Merge pull request #117 from GreenBankObservatory/release_resolve_con…

…flicts Release resolve conflicts
GreenBankObservatory · Nov 20, 2023 · 501448a · 501448a
2 parents 365407f + 8838c5e
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diff --git a/.github/workflows/hatch-and-pytest.yml b/.github/workflows/hatch-and-pytest.yml
@@ -5,9 +5,10 @@ name: Build and Pytest
 
 on:
   push:
-    branches: [ "main", "release-0.2.0", "cat-devel", "mwp-devel", "pedro-devel" ]
+    branches: [ "main", "release-*", "cat-devel", "mwp-devel", "pedro-devel", "evan-devel" ]
   pull_request:
-    branches: [ "main", "release-0.2.0", "cat-devel", "mwp-devel", "pedro-devel" ]
+    branches: [ "main", "release-*", "cat-devel", "mwp-devel", "pedro-devel", "evan-devel" ]
+  workflow_dispatch: # needed for "Run" button to show up in action
 jobs:
   build:
     runs-on:  ${{ matrix.os }}
@@ -17,7 +18,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, windows-latest, macos-latest]
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.9", "3.10", "3.11"]
 
     steps:
     - uses: actions/checkout@v3
@@ -28,6 +29,7 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
+        python -m pip install flake8 pytest
         pip install -r requirements.txt
         pip install -e .
     - name: Build with hatch

diff --git a/.github/workflows/pre-commit.yml b/.github/workflows/pre-commit.yml
@@ -0,0 +1,20 @@
+name: pre-commit
+
+on:
+  pull_request:
+  push:
+    branches: [main, release*]
+
+
+jobs:
+  pre-commit:
+    env:
+      SKIP: ruff
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+    - uses: actions/setup-python@v4
+      with:
+        # must match the version in .pre-commit-config.yaml:default_language_version.python
+        python-version: '3.9'
+    - uses: pre-commit/[email protected]
diff --git a/.github/workflows/pyinstaller.yml b/.github/workflows/pyinstaller.yml
@@ -16,7 +16,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, windows-latest, macos-latest]
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.9", "3.10", "3.11"]
 
     steps:
       - uses: actions/checkout@v3

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
@@ -4,6 +4,7 @@ on:
   release:
     types: [ published ]
   workflow_dispatch:
+
 jobs:
   build:
     runs-on:  ${{ matrix.os }}

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -9,6 +9,7 @@ repos:
     rev: v4.4.0
     hooks:
       - id: trailing-whitespace
+        exclude: '(notebooks|attic|benchmark|testdata)/.*'
       - id: end-of-file-fixer
         exclude: LICENSE
       - id: check-yaml
@@ -24,13 +25,12 @@ repos:
     rev: 5.12.0
     hooks:
       - id: isort
-        args: ["--profile", "black", "--filter-files"]
-        exclude: ^notebooks/
+        exclude: '(notebooks|attic|benchmark|testdata)/.*'
   - repo: 'https://github.com/psf/black'
     rev: 23.1.0
     hooks:
       - id: black
-        exclude: ^notebooks/
+        exclude: '(notebooks|attic|benchmark|testdata)/.*'
 #  - repo: https://github.com/jazzband/pip-tools
 #    rev: 6.12.3
 #    hooks:

diff --git a/README.md b/README.md
@@ -1,16 +1,16 @@
 [![Documentation Status](https://readthedocs.org/projects/dysh/badge/?version=latest)](https://dysh.readthedocs.io/en/latest/?badge=latest)
 
-# Dysh
+# dysh
 
-*Dysh* is a Python spectral line data reduction and analysis program for singledish data with specific emphasis on data from the Green Bank Telescope.  It is currently under development in collaboration between the [Green Bank Observatory](https:/greenbankobservatory.org) and the Laboratory for Millimeter-Wave Astronomy (LMA) at [University of Maryland (UMD)](https://www.astro.umd.edu).  It is intended to be a full replacement for the GBO's current reduction package [GBTIDL](https://www.gb.nrao.edu/GBT/DA/gbtidl/users_guide/).
+*dysh* is a Python spectral line data reduction and analysis program for singledish data with specific emphasis on data from the Green Bank Telescope.  It is currently under development in collaboration between the [Green Bank Observatory](https:/greenbankobservatory.org) and the Laboratory for Millimeter-Wave Astronomy (LMA) at [University of Maryland (UMD)](https://www.astro.umd.edu).  It is intended to be a full replacement for the GBO's current reduction package [GBTIDL](https://www.gb.nrao.edu/GBT/DA/gbtidl/users_guide/).
 
