/core.py → src/ptychodus/model/tike/core.py b/ptychodus/model/tike/core.py → src/ptychodus/model/tike/core.py
diff --git a/ptychodus/model/tike/reconstructor.py → src/ptychodus/model/tike/reconstructor.py b/ptychodus/model/tike/reconstructor.py → src/ptychodus/model/tike/reconstructor.py
diff --git a/ptychodus/model/tike/settings.py → src/ptychodus/model/tike/settings.py b/ptychodus/model/tike/settings.py → src/ptychodus/model/tike/settings.py
diff --git a/ptychodus/model/visualization/__init__.py → ...ptychodus/model/visualization/__init__.py b/ptychodus/model/visualization/__init__.py → ...ptychodus/model/visualization/__init__.py
diff --git a/ptychodus/model/visualization/colorAxis.py → ...tychodus/model/visualization/colorAxis.py b/ptychodus/model/visualization/colorAxis.py → ...tychodus/model/visualization/colorAxis.py
diff --git a/ptychodus/model/visualization/colorModel.py → ...ychodus/model/visualization/colorModel.py b/ptychodus/model/visualization/colorModel.py → ...ychodus/model/visualization/colorModel.py
diff --git a/...model/visualization/colorModelRenderer.py → ...model/visualization/colorModelRenderer.py b/...model/visualization/colorModelRenderer.py → ...model/visualization/colorModelRenderer.py
diff --git a/ptychodus/model/visualization/colormap.py → ...ptychodus/model/visualization/colormap.py b/ptychodus/model/visualization/colormap.py → ...ptychodus/model/visualization/colormap.py
diff --git a/...s/model/visualization/colormapRenderer.py → ...s/model/visualization/colormapRenderer.py b/...s/model/visualization/colormapRenderer.py → ...s/model/visualization/colormapRenderer.py
diff --git a/ptychodus/model/visualization/components.py → ...ychodus/model/visualization/components.py b/ptychodus/model/visualization/components.py → ...ychodus/model/visualization/components.py
diff --git a/ptychodus/model/visualization/core.py → src/ptychodus/model/visualization/core.py b/ptychodus/model/visualization/core.py → src/ptychodus/model/visualization/core.py
diff --git a/ptychodus/model/visualization/renderer.py → ...ptychodus/model/visualization/renderer.py b/ptychodus/model/visualization/renderer.py → ...ptychodus/model/visualization/renderer.py
diff --git a/...dus/model/visualization/transformation.py → ...dus/model/visualization/transformation.py b/...dus/model/visualization/transformation.py → ...dus/model/visualization/transformation.py
diff --git a/ptychodus/model/workflow/__init__.py → src/ptychodus/model/workflow/__init__.py b/ptychodus/model/workflow/__init__.py → src/ptychodus/model/workflow/__init__.py
diff --git a/ptychodus/model/workflow/api.py → src/ptychodus/model/workflow/api.py b/ptychodus/model/workflow/api.py → src/ptychodus/model/workflow/api.py
diff --git a/ptychodus/model/workflow/authorizer.py → src/ptychodus/model/workflow/authorizer.py b/ptychodus/model/workflow/authorizer.py → src/ptychodus/model/workflow/authorizer.py
diff --git a/ptychodus/model/workflow/core.py → src/ptychodus/model/workflow/core.py b/ptychodus/model/workflow/core.py → src/ptychodus/model/workflow/core.py
diff --git a/ptychodus/model/workflow/executor.py → src/ptychodus/model/workflow/executor.py b/ptychodus/model/workflow/executor.py → src/ptychodus/model/workflow/executor.py
diff --git a/ptychodus/model/workflow/globus.py → src/ptychodus/model/workflow/globus.py b/ptychodus/model/workflow/globus.py → src/ptychodus/model/workflow/globus.py
diff --git a/ptychodus/model/workflow/locator.py → src/ptychodus/model/workflow/locator.py b/ptychodus/model/workflow/locator.py → src/ptychodus/model/workflow/locator.py
diff --git a/ptychodus/model/workflow/settings.py → src/ptychodus/model/workflow/settings.py b/ptychodus/model/workflow/settings.py → src/ptychodus/model/workflow/settings.py
