Merge pull request #36 from simontorres/change_field_separator

Change field separator closes #31 #34 #35
soar-telescope · Jan 26, 2021 · ef7cf8c · ef7cf8c
2 parents c452359 + 968351b
commit ef7cf8c
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diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -6,7 +6,7 @@ sphinx:
 formats: all
 
 python:
-  version: 3.5
+  version: 3.7
   install:
     - method: pip
       path: .

diff --git a/.travis.yml b/.travis.yml
diff --git a/CHANGES.rst b/CHANGES.rst
@@ -1,3 +1,13 @@
+.. _v1.0.0:
+
+1.0.0
+=====
+
+- Removed Travis CI [#31]
+- Replaced separator to double underscore [#34, #35]
+- Updated documentation.
+
+
 .. _v0.3.6:
 
 0.3.6

diff --git a/README.md b/README.md
@@ -3,7 +3,7 @@
 
 # Goodman Focus Finder
 
-[![Build Status](https://travis-ci.org/soar-telescope/goodman_focus.svg?branch=master)](https://travis-ci.org/soar-telescope/goodman_focus)
+![Goodman Focus](https://github.com/soar-telescope/goodman_focus/workflows/Goodman%20Focus/badge.svg)
 [![Coverage Status](https://coveralls.io/repos/github/soar-telescope/goodman_focus/badge.svg?branch=master)](https://coveralls.io/github/soar-telescope/goodman_focus?branch=master)
 [![Documentation Status](https://readthedocs.org/projects/goodman-focus/badge/?version=latest)](https://goodman-focus.readthedocs.io/en/latest/?badge=latest)
 [![pypi](https://img.shields.io/pypi/v/goodman_focus.svg?style=flat)](https://pypi.org/project/goodman-focus/)

diff --git a/docs/conf.py b/docs/conf.py
@@ -44,7 +44,6 @@
     'sphinx.ext.autodoc',
     'sphinx.ext.intersphinx',
     'sphinxcontrib.napoleon',
-    'm2r',
     'matplotlib.sphinxext.plot_directive',
 ]
 
@@ -54,7 +53,7 @@
 # The suffix(es) of source filenames.
 # You can specify multiple suffix as a list of string:
 #
-source_suffix = ['.rst', '.md']
+source_suffix = ['.rst']
 # source_suffix = '.rst'
 
 # The master toctree document.

diff --git a/docs/index.rst b/docs/index.rst
@@ -6,8 +6,8 @@
 Welcome to Goodman Focus' documentation!
 ========================================
 
-.. image:: https://travis-ci.org/soar-telescope/goodman_focus.svg?branch=master
-    :target: https://travis-ci.org/soar-telescope/goodman_focus
+.. image:: https://github.com/soar-telescope/goodman_focus/workflows/Goodman%20Focus/badge.svg
+    :alt: Goodman Focus
 .. image:: https://coveralls.io/repos/github/soar-telescope/goodman_focus/badge.svg?branch=master
     :target: https://coveralls.io/github/soar-telescope/goodman_focus?branch=master
 .. image:: https://readthedocs.org/projects/goodman-focus/badge/?version=latest
@@ -25,8 +25,6 @@ different focus values. It works for imaging and for spectroscopy.
 
 This tool requires python `3.6` at least to work. It will not install with `3.5`.
 
-We recommend using `astroconda <https://astroconda.readthedocs.io/en/latest/>`_ since it is easier.
-
 
 .. toctree::
    :maxdepth: 2

diff --git a/docs/usingit.rst b/docs/usingit.rst
@@ -90,7 +90,7 @@ Interpreting Results
 
 The terminal version will print a message like this
 
-  ``[17:16:06][INFO]: Best Focus for mode SP_Red_400m2_GG455 is -1032.6413206603302``
+  ``[17:16:06][INFO]: Best Focus for mode SP__Red__400m2__GG455 is -1032.6413206603302``
 
 
 Using it as a library will return a dictionary with the following values.
@@ -100,16 +100,16 @@ explained in :ref:`decoding-mode-name`
 
