Merge pull request #33 from pllim/pr26-follow-up

Clean up PR 26 etc

.github/workflows/ci_workflows.yml

@@ -49,8 +49,10 @@ jobs:
         python -m pip install --upgrade pip setuptools
         python -m pip install 'numpy<1.19'
         python -m pip install -e .[test,all]
-    - name: Test without optional deps
-      run: pytest --open-files --remote-data
+    - name: Test with stable deps and coverage
+      run: pytest --cov=./ --cov-report=xml --open-files --remote-data
+    - name: Coverage report
+      uses: codecov/codecov-action@v1
 
   dev_deps_tests:
     runs-on: ubuntu-latest

README.rst

@@ -1,13 +1,18 @@
 exovetter: Exoplanet Vetting
-----------------------------
+============================
 
 .. image:: https://readthedocs.org/projects/exovetter/badge/?version=latest
     :target: https://exovetter.readthedocs.io/en/latest/?badge=latest
     :alt: Documentation Status
 
 .. image:: https://github.com/spacetelescope/exovetter/workflows/CI/badge.svg
+    :target: https://github.com/spacetelescope/exovetter/actions
     :alt: Github Actions CI Status
 
+.. image:: https://codecov.io/gh/spacetelescope/exovetter/branch/master/graph/badge.svg?token=H3UC4Q0H6R
+    :target: https://codecov.io/gh/spacetelescope/exovetter
+    :alt: Coverage report
+
 .. image:: http://img.shields.io/badge/powered%20by-AstroPy-orange.svg?style=flat
     :target: http://www.astropy.org
     :alt: Powered by Astropy Badge

docs/api.rst

@@ -18,3 +18,10 @@ Reference/API
 
 .. automodapi:: exovetter.transit_coverage
     :no-inheritance-diagram:
+
+.. automodapi:: exovetter.model
+    :no-inheritance-diagram:
+
+.. automodapi:: exovetter.const
+    :no-inheritance-diagram:
+    :include-all-objects:

exovetter/const.py

@@ -1,16 +1,32 @@
+"""Constants and units for exoplanet vetting."""
+
 import astropy.units as u
 
-"""
-Useful constants for exoplanet vetting
-"""
+__all__ = ['bjd', 'bkjd', 'btjd', 'bet', 'ppk', 'ppm', 'frac_amp']
+
+# TODO: Improve docstrings
 
 # Time offset constants
+
 bjd = 0 * u.day
+"""BJD"""
+
 bkjd = bjd - 2_454_833 * u.day
+"""BKJD"""
+
 btjd = bjd - 2_457_000 * u.day
-bet = bjd - 2_451_544.5 * u.day  # Barycentric Emphemeris time
+"""BTJD"""
+
+bet = bjd - 2_451_544.5 * u.day
+"""Barycentric Emphemeris Time (BET)"""
 
 # Handy units to express depth
+
 ppk = 1e-3 * u.dimensionless_unscaled
+"""PPK"""
+
 ppm = 1e-3 * ppk
+"""PPM"""
+
 frac_amp = u.dimensionless_unscaled
+"""Frac amp"""

exovetter/lpp.py

@@ -8,6 +8,9 @@
 import warnings
 
 import numpy as np
+from astropy import units as u
+from astropy.utils.data import download_file, _is_url
+from scipy import io as spio
 
 __all__ = ['compute_lpp_Transitmetric', 'runningMedian', 'foldBinLightCurve',
            'computeRawLPPTransitMetric', 'knnDistance_fromKnown',
@@ -345,16 +348,21 @@ def __init__(self, tce, lc, lc_name="flux", default_snr=10.):
 
         self.check_tce(tce, default_snr)
 
-        self.tzero = tce['tzero']
-        self.dur = tce['duration']
-        self.period = tce['period']
+        # FIXME: This looks more correct but fails the test.
+        # from exovetter import const as exo_const
+        # self.tzero = tce.get_epoch(
+        #     getattr(exo_const, lc.time_format)).to_value(u.day)
+
+        self.tzero = tce['epoch'].to_value(u.day)
+        self.dur = tce['duration'].to_value(u.hr)
+        self.period = tce['period'].to_value(u.day)
 
         self.mes = default_snr
         if 'snr' in tce.keys():
             self.mes = tce['snr']
 
         self.time = lc.time
-        self.flux = lc.__dict__[lc_name]  # TODO: Use getattr?
+        self.flux = getattr(lc, lc_name)
 
