Merge pull request #48 from nfsi-canada/v021

V021

Author: paudetseis

README.md

@@ -12,7 +12,7 @@ can be used through command-line scripts.
 
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4281480.svg)](https://doi.org/10.5281/zenodo.4281480)
 [![build](https://github.com/nfsi-canada/OBStools/workflows/Build/badge.svg)](https://github.com/nfsi-canada/OBStools/actions)
-[![codecov](https://codecov.io/gh/nfsi-canada/OBStools/branch/master/graph/badge.svg)](https://codecov.io/gh/nfsi-canada/OBStools)
+<!-- [![codecov](https://codecov.io/gh/nfsi-canada/OBStools/branch/master/graph/badge.svg)](https://codecov.io/gh/nfsi-canada/OBStools) -->
 
 Installation, API documentation, scripts and tutorials are described at https://nfsi-canada.github.io/OBStools/
 

docs/atacr.rst

@@ -103,6 +103,17 @@ Usage
 .. code-block::
 
     $ comply_calculate -h
+
+    #################################################################################
+    #                            _                    _            _       _        #
+    #   ___ ___  _ __ ___  _ __ | |_   _     ___ __ _| | ___ _   _| | __ _| |_ ___  #
+    #  / __/ _ \| '_ ` _ \| '_ \| | | | |   / __/ _` | |/ __| | | | |/ _` | __/ _ \ #
+    # | (_| (_) | | | | | | |_) | | |_| |  | (_| (_| | | (__| |_| | | (_| | ||  __/ #
+    #  \___\___/|_| |_| |_| .__/|_|\__, |___\___\__,_|_|\___|\__,_|_|\__,_|\__\___| #
+    #                     |_|      |___/_____|                                      #
+    #                                                                               #
+    #################################################################################
+
     usage: comply_calculate [options] <Station Database>
 
     Script used to calculate compliance functions between various components. The noise data can be those obtained
@@ -189,6 +200,17 @@ In this case we do not need to specify any option and type in a terminal:
 
     $ comply_calculate M08A.pkl
 
+    #################################################################################
+    #                            _                    _            _       _        #
+    #   ___ ___  _ __ ___  _ __ | |_   _     ___ __ _| | ___ _   _| | __ _| |_ ___  #
+    #  / __/ _ \| '_ ` _ \| '_ \| | | | |   / __/ _` | |/ __| | | | |/ _` | __/ _ \ #
+    # | (_| (_) | | | | | | |_) | | |_| |  | (_| (_| | | (__| |_| | | (_| | ||  __/ #
+    #  \___\___/|_| |_| |_| .__/|_|\__, |___\___\__,_|_|\___|\__,_|_|\__,_|\__\___| #
+    #                     |_|      |___/_____|                                      #
+    #                                                                               #
+    #################################################################################
+
+
     Path to COMPL_STA/7D.M08A doesn't exist - creating it
      
      

docs/comply.rst

@@ -29,7 +29,7 @@
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
-extensions = ['sphinx.ext.autodoc', 'sphinx.ext.napoleon']
+extensions = ['sphinx.ext.autodoc', 'sphinx.ext.napoleon', 'sphinx.ext.viewcode']
 
 autodoc_member_order = 'bysource'
 

docs/conf.py

@@ -16,8 +16,6 @@ can be used through command-line scripts.
    :target: https://doi.org/10.5281/zenodo.4281480
 .. image:: https://github.com/nfsi-canada/OBStools/workflows/Build/badge.svg
    :target: https://github.com/nfsi-canada/OBStools/actions
-.. image:: https://codecov.io/gh/nfsi-canada/OBStools/branch/master/graph/badge.svg
-   :target: https://codecov.io/gh/nfsi-canada/OBStools
 
 .. toctree::
    :maxdepth: 1

docs/index.rst

@@ -1,5 +1,5 @@
 project('rfpy', 'c',
-  version : '0.2.0',
+  version : '0.2.1',
   license: 'MIT',
   meson_version: '>=0.64.0',
 )

meson.build

@@ -24,7 +24,7 @@
 Licence
 -------
 
-Copyright 2019 Pascal Audet & Helen Janiszewski
+Copyright 2019 Pascal Audet
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal
@@ -50,19 +50,14 @@
 Dependencies
 ++++++++++++
 
-The current version has been tested using **Python 3.10** \
-The following package is required before install ``obstools``:
-
-- `stdb <https://github.com/paudetseis/StDb>`_
-
-Other required packages (e.g., ``obspy``)
-will be automatically installed by ``stdb``.
+- `stdb <https://github.com/schaefferaj/StDb>`_
+- `obspy <https://github.com/obspy/obspy>`_
 
 Conda environment
 +++++++++++++++++
 
 We recommend creating a custom ``conda`` environment
-where ``OBStools`` can be installed along with some of its dependencies.
+where ``OBStools`` can be installed along with its dependencies.
 
 .. sourcecode:: bash
 
@@ -78,14 +73,14 @@
 
 .. sourcecode:: bash
 
-   pip install stdb
+   pip install git+https://github.com/schaefferaj/stdb
 
 Installing development branch on GitHub
 +++++++++++++++++++++++++++++++++++++++
 
 .. sourcecode:: bash
 
-   pip install obstools@git+https://github.com/nfsi-canada/obstools
+   pip install git+https://github.com/nfsi-canada/obstools
 
 Installing from source
 ++++++++++++++++++++++
@@ -103,11 +98,75 @@
 
    pip install .
 
+Using local data
+----------------
+
+The various scripts packaged with ``OrientPy`` use FDSN web services
+through and ``ObsPy`` `Client` to load waveform data. For waveform
+data locally stored on your hard drive, the scripts can use a `Client`
+that reads a `SeisComP Data Structure 
+<https://docs.obspy.org/packages/autogen/obspy.clients.filesystem.sds.html>`_ 
+archive containing SAC or miniSEED waveform data. Check out the scripts 
+``bng_calc`` and ``dl_calc`` below and the argument ``--local-data`` and 
+``--dtype`` for more details.
+
+Station Metadata
+++++++++++++++++
+
+If you have data stored locally on your drive, it is likely you also
+have a station `XML <https://www.fdsn.org/xml/station/>`_ file
+containing the metadata. The corresponding ObsPy documentation is
+`here <https://docs.obspy.org/packages/obspy.core.inventory.html>`_. 
+
+To convert the station `XML` file to an input that can be read by
+``OrientPy``, you run the command ``gen_stdb station.xml`` (only
+available on StDb version 0.2.7), which will create the file
+``station.pkl``. If you don't have a station `XML` file but you have
+a dataless SEED file, you can convert it first to `XML` using `this
+tools <https://seiscode.iris.washington.edu/projects/stationxml-converter>`_.
+
+Waveform Data
++++++++++++++
+
+The SDS folder containing the waveform data has the structure:
+
+.. code-block:: python
+
+   archive
+     + year
+       + network code
+         + station code
+           + channel code + type
+             + one file per day and location, e.g. NET.STA.LOC.CHAN.TYPE.YEAR.DOY
+
+
+For example:
+
+.. code-block:: python
+
+   SDS/
+     2014/
+       YH/
+         LOBS3/
+           HH1.D/ 
+             YH.LOBS3..CH1.D.2014.332
+             ...
+
+
+Note, the filename does not include the extension (`.MSEED` or `.SAC`),
+and the characters `.D` (for type Data) that appear in both the
+channel code and the filename. Note also the two dots (`..`). If
+there is a location code, it should appear between those dots (e.g.,
+for a location code `10`, the corresponding filename should be
+`YH.LOBS3.10.HH1.D.2014.332`). There is no location code for the 
+YH.LOBS3 data, and this field is simply absent from the filenames.
+Finally, the day-of-year (DOY) field must be zero-padded to be exactly
+3 characters.
 """
 
-__version__ = '0.2.0'
+__version__ = '0.2.1'
 
-__author__ = 'Pascal Audet & Helen Janiszewski'
+__author__ = 'Pascal Audet'
 
 from . import atacr
 from . import comply