From 2e6ee5d32b17d81cb0015427d2a5a4807371db99 Mon Sep 17 00:00:00 2001
From: Jeremy Fee <jmfee@usgs.gov>
Date: Wed, 20 Jan 2016 15:40:53 -0700
Subject: [PATCH] Update documentation examples, setup.py package list

---
 docs/algorithms/DeltaF_usage.md |  4 ++--
 docs/algorithms/XYZ_usage.md    |  4 ++--
 docs/api.md                     | 10 +++++-----
 docs/usage.md                   |  6 ++++--
 setup.py                        |  1 +
 5 files changed, 14 insertions(+), 11 deletions(-)

diff --git a/docs/algorithms/DeltaF_usage.md b/docs/algorithms/DeltaF_usage.md
index ff93d7746..beb0b2d02 100644
--- a/docs/algorithms/DeltaF_usage.md
+++ b/docs/algorithms/DeltaF_usage.md
@@ -6,7 +6,7 @@ and a scalar total-field measurement made by independent sensors.  Read more
 about the [DeltaF Algorithm](./DeltaF.md).
 
 
-`geomag.py --deltaf {geo, obs, obsd}`
+`geomag.py --algorithm deltaf [--deltaf-from {geo, obs, obsd}]`
 
 
 ### Reference Frames
@@ -21,7 +21,7 @@ about the [DeltaF Algorithm](./DeltaF.md).
 To compute DeltaF from  HEZF data for Tucson observatory:
 ```
 geomag.py \
-    --deltaf obs \
+    --algorithm deltaf \
     --observatory TUC \
     --type variation \
     --interval minute \
diff --git a/docs/algorithms/XYZ_usage.md b/docs/algorithms/XYZ_usage.md
index b01fdd8be..d154887f8 100644
--- a/docs/algorithms/XYZ_usage.md
+++ b/docs/algorithms/XYZ_usage.md
@@ -5,7 +5,7 @@ The XYZ Algorithm rotates between `geographic`, `observatory`, and `magnetic`,
 channel orientations.  Read more about the [XYZ Algorithm](./XYZ.md).
 
 
-`geomag.py --xyz {geo, mag, obs, obsd} {geo, mag, obs, obsd}`
+`geomag.py --algorithm xyz [--xyz-from {geo,mag,obs,obsd}] [--xyz-to {geo,mag,obs,obsd}]`
 
 ### Reference Frames
 
@@ -30,7 +30,7 @@ There are 3 reference frames in this library.
 To convert HEZF data in pcdcp files to XYZF for Tucson observatory for all of
 March 2013 output to iaga2002 files:
 
-      geomag.py --xyz obs geo --observatory TUC \
+      geomag.py --algorithm xyz --observatory TUC \
       --starttime 2013-03-01T00:00:00Z --endtime 2013-03-31T23:59:00Z \
       --input-pcdcp-url file://data-pcdcp/./%(OBS)s%(year)s%(julian)s.%(i)s \
       --output-iaga-url file://data-iaga/./$(obs)s%(Y)s%(j)s.%(i)s \
diff --git a/docs/api.md b/docs/api.md
index 15c8df354..61ef90e05 100644
--- a/docs/api.md
+++ b/docs/api.md
@@ -44,11 +44,11 @@ Exception base class is `geomagio.TimeseriesFactoryException`.
 
 ## Algorithms
 
-Base class is `geomagio.Algorithm`
-Exception base class is `geomagio.AlgorithmException`
+Base class is `geomagio.algorithm.Algorithm`
+Exception base class is `geomagio.algorithm.AlgorithmException`
 
-- Delta F `geomagio.DeltaFAlgorithm`
-- XYZ `geomagio.XYZAlgorithm`
+- Delta F `geomagio.algorithm.DeltaFAlgorithm`
+- XYZ `geomagio.algorithm.XYZAlgorithm`
 
 
 ## Example
@@ -60,7 +60,7 @@ The following example:
 - Plots the data using matplotlib
 
 ```python
-from geomagio import XYZAlgorithm
+from geomagio.algorithm import XYZAlgorithm
 from geomagio.edge import EdgeFactory
 from obspy.core import UTCDateTime
 
diff --git a/docs/usage.md b/docs/usage.md
index bc28f80a4..a0bc321e6 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -68,10 +68,12 @@ There are flags to specify certain algorithms should be run against the data.
 
 #### XYZ ####
 
-`--xyz {geo, mag, obs, obsd} {geo, mag, obs, obsd}`
+`--algorithm xyz`
+`--xyz-from {geo, mag, obs, obsd}` (default is `obs`)
+`--xyz-to {geo, mag, obs, obsd}` (default is `geo`)
 
 #### [XYZ Usage](./algorithms/XYZ_usage.md) ####
-Rotate data from HEZ or HDZ to XYZ and back.
+Rotate data from HEZ (obs) or HDZ (mag) to XYZ (geo) and back.
 
 Extensive explanation of all input and output methods:
 [IO Methods](./io.md)
diff --git a/setup.py b/setup.py
index 0257b0d1d..84ef2911c 100644
--- a/setup.py
+++ b/setup.py
@@ -7,6 +7,7 @@ setup(
     url='https://github.com/usgs/geomag-algorithms',
     packages=[
         'geomagio',
+        'geomagio.algorithm',
         'geomagio.iaga2002',
         'geomagio.imfv283',
         'geomagio.edge',
-- 
GitLab