Pre commit

.coveragerc

@@ -3,4 +3,3 @@ omit = */tests/*
 
 [report]
 omit = */tests/*
-

.flake8

@@ -0,0 +1,38 @@
+[flake8]
+ignore =
+    E203  # No space before colon
+    W503
+    C408  # Ignore using dict() function.
+    D107  # Missing docstring in __init__ (we do it in the class)
+    D401  # "First line should be in imperative mood" -- this doesn't work for properties, see https://github.com/PyCQA/pydocstyle/issues/301
+    A003  # allow method names to be the same as python builtins
+    RST210  # inline strong start-string without end-string. This is OK in the case of **kwargs in parameters.
+    D     # TODO: add doc checks back in by removing this line!
+    E501  # TODO: add this back in to ensure lines aren't too long!
+    T001  # Allow print statements (eventually should use logging instead...)
+    B008  # allow function calls in argument defaults.
+    A002  # allow arguments to shadow python builtins
+max-line-length = 88
+# TODO: max-complexity should be 18!
+max-complexity = 75
+per-file-ignores =
+    docs/conf.py:D,A
+    */__init__.py:F401
+    scripts/*:T001,T201
+rst-roles =
+    class
+    func
+    mod
+    data
+    const
+    meth
+    attr
+    exc
+    obj
+rst-directives =
+    note
+    warning
+    versionadded
+    versionchanged
+    deprecated
+    seealso

.gitignore

@@ -11,3 +11,5 @@ eggs/
 *egg-info
 *GIT_INFO
 *ipynb_checkpoints
+hera_pspec/_version.py
+.vscode/

.pre-commit-config.yaml

@@ -0,0 +1,45 @@
+exclude: 'setup.py|hera_pspec/data/|pipelines/web_ui/w3.css'
+
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.2.0
+    hooks:
+    - id: trailing-whitespace
+    - id: check-added-large-files
+    - id: check-ast
+    - id: check-json
+    # - id: check-merge-conflict
+    - id: check-xml
+    - id: check-yaml
+      args: ['--unsafe']  # Only check syntax rather than try to load.
+    - id: debug-statements
+    - id: end-of-file-fixer
+    - id: requirements-txt-fixer
+    - id: mixed-line-ending
+      args: ['--fix=no']
+
+  - repo: https://github.com/PyCQA/flake8
+    rev: 4.0.1  # pick a git hash / tag to point to
+    hooks:
+    -   id: flake8
+        additional_dependencies:
+          - flake8-rst-docstrings
+          - flake8-docstrings
+          - flake8-builtins
+          - flake8-logging-format
+          - flake8-rst-docstrings
+          - flake8-rst
+          - flake8-markdown
+          - flake8-bugbear
+          - flake8-comprehensions
+          - flake8-print
+
+  - repo: https://github.com/psf/black
+    rev: 22.3.0
+    hooks:
+    - id: black
+
+  - repo: https://github.com/pre-commit/pygrep-hooks
+    rev: v1.9.0
+    hooks:
+      - id: rst-backticks

CHANGELOG.md

@@ -1,12 +1,12 @@
 v0.2.0 (2019-08-09)
     * Python 3 compatibility.
-    * Allow cross-polarization spectra to be calculated as long as they 
+    * Allow cross-polarization spectra to be calculated as long as they
       aren't beam-normalized; polarizations now specified as polpairs.
     * Time-dependent noise power spectra capability in generate_noise.
     * Methods to fetch redundant baselines/blpairs from UVPSpec objects.
-    * Exact normalization mode (Saurabh Singh) with optimization (Ronan 
+    * Exact normalization mode (Saurabh Singh) with optimization (Ronan
       Legin).
-    * Updated covariance handling, incl. averaging and analytic variance 
+    * Updated covariance handling, incl. averaging and analytic variance
       (Jianrong Tan).
     * New 'lazy covariance' weighting mode (Aaron Ewall-Wice).
     * Fix bug where little_h was passed incorrectly (Zachary Martinot).
@@ -15,6 +15,6 @@ v0.2.0 (2019-08-09)
     * Various minor interface changes and improved tests.
 
 v0.1.0 (2018-07-18)
-    * Initial release; implements core functionality, 
+    * Initial release; implements core functionality,
       documentation, and tests.
     * Includes basic pipeline run scripts.

README.md

@@ -4,23 +4,23 @@
 [![codecov](https://codecov.io/gh/HERA-Team/hera_pspec/branch/master/graph/badge.svg)](https://codecov.io/gh/HERA-Team/hera_pspec)
 [![Documentation](https://readthedocs.org/projects/hera-pspec/badge/?version=latest)](https://readthedocs.org/projects/hera-pspec/badge/?version=latest)
 
-The ``hera_pspec`` library provides all of the tools and data structures needed to perform a delay 
-spectrum analysis on interferometric data. The input data can be in any format supported by ``pyuvdata``, 
+The ``hera_pspec`` library provides all of the tools and data structures needed to perform a delay
+spectrum analysis on interferometric data. The input data can be in any format supported by ``pyuvdata``,
 and the output data are stored in HDF5 containers.
 
 For usage examples and documentation, see http://hera-pspec.readthedocs.io/en/latest/.
 
 ## Installation
 Preferred method of installation for users is simply `pip install .`
-(or `pip install git+https://github.com/HERA-Team/hera_pspec`). This will install 
+(or `pip install git+https://github.com/HERA-Team/hera_pspec`). This will install
 required dependencies. See below for manual dependency management.
- 
+
 ### Dependencies
 If you are using `conda`, you may wish to install the following dependencies manually
 to avoid them being installed automatically by `pip`::
 
     $ conda install -c conda-forge "numpy>=1.15" "astropy>=2.0" h5py pyuvdata scipy matplotlib pyyaml
-    
+
 ### Developing
 If you are developing `hera_pspec`, it is preferred that you do so in a fresh `conda`
 environment. The following commands will install all relevant development packages::
@@ -30,9 +30,9 @@ environment. The following commands will install all relevant development packag
     $ conda create -n hera_pspec python=3
     $ conda activate hera_pspec
     $ conda env update -n hera_pspec -f ci/hera_pspec_tests.yml
-    $ pip install -e . 
+    $ pip install -e .
 
-This will install extra dependencies required for testing/development as well as the 
+This will install extra dependencies required for testing/development as well as the
 standard ones.
 
 ### Running Tests
@@ -42,10 +42,10 @@ From the source `hera_pspec` directory run: `pytest`.
 
 ## Running `hera_pspec`
 
-See the documentation for an 
-[overview and examples](http://hera-pspec.readthedocs.io/en/latest/pspec.html) 
-of how to run `hera_pspec`. There are also some example Jupyter notebooks, 
-including [`examples/PS_estimation_examples.ipynb`](examples/PS_estimation_example.ipynb) 
-(a brief tutorial on how to create delay spectra), and 
-[`examples/PSpecBeam_tutorial.ipynb`](examples/PSpecBeam_tutorial.ipynb) (a brief 
+See the documentation for an
+[overview and examples](http://hera-pspec.readthedocs.io/en/latest/pspec.html)
+of how to run `hera_pspec`. There are also some example Jupyter notebooks,
+including [`examples/PS_estimation_examples.ipynb`](examples/PS_estimation_example.ipynb)
+(a brief tutorial on how to create delay spectra), and
+[`examples/PSpecBeam_tutorial.ipynb`](examples/PSpecBeam_tutorial.ipynb) (a brief
 tutorial on handling beam objects).

ci/hera_pspec_tests.yml

@@ -22,4 +22,3 @@ dependencies:
     - git+https://github.com/RadioAstronomySoftwareGroup/pyuvdata
     - git+https://github.com/HERA-Team/uvtools
     - git+https://github.com/HERA-Team/hera_cal
-

docs/Makefile

@@ -17,4 +17,4 @@ help:
 # Catch-all target: route all unknown targets to Sphinx using the new
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
 %: Makefile
-	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)