Merge pull request #246 from simontorres/documentation_updates

Documentation updates, also changed dcr installation
soar-telescope · Oct 18, 2018 · f53982f · f53982f
2 parents b6412e3 + b2165f3
commit f53982f
Show file tree

Hide file tree

Showing 26 changed files with 263 additions and 182 deletions.
diff --git a/.travis.yml b/.travis.yml
@@ -8,12 +8,12 @@ branches:
   - master
   - development
 
-before_install:
-- ./install_dcr.sh
+# before_install:
+# - ./install_dcr.sh
 
 
 install:
-- export PATH="$PATH:$HOME/build/soar-telescope/goodman_pipeline/dcrbin"
+# - export PATH="$PATH:$HOME/build/soar-telescope/goodman_pipeline/dcrbin"
 
 - sudo apt-get update
 
@@ -40,8 +40,8 @@ install:
 - source activate goodman_pipeline
 
 # install
-- python setup.py test
 - python setup.py install
+- python setup.py test
 
 script:
 - pytest

diff --git a/README.md b/README.md
@@ -32,8 +32,8 @@ If you wish to know more about the instrument please check the
 If you are having trouble operating the Goodman Pipeline we suggest the following
 procedure.
 
-* Check [existing issues](https://github.com/soar-telescope/goodman/issues) or 
-open a [new Issue](https://github.com/soar-telescope/goodman/issues/new) on GitHub.
+* Check [existing issues](https://github.com/soar-telescope/goodman_pipeline/issues) or 
+open a [new Issue](https://github.com/soar-telescope/goodman_pipeline/issues/new) on GitHub.
 
