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8 changes: 4 additions & 4 deletions .codecov.yml
Original file line number Diff line number Diff line change
@@ -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]
19 changes: 16 additions & 3 deletions .codespell/ignore_words.txt
Original file line number Diff line number Diff line change
Expand Up @@ -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
31 changes: 21 additions & 10 deletions .github/ISSUE_TEMPLATE/release_checklist.md
Original file line number Diff line number Diff line change
Expand Up @@ -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.
15 changes: 15 additions & 0 deletions .github/PULL_REQUEST_TEMPLATE/pull_request_template.md
Original file line number Diff line number Diff line change
@@ -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).
-->
6 changes: 4 additions & 2 deletions .github/workflows/build-wheel-release-upload.yml
Original file line number Diff line number Diff line change
Expand Up @@ -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 }}
6 changes: 3 additions & 3 deletions .github/workflows/check-news-item.yml
Original file line number Diff line number Diff line change
Expand Up @@ -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
4 changes: 2 additions & 2 deletions .github/workflows/matrix-and-codecov-on-merge-to-main.yml
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down
12 changes: 12 additions & 0 deletions .github/workflows/publish-docs-on-release.yml
Original file line number Diff line number Diff line change
@@ -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
7 changes: 2 additions & 5 deletions .github/workflows/tests-on-pr.yml
Original file line number Diff line number Diff line change
@@ -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
Expand Down
8 changes: 1 addition & 7 deletions .gitignore
Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,7 @@ __pycache__/
.Python
env/
build/
_build/
develop-eggs/
dist/
downloads/
Expand Down Expand Up @@ -90,10 +91,3 @@ target/

# Ipython Notebook
.ipynb_checkpoints

# version information
setup.cfg
/src/diffpy/*/version.cfg

# Rever
rever/
38 changes: 29 additions & 9 deletions .pre-commit-config.yaml
Original file line number Diff line number Diff line change
@@ -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
Expand Down Expand Up @@ -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]
13 changes: 13 additions & 0 deletions .readthedocs.yaml
Original file line number Diff line number Diff line change
@@ -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
4 changes: 2 additions & 2 deletions CHANGELOG.rst
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
=============
Release Notes
Release notes
=============

.. current developments
Expand Down Expand Up @@ -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


Expand Down
2 changes: 1 addition & 1 deletion CODE-OF-CONDUCT.rst
Original file line number Diff line number Diff line change
Expand Up @@ -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.

Expand Down
2 changes: 1 addition & 1 deletion LICENSE.rst
Original file line number Diff line number Diff line change
Expand Up @@ -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:
Expand Down
8 changes: 5 additions & 3 deletions README.rst
Original file line number Diff line number Diff line change
Expand Up @@ -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|

Expand All @@ -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
Expand Down Expand Up @@ -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
---------------
Expand All @@ -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
-------

Expand Down
12 changes: 7 additions & 5 deletions devutils/sgtbx_extra_groups.py
Original file line number Diff line number Diff line change
@@ -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.
"""
Expand Down Expand Up @@ -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())
Expand Down
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