Cookierelease: setup src folder structure

src/diffpy/__init__.py

@@ -0,0 +1,23 @@
+#!/usr/bin/env python
+##############################################################################
+#
+# (c) 2024 The Trustees of Columbia University in the City of New York.
+# All rights reserved.
+#
+# File coded by: Billinge Group members and community contributors.
+#
+# See GitHub contributions for a more detailed list of contributors.
+# https://github.com/diffpy/diffpy.nmf_mapping/graphs/contributors
+#
+# See LICENSE.rst for license information.
+#
+##############################################################################
+
+"""Blank namespace package for module diffpy."""
+
+
+from pkgutil import extend_path
+
+__path__ = extend_path(__path__, __name__)
+
+# End of file

src/diffpy/nmf_mapping/__init__.py

@@ -0,0 +1,24 @@
+#!/usr/bin/env python
+##############################################################################
+#
+# (c) 2024 The Trustees of Columbia University in the City of New York.
+# All rights reserved.
+#
+# File coded by: Billinge Group members and community contributors.
+#
+# See GitHub contributions for a more detailed list of contributors.
+# https://github.com/diffpy/diffpy.nmf_mapping/graphs/contributors
+#
+# See LICENSE.rst for license information.
+#
+##############################################################################
+
+"""Run NMF analysis on PDF and XRD data"""
+
+# package version
+from diffpy.nmf_mapping.version import __version__
+
+# silence the pyflakes syntax checker
+assert __version__ or True
+
+# End of file

diffpy/nmf_mapping/nmf_mapping/nmf_mapping_code.py → src/diffpy/nmf_mapping/nmf_mapping_code.py

@@ -11,11 +11,12 @@
 import numpy as np
 import pandas as pd
 from bg_mpl_stylesheets.styles import all_styles
-from diffpy.utils.parsers.loaddata import loadData
 from scipy import interpolate
 from sklearn.decomposition import NMF, PCA
 from sklearn.exceptions import ConvergenceWarning
 
+from diffpy.utils.parsers.loaddata import loadData
+
 plt.style.use(all_styles["bg_style"])
 warnings.filterwarnings("ignore", category=FutureWarning)
 warnings.filterwarnings("ignore", category=ConvergenceWarning)

src/diffpy/nmf_mapping/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": "[email protected]"}
+    with open(home_dir / "diffpyconfig.json", "w") as f:
+        json.dump(home_config_data, f)
+
+    yield tmp_path

src/diffpy/nmf_mapping/tests/debug.py

@@ -0,0 +1,35 @@
+#!/usr/bin/env python
+##############################################################################
+#
+# (c) 2024 The Trustees of Columbia University in the City of New York.
+# All rights reserved.
+#
+# File coded by: Billinge Group members and community contributors.
+#
+# See GitHub contributions for a more detailed list of contributors.
+# https://github.com/diffpy/diffpy.nmf_mapping/graphs/contributors
+#
+# See LICENSE.rst for license information.
+#
+##############################################################################
+
+"""
+Convenience module for debugging the unit tests using
+
+python -m diffpy.nmf_mapping.tests.debug
+
+Exceptions raised by failed tests or other errors are not caught.
+"""
+
+
+if __name__ == "__main__":
+    import sys
+
+    from diffpy.nmf_mapping.tests import testsuite
+
+    pattern = sys.argv[1] if len(sys.argv) > 1 else ""
+    suite = testsuite(pattern)
+    suite.debug()
+
+
+# End of file

src/diffpy/nmf_mapping/tests/run.py

@@ -0,0 +1,34 @@
+#!/usr/bin/env python
+##############################################################################
+#
+# (c) 2024 The Trustees of Columbia University in the City of New York.
+# All rights reserved.
+#
+# File coded by: Billinge Group members and community contributors.
+#
+# See GitHub contributions for a more detailed list of contributors.
+# https://github.com/diffpy/diffpy.nmf_mapping/graphs/contributors
+#
+# See LICENSE.rst for license information.
+#
+##############################################################################
+"""Convenience module for executing all unit tests with
+python -m \.tests.run
+"""
+
+import sys
+
+import pytest
+
+if __name__ == "__main__":
+    # show output results from every test function
+    args = ["-v"]
+    # show the message output for skipped and expected failure tests
+    if len(sys.argv) > 1:
+        args.extend(sys.argv[1:])
+    print("pytest arguments: {}".format(args))
+    # call pytest and exit with the return code from pytest
+    exit_res = pytest.main(args)
+    sys.exit(exit_res)
+
+# End of file

src/diffpy/nmf_mapping/version.py

@@ -0,0 +1,26 @@
+#!/usr/bin/env python
+##############################################################################
+#
+# (c) 2024 The Trustees of Columbia University in the City of New York.
+# All rights reserved.
+#
+# File coded by: Billinge Group members and community contributors.
+#
+# See GitHub contributions for a more detailed list of contributors.
+# https://github.com/diffpy/diffpy.nmf_mapping/graphs/contributors
+#
+# See LICENSE.rst for license information.
+#
+##############################################################################
+
+"""Definition of __version__."""
+
+#  We do not use the other three variables, but can be added back if needed.
+#  __all__ = ["__date__", "__git_commit__", "__timestamp__", "__version__"]
+
+# obtain version information
+from importlib.metadata import version
+
+__version__ = version("diffpy.nmf_mapping")
+
+# End of file