.gitignore

@@ -3,17 +3,22 @@ dist/*
 *.pyc
 *.pyd
 *egg-info*
-
+*.so
 .eggs
 doctrees
-/docs/_build
-/.project
-/.pydevproject
-/.settings/org.eclipse.core.resources.prefs
-/wetb/gtsdf/tests/tmp
-/wetb/dlc/tests/test_files/res_all
-/wetb/dlc/tests/test_files/res2_all
-/wetb/hawc2/ascii2bin/ascii2bin_dist
-/wetb/hawc2/tests/test_files/htcfiles/tmp.htc
-/wetb/hawc2/ascii2bin/tests/test_files/Hawc2ascii_bin.sel
-/wetb/hawc2/ascii2bin/tests/test_files/Hawc2ascii_bin.dat
+docs/_build
+.project
+.pydevproject
+.settings/org.eclipse.core.resources.prefs
+wetb/gtsdf/tests/tmp
+wetb/dlc/tests/test_files/res_all
+wetb/dlc/tests/test_files/res2_all
+wetb/hawc2/ascii2bin/ascii2bin_dist
+wetb/hawc2/tests/test_files/htcfiles/tmp.htc
+wetb/hawc2/ascii2bin/tests/test_files/Hawc2ascii_bin.sel
+wetb/hawc2/ascii2bin/tests/test_files/Hawc2ascii_bin.dat
+wetb/prepost/tests/data/demo_dlc/remote*
+
+/wetb/fatigue_tools/rainflowcounting/compile.py
+/docs/api
+/htmlcov

.gitlab-ci.yml

 before_script:
   - apt-get update
+  # uncomment first time
+  #- rm -rf TestFiles
+  #- git submodule update --init
+  - git submodule sync
+  - git submodule update
+
 
 test-3.4:
   image: mmpe/wetb
   script:
-  - python3 setup.py test
\ No newline at end of file
+  #- python3 setup.py test
+  - python3 -m pytest --cov=wetb
+   

.gitmodules

+[submodule "TestFiles"]
+	path = TestFiles
+	url = https://gitlab.windenergy.dtu.dk/toolbox/TestFiles.git

AUTHORS.rst

@@ -3,4 +3,5 @@ Developers
 ==========
 
 * Mads Mølgaard Pedersen
-* David Verelst
+* David R.S. Verelst
+* Carlo Tibaldi

CONTRIBUTING.md

+Contributions
+-------------
+
+If you make a change in the toolbox, that others can benefit from please make a merge request.
+
+If you can, please submit a merge request with the fix or improvements including tests.
+
+The workflow to make a merge request is as follows:
+
+
+-Create a feature branch, branch away from master
+-Write tests and code
+-Push the commit(s) to your fork
+-Submit a merge request (MR) to the master branch of
+-Link any relevant issues in the merge request description and leave a comment on them with a link back to the MR
+-Your tests should run as fast as possible, and if it uses test files, these files should be as small as possible.
+-Please keep the change in a single MR as small as possible. Split the functionality if you can
\ No newline at end of file