 ## Development Team
 

diff --git a/docs/_install_dcr.rst b/docs/_install_dcr.rst
@@ -0,0 +1,93 @@
+.. _dcr:
+
+Installing DCR
+**************
+
+.. admonition:: Acknowledgement Note
+
+  Please cite: Pych, W., 2004, PASP, 116, 148
+
+In terms of cosmic ray rejection we shifted to a non-python package because the
+results were much better compared to LACosmic's implementation in Astropy.
+LACosmic was not designed to work with spectroscopy. Though since version
+:ref:`1.1.0 <v1.1.0>` we shifted from Astropy to Astroscrappy's implementation
+of LACosmic.
+
+The latest version of the Goodman Spectroscopic Pipeline uses a modified version
+of ``dcr`` to help with the pipeline's workflow. It is included under
+
+  ``<path_to_download_location>/goodman_pipeline/goodman_pipeline/data/dcr-source/dcr/``
+
+``goodman_pipeline-<version>`` is the folder that will be created once you untar or unzip the latest
+release of the |pipeline name|.
+
+.. important::
+
+    The changes we made to DCR include deletion of all ``HISTORY`` and ``COMMENT`` keywords,
+    which we don't use in the pipeline. And addition of a couple of custom
+    keywords, such as: ``GSP_FNAM``, which stores the name of the file being
+    created. ``GSP_DCRR`` which stores the reference to the paper to cite.
+
+
+You are still encouraged to visit the official
+`Link <http://users.camk.edu.pl/pych/DCR/>`_. We remind again that users of the
+Goodman Pipeline should cite the DCR paper with the reference indicated above.
+
+Compiling DCR
+^^^^^^^^^^^^^
+
+Compiling ``dcr`` is actually very simple.
+
+  ``cd <path_to_download_location>/goodman_pipeline/goodman_pipeline/data/dcr-source/dcr/``
+
+Then simply type:
+
+  ``make``
+
+This will compile `dcr` and also it will create other files. The executable
+binary here is ``dcr``.
+
+We have successfully compiled *dcr* right out the box in several platforms, such as:
+
+- Ubuntu 16.04
+- Centos 7.1, 7.4
+- MacOS Sierra
+- Solaris 11
+
+
+Installing the DCR binary
+^^^^^^^^^^^^^^^^^^^^^^^^^
+
+This is a suggested method. If you are not so sure what you are doing, we
+recommend you follow the steps shown below. If you are a more advanced user and
+you want to do it your own way, all you have to achieve is to have the ``dcr``
+executable binary in your ``$PATH`` variable.
+
+1. Open a terminal
+2. In your home directory create a hidden directory ``.bin`` (Home directory
+   should be the default when you open a new terminal window)
+
+   ``mkdir ~/.bin``
+
+3. Move the binary of your choice and rename it ``dcr``. If you compiled it,
+   most likely it's already called ``dcr`` so you can ignore the renaming part of
+   this step.
+
+   ``mv dcr.Ubuntu16.04 ~/.bin/dcr``
+
+   Or
+
+   ``mv dcr ~/.bin/dcr``
+
+4. Add your ``$HOME/.bin`` directory to your ``$PATH`` variable. Open the file
+   ``.bashrc`` and add the following line.
+
+   ``export PATH=$PATH:/home/myusername/.bin``
+
+   Where ``/home/myusername`` is of course your home directory.
+
+5. Close and reopen the terminal or load the ``.bashrc`` file.
+
+    ``source ~/.bashrc``
+
+.. include:: _shortcuts.rst
diff --git a/docs/img/cvso166_400m2_gg455_2.png → docs/_static/cvso166_400m2_gg455_2.png b/docs/img/cvso166_400m2_gg455_2.png → docs/_static/cvso166_400m2_gg455_2.png
diff --git a/docs/img/cvso2016_Ha_auto_wl_solution2.png → ..._static/cvso2016_Ha_auto_wl_solution2.png b/docs/img/cvso2016_Ha_auto_wl_solution2.png → ..._static/cvso2016_Ha_auto_wl_solution2.png
diff --git a/docs/img/cvso2016_Ha_auto_wl_solution_1.png → ...static/cvso2016_Ha_auto_wl_solution_1.png b/docs/img/cvso2016_Ha_auto_wl_solution_1.png → ...static/cvso2016_Ha_auto_wl_solution_1.png
diff --git a/docs/img/cvso2016_Ha_auto_wl_solution_3.png → ...static/cvso2016_Ha_auto_wl_solution_3.png b/docs/img/cvso2016_Ha_auto_wl_solution_3.png → ...static/cvso2016_Ha_auto_wl_solution_3.png
diff --git a/docs/img/eg21_1200M5_GG455.png → docs/_static/eg21_1200M5_GG455.png b/docs/img/eg21_1200M5_GG455.png → docs/_static/eg21_1200M5_GG455.png
diff --git a/docs/img/lamp1D_example.png → docs/_static/lamp1D_example.png b/docs/img/lamp1D_example.png → docs/_static/lamp1D_example.png
diff --git a/docs/img/lst → docs/_static/lst b/docs/img/lst → docs/_static/lst
diff --git a/docs/img/realvnc.png → docs/_static/realvnc.png b/docs/img/realvnc.png → docs/_static/realvnc.png
diff --git a/docs/img/realvnc1.png → docs/_static/realvnc1.png b/docs/img/realvnc1.png → docs/_static/realvnc1.png
diff --git a/docs/img/realvnc_login.png → docs/_static/realvnc_login.png b/docs/img/realvnc_login.png → docs/_static/realvnc_login.png
diff --git a/docs/img/reminavnc.png → docs/_static/reminavnc.png b/docs/img/reminavnc.png → docs/_static/reminavnc.png
diff --git a/docs/img/screenshot_1.png → docs/_static/screenshot_1.png b/docs/img/screenshot_1.png → docs/_static/screenshot_1.png
diff --git a/docs/_static/soar_logo.png b/docs/_static/soar_logo.png
diff --git a/docs/img/soardata3-terminal.png → docs/_static/soardata3-terminal.png b/docs/img/soardata3-terminal.png → docs/_static/soardata3-terminal.png
diff --git a/...a_automated_solution_GSPEC_2018-03-22.png → ...a_automated_solution_GSPEC_2018-03-22.png b/...a_automated_solution_GSPEC_2018-03-22.png → ...a_automated_solution_GSPEC_2018-03-22.png
diff --git a/docs/_working_with_virtualenv.rst b/docs/_working_with_virtualenv.rst
@@ -11,16 +11,18 @@ If you know nothing about them we recommend you to start in the `Conda site <htt
 
 For the purpose of this manual we will just say that a *Virtual Environment*
 lets you have a custom set of libraries/tools in one place, and most importantly
-is independent of your host system. Installation will not be discussed here but
+it adds a layer of isolation from your host system. Installation will not be discussed here but
 you can visit `this link <https://conda.io/docs/user-guide/tasks/manage-environments.html>`_
 for information.
 
+Here is a quick overview of the basic operations with virtual environments.
+
 Discover what environments exist in your system.
   ``conda env list``
 
   Will print a list where the first column is the name.
 
-Activate (enter) the virtual Environment.
+Activate the virtual Environment.
   ``source activate <venv-name>``
 
   Where ``<venv-name>`` is the name of your virtual environment. Your shell's
@@ -29,7 +31,7 @@ Activate (enter) the virtual Environment.
   ``(<venv-name>) [user@hostname folder-name]$``
 
 
-Deactivate (leave) the virtual environment.
+Deactivate the virtual environment.
   ``source deactivate``
 
   This time the prompt will change again to:

diff --git a/docs/conf.py b/docs/conf.py
@@ -111,6 +111,8 @@
 
 html_theme = 'sphinx_rtd_theme'
 
+html_logo = '_static/soar_logo.png'
+
 html_context = {'license': 'BSD 3-Clause License'}
 
 # Theme options are theme-specific and customize the look and feel of a theme