Merge pull request #105 from GreenBankObservatory/multifits

Multifits

.github/workflows/build.yml

@@ -1,9 +1,8 @@
-name: hatch build
+name: Build with hatch
 
 on:
   release:
-    types: 
-      - [created]
+    types: [created]
   workflow_dispatch: # needed for "Run" button to show up in action menu
 
 jobs:
@@ -15,7 +14,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest]
-        python-version: "3.x"
+        python-version: ["3.x"]
     steps:
     - uses: actions/checkout@v3
     - name: Set up Python ${{ matrix.python-version }}
@@ -25,8 +24,8 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install -r requirements-dev.txt
+        pip install -r requirements_dev.txt
         pip install -e .
-    - hatch: Build with hatch
+    - name: Build with hatch
       run: |
         hatch build -c 

.github/workflows/python-package.yml

@@ -8,6 +8,7 @@ on:
     branches: [ "main", "release-0.1.0", "cat-devel", "mwp-devel", "pedro-devel" ]
   pull_request:
     branches: [ "main", "release-0.1.0", "cat-devel", "mwp-devel", "pedro-devel" ]
+  workflow_dispatch: # needed for "Run" button to show up in action 
 jobs:
   build:
     runs-on:  ${{ matrix.os }}
@@ -32,4 +33,4 @@ jobs:
         pip install -e .
     - name: Test with pytest
       run: |
-        pytest
+        pytest

.github/workflows/release.yml

@@ -1,15 +1,14 @@
+name: Publish Release to PyPi
+
 on:
   release:
-    types: 
-      - published
-
-name: release
-
+    types: [ published ]
+  workflow_dispatch:
 jobs:
   build:
     runs-on:  ${{ matrix.os }}
     environment: release
-    
+
     strategy:
       fail-fast: false
       matrix:
@@ -26,8 +25,9 @@ jobs:
         python -m pip install --upgrade pip
         pip install -r requirements-dev.txt
         pip install -e .
-    - hatch: Build with hatch
-        hatch build -c 
+    - name: Build with hatch
+      run: |
+        hatch build -c
 
   pypi-publish:
     name: upload release to PyPI

.github/workflows/testworkflow.yml

@@ -0,0 +1,16 @@
+name: TestWorkflow
+
+on:
+  release:
+    types: [created]
+  workflow_dispatch:
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Run a one-line script
+        run: echo Hello, world!

.pre-commit-config.yaml

@@ -1,7 +1,7 @@
 ---
 # See https://pre-commit.com for more information
 default_language_version:
-  python: python3.8
+  python: python3.10
 
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
@@ -26,10 +26,12 @@ repos:
     rev: 5.12.0
     hooks:
       - id: isort
+        exclude: ^notebooks/
   - repo: 'https://github.com/psf/black'
     rev: 23.1.0
     hooks:
       - id: black
+        exclude: ^notebooks/
   - repo: https://github.com/jazzband/pip-tools
     rev: 6.12.3
     hooks:

.readthedocs.yaml

@@ -17,7 +17,7 @@ build:
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
-   configuration: docs/conf.py
+   configuration: docs/source/conf.py
 
 # If using Sphinx, optionally build your docs in additional formats such as PDF
 # formats:

README.md

@@ -1,3 +1,5 @@
+[![Documentation Status](https://readthedocs.org/projects/dysh/badge/?version=latest)](https://dysh.readthedocs.io/en/latest/?badge=latest)
+
 # 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/).
@@ -14,7 +16,7 @@ Dysh is most easily installed with *pip*, which will take care of any dependenci
     $ pip install dysh
 ```
 
-#### From github
+#### From GitHub
 To install from github without creating a separate virtual environment: 
 
 ```bash

docs/.env.template

@@ -0,0 +1,8 @@
+# Template environment file for building the docs
+# Copy this to .env, then edit all indicated lines
+
+export DOCS_ROOT=""  # EDIT ME
+export DOCS_HOST=""  # EDIT ME
+export DOCS_PORT=""  # EDIT ME
+
+alias startdocs="cd $DOCS_ROOT && source docs-env/bin/activate && cd source && sphinx-autobuild . _build -b html --host $DOCS_HOST --port $DOCS_PORT"

docs/requirements.txt

@@ -1,13 +1,72 @@
-myst_parser
-numpydoc
-sphinx
-sphinx-automodapi
-sphinxcontrib-applehelp
-sphinxcontrib-devhelp
-sphinxcontrib-htmlhelp
-sphinxcontrib-jsmath
-sphinxcontrib-qthelp
-sphinxcontrib-serializinghtml
-sphinxcontrib-websupport
-sphinx_rtd_theme
-sphinxcontrib_mermaid
+alabaster==0.7.13
+asdf==2.15.1
+asdf-astropy==0.4.0
+asdf-coordinates-schemas==0.2.0
+asdf-standard==1.0.3
+asdf-transform-schemas==0.3.0
+asdf-unit-schemas==0.1.0
+asdf-wcs-schemas==0.1.1
+astropy==5.3.2
+attrs==23.1.0
+Babel==2.12.1
+certifi==2023.7.22
+charset-normalizer==3.2.0
+colorama==0.4.6
+contourpy==1.1.0
+cycler==0.11.0
+docutils==0.18.1
+fonttools==4.42.1
+gwcs==0.18.3
+idna==3.4
+imagesize==1.4.1
+importlib-metadata==6.8.0
+importlib-resources==6.0.1
+Jinja2==3.1.2
+jmespath==1.0.1
+jsonschema==4.19.0
+jsonschema-specifications==2023.7.1
+kiwisolver==1.4.4
+livereload==2.6.3
+markdown-it-py==3.0.0
+MarkupSafe==2.1.3
+matplotlib==3.7.2
+mdit-py-plugins==0.4.0
+mdurl==0.1.2
+myst-parser==2.0.0
+ndcube==2.1.3
+numpy==1.25.2
+numpydoc==1.5.0
+packaging==23.1
+pandas==2.0.3
+Pillow==10.0.0
+pyerfa==2.0.0.3
+Pygments==2.16.1
+pyparsing==3.0.9
+python-dateutil==2.8.2
+pytz==2023.3
+PyYAML==6.0.1
+referencing==0.30.2
+requests==2.31.0
+rpds-py==0.9.2
+scipy==1.11.2
+semantic-version==2.10.0
+six==1.16.0
+snowballstemmer==2.2.0
+specutils==1.11.0
+Sphinx==7.2.2
+sphinx-autobuild==2021.3.14
+sphinx-automodapi==0.16.0
+sphinx-rtd-theme==1.3.0
+sphinxcontrib-applehelp==1.0.7
+sphinxcontrib-devhelp==1.0.5
+sphinxcontrib-htmlhelp==2.0.4
+sphinxcontrib-jquery==4.1
+sphinxcontrib-jsmath==1.0.1
+sphinxcontrib-mermaid==0.9.2
+sphinxcontrib-qthelp==1.0.6
+sphinxcontrib-serializinghtml==1.1.9
+sphinxcontrib-websupport==1.2.6
+tornado==6.3.3
+tzdata==2023.3
+urllib3==2.0.4
+zipp==3.16.2

docs/source/_static/css/custom.css

@@ -0,0 +1,11 @@
+/* Remove width restriction on content so that diagrams
+   are more visible */
+   .wy-nav-content {
+      max-width: none;
+  }
+
+  /* Override the logo/searchbar background color;
+     it conflicts with the logo color */
+  .wy-side-nav-search {
+      background-color: #C6B9D2;
+  }

docs/conf.py → docs/source/conf.py

@@ -14,11 +14,9 @@
 #
 import os
 import sys
-sys.path.insert(0, os.path.abspath('..'))
-sys.path.insert(0, os.path.abspath('../src'))
-sys.path.insert(0, os.path.abspath('../src/dysh'))
-#sys.path.insert(0, os.path.abspath('../src'))
-# sys.path.insert(0, os.path.abspath('.'))
+
+sys.path.insert(0, os.path.abspath('../../src'))
+sys.path.insert(0, os.path.abspath('.'))
 
 import dysh
 # -- Project information -----------------------------------------------------
@@ -57,8 +55,7 @@
     "sphinx.ext.ifconfig",
     "sphinx.ext.viewcode",
     "sphinxcontrib.mermaid",
-    "numpydoc",
-#    "sphinx_automodapi.automodapi",
+    "numpydoc"
 ]
 
 numpydoc_show_class_members = True
@@ -109,8 +106,7 @@
 #
 # TODO: consider using sphinx_sizzle_theme, so we get tooltip definitions?
 html_theme = "sphinx_rtd_theme"
-
-# html_logo = "_static/gbors_logo.png"
+html_logo = "_static/icon/logo.svg"
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
@@ -121,7 +117,7 @@
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ["static"]
+html_static_path = ["_static"]
 
 # Custom sidebar templates, must be a dictionary that maps document names
 # to template names.
@@ -201,6 +197,7 @@
 default_role = 'obj'
 
 # -- Extension configuration -------------------------------------------------
+numpydoc_class_members_toctree = False
 
 # -- Options for intersphinx extension ---------------------------------------
 
@@ -224,6 +221,6 @@
 
 # These paths are either relative to html_static_path
 # or fully qualified paths (eg. https://...)
-#html_css_files = [
-#    "css/custom.css",
-#]
+html_css_files = [
+    "css/custom.css",
+]

docs/source/design/index.rst

@@ -0,0 +1,10 @@
+******
+Design
+******
+
+Stuff about the overall design
+
+.. toctree::
+   :maxdepth: 2
+
+   sdfits_loaders