README

+|build status| |coverage report|
+
+Introduction
+============
+
+The Wind Energy Toolbox (or ``wetb``, pronounce as wee-tee-bee) is a
+collection of Python scripts that facilitate working with (potentially a
+lot) of HAWC2, HAWCStab2, FAST or other text input based simulation
+tools.
+
+Note that this toolbox is very much a WIP (work in progress). For
+example, some of the functions in the `prepost <#prepost>`__ module have
+a similar functions in `Hawc2io <wetb/hawc2/Hawc2io.py>`__. These
+different implementations will be merged in due time.
+
+Both Python2 and Python3 are supported.
+
+Installation
+============
+
+-  `Simple user <docs/install.md>`__
+-  `Developer/contributor <docs/developer-guide.md>`__
+
+Contents of WindEnergyToolbox, `wetb <wetb>`__
+==============================================
+
+Overview
+~~~~~~~~
+
+-  `hawc2 <#hawc2>`__
+-  `gtsdf <#gtsdf>`__
+-  `fatigue\_tools <#fatigue_tools>`__
+-  `wind <#wind>`__
+-  `dlc <#dlc>`__
+-  `prepost <#prepost>`__
+-  `fast <#fast>`__
+-  `utils <#utils>`__
+
+`hawc2 <wetb/hawc2>`__
+~~~~~~~~~~~~~~~~~~~~~~
+
+-  `Hawc2io <wetb/hawc2/Hawc2io.py>`__: Read binary, ascii and flex
+   result files
+-  `sel\_file <wetb/hawc2/sel_file.py>`__: Read/write \*.sel (sensor
+   list) files
+-  `htc\_file <wetb/hawc2/htc_file.py>`__: Read/write/manipulate htc
+   files
+-  `ae\_file <wetb/hawc2/ae_file.py>`__: Read AE (aerodynamic blade
+   layout) files
+-  `pc\_file <wetb/hawc2/pc_file.py>`__: Read PC (profile coefficient)
+   files
+-  `st\_file <wetb/hawc2/st_file.py>`__: Read ST (structural properties)
+   files
+-  `shear\_file <wetb/hawc2/shear_file.py>`__: Create user defined shear
+   file
+-  `at\_time\_file <wetb/hawc2/at_time_file.py>`__: Read at
+   output\_at\_time files
+-  `log\_file <wetb/hawc2/log_file.py>`__: Read and interpret log files
+-  `ascii2bin <wetb/hawc2/ascii2bin>`__: Compress HAWC2 ascii result
+   files to binary
+
+`gtsdf <wetb/gtsdf>`__
+~~~~~~~~~~~~~~~~~~~~~~
+
+General Time Series Data Format, a binary hdf5 data format for storing
+time series data. - `gtsdf <wetb/gtsdf/gtsdf.py>`__: read/write/append
+gtsdf files - `unix\_time <wetb/gtsdf/unix_time.py>`__: convert between
+datetime and unix time (seconds since 1/1/1970)
+
+`fatigue\_tools <wetb/fatigue_tools>`__
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+-  `fatigue <wetb/fatigue_tools/fatigue.py>`__: Rainflow counting, cycle
+   matrix and equivalent loads
+-  `bearing\_damage <wetb/fatigue_tools/bearing_damage.py>`__: Calculate
+   a comparable measure of bearing damage
+
+`wind <wetb/wind>`__
+~~~~~~~~~~~~~~~~~~~~
+
+-  `shear <wetb/wind/shear.py>`__: Calculate and fit wind shear
+
+`dlc <wetb/dlc>`__
+~~~~~~~~~~~~~~~~~~
+
+Module for working with "Design load cases" (Code independent) -
+`high\_level <wetb/dlc/high_level.py>`__ Class for working with the
+highlevel dlc excell sheet
+
+`prepost <wetb/prepost>`__
+~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Module for creating an arbitrary number of HAWC2 simulations, and
+optionally corresponding execution scripts for a PBS Torque cluster
+(Linux), simple bash (Linux), or Windows batch scripts. A
+post-processing module is also included that calculates statistical
+parameters, performs rainflow counting for fatigue load calculations,
+and create load envelopes.
+
+Additional documentation can be found here:
+
+-  `Getting started with DLBs <docs/getting-started-with-dlbs.md>`__
+
+   -  `Generate DLB spreadsheets <docs/generate-spreadsheet.md>`__
+   -  `Auto-generation of Design Load Cases <docs/howto-make-dlcs.md>`__
+   -  `House rules for storing results on
+      ``mimer/hawc2sim`` <docs/houserules-mimerhawc2sim.md>`__
+   -  `How to use the Statistics
+      DataFrame <docs/using-statistics-df.md>`__
+
+`fast <wetb/fast>`__
+~~~~~~~~~~~~~~~~~~~~
+
+Tools for working with NREL's FAST code (An aeroelastic computer-aided
+engineering (CAE) tool for horizontal axis wind turbines) -
+`fast\_io <wetb/fast/fast_io.py>`__: Read binary and ascii result files
+
+`utils <wetb/utils>`__
+~~~~~~~~~~~~~~~~~~~~~~
+
+Other functions - `geometry <wetb/utils/geometry.py>`__: Different kind
+of geometry conversion functions -
+`process\_exec <wetb/utils/process_exec.py>`__: Run system command in
+subprocess - `timing <wetb/utils/timing.py>`__: Decorators for
+evaluating execution time of functions -
+`caching <wetb/utils/caching.py>`__: Decorators to create cached
+(calculate once) functions and properties
+
+.. |build status| image:: https://gitlab.windenergy.dtu.dk/toolbox/WindEnergyToolbox/badges/master/build.svg
+   :target: https://gitlab.windenergy.dtu.dk/toolbox/WindEnergyToolbox/commits/master
+.. |coverage report| image:: https://gitlab.windenergy.dtu.dk/toolbox/WindEnergyToolbox/badges/master/coverage.svg
+   :target: https://gitlab.windenergy.dtu.dk/toolbox/WindEnergyToolbox/commits/master

README.md

 
+[![build status](https://gitlab.windenergy.dtu.dk/toolbox/WindEnergyToolbox/badges/master/build.svg)](https://gitlab.windenergy.dtu.dk/toolbox/WindEnergyToolbox/commits/master)
+[![coverage report](https://gitlab.windenergy.dtu.dk/toolbox/WindEnergyToolbox/badges/master/coverage.svg)](https://gitlab.windenergy.dtu.dk/toolbox/WindEnergyToolbox/commits/master)
+
 # Introduction
 
 The Wind Energy Toolbox (or ```wetb```, pronounce as wee-tee-bee) is a collection
@@ -10,72 +13,12 @@ some of the functions in the [prepost](#prepost) module have a similar functions
 in [Hawc2io](wetb/hawc2/Hawc2io.py). These different implementations will be
 merged in due time.
 
-
-# Python 3
-
-This module currently only works under Python 3. If you are working in Python 2,
-this could be a good moment to consider switching. If you are bound to Python 2
-due to critical 3th party dependencies you are encouraged to cast your vote for
-Python 2 compatibility in
-[issue 1](https://gitlab.windenergy.dtu.dk/toolbox/WindEnergyToolbox/issues/1).
-
-Switching to Python 3 is in general a very good idea especially since Python 3.5
-was released. Some even dare to say it
-[is like eating your vegetables](http://nothingbutsnark.svbtle.com/porting-to-python-3-is-like-eating-your-vegetables).
-
-You can automatically convert your code from Python 2 to 3 using the
-[2to3](https://docs.python.org/2/library/2to3.html) utility which is included
-in Python 2.7 by default. You can also write code that is compatible with both
-2 and 3 at the same time (you can find additional resources in
-[issue 1](https://gitlab.windenergy.dtu.dk/toolbox/WindEnergyToolbox/issues/1)).
-
-
-# Dependencies
-
-* [numpy](http://www.numpy.org/)
-
-* [scipy](http://scipy.org/scipylib/)
-
-* [pandas](http://pandas.pydata.org/)
-
-* xlrd
-
-* h5py
-
-* [matplotlib](http://matplotlib.org/)
-
-* [pytables](http://www.pytables.org/)
-
-* [pyscaffold](http://pyscaffold.readthedocs.org/en/)
-
-* pytest
-
-* six
-
+Both Python2 and Python3 are supported.
 
 # Installation
 
-Detailed installation instructions, including how to install Python from scratch,
-are described in the [detailed installation manual](docs/install-manual-detailed.md).
-
-
-If you now what you are doing, you can install as follows:
-
-```
-python setup.py
-```
-
-Or create a binary wheel distribution package with:
-
-```
-python setup.py bdist_wheel -d dist
-```
-
-
-# Tests
-
-Only a small part of the code is covered by unittests currently. More tests are
-forthcoming.
+- [Simple user](docs/install.md)
+- [Developer/contributor](docs/developer-guide.md)
 
 
 # Contents of WindEnergyToolbox, [wetb](wetb)
@@ -97,6 +40,7 @@ forthcoming.
 - [htc_file](wetb/hawc2/htc_file.py): Read/write/manipulate htc files
 - [ae_file](wetb/hawc2/ae_file.py): Read AE (aerodynamic blade layout) files
 - [pc_file](wetb/hawc2/pc_file.py): Read PC (profile coefficient) files
+- [st_file](wetb/hawc2/st_file.py): Read ST (structural properties) files
 - [shear_file](wetb/hawc2/shear_file.py): Create user defined shear file
 - [at_time_file](wetb/hawc2/at_time_file.py): Read at output_at_time files
 - [log_file](wetb/hawc2/log_file.py): Read and interpret log files
@@ -112,7 +56,7 @@ General Time Series Data Format, a binary hdf5 data format for storing time seri
 - [bearing_damage](wetb/fatigue_tools/bearing_damage.py): Calculate a comparable measure of bearing damage
 
 ### [wind](wetb/wind)
-- [shear](wetb/wind/shear.py): Calculate and fit wind shear 
+- [shear](wetb/wind/shear.py): Calculate and fit wind shear
 
 ### [dlc](wetb/dlc)
 Module for working with "Design load cases" (Code independent)
@@ -125,6 +69,14 @@ corresponding execution scripts for a PBS Torque cluster (Linux), simple bash
 that calculates statistical parameters, performs rainflow counting for fatigue
 load calculations, and create load envelopes.
 
+Additional documentation can be found here:
+
+- [Getting started with DLBs](docs/getting-started-with-dlbs.md)
+    - [Generate DLB spreadsheets](docs/generate-spreadsheet.md)
+    - [Auto-generation of Design Load Cases](docs/howto-make-dlcs.md)
+    - [House rules for storing results on ```mimer/hawc2sim```](docs/houserules-mimerhawc2sim.md)
+    - [How to use the Statistics DataFrame](docs/using-statistics-df.md)
+
 ### [fast](wetb/fast)
 Tools for working with NREL's FAST code (An aeroelastic computer-aided engineering (CAE) tool for horizontal axis wind turbines)
 - [fast_io](wetb/fast/fast_io.py): Read binary and ascii result files
@@ -136,9 +88,3 @@ Other functions
 - [timing](wetb/utils/timing.py): Decorators for evaluating execution time of functions
 - [caching](wetb/utils/caching.py): Decorators to create cached (calculate once) functions and properties
 
-
-# Note
-
-This project has been set up using PyScaffold 2.5. For details and usage
-information on PyScaffold see http://pyscaffold.readthedocs.org/.
-

