Autoformatting (#99)

Adds automatic formatting and CI checks.

* Autoformatting

* Autoformat

* Add precommit

* Add dev deps

* M2

* Fix file

* Fixes

* Add CI options

* Pre-commit fix

* Clean up

* Readme

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Add pre-commit-ci

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

.pre-commit-config.yaml

@@ -0,0 +1,28 @@
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v3.2.0
+    hooks:
+    -   id: trailing-whitespace
+    -   id: end-of-file-fixer
+    -   id: check-yaml
+    -   id: check-added-large-files
+-   repo: https://github.com/psf/black
+    rev: 23.3.0
+    hooks:
+    -   id: black
+-   repo: https://github.com/PyCQA/isort
+    rev: 5.12.0
+    hooks:
+    -   id: isort
+        args: ["--profile=black"]
+ci:
+    autofix_commit_msg: |
+        [pre-commit.ci] auto fixes from pre-commit.com hooks
+
+        for more information, see https://pre-commit.ci
+    autofix_prs: true
+    autoupdate_branch: ''
+    autoupdate_commit_msg: '[pre-commit.ci] pre-commit autoupdate'
+    autoupdate_schedule: weekly
+    skip: []
+    submodules: false

MANIFEST.in

@@ -4,4 +4,3 @@ include RMtools_1D/cats/*
 include RMtools_1D/data/*
 include RMtools_1D/README.txt
 include RMtools_3D/README.txt
-

README.md

@@ -1,3 +1,5 @@
+![Tests](https://github.com/CIRADA-Tools/RM-tools/actions/workflows/python-package.yml/badge.svg) [![pre-commit.ci status](https://results.pre-commit.ci/badge/github/CIRADA-Tools/RM-Tools/master.svg)](https://results.pre-commit.ci/latest/github/CIRADA-Tools/RM-Tools/master)
+
 # RM-Tools
 
 RM-synthesis, RM-clean and QU-fitting on polarised radio spectra
@@ -6,48 +8,64 @@ RM-synthesis, RM-clean and QU-fitting on polarised radio spectra
  polarised radio spectra.
 
 
- Initial version by Cormac R. Purcell  
+ Initial version by Cormac R. Purcell
  Currently hosted by CIRADA and maintained by Cameron Van Eck
 
 Version 1.2 is now released! Check the wiki for new functionality.
 
+## Installation / Usage
 Installation, usage instructions and detailed algorithm information can be found in the [wiki](https://github.com/CIRADA-Tools/RM-Tools/wiki).
 
-Structure:  
-RMtools_1D  ... Toolkit to produce Faraday spectra of single pixels.  
-RMtools_3D  ... Toolkit to produce Faraday depth cubes.  
-RMutils     ... Utilities for interacting with polarized data and Faraday depth 
-
-This will make the following modules importable in Python: RMtools_1D, RMtools_3D, RMutil
+## Structure:
+- RMtools_1D  ... Toolkit to produce Faraday spectra of single pixels.
+- RMtools_3D  ... Toolkit to produce Faraday depth cubes.
+- RMutils     ... Utilities for interacting with polarized data and Faraday depth
 
 ![RM-Tools component diagram](https://github.com/CIRADA-Tools/RM-Tools/wiki/diagram.png)
 
-Five terminal commands are added to invoke the main tools:  
-rmsynth1d  
-rmclean1d  
-rmsynth3d  
-rmclean3d  
-qufit
+Five terminal commands are added to invoke the main tools:
+- `rmsynth1d`
+- `rmclean1d`
+- `rmsynth3d`
+- `rmclean3d`
+- `qufit`
 
 Use these commands with a -h flag to get information on the usage of each. Full documentation is on the [wiki](https://github.com/CIRADA-Tools/RM-Tools/wiki).
 
-The following terminal commands are available to access the [additional tools](https://github.com/CIRADA-Tools/RM-Tools/wiki/Tools):  
-rmtools_freqfile  
-rmtools_calcRMSF  
-rmtools_testdata1D  
-rmtools_createchunks  
-rmtools_assemblechunks  
-rmtools_fitIcube  
-rmtools_peakfitcube  
-rmtools_testdata3D  
-rmtools_extractregion
-
+The following terminal commands are available to access the [additional tools](https://github.com/CIRADA-Tools/RM-Tools/wiki/Tools):
+- `rmtools_freqfile`
+- `rmtools_calcRMSF`
+- `rmtools_testdata1D`
+- `rmtools_createchunks`
+- `rmtools_assemblechunks`
+- `rmtools_fitIcube`
+- `rmtools_peakfitcube`
+- `rmtools_testdata3D`
+- `rmtools_extractregion`
 
-If you use this package in a publication, please cite the [ASCL entry](https://ui.adsabs.harvard.edu/abs/2020ascl.soft05003P/abstract) for the time being.  
-A paper with a full description of the package is being prepared but is not available yet.
 
-Questions, bug reports, and feature requests can be posted to the GitHub issues page or sent to Cameron Van Eck, cameron.vaneck (at) anu.edu.au.
+## Citing
+If you use this package in a publication, please cite the [ASCL entry](https://ui.adsabs.harvard.edu/abs/2020ascl.soft05003P/abstract) for the time being. A paper with a full description of the package is being prepared but is not available yet.
 
 More information on the Canadian Initiative for Radio Astronomy Data Analysis (CIRADA) can be found at cirada.ca.
 
-![Tests](https://github.com/CIRADA-Tools/RM-tools/actions/workflows/python-package.yml/badge.svg)
+RM-Tools is open source under an MIT License.
+
+## Contributing
+Contributions are welcome. Questions, bug reports, and feature requests can be posted to the GitHub issues page or sent to Cameron Van Eck, cameron.vaneck (at) anu.edu.au.
+
+The development dependencies can be installed via `pip` from PyPI:
+```bash
+pip install "RM-Tools[dev]"
+```
+or for a local clone:
+```bash
+cd RM-Tools
+pip install ".[dev]"
+```
+
+Code formatting and style is handled by `black` and `isort`, with tests run by `pytest`. A `pre-commit` hook is available to handle the autoformatting. After installing the `dev` dependencies, you can install the hooks by running:
+```bash
+cd RM-Tools
+pre-commit install
+```

RMtools_1D/README.txt

@@ -41,4 +41,3 @@
 ./do_QUfit_1D_mnest.py data/Source1.dat -m 1 -p
 ./do_QUfit_1D_mnest.py data/Source2.dat -m 3 -p
 ./do_QUfit_1D_mnest.py data/Source3.dat -m 3 -p
-

RMtools_1D/__init__.py

@@ -1,2 +1,3 @@
 import pkg_resources
-__version__ = pkg_resources.get_distribution("RM-Tools").version
+
+__version__ = pkg_resources.get_distribution("RM-Tools").version