Recut - codecov in PR, Codespell, release checklist (#136)

* modify codecov.yml, remove .coveragerc, add news

* Add news for codecov

Author: bobleesj

.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]

.coveragerc

@@ -13,10 +13,16 @@ assignees: ""
 - [ ] 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 and
-  tested
-- [ ] Successfully run any tutorial examples or do functional testing in some other way.
+- [ ] Installation instructions in the README, documentation and on the website (e.g., diffpy.org) updated.
+- [ ] Successfully run any tutorial examples or do functional testing with the latest Python version
 - [ ] Grammar and writing quality have been checked (no typos).
 
 Please mention @sbillinge when you are ready for release. Include any additional comments necessary, such as
-version information and details about the pre-release.
+version information and details about the pre-release here:
+
+### 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.
+- [ ]  Documentation (README, tutorials, API references, and websites) is deployed without broken links or missing figures.

.github/ISSUE_TEMPLATE/release_checklist.md

@@ -1,4 +1,4 @@
-name: Release (GitHub/PyPI)
+name: Release (GitHub/PyPI) and Deploy Docs
 
 on:
   workflow_dispatch:
@@ -8,8 +8,6 @@ on:
 
 jobs:
   release:
-    permissions:
-      contents: write
     uses: Billingegroup/release-scripts/.github/workflows/_build-wheel-release-upload.yml@v0
     with:
       project: diffpy.snmf

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

@@ -1,6 +1,6 @@
 **Added:**
 
-* Codecov coverage report in PR
+* Coverage report in each PR
 
 **Changed:**
 

news/codecov.rst

@@ -11,7 +11,7 @@ authors = [
 maintainers = [
   { name="Simon J.L. Billinge group", email="simon.billinge@gmail.com" },
 ]
-description = "A python package implementing the stretched NMF algorithm."
+description = "Python package implementing the stretched NMF algorithm."
 keywords = ['diffpy', 'PDF']
 readme = "README.rst"
 requires-python = ">=3.11, <3.14"
@@ -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',
 ]
@@ -57,7 +57,7 @@ dependencies = {file = ["requirements/pip.txt"]}
 [tool.codespell]
 exclude-file = ".codespell/ignore_lines.txt"
 ignore-words = ".codespell/ignore_words.txt"
-skip = "*.cif"
+skip = "*.cif,*.dat"
 
 [tool.black]
 line-length = 115