TestFiles @ cf64c48f

+Subproject commit cf64c48ffb671d35a457d0539e078bfe3eb07f0b

docs/configure-wine.md

+Background Information Regarding Wine
+-------------------------------------
+
+> Note that the steps described here are executed automatically by the
+configuration script [```config-wine-hawc2.sh```]
+(https://gitlab.windenergy.dtu.dk/toolbox/pbsutils/blob/master/config-wine-hawc2.sh)
+in ```pbsutils```.
+
+
+Configure Wine for Gorm
+------------------------
+
+You will also need to configure wine and place the HAWC2 executables in a
+directory that wine knows about. First, activate the correct wine environment by
+typing in a shell in the Gorm's home directory (it can be activated with
+ssh (Linux, Mac) or putty (MS Windows)):
+
+```
+g-000 $ WINEARCH=win32 WINEPREFIX=~/.wine32 wine test.exe
+```
+
+Optionally, you can also make an alias (a short format for a longer, more complex
+command). In the ```.bashrc``` file in your home directory
+(```/home/$USER/.bash_profile```), add at the bottom of the file:
+
+```
+alias wine32='WINEARCH=win32 WINEPREFIX=~/.wine32 wine'
+```
+
+Add a folder called ```~/wine_exe/win32``` to your wine system's PATH so we can
+copy all the HAWC2 executables in here:
+
+```
+$EXE_DIR_WINE="z:/home/$USER/wine_exe/win32/"
+printf 'REGEDIT4\n[HKEY_CURRENT_USER\\Environment]\n"PATH"="'"$EXE_DIR_WINE"'"\n' >> ./tmp.reg
+WINEARCH=win32 WINEPREFIX=~/.wine32 wine regedit ./tmp.reg
+rm ./tmp.reg
+```
+
+And now copy all the HAWC2 executables, DLL's (including the license manager)
+to your wine directory. You can copy all the required executables, dll's and
+the license manager are located at ```/home/MET/hawc2exe```. The following
+command will update your local directory with any new executables that have
+been placed in ```/home/MET/hawc2exe/win32/```:
+
+```
+g-000 $ rsync -a /home/MET/hawc2exe/win32/* /home/$USER/wine_exe/win32/
+```
+
+Notice that the HAWC2 executable names are ```hawc2-latest.exe```,
+```hawc2-118.exe```, etc. By default the latest version will be used and the user
+does not need to specify this. However, when you need to compare different version
+you can easily do so by specifying which case should be run with which
+executable. The file ```hawc2-latest.exe``` will always be the latest HAWC2
+version at ```/home/MET/hawc2exe/```. When a new HAWC2 is released you can
+simply copy all the files from there again to update.
+
+
+Configure Wine for Jess
+------------------------
+
+Same principles apply to Jess, and  [```config-wine-hawc2.sh```]
+(https://gitlab.windenergy.dtu.dk/toolbox/pbsutils/blob/master/config-wine-hawc2.sh)
+can be used to initialize and configure your wine environment.
+
+Note that due to a bug in the specific version of wine that is installed on
+Jess, ```config-wine-hawc2.sh``` will apply the following command to fix this.
+It is important to note that this fix will have to be executed on each node at
+the beginning of each new session:
+
+```
+j-000 $ WINEARCH=win32 WINEPREFIX=~/.wine32 winefix
+```
+
+```winefix``` is automatically included in the ```pbs_in``` scripts genetrated
+by the toolbox.
+