diff --git a/ptychodus/model/workflow/status.py → src/ptychodus/model/workflow/status.py b/ptychodus/model/workflow/status.py → src/ptychodus/model/workflow/status.py
diff --git a/ptychodus/plugins/aps2idDiffractionFile.py → ...tychodus/plugins/aps2idDiffractionFile.py b/ptychodus/plugins/aps2idDiffractionFile.py → ...tychodus/plugins/aps2idDiffractionFile.py
diff --git a/ptychodus/plugins/csvObjectFile.py → src/ptychodus/plugins/csvObjectFile.py b/ptychodus/plugins/csvObjectFile.py → src/ptychodus/plugins/csvObjectFile.py
diff --git a/ptychodus/plugins/csvProbeFile.py → src/ptychodus/plugins/csvProbeFile.py b/ptychodus/plugins/csvProbeFile.py → src/ptychodus/plugins/csvProbeFile.py
diff --git a/ptychodus/plugins/cxiDiffractionFile.py → src/ptychodus/plugins/cxiDiffractionFile.py b/ptychodus/plugins/cxiDiffractionFile.py → src/ptychodus/plugins/cxiDiffractionFile.py
diff --git a/ptychodus/plugins/cxiProbeFile.py → src/ptychodus/plugins/cxiProbeFile.py b/ptychodus/plugins/cxiProbeFile.py → src/ptychodus/plugins/cxiProbeFile.py
diff --git a/ptychodus/plugins/cxiScanFile.py → src/ptychodus/plugins/cxiScanFile.py b/ptychodus/plugins/cxiScanFile.py → src/ptychodus/plugins/cxiScanFile.py
diff --git a/ptychodus/plugins/deconvolution.py → src/ptychodus/plugins/deconvolution.py b/ptychodus/plugins/deconvolution.py → src/ptychodus/plugins/deconvolution.py
diff --git a/ptychodus/plugins/delimitedScanFile.py → src/ptychodus/plugins/delimitedScanFile.py b/ptychodus/plugins/delimitedScanFile.py → src/ptychodus/plugins/delimitedScanFile.py
diff --git a/ptychodus/plugins/fresnelZonePlate.py → src/ptychodus/plugins/fresnelZonePlate.py b/ptychodus/plugins/fresnelZonePlate.py → src/ptychodus/plugins/fresnelZonePlate.py
diff --git a/ptychodus/plugins/h5DiffractionFile.py → src/ptychodus/plugins/h5DiffractionFile.py b/ptychodus/plugins/h5DiffractionFile.py → src/ptychodus/plugins/h5DiffractionFile.py
diff --git a/ptychodus/plugins/h5ProductFile.py → src/ptychodus/plugins/h5ProductFile.py b/ptychodus/plugins/h5ProductFile.py → src/ptychodus/plugins/h5ProductFile.py
diff --git a/ptychodus/plugins/lclsFileReaders.py → src/ptychodus/plugins/lclsFileReaders.py b/ptychodus/plugins/lclsFileReaders.py → src/ptychodus/plugins/lclsFileReaders.py
diff --git a/ptychodus/plugins/lynxDiffractionFile.py → src/ptychodus/plugins/lynxDiffractionFile.py b/ptychodus/plugins/lynxDiffractionFile.py → src/ptychodus/plugins/lynxDiffractionFile.py
diff --git a/ptychodus/plugins/lynxOrchestraScanFile.py → ...tychodus/plugins/lynxOrchestraScanFile.py b/ptychodus/plugins/lynxOrchestraScanFile.py → ...tychodus/plugins/lynxOrchestraScanFile.py
diff --git a/...hodus/plugins/lynxSoftGlueZynqScanFile.py → ...hodus/plugins/lynxSoftGlueZynqScanFile.py b/...hodus/plugins/lynxSoftGlueZynqScanFile.py → ...hodus/plugins/lynxSoftGlueZynqScanFile.py
diff --git a/ptychodus/plugins/matObjectFile.py → src/ptychodus/plugins/matObjectFile.py b/ptychodus/plugins/matObjectFile.py → src/ptychodus/plugins/matObjectFile.py
diff --git a/ptychodus/plugins/matProbeFile.py → src/ptychodus/plugins/matProbeFile.py b/ptychodus/plugins/matProbeFile.py → src/ptychodus/plugins/matProbeFile.py
diff --git a/ptychodus/plugins/mdaScanFile.py → src/ptychodus/plugins/mdaScanFile.py b/ptychodus/plugins/mdaScanFile.py → src/ptychodus/plugins/mdaScanFile.py
diff --git a/ptychodus/plugins/nanoMaxScanFile.py → src/ptychodus/plugins/nanoMaxScanFile.py b/ptychodus/plugins/nanoMaxScanFile.py → src/ptychodus/plugins/nanoMaxScanFile.py
diff --git a/ptychodus/plugins/neXus/__init__.py → src/ptychodus/plugins/neXus/__init__.py b/ptychodus/plugins/neXus/__init__.py → src/ptychodus/plugins/neXus/__init__.py
