Skip to content
Draft
Changes from 1 commit
Commits
Show all changes
40 commits
Select commit Hold shift + click to select a range
88a3e0f
Update documentation for the relationship between CIF grammar and the…
janbridley Dec 8, 2025
39a9396
Fix string format
janbridley Dec 8, 2025
e283d39
Unix-style wildcards doc
janbridley Dec 8, 2025
aaf5ad5
Remove exclamation points
janbridley Dec 8, 2025
c498b9d
Clean up development guide
janbridley Dec 8, 2025
6db5a2a
Swap to RST link style for doc comment
janbridley Dec 8, 2025
f77c6f8
Update type hints
janbridley Dec 8, 2025
5e82c5c
Add type hints where they cannot be inferred
janbridley Dec 8, 2025
4d0ba4d
Standardize error handling for gemmi tests
janbridley Dec 8, 2025
d032730
Clean up unused TODOs
janbridley Dec 8, 2025
ea0e515
One straggler TODO
janbridley Dec 8, 2025
92ef1f3
Note TODO
janbridley Dec 8, 2025
3550eae
Swap note -> attention admonition
janbridley Dec 8, 2025
8b0e7ff
Swap to caution
janbridley Dec 8, 2025
81ef61a
One more caution
janbridley Dec 8, 2025
f9522b7
Add GSD requirement for testing
janbridley Dec 8, 2025
c66d871
Fix typos
janbridley Dec 8, 2025
2fef24d
Add HOOMD-Blue example and examples toc section
janbridley Dec 8, 2025
e083212
Add LAMMPS example
janbridley Dec 8, 2025
fe34e8d
Fix LAMMPS example
janbridley Dec 8, 2025
13b2823
Remove unused line
janbridley Dec 8, 2025
9398394
Add noisy data and fix headers
janbridley Dec 8, 2025
6357459
Final title
janbridley Dec 8, 2025
a8d80f4
Doctest LAMMPS output
janbridley Dec 8, 2025
239dc7e
Add example on numerical precision
janbridley Dec 9, 2025
81b0771
Update requirements file for py3.14
janbridley Dec 9, 2025
6ec6f29
Update changelog.rst
janbridley Dec 9, 2025
1b5be04
Fix label in CHANGELOG
janbridley Dec 9, 2025
ab33ab2
Pre-compile patterns for unit cell evaluation
janbridley Dec 10, 2025
4129943
Add example for setting Wyckoff sites
janbridley Dec 10, 2025
fbf40fb
Fix doctest-requires
janbridley Dec 10, 2025
21a5c3f
Add warning for setting structure
janbridley Dec 10, 2025
2287526
Fix type annotation
janbridley Dec 10, 2025
a624d3a
Include only necessary data
janbridley Dec 10, 2025
d3c189c
Merge branch 'doc/grammar' into feat/set_basis
janbridley Dec 10, 2025
84c08e3
sphinx-inline-tabs
janbridley Dec 12, 2025
6ca3a23
Description of Wyckoff postions
janbridley Dec 12, 2025
02c7740
Move up table and fix formatting
janbridley Dec 12, 2025
0860b82
Merge branch 'main' into feat/set_basis
janbridley Dec 12, 2025
ff427e7
Restore heading
janbridley Dec 12, 2025
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
Prev Previous commit
Next Next commit
Clean up development guide
  • Loading branch information
janbridley committed Dec 8, 2025
commit c498b9db180c28229259b7b89dc29371ae8ad58a
24 changes: 16 additions & 8 deletions doc/source/development.rst
Original file line number Diff line number Diff line change
Expand Up @@ -5,9 +5,11 @@ Development Guide
=================


All contributions to **parsnip** are welcome!
Developers are invited to contribute to the framework by pull request to the package repository on `GitHub`_, and all users are welcome to provide contributions in the form of **user feedback** and **bug reports**.
We recommend discussing new features in form of a proposal on the issue tracker for the appropriate project prior to development.
All contributions to **parsnip** are welcome! Developers are invited to contribute to
the framework by pull request to the package repository on `GitHub`_, and all users are
welcome to provide contributions in the form of **user feedback** and **bug reports**.
We recommend discussing new features in form of a proposal on the issue tracker for the
appropriate project prior to development.

.. _github: https://github.com/glotzerlab/parsnip

Expand All @@ -16,10 +18,12 @@ General Guidelines

All code contributed to **parsnip** must adhere to the following guidelines:

* Hard dependencies (those that end users must install to use **parsnip**) are *strongly* discouraged, and should be avoided where possible. Additional dependencies required by developers (those used to run tests or build docs) are allowed where necessary.
* Hard dependencies (those that end users must install to use **parsnip**) are *strongly* discouraged, and should be avoided where possible. Additional dependencies required by developers (those used to run tests or build docs) are allowed if necessary.
* All code should adhere to the source code conventions and satisfy the documentation and testing requirements discussed below.

As portability is a primary feature of **parsnip**, tests are run run on Python versions 3.7 and later. However, first class support should only be expected for versions covered by `NEP 29`_.
As portability is a primary feature of **parsnip**, tests are run run on Python versions
3.9 and later. However, first class support should only be expected for versions covered
by `NEP 29`_.

.. _NEP 29: https://numpy.org/neps/nep-0029-deprecation_policy.html

Expand All @@ -43,9 +47,10 @@ API documentation should be written as part of the docstrings of the package in
Docstrings are automatically validated using `pydocstyle <http://www.pydocstyle.org/>`_ whenever the ruff prek hooks are run.
The `official documentation <https://parsnip.readthedocs.io/>`_ is generated from the docstrings using `Sphinx <http://www.sphinx-doc.org/en/stable/index.html>`_.

In addition to API documentation, inline comments are strongly encouraged.
Code should be written as transparently as possible, so the primary goal of documentation should be explaining the algorithms or mathematical concepts underlying the code.
Multiline comments for regex strings may sometimes be necessary.
In addition to API documentation, inline comments are strongly encouraged. Code should
be written as transparently as possible, so the primary goal of documentation should
be explaining the algorithms or mathematical concepts underlying the code.


Building Documentation
^^^^^^^^^^^^^^^^^^^^^^
Expand All @@ -65,4 +70,7 @@ All code should include a set of tests which validate correct behavior.
All tests should be placed in the ``tests`` folder at the root of the project.
In general, most parts of parsnip primarily require `unit tests <https://en.wikipedia.org/wiki/Unit_testing>`_, but where appropriate `integration tests <https://en.wikipedia.org/wiki/Integration_testing>`_ are also welcome. Core functions should be tested against the sample CIF files included in ``tests/sample_data``.
Tests in **parsnip** use the `pytest <https://docs.pytest.org/>`__ testing framework.
Doctests are automatically integrated with ``pytest`` via
`pytest-doctestplus <https://github.com/scientific-python/pytest-doctestplus>`_.

To run the tests, simply execute ``pytest`` at the root of the repository.
Loading