diffpy.labpdfproc 0.3.1rc4__tar.gz → 0.4.0rc0__tar.gz

{diffpy_labpdfproc-0.3.1rc4 → diffpy_labpdfproc-0.4.0rc0}/MANIFEST.in

@@ -3,7 +3,6 @@ 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.

{diffpy_labpdfproc-0.3.1rc4 → diffpy_labpdfproc-0.4.0rc0}/PKG-INFO

@@ -1,9 +1,10 @@
 Metadata-Version: 2.4
 Name: diffpy.labpdfproc
-Version: 0.3.1rc4
+Version: 0.4.0rc0
 Summary: Tools for processing x-ray powder diffraction data from laboratory sources.
 Author-email: Yucong Chen <yc4372@columbia.edu>, Till Schertenleib <ts@chem.ku.dk>, Caden Myers <cjm2304@columbia.edu>, Simon Billinge <sbillinge@ucsb.edu>
 Maintainer-email: Simon Billinge <sbillinge@ucsb.edu>
+License-Expression: BSD-3-Clause
 Project-URL: Homepage, https://github.com/diffpy/diffpy.labpdfproc/
 Project-URL: Issues, https://github.com/diffpy/diffpy.labpdfproc/issues/
 Keywords: powder XRD,absorption correction,PDF,diffpy
@@ -11,19 +12,16 @@ Classifier: Development Status :: 5 - Production/Stable
 Classifier: Environment :: Console
 Classifier: Intended Audience :: Developers
 Classifier: Intended Audience :: Science/Research
-Classifier: License :: OSI Approved :: BSD License
 Classifier: Operating System :: MacOS :: MacOS X
 Classifier: Operating System :: Microsoft :: Windows
 Classifier: Operating System :: POSIX
 Classifier: Operating System :: Unix
-Classifier: Programming Language :: Python :: 3.10
-Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
 Classifier: Programming Language :: Python :: 3.14
 Classifier: Topic :: Scientific/Engineering :: Physics
 Classifier: Topic :: Scientific/Engineering :: Chemistry
-Requires-Python: <3.15,>=3.10
+Requires-Python: <3.15,>=3.12
 Description-Content-Type: text/x-rst
 License-File: LICENSE.rst
 License-File: AUTHORS.rst
@@ -51,8 +49,8 @@ Dynamic: license-file
 .. |Black| image:: https://img.shields.io/badge/code_style-black-black
         :target: https://github.com/psf/black
 
-.. |CI| image:: https://github.com/diffpy/diffpy.labpdfproc/actions/workflows/matrix-and-codecov-on-merge-to-main.yml/badge.svg
-        :target: https://github.com/diffpy/diffpy.labpdfproc/actions/workflows/matrix-and-codecov-on-merge-to-main.yml
+.. |CI| image:: https://github.com/diffpy/diffpy.labpdfproc/actions/workflows/matrix-and-codecov.yml/badge.svg
+        :target: https://github.com/diffpy/diffpy.labpdfproc/actions/workflows/matrix-and-codecov.yml
 
 .. |Codecov| image:: https://codecov.io/gh/diffpy/diffpy.labpdfproc/branch/main/graph/badge.svg
         :target: https://codecov.io/gh/diffpy/diffpy.labpdfproc

{diffpy_labpdfproc-0.3.1rc4 → diffpy_labpdfproc-0.4.0rc0}/README.rst

@@ -15,8 +15,8 @@
 .. |Black| image:: https://img.shields.io/badge/code_style-black-black
         :target: https://github.com/psf/black
 
-.. |CI| image:: https://github.com/diffpy/diffpy.labpdfproc/actions/workflows/matrix-and-codecov-on-merge-to-main.yml/badge.svg
-        :target: https://github.com/diffpy/diffpy.labpdfproc/actions/workflows/matrix-and-codecov-on-merge-to-main.yml
+.. |CI| image:: https://github.com/diffpy/diffpy.labpdfproc/actions/workflows/matrix-and-codecov.yml/badge.svg
+        :target: https://github.com/diffpy/diffpy.labpdfproc/actions/workflows/matrix-and-codecov.yml
 
