testing documentation

ashleychontos · Nov 6, 2022 · 4aaaf93 · 4aaaf93
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diff --git a/docs/library/about.rst b/docs/library/about.rst
@@ -63,60 +63,60 @@ Related Tools
 Several tools have been developed to solve related scientific and data analysis problems. We have compiled 
 a list of software packages that perform similar or complementary analyses.
 
- * `AMP`:
+ * ``AMP``:
     - language: 
     - reference:
     - documentation: no
     - publicly available: no
     - requires license: n/a
 
- * `A2Z`: determining global parameters of the oscillations of solar-like stars
+ * ``A2Z``: determining global parameters of the oscillations of solar-like stars
     - language: `?`
-    - reference: `yes<https://ui.adsabs.harvard.edu/abs/2010A%26A...511A..46M>`_
+    - reference: `yes <https://ui.adsabs.harvard.edu/abs/2010A%26A...511A..46M>`_ 
     - documentation: no
     - publicly available: no
     - requires license: n/a
 
- * `Background`: an extension of ``DIAMONDS`` that fits the background signal of solar-like oscillators 
+ * ``Background``: an extension of ``DIAMONDS`` that fits the background signal of solar-like oscillators 
     - language: `c++11`
     - reference: no
     - documentation: no
-    - publicly available: `yes<https://github.com/EnricoCorsaro/Background>`_
+    - publicly available: `yes <https://github.com/EnricoCorsaro/Background>`_ 
     - requires license: no
 
- * `CAN`: on the detection of Lorentzian profiles in a power spectrum
+ * ``CAN``: on the detection of Lorentzian profiles in a power spectrum
     - language: `?`
-    - reference: `yes<https://ui.adsabs.harvard.edu/abs/2009A%26A...506.1043G>`_
+    - reference: `yes <https://ui.adsabs.harvard.edu/abs/2009A%26A...506.1043G>`_ 
     - documentation: no
     - publicly available: no
     - requires license: n/a
 
- * `COR`: on detecting the large separation in the autocorrelation of stellar oscillation times series
+ * ``COR``: on detecting the large separation in the autocorrelation of stellar oscillation times series
     - language: `?`
-    - reference: `yes<https://ui.adsabs.harvard.edu/abs/2009A%26A...508..877M>`_
+    - reference: `yes <https://ui.adsabs.harvard.edu/abs/2009A%26A...508..877M>`_ 
     - documentation: no
     - publicly available: no
     - requires license: n/a
 
- * `DIAMONDS`: high-DImensional And multi-MOdal NesteD Sampling
+ * ``DIAMONDS``: high-DImensional And multi-MOdal NesteD Sampling
     - language: `c++11`
-    - reference: `yes<https://ui.adsabs.harvard.edu/abs/2014A%26A...571A..71C>`_
-    - documentation: `yes<https://diamonds.readthedocs.io/en/latest/>`_
-    - publicly available: `yes<https://github.com/EnricoCorsaro/DIAMONDS>`_
+    - reference: `yes <https://ui.adsabs.harvard.edu/abs/2014A%26A...571A..71C>`_ 
+    - documentation: `yes <https://diamonds.readthedocs.io/en/latest/>`_ 
+    - publicly available: `yes <https://github.com/EnricoCorsaro/DIAMONDS>`_ 
     - requires license: n/a
 
- * `DLB`:
+ * ``DLB``:
     - language: `?`
     - reference: no
     - documentation: n/a
     - publicly available: no
     - requires license: n/a 
 
- * `FAMED`: Fast & AutoMated pEakbagging with Diamonds
+ * ``FAMED``: Fast & AutoMated pEakbagging with Diamonds
     - language: `IDL` (currently being developed in `Python`)
-    - reference: `yes<https://ui.adsabs.harvard.edu/abs/2020A%26A...640A.130C>`_
-    - documentation: `yes<https://famed.readthedocs.io/en/latest/>`_
-    - publicly available: `yes<https://github.com/EnricoCorsaro/FAMED>`_
+    - reference: `yes <https://ui.adsabs.harvard.edu/abs/2020A%26A...640A.130C>`_ 
+    - documentation: `yes <https://famed.readthedocs.io/en/latest/>`_ 
+    - publicly available: `yes <https://github.com/EnricoCorsaro/FAMED>`_ 
     - requires license: yes
 
  * Flicker Flipper?: 
@@ -126,51 +126,51 @@ a list of software packages that perform similar or complementary analyses.
     - publicly available: 
     - requires license: n/a
 
