docs updated. added apps docs

docs/api/core.rst

@@ -9,6 +9,14 @@ sigpyproc.core.stats
    :undoc-members:
    :show-inheritance:
 
+sigpyproc.core.rfi
+--------------------
+
+.. automodule:: sigpyproc.core.rfi
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 
 sigpyproc.core.kernels
 ----------------------

docs/api/io.rst

@@ -24,3 +24,11 @@ sigpyproc.io.fileio
    :members:
    :undoc-members:
    :show-inheritance:
+
+sigpyproc.io.pfits
+-------------------
+
+.. automodule:: sigpyproc.io.pfits
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/cmd.rst

@@ -0,0 +1,18 @@
+Command line utilities
+======================
+
+.. click:: sigpyproc.apps.spp_header:main
+   :prog: spp_header
+   :nested: full
+
+.. click:: sigpyproc.apps.spp_decimate:main
+   :prog: spp_decimate
+   :nested: full
+
+.. click:: sigpyproc.apps.spp_extract:main
+   :prog: spp_extract
+   :nested: full
+
+.. click:: sigpyproc.apps.spp_clean:main
+   :prog: spp_clean
+   :nested: full

docs/conf.py

@@ -41,6 +41,7 @@
     "sphinx.ext.napoleon",
     "sphinx.ext.intersphinx",
     "myst_nb",
+    "sphinx_click",
 ]
 
 # Add any paths that contain templates here, relative to this directory.

docs/index.rst

@@ -41,6 +41,7 @@ Contents
   :caption: User Guide
 
   install
+  cmd
   modules
   dev
   changes

docs/install.rst

@@ -22,8 +22,11 @@ Some of the required dependencies are:
 - `astropy <https://www.astropy.org>`_
 - `numba <https://numba.pydata.org>`_
 - `bottleneck <https://bottleneck.readthedocs.io>`_
+- `h5py <https://docs.h5py.org/en/stable/>`_
 - `attrs <https://attrs.org>`_
 - `rich <https://rich.readthedocs.io>`_
+- `click <https://click.palletsprojects.com/en/latest/>`_
+- `iqrm <https://github.com/v-morello/iqrm>`_
 
 
 .. _source:

setup.cfg

@@ -55,6 +55,7 @@ docs =
     sphinx>=4.4.0
     sphinx-book-theme>=0.2.0
     myst-nb
+    sphinx-click
 
 develop =
     wemake-python-styleguide

sigpyproc/base.py

@@ -823,7 +823,7 @@ def clean_rfi(
 
         Returns
         -------
-        tuple[str, RFIMask]
+        tuple(str, :class:`~sigpyproc.core.rfi.RFIMask`)
             Filename and mask of cleaned data
 
         Raises

sigpyproc/core/rfi.py

@@ -23,7 +23,7 @@ def double_mad_mask(array: npt.ArrayLike, threshold: float = 3) -> np.ndarray:
 
     Returns
     -------
-    numpy.ndarray
+    :py:obj:`~numpy.ndarray`
         The mask for the array.
 
     Raises

sigpyproc/core/stats.py

@@ -64,7 +64,7 @@ def zscore_mad(array: npt.ArrayLike) -> np.ndarray:
 
     Returns
     -------
-    numy.ndarray
+    :py:obj:`~numpy.ndarray`
         The modified z-score of the array.
 
     Notes
@@ -95,7 +95,7 @@ def zscore_double_mad(array: npt.ArrayLike) -> np.ndarray:
 
     Returns
     -------
-    numy.ndarray
+    :py:obj:`~numpy.ndarray`
         The modified z-score of the array.
 
     Notes

sigpyproc/io/pfits.py

@@ -122,7 +122,7 @@ def location(self) -> EarthLocation:
 
     @property
     def receiver(self) -> Receiver:
-        """sigpyproc.io.hdu.Receiver: Receiver information."""
+        """:class:`~sigpyproc.io.hdu.Receiver`: Receiver information."""
         return Receiver(
             name=self.header["FRONTEND"],
             nrcvr=self.header["NRCVR"],
@@ -136,7 +136,7 @@ def receiver(self) -> Receiver:
 
     @property
     def backend(self) -> Backend:
-        """sigpyproc.io.hdu.Backend: Backend information."""
+        """:class:`~sigpyproc.io.hdu.Backend`: Backend information."""
         return Backend(
             name=self.header["BACKEND"],
             phase=self.header["BE_PHASE"],
@@ -165,7 +165,7 @@ def date_obs(self) -> Time:
 
     @property
     def freqs(self) -> FrequencyChannels:
-        """sigpyproc.utils.FrequencyChannels: Frequency channels."""
+        """:class:`~sigpyproc.utils.FrequencyChannels`: Frequency channels."""
         return FrequencyChannels.from_pfits(
             self.header["OBSFREQ"], self.header["OBSBW"], self.header["OBSNCHAN"]
         )

sigpyproc/readers.py

@@ -170,12 +170,12 @@ def __init__(self, filename: str) -> None:
 
     @property
     def pri_hdr(self) -> pfits.PrimaryHdr:
-        """:class:`~sigpyproc.io.hdu.PFITSPrimaryHdr`: Primary header of input file."""
+        """:class:`~sigpyproc.io.pfits.PrimaryHdr`: Primary header of input file."""
         return self._fitsfile.pri_hdr
 
     @property
     def sub_hdr(self) -> pfits.SubintHdr:
-        """:class:`~sigpyproc.io.hdu.PFITSSubintHdr`: Subint header of input file."""
+        """:class:`~sigpyproc.io.pfits.SubintHdr`: Subint header of input file."""
         return self._fitsfile.sub_hdr
 
     @property