 ## 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 3.9+ 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).
+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).
 
 ```bash
     $ pip install dysh

diff --git a/attic/sdfitsload.py b/attic/sdfitsload.py
@@ -93,7 +93,7 @@ def dcmeantsys(calon, caloff, tcal, mode=0, fedge=10, nedge=None):
     mode=1     do the mean after the division
     """
     nchan = len(calon)
-    if nedge == None:
+    if nedge is None:
         nedge = nchan // fedge  # 10 %
     if mode == 0:
         meanoff = np.mean(caloff[nedge:-nedge])

diff --git a/benchmark/revisedstructure.py b/benchmark/revisedstructure.py
@@ -9,9 +9,9 @@
 
 import numpy as np
 from astropy.table import Table, vstack
-from specutils import SpectralRegion, Spectrum1D, SpectrumList
+from specutils import SpectralRegion
 
-from dysh.sdfitsload import Obsblock, SDFITSLoad, baseline, get_size
+from dysh.sdfitsload import SDFITSLoad, baseline
 
 if __name__ == "__main__":
     parser = argparse.ArgumentParser(prog="revisedstructure")

diff --git a/docs/source/design/sdfits_loaders.rst b/docs/source/design/sdfits_loaders.rst
@@ -7,15 +7,15 @@ Motivation
 
 Although the initial design will be for GBT data, a goal is for `dysh` to be easily modifiable for any single-dish radio telescope. Thus came the idea of an SDFITS loader which would standardize inputs.
 
-Obsblock
-========
+ScanBlock
+=========
 
-Here's the class diagram for an `Obsblock` and its derived classes.
+Here's the class diagram for an `ScanBlock` and its derived classes.
 
 .. mermaid::
 
     classDiagram
-        class Obsblock{
+        class ScanBlock{
             metadata
             spectra
             summary()
@@ -35,23 +35,18 @@ Here's the class diagram for an `Obsblock` and its derived classes.
             spectra
             fold()
         }
-        class NodScan{
+        class SubBeamNodScan{
             metadata
             spectra
         }
         class OTFScan{
             metadata
             spectra
         }
-        class ScanAvg{
-            metadata
-            spectra
-        }
-        Obsblock <|-- PSScan
-        Obsblock <|-- FSScan
-        Obsblock <|-- NodScan
-        Obsblock <|-- OTFScan
-        Obsblock <|-- ScanAvg
+        ScanBlock <|-- PSScan
+        ScanBlock <|-- FSScan
+        ScanBlock <|-- NodScan
+        ScanBlock <|-- OTFScan
 
 That's probably not super accurate. I just copied the diagram in the stakeholder presentation from last May.
 
@@ -64,7 +59,7 @@ SDFITSLoad
         class SDFITSLoad{
             _filename
             _bintable
-            _ptable
+            _index
             _binheader
             _data
             _hdu

diff --git a/docs/source/for_developers/git_workflows.rst b/docs/source/for_developers/git_workflows.rst
@@ -43,7 +43,7 @@ Releases
 Release branches will be locked once work on the next release begins.
 
 Setting up your own development branch
-========
+======================================
 
 In the directory you want to work in, set up the repo:
 

diff --git a/docs/source/getting_started/install.rst b/docs/source/getting_started/install.rst
@@ -2,7 +2,7 @@
 Installing ``dysh``
 *******************
 
-``dysh`` requires Python 3.8+ and recent versions of
+``dysh`` requires Python 3.9+ and recent versions of
 `astropy <https://astropy.org>`_,
 `numpy <https://numpy.org>`_,
 `scipy <https://scipy.org>`_,

diff --git a/docs/source/getting_started/tutorials/GBT/tutorial-positionswitch.rst b/docs/source/getting_started/tutorials/GBT/tutorial-positionswitch.rst
@@ -44,6 +44,9 @@ In a `Python` instance, type
 
 Keep the `Python` instance open, we will start working with `dysh` now.
 
+.. note::
+    The data used for this tutorial is ~800 MB. Make sure you have enough disk space and bandwidth to download it.
+
 Inspecting the raw data
 -----------------------
 

diff --git a/docs/source/modules/dysh.spectra.rst b/docs/source/modules/dysh.spectra.rst
@@ -27,10 +27,3 @@ Scan
    :members:
    :undoc-members:
    :show-inheritance:
-
-Obsblock
---------
-.. automodule:: dysh.spectra.obsblock
-   :members:
-   :undoc-members:
-   :show-inheritance: