Added links to sections, and updated sections for MAC101

docs/source/mac_101.rst

@@ -1,3 +1,5 @@
+
+.. _MAC101:
 ==========================
 MAC 101: An Introduction
 ==========================
@@ -11,6 +13,113 @@ to SSH onto a remote computer, and more.
 .. contents:: Table of Contents
     :local:
 
+--------------------------
+What your MAC should have
+--------------------------
+
+Your MAC already comes with pre-installed packages, but some of the 
+packages that you may need are not *entirely* ready to be used.
+The first packages that you may need to install are the following:
+
+.. _Xcode:
+^^^^^^^^^^^^^^^^^^^^
+Xcode
+^^^^^^^^^^^^^^^^^^^^
+
+`Xcode <https://developer.apple.com/xcode/>`_ is an editor that you 
+can use to edit and run your scripts.
+
+.. note::
+
+    In my opinion, `Sublime Text <https://www.sublimetext.com/>`_ is a 
+    much better editor than Xcode is, because it has a lot more 
+    integrations and feautures than Xcode does.
+
+After having downloaded and installed Xcode, there are a few commands that 
+need to be run in order to let other programs run, i.e. 
+**`Xcode Command-line Tools <https://railsapps.github.io/xcode-command-line-tools.html>`_**.
+
+You should run the following commands from the Terminal:
+
+.. code-block::
+
+    xcode-select --install
+
+and verify that you've installed Xcode Command Line Tools successfully:
+
+.. code-block::
+
+    $ xcode-select -p
+    /Applications/Xcode.app/Contents/Developer
+
+Just to be certain, verify that **gcc** is installed:
+
+.. code::
+
+    $ gcc --version
+    gcc-7 (Homebrew GCC 7.2.0) 7.2.0
+    Copyright (C) 2017 Free Software Foundation, Inc.
+    This is free software; see the source for copying conditions.  There is NO
+    warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+
+For more information, read `this <https://railsapps.github.io/xcode-command-line-tools.html>`_
+to know more about **Xcode Command Line Tools**.
+
+
+.. _LaTeX:
+^^^^^^^^^^^^^^^^^^^^
+LaTeX
+^^^^^^^^^^^^^^^^^^^^
+
+Another important package that you need to install whenever you get a new 
+MAC is **LaTeX**.  LaTeX is a *document preparation system* that lets you 
+present your work or documents in a presentable format. LaTeX is 
+also used a lot by scientific journals, i.e. **Astrophysical Journal**, 
+**`Monthly Notices of the Royal Astronomical Society <https://academic.oup.com/mnras>`_**.
+
+To download LaTeX on a MAC, you need to download **MacTEX**.
+This can be found at `https://www.tug.org/mactex/ <https://www.tug.org/mactex/>`_.
+
+After downloading the necessary :code:`.pkg` file, you will be able to 
+execute and run LaTeX on your computer.
+
+For a tutorial on how to use LaTeX, go to the links in LaTeX_links_.
+
+.. _VPN:
+^^^^^^^^^^^^^^^^^^^^
+Vanderbilt VPN
+^^^^^^^^^^^^^^^^^^^^
+
+Sometimes you will need to access remote servers from outside Vanderbilt.
+To do this you will need to set up a **VPN** connections.
+In order to do this, you will need to install the 
+`Pulse Secure VPN <https://it.vanderbilt.edu/security/secure-communications/remote-access/>`_
+client. This will will let you connect remotely to servers hosted at Vanderbilt .
+
+
+.. _MAC_Time_Machine:
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+MAC Time Machine & Backup
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+When you get a MAC, you have the option to set up 
+`Time Machine <https://support.apple.com/en-us/HT201250>`_. Time Machine 
+lets you back up your entire computer, so that you don't loose any 
+important file.
+
+I **strongly** suggest buying a hard drive (>1TB) to back up all of your 
+files. I find the hard drives from *Western Digital* quite useful.
+In case you're interested, see `here <https://www.wdc.com/products/personal-cloud-storage.html>`_.
+
+.. note::
+
+    It is **extremely** important that you back up your computer at least a few 
+    times a week. If not, you may end up loosing a substantial amount of 
+    files (and your work!) if your computer fails. So this should be one 
+    of the **first things** that you do when having a Mac.
+
+
+.. _SSH:
 -------------
 SSH
 -------------
@@ -95,7 +204,7 @@ your password anytime that you want to access the remote server.
 
 This can be solved by using **:code:`SSH keys`**.
 
-
+.. _SSH_Keys:
 ^^^^^^^^^^^^^
 SSH-Keys
 ^^^^^^^^^^^^^
@@ -153,6 +262,7 @@ replacing :code:`key` with the name of the actual SSH-key.
     them. (But they would have to know which server to connect to, which 
     "config" file will provide!)
 