 .. code-block:: python
 
-  {'IM_Red_g-SDSS': -571.4837418709354,
-   'IM_Red_i-SDSS': -802.567783891946,
-   'IM_Red_r-SDSS': -573.8694347173587,
-   'IM_Red_z-SDSS': -1161.5072536268135,
-   'SP_Red_400m1_NOFILTER': -492.0760380190095,
-   'SP_Red_400m2_GG455': -1032.6413206603302}
+  {'IM__Red__g-SDSS': -571.4837418709354,
+   'IM__Red__i-SDSS': -802.567783891946,
+   'IM__Red__r-SDSS': -573.8694347173587,
+   'IM__Red__z-SDSS': -1161.5072536268135,
+   'SP__Red__400m1__NOFILTER': -492.0760380190095,
+   'SP__Red__400m2__GG455': -1032.6413206603302}
 
 
 It is also possible to obtain a plot, from terminal, use ``--plot-results``.
-Below is a repreduction of results obtained  with test data.
+Below is a reproduction of results obtained  with test data.
 
 .. plot::
 
@@ -118,7 +118,7 @@ Below is a repreduction of results obtained  with test data.
   import matplotlib.pyplot as plt
 
   best_focus = -571.483741871
-  mode_name = 'IM_Red_g-SDSS'
+  mode_name = 'IM__Red__g-SDSS'
 
   data = {'file': ['0186_focus_gp.fits',
                    '0187_focus_gp.fits',
@@ -187,21 +187,26 @@ The mode name is different for Imaging and Spectroscopy, since for imaging
 the important settings are the instrument and the filter and for spectroscopy
 the important values come from the instrument, the grating and observing mode and
 filter from second filter wheel. Below, the word inside the parenthesis represents
-a kewyword from the header.
+a keyword from the header.
+
+.. warning::
+  Be aware that the separator string is a ``double underscore``. This change
+  was necessary to avoid confusion with single underscores used in certain
+  keyword values.
 
 For imaging:
 
-  ``IM_(INSTCONF)_(FILTER)``
+  ``IM__(INSTCONF)__(FILTER)``
 
 for example:
 
-  ``IM_Red_g-SDSS``
+  ``IM__Red__g-SDSS``
 
 For spectroscopy:
 
-  ``SP_(INSTCONF)_(WAVMODE)_(FILTER2)``
+  ``SP__(INSTCONF)__(WAVMODE)__(FILTER2)``
 
 
 for example:
 
-  ``SP_Red_400m2_GG455``
+  ``SP__Red__400m2__GG455``
diff --git a/environment.yml b/environment.yml
@@ -10,6 +10,6 @@ dependencies:
   - pip:
       - ccdproc
       - coveralls
-      - m2r
+      - sphinx_rtd_theme
       - sphinx
       - sphinxcontrib.napoleon
diff --git a/goodman_focus/goodman_focus.py b/goodman_focus/goodman_focus.py
@@ -168,11 +168,10 @@ def get_fwhm(peaks, values, x_axis, profile, model, sigma=3, maxiter=3):
         peaks (numpy.ndarray): An array of peaks present in the profile.
         values (numpy.ndarray): An array of values at peak location.
         x_axis (numpy.ndarray): X-axis for the profile, usually is equivalent to
-        `range(len(profile))`.
-        profile (numpy.ndarray): 1-dimensional profile of the image being
-         analyzed.
+         `range(len(profile))`.
+        profile (numpy.ndarray): 1-dimensional profile of the image being analyzed.
         model (Model): A model to fit to each peak location. `Gaussian1D` and
-        `Moffat1D` are supported.
+         `Moffat1D` are supported.
         sigma (int): Number sigmas to use on sigma-clipping
         maxiter (int): Maximum number of sigma-clipping iterations
 
