Run pre-commit hooks on all files

Also:

- Update pre-commit hooks via autoupdate
- Tweak config of various hooks
- Add pip-compile hook

.github/workflows/pre-commit.yml

@@ -0,0 +1,14 @@
+name: pre-commit
+
+on:
+  pull_request:
+  push:
+    branches: [release-0.1.0-precommit]
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+    - uses: actions/setup-python@v3
+    - uses: pre-commit/action@v3.0.0

.github/workflows/python-package.yml

@@ -11,7 +11,7 @@ on:
 jobs:
   build:
     runs-on:  ${{ matrix.os }}
-    
+
     strategy:
       fail-fast: false
       matrix:
@@ -32,4 +32,4 @@ jobs:
         pip install -e .
     - name: Test with pytest
       run: |
-        pytest
+        pytest

.github/workflows/release-test.yml

@@ -1,6 +1,6 @@
 on:
   testrelease:
-    types: 
+    types:
       - published
 
 name: testrelease

.github/workflows/release.yml

@@ -1,6 +1,6 @@
 on:
   release:
-    types: 
+    types:
       - published
 
 name: release

.pre-commit-config.yaml

@@ -1,7 +1,7 @@
 ---
 # See https://pre-commit.com for more information
 default_language_version:
-  python: python3.8
+  python: python3.11
 
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
@@ -10,10 +10,7 @@ repos:
     hooks:
       - id: trailing-whitespace
       - id: end-of-file-fixer
-        exclude: LICENSE
       - id: check-yaml
-      # Might make sense once everything is at Python 3
-      # - id: check-ast
       - id: check-added-large-files
         args:
           - '--maxkb=1024'
@@ -27,12 +24,24 @@ repos:
     hooks:
       - id: isort
   - repo: 'https://github.com/psf/black'
-    rev: 23.1.0
+    rev: 23.7.0
     hooks:
       - id: black
+  - repo: 'https://github.com/PyCQA/autoflake'
+    rev: v2.2.0
+    hooks:
+      - id: autoflake
+  - repo: 'https://github.com/PyCQA/docformatter'
+    rev: v1.7.5
+    hooks:
+      - id: docformatter
+        args:
+            - '--in-place'
+            - '--config=./pyproject.toml'
   - repo: https://github.com/jazzband/pip-tools
-    rev: 6.12.3
+    rev: 7.1.0
     hooks:
       - id: pip-compile
+        files: pyproject.toml
         args:
           - '--resolver=backtracking'

README.md

@@ -5,7 +5,7 @@
 ## Getting Started
 ### Installation
 
-Dysh requires Python 3.8+ and recent versions of [astropy]( https://astropy.org), [numpy](https://numpy.org), [scipy](https://scipy.org), [pandas](https://pandas.pydata.org), [specutils](https://specutils.readthedocs.io/en/stable/),  and [matplotlib](https://matplotlib.org). 
+Dysh requires Python 3.8+ and recent versions of [astropy]( https://astropy.org), [numpy](https://numpy.org), [scipy](https://scipy.org), [pandas](https://pandas.pydata.org), [specutils](https://specutils.readthedocs.io/en/stable/),  and [matplotlib](https://matplotlib.org).
 
 #### With pip from PyPi
 Dysh is most easily installed with *pip*, which will take care of any dependencies.  The packaged code is hosted at the [Python Packaging Index](https://pypi.org/project/dysh).
@@ -15,7 +15,7 @@ Dysh is most easily installed with *pip*, which will take care of any dependenci
 ```
 
 #### From github
-To install from github without creating a separate virtual environment: 
+To install from github without creating a separate virtual environment:
 
 ```bash
     $ git clone git@github.com:GreenBankObservatory/dysh.git
@@ -64,7 +64,7 @@ The virtual environment will be created the first time; subsequent invoking ``ha
 
 ```bash
     (dysh) $ exit
-    $ 
+    $
 ```
 
 4.  Each time when you come back in this directory without being in this virtual environment, you'll need to load the virtual environment
@@ -80,4 +80,3 @@ The virtual environment will be created the first time; subsequent invoking ``ha
 ```bash
     $ pytest
 ```
-

benchmark/README.md

@@ -1,12 +1,12 @@
 # Notes for benchmarking Dysh
 
-The purpose of  benchmarking is to test performance  of 
+The purpose of  benchmarking is to test performance  of
 
-- opening/loading an SDFITS file/hdu 
+- opening/loading an SDFITS file/hdu
 - optionally creating an index of some sort (GBTIDL or pandas)
 - creating spectra from each DATA row of the SDFITS table.
 - remove baselines of order 1, 2, and 3 from each spectrum.
- 
+
 Timing is 'wall clock time', i.e., it includes and kernel/sleep operations.  In python, we are using  *time.perfcounter_ns()*
 
 ## Avoiding File caching
@@ -22,7 +22,7 @@ The OMP_NUM_THREADS environment variable sets the number of threads to use for
 and
     setenv OMP_NUM_THREADS 1
 
-## SDFITS Files 
+## SDFITS Files
 
 The standard set of SDFITS files to run the benchmark on are in /lma1/mpound/GBT/examples/ on LMA machines and /home/scratch/mpound/examples in GBO machines.  The files are (in ascending order of size):
 
@@ -33,15 +33,15 @@ The standard set of SDFITS files to run the benchmark on are in /lma1/mpound/GBT
 - onoff-L/data/TGBT21A_501_11.raw.vegas.fits
 - mapping-L/data/TGBT17A_506_11.raw.vegas/
 TGBT17A_506_11.raw.vegas.A.fits
-- nod-KFPA/data/TGBT22A_503_02.raw.vegas/TGBT22A_503_02.raw.vegas.F.fits 
+- nod-KFPA/data/TGBT22A_503_02.raw.vegas/TGBT22A_503_02.raw.vegas.F.fits
 - mixed-fs-ps/data/AGBT16B_225_05/AGBT16B_225_05.raw.vegas/AGBT16B_225_05.raw.vegas.B.fits
 
 ## Code details
 1. Benchmark code is in the subdirectory *benchmark*
 2. The python benchmark code is *revisedstructure.py* and is invoked with *benchmark_py.csh*
     -  To run it, you have to have dysh installed.  This is done with hatch and I haven't written up the notes for that yet!
     - It has various options to turn on/off pieces of the benchmark, see *revisedstructure.py -h*
- 
+
 ## Output
 Output should be into a (IPAC-formatted) table with the following columns:
 
@@ -50,7 +50,7 @@ Output should be into a (IPAC-formatted) table with the following columns:
 - N_hdu - number of HDU in the file
 - HDU - number of the HDU for which this row contains the benchmark
 - N_rows - number of rows in this HDU
-- N_chan - number of chan per spectum in this HDU  
+- N_chan - number of chan per spectum in this HDU
 - Load - time to load/read the SDFITs file, in ms .  e.g. astropy.io.fits.open()
 - Index - time to create index (e.g. pandas, GBTIDL) in ms
 - Create_Obslocks - time to create Spectrum object for every row of HDU, in ms
@@ -62,4 +62,3 @@ The python script *makeplots.py* will make some standard  plots given the IPAC f
 
     ./makeplots.py -f tab_omp=1.out -t "Timing for Load/Obsblocks/Baseline (OMP=1)" -o t1.png
     ./makeplots.py -f tab_omp_unset.out -t "Timing for Load/Obsblocks/Baseline (OMP unset)" -o t2.png
-

benchmark/benchmark_py.csh

@@ -2,7 +2,7 @@
 #set path = ( . $path )
 #
 # BE sure to echo 1 > /proc/sys/vm/drop_caches before running this.
-unsetenv OMP_NUM_THREADS 
+unsetenv OMP_NUM_THREADS
 set root = "/data/gbt/examples/"
 #set root = "/lma1/mpound/GBT/examples/"
 #set root = "/home/scratch/mpound/examples/"