- * `KAB`: automated asteroseismic analysis of solar-type stars
+ * ``KAB``: automated asteroseismic analysis of solar-type stars
     - language: `?`
-    - reference: `yes<https://ui.adsabs.harvard.edu/abs/2010arXiv1003.4167K>`_
+    - reference: `yes <https://ui.adsabs.harvard.edu/abs/2010arXiv1003.4167K>`_ 
     - documentation: no
     - publicly available: no
     - requires license: n/a
 
- * `lightkurve`: a friendly Python package for making discoveries with *Kepler* & TESS
+ * ``lightkurve``: a friendly Python package for making discoveries with *Kepler* & TESS
     - language: `Python`
     - reference: no
-    - documentation: `yes<https://docs.lightkurve.org>`_
-    - publicly available: `yes<https://github.com/lightkurve/lightkurve>`_
+    - documentation: `yes <https://docs.lightkurve.org>`_ 
+    - publicly available: `yes <https://github.com/lightkurve/lightkurve>`_ 
     - requires license: no 
 
- * `OCT`: automated pipeline for extracting oscillation parameters of solar-like main-sequence stars
+ * ``OCT``: automated pipeline for extracting oscillation parameters of solar-like main-sequence stars
     - language: `?`
-    - reference: `yes<https://ui.adsabs.harvard.edu/abs/2010MNRAS.402.2049H>`_
+    - reference: `yes <https://ui.adsabs.harvard.edu/abs/2010MNRAS.402.2049H>`_ 
     - documentation: no
     - publicly available: no
     - requires license: n/a
 
- * `ORK`: using the comb response function method to identify spacings
+ * ``ORK``: using the comb response function method to identify spacings
     - language: `?`
-    - reference: `yes<https://ui.adsabs.harvard.edu/abs/2008ApJ...676.1248B>`_
+    - reference: `yes <https://ui.adsabs.harvard.edu/abs/2008ApJ...676.1248B>`_ 
     - documentation: no
     - publicly available: no
     - requires license: n/a
 
- * `QML`: a power-spectrum autocorrelation technique to detect global asteroseismic parameters
+ * ``QML``: a power-spectrum autocorrelation technique to detect global asteroseismic parameters
     - language: `?`
-    - reference: `yes<https://ui.adsabs.harvard.edu/abs/2011arXiv1104.0631V>`_
+    - reference: `yes <https://ui.adsabs.harvard.edu/abs/2011arXiv1104.0631V>`_ 
     - documentation: no
     - publicly available: no
     - requires license: n/a
 
- * `PBjam`: a python package for automating asteroseismology of solar-like oscillators
+ * ``PBjam``: a python package for automating asteroseismology of solar-like oscillators
     - language: `Python`
-    - reference: yes <https://ui.adsabs.harvard.edu/abs/2021AJ....161...62N>
-    - documentation: `yes<https://pbjam.readthedocs.io/en/latest/>`_
-    - publicly available: `yes<https://github.com/grd349/PBjam>`_
+    - reference: `yes <https://ui.adsabs.harvard.edu/abs/2021AJ....161...62N>`_ 
+    - documentation: `yes <https://pbjam.readthedocs.io/en/latest/>`_ 
+    - publicly available: `yes <https://github.com/grd349/PBjam>`_ 
     - requires license: no 
 
- * `SYD`: automated extraction of oscillation parameters for *Kepler* observations of solar-type stars
+ * ``SYD``: automated extraction of oscillation parameters for *Kepler* observations of solar-type stars
     - language: `IDL`
-    - reference: `yes<https://ui.adsabs.harvard.edu/abs/2009CoAst.160...74H>`_
+    - reference: `yes <https://ui.adsabs.harvard.edu/abs/2009CoAst.160...74H>`_ 
     - documentation: no
     - publicly available: no
     - requires license: yes

diff --git a/src/pysyd/__init__.py b/src/pysyd/__init__.py
@@ -19,7 +19,7 @@
 __author__ = "Ashley Chontos<[email protected]>"
 __license__ = "MIT"
 __description__ = "Automated measurements of global asteroseismic parameters"
-__version__ = '6.10.0'
+__version__ = '6.10.1a'
 
