Merge pull request #139 from TingwenZhang/level-5-2

skpkg: new files

Author: sbillinge

.codecov.yml

@@ -1,14 +1,14 @@
 coverage:
   status:
-    project:  # more options at https://docs.codecov.com/docs/commit-status
+    project: # more options at https://docs.codecov.com/docs/commit-status
       default:
         target: auto # use the coverage from the base commit, fail if coverage is lower
-        threshold: 0%  # allow the coverage to drop by
+        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]
+  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_words.txt

@@ -4,8 +4,21 @@
 ;; abbreviation for "materials" often used in a journal title
 mater
 
-;; alternative use of socioeconomic
-socio-economic
-
 ;; Frobenius norm used in np.linalg.norm
 fro
+
+;; "discus" is the name of a software package
+discus
+DISCUS
+
+;; chemical elements
+Te
+Nd
+
+;; /src/diffpy/structure/parsers/p_pdb.py:100
+;; pdb identifier
+CONECT
+
+;; /src/diffpy/structure/parsers/p_xcfg.py:452
+;; used in a function
+BU

.github/ISSUE_TEMPLATE/release_checklist.md

@@ -6,30 +6,41 @@ labels: "release"
 assignees: ""
 ---
 
-### PyPI/GitHub release checklist:
+### 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.
+      missing), tutorials, and other human-written text is up-to-date with any changes in the code.
+- [ ] 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.
 
-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:
+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:
 
-### conda-forge release checklist:
+### PyPI/GitHub full-release preparation checklist:
 
-<!-- After @sbillinge releases the PyPI package, please check the following when creating a PR for conda-forge release.-->
+- [ ] Create a new conda environment and install the rc from PyPI (`pip install <package-name>==??`)
+- [ ] License information on PyPI is correct.
+- [ ] Docs are deployed successfully to `https://<github-username-or-orgname>/<package-name>`.
+- [ ] Successfully run all tests, tutorial examples or do functional testing.
 
+Please let the maintainer know that all checks are done and the package is ready for full release.
+
+### conda-forge release preparation checklist:
+
+<!-- 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.
-- [ ] All relevant issues in the feedstock are addressed in the release PR.
+- [ ] Close any open issues on the feedstock. Reach out to the maintainer if you have questions.
+- [ ] Tag the maintainer for conda-forge release.
 
 ### 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.
+- [ ] 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/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

@@ -4,13 +4,15 @@ 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:
-    uses: Billingegroup/release-scripts/.github/workflows/_build-wheel-release-upload.yml@v0
+    uses: scikit-package/release-scripts/.github/workflows/_build-wheel-release-upload.yml@v0
     with:
       project: diffpy.structure
+      c_extension: false
+      maintainer_GITHUB_username: sbillinge
     secrets:
       PYPI_TOKEN: ${{ secrets.PYPI_TOKEN }}
       PAT_TOKEN: ${{ secrets.PAT_TOKEN }}

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

@@ -3,10 +3,10 @@ name: Check for News
 on:
   pull_request_target:
     branches:
-    - main
+      - main
 
 jobs:
-  build:
-    uses: Billingegroup/release-scripts/.github/workflows/_check-news-item.yml@v0
+  check-news-item:
+    uses: scikit-package/release-scripts/.github/workflows/_check-news-item.yml@v0
     with:
       project: diffpy.structure

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

@@ -11,8 +11,8 @@ on:
   workflow_dispatch:
 
 jobs:
-  coverage:
-    uses: Billingegroup/release-scripts/.github/workflows/_matrix-and-codecov-on-merge-to-main.yml@v0
+  matrix-coverage:
+    uses: scikit-package/release-scripts/.github/workflows/_matrix-and-codecov-on-merge-to-main.yml@v0
     with:
       project: diffpy.structure
       c_extension: false

.github/workflows/publish-docs-on-release.yml

@@ -0,0 +1,12 @@
+name: Deploy Documentation on Release
+
+on:
+  workflow_dispatch:
+
+jobs:
+  docs:
+    uses: scikit-package/release-scripts/.github/workflows/_publish-docs-on-release.yml@v0
+    with:
+      project: diffpy.structure
+      c_extension: false
+      headless: false

