Merge branch 'v3.3.0' into iterpars-behavior

Author: stevenhua0320

.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 }}

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