docs/developer-guide.md

+# Developer guide
+
+Thank you for your interest in developing wetb. This guide details how to
+contribute to wetb in a way that is efficient for everyone.
+
+
+## Contents
+
+- [Fork](#fork-project)
+- [Requirements](#requirements)
+- [Install Python](#install-python)
+- [Install/build dependencies](#installbuild-dependencies)
+- [Get wetb](#get-wetb)
+- [Install wetb](#install-wetb)
+- [Contributions](#contributions)
+- [Upload contributions](#upload-contributions)
+- [Make and upload wheels](#make-and-upload-wheels)
+
+
+## Fork project
+
+We prefer that you make your contributions in your own fork of the project,
+[make your changes](#Contributions) and [make a merge request](#Upload contributions).
+
+The project can be forked to your own user account via the \<Fork\> button on
+the [frontpage](https://gitlab.windenergy.dtu.dk/toolbox/WindEnergyToolbox)
+
+
+## Requirements
+
+
+### Command line
+
+This guide will use the command line (aka command prompt) frequently.
+You can launch a Windows terminal as follows: press Start> and type
+"cmd" + \<Enter\>. A link to the command prompt should be visible now.
+
+In case you want an alternative, more capable windows terminal, you could consider
+using [ConEmu](https://conemu.github.io/) (this is optional).
+
+> ConEmu-Maximus5 is a Windows console emulator with tabs, which presents
+> multiple consoles and simple GUI applications as one customizable GUI window
+> with various features.
+
+
+### Git
+
+* Download and install Git version control system for Windows 64-bit
+[here](https://git-scm.com/download/win). Only select the Windows Portable
+option if you know what you are doing or if you do not have administrative
+rights on your computer.
+
+* Git comes with a simple GUI, but there are more and different options available
+if you are not happy with it, see [here](https://git-scm.com/downloads/guis).
+
+* On windows we highly recommend [tortoisegit](https://tortoisegit.org/). It
+is a gui integrated into the windows explorer.
+
+
+## Install Python
+
+For all platforms we recommend that you download and install the Anaconda -
+a professional grade, full blown scientific Python distribution.
+
+
+### Installing Anaconda, activate root environment
+
+* Download and install Anaconda (Python 3.5 version, 64 bit installer is
+recommended) from <https://www.continuum.io/downloads>
+
+> Note: The Python 2.7 or Python 3.5 choice of Anaconda only affects the
+root environment. You can always create additional environments using other
+Python versions, see below.
+
+* Update the root Anaconda environment (type in a terminal):
+
+```
+>> conda update --all
+```
+
+* Activate the Anaconda root environment in a terminal as follows:
+
+```
+>> activate
+```
+
+and your terminal will do something like:
+```
+C:\Users\> activate
+(root) C:\Users\>
+```
+note that the name of the environment is now a prefix before the current path.
+
+use ```deactivate``` to deactivate the environment.
+
+
+### Optionally, create other independent Anaconda environments
+
+By using environments you can manage different Python installations with
+different versions on your system. Creating environments is as easy as:
+
+```
+>> conda create -n py27 python=2.7
+>> conda create -n py34 python=3.4
+>> conda create -n py35 python=3.5
+```
+
+These environments can be activated as follows:
+
+```
+>> activate py27
+>> activate py34
+>> activate py35
+```
+
+The Python distribution in use will now be located in e.g. \<path_to_anaconda\>/env/py35/
+
+use ```deactivate``` to deactivate the environment.
+
+
+## Install/build dependencies
+
+- Compiler (```wetb``` contains cython extensions that require a compiler):
+    - Linux: gcc (should be installed by default)
+    - Windows:
+        - Python 2.7: [Microsoft Visual C++ Compiler for Python 2.7](http://aka.ms/vcpython27),
+        or the [direct link](https://www.microsoft.com/en-gb/download/details.aspx?id=44266).
+        - Python 3.4: MS Visual Studio 2010
+        - Python 3.5: MS Visual Studio 2015 or [Visual C++ Build Tools](http://landinghub.visualstudio.com/visual-cpp-build-tools)
+        - Only one MS Visual Studio version can be installed, but you can for
+        example install MS Visual Studio 2010 alongside the Visual C++ Build Tools.
+- [numpy](http://www.numpy.org/)
+- [cython](http://cython.org/)
+- [scipy](http://scipy.org/scipylib/)
+- [pandas](http://pandas.pydata.org/)
+- xlrd and xlwt from [python-excel](http://www.python-excel.org/)
+- [openpyxl](http://openpyxl.readthedocs.org/en/default/)
+- [h5py](http://www.h5py.org/)
+- [matplotlib](http://matplotlib.org/)
+- [pytables](http://www.pytables.org/)
+- [pyscaffold](http://pyscaffold.readthedocs.org/en/)
+- [pytest](https://pypi.python.org/pypi/pytest)
+- [pytest-cov](https://pypi.python.org/pypi/pytest-cov/)
+- six, [future](http://python-future.org/index.html)
+- nose, sphinx, blosc, pbr, psutil, coverage, setuptools_scm
+- [parimeko](http://www.paramiko.org/)
+- [sshtunnel](https://github.com/pahaz/sshtunnel)
+- [pandoc](http://pandoc.org/) , [pypandoc](https://pypi.python.org/pypi/pypandoc):
+convert markdown formatted readme file to rst for PyPi compatibility. See also
+issue #22. ```pandoc``` is available in Anaconda. When installing
+```pypandoc``` via pip, you have to install ```pandoc``` via your package
+manager (Linux/Mac).
+- [twine](https://pypi.python.org/pypi/twine): upload package to
+[PyPi](https://pypi.python.org/pypi)
+
+Install the necessary Python dependencies using the conda package manager:
+
+```
+>> conda install setuptools_scm future h5py pytables pytest pytest-cov nose sphinx blosc pbr paramiko
+>> conda install scipy pandas matplotlib cython xlrd coverage xlwt openpyxl psutil pandoc
+>> conda install -c conda-forge pyscaffold sshtunnel twine pypandoc --no-deps
+```
+
+Note that ```--no-deps``` avoids that newer packages from the channel
+```conda-forge``` will be used instead of those from the default ```anaconda```
+channel. Depending on which packages get overwritten, this might brake your
+Anaconda root environment. As such, using ```--no-deps``` should be
+used for safety (especially when operating from the root environment).
+
+Note that:
+
+- With Python 2.7, blosc fails to install.
+- With Python 3.6, twine, pypandoc fails to install.
+
+
+## Get wetb
+
+Copy the https - link on the front page of your fork of wetb
+
+```
+>> git clone <https-link>
+```
+
+or via tortoise-git:
+
+- Right-click in your working folder
+- "Git Clone..."
+- \<Ok\>
+
+
+## Install wetb
+
+```
+>> cd WindEnergyToolbox
+>> pip install -e . --no-deps
+```
+
+Note that the ```--no-deps``` option here is used for the same reason as explained
+above for the ```conda-forge``` channel: it is to avoid that pip will replace
+newer packages compared to the ones as available in the ```Anaconda``` channel.
+
+
+## Update wetb
+
+```
+>> cd WindEnergyToolbox
+>> git pull
+>> pip install -e . --no-deps
+```
+
+
+## Run tests
+
+Note that the test should be executed from a clean repository and which is not
+used as a development installation with ```pip install -e .```. For example,
+create a clone of your local git repository in which your development takes
+place, but name the top level folder to something else:
+
+```
+>> git clone WindEnergyToolbox/ wetb_tests
+>> cd wetb_tests
+```
+
+In order to make sure your git repository is clean, this will remove all
+untracked files, and undo all untracked changes. WARNING: you will loose all
+untracked files and changes!!
+```
+>> git clean -df & git checkout .
+```
+
+Now we have clean repository that is not used as a development installation
+directory, and we simply track our own local development git repository.
+Use ```git pull``` to get the latest local commits.
+
+```
+>> python -m pytest --cov=wetb
+```
+
+
+## Contributions
+
+If you make a change in the toolbox, that others can benefit from please make a merge request.
+
+If you can, please submit a merge request with the fix or improvements including tests.
+
+The workflow to make a merge request is as follows:
+
+- Create a feature branch, branch away from master
+- Write tests and code
+- Push the commit(s) to your fork
+- Submit a merge request (MR) to the master branch of
+- Link any relevant issues in the merge request description and leave a comment on them with a link back to the MR
+- Your tests should run as fast as possible, and if it uses test files, these files should be as small as possible.
+- Please keep the change in a single MR as small as possible. Split the functionality if you can
+
+
+## Upload contributions
+
+To be written
+
+
+## Make and upload wheels to PyPi
+
+Workflow for creating and uploading wheels is as follows:
+
+- Make tag: ```git tag "vX.Y.Z"```, and push tag to remote: ```git push --tags```
+- In order to have a clean version number (which is determined automagically)
+make sure your git working directory is clean (no uncommitted changes etc).
+- ```pip install -e . --upgrade```
+- ```python setup.py bdist_wheel -d dist``` (wheel includes compiled extensions)
+- On Linux you will have to rename the binary wheel file
+(see [PEP 513](https://www.python.org/dev/peps/pep-0513/) for a background discussion):
+    - from: ```wetb-0.0.5-cp35-cp35m-linux_x86_64.whl```
+    - to: ```wetb-0.0.5-cp35-cp35m-manylinux1_x86_64.whl```
+- ```python setup.py sdist -d dist``` (for general source distribution installs)
+- ```twine upload dist/*```
+
+In case of problems:
+
+- Make sure the version tag is compliant with
+[PEP 440](https://www.python.org/dev/peps/pep-0440/), otherwise ```twine upload```
+will fail. This means commit hashes can not be part of the version number.
+Note that when your git working directory is not clean, the scheme for automatic
+versioning number will add ```dirty``` to the version number.
+

docs/generate-spreadsheet.md

+Auto-generation of DLB Spreadsheets
+===================================
+
+Introduction
+------------
+
+This manual explains how to automatically generate the set of spreadsheets that
+defines a DLB and is required as input to the pre-processor.
+
+This tool comes handy in the following scenarios:
+* a DLB for a new turbine needs to be generated;
+* a different wind turbine class needs to be evaluated;
+* a new parameter needs to be included in the htc file;
+* different parameters variations are required, e.g. different wind speed range or different number of turbulent seed.
+
+The generator of the cases uses an input spreadsheet where the cases are defined
+in a more compact way. 
+The tool is based on the "tags" concept that is used for the generation of the htc files.
+
+Main spreadsheet
+----------------
+
+A main spreadsheet is used to defines all the DLC of the DLB. The file specifies the tags that are then required in the htc files.
+
+The file has:
+* a Main sheet where some wind turbines parameters are defined, the tags are initialized, and the definitions of turbulence and gusts are given.
+* a series of other sheets, each defining a DLC. In these sheets the tags that changes in that DLC are defined.
+
+The tags are divided into three possible different categories:
+* Constants (C). Constants are tags that do not change in a DLC, e.g. simulation time, output format, ...;
+* Variables (V). Variables are tags that define the number of cases in a DLC through their combinations, e.g. wind speed, number of turbulence seeds, wind direction, ..;
+* Functions (F). Functions are tags that depend on other tags through an expression, e.g. turbulence intensity, case name, ....
+
+In each sheet the type of tag is defined in the line above the tag by typing one of the letters C, V, or F.
+
+Functions (F) tags
+------------------
+
+* Numbers can be converted to strings (for example when a tag refers to a file name) 
+by using double quotes ```"``` for Functions (F):
+    * ```"wdir_[wdir]deg_wsp_[wsp]ms"``` will result in the tags ``` [wdir]``` 
+    and ```[wsp]```  being replaced with formatted text.
+    * following formatting rules are used:
+        * ```[wsp]```, ```[gridgustdelay]``` : ```02i```
+        * ```[wdir]```, ```[G_phi0]``` : ```03i```
+        * ```[Hs]```, ```[Tp]``` : ```05.02f```
+        * all other tags: ```04i```
+    * Only numbers in tags with double quotes are formatted. In all other cases
+    there is no formatting taking place and hence no loss of precision occurs.
+    * In this context, when using quotes, always use double quotes like ```"```.
+    Do not use single quotes ```'``` or any other quote character.
+
+Variable (V) tags
+-----------------
+
+* ```[seed]``` and ```[wave_seed]``` are special variable tags. Instead of defining
+a range of seeds, the user indicates the number of seeds to be used.
+* ```[wsp]``` is a required variable tag
+* ```[seed]``` should be placed in a column BEFORE ```[wsp]```
+
+Generate the files
+------------------
+
+To generate the files defining the different DLC the following lines need to be executed:
+    
+    export PATH=/home/python/miniconda3/bin:$PATH
+    source activate wetb_py3
+    python /home/MET/repositories/toolbox/WindEnergyToolbox/wetb/prepost/GenerateDLCs.py --folder=DLCs 
+    
+the first two lines activate the virtual environment. The third calls the routine *GenerateDLCs.py * that generates the files.
+The routine should be called from the folder *htc* where also the master spreadsheet *DLCs.xlsx* need to be located.
+The generated files are placed in the folder *DLCs*.