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

@@ -1,15 +1,12 @@
 name: Tests on PR
 
 on:
-  push:
-    branches:
-      - main
   pull_request:
   workflow_dispatch:
 
 jobs:
-  validate:
-    uses: Billingegroup/release-scripts/.github/workflows/_tests-on-pr.yml@v0
+  tests-on-pr:
+    uses: scikit-package/release-scripts/.github/workflows/_tests-on-pr.yml@v0
     with:
       project: diffpy.structure
       c_extension: false

.gitignore

@@ -10,6 +10,7 @@ __pycache__/
 .Python
 env/
 build/
+_build/
 develop-eggs/
 dist/
 downloads/
@@ -90,10 +91,3 @@ target/
 
 # Ipython Notebook
 .ipynb_checkpoints
-
-# version information
-setup.cfg
-/src/diffpy/*/version.cfg
-
-# Rever
-rever/

.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
@@ -44,3 +44,23 @@ 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
+  # 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

CHANGELOG.rst

@@ -1,5 +1,5 @@
 =============
-Release Notes
+Release notes
 =============
 
 .. current developments
@@ -28,7 +28,7 @@ Release Notes
 **Fixed:**
 
 * Add getting started section and re-arrange install success check instructions
-* Added termial script for transtru app in pyproject.toml
+* Added terminal script for transtru app in pyproject.toml
 * Changed requires-python to align with classifiers
 
 

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

@@ -15,7 +15,7 @@ Copyright (c) 2014, Australian Synchrotron Research Program Inc., ("ASRP")
 
 Copyright (c) 2014-2019, Brookhaven Science Associates, Brookhaven National Laboratory
 
-Copyright (c) 2024, The Trustees of Columbia University in the City of New York.
+Copyright (c) 2024-2025, The Trustees of Columbia University in the City of New York.
 All rights reserved.
 
 The "DiffPy-CMI" is distributed subject to the following license conditions:

README.rst

@@ -8,7 +8,7 @@
         :target: https://diffpy.github.io/diffpy.structure
         :height: 100px
 
-|PyPi| |Forge| |PythonVersion| |PR|
+|PyPI| |Forge| |PythonVersion| |PR|
 
 |CI| |Codecov| |Black| |Tracking|
 
@@ -26,7 +26,7 @@
 
 .. |PR| image:: https://img.shields.io/badge/PR-Welcome-29ab47ff
 
-.. |PyPi| image:: https://img.shields.io/pypi/v/diffpy.structure
+.. |PyPI| image:: https://img.shields.io/pypi/v/diffpy.structure
         :target: https://pypi.org/project/diffpy.structure/
 
 .. |PythonVersion| image:: https://img.shields.io/pypi/pyversions/diffpy.structure
@@ -132,7 +132,7 @@ trying to commit again.
 
 Improvements and fixes are always appreciated.
 
-Before contribuing, please read our `Code of Conduct <https://github.com/diffpy/diffpy.structure/blob/main/CODE-OF-CONDUCT.rst>`_.
+Before contributing, please read our `Code of Conduct <https://github.com/diffpy/diffpy.structure/blob/main/CODE-OF-CONDUCT.rst>`_.
 
 Acknowledgement
 ---------------
@@ -143,6 +143,8 @@ originate from the `pymmlib project <http://pymmlib.sourceforge.net>`_.
 Less common settings of space groups were generating using the
 `Computational Crystallography Toolbox <http://cctbx.sourceforge.net>`_.
 
+``diffpy.structure`` is built and maintained with `scikit-package <https://scikit-package.github.io/scikit-package/>`_.
+
 Contact
 -------
 

devutils/sgtbx_extra_groups.py

@@ -1,10 +1,11 @@
 #!/usr/bin/env python
 
-"""Quick and extremely dirty script for generating code for SpaceGroup that
-are defined in cctbx, but not in mmLib.  It was used to generate module
-sgtbxspacegroups.
+"""Quick and extremely dirty script for generating code for SpaceGroup
+that are defined in cctbx, but not in mmLib.  It was used to generate
+module sgtbxspacegroups.
 
-This is a utility script that should not be included with code distribution.
+This is a utility script that should not be included with code
+distribution.
 
 Not to be included with code distributions.
 """
@@ -40,7 +41,8 @@ def tupleToSGArray(tpl):
 
 
 def mmSpaceGroupFromSymbol(symbol):
-    """Construct SpaceGroup instance from a string symbol using sgtbx data."""
+    """Construct SpaceGroup instance from a string symbol using sgtbx
+    data."""
     sginfo = sgtbx.space_group_info(symbol)
     symop_list = []
     symop_list = getSymOpList(sginfo.group())