Recut - support Py3.13, add checklist, codespell

.codecov.yml

@@ -1,34 +1,14 @@
-# codecov can find this file anywhere in the repo, so we don't need to clutter
-# the root folder.
-#comment: false
-
-codecov:
-  notify:
-    require_ci_to_pass: no
-
 coverage:
   status:
-    patch:
+    project:  # more options at https://docs.codecov.com/docs/commit-status
       default:
-        target: '70'
-        if_no_uploads: error
-        if_not_found: success
-        if_ci_failed: failure
-    project:
-      default: false
-      library:
-        target: auto
-        if_no_uploads: error
-        if_not_found: success
-        if_ci_failed: error
-        paths: '!*/tests/.*'
-
-      tests:
-        target: 97.9%
-        paths: '*/tests/.*'
-        if_not_found: success
-
-flags:
-  tests:
-    paths:
-      - tests/
+        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]

.codespell/ignore_lines.txt

@@ -0,0 +1,2 @@
+;; Please include filenames and explanations for each ignored line.
+;; See https://docs.openverse.org/meta/codespell.html for docs.

.codespell/ignore_words.txt

@@ -0,0 +1,17 @@
+;; Please include explanations for each ignored word (lowercase).
+;; See https://docs.openverse.org/meta/codespell.html for docs.
+
+;; abbreviation for "materials" often used in a journal title
+mater
+
+;; alternative use of socioeconomic
+socio-economic
+
+;; Frobenius norm used in np.linalg.norm
+fro
+
+;; class name within distutils module
+ccompiler
+
+;; structure file format
+discus

.github/ISSUE_TEMPLATE/bug_feature.md

@@ -0,0 +1,16 @@
+---
+name: Bug Report or Feature Request
+about: Report a bug or suggest a new feature!
+title: ""
+labels: ""
+assignees: ""
+---
+
+### Problem
+
+<!--
+For a bug report, please copy and paste any error messages from the application or command-line here.
+For a feature request, please state how the new functionality could benefit the community.
+-->
+
+### Proposed solution

.github/ISSUE_TEMPLATE/release_checklist.md

@@ -0,0 +1,44 @@
+---
+name: Release
+about: Checklist and communication channel for PyPI and GitHub release
+title: "Ready for <version-number> PyPI/GitHub release"
+labels: "release"
+assignees: ""
+---
+
+### PyPI/GitHub rc-release preparation checklist:
+
+- [ ] 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.
+- [ ] Installation instructions in the README, documentation and on the website (e.g., diffpy.org) are updated.
+- [ ] Successfully run any tutorial examples or do functional testing with the latest Python version.
+- [ ] Grammar and writing quality are checked (no typos).
+
+Please mention @sbillinge here when you are ready for PyPI/GitHub release. Include any additional comments necessary, such as version information and details about the pre-release here:
+
+### PyPI/GitHub  full-release preparation checklist:
+- [ ] Create a new conda environment and install the rc from pypi (`pip install <package-name>=??`)
+- [ ] License information at Pypi is verified as correct.
+- [ ] Docs deployed successfully to `<package-name>.github.io`
+- [ ] Successfully run all tests, tutorial examples or do functional testing
+
+Please let  @sbillinge know that all checks are done and package is ready for full release.
+
+### conda-forge release preparation checklist:
+
+<!-- After @sbillinge 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.
+- [ ] Close any open issues on the feedstock.  Reach out to @bobleesj if you have questions
+- [ ] let @sbillinge and @bobleesj when this is ready
+
+### Post-release checklist
+
+<!-- Before closing this issue, please complete the following: -->
+
+- [ ]  Run tutorial examples and conduct functional testing using the installation guide in the README. Attach screenshots/results as comments.
+- [ ]  Documentation (README, tutorials, API references, and websites) is deployed without broken links or missing figures.

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

@@ -0,0 +1,16 @@
+name: Release (GitHub/PyPI) and Deploy Docs
+
+on:
+  workflow_dispatch:
+  push:
+    tags:
+      - '*'  # Trigger on all tags initially, but tag and release privilege are verified in _build-wheel-release-upload.yml
+
+jobs:
+  release:
+    uses: Billingegroup/release-scripts/.github/workflows/_build-wheel-release-upload.yml@v0
+    with:
+      project: diffpy.pdffit2
+    secrets:
+      PYPI_TOKEN: ${{ secrets.PYPI_TOKEN }}
+      PAT_TOKEN: ${{ secrets.PAT_TOKEN }}

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

@@ -6,7 +6,7 @@ on:
     - main
 
 jobs:
-  build:
+  check-news-item:
     uses: Billingegroup/release-scripts/.github/workflows/_check-news-item.yml@v0
     with:
       project: diffpy.pdffit2

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

@@ -11,7 +11,7 @@ on:
   workflow_dispatch:
 
 jobs:
-  coverage:
+  matrix-coverage:
     uses: Billingegroup/release-scripts/.github/workflows/_matrix-and-codecov-on-merge-to-main.yml@v0
     with:
       project: diffpy.pdffit2

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

@@ -8,9 +8,11 @@ on:
   workflow_dispatch:
 
 jobs:
-  validate:
+  tests-on-pr:
     uses: Billingegroup/release-scripts/.github/workflows/_tests-on-pr.yml@v0
     with:
       project: diffpy.pdffit2
       c_extension: true
       headless: false
+    secrets:
+      CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

.pre-commit-config.yaml

@@ -16,7 +16,10 @@ repos:
       - id: check-yaml
       - id: end-of-file-fixer
       - id: trailing-whitespace
-        exclude: '\.(rst|txt)$'
+      - 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:
@@ -41,3 +44,9 @@ repos:
         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

AUTHORS.rst

@@ -1,7 +1,7 @@
 Authors
 =======
 
-Billinge Group and community contibutors.
+Billinge Group and community contributors.
 
 ----
 
@@ -17,7 +17,7 @@ Previous significant contributors to this code were
 
     Pavol Juhas,  Chris Farrow, Jacques Bloch, Wenduo Zhou
 
-Please see the github contributions and the header of each source file 
+Please see the github contributions and the header of each source file
 for a detailed list of
 contributors.  This is an open-source project and we hope and expect
 that the list of contributors will expand with time.  Many thanks to

README.rst

@@ -121,7 +121,7 @@ and run the following ::
         pip install .
 
 To confirm that the installation was successful, run the following in a terminal ::
-                
+
         python -c "import diffpy.pdffit2; print(diffpy.pdffit2.__version__)"
 
 Support and Contribute

doc/source/examples.rst

@@ -59,7 +59,7 @@ The first example shows how to calculates the PDF for FCC nickel and saves the r
     # display plot window, this must be the last command in the script
     plt.show()
 
-The scripts can be downloaded :download:`here <examples/Ni_calculation.py>`. 
+The scripts can be downloaded :download:`here <examples/Ni_calculation.py>`.
 
 =======================================
 Example 2: Performing simple refinement

news/py313.rst

@@ -0,0 +1,23 @@
+**Added:**
+
+* Python 3.13 support
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* Python 3.10 support
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>

pyproject.toml

@@ -12,9 +12,9 @@ maintainers = [
   { name="Simon J.L. Billinge group", email="[email protected]" },
 ]
 description = "PDFfit2 - real space structure refinement program."
-keywords = ['PDF structure refinement']
+keywords = ["PDF", "structure refinement"]
 readme = "README.rst"
-requires-python = ">=3.10"
+requires-python = ">=3.11, <3.14"
 classifiers = [
         'Development Status :: 5 - Production/Stable',
         'Environment :: Console',
@@ -25,9 +25,9 @@ classifiers = [
         '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',
         'Topic :: Scientific/Engineering :: Physics',
         'Topic :: Scientific/Engineering :: Chemistry',
 ]
@@ -51,6 +51,11 @@ namespaces = false  # to disable scanning PEP 420 namespaces (true by default)
 [tool.setuptools.dynamic]
 dependencies = {file = ["requirements/pip.txt"]}
 
+[tool.codespell]
+exclude-file = ".codespell/ignore_lines.txt"
+ignore-words = ".codespell/ignore_words.txt"
+skip = "*.cif,*.dat,*.cc,*.h"
+
 [tool.black]
 line-length = 115
 include = '\.pyi?$'

src/diffpy/pdffit2/pdffit.py

@@ -301,7 +301,7 @@ def calc(self):
 
         Raises:
             pdffit2.calculationError when allocated space cannot
-            accomodate calculation
+            accommodate calculation
             pdffit.unassignedError when space for calculation has not been
             allocated
         """
@@ -572,7 +572,7 @@ def getR(self):
 
         This function should only be called after data has been loaded or
         calculated. Before a refinement, the list of r-points will reflect the
-        data. Afterwords, they will reflect the fit range.
+        data. Afterwards, they will reflect the fit range.
 
         Raises: pdffit2.unassignedError if no data exists
 
@@ -599,7 +599,7 @@ def getpdf_obs(self):
 
         This function should only be called after data has been loaded or
         calculated. Before a refinement, the list of r-points will reflect the
-        data. Afterwords, they will reflect the fit range.
+        data. Afterwards, they will reflect the fit range.
 
         Raises: pdffit2.unassignedError if no data exists
 
@@ -613,7 +613,7 @@ def getpdf_diff(self):
 
         This function should only be called after data has been loaded or
         calculated. Before a refinement, the list of r-points will reflect the
-        data. Afterwords, they will reflect the fit range.
+        data. Afterwards, they will reflect the fit range.
 
         Raises: pdffit2.unassignedError if no data exists
 
@@ -880,7 +880,7 @@ def blen(self, *args):
                 if isinstance(a2, numbers.Integral):
                     a2 = atom_types[a2 - 1]
             except IndexError:
-                # index of non-existant atom type
+                # index of non-existent atom type
                 return
             # arguments are OK here, get bond length dictionary
             bld = pdffit2.bond_length_types(self._handle, a1, a2, lb, ub)
@@ -930,8 +930,8 @@ def bond_length_types(self, a1, a2, lb, ub):
 
         Return a dictionary of distance data containing
 
-        dij  : list of bond lenghts within given bounds
-        ddij : list of bond legnth standard deviations
+        dij  : list of bond lengths within given bounds
+        ddij : list of bond length standard deviations
         ij0  : pairs of atom indices starting from 0
         ij1  : pairs of atom indices starting from 1