Merge branch 'main' of https://github.com/sblunt/orbitize into plot_all_orbits

Author: manduhmia

.github/workflows/joss-compile.yml

@@ -0,0 +1,23 @@
+on: [push]
+
+jobs:
+  paper:
+    runs-on: ubuntu-latest
+    name: Paper Draft
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Build draft PDF
+        uses: openjournals/openjournals-draft-action@master
+        with:
+          journal: joss
+          # This should be the path to the paper within your repo.
+          paper-path: paper/paper.md
+      - name: Upload
+        uses: actions/upload-artifact@v1
+        with:
+          name: paper
+          # This is the output path where Pandoc will write the compiled
+          # PDF. Note, this should be the same directory as the input
+          # paper.md
+          path: paper/paper.pdf

.github/workflows/python-package.yml

@@ -0,0 +1,48 @@
+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+
+name: CI tests
+
+on:
+  push:
+    branches: 
+      - '*' # run on all
+  pull_request:
+    branches: 
+      - '*'
+
+jobs:
+  build:
+
+    runs-on: macos-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.10", "3.11", "3.12"]
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v3
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install flake8 pytest pytest-cov
+        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+    - name: Lint with flake8
+      run: |
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    - name: Test with pytest
+      run: |
+        pytest --cov
+    - name: Coveralls GitHub Action
+      if: ${{ matrix.python-version }} == '3.12'
+      uses: coverallsapp/github-action@v2
+      with:
+        parallel: true
+        flag-name: run-$
+

.github/workflows/run-notebooks.yml

@@ -0,0 +1,36 @@
+name: Test jupyter notebook tutorials
+
+on:
+  push:
+    branches: 
+      - main # only rerun tutorials when making PRs or changing main
+      - v3
+  pull_request:
+    branches: 
+      - '*'
+
+jobs:
+  build:
+
+    runs-on: macos-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.12"]
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v3
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install jupyter setuptools wheel nbmake
+        python -m pip install -r requirements.txt
+        python -m pip install . --no-build-isolation
+    - name: Run tutorial notebooks
+      run: |
+        py.test --nbmake --nbmake-timeout=3000 docs/tutorials/*.ipynb
+      

.gitignore

@@ -3,12 +3,14 @@ orbitize/example_data/rebound*.csv
 orbitize/example_data/*test.hdf5
 .vscode/launch.json
 .vscode/settings.json
+*.DS_Store
 
 # images & storage files generated by tutorials
 *.hdf5
 !orbitize/example_data/v1_posterior.hdf5
 *.fits
 *.png
+!docs/tutorials/eift_hd206893.png
 tests/test_results.h5
 tests/multiplanet*test.csv
 

.readthedocs.yaml

@@ -0,0 +1,20 @@
+version: 2
+
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.10"
+
+sphinx:
+  configuration: docs/conf.py
+
+formats:
+   - pdf
+   - epub
+
+python:
+   install:
+   - requirements: requirements.txt # orbitize requirements
+   - requirements: docs/requirements.txt # docs-building requirements
+   - method: pip
+     path: . # install orbitize

.travis.yml

@@ -4,7 +4,7 @@
 
 Orbit-fitting for directly imaged objects. For installation instructions, tutorials, and detailed documentation, start [here](http://orbitize.readthedocs.io/en/latest/).
 
-[![Build Status](https://app.travis-ci.com/sblunt/orbitize.svg?branch=main)](https://app.travis-ci.com/sblunt/orbitize)
+![Build Status](https://github.com/sblunt/orbitize/actions/workflows/python-package.yml/badge.svg)
 [![Coverage Status](https://coveralls.io/repos/github/sblunt/orbitize/badge.svg?branch=main)](https://coveralls.io/github/sblunt/orbitize?branch=main)
 [![Documentation Status](https://readthedocs.org/projects/orbitize/badge/?version=latest)](http://orbitize.readthedocs.io/en/latest/?badge=latest)
 [![PyPI version](https://badge.fury.io/py/orbitize.svg)](https://badge.fury.io/py/orbitize)

README.md

@@ -22,7 +22,10 @@
 #
 import os
 import sys
-sys.path.insert(0, os.path.abspath('./../orbitize')) # location of orbitize files with docstrings
+
+sys.path.insert(
+    0, os.path.abspath("./../orbitize")
+)  # location of orbitize files with docstrings
 