         # make sure flux is zero norm.
         if np.round(np.median(self.flux)) != 0:
@@ -387,13 +395,9 @@ class Loadmap:
         If URL is provided, it will be cached using :ref:`astropy:utils-data`
 
     """
-    builtin_mat = 'https://stsci.box.com/s/s2jup12rcjn05qll598h33bwycjeym8x'
-    # builtin_mat = 'https://sourceforge.net/p/lpptransitlikemetric/code/HEAD/tree/data/maps/combMapDR25AugustMapDV_6574.mat?format=raw'  # noqa: E501
+    builtin_mat = 'https://stsci.box.com/shared/static/1ffi1t1fhae82d7xeqexw4ymlhlk0ov4.mat'  # noqa
 
     def __init__(self, filename=None):
-        from astropy.utils.data import download_file, _is_url
-        from scipy import io as spio
-
         if filename is None:
             filename = self.builtin_mat
 

exovetter/model.py

@@ -1,19 +1,58 @@
-# -*- coding: utf-8 -*-
-"""
-Repository of transit models.
+"""Module to handle transit models.
+
+Available models:
+
+* Boxcar
+* Trapezoid (to be added in the future)
 
-Currently, only the box car model is implemented, need a
-trapezoid model here too.
+Developer notes
+===============
+
+For each model type, create 2 functions:
+
+1. ``create_<modelname>_model_for_tce``: Takes a TCE as input.
+2. ``create_<modelname>``: Takes more fundamental times
+   (e.g., numpy arrays, floats).
 
-For each model type create 2 functions, one that takes a TCE as input,
-and one that takes more fundamental times (numpy arrays, floats, etc.)
 """
+# TODO: See https://github.com/spacetelescope/exovetter/issues/32
+# FIXME: Improve docstrings.
 
-import astropy.units as u
 import numpy as np
+from astropy import units as u
+
+__all__ = ['create_box_model_for_tce', 'create_box_model']
 
 
 def create_box_model_for_tce(tce, times, time_offset):
+    """Create boxcar model for a given TCE.
+
+    Parameters
+    ----------
+    tce : `~exovetter.tce.Tce`
+        Threshold Crossing Event.
+
+    times : `~astropy.units.Quantity`
+        Times.
+
+    time_offset : `~astropy.units.Quantity`
+        Time offset for :meth:`exovetter.tce.Tce.get_epoch`.
+
+    Returns
+    -------
+    flux : `~astropy.units.Quantity`
+        Flux from boxcar model.
+
+    Raises
+    ------
+    ValueError
+        Invalid input.
+
+    See also
+    --------
+    create_box_model
+
+    """
     if not tce.validate():
         raise ValueError("Required quantities missing from TCE")
 
@@ -35,22 +74,51 @@ def create_box_model_for_tce(tce, times, time_offset):
 
 
 def create_box_model(times, period, epoch, duration, depth):
+    """Create boxcar model.
+
+    Parameters
+    ----------
+    times : array
+        Times.
+
+    period : float
+        Period.
+
+    epoch : float
+        Epoch.
+
+    duration  : float
+        Duration.
+
+    depth : `~astropy.units.Quantity`
+        Depth.
+
+    Returns
+    -------
+    flux : `~astropy.units.Quantity`
+        Flux from boxcar model, in the same unit as ``depth``.
+
+    See also
+    --------
+    create_box_model_for_tce
+
+    """
     # Make epoch the start of the transit, not the midpoint
-    epoch -= duration / 2.0
+    epoch -= duration * 0.5
 
     mnT = np.min(times)
     mxT = np.max(times)
 
     e0 = int(np.floor((mnT - epoch) / period))
     e1 = int(np.floor((mxT - epoch) / period))
 
-    flux = 0.0 * times
+    flux = np.zeros_like(times)
+    depth_values = depth.to_value()
     for i in range(e0, e1 + 1):
         t0 = period * i + epoch
         t1 = t0 + duration
-        # print(i, t0, t1)
 
         idx = (t0 <= times) & (times <= t1)
-        flux[idx] -= depth.to_value()
+        flux[idx] -= depth_values
 
     return flux * depth.unit