Merge pull request #395 from Allonck/updateDocs

Update docs and change variable name

docs/_cosmic_ray_removal.rst

@@ -46,4 +46,9 @@ methods.
 Asymetric binnings have not been tested but the pipeline only takes in
 consideration the dispersion axis to decide. This does not mean that the spatial
 binning does not impact the performance of any of the methods, we just don't
-know it yet.
+know it yet.
+
+.. note::
+
+  The prefix ``c`` is added to all the comparison lamps, despite they not being
+  affected by cosmic rays.

docs/_observing.rst

@@ -49,7 +49,8 @@ Observing for Radial Velocity
 
 Radial velocity measurements are possible with the |goodman HTS| but you have
 to be careful. A very detailed description of the procedures and what you can
-expect was prepared and is available  `HERE <http://www.ctio.noao.edu/soar/sites/default/files/GOODMAN/goodman_rv.pdf>`_.
+expect was prepared and is available  `here <https://noirlab.edu/science/sites/default/files/media/archives/documents/scidoc0489.pdf>`_
+and `here <https://noirlab.edu/science/sites/default/files/media/archives/documents/scidoc0490.pdf>`_ .
 
 Please read it carefully so you don't find any surprises when trying to reduce
 your data.

docs/install.rst

@@ -39,8 +39,9 @@ This installation was tested on MacOS High Sierra.
 
 2. Download Anaconda or Miniconda
 
-  ``curl https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh --output miniconda.sh``
+  ``curl https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-arm64.sh --output miniconda.sh``
 
+If you have a different processor like intel, you can search miniconda installer url for your system.
 
 Common Steps
 ************

goodman_pipeline/core/core.py

@@ -302,7 +302,7 @@ def call_cosmic_rejection(ccd,
             log.info('Setting cosmic ray rejection method to:'
                      ' {:s}'.format(method))
 
-    if ccd.header['OBSTYPE'] == 'COMP' and method != 'none':
+    if ccd.header['OBSTYPE'] in ['COMP', 'ARC'] and method != 'none':
         log.info("Changing cosmic ray rejection method from '{:s}' to 'none'"
                  " for comparison lamp. Prefix 'c' will be added "
                  "anyway.".format(method))
@@ -317,11 +317,11 @@ def call_cosmic_rejection(ccd,
                     'the mask use --keep-cosmic-files')
 
         if not os.path.isfile(os.path.join(red_path, 'dcr.par')):
-            _create = GenerateDcrParFile()
+            generate_dcr_parameters_file = GenerateDcrParFile()
             _instrument = ccd.header['INSTCONF']
             _binning, _ = ccd.header['CCDSUM'].split()
 
-            _create(instrument=_instrument, binning=_binning, path=red_path)
+            generate_dcr_parameters_file(instrument=_instrument, binning=_binning, path=red_path)
 
         #out_prefix = prefix + out_prefix #Move line here
 

goodman_pipeline/core/tests/test_core.py

@@ -511,6 +511,22 @@ def test_call_cosmic_rejection_comp_lamp(self):
                          ccd.header['GSP_FNAM'])
         self.assertEqual('none', ccd.header['GSP_COSM'])
 
+    def test_call_cosmic_rejection_arc_lamp(self):
+        self.ccd.header.set('OBSTYPE', value='ARC')
+        prefix = 'new_'
+        ccd, out_prefix = call_cosmic_rejection(ccd=self.ccd,
+                                                image_name=self.file_name,
+                                                out_prefix=self.out_prefix,
+                                                red_path=self.red_path,
+                                                keep_files=True,
+                                                prefix=prefix,
+                                                method='dcr',
+                                                save=True)
+        self.assertEqual(prefix + self.out_prefix, out_prefix)
+        self.assertEqual(f"{prefix}{self.out_prefix}_{self.file_name}",
+                         ccd.header['GSP_FNAM'])
+        self.assertEqual('none', ccd.header['GSP_COSM'])
+
     def test_call_cosmic_rejection_not_implemented_error(self):
         prefix = 'new_'
         self.assertRaises(NotImplementedError,