 .. |Codecov| image:: https://codecov.io/gh/diffpy/diffpy.labpdfproc/branch/main/graph/badge.svg
         :target: https://codecov.io/gh/diffpy/diffpy.labpdfproc

{diffpy_labpdfproc-0.3.1rc4 → diffpy_labpdfproc-0.4.0rc0}/pyproject.toml

@@ -1,5 +1,5 @@
 [build-system]
-requires = ["setuptools>=62.0", "setuptools-git-versioning>=2.0"]
+requires = ["setuptools>=77", "setuptools-git-versioning>=2.0"]
 build-backend = "setuptools.build_meta"
 
 [project]
@@ -17,19 +17,18 @@ maintainers = [
 description = "Tools for processing x-ray powder diffraction data from laboratory sources."
 keywords = ['powder XRD', 'absorption correction', 'PDF', 'diffpy']
 readme = "README.rst"
-requires-python = ">=3.10, <3.15"
+license = "BSD-3-Clause"
+license-files = ["LICENSE*.rst", "AUTHORS.rst"]
+requires-python = ">=3.12, <3.15"
 classifiers = [
         'Development Status :: 5 - Production/Stable',
         'Environment :: Console',
         'Intended Audience :: Developers',
         'Intended Audience :: Science/Research',
-        'License :: OSI Approved :: BSD License',
         'Operating System :: MacOS :: MacOS X',
         'Operating System :: Microsoft :: Windows',
         'Operating System :: POSIX',
         'Operating System :: Unix',
-        'Programming Language :: Python :: 3.10',
-        'Programming Language :: Python :: 3.11',
         'Programming Language :: Python :: 3.12',
         'Programming Language :: Python :: 3.13',
         'Programming Language :: Python :: 3.14',
@@ -47,18 +46,18 @@ 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)
 exclude = ["diffpy.labpdfproc.tests*"]  # exclude packages matching these glob patterns (empty by default)
-namespaces = false  # to disable scanning PEP 420 namespaces (true by default)
+namespaces = true  # to disable scanning PEP 420 namespaces (true by default)
 
 [tool.setuptools.package-data]
 "diffpy.labpdfproc" = ["data/*"]
 
+[project.scripts]
+labpdfproc = "diffpy.labpdfproc.labpdfprocapp:main"
+
 [tool.setuptools.dynamic]
 dependencies = {file = ["requirements/pip.txt"]}
 

{diffpy_labpdfproc-0.3.1rc4 → diffpy_labpdfproc-0.4.0rc0}/requirements/conda.txt

@@ -3,3 +3,4 @@ diffpy.utils
 pandas
 scipy
 wxpython
+gooey

{diffpy_labpdfproc-0.3.1rc4 → diffpy_labpdfproc-0.4.0rc0}/src/diffpy/labpdfproc/labpdfprocapp.py

@@ -131,20 +131,14 @@ def _add_credit_args(parser, use_gui=False):
 
 
 def _save_corrected(corrected, input_path, args):
-    outfile = args.output_directory / (input_path.stem + "_corrected.chi")
-    if outfile.exists() and not args.force:
-        print(f"WARNING: {outfile} exists. Use --force to overwrite.")
-        return
+    outfile = args.output_directory / (f"{input_path.stem}-mud-corrected.chi")
     corrected.metadata = corrected.metadata or {}
     corrected.dump(str(outfile), xtype=args.xtype)
     print(f"Saved corrected data to {outfile}")
 
 
 def _save_correction(correction, input_path, args):
-    corrfile = args.output_directory / (input_path.stem + "_cve.chi")
-    if corrfile.exists() and not args.force:
-        print(f"WARNING: {corrfile} exists. Use --force to overwrite.")
-        return
+    corrfile = args.output_directory / (f"{input_path.stem}-cve.chi")
     correction.metadata = correction.metadata or {}
     correction.dump(str(corrfile), xtype=args.xtype)
     print(f"Saved correction data to {corrfile}")
@@ -312,7 +306,9 @@ def get_args_gui():
 
 def get_args_cli(override=None):
     parser = create_parser(use_gui=False)
-    return parser.parse_args(override)
+    argv = override if override is not None else sys.argv[1:]
+    argv = [arg for arg in argv if arg != "--ignore-gooey"]
+    return parser.parse_args(argv)
 
 
 def main():