 
 # -- General configuration ------------------------------------------------
@@ -35,38 +38,41 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
-    'sphinx_rtd_theme',
-    'sphinx.ext.autodoc',
-    'sphinx.ext.doctest',
-    'sphinx.ext.todo',
-    'sphinx.ext.mathjax',
-    'sphinx.ext.napoleon', # allows Google style-guide docs to render more prettily
-    'sphinx.ext.viewcode',
-    'nbsphinx'
-    ]
+    "sphinx_rtd_theme",
+    "sphinx.ext.autodoc",
+    "sphinx.ext.doctest",
+    "sphinx.ext.todo",
+    "sphinx.ext.mathjax",
+    "sphinx.ext.napoleon",  # allows Google style-guide docs to render more prettily
+    "sphinx.ext.viewcode",
+    "nbsphinx",
+]
 
 # Disable notebook timeout
 nbsphinx_timeout = -1
 
+# Only re-run notebooks that have no outputs
+nbsphinx_execute = "auto"
+
 # Allow notebook errors
-nbsphinx_allow_errors = True
+nbsphinx_allow_errors = False
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # The suffix(es) of source filenames.
 # You can specify multiple suffix as a list of string:
 #
 # source_suffix = ['.rst', '.md']
-source_suffix = '.rst'
+source_suffix = ".rst"
 
 # The master toctree document.
-master_doc = 'index'
+master_doc = "index"
 
 # General information about the project.
-project = 'orbitize'
-copyright = '2018, Sarah Blunt, Jason Wang, Isabel Angelo, Henry Ngo, et al'
-author = 'Sarah Blunt, Jason Wang, Isabel Angelo, Henry Ngo, et al'
+project = "orbitize"
+copyright = "2018, Sarah Blunt, Jason Wang, Isabel Angelo, Henry Ngo, et al"
+author = "Sarah Blunt, Jason Wang, Isabel Angelo, Henry Ngo, et al"
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
@@ -75,7 +81,7 @@
 # The short X.Y version.
 version = orbitize.__version__
 # The full version, including alpha/beta/rc tags.
-#release = '0.1'
+# release = '0.1'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -90,7 +96,7 @@
 exclude_patterns = []
 
 # The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
+pygments_style = "sphinx"
 
 # If true, `todo` and `todoList` produce output, else they produce nothing.
 todo_include_todos = True
@@ -101,7 +107,7 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'sphinx_rtd_theme'
+html_theme = "sphinx_rtd_theme"
 
 # 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
@@ -111,12 +117,12 @@
 
 # The name of an image file (relative to this directory) to place at the top
 # of the sidebar.
-#html_logo = 'orbitize_logo_150.png'
+# html_logo = 'orbitize_logo_150.png'
 
 # The name of an image file (within the static path) to use as favicon of the
 # docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
 # pixels large.
-html_favicon = 'favicon.ico'
+html_favicon = "favicon.ico"
 
 # 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,
@@ -129,17 +135,17 @@
 # This is required for the alabaster theme
 # refs: http://alabaster.readthedocs.io/en/latest/installation.html#sidebars
 html_sidebars = {
-    '**': [
-        'relations.html',  # needs 'show_related': True theme option to display
-        'searchbox.html',
+    "**": [
+        "relations.html",  # needs 'show_related': True theme option to display
+        "searchbox.html",
     ]
 }
 
 
 # -- Options for HTMLHelp output ------------------------------------------
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'orbitizedoc'
+htmlhelp_basename = "orbitizedoc"
 
 
 # -- Options for LaTeX output ---------------------------------------------
@@ -148,15 +154,12 @@
     # The paper size ('letterpaper' or 'a4paper').
     #
     # 'papersize': 'letterpaper',
-
     # The font size ('10pt', '11pt' or '12pt').
     #
     # 'pointsize': '10pt',
-
     # Additional stuff for the LaTeX preamble.
     #
     # 'preamble': '',
-
     # Latex figure (float) alignment
     #
     # 'figure_align': 'htbp',
@@ -166,19 +169,21 @@
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-    (master_doc, 'orbitize.tex', 'orbitize Documentation',
-     'Sarah Blunt, Jason Wang, Henry Ngo, et al.', 'manual'),
+    (
+        master_doc,
+        "orbitize.tex",
+        "orbitize Documentation",
+        "Sarah Blunt, Jason Wang, Henry Ngo, et al.",
+        "manual",
+    ),
 ]
 
 
 # -- Options for manual page output ---------------------------------------
 
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
-man_pages = [
-    (master_doc, 'orbitize', 'orbitize Documentation',
-     [author], 1)
-]
+man_pages = [(master_doc, "orbitize", "orbitize Documentation", [author], 1)]
 
 
 # -- Options for Texinfo output -------------------------------------------
@@ -187,10 +192,13 @@
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-    (master_doc, 'orbitize', 'orbitize Documentation',
-     author, 'orbitize', 'One line description of project.',
-     'Miscellaneous'),
+    (
+        master_doc,
+        "orbitize",
+        "orbitize Documentation",
+        author,
+        "orbitize",
+        "One line description of project.",
+        "Miscellaneous",
+    ),
 ]
-
-
-