Merge pull request #339 from sblunt/github-actions

GitHub actions

.github/workflows/python-package.yml

@@ -1,18 +1,19 @@
 # This workflow will install Python dependencies, run tests and lint with a variety of Python versions
-# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
 
-name: Python package
+name: CI tests
 
 on:
   push:
-    branches: [ "main" ]
+    branches: 
+      - '*' # run on all
   pull_request:
-    branches: [ "main" ]
+    branches: 
+      - '*'
 
 jobs:
   build:
 
-    runs-on: ubuntu-latest
+    runs-on: macos-latest
     strategy:
       fail-fast: false
       matrix:

docs/conf.py

@@ -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
 
+# Always re-run notebooks when building docss
+nbsphinx_execute = "always"
+
 # 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",
+    ),
 ]
-
-
-

orbitize/radvel_utils/compute_sep.py

@@ -1,90 +1,2 @@
-import numpy as np
-import pandas as pd
-from astropy import units as u
-
-from radvel.basis import Basis
-from radvel.utils import Msini
-from orbitize.basis import tp_to_tau
-from orbitize.kepler import calc_orbit
-
-def compute_sep(
-    df, epochs, basis, m0, m0_err, plx, plx_err, n_planets=1, pl_num=1
-):
-    """
-    Computes a sky-projected angular separation posterior given a 
-    RadVel-computed DataFrame.
-
-    Args:
-        df (pd.DataFrame): Radvel-computed posterior (in any orbital basis)
-        epochs (np.array of astropy.time.Time): epochs at which to compute 
-            separations
-        basis (str): basis string of input posterior (see 
-            radvel.basis.BASIS_NAMES` for the full list of possibilities). 
-        m0 (float): median of primary mass distribution (assumed Gaussian).
-        m0_err (float): 1sigma error of primary mass distribution 
-            (assumed Gaussian).
-        plx (float): median of parallax distribution (assumed Gaussian).
-        plx_err: 1sigma error of parallax distribution (assumed Gaussian).
-        n_planets (int): total number of planets in RadVel posterior
-        pl_num (int): planet number used in RadVel fits (e.g. a RadVel label of 
-            'per1' implies `pl_num` == 1) 
-
-    Example:
-
-        >> df = pandas.read_csv('sample_radvel_chains.csv.bz2', index_col=0)
-        >> epochs = astropy.time.Time([2022, 2024], format='decimalyear')
-        >> seps, df_orb = compute_sep(
-               df, epochs, 'per tc secosw sesinw k', 0.82, 0.02, 312.22, 0.47
-           )
-
-    Returns:
-        tuple of:
-            np.array of size (len(epochs) x len(df)): sky-projected angular 
-                separations [mas] at each input epoch
-            pd.DataFrame: corresponding orbital posterior in orbitize basis
-    """
-
-    myBasis = Basis(basis, n_planets)
-    df = myBasis.to_synth(df)
-    chain_len = len(df)
-    tau_ref_epoch = 58849
-
-    # convert RadVel posteriors -> orbitize posteriors
-    m_st = np.random.normal(m0, m0_err, size = chain_len)
-    semiamp = df['k{}'.format(pl_num)].values
-    per_day = df['per{}'.format(pl_num)].values
-    period_yr = per_day / 365.25
-    ecc = df['e{}'.format(pl_num)].values
-    msini = (
-        Msini(semiamp, per_day, m_st, ecc, Msini_units='Earth') * 
-        (u.M_earth / u.M_sun).to('')
-    )
-    cosi = (2. * np.random.random(size = chain_len)) - 1.
-    inc = np.arccos(cosi)
-    m_pl = msini / np.sin(inc)
-    mtot = m_st + m_pl
-    sma = (period_yr**2 * mtot)**(1/3)
-    omega_st_rad = df['w{}'.format(pl_num)].values
-    omega_pl_rad = omega_st_rad + np.pi
-    parallax = np.random.normal(plx, plx_err, size = chain_len)
-    lan = np.random.random_sample(size = chain_len) * 2. * np.pi
-    tp_mjd = df['tp{}'.format(pl_num)].values - 2400000.5
-    tau = tp_to_tau(tp_mjd, tau_ref_epoch, period_yr)
-
-    # compute projected separation in mas
-    raoff, deoff, _ = calc_orbit(
-        epochs.mjd, sma, ecc, inc, 
-        omega_pl_rad, lan, tau, 
-        parallax, mtot, tau_ref_epoch=tau_ref_epoch
-    )
-    seps = np.sqrt(raoff**2 + deoff**2)
-
-    df_orb = pd.DataFrame(
-        np.transpose([sma, ecc, inc, omega_pl_rad, lan, tau, parallax, m_st, m_pl]), 
-        columns=[
-            'sma', 'ecc', 'inc_rad', 'omega_pl_rad', 'lan_rad', 'tau_58849', 
-            'plx', 'm_st', 'mp'
-        ]
-    )
-
-    return seps, df_orb
+def compute_sep(df, epochs, basis, m0, m0_err, plx, plx_err, n_planets=1, pl_num=1):
+    raise ModuleNotFoundError("This functionaity is deprecated. See sblunt/orbitize_radvel_utils.")

requirements.txt

@@ -10,7 +10,6 @@ deprecation
 cython
 pytest
 pandas
-radvel
 pyerfa
 astroquery
 sphinx