skpkg: migrate src folder, migrate test folder

src/diffpy/__init__.py

@@ -1,18 +1,14 @@
 #!/usr/bin/env python
 ##############################################################################
 #
-# dpx.pdfgetxgui    by Simon J. L. Billinge group
-#                   (c) 2012 Trustees of the Columbia University
-#                   in the City of New York.  All rights reserved.
+# (c) 2012-2025 The Trustees of Columbia University in the City of New York.
+# All rights reserved.
 #
-# File coded by:    Xiaohao Yang
+# File coded by: Xiaohao Yang and Billinge Group members.
 #
-# See AUTHORS.txt for a list of people who contributed.
-# See LICENSE.txt for license information.
+# See GitHub contributions for a more detailed list of contributors.
+# https://github.com/diffpy/diffpy.srxplanargui/graphs/contributors
+#
+# See LICENSE.rst for license information.
 #
 ##############################################################################
-"""Blank namespace package."""
-
-__import__("pkg_resources").declare_namespace(__name__)
-
-# End of file

src/diffpy/srxplanargui/__init__.py

@@ -1,19 +1,23 @@
 #!/usr/bin/env python
 ##############################################################################
 #
-# dpx.pdfgetxgui    by Simon J. L. Billinge group
-#                   (c) 2012 Trustees of the Columbia University
-#                   in the City of New York.  All rights reserved.
+# (c) 2012-2025 The Trustees of Columbia University in the City of New York.
+# All rights reserved.
 #
-# File coded by:    Xiaohao Yang
+# File coded by: Xiaohao Yang, Billinge Group members.
 #
-# See AUTHORS.txt for a list of people who contributed.
-# See LICENSE.txt for license information.
+# See GitHub contributions for a more detailed list of contributors.
+# https://github.com/diffpy/diffpy.srxplanargui/graphs/contributors
+#
+# See LICENSE.rst for license information.
 #
 ##############################################################################
+"""xPDFsuite, a software for PDF transformation and visualization."""
 
+# package version
+from diffpy.srxplanargui.version import __version__  # noqa
 
-# obtain version information
-# from diffpy.srxplanargui.version import __version__
+# silence the pyflakes syntax checker
+assert __version__ or True
 
 # End of file

src/diffpy/srxplanargui/imageplot.py

@@ -101,38 +101,50 @@ class ImagePlot(HasTraits):
     )
     avgmask = DelegatesTo(
         "srxconfig",
-        desc=("Mask the pixels too bright or too dark compared to"
-              " the average intensity at the similar diffraction angle"),
+        desc=(
+            "Mask the pixels too bright or too dark compared to"
+            " the average intensity at the similar diffraction angle"
+        ),
     )
     brightpixelr = DelegatesTo(
         "srxconfig",
-        desc=("Pixels with intensity large than this relative threshold"
-              " (times the local environment) value will be masked"),
+        desc=(
+            "Pixels with intensity large than this relative threshold"
+            " (times the local environment) value will be masked"
+        ),
     )
     brightpixelsize = DelegatesTo(
         "srxconfig", desc="Size of testing area for detecting bright pixels"
     )
     darkpixelr = DelegatesTo(
         "srxconfig",
-        desc=("Pixels with intensity less than this relative threshold"
-              " (times the local environment) value will be masked"),
+        desc=(
+            "Pixels with intensity less than this relative threshold"
+            " (times the local environment) value will be masked"
+        ),
     )
     avgmaskhigh = DelegatesTo(
         "srxconfig",
-        desc=("Comparing to the average intensity at "
-              "similar diffraction angle, \npixels with intensity larger than"
-              " avg_int*high will be masked"),
+        desc=(
+            "Comparing to the average intensity at "
+            "similar diffraction angle, \npixels with intensity larger than"
+            " avg_int*high will be masked"
+        ),
     )
     avgmasklow = DelegatesTo(
         "srxconfig",
-        desc=("Comparing to the average intensity at "
-              "similar diffraction angle, \npixels with intensity less than "
-              "avg_int*low will be masked"),
+        desc=(
+            "Comparing to the average intensity at "
+            "similar diffraction angle, \npixels with intensity less than "
+            "avg_int*low will be masked"
+        ),
     )
     cropedges = DelegatesTo(
         "srxconfig",
-        desc=("The number of pixels masked"
-              " at each edge (left, right, top, bottom)"),
+        desc=(
+            "The number of pixels masked"
+            " at each edge (left, right, top, bottom)"
+        ),
     )
 
     def createPlot(self):
@@ -231,7 +243,7 @@ def addPointMask(self, ndx, remove=None):
         """Param ndx -- (x,y) float."""
         x, y = ndx
         r = self.pts - np.array((x, y))
-        r = np.sum(r ** 2, axis=1)
+        r = np.sum(r**2, axis=1)
         mask = r < ((self.pointmaskradius + 1) ** 2)
         mask = mask.reshape(self.staticmask.shape)
         if remove:
@@ -318,9 +330,11 @@ def _enableMaskEditing(self):
             self.plot.tools.remove(self.pan)
         self.plot.overlays.append(self.lstool)
         self.titlebak = self.plot.title
-        self.plot.title = ("Click: add a vertex; "
-                           "<Ctrl>+Click: remove a vertex; \n          "
-                           "<Enter>: finish the selection")
+        self.plot.title = (
+            "Click: add a vertex; "
+            "<Ctrl>+Click: remove a vertex; \n          "
+            "<Enter>: finish the selection"
+        )
         return
 
     def _disableMaskEditing(self):

src/diffpy/srxplanargui/srxplanargui_app.py

@@ -0,0 +1,33 @@
+import argparse
+
+from diffpy.srxplanargui.version import __version__  # noqa
+
+
+def main():
+    parser = argparse.ArgumentParser(
+        prog="diffpy.srxplanargui",
+        description=(
+            "xPDFsuite, a software for PDF transformation and visualization.\n\n"
+            "For more information, visit: "
+            "https://github.com/diffpy/diffpy.srxplanargui/"
+        ),
+        formatter_class=argparse.RawDescriptionHelpFormatter,
+    )
+
+    parser.add_argument(
+        "--version",
+        action="store_true",
+        help="Show the program's version number and exit",
+    )
+
+    args = parser.parse_args()
+
+    if args.version:
+        print(f"diffpy.srxplanargui {__version__}")
+    else:
+        # Default behavior when no arguments are given
+        parser.print_help()
+
+
+if __name__ == "__main__":
+    main()

src/diffpy/srxplanargui/version.py

@@ -1,28 +1,26 @@
 #!/usr/bin/env python
 ##############################################################################
 #
-# diffpy.srxplanar  by DANSE Diffraction group
-#                   Simon J. L. Billinge
-#                   (c) 2010 Trustees of the Columbia University
-#                   in the City of New York.  All rights reserved.
+# (c) 2012-2025 The Trustees of Columbia University in the City of New York.
+# All rights reserved.
 #
-# File coded by:    Xiaohao Yang
+# File coded by: Xiaohao Yang, Billinge Group members.
 #
-# See AUTHORS.txt for a list of people who contributed.
-# See LICENSENOTICE.txt for license information.
+# See GitHub contributions for a more detailed list of contributors.
+# https://github.com/diffpy/diffpy.srxplanargui/graphs/contributors  # noqa: E501
+#
+# See LICENSE.rst for license information.
 #
 ##############################################################################
-"""Definition of __version__ and __date__ for this package."""
-
-# obtain version information
-from pkg_resources import get_distribution
+"""Definition of __version__."""
 
-_pkgname = __name__.rsplit(".", 1)[0]
-__version__ = get_distribution(_pkgname).version
+#  We do not use the other three variables, but can be added back if needed.
+#  __all__ = ["__date__", "__git_commit__", "__timestamp__", "__version__"]
 
-# we assume that tag_date was used and __version__ ends in YYYYMMDD
-__date__ = (
-    __version__[-8:-4] + "-" + __version__[-4:-2] + "-" + __version__[-2:]
-)
+# obtain version information
+from importlib.metadata import PackageNotFoundError, version
 
-# End of file
+try:
+    __version__ = version("diffpy.srxplanargui")
+except PackageNotFoundError:
+    __version__ = "unknown"

tests/conftest.py

@@ -0,0 +1,19 @@
+import json
+from pathlib import Path
+
+import pytest
+
+
+@pytest.fixture
+def user_filesystem(tmp_path):
+    base_dir = Path(tmp_path)
+    home_dir = base_dir / "home_dir"
+    home_dir.mkdir(parents=True, exist_ok=True)
+    cwd_dir = base_dir / "cwd_dir"
+    cwd_dir.mkdir(parents=True, exist_ok=True)
+
+    home_config_data = {"username": "home_username", "email": "home@email.com"}
+    with open(home_dir / "diffpyconfig.json", "w") as f:
+        json.dump(home_config_data, f)
+
+    yield tmp_path

tests/test_version.py

@@ -0,0 +1,10 @@
+"""Unit tests for __version__.py."""
+
+import diffpy.srxplanargui  # noqa
+
+
+def test_package_version():
+    """Ensure the package version is defined and not set to the initial
+    placeholder."""
+    assert hasattr(diffpy.srxplanargui, "__version__")
+    assert diffpy.srxplanargui.__version__ != "0.0.0"