diff --git a/...dus/plugins/neXus/neXusDiffractionFile.py → ...dus/plugins/neXus/neXusDiffractionFile.py b/...dus/plugins/neXus/neXusDiffractionFile.py → ...dus/plugins/neXus/neXusDiffractionFile.py
diff --git a/...odus/plugins/neXus/velociprobeScanFile.py → ...odus/plugins/neXus/velociprobeScanFile.py b/...odus/plugins/neXus/velociprobeScanFile.py → ...odus/plugins/neXus/velociprobeScanFile.py
diff --git a/ptychodus/plugins/npyDiffractionFile.py → src/ptychodus/plugins/npyDiffractionFile.py b/ptychodus/plugins/npyDiffractionFile.py → src/ptychodus/plugins/npyDiffractionFile.py
diff --git a/ptychodus/plugins/npyObjectFile.py → src/ptychodus/plugins/npyObjectFile.py b/ptychodus/plugins/npyObjectFile.py → src/ptychodus/plugins/npyObjectFile.py
diff --git a/ptychodus/plugins/npyProbeFile.py → src/ptychodus/plugins/npyProbeFile.py b/ptychodus/plugins/npyProbeFile.py → src/ptychodus/plugins/npyProbeFile.py
diff --git a/ptychodus/plugins/npzDiffractionFile.py → src/ptychodus/plugins/npzDiffractionFile.py b/ptychodus/plugins/npzDiffractionFile.py → src/ptychodus/plugins/npzDiffractionFile.py
diff --git a/ptychodus/plugins/npzProductFile.py → src/ptychodus/plugins/npzProductFile.py b/ptychodus/plugins/npzProductFile.py → src/ptychodus/plugins/npzProductFile.py
diff --git a/ptychodus/plugins/objectPhaseCentering.py → ...ptychodus/plugins/objectPhaseCentering.py b/ptychodus/plugins/objectPhaseCentering.py → ...ptychodus/plugins/objectPhaseCentering.py
diff --git a/...hodus/plugins/ptychoShelvesProductFile.py → ...hodus/plugins/ptychoShelvesProductFile.py b/...hodus/plugins/ptychoShelvesProductFile.py → ...hodus/plugins/ptychoShelvesProductFile.py
diff --git a/ptychodus/plugins/ptychoShelvesScanFile.py → ...tychodus/plugins/ptychoShelvesScanFile.py b/ptychodus/plugins/ptychoShelvesScanFile.py → ...tychodus/plugins/ptychoShelvesScanFile.py
diff --git a/ptychodus/plugins/tiffDiffractionFile.py → src/ptychodus/plugins/tiffDiffractionFile.py b/ptychodus/plugins/tiffDiffractionFile.py → src/ptychodus/plugins/tiffDiffractionFile.py
diff --git a/ptychodus/plugins/upscaling.py → src/ptychodus/plugins/upscaling.py b/ptychodus/plugins/upscaling.py → src/ptychodus/plugins/upscaling.py
diff --git a/ptychodus/plugins/workflow.py → src/ptychodus/plugins/workflow.py b/ptychodus/plugins/workflow.py → src/ptychodus/plugins/workflow.py
diff --git a/ptychodus/plugins/xrfMapsFile.py → src/ptychodus/plugins/xrfMapsFile.py b/ptychodus/plugins/xrfMapsFile.py → src/ptychodus/plugins/xrfMapsFile.py
diff --git a/ptychodus/ptychodusAdImageProcessor.py → src/ptychodus/ptychodusAdImageProcessor.py b/ptychodus/ptychodusAdImageProcessor.py → src/ptychodus/ptychodusAdImageProcessor.py
diff --git a/ptychodus/ptychodusFuncXPolarisConfig.py → src/ptychodus/ptychodusFuncXPolarisConfig.py b/ptychodus/ptychodusFuncXPolarisConfig.py → src/ptychodus/ptychodusFuncXPolarisConfig.py
diff --git a/ptychodus/ptychodus_bdp.py → src/ptychodus/ptychodus_bdp.py b/ptychodus/ptychodus_bdp.py → src/ptychodus/ptychodus_bdp.py
diff --git a/ptychodus/view/__init__.py → src/ptychodus/view/__init__.py b/ptychodus/view/__init__.py → src/ptychodus/view/__init__.py
diff --git a/ptychodus/view/automation.py → src/ptychodus/view/automation.py b/ptychodus/view/automation.py → src/ptychodus/view/automation.py
diff --git a/ptychodus/view/core.py → src/ptychodus/view/core.py b/ptychodus/view/core.py → src/ptychodus/view/core.py
diff --git a/ptychodus/view/image.py → src/ptychodus/view/image.py b/ptychodus/view/image.py → src/ptychodus/view/image.py
diff --git a/ptychodus/view/make_qrc.sh → src/ptychodus/view/make_qrc.sh b/ptychodus/view/make_qrc.sh → src/ptychodus/view/make_qrc.sh
diff --git a/ptychodus/view/object.py → src/ptychodus/view/object.py b/ptychodus/view/object.py → src/ptychodus/view/object.py
diff --git a/ptychodus/view/patterns.py → src/ptychodus/view/patterns.py b/ptychodus/view/patterns.py → src/ptychodus/view/patterns.py
diff --git a/ptychodus/view/probe.py → src/ptychodus/view/probe.py b/ptychodus/view/probe.py → src/ptychodus/view/probe.py
diff --git a/ptychodus/view/product.py → src/ptychodus/view/product.py b/ptychodus/view/product.py → src/ptychodus/view/product.py
diff --git a/ptychodus/view/ptychodus.svg → src/ptychodus/view/ptychodus.svg b/ptychodus/view/ptychodus.svg → src/ptychodus/view/ptychodus.svg
diff --git a/ptychodus/view/ptychonn.py → src/ptychodus/view/ptychonn.py b/ptychodus/view/ptychonn.py → src/ptychodus/view/ptychonn.py
diff --git a/ptychodus/view/reconstructor.py → src/ptychodus/view/reconstructor.py b/ptychodus/view/reconstructor.py → src/ptychodus/view/reconstructor.py
diff --git a/ptychodus/view/repository.py → src/ptychodus/view/repository.py b/ptychodus/view/repository.py → src/ptychodus/view/repository.py
diff --git a/ptychodus/view/resources.py → src/ptychodus/view/resources.py b/ptychodus/view/resources.py → src/ptychodus/view/resources.py
diff --git a/ptychodus/view/resources.qrc → src/ptychodus/view/resources.qrc b/ptychodus/view/resources.qrc → src/ptychodus/view/resources.qrc
diff --git a/ptychodus/view/scan.py → src/ptychodus/view/scan.py b/ptychodus/view/scan.py → src/ptychodus/view/scan.py
diff --git a/ptychodus/view/settings.py → src/ptychodus/view/settings.py b/ptychodus/view/settings.py → src/ptychodus/view/settings.py
diff --git a/ptychodus/view/test.py → src/ptychodus/view/test.py b/ptychodus/view/test.py → src/ptychodus/view/test.py
diff --git a/ptychodus/view/visualization.py → src/ptychodus/view/visualization.py b/ptychodus/view/visualization.py → src/ptychodus/view/visualization.py
diff --git a/ptychodus/view/widgets/__init__.py → src/ptychodus/view/widgets/__init__.py b/ptychodus/view/widgets/__init__.py → src/ptychodus/view/widgets/__init__.py
diff --git a/ptychodus/view/widgets/angleWidget.py → src/ptychodus/view/widgets/angleWidget.py b/ptychodus/view/widgets/angleWidget.py → src/ptychodus/view/widgets/angleWidget.py
diff --git a/...odus/view/widgets/comboBoxItemDelegate.py → ...odus/view/widgets/comboBoxItemDelegate.py b/...odus/view/widgets/comboBoxItemDelegate.py → ...odus/view/widgets/comboBoxItemDelegate.py
diff --git a/ptychodus/view/widgets/decimalLineEdit.py → ...ptychodus/view/widgets/decimalLineEdit.py b/ptychodus/view/widgets/decimalLineEdit.py → ...ptychodus/view/widgets/decimalLineEdit.py
diff --git a/ptychodus/view/widgets/decimalSlider.py → src/ptychodus/view/widgets/decimalSlider.py b/ptychodus/view/widgets/decimalSlider.py → src/ptychodus/view/widgets/decimalSlider.py
diff --git a/ptychodus/view/widgets/exceptionDialog.py → ...ptychodus/view/widgets/exceptionDialog.py b/ptychodus/view/widgets/exceptionDialog.py → ...ptychodus/view/widgets/exceptionDialog.py
diff --git a/ptychodus/view/widgets/groupBox.py → src/ptychodus/view/widgets/groupBox.py b/ptychodus/view/widgets/groupBox.py → src/ptychodus/view/widgets/groupBox.py
diff --git a/ptychodus/view/widgets/lengthWidget.py → src/ptychodus/view/widgets/lengthWidget.py b/ptychodus/view/widgets/lengthWidget.py → src/ptychodus/view/widgets/lengthWidget.py
diff --git a/...s/view/widgets/progressBarItemDelegate.py → ...s/view/widgets/progressBarItemDelegate.py b/...s/view/widgets/progressBarItemDelegate.py → ...s/view/widgets/progressBarItemDelegate.py
diff --git a/ptychodus/view/widgets/uuidLineEdit.py → src/ptychodus/view/widgets/uuidLineEdit.py b/ptychodus/view/widgets/uuidLineEdit.py → src/ptychodus/view/widgets/uuidLineEdit.py
diff --git a/ptychodus/view/workflow.py → src/ptychodus/view/workflow.py b/ptychodus/view/workflow.py → src/ptychodus/view/workflow.py