{diffpy_labpdfproc-0.3.1rc4 → diffpy_labpdfproc-0.4.0rc0}/src/diffpy/labpdfproc/tools.py

@@ -113,8 +113,10 @@ def _expand_user_input(args):
 
 
 def set_input_lists(args):
-    """Set input directory and files. It takes cli inputs, checks if
-    they are files or directories and creates a list of files to be
+    """Set input directory and files.
+
+    It takes cli inputs, checks if they are files or directories
+    and creates a list of files to be
     processed which is stored in the args Namespace.
 
     Parameters
@@ -132,7 +134,6 @@ def set_input_lists(args):
     args : argparse.Namespace
         The updated arguments with the modified input list.
     """
-
     input_paths = []
     args = _expand_user_input(args)
     for input_name in args.input:
@@ -224,7 +225,6 @@ def load_wavelength_from_config_file(args):
     args : argparse.Namespace
         The updated arguments with the updated wavelength and anode type.
     """
-
     if args.wavelength is not None:
         return normalize_wavelength(args)
 
@@ -453,7 +453,6 @@ def load_user_metadata(args):
         The updated argparse Namespace
         with user metadata inserted as key-value pairs.
     """
-
     reserved_keys = set(vars(args).keys())
 
     if args.user_metadata:
@@ -479,10 +478,12 @@ def load_user_metadata(args):
 
 
 def load_user_info(args):
-    """Load user info into args. If none is provided, call
-    check_and_build_global_config function from diffpy.utils to prompt
-    the user for inputs. Otherwise, call get_user_info with the provided
-    arguments.
+    """Load user info into args.
+
+    If none is provided, call check_and_build_global_config
+    function from diffpy.utils to prompt
+    the user for inputs. Otherwise, call get_user_info
+    with the provided arguments.
 
     Parameters
     ----------
@@ -528,10 +529,33 @@ def load_package_info(args):
     return args
 
 
+def _check_saved_file_exists(args):
+    """Check if the output files already exist based on the input paths
+    and output directory."""
+    existing_files = []
+    for path in args.input_paths:
+        outfile = args.output_directory / (f"{path.stem}-mud-corrected.chi")
+        if outfile.exists() and not args.force:
+            existing_files.append(outfile)
+        if args.output_correction:
+            corrfile = args.output_directory / (f"{path.stem}-cve.chi")
+            if corrfile.exists() and not args.force:
+                existing_files.append(corrfile)
+    if existing_files:
+        existing_files_str = "\n".join(str(f) for f in existing_files)
+        raise FileExistsError(
+            "The following output files already exist:"
+            f"\n{existing_files_str}\n"
+            "Use --force to overwrite them."
+        )
+
+
 def preprocessing_args(args):
-    """Perform preprocessing on the provided args. The process includes
-    loading package and user information, setting input, output,
-    wavelength, anode type, xtype, mu*D, and loading user metadata.
+    """Perform preprocessing on the provided args.
+
+    The process includes loading package and user information,
+    setting input, output, wavelength, anode type, xtype,
+    mu*D, and loading user metadata.
 
     Parameters
     ----------
@@ -542,6 +566,11 @@ def preprocessing_args(args):
     -------
     args : argparse.Namespace
         The updated argparse Namespace with arguments preprocessed.
+
+    Raises
+    ------
+    FileExistsError
+        If the output files already exist and --force is not used.
     """
     args = load_wavelength_from_config_file(args)
     args = set_mud(args)
@@ -552,6 +581,7 @@ def preprocessing_args(args):
     args = load_user_metadata(args)
     args = load_user_info(args)
     args = load_package_info(args)
+    _check_saved_file_exists(args)
     return args
 
 

{diffpy_labpdfproc-0.3.1rc4 → diffpy_labpdfproc-0.4.0rc0}/src/diffpy.labpdfproc.egg-info/PKG-INFO

@@ -1,9 +1,10 @@
 Metadata-Version: 2.4
 Name: diffpy.labpdfproc
-Version: 0.3.1rc4
+Version: 0.4.0rc0
 Summary: Tools for processing x-ray powder diffraction data from laboratory sources.
 Author-email: Yucong Chen <yc4372@columbia.edu>, Till Schertenleib <ts@chem.ku.dk>, Caden Myers <cjm2304@columbia.edu>, Simon Billinge <sbillinge@ucsb.edu>
 Maintainer-email: Simon Billinge <sbillinge@ucsb.edu>
+License-Expression: BSD-3-Clause
 Project-URL: Homepage, https://github.com/diffpy/diffpy.labpdfproc/
 Project-URL: Issues, https://github.com/diffpy/diffpy.labpdfproc/issues/
 Keywords: powder XRD,absorption correction,PDF,diffpy
@@ -11,19 +12,16 @@ Classifier: Development Status :: 5 - Production/Stable
 Classifier: Environment :: Console
 Classifier: Intended Audience :: Developers
 Classifier: Intended Audience :: Science/Research
-Classifier: License :: OSI Approved :: BSD License
 Classifier: Operating System :: MacOS :: MacOS X
 Classifier: Operating System :: Microsoft :: Windows
 Classifier: Operating System :: POSIX
 Classifier: Operating System :: Unix
-Classifier: Programming Language :: Python :: 3.10
-Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
 Classifier: Programming Language :: Python :: 3.14
 Classifier: Topic :: Scientific/Engineering :: Physics
 Classifier: Topic :: Scientific/Engineering :: Chemistry
-Requires-Python: <3.15,>=3.10
+Requires-Python: <3.15,>=3.12
 Description-Content-Type: text/x-rst
 License-File: LICENSE.rst
 License-File: AUTHORS.rst
@@ -51,8 +49,8 @@ Dynamic: license-file
 .. |Black| image:: https://img.shields.io/badge/code_style-black-black
         :target: https://github.com/psf/black
 
-.. |CI| image:: https://github.com/diffpy/diffpy.labpdfproc/actions/workflows/matrix-and-codecov-on-merge-to-main.yml/badge.svg
-        :target: https://github.com/diffpy/diffpy.labpdfproc/actions/workflows/matrix-and-codecov-on-merge-to-main.yml
+.. |CI| image:: https://github.com/diffpy/diffpy.labpdfproc/actions/workflows/matrix-and-codecov.yml/badge.svg
+        :target: https://github.com/diffpy/diffpy.labpdfproc/actions/workflows/matrix-and-codecov.yml
 
 .. |Codecov| image:: https://codecov.io/gh/diffpy/diffpy.labpdfproc/branch/main/graph/badge.svg
         :target: https://codecov.io/gh/diffpy/diffpy.labpdfproc

{diffpy_labpdfproc-0.3.1rc4 → diffpy_labpdfproc-0.4.0rc0}/src/diffpy.labpdfproc.egg-info/SOURCES.txt

@@ -1,16 +1,7 @@
-.codecov.yml
-.flake8
-.isort.cfg
-.pre-commit-config.yaml
-.readthedocs.yaml
 AUTHORS.rst
-CHANGELOG.rst
-CODE-OF-CONDUCT.rst
 LICENSE.rst
 MANIFEST.in
 README.rst
-cookiecutter.json
-environment.yml
 pyproject.toml
 requirements/build.txt
 requirements/conda.txt

{diffpy_labpdfproc-0.3.1rc4 → diffpy_labpdfproc-0.4.0rc0}/tests/conftest.py

@@ -13,7 +13,8 @@ def user_filesystem(tmp_path):
     home_dir.mkdir(parents=True, exist_ok=True)
     test_dir = base_dir / "test_dir"
     test_dir.mkdir(parents=True, exist_ok=True)
-
+    output_dir = base_dir / "output_dir"
+    output_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"
@@ -59,6 +60,10 @@ def user_filesystem(tmp_path):
         f.write("good_data.xy \n")
         f.write(f"{str(input_dir.resolve() / 'good_data.txt')}\n")
 
+    with open(output_dir / "good_data-mud-corrected.chi", "w") as f:
+        f.write(chi_data)
+    with open(output_dir / "good_data-cve.chi", "w") as f:
+        f.write(chi_data)
     home_config_data = {
         "wavelength": 0.3,
         "owner_name": "home_username",

{diffpy_labpdfproc-0.3.1rc4 → diffpy_labpdfproc-0.4.0rc0}/tests/test_tools.py

@@ -847,3 +847,38 @@ def test_load_metadata(mocker, user_filesystem, inputs, expected):
             **expected,
         }
         assert actual_metadata == expected_metadata
+
+
+def test_preprocess_args_bad(user_filesystem, monkeypatch):
+    # Case: user tries to run absorption correction, but the output
+    # filenames already for *-mud-corrected.chi and *-cve.chi exists.
+    # expected: preprocess_args catches this early and raises an Error
+    cwd = Path(user_filesystem)
+    home_dir = cwd / "home_dir"
+    # set cwd so program can find diffpyconfig.json
+    monkeypatch.setattr("pathlib.Path.home", lambda _: home_dir)
+    input_data_file = str(user_filesystem / "good_data.chi")
+    existing_corrected_file = str(
+        user_filesystem / "output_dir" / "good_data-mud-corrected.chi"
+    )
+    existing_corrected_cve_file = str(
+        user_filesystem / "output_dir" / "good_data-cve.chi"
+    )
+    cli_inputs = [
+        "mud",
+        input_data_file,
+        "2.5",
+        "-o",
+        str(user_filesystem / "output_dir"),
+        "-c",  # -c flag saves the cve file
+    ]
+    args = get_args_cli(cli_inputs)
+    args = set_input_lists(args)
+    msg = (
+        "The following output files already exist:"
+        f"\n{existing_corrected_file}\n"
+        f"{existing_corrected_cve_file}\n"
+        "Use --force to overwrite them."
+    )
+    with pytest.raises(FileExistsError, match=re.escape(msg)):
+        preprocessing_args(args)

{diffpy_labpdfproc-0.3.1rc4 → diffpy_labpdfproc-0.4.0rc0}/tests/test_version.py

@@ -1,6 +1,6 @@
 """Unit tests for __version__.py."""
 
-import diffpy.labpdfproc
+import diffpy.labpdfproc  # noqa
 
 
 def test_package_version():

diffpy_labpdfproc-0.3.1rc4/.codecov.yml

@@ -1,14 +0,0 @@
-coverage:
-  status:
-    project: # more options at https://docs.codecov.com/docs/commit-status
-      default:
-        target: auto # use the coverage from the base commit, fail if coverage is lower
-        threshold: 0% # allow the coverage to drop by
-
-comment:
-  layout: " diff, flags, files"
-  behavior: default
-  require_changes: false
-  require_base: false # [true :: must have a base report to post]
-  require_head: false # [true :: must have a head report to post]
-  hide_project_coverage: false # [true :: only show coverage on the git diff aka patch coverage]

diffpy_labpdfproc-0.3.1rc4/.flake8

@@ -1,13 +0,0 @@
-# As of now, flake8 does not natively support configuration via pyproject.toml
-# https://github.com/microsoft/vscode-flake8/issues/135
-[flake8]
-exclude =
-    .git,
-    __pycache__,
-    build,
-    dist,
-    docs/source/conf.py
-max-line-length = 79
-# Ignore some style 'errors' produced while formatting by 'black'
-# https://black.readthedocs.io/en/stable/guides/using_black_with_other_tools.html#labels-why-pycodestyle-warnings
-extend-ignore = E203

diffpy_labpdfproc-0.3.1rc4/.isort.cfg

@@ -1,5 +0,0 @@
-[settings]
-# Keep import statement below line_length character limit
-line_length = 79
-multi_line_output = 3
-include_trailing_comma = True

diffpy_labpdfproc-0.3.1rc4/.pre-commit-config.yaml

@@ -1,66 +0,0 @@
-default_language_version:
-  python: python3
-ci:
-  autofix_commit_msg: |
-    [pre-commit.ci] auto fixes from pre-commit hooks
-  autofix_prs: true
-  autoupdate_branch: "pre-commit-autoupdate"
-  autoupdate_commit_msg: "[pre-commit.ci] pre-commit autoupdate"
-  autoupdate_schedule: monthly
-  skip: [no-commit-to-branch]
-  submodules: false
-repos:
-  - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
-    hooks:
-      - id: check-yaml
-      - id: end-of-file-fixer
-      - id: trailing-whitespace
-      - id: check-case-conflict
-      - id: check-merge-conflict
-      - id: check-toml
-      - id: check-added-large-files
-  - repo: https://github.com/psf/black
-    rev: 24.4.2
-    hooks:
-      - id: black
-  - repo: https://github.com/pycqa/flake8
-    rev: 7.0.0
-    hooks:
-      - id: flake8
-  - repo: https://github.com/pycqa/isort
-    rev: 5.13.2
-    hooks:
-      - id: isort
-        args: ["--profile", "black"]
-  - repo: https://github.com/kynan/nbstripout
-    rev: 0.7.1
-    hooks:
-      - id: nbstripout
-  - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
-    hooks:
-      - id: no-commit-to-branch
-        name: Prevent Commit to Main Branch
-        args: ["--branch", "main"]
-        stages: [pre-commit]
-  - repo: https://github.com/codespell-project/codespell
-    rev: v2.3.0
-    hooks:
-      - id: codespell
-        additional_dependencies:
-          - tomli
-  # prettier - multi formatter for .json, .yml, and .md files
-  - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: f12edd9c7be1c20cfa42420fd0e6df71e42b51ea # frozen: v4.0.0-alpha.8
-    hooks:
-      - id: prettier
-        additional_dependencies:
-          - "prettier@^3.2.4"
-  # docformatter - PEP 257 compliant docstring formatter
-  - repo: https://github.com/s-weigand/docformatter
-    rev: 5757c5190d95e5449f102ace83df92e7d3b06c6c
-    hooks:
-      - id: docformatter
-        additional_dependencies: [tomli]
-        args: [--in-place, --config, ./pyproject.toml]

diffpy_labpdfproc-0.3.1rc4/.readthedocs.yaml

@@ -1,13 +0,0 @@
-version: 2
-
-build:
-  os: "ubuntu-22.04"
-  tools:
-    python: "latest"
-
-python:
-  install:
-    - requirements: requirements/docs.txt
-
-sphinx:
-  configuration: docs/source/conf.py

diffpy_labpdfproc-0.3.1rc4/CHANGELOG.rst

@@ -1,106 +0,0 @@
-=============
-Release notes
-=============
-
-.. current developments
-
-0.3.0
-=====
-
-**Added:**
-
-* Functionalities to estimate mu*D theoretically.
-* Added published reference to ``README.rst``.
-* Fast calculation supports values up to muD = 7
-* Recookiecut with updated ``scikit-package`` to enable docs preview in PRs.
-* Updated package standards to scikit-package 0.3.0.
-* Added ``cookiecutter.json`` file for the ``package update`` command.
-* Functionality to read wavelength and anode type directly from a diffpy configuration file.
-* Utility and example documentation for ``tools`` module.
-* Gooey support so that the app can be run with GUI
-* Coverage report in each PR
-* doi in Readme for papers.
-* Support for independent variables other than two-theta.
-* new subcommand ``applymud`` to run the original absorption correction process through CLI.
-* Utility and example documentation for the main module.
-* Added documentation for new CLI updates.
-* Documentation for functions module.
-* Spelling check via Codespell in pre-commit
-* Python 3.13 support
-* Functionality in `load_user_info` to enable user to enter an ORCID.
-
-**Changed:**
-
-* Default to brute-force computation when muD < 0.5 or > 7.
-* Print a warning message instead of error, explicitly stating the input muD value
-* Functions that use DiffractionObject` in `diffpy.utils` to follow the new API.
-* Workflow for loading wavelength - raise an error when both wavelength and anode type are specified.
-* Readme: muD now requires the ``--mud`` flag instead of a required argument.
-* Made muD an optional argument and provided different options (manually entry / z-scan file path) for users to specify muD
-* Increased the number of significant figures for wavelength and separated values for Ka1 and Ka2.
-* hyphens / underscores format according to new scikit-package group standard.
-* GitHub workflows for renamed test file.
-* Return a ``ValueError`` if no wavelength is found on config file or if its not specified.
-* Compartmentalize commands into the subcommands ``mud``, ``zscan``, and ``sample``. See documentation for more info.
-* Changed ``doc`` to ``docs`` and ``CODE_OF_CONDUCT.rst`` to ``CODE-OF-CONDUCT.rst`` to comply with scikit-package standards.
-* All function docstrings and tests to be more informative, incorporating new ORCID function and improving overall clarity.
-
-**Fixed:**
-
-* duplicated wavelength information in output files
-
-**Removed:**
-
-* Remove the import of extend_path from pkgutil in diffpy/__init__.py since we are not strictly following the Python namespace package convention.
-
-
-0.2.0
-=====
-
-**Added:**
-
-* Support for Python 3.13
-
-**Removed:**
-
-* Support for Python 3.10
-
-
-0.1.3
-=====
-
-**Added:**
-
-* generate package API doc
-* redo cookiecutter to add issue templates and update readme
-
-
-0.1.2
-=====
-
-**Added:**
-
-* polynomial interpolation as the default method for cve computation.
-
-**Fixed:**
-
-* add PyPI packages under pip.txt
-
-
-
-0.1.1
-=====
-
-
-
-0.1.1
-=====
-
-
-
-0.1.0
-=====
-
-
-
-Initial release of labPDFproc.  Please see README and documentation for details

diffpy_labpdfproc-0.3.1rc4/CODE-OF-CONDUCT.rst

@@ -1,133 +0,0 @@
-=====================================
- Contributor Covenant Code of Conduct
-=====================================
-
-Our Pledge
-----------
-
-We as members, contributors, and leaders pledge to make participation in our
-community a harassment-free experience for everyone, regardless of age, body
-size, visible or invisible disability, ethnicity, sex characteristics, gender
-identity and expression, level of experience, education, socioeconomic status,
-nationality, personal appearance, race, caste, color, religion, or sexual
-identity and orientation.
-
-We pledge to act and interact in ways that contribute to an open, welcoming,
-diverse, inclusive, and healthy community.
-
-Our Standards
--------------
-
-Examples of behavior that contributes to a positive environment for our
-community include:
-
-* Demonstrating empathy and kindness toward other people
-* Being respectful of differing opinions, viewpoints, and experiences
-* Giving and gracefully accepting constructive feedback
-* Accepting responsibility and apologizing to those affected by our mistakes,
-  and learning from the experience
-* Focusing on what is best not just for us as individuals, but for the overall
-  community
-
-Examples of unacceptable behavior include:
-
-* The use of sexualized language or imagery, and sexual attention or advances of
-  any kind
-* Trolling, insulting or derogatory comments, and personal or political attacks
-* Public or private harassment
-* Publishing others' private information, such as a physical or email address,
-  without their explicit permission
-* Other conduct which could reasonably be considered inappropriate in a
-  professional setting
-
-Enforcement Responsibilities
-----------------------------
-
-Community leaders are responsible for clarifying and enforcing our standards of
-acceptable behavior and will take appropriate and fair corrective action in
-response to any behavior that they deem inappropriate, threatening, offensive,
-or harmful.
-
-Community leaders have the right and responsibility to remove, edit, or reject
-comments, commits, code, wiki edits, issues, and other contributions that are
-not aligned to this Code of Conduct, and will communicate reasons for moderation
-decisions when appropriate.
-
-Scope
------
-
-This Code of Conduct applies within all community spaces, and also applies when
-an individual is officially representing the community in public spaces.
-Examples of representing our community include using an official email address,
-posting via an official social media account, or acting as an appointed
-representative at an online or offline event.
-
-Enforcement
------------
-
-Instances of abusive, harassing, or otherwise unacceptable behavior may be
-reported to the community leaders responsible for enforcement at
-sbillinge@ucsb.edu. All complaints will be reviewed and investigated promptly and fairly.
-
-All community leaders are obligated to respect the privacy and security of the
-reporter of any incident.
-
-Enforcement Guidelines
-----------------------
-
-Community leaders will follow these Community Impact Guidelines in determining
-the consequences for any action they deem in violation of this Code of Conduct:
-
-1. Correction
-****************
-
-**Community Impact**: Use of inappropriate language or other behavior deemed
-unprofessional or unwelcome in the community.
-
-**Consequence**: A private, written warning from community leaders, providing
-clarity around the nature of the violation and an explanation of why the
-behavior was inappropriate. A public apology may be requested.
-
-2. Warning
-*************
-
-**Community Impact**: A violation through a single incident or series of
-actions.
-
-**Consequence**: A warning with consequences for continued behavior. No
-interaction with the people involved, including unsolicited interaction with
-those enforcing the Code of Conduct, for a specified period of time. This
-includes avoiding interactions in community spaces as well as external channels
-like social media. Violating these terms may lead to a temporary or permanent
-ban.
-
-3. Temporary Ban
-******************
-
-**Community Impact**: A serious violation of community standards, including
-sustained inappropriate behavior.
-
-**Consequence**: A temporary ban from any sort of interaction or public
-communication with the community for a specified period of time. No public or
-private interaction with the people involved, including unsolicited interaction
-with those enforcing the Code of Conduct, is allowed during this period.
-Violating these terms may lead to a permanent ban.
-
-4. Permanent Ban
-******************
-
-**Community Impact**: Demonstrating a pattern of violation of community
-standards, including sustained inappropriate behavior, harassment of an
-individual, or aggression toward or disparagement of classes of individuals.
-
-**Consequence**: A permanent ban from any sort of public interaction within the
-community.
-
-Attribution
------------
-
-This Code of Conduct is adapted from the `Contributor Covenant <https://www.contributor-covenant.org/version/2/1/code_of_conduct.html>`_.
-
-Community Impact Guidelines were inspired by `Mozilla's code of conduct enforcement ladder <https://github.com/mozilla/inclusion>`_.
-
-For answers to common questions about this code of conduct, see the `FAQ <https://www.contributor-covenant.org/faq>`_. `Translations are available <https://www.contributor-covenant.org/translations>`_

diffpy_labpdfproc-0.3.1rc4/cookiecutter.json

@@ -1,20 +0,0 @@
-{
-  "author_names": "Yucong Chen, Till Schertenleib, Caden Myers, Simon Billinge",
-  "author_emails": "yc4372@columbia.edu, ts@chem.ku.dk, cjm2304@columbia.edu, sbillinge@ucsb.edu",
-  "maintainer_names": "Simon Billinge",
-  "maintainer_emails": "sbillinge@ucsb.edu",
-  "maintainer_github_usernames": "sbillinge",
-  "contributors": "Yucong Chen, Till Schertenleib, Caden Myers, Billinge Group members",
-  "license_holders": "The Trustees of Columbia University in the City of New York",
-  "project_name": "diffpy.labpdfproc",
-  "github_username_or_orgname": "diffpy",
-  "github_repo_name": "diffpy.labpdfproc",
-  "conda_pypi_package_dist_name": "diffpy.labpdfproc",
-  "package_dir_name": "diffpy.labpdfproc",
-  "project_short_description": "Tools for processing x-ray powder diffraction data from laboratory sources.",
-  "project_keywords": "powder XRD, absorption correction, PDF, diffpy",
-  "minimum_supported_python_version": "3.12",
-  "maximum_supported_python_version": "3.14",
-  "project_needs_c_code_compiled": "No",
-  "project_has_gui_tests": "No"
-}

diffpy_labpdfproc-0.3.1rc4/environment.yml

@@ -1,6 +0,0 @@
-name: diffpy.labpdfproc
-channels:
-  - conda-forge
-dependencies:
-  - python=3
-  - pip