docs/getting-started-with-dlbs.md

+# Getting started with generating DLBs for HAWC2
+
+Note that DLB stands for Design Load Basis. It refers to a set of cases that are
+used to evaluate the fitness of a certain design. An example of a DLB definition
+is the IEC 61400-1ed3.
+
+
+## Overview
+
+This document intends to provide an extremely brief overview of how to run a set
+of HAWC2 simulations using the Gorm cluster at DTU and the Mimer storage.
+This document is a work in progress, and is by no means exhaustive.
+
+
+## Resources
+
+The majority of this information can be found in the Wind Energy Toolbox
+documentation. In particular, [generate-spreadsheet](docs/generate-spreadsheet.md)
+discusses how to use a "master" Excel spreadsheet to generate the subordinate
+Excel spreadsheets that will later be used to create the necessary HTC files.
+[howto-make-dlcs](docs/howto-make-dlcs.md) discusses how to create htc files
+from the subordinate spreadsheets, submit those HTC files to the cluster,
+and post-process results.
+[houserules-mimerhawc2sim](docs/houserules-mimerhawc2sim.md) has some
+"house rules" on storing simulations on mimer.
+[using-statistics-df.md](docs/using-statistics-df) has some information
+on loading the post-processing statistics using Python.
+
+
+## Steps
+
+##### 1. Make sure that you can access the cluster/mimer.
+See the instructions on [this page](docs/howto-make-dlcs.md).
+
+##### 2. Create a Set ID folder for this project/simulation.
+You should find that, within a given turbine model, the folder structure is
+similar to the following:
+
+```
+|-- DTU10MW/
+|   |-- AA0001
+|   |   |-- ...
+|   |-- AA0002
+|   |   |-- ...
+|   |-- ...
+|   |-- AB0001
+|   |-- ...
+|-- AA_log_DTUMW.xlsx
+|-- AB_log_DTUMW.xlsx
+|-- ...
+```
+
+Here, each of these alphanumeric folders are "set IDs", and you should have a
+unique set ID for each set of simulations. Detailed house rules on how you
+should store data on mimer can be found in the
+[houserules-mimerhawc2sim](docs/houserules-mimerhawc2sim.md) document.
+
+There are two steps to creating your new set ID folder:
+1. Determine if you need to create a new turbine model folder. You should only
+do this when the turbulence box size changes (e.g., if the rotor size changes)
+or if you have a model that's never been simulated on mimer.
+2. Determine your set ID code. There are two scenarios:
+    * No one else in your project has run simulations on mimer. In this case,
+    create a new set ID alpha code (e.g., "AA", "AB", etc.). 
+    * Simulations for this project/turbine configuration already exist. In this
+    case, use a pre-existing set ID alpha code and add one to the most recent
+    Set ID (e.g., if "AB0008" exists, your new folder should be "AB0009").  
+    
+##### 3. Add proper log files for your Set ID folder.
+See the [house rules](docs/houserules-mimerhawc2sim.md) regarding log files.
+
+##### 4. Add your model files.
+Within your new Set ID folder, add your HAWC2 model files. Keep a folder
+structure similar to this:
+
+```
+|-- control/
+|   |-- ...
+|-- data/
+|   |-- ...
+|-- htc/
+|   |-- _master/
+|   |   |-- TURB_master_AA0001.htc
+|   |-- DLCs.xlsx
+```
+
+Your master htc file, stored in ```htc/_master/```, can take any desired naming
+convention, but it must have ```_master_``` in the name or future scripts will
+abort. ```htc/DLCs.xlsx``` is your master Excel file that will create the 
+subordinate Excel files in the coming steps.
+
+##### 5. Create your subordinate Excel files.
+From a terminal, change to your htc directory. Then run the following code:
+
+```
+$ export PATH=/home/python/miniconda3/bin:$PATH
+$ source activate wetb_py3
+$ python /home/MET/repositories/toolbox/WindEnergyToolbox/wetb/prepost/GenerateDLCs.py --folder=DLCs
+$ source deactivate
+```
+
+This will create a subfolders DLCs and fill that new subfolder with the created
+subordinate Excel files.
+
+##### 6. Create your htc files and PBS job scripts .
+These files and scripts are generated from the subordinate Excel files from
+Step 5. To do this, in the terminal, change up a level to your Set ID folder
+(e.g., to folder "AB0001"). Then run this code
+
+```
+$ qsub-wrap.py -f /home/MET/repositories/toolbox/WindEnergyToolbox/wetb/prepost/dlctemplate.py --prep
+```
+
+Your htc files should now be placed in subfolders in the htc folder, and PBS
+job files should be in folder ```pbs_in```.
+
+##### 7. Launch the htc files to the cluster.
+Use the ```launch.py``` function to launch the jobs on the cluster.
+For example, the following code will launch the jobs in folder ```pbs_in``` on
+100 nodes. You must be in the top-level Set ID folder for this to work (e.g.,
+in folder "AB0001").
+
+```
+$ launch.py -n 100 -p pbs_in/
+```
+
+There are many launch options available. You can read more about the options
+and querying the cluster configurations/status/etc. on 
+[this page](docs/howto-make-dlcs.md), or you can use the ```launchy.py```
+help function to print available launch options:
+
+```
+$ launch.py --help
+```
+
+##### 8. Post-process results.
+
+The wetb function ```qsub-wrap.py``` can not only generate htc files but also 
+post-process results. For example, here is code to check the log files
+and calculate the statistics, the AEP and the lifetime equivalent loads
+(must be executed from the top-level Set ID folder):
+
+```
+$ qsub-wrap.py -f /home/MET/repositories/toolbox/WindEnergyToolbox/wetb/prepost/dlctemplate.py --years=25 --neq=1e7 --stats --check_logs --fatigue
+```
+
+More details regarding loading the post-processed with statistics dataframes
+can be found here: [using-statistics-df](docs/using-statistics-df.md).
+

