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Dev #60

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merged 5 commits into from
Oct 13, 2024
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Dev #60

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30620f3
Add repostatus.org badge and reorder Project badges
jsdodge Oct 12, 2024
20f3ee1
Update documentation for linting with Hatch
jsdodge Oct 12, 2024
a59e113
Update documentation to include instructions for type checking
jsdodge Oct 12, 2024
0cd0ce2
Bump version; update changelog
jsdodge Oct 13, 2024
f67c651
Revise JOSS paper; update changelog
jsdodge Oct 13, 2024
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12 changes: 12 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -5,6 +5,17 @@
Please follow the guidelines at [Common Changelog](https://common-changelog.org)
for maintaining this file.

## [0.5.3] - 2024-10-12

### Fixed
- Fix documentation error in the Contributing section
- Fix typographical errors in JOSS paper

### Added
- Add [repostatus.org](https://www.repostatus.org/) badge
- Add documentation on type checking in the Contributing section
- Add student acknowledgements to JOSS paper

## [0.5.2] - 2024-09-11

### Changed
Expand Down Expand Up @@ -263,6 +274,7 @@ _Changelog introduced._

- Remove `tdtf`

[0.5.3]: https://github.com/dodge-research-group/thztools/releases/tag/v0.5.3
[0.5.2]: https://github.com/dodge-research-group/thztools/releases/tag/v0.5.2
[0.5.1]: https://github.com/dodge-research-group/thztools/releases/tag/v0.5.1
[0.5.0]: https://github.com/dodge-research-group/thztools/releases/tag/v0.5.0
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12 changes: 6 additions & 6 deletions README.md
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Expand Up @@ -15,12 +15,12 @@ to use statistically optimal methods for doing this analysis, as described in [L

This is *beta* software that is currently under development.

| Information | Links |
|:------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| **Project** | [![DOI](https://zenodo.org/badge/569133241.svg)](https://zenodo.org/doi/10.5281/zenodo.10100093) ![PyPI - Status](https://img.shields.io/pypi/status/thztools) ![PyPI - Python Version](https://img.shields.io/pypi/pyversions/thztools) ![PyPI - Version](https://img.shields.io/pypi/v/thztools) [![Anaconda-Server Badge](https://anaconda.org/conda-forge/thztools/badges/version.svg)](https://anaconda.org/conda-forge/thztools) ![GitHub](https://img.shields.io/github/license/dodge-research-group/thztools) [![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff) [![Common Changelog](https://common-changelog.org/badge.svg)](https://common-changelog.org) [![Contributor Covenant](https://img.shields.io/badge/Contributor%20Covenant-2.1-4baaaa.svg)](code_of_conduct.md) |
| **Build** | ![GitHub Workflow Status](https://img.shields.io/github/actions/workflow/status/dodge-research-group/thztools/sphinx.yml?label=build%3Adocs) ![GitHub Workflow Status](https://img.shields.io/github/actions/workflow/status/dodge-research-group/thztools/pytest-with-coverage.yml?label=build%3Atests%20(conda)) ![GitHub Workflow Status](https://img.shields.io/github/actions/workflow/status/dodge-research-group/thztools/test-pip.yml?label=build%3Atests%20(pip)) [![codecov](https://codecov.io/gh/dodge-research-group/thztools/branch/dev/graph/badge.svg?token=U8PLKTQ7AH)](https://codecov.io/gh/dodge-research-group/thztools) |
| **Documentation** | https://dodge-research-group.github.io/thztools/ |
| **Cite** | L. Mohtashemi et al., *Opt. Express* **29**, 4912 (2021). [(DOI)](https://doi.org/10.1364/OE.417724) |
| Information | Links |
|:------------------|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| **Project** | [![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active) ![GitHub](https://img.shields.io/github/license/dodge-research-group/thztools) ![PyPI - Status](https://img.shields.io/pypi/status/thztools) ![PyPI - Version](https://img.shields.io/pypi/v/thztools) [![Anaconda-Server Badge](https://anaconda.org/conda-forge/thztools/badges/version.svg)](https://anaconda.org/conda-forge/thztools) ![PyPI - Python Version](https://img.shields.io/pypi/pyversions/thztools) [![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff) [![Common Changelog](https://common-changelog.org/badge.svg)](https://common-changelog.org) [![Contributor Covenant](https://img.shields.io/badge/Contributor%20Covenant-2.1-4baaaa.svg)](code_of_conduct.md) [![DOI](https://zenodo.org/badge/569133241.svg)](https://zenodo.org/doi/10.5281/zenodo.10100093) |
| **Build** | ![GitHub Workflow Status](https://img.shields.io/github/actions/workflow/status/dodge-research-group/thztools/sphinx.yml?label=build%3Adocs) ![GitHub Workflow Status](https://img.shields.io/github/actions/workflow/status/dodge-research-group/thztools/pytest-with-coverage.yml?label=build%3Atests%20(conda)) ![GitHub Workflow Status](https://img.shields.io/github/actions/workflow/status/dodge-research-group/thztools/test-pip.yml?label=build%3Atests%20(pip)) [![codecov](https://codecov.io/gh/dodge-research-group/thztools/branch/dev/graph/badge.svg?token=U8PLKTQ7AH)](https://codecov.io/gh/dodge-research-group/thztools) |
| **Documentation** | https://dodge-research-group.github.io/thztools/ |
| **Cite** | L. Mohtashemi et al., *Opt. Express* **29**, 4912 (2021). [(DOI)](https://doi.org/10.1364/OE.417724) |

The original MATLAB code is available at [Zenodo](https://zenodo.org/record/4876388).

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8 changes: 6 additions & 2 deletions docs/source/contributing.rst
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Expand Up @@ -72,9 +72,13 @@ To execute tests with ``pytest``::

hatch run test

To lint the code base with ``ruff`` and apply ``black`` format rules::
To lint the code base with ``ruff``::

hatch run lint:all
hatch fmt

To run type checking with ``mypy``::

hatch run lint:typing

To build the documentation with ``sphinx`` and test examples with ``doctest``::

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12 changes: 8 additions & 4 deletions paper/paper.md
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Expand Up @@ -49,7 +49,7 @@ bibliography: paper.bib
Terahertz time-domain spectroscopy (THz-TDS) uses short electromagnetic pulses
to probe the electromagnetic response of matter over frequencies from about
0.1 THz to about 10 THz, where
1 THz = 10<sup>12</sup> Hz [@neu2018a]. A typical measurement
1 THz = 10^12^ Hz [@neu2018a]. A typical measurement
compares two electromagnetic pulses, one of which has interacted with a material
and another which has not. The pulses are measured as a function of time, but
the electromagnetic properties of matter are most naturally described as a
Expand All @@ -68,7 +68,7 @@ using a maximum-likelihood estimation procedure in the time
domain [@mohtashemi2021]. To support this mode of analysis, the `THzTools`
package provides functionality and documentation that are unavailable in
existing THz-TDS analysis software [@peretti2019; @tayvah2021; @lee2023]. It
provides functions to simulate THz-TDS measurements, apply a freqeuncy response
provides functions to simulate THz-TDS measurements, apply a frequency response
function to a THz-TDS waveform, characterize the noise of a THz-TDS system, and
fit a parameterized frequency response function to a pair of input and output
waveforms.
Expand All @@ -79,7 +79,11 @@ this codebase to Python, we introduced new functionality, optimized the code for
speed and efficiency, and revised the user interface to make it easier to use.

# Acknowledgements
J. S. D. acknowledges support from the Natural Sciences and Engineering
Research Council of Canada (NSERC).
J. P. L. and S. H.-G. acknowledge support from Mitacs Globalink Research
Internship Program. A. N. acknowledges support from the Natural Sciences and
Engineering Research Council of Canada Collaborative Research and Training
Experience (NSERC CREATE) Program in Quantum Computing. J. S. D. acknowledges
support from the Natural Sciences and Engineering Research Council of Canada
(NSERC).

# References
2 changes: 1 addition & 1 deletion src/thztools/__about__.py
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__version__ = "0.5.2"
__version__ = "0.5.3"
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