@@ -496,14 +495,14 @@ def _get_mode_name(group):
             subset=['INSTCONF', 'FILTER', 'FILTER2', 'WAVMODE'], keep='first')
 
         if unique_values['WAVMODE'].values == ['IMAGING']:
-            mode_name = 'IM_{}_{}'.format(
-                unique_values['INSTCONF'].values[0],
-                unique_values['FILTER'].values[0])
+            mode_name = '__'.join(['IM',
+                                   str(unique_values['INSTCONF'].values[0]),
+                                   str(unique_values['FILTER'].values[0])])
         else:
-            mode_name = 'SP_{}_{}_{}'.format(
-                unique_values['INSTCONF'].values[0],
-                unique_values['WAVMODE'].values[0],
-                unique_values['FILTER2'].values[0])
+            mode_name = '__'.join(['SP',
+                                   str(unique_values['INSTCONF'].values[0]),
+                                   str(unique_values['WAVMODE'].values[0]),
+                                   str(unique_values['FILTER2'].values[0])])
         mode_name = re.sub('[<> ]', '', mode_name)
         # mode_name = re.sub('[- ]', '_', mode_name)
         return mode_name
@@ -592,39 +591,5 @@ def run_goodman_focus(args=None):   # pragma: no cover
         log.info("Mode: {} Best Focus: {}".format(key, result[key]))
 
 
-# def run_goodman_focus_list(args=None):   # pragma: no cover
-#     """Entrypoint
-#
-#     Args:
-#         args (list): (optional) a list of arguments and respective values.
-#
-#     """
-#     args = get_args(arguments=args)
-#     goodman_focus = GoodmanFocus(data_path=args.data_path,
-#                                  file_pattern=args.file_pattern,
-#                                  obstype=args.obstype,
-#                                  features_model=args.features_model,
-#                                  plot_results=args.plot_results,
-#                                  debug=args.debug)
-#
-#     file_list = ['0016_foc_400m2.fits',
-#                  '0018_foc_400m2.fits',
-#                  '0020_foc_400m2.fits',
-#                  '0022_foc_400m2.fits',
-#                  '0024_foc_400m2.fits',
-#                  '0026_foc_400m2.fits',
-#                  '0028_foc_400m2.fits',
-#                  '0017_foc_400m2.fits',
-#                  '0019_foc_400m2.fits',
-#                  '0021_foc_400m2.fits',
-#                  '0023_foc_400m2.fits',
-#                  '0025_foc_400m2.fits',
-#                  '0027_foc_400m2.fits']
-#
-#     result = goodman_focus(files=file_list)
-#     print(result)
-
-
 if __name__ == '__main__':   # pragma: no cover
-    # full_path = '/user/simon/data/soar/work/focus2'
     run_goodman_focus()
diff --git a/goodman_focus/tests/test_goodman_focus.py b/goodman_focus/tests/test_goodman_focus.py
@@ -221,15 +221,15 @@ def setUp(self):
 
     def test_imaging_mode(self):
         df = pandas.DataFrame(self.data)
-        expected_name = 'IM_Blue_FILTER-X'
+        expected_name = 'IM__Blue__FILTER-X'
         mode_name = GoodmanFocus._get_mode_name(group=df)
         self.assertEqual(mode_name, expected_name)
 
     def test_spectroscopy_mode(self):
         self.data['WAVMODE'] = ['400  z1'] * 5
         df = pandas.DataFrame(self.data)
 
-        expected_name = 'SP_Blue_400z1_NOFILTER'
+        expected_name = 'SP__Blue__400z1__NOFILTER'
 
         mode_name = GoodmanFocus._get_mode_name(group=df)
 

diff --git a/goodman_focus/version.py b/goodman_focus/version.py
@@ -1,2 +1,2 @@
 # This is an automatic generated file please do not edit
-__version__ = '0.3.5'
+__version__ = '0.3.7'
diff --git a/pyproject.toml b/pyproject.toml
@@ -0,0 +1,7 @@
+[build-system]
+
+requires = ["setuptools",
+            "setuptools_scm",
+            "wheel"]
+
+build-backend = 'setuptools.build_meta'
diff --git a/setup.cfg b/setup.cfg
@@ -32,4 +32,4 @@ install_requires =
     sphinx
 
 # version should be PEP440 compatible (http://www.python.org/dev/peps/pep-0440)
-version = 0.3.6
+version = 1.0.0