fix: merge from main to resolve conflicts

Author: yucongalicechen

.codespell/ignore_words.txt

@@ -4,8 +4,5 @@
 ;; abbreviation for "materials" often used in a journal title
 mater
 
-;; alternative use of socioeconomic
-socio-economic
-
 ;; Frobenius norm used in np.linalg.norm
 fro

.github/PULL_REQUEST_TEMPLATE/pull_request_template.md

@@ -0,0 +1,15 @@
+### What problem does this PR address?
+
+<!-- Provide a brief overview and link to the issue. Attach outputs, including screenshots (before/after), if helpful for the reviewer. -->
+
+### What should the reviewer(s) do?
+
+<!-- Merge the code, provide feedback, initiate a discussion, etc. -->
+
+<!--
+Use the following checklist items when applicable (select only what applies):
+- [ ] This PR introduces a public-facing change (e.g., figures, CLI input/output, API).
+    - [ ] Documentation (e.g., tutorials, examples, README) has been updated.
+    - [ ] A tracking issue or plan to update documentation exists.
+- [ ] This PR affects internal functionality only (no user-facing change).
+-->

.github/workflows/build-wheel-release-upload.yml

@@ -4,7 +4,7 @@ on:
   workflow_dispatch:
   push:
     tags:
-      - '*'  # Trigger on all tags initially, but tag and release privilege are verified in _build-wheel-release-upload.yml
+      - "*" # Trigger on all tags initially, but tag and release privilege are verified in _build-wheel-release-upload.yml
 
 jobs:
   release:

.github/workflows/check-news-item.yml

@@ -3,7 +3,7 @@ name: Check for News
 on:
   pull_request_target:
     branches:
-    - main
+      - main
 
 jobs:
   check-news-item:

.github/workflows/matrix-and-codecov-on-merge-to-main.yml

@@ -23,7 +23,7 @@ jobs:
         os: [ubuntu-latest, windows-latest, macos-13, macos-14]
         python-version: ["3.11", "3.12", "3.13"]
     env:
-          LATEST_PYTHON_VERSION: "3.13"
+      LATEST_PYTHON_VERSION: "3.13"
     steps:
       - name: Check out diffpy.labpdfproc
         uses: actions/checkout@v4

.github/workflows/tests-on-pr.yml

@@ -39,7 +39,6 @@ jobs:
           pip install gooey
           python -m pip install . --no-deps
 
-
       - name: Validate diffpy.labpdfproc
         run: |
           pytest --cov

.pre-commit-config.yaml

@@ -1,14 +1,14 @@
 default_language_version:
-    python: python3
+  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
+  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
@@ -47,6 +47,20 @@ repos:
   - repo: https://github.com/codespell-project/codespell
     rev: v2.3.0
     hooks:
-    - id: codespell
-      additional_dependencies:
-        - tomli
+      - 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]

.readthedocs.yaml

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

CODE_OF_CONDUCT.rst

@@ -8,7 +8,7 @@ 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, socio-economic status,
+identity and expression, level of experience, education, socioeconomic status,
 nationality, personal appearance, race, caste, color, religion, or sexual
 identity and orientation.
 

LICENSE.rst

@@ -1,7 +1,6 @@
 BSD 3-Clause License
 
-Copyright (c) 2024, The Trustees of Columbia University
-in the City of New York.
+Copyright (c) 2025, The Trustees of Columbia University in the City of New York.
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

news/recut2.rst

@@ -0,0 +1,23 @@
+**Added:**
+
+* Recookiecut with updated ``scikit-package`` to enable docs preview in PRs.
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>

src/diffpy/labpdfproc/__init__.py

@@ -12,9 +12,8 @@
 # See LICENSE.rst for license information.
 #
 ##############################################################################
-
-"""Tools for processing x-ray powder diffraction data
-from laboratory sources."""
+"""Tools for processing x-ray powder diffraction data from laboratory
+sources."""
 
 # package version
 from diffpy.labpdfproc.version import __version__

src/diffpy/labpdfproc/functions.py

@@ -40,8 +40,8 @@ def __init__(
         self._get_grid_points()
 
     def _get_grid_points(self):
-        """Given a radius and a grid size,
-        return a grid of points to uniformly sample that circle."""
+        """Given a radius and a grid size, return a grid of points to uniformly
+        sample that circle."""
         xs = np.linspace(-self.radius, self.radius, self.npoints)
         ys = np.linspace(-self.radius, self.radius, self.npoints)
         self.grid = {
@@ -50,8 +50,8 @@ def _get_grid_points(self):
         self.total_points_in_grid = len(self.grid)
 
     def _get_entry_exit_coordinates(self, coordinate, angle):
-        """Get the coordinates where the beam enters and leaves the circle
-        for a given angle and grid point.
+        """Get the coordinates where the beam enters and leaves the circle for
+        a given angle and grid point.
 
         It is calculated in the following way:
         For the entry coordinate,
@@ -108,9 +108,8 @@ def _get_entry_exit_coordinates(self, coordinate, angle):
         return entry_point, exit_point
 
     def _get_path_length(self, grid_point, angle):
-        """Return the path length of
-        a horizontal line entering the circle at the same height
-        to the grid point then exiting at angle.
+        """Return the path length of a horizontal line entering the circle at
+        the same height to the grid point then exiting at angle.
 
         Parameters
         ----------
@@ -137,8 +136,8 @@ def _get_path_length(self, grid_point, angle):
         return total_distance, primary_distance, secondary_distance
 
     def set_distances_at_angle(self, angle):
-        """Given an angle, set the distances from the grid points
-        to the entry and exit coordinates.
+        """Given an angle, set the distances from the grid points to the entry
+        and exit coordinates.
 
         Parameters
         ----------
@@ -171,9 +170,11 @@ def set_muls_at_angle(self, angle):
 
 
 def _cve_brute_force(input_pattern, mud):
-    """Compute cve for the given mud on a global grid
-    using the brute-force method.
-    Assume mu=mud/2, given that the same mu*D yields the same cve and D/2=1.
+    """Compute cve for the given mud on a global grid using the brute-force
+    method.
+
+    Assume mu=mud/2, given that the same mu*D yields the same cve and
+    D/2=1.
     """
     mu_sample_invmm = mud / 2
     abs_correction = Gridded_circle(
@@ -201,10 +202,8 @@ def _cve_brute_force(input_pattern, mud):
 
 
 def _cve_polynomial_interpolation(input_pattern, mud):
-    """Compute cve using polynomial interpolation method,
-    default to brute-force computation if mu*D is
-    out of the range (0.5 to 7).
-    """
+    """Compute cve using polynomial interpolation method, default to brute-
+    force computation if mu*D is out of the range (0.5 to 7)."""
     if mud > 7 or mud < 0.5:
         warnings.warn(
             f"Input mu*D = {mud} is out of the acceptable range "
@@ -287,8 +286,8 @@ def compute_cve(
 
 
 def apply_corr(input_pattern, absorption_correction):
-    """Apply absorption correction to the given diffraction object
-    with the correction diffraction object.
+    """Apply absorption correction to the given diffraction object with the
+    correction diffraction object.
 
     Parameters
     ----------

src/diffpy/labpdfproc/tools.py

@@ -112,10 +112,9 @@ 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 processed
-    which is stored in the args Namespace.
+    """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
     ----------
@@ -276,8 +275,8 @@ def set_wavelength(args):
 
 
 def set_xtype(args):
-    """Set the xtype based on the given input arguments,
-    raise an error if xtype is not one of {*XQUANTITIES, }.
+    """Set the xtype based on the given input arguments, raise an error if
+    xtype is not one of {*XQUANTITIES, }.
 
     Parameters
     ----------
@@ -333,8 +332,8 @@ def _parse_theoretical_input(input_str):
 
 
 def _set_theoretical_mud(args):
-    """Theoretical estimation of mu*D from
-    sample composition, energy, sample mass density, and capillary diameter"""
+    """Theoretical estimation of mu*D from sample composition, energy, sample
+    mass density, and capillary diameter."""
     sample_composition, energy, sample_mass_density, diameter = (
         _parse_theoretical_input(args.theoretical_estimation)
     )
@@ -387,8 +386,8 @@ def _load_key_value_pair(s):
 
 
 def load_user_metadata(args):
-    """Load user metadata into args,
-    raise ValueError if it is in incorrect format.
+    """Load user metadata into args, raise ValueError if it is in incorrect
+    format.
 
     Parameters
     ----------
@@ -427,10 +426,9 @@ 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
     ----------
@@ -457,8 +455,8 @@ def load_user_info(args):
 
 
 def load_package_info(args):
-    """Load diffpy.labpdfproc package name and version into args
-    using get_package_info function from diffpy.utils.
+    """Load diffpy.labpdfproc package name and version into args using
+    get_package_info function from diffpy.utils.
 
     Parameters
     ----------
@@ -477,10 +475,9 @@ def load_package_info(args):
 
 
 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
     ----------
@@ -504,8 +501,8 @@ def preprocessing_args(args):
 
 
 def load_metadata(args, filepath):
-    """Load the relevant metadata from args
-    to write into the header of the output files.
+    """Load the relevant metadata from args to write into the header of the
+    output files.
 
     Parameters
     ----------

src/diffpy/labpdfproc/version.py

@@ -12,7 +12,6 @@
 # See LICENSE.rst for license information.
 #
 ##############################################################################
-
 """Definition of __version__."""
 
 #  We do not use the other three variables, but can be added back if needed.

tests/test_version.py

@@ -1,11 +1,10 @@
-"""Unit tests for __version__.py
-"""
+"""Unit tests for __version__.py."""
 
 import diffpy.labpdfproc
 
 
 def test_package_version():
-    """Ensure the package version is defined
-    and not set to the initial placeholder."""
+    """Ensure the package version is defined and not set to the initial
+    placeholder."""
     assert hasattr(diffpy.labpdfproc, "__version__")
     assert diffpy.labpdfproc.__version__ != "0.0.0"