Updated the install instructions for Ubuntu 18.04

.gitignore

@@ -108,3 +108,4 @@ reports/
 .Rhistory
 sn_profile_*/
 settings.dcf
+tests/fakedata_generation/

docs/features/extracted.rst

@@ -749,7 +749,7 @@ The differences between both API versions are:
     - Unified level of sleep. For intraday data, we unify sleep levels of each sleep record with a column named "unified_level". Based on `this Fitbit forum post`_ , we merge levels into two categories:
         - For the "classic" type: unified_level is one of {0, 1} where 0 means awake and groups "awake" + "restless", while 1 means asleep and groups "asleep".
         - For the "stages" type, unified_level is one of {0, 1} where 0 means awake and groups "wake" while 1 means asleep and groups "deep" + "light" + "rem".
-    - Short Data. In `v1.2`, records of type "stages" contain "shortData_" in addition to "data". We merge "data" part and "shortData" part to extract intraday data. 
+    - Short Data. In `v1.2`, records of type "stages" contain "shortData" in addition to "data". We merge "data" part and "shortData" part to extract intraday data. 
         - The "data" grouping displays the sleep stages and any wake periods > 3 minutes (180 seconds).
         - The "shortData" grouping displays the short wake periods representing physiological awakenings that are <= 3 minutes (180 seconds).
     - The following columns of Summary data are not computed by RAPIDS but taken directly from columns with a similar name provided by the API: `efficiency`, `minutes_after_wakeup`, `minutes_asleep`, `minutes_awake`, `minutes_to_fall_asleep`, `minutes_in_bed`, `is_main_sleep` and `type`

docs/usage/faq.rst

@@ -26,16 +26,20 @@ Frequently Asked Questions
 
 Please make sure the ``MY_GROUP`` in ``config.yaml`` and ``.env`` match.
 
+
+
 2. Cannot start mysql in linux via ``brew services start mysql``
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 use the following command instead:
 
 ``mysql.server start``
 
+
 3. Every time I run ``snakemake -R download_dataset`` all rules are executed
 """"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 This is expected behavior. The advantage of using ``snakemake`` under the hood is that every time a file containing data is modified every rule that depends on that file will be re-executed to update their results. In this case, since ``download_dataset`` updates all the raw data, and you are forcing the rule with the flag ``-R`` every single rule that depends on those raw files will be executed.
 
+
 4. Got an error ``Table XXX doesn't exist`` while running the download_dataset rule.
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 ::
@@ -47,3 +51,92 @@ This is expected behavior. The advantage of using ``snakemake`` under the hood i
 
 **Solution:**
 Please make sure the sensors listed in SENSORS in ``config.yaml`` match your database tables.
+
+
+
+5. How do I install on Ubuntu 16.04
+""""""""""""""""""""""""""""""""""""
+
+#. Install dependencies (Homebrew - if not installed):
+
+    - ``sudo apt-get install libmariadb-client-lgpl-dev libxml2-dev libssl-dev``
+    - Install brew_ for linux and add the following line to ~/.bashrc: ``export PATH=$HOME/.linuxbrew/bin:$PATH``
+    - ``source ~/.bashrc``
+
+#. Install MySQL
+
+    - ``brew install mysql``
+    - ``brew services start mysql``
+
+#. Install R, pandoc and rmarkdown:
+
+    - ``brew install r``
+    - ``brew install gcc@6`` (needed due to this bug_)
+    - ``HOMEBREW_CC=gcc-6 brew install pandoc``
+
+#. Install miniconda using these instructions_
+
+#. Clone our repo:
+
+    - ``git clone https://github.com/carissalow/rapids``
+
+#. Create a python virtual environment:
+
+    - ``cd rapids``
+    - ``conda env create -f environment.yml -n MY_ENV_NAME``
+    - ``conda activate MY_ENV_NAME``
+
+#. Install R packages and virtual environment:
+
+    - ``snakemake renv_install``
+    - ``snakemake renv_init``
+    - ``snakemake renv_restore``
+        - This step could take several minutes to complete. Please be patient and let it run until completion. 
+
+#. See :ref:`Usage section <usage-section>`.
+
+
+
+6. Configuration failed for package ``RMySQL``
+""""""""""""""""""""""""""""""""""""""""""""""""
+::
+
+    --------------------------[ ERROR MESSAGE ]----------------------------
+    <stdin>:1:10: fatal error: mysql.h: No such file or directory
+    compilation terminated.
+    -----------------------------------------------------------------------
+    ERROR: configuration failed for package 'RMySQL'
+
+sudo apt install libmariadbclient-dev
+
+
+
+7. No package ``libcurl`` found
+"""""""""""""""""""""""""""""""""
+
+The  ``libcurl`` needs to installed using the following command
+
+``sudo apt install libcurl4-openssl-dev``
+
+
+
+8. Configuration failed because ``openssl`` was not found.
+"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+
+Install the ``openssl`` library using the following command
+
+``sudo apt install libssl-dev``
+
+
+9. Configuration failed because ``libxml-2.0`` was not found
+"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+
+Install the ``xml`` library using the following command 
+
+``sudo apt install libxml2-dev``
+
+.. ------------------------ Links --------------------------- ..
+
+.. _bug: https://github.com/Homebrew/linuxbrew-core/issues/17812
+.. _instructions: https://docs.conda.io/projects/conda/en/latest/user-guide/install/linux.html
+.. _brew: https://docs.brew.sh/Homebrew-on-Linux

docs/usage/installation.rst

@@ -48,28 +48,47 @@ macOS (tested on Catalina 10.15)
 #. See Usage section below. 
 
 
-Linux (tested on Ubuntu 16.04)
+Linux (tested on Ubuntu 18.04)
 ------------------------------
 
-#. Install dependencies (Homebrew - if not installed):
+#. Install dependencies :
 
-    - ``sudo apt-get install libmariadb-client-lgpl-dev libxml2-dev libssl-dev``
+    - ``sudo apt install libcurl4-openssl-dev``
-    - Install brew_ for linux and add the following line to ~/.bashrc: ``export PATH=$HOME/.linuxbrew/bin:$PATH``
+    - ``sudo apt install libssl-dev``
+    - ``sudo apt install libxml2-dev``
+
+    (Homebrew - if not installed)
+    
+    - Install brew_ for linux 
+    - add the following line to ~/.bashrc: ``export PATH=$HOME/.linuxbrew/bin:$PATH``
     - ``source ~/.bashrc``
 
 #. Install MySQL
 
-    - ``brew install mysql``
+    - ``sudo apt install-mysql``
-    - ``brew services start mysql``
+    - ``sudo apt install libmariadbclient-dev``
+    - (OPTIONAL) ``sudo apt install mysql-server``
 
-#. Install R, pandoc and rmarkdown:
 
-    - ``brew install r``
+#. Install R
-    - ``brew install gcc@6`` (needed due to this bug_)
+
-    - ``HOMEBREW_CC=gcc-6 brew install pandoc``
+    - ``sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9``
+    - ``sudo add-apt-repository 'deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran40/'``
+    - ``sudo apt update``
+    - ``sudo apt install r-base``
+
+#. Install PANDOC
+
+    - ``sudo apt install pandoc``
+
+#. Install GIT
+
+    - ``sudo apt install git``
 
 #. Install miniconda using these instructions_ 
 
+#. Restart your current shell
+
 #. Clone our repo:
 
     - ``git clone https://github.com/carissalow/rapids``
@@ -83,13 +102,14 @@ Linux (tested on Ubuntu 16.04)
 #. Install R packages and virtual environment:
 
     - ``snakemake renv_install``
-    - ``snakemake renv_init``
     - ``snakemake renv_restore``
         - This step could take several minutes to complete. Please be patient and let it run until completion. 
 
 #. See Usage section below.
 
 
+.. _usage-section:
+
 Usage
 ======
 Once RAPIDS is installed, follow these steps to start processing mobile data.

docs/usage/quick_rule.rst

@@ -1,4 +1,5 @@
 .. _minimal-working-example:
+
 Minimal Working Example 
 =======================