 __all__ = ['cli','models','pipeline','plots','target','utils']
 

diff --git a/src/pysyd/pipeline.py b/src/pysyd/pipeline.py
@@ -17,7 +17,7 @@
 
 
 def check(args):
-    """
+    """Check target
     
     This is intended to be a way to check a target before running it by plotting the
     times series data and/or power spectrum. This works in the most basic way  but has
@@ -28,9 +28,9 @@ def check(args):
             the command line arguments
     
     .. important::
-        has not been extensively tested
+        has not been extensively tested - also it is exactly the same as "load" so think 
+        through if this is actually needed and decided which is easier to understand
 
-    
     """
     star = load(args)
     plots.check_data(star)
@@ -48,10 +48,9 @@ def fun(args):
 
 
 def load(args):
-    """
+    """Load target
     
-    Module to load in all relevant information and dictionaries
-    required to run the pipeline
+    Load in a given target to check data or figures
     
     .. note::
         this does *not* load in a target or target data, this is purely
@@ -61,20 +60,6 @@ def load(args):
     Parameters
         args : argparse.Namespace
             the command line arguments
-        star : object, optional
-            pretty sure this is only used from jupyter notebook
-        verbose : bool, optional
-            again, this is only used if not using command line
-        command : str, optional
-            which of the 5 ``pysyd.pipeline`` modes to execute from the notebook
-
-    Returns
-        single : target.Target
-            current data available for the provided target
-
-    Deprecated
-        single : target.Target
-            current data available for the provided target
 
     """
     if args.data:
@@ -91,13 +76,12 @@ def load(args):
     params.add_targets(stars=args.stars)
     # Load target data
     star = Target(args.stars[0], params)
-    return star
 
 
 def parallel(args):
-    """
+    """Parallel execution
     
-    Run ``pySYD`` in parallel for a large number of stars
+    Run ``pySYD`` concurrently for a large number of stars
 
     Parameters
         args : argparse.Namespace
@@ -113,23 +97,23 @@ def parallel(args):
     params = utils.Parameters(args=args)
     if args.stars is None:
         try:
-            args.stars = params.load_starlist()
+            args.stars = params._load_starlist()
         except utils.InputError as error:
             print(error.msg)
             return
     # Add target stars
     params.add_targets(stars=args.stars)
     # Creates the separate, asyncrhonous (nthread) processes
     pool = mp.Pool(args.n_threads)
-    result_objects = [pool.apply_async(pipe, args=(group, params)) for group in params.params['groups']]
+    result_objects = [pool.apply_async(_pipe, args=(group, params)) for group in params.params['groups']]
     results = [r.get() for r in result_objects]
     pool.close()
     pool.join()               # postpones execution of the next line until all processes finish
     # Concatenates output into two files
-    utils.scrape_output(params)
+    utils._scrape_output(params)
 
 
-def pipe(group, params, progress=False):
+def _pipe(group, params, progress=False):
     """
 
     This function is called by both :mod:`pysyd.pipeline.run` and :mod:`pysyd.pipeline.parallel`
@@ -150,7 +134,7 @@ def pipe(group, params, progress=False):
 
 
 def plot(args):
-    """
+    """Make plots
     
     Module to load in all relevant information and dictionaries
     required to run the pipeline
@@ -178,40 +162,41 @@ def plot(args):
 
 
 def run(args):
-    """
+    """Run pySYD
     
-    Main function to initiate the pySYD pipeline (consecutively, not
-    in parallel)
+    Main function to initiate the pySYD pipeline for one or many stars (the latter is run
+    consecutively *not* concurrently)
 
     Parameters
         args : argparse.Namespace
             the command line arguments
 
     Methods
-        pipe
+        :mod:`pysyd.utils.Parameters`
+        :mod:`pysyd.pipeline.pipe`
+        :mod:`pysyd.utils._scrape_output`
 
     .. seealso:: :mod:`pysyd.pipeline.parallel`
 
-
     """
     # Load default pySYD parameters
     params = utils.Parameters(args=args)
     if args.stars is None:
         try:
-            args.stars = params.load_starlist()
+            args.stars = params._load_starlist()
         except utils.InputError as error:
             print(error.msg)
             return
     # Update with CL options
     params.add_targets(stars=args.stars)
     # Run single batch of stars
-    pipe(args.stars, params)
+    _pipe(args.stars, params)
     # Concatenates output into two files
-    utils.scrape_output(params)
+    utils._scrape_output(params)
 
 
 def setup(args):
-    """
+    """Quick software setup
     
     Running this after installation will create the appropriate directories in the current working
     directory as well as download example data and files to test your pySYD installation