+.. _SSH_Config:
 ^^^^^^^^^^^^^^^^^
 SSH Config file
 ^^^^^^^^^^^^^^^^^
@@ -217,6 +327,7 @@ This will make **git** to use the public key :code:`github_key`, which
 you should have created already. If not, follow these instructions
 `here <https://help.github.com/articles/connecting-to-github-with-ssh/>`_.
 
+.. _SSH_X11:
 """"""""""""""""""""""""""
 Forwarding X11 (MACs only)
 """"""""""""""""""""""""""

docs/source/python_intro.rst

@@ -1,3 +1,4 @@
+.. _Python101:
 ================================================
 Python 101 - Anaconda, environments, and more
 ================================================
@@ -8,6 +9,7 @@ in order to property use python in your projects.
 .. contents:: Table of Contents
     :local:
 
+.. _Python_Anaconda:
 --------------------
 Anaconda
 --------------------
@@ -24,10 +26,11 @@ From their website:
     deliver actionable insights that drive businesses and industries forward.
 
 
-Having *Ananconda* installed on your computer is important, since it 
+Having **Ananconda* installed on your computer is important, since it 
 allows you to not worry about installing missing dependencies, 
 creates environments for you projects, etc.
 
+.. _Python_Anaconda_Install:
 ^^^^^^^^^^^^^^^^^^^^^
 Installing Anaconda
 ^^^^^^^^^^^^^^^^^^^^^
@@ -71,6 +74,7 @@ terminal:
     home directory**, e.g. a computer hosted by 
     `ACCRE <http://www.accre.vanderbilt.edu/>`_.
 
+.. _Anaconda_Environments:
 ^^^^^^^^^^^^^^^^^^^^^^^
 Managing environments
 ^^^^^^^^^^^^^^^^^^^^^^^
@@ -126,7 +130,7 @@ For more information, see `<https://conda.io/docs/user-guide/tasks/manage-enviro
     are in the directory. For more information on how to install it and 
     use it, see `<https://github.com/chdoig/conda-auto-env>`_.
 
-
+.. _Code_Structure:
 ----------------------------
 Structuring your code
 ----------------------------
@@ -139,6 +143,7 @@ in mind when you're structuring your project will allow others to
 look at your code, understand it well enough to be able to **recreate** 
 your results.
 
+.. _Code_Cookiecutter:
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 Cookiecutter and Folder Structure
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -225,7 +230,7 @@ Once you have cloned and answered the questions by *cookiecutter*,
 you will have a directory with a folder structure that allows for 
 easy reproducibility.
 
-
+.. _Python_Environment:
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 Editing your environment
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

docs/source/useful_links.rst

@@ -1,3 +1,4 @@
+.. _Useful_links:
 =============================
 Useful links and Resources
 =============================
@@ -9,6 +10,7 @@ It includes links from science, coding, machine learning, etc.
 .. contents:: Table of Contents
     :local:
 
+.. _General_links:
 -----------------
 General
 -----------------
@@ -19,12 +21,14 @@ General
 - `AstroBrew Schedule <https://as.vanderbilt.edu/astronomy/category/astrobrew/>`_
 - `Vandy Astronomy - Workshops and Seminars <https://vandyastroml.github.io>`_ Main Website for the Astronomy Workshops and Seminars at Vanderbilt
 
+.. _MAC_links:
 ----------------------------------
 MAC-related (if applicable)
 ----------------------------------
 - `Setting up a MAC <http://www.astrobetter.com/wiki/Wiki+Home>`_
 - `Apps for MACs <http://www.astrobetter.com/wiki/tiki-index.php?page=Mac+Apps>`_
 
+.. _Reading_Papers_links:
 -----------------
 Reading Papers
 -----------------
@@ -40,32 +44,37 @@ Reading Papers
 - `Benty Fields <https://www.benty-fields.com/>`_ - Selected papers to use. It uses ML to suggest you new papers.
 - `AAS Nova <http://aasnova.org/>`_ - Research highlights from the journals of the American Astronomical Society
 
+.. _Paper_Management_links:
 -----------------
 Paper Management
 -----------------
 
 - `Mendeley <https://www.mendeley.com/>`_
 
+.. _Taking_Notesv:
 -------------------
 Taking Notes
 -------------------
 
 - `Evernote <https://evernote.com/>`_
 - `OneNote <https://www.onenote.com/>`_
 
+.. _Collaborations_links:
 -------------------
 Collaborations
 -------------------
 
 - `Slack <https://slack.com/>`_
 
+.. _Conferences_links:
 -----------------
 Conferences
 -----------------
 - `Python in Astronomy <http://openastronomy.org/pyastro/>`_
 - `Canadian Astronomy Data Centre <http://www1.cadc-ccda.hia-iha.nrc-cnrc.gc.ca/en/meetings/>`_
 - `Conference Management Software for Astronomy <https://www.conference-service.com/conferences/gravitation-and-cosmology.html>`_
 
+.. _General_Learning_links:
 -----------------
 General Learning
 -----------------
@@ -77,6 +86,7 @@ General Learning
 - `World Science Festival <https://www.worldsciencefestival.com/>`_
 - `TED Talks <https://www.ted.com/>`_
 
+.. _Python_Anaconda_links:
 -------------------
 Python & Anaconda
 -------------------
@@ -88,6 +98,7 @@ Python & Anaconda
 - `Astro ML <http://www.astroml.org/>`_ - Machine Learning and Data Mining for Astronomy
 - `Cython Tutorial <https://cython.readthedocs.io/en/latest/src/tutorial/cython_tutorial.html>`_
 
+.. _Interesting_Python_Packages_links:
 ----------------------------------
 Interesting Python Packages
 ----------------------------------
@@ -97,14 +108,17 @@ Interesting Python Packages
 - `Pandas <https://pandas.pydata.org/>`_ and `Tutorial <https://www.tutorialspoint.com/python_pandas/>`_
 - `Scikit-Learn <http://scikit-learn.org/>`_
 
+.. _Code_Editors_links:
 -------------------
 Code Editors
 -------------------
 
 - `Sublime Text 3 <https://www.sublimetext.com/>`_
 - `PyCharm <https://www.jetbrains.com/pycharm/>`_
+- `Atom Editor <https://atom.io/>`_ - Similar to Sublime Text.
 - `VIM for Beginners <https://computers.tutsplus.com/tutorials/vim-for-beginners--cms-21118>`_
 
+.. _Code_Structure_links:
 -------------------
 Code Structure
 -------------------
@@ -113,6 +127,7 @@ Code Structure
 - `Markdown CheatSheet <https://github.com/adam-p/markdown-here/wiki/Markdown-Cheatsheet>`_
 - `Restructured Text (reST) CheatSheet <https://github.com/ralsina/rst-cheatsheet/blob/master/rst-cheatsheet.rst>`_
 
+.. _Version_Control_links:
 -----------------
 Version Control
 -----------------
@@ -122,20 +137,23 @@ Version Control
 - `Git tutorials and training <https://www.atlassian.com/git/tutorials/>`_ by Atlassian
 - `Bitbucket <https://bitbucket.org/>`_
 
+.. _SSH_Keys_links:
 -----------------
 SSH Keys
 -----------------
 
 - `How to Set up SSH Keys <https://www.digitalocean.com/community/tutorials/how-to-set-up-ssh-keys--2>`_
 - `Connecting to Github with SSH <https://help.github.com/articles/connecting-to-github-with-ssh/>`_
 
+.. _LaTeX_links:
 -----------------
 LaTeX
 -----------------
 
 - `Installing LaTeX <http://www.astrobetter.com/blog/2010/07/06/install-latex/>`_
 - `Learn LaTeX in 30 minutes <https://www.sharelatex.com/learn/Learn_LaTeX_in_30_minutes>`_
 
+.. _Online_Presentations_links:
 -----------------------
 Online Presentations
 -----------------------
@@ -145,6 +163,7 @@ Online Presentations
 - `Galaxy Formation Conferences - Lectures and Videos <http://astro.dur.ac.uk/Gal2011/talks.php>`_
 - 
 
+.. _Machine_Learning_links:
 -----------------
 Machine Learning
 -----------------
@@ -157,6 +176,7 @@ Machine Learning
 - `Introductory Applied Machine Learning <https://www.coursera.org/learn/python-machine-learning>`_
 - `Udacity's Deep Learning course <https://www.udacity.com/course/deep-learning--ud730>`_
 
+.. _Papers_links:
 -----------------
 Papers
 -----------------
@@ -165,6 +185,7 @@ Papers
 - `"Ten Simple Rules for Making Research Software More Robust" <https://arxiv.org/abs/1610.04546>`_ by Morgan Taschuk et al. (2017)
 - `Interactive Notebooks: Sharing the Code <http://www.nature.com/news/interactive-notebooks-sharing-the-code-1.16261>`_ by Helen Shen
 
+.. _Interesting_Books_links:
 ---------------------
 Interesting Books
 ---------------------
@@ -177,6 +198,7 @@ Interesting Books
 - `Introduction to Cosmology <https://www.amazon.com/Introduction-Cosmology-Barbara-Ryden/dp/0805389121/ref=pd_sim_14_1?ie=UTF8&dpID=41E27ZCFRKL&dpSrc=sims&preST=_AC_UL160_SR130,160_&psc=1&refRID=Q3QMV7G3AF4RG508TDM6>`_ by Barbara Ryden or the `PDF version <http://atlas.physics.arizona.edu/~kjohns/downloads/lsst/Ryden_IntroCosmo.pdf>`_
 - `An Introduction to Modern Astrophysics <https://www.amazon.com/Introduction-Modern-Astrophysics-2nd/dp/0805304029>`_ by Bradley Carroll
 
+.. _Jobs_and_Applications_links:
 ----------------------
 Jobs and Applications
 ----------------------