Merge pull request #2514 from cta-observatory/fix_doc_examples

fix some documentation bugs

docs/api-reference/atmosphere/index.rst

@@ -15,3 +15,4 @@ Reference/API
 =============
 
 .. automodapi:: ctapipe.atmosphere
+    :inherited-members:

docs/user-guide/tools.rst

@@ -14,12 +14,20 @@ You can get a list of all available command-line tools by typing
 Data Processing Tools
 =====================
 
-* ``ctapipe-process``: input R0, R1, or DL0 data and output DL1/DL2 data in HDF5 format
-* ``ctapipe-merge``: merge DL1-DL2 data files into a single file
-* ``ctapipe-reconstruct-muons``: detect and parameterize muons (deprecated, to be merged with process tool)
-
+* ``ctapipe-quickstart``: create some default analysis configurations and a working directory
+* ``ctapipe-process``: Process event data in any supported format from R0/R1/DL0 to DL1 or DL2 HDF5 files.
+* ``ctapipe-apply-models``: Tool to apply machine learning models in bulk (as opposed to event by event).
+* ``ctapipe-train-disp-reconstructor`` : Train the ML models for the  `ctapipe.reco.DispReconstructor` (monoscopic reconstruction)
+* ``ctapipe-train-energy-regressor``:  Train the ML models for the `ctapipe.reco.EnergyRegressor` (energy estimation)
+* ``ctapipe-train-particle-classifier``: Train the ML models for the  `ctapipe.reco.ParticleClassifier` (gamma-hadron separation)
+
+File Management Tools:
+======================
+* ``ctapipe-merge``:   Merge multiple ctapipe HDF5 files into one
+* ``ctapipe-fileinfo``:  Display information about ctapipe HDF5 output files
 
 Other Tools
 ===========
 
-* ``ctapipe-dump-instrument``: writes instrumental info from any supported event input file, and writes them out as FITS files for external use.
+* ``ctapipe-info``:  print information about your ctapipe installation and its command-line tools.
+* ``ctapipe-dump-instrument``: writes instrumental info from any supported event input file, and writes them out as FITS or ECSV files for external use.

examples/visualization/camera_display.py

@@ -77,24 +77,25 @@
 # top of the camera (when parked) is aligned to the X-axis. To show the
 # camera in another orientation, it’s useful to apply a coordinate
 # transform to the ``CameraGeometry`` before passing it to the
-# ``CameraDisplay``. The following ``Frames`` are supported: \*
-# ``EngineeringCameraFrame`` : similar to CameraFrame, but with the top of
-# the camera aligned to the Y axis \* ``TelescopeFrame``: In *degrees* (on
-# the sky) coordinates relative to the telescope Alt/Az pointing position,
-# with the Alt axis pointing upward.
+# ``CameraDisplay``. The following ``Frames`` are supported:
 #
+#     * ``CameraFrame``: The frame used by SimTelArray, with the top
+#       of the camera on the x-axis
+#     * ``EngineeringCameraFrame``: similar to CameraFrame, but with
+#       the top of the camera aligned to the Y axis
+#     * ``TelescopeFrame``: In *degrees* (on the sky) coordinates
+#       relative to the telescope Alt/Az pointing position,
+#       with the Alt axis pointing upward.
+#
+# Note the the name of the Frame appears in the lower-right corner
+
 
 fig, ax = plt.subplots(1, 3, figsize=(15, 4))
 CameraDisplay(geom, image=image, ax=ax[0])
 CameraDisplay(geom.transform_to(EngineeringCameraFrame()), image=image, ax=ax[1])
 CameraDisplay(geom.transform_to(TelescopeFrame()), image=image, ax=ax[2])
 
 
-######################################################################
-# Note the the name of the Frame appears in the lower-right corner
-#
-
-
 ######################################################################
 # For the rest of this demo, let’s use the ``TelescopeFrame``
 #

src/ctapipe/atmosphere.py

@@ -315,7 +315,7 @@ class FiveLayerAtmosphereDensityProfile(AtmosphereDensityProfile):
 
     Layer 5 is modeled with:
 
-    ..math:: T(h) = a_5 - b_5 \frac{h}{c_5}
+    .. math:: T(h) = a_5 - b_5 \frac{h}{c_5}
 
     References
     ----------

src/ctapipe/coordinates/ground_frames.py

@@ -3,15 +3,6 @@
 this different systems. Frames and transformations are defined using
 the astropy.coordinates framework. This module defines transformations
 for ground based cartesian and planar systems.
-
-For examples on usage see examples/coordinate_transformations.py
-
-This code is based on the coordinate transformations performed in the
-read_hess code
-
-TODO:
-
-- Tests Tests Tests!
 """
 import astropy.units as u
 import numpy as np

src/ctapipe/coordinates/nominal_frame.py

@@ -39,11 +39,11 @@ class NominalFrame(BaseCoordinateFrame):
     Attributes
     ----------
 
-    origin: SkyCoord[AltAz]
+    origin: astropy.coordinates.SkyCoord[AltAz]
         Origin of this frame as a HorizonCoordinate
-    obstime: Tiem
+    obstime: astropy.time.Time
         Observation time
-    location: EarthLocation
+    location: astropy.coordinates.EarthLocation
         Location of the telescope
     """
 

src/ctapipe/core/telescope_component.py

@@ -270,7 +270,7 @@ class TelescopeParameter(List):
     Examples
     --------
 
-    .. code-block: python
+    .. code-block:: python
 
         tel_param = [
             ('type', '*', 5.0),                       # default for all
@@ -280,7 +280,7 @@ class TelescopeParameter(List):
             ('id', 34, 4.0),                   # override telescope 34 specifically
         ]
 
-    .. code-block: python
+    .. code-block:: python
 
         tel_param = 4.0  # sets this value for all telescopes