docs/houserules-mimerhawc2sim.md

+
+House Rules for ```mimer/hawc2sim``` and HAWC2 model folder structure
+=====================================================================
+
+
+Objectives
+----------
+
+* Re-use turbulence boxes (save disk space)
+* Find each others simulations, review, re-run
+* Find working examples of simulations, DLB's
+* Avoid running the same DLB, simulations more than once
+
+* Disk usage quota review: administrators will create an overview of disk usage
+as used per turbine and user.
+
+
+Basic structure
+---------------
+
+The HAWC2 simulations are located on the data capacitor [mimer]
+(http://mimer.risoe.dk/mimerwiki), on the following address:
+
+```
+# on Windows, use the following address when mapping a new network drive
+\\mimer\hawc2sim
+
+# on Linux you can use sshfs or mount -t cifs
+//mimer.risoe.dk/hawc2sim
+```
+
+The following structure is currently used for this ```hawc2sim``` directory:
+* turbine model (e.g. DTU10MW, NREL5MW, etc)
+    * set ID: 2 alphabetic characters followed by 4 numbers (e.g. AA0001)
+* letters are task/project oriented, numbers are case oriented
+
+For example:
+* DTU10MW
+    * AA0001
+    * AA0002
+    * AB0001
+    * log_AA.xlsx
+    * log_BB.xlsx
+    * log_overview.xlsx
+* NREL5MW
+    * AA0001
+    * AA0002
+    * BA0001
+    * log_AA.xlsx
+    * log_BB.xlsx
+    * log_overview.xlsx
+
+
+House rules
+-----------
+
+* New Turbine model folder when a new size of the turbulence box is required
+(i.e. when the rotor size is different)
+* One "set ID" refers to one analysis, and it might contain more than one DLB
+	* If you realize more cases have to be included, add them in the same
+	"set ID". Don't start new "set ID" numbers.
+	* Each "set ID" number consists of 2 alphabetic followed by 4
+	numerical characters.
+* Log file
+	* Indicate which DLB used for the given "set ID" in the log file
+	* Indicate the changes wrt to a previous "set ID"
+	* Write clear and concise log messages so others can understand what
+	analysis or which DLB is considered
+	* Indicate in the log if something works or not.
+	* Indicate if a certain "set ID" is used for a certain publication or report
+* Keep a log file of the different letters. For instance AA might refer to load
+simulations carried out within a certain project
+* When results are outdated or wrong, delete the log and result files, but keep
+the htc, data and pbs input files so the "set ID" could be re-run again in the
+future. This is especially important if the given "set ID" has been used in a
+publication, report or Master/PhD thesis.
+
+
+File permissions
+----------------
+
+* By default only the person who generated the simulations within a given
+"set ID" can delete or modify the input files, other users have only read access.
+If you want to give everyone read and write access, you do:
+
+```
+# replace demo/AA0001 with the relevant turbine/set id
+g-000 $ cd /mnt/mimer/hawc2sim/demo
+g-000 $ chmod 777 -R AA0001
+```
+
+
+HAWC2 folder structure
+----------------------
+
+The current DLB setup assumes the following HAWC2 model folder structure:
+
+```
+|-- control
+|   |-- ...
+|-- data
+|   |-- ...
+|-- htc
+|   |-- DLCs
+|   |   |-- dlc12_iec61400-1ed3.xlsx
+|   |   |-- dlc13_iec61400-1ed3.xlsx
+|   |   |-- ...
+|   |-- _master
+|   |   `-- dtu10mw_master_C0013.htc
+```
+
+The load case definitions should be placed in Excel spreadsheets with a
+```*.xlsx``` extension. The above example shows one possible scenario whereby
+all the load case definitions are placed in ```htc/DLCs``` (all folder names
+are case sensitive). Alternatively, one can also place the spreadsheets in
+separate sub folders, for example:
+
+```
+|-- control
+|   |-- ...
+|-- data
+|   |-- ...
+|-- htc
+|   |-- dlc12_iec61400-1ed3
+|   |   |-- dlc12_iec61400-1ed3.xlsx
+|   |-- dlc13_iec61400-1ed3
+|   |   |-- dlc13_iec61400-1ed3.xlsx
+```
+
+In order to use this auto-configuration mode, there can only be one master file
+in ```_master``` that contains ```_master_``` in its file name.
+
+For the NREL5MW and the DTU10MW HAWC2 models, you can find their respective
+master files and DLC definition spreadsheet files on ```mimer/hawc2sim```.
+

docs/install-anaconda.md

+
+# Installation manual
+
+
+## Anaconda or Miniconda on Linux
+
+```
+conda update --all
+conda create -n wetb_py3 python=3.5
+source activate wetb_py3
+conda install setuptools_scm future h5py pytables pytest nose sphinx blosc psutil
+conda install scipy pandas matplotlib cython xlrd coverage xlwt openpyxl paramiko
+conda install -c https://conda.anaconda.org/conda-forge pyscaffold pytest-cov
+```
+
+## Anaconda or Miniconda on Windows
+
+```
+conda update --all
+conda create -n wetb_py3 python=3.4
+source activate wetb_py3
+conda install setuptools_scm future h5py pytables pytest nose sphinx psutil
+conda install scipy pandas matplotlib cython xlrd coverage xlwt openpyxl paramiko
+conda install -c https://conda.anaconda.org/conda-forge pyscaffold pytest-cov
+```
+

docs/install-manