MANIFEST.in, README.rst, pyproject.toml, tests/conftest.py

Author: yucongalicechen

MANIFEST.in

@@ -3,6 +3,7 @@ graft tests
 graft requirements
 
 include AUTHORS.rst LICENSE*.rst README.rst
+include src/diffpy/labpdfproc/data *
 
 # Exclude all bytecode files and __pycache__ directories
 global-exclude *.py[cod]  # Exclude all .pyc, .pyo, and .pyd files.

README.rst

@@ -37,7 +37,28 @@
 
 Tools for processing x-ray powder diffraction data from laboratory sources.
 
-* LONGER DESCRIPTION HERE
+PDFgetX3 has revolutionized how PDF methods can be applied to solve nanostructure problems.
+However, the program was designed for use with Rapid Acquisition PDF (RAPDF) data from synchrotron sources.
+A key approximation inherent in the use of PDFgetX3 for RAPDF data is that absorption effects are negligible.
+This is typically not the case for laboratory x-ray diffractometers, where absorption effects can be significant.
+
+This app is designed to preprocess data from laboratory x-ray diffractometers before using PDFgetX3 to obtain PDFs.
+The app currently carries out an absorption correction assuming a parallel beam capillary geometry
+which is the most common geometry for lab PDF measurements.
+
+The theory is described in the following paper:
+
+An ad hoc Absorption Correction for Reliable
+Pair-Distribution Functions from Low Energy x-ray Sources,
+Yucong Chen, Till Schertenleib, Andrew Yang, Pascal Schouwink,
+Wendy L. Queen and Simon J. L. Billinge, in preparation.
+
+The related experimental data acquisition protocols are described in the following paper:
+
+Protocols for Obtaining Reliable PDFs from Laboratory
+x-ray Sources Using PDFgetX3,
+Till Schertenleib, Daniel Schmuckler, Yucong Chen, Geng Bang Jin,
+Wendy L. Queen and Simon J. L. Billinge, in preparation.
 
 For more information about the diffpy.labpdfproc library, please consult our `online documentation <https://diffpy.github.io/diffpy.labpdfproc>`_.
 
@@ -81,6 +102,27 @@ and run the following ::
 
         pip install .
 
+Example
+-------
+
+Navigate to the directory that contains 1D diffraction patterns that you would like to process.
+Activate the conda environment (`conda activate diffpy.labpdfproc_env`) that contains the package and run the following command ::
+
+        labpdfproc <muD> <path/to/inputfile.txt>
+
+Here replace <muD> with the value of muD for your sample
+and <path/to/inputfile.txt> with the path and filename of your input file.
+For example, if the uncorrected data case is called zro2_mo.xy and is in the current directory
+and it has a muD of 2.5 then the command would be ::
+
+        labpdfproc 2.5 zro2_mo.xy
+
+Please type ::
+
+        labpdfproc --help
+
+for more information on the available options.
+
 Support and Contribute
 ----------------------
 
@@ -109,7 +151,7 @@ trying to commit again.
 
 Improvements and fixes are always appreciated.
 
-Before contribuing, please read our `Code of Conduct <https://github.com/diffpy/diffpy.labpdfproc/blob/main/CODE_OF_CONDUCT.rst>`_.
+Before contributing, please read our `Code of Conduct <https://github.com/diffpy/diffpy.labpdfproc/blob/main/CODE_OF_CONDUCT.rst>`_.
 
 Contact
 -------

pyproject.toml

@@ -42,6 +42,9 @@ template = "{tag}"
 dev_template = "{tag}"
 dirty_template = "{tag}"
 
+[project.scripts]
+labpdfproc = "diffpy.labpdfproc.labpdfprocapp:main"
+
 [tool.setuptools.packages.find]
 where = ["src"]  # list of folders that contain the packages (["."] by default)
 include = ["*"]  # package names should match these glob patterns (["*"] by default)

tests/conftest.py

@@ -7,10 +7,45 @@
 @pytest.fixture
 def user_filesystem(tmp_path):
     base_dir = Path(tmp_path)
+    input_dir = base_dir / "input_dir"
+    input_dir.mkdir(parents=True, exist_ok=True)
     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)
+
+    chi_data = "dataformat = twotheta\n mode = xray\n # chi_Q chi_I\n 1 2\n 3 4\n 5 6\n 7 8\n"
+    xy_data = "1 2\n 3 4\n 5 6\n 7 8"
+    unreadable_data = "This is a file with no data that is non-readable by " "LoadData"
+    binary_data = b"\x00\x01\x02\x03\x04"
+
+    with open(base_dir / "good_data.chi", "w") as f:
+        f.write(chi_data)
+    with open(base_dir / "good_data.xy", "w") as f:
+        f.write(xy_data)
+    with open(base_dir / "good_data.txt", "w") as f:
+        f.write(chi_data)
+    with open(base_dir / "unreadable_file.txt", "w") as f:
+        f.write(unreadable_data)
+    with open(base_dir / "binary.pkl", "wb") as f:
+        f.write(binary_data)
+
+    with open(input_dir / "good_data.chi", "w") as f:
+        f.write(chi_data)
+    with open(input_dir / "good_data.xy", "w") as f:
+        f.write(xy_data)
+    with open(input_dir / "good_data.txt", "w") as f:
+        f.write(chi_data)
+    with open(input_dir / "unreadable_file.txt", "w") as f:
+        f.write(unreadable_data)
+    with open(input_dir / "binary.pkl", "wb") as f:
+        f.write(binary_data)
+
+    with open(input_dir / "file_list.txt", "w") as f:
+        f.write("good_data.chi \n good_data.xy \n good_data.txt \n missing_file.txt")
+    with open(input_dir / "file_list_example2.txt", "w") as f:
+        f.write("input_dir/*.txt \n")
+        f.write("input_dir/good_data.chi \n")
+        f.write("good_data.xy \n")
+        f.write(f"{str(input_dir.resolve() / 'good_data.txt')}\n")
 
     home_config_data = {"username": "home_username", "email": "[email protected]"}
     with open(home_dir / "diffpyconfig.json", "w") as f: