merge v3.3.0 into main

.codecov.yml

@@ -5,6 +5,9 @@ coverage:
         target: auto # use the coverage from the base commit, fail if coverage is lower
         threshold: 0% # allow the coverage to drop by
 
+  ignore:
+    - "tests/test_speed.py" # ignore performance testing in test coverage.
+
 comment:
   layout: " diff, flags, files"
   behavior: default

.github/ISSUE_TEMPLATE/release_checklist.md

@@ -11,12 +11,13 @@ assignees: ""
 - [ ] All PRs/issues attached to the release are merged.
 - [ ] All the badges on the README are passing.
 - [ ] License information is verified as correct. If you are unsure, please comment below.
-- [ ] Locally rendered documentation contains all appropriate pages, including API references (check no modules are
-      missing), tutorials, and other human-written text is up-to-date with any changes in the code.
+- [ ] Locally rendered documentation contains all appropriate pages, tutorials, and other human-written text is up-to-date with any changes in the code.
+- [ ] All API references are included. To check this, run `conda install scikit-package` and then `package build api-doc`. Review any edits made by rerendering the docs locally.
 - [ ] Installation instructions in the README, documentation, and the website are updated.
 - [ ] Successfully run any tutorial examples or do functional testing with the latest Python version.
 - [ ] Grammar and writing quality are checked (no typos).
 - [ ] Install `pip install build twine`, run `python -m build` and `twine check dist/*` to ensure that the package can be built and is correctly formatted for PyPI release.
+- [ ] Dispatch matrix testing to test the release on all Python versions and systems. If you do not have permission to run this workflow, tag the maintainer and say `@maintainer, please dispatch matrix testing workflow`.
 
 Please tag the maintainer (e.g., @username) in the comment here when you are ready for the PyPI/GitHub release. Include any additional comments necessary, such as version information and details about the pre-release here:
 
@@ -34,7 +35,7 @@ Please let the maintainer know that all checks are done and the package is ready
 <!-- After the maintainer releases the PyPI package, please check the following when creating a PR for conda-forge release.-->
 
 - [ ] Ensure that the full release has appeared on PyPI successfully.
-- [ ] New package dependencies listed in `conda.txt` and `test.txt` are added to `meta.yaml` in the feedstock.
+- [ ] New package dependencies listed in `conda.txt` and `tests.txt` are added to `meta.yaml` in the feedstock.
 - [ ] Close any open issues on the feedstock. Reach out to the maintainer if you have questions.
 - [ ] Tag the maintainer for conda-forge release.
 

.github/workflows/build-and-publish-docs-on-dispatch.yml

@@ -0,0 +1,18 @@
+name: Build and Publish Docs on Dispatch
+
+on:
+  workflow_dispatch:
+
+jobs:
+  get-python-version:
+    uses: scikit-package/release-scripts/.github/workflows/_get-python-version-latest.yml@v0
+    with:
+      python_version: 0
+
+  docs:
+    uses: scikit-package/release-scripts/.github/workflows/_release-docs.yml@v0
+    with:
+      project: diffpy.srfit
+      c_extension: false
+      headless: false
+      python_version: ${{ fromJSON(needs.get-python-version.outputs.latest_python_version) }}

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

@@ -1,4 +1,4 @@
-name: Release (GitHub/PyPI) and Deploy Docs
+name: Build Wheel, Release on GitHub/PyPI, and Deploy Docs
 
 on:
   workflow_dispatch:
@@ -7,12 +7,12 @@ on:
       - "*" # Trigger on all tags initially, but tag and release privilege are verified in _build-wheel-release-upload.yml
 
 jobs:
-  release:
+  build-release:
     uses: scikit-package/release-scripts/.github/workflows/_build-wheel-release-upload.yml@v0
     with:
       project: diffpy.srfit
       c_extension: false
-      maintainer_GITHUB_username: sbillinge
+      maintainer_GITHUB_username: cadenmyers13, sbillinge
     secrets:
       PYPI_TOKEN: ${{ secrets.PYPI_TOKEN }}
       PAT_TOKEN: ${{ secrets.PAT_TOKEN }}

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

@@ -1,6 +1,9 @@
-name: CI
+name: Matrix and Codecov
 
 on:
+  # push:
+  #   branches:
+  #     - main
   release:
     types:
       - prereleased

.pre-commit-config.yaml

@@ -11,7 +11,7 @@ ci:
   submodules: false
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v6.0.0
     hooks:
       - id: check-yaml
       - id: end-of-file-fixer
@@ -21,46 +21,47 @@ repos:
       - id: check-toml
       - id: check-added-large-files
   - repo: https://github.com/psf/black
-    rev: 24.4.2
+    rev: 26.3.1
     hooks:
       - id: black
   - repo: https://github.com/pycqa/flake8
-    rev: 7.0.0
+    rev: 7.3.0
     hooks:
       - id: flake8
   - repo: https://github.com/pycqa/isort
-    rev: 5.13.2
+    rev: 8.0.1
     hooks:
       - id: isort
         args: ["--profile", "black"]
   - repo: https://github.com/kynan/nbstripout
-    rev: 0.7.1
+    rev: 0.9.1
     hooks:
       - id: nbstripout
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v6.0.0
     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
+    rev: v2.4.2
     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
+    rev: 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
+  - repo: https://github.com/PyCQA/docformatter
+    rev: v1.7.7
     hooks:
       - id: docformatter
+        language_version: python3.13
         additional_dependencies: [tomli]
         args: [--in-place, --config, ./pyproject.toml]

AUTHORS.rst

@@ -1,7 +1,7 @@
 Authors
 =======
 
-Christopher Farrow, Pavol Juhas, Simon J. L. Billinge, and members of the Billinge Group
+Christopher Farrow, Pavol Juhas, Caden Myers, Simon J. L. Billinge, and members of the Billinge Group
 
 Contributors
 ------------

CODE-OF-CONDUCT.rst

@@ -67,7 +67,7 @@ Enforcement
 
 Instances of abusive, harassing, or otherwise unacceptable behavior may be
 reported to the community leaders responsible for enforcement at
-sb2896@columbia.edu. All complaints will be reviewed and investigated promptly and fairly.
+cjm2304@columbia.edu and 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.

LICENSE.rst

@@ -9,7 +9,7 @@ OPEN SOURCE LICENSE AGREEMENT
 - Copyright (c) 2008-2012, The Trustees of Columbia University in the City of New York
 - Copyright (c) 2014-2019, Brookhaven Science Associates, Brookhaven National Laboratory
 - Copyright (c) 2020-2025, The Trustees of Columbia University in the City of New York
-
+- Copyright (c) 2026-present, The DiffPy Team.
 
 The "DiffPy-CMI" is distributed subject to the following license conditions:
 

MANIFEST.in

@@ -11,4 +11,3 @@ global-exclude __pycache__  # Exclude Python cache directories.
 global-exclude .git*  # Exclude git files and directories.
 global-exclude .idea  # Exclude PyCharm project settings.
 exclude .codecov.yml
-exclude .coveragerc

README.rst

@@ -25,6 +25,7 @@
         :target: https://anaconda.org/conda-forge/diffpy.srfit
 
 .. |PR| image:: https://img.shields.io/badge/PR-Welcome-29ab47ff
+        :target: https://github.com/diffpy/diffpy.srfit/pulls
 
 .. |PyPI| image:: https://img.shields.io/pypi/v/diffpy.srfit
         :target: https://pypi.org/project/diffpy.srfit/
@@ -38,7 +39,7 @@
 diffpy.srfit
 ============
 
-Configurable code for solving atomic structures.
+Generalized code base for modeling problems.
 
 The diffpy.srfit package provides the framework for building a global optimizer
 on the fly from components such as function calculators (that calculate
@@ -62,6 +63,23 @@ obtain the total cost function. Additionally, diffpy.srfit is designed to be
 extensible, allowing the user to integrate external calculators to perform
 co-refinements with other techniques.
 
+
+SrFit has tools for coherently combining known information about a
+material to derive other properties, in particular material structure.
+SrFit allows the customization and creation of structure
+representations, profile calculators, constraints, restraints and file
+input parsers. The customized pieces can be glued together within SrFit
+to optimize a structure, or other physically relevant information from
+one or more experimental profiles. Other known information about the
+system of interest can be included with arbitrarily complex constraints
+and restraints. In this way, the end user creates a customized fitting
+application that suits the problem to the available information.
+
+The subpackages herein define various pieces of the SrFit framework.
+Developers are encouraged to work through the examples described in the
+documentation to learn how to use and customize the various parts of
+SrFit.
+
 For more information about the diffpy.srfit library, please consult our `online documentation <https://diffpy.github.io/diffpy.srfit>`_.
 
 Citation
@@ -94,10 +112,6 @@ The following creates and activates a new environment named ``diffpy.srfit_env``
         conda create -n diffpy.srfit_env diffpy.srfit
         conda activate diffpy.srfit_env
 
-To confirm that the installation was successful, type ::
-
-        python -c "import diffpy.srfit; print(diffpy.srfit.__version__)"
-
 The output should print the latest version displayed on the badges above.
 
 This will install the minimal `diffpy.srfit` installation.  It will often be used
@@ -136,6 +150,19 @@ and run the following ::
 
         pip install .
 
+This package also provides command-line utilities. To check the software has been installed correctly, type ::
+
+        diffpy.srfit --version
+
+You can also type the following command to verify the installation. ::
+
+        python -c "import diffpy.srfit; print(diffpy.srfit.__version__)"
+
+
+To view the basic usage and available commands, type ::
+
+        diffpy.srfit -h
+
 Getting Started
 ---------------
 
@@ -167,12 +194,12 @@ trying to commit again.
 
 Improvements and fixes are always appreciated.
 
-Before contributing, please read our `Code of Conduct <https://github.com/diffpy/diffpy.srfit/blob/main/CODE_OF_CONDUCT.rst>`_.
+Before contributing, please read our `Code of Conduct <https://github.com/diffpy/diffpy.srfit/blob/main/CODE-OF-CONDUCT.rst>`_.
 
 Contact
 -------
 
-For more information on diffpy.srfit please visit the project `web-page <https://diffpy.github.io/>`_ or email Simon Billinge at sb2896@columbia.edu.
+For more information on diffpy.srfit please visit the project `web-page <https://diffpy.github.io/>`_ or email the maintainers ``Caden Myers (cjm2304@columbia.edu) and Simon J. L. Billinge (sbillinge@ucsb.edu)``.
 
 Acknowledgements
 ----------------

cookiecutter.json

@@ -0,0 +1,20 @@
+{
+  "author_names": "Christopher Farrow, Pavol Juhas, Caden Myers, Simon J. L. Billinge",
+  "author_emails": "farrowch@gmail.com, pavol.juhas@gmail.com, cjm2304@columbia.edu, sbillinge@ucsb.edu",
+  "maintainer_names": "Caden Myers, Simon J. L. Billinge",
+  "maintainer_emails": "cjm2304@columbia.edu, sbillinge@ucsb.edu",
+  "maintainer_github_usernames": "cadenmyers13, sbillinge",
+  "contributors": "Christopher Farrow, Pavol Juhas, Caden Myers, Simon J. L. Billinge, and members of the DiffPy community.",
+  "license_holders": "The DiffPy Team",
+  "project_name": "diffpy.srfit",
+  "github_username_or_orgname": "diffpy",
+  "github_repo_name": "diffpy.srfit",
+  "conda_pypi_package_dist_name": "diffpy.srfit",
+  "package_dir_name": "diffpy.srfit",
+  "project_short_description": "Generalized code base for modeling problems.",
+  "project_keywords": "regression, modeling, fitting, diffraction, PDF",
+  "minimum_supported_python_version": "3.11",
+  "maximum_supported_python_version": "3.13",
+  "project_needs_c_code_compiled": "No",
+  "project_has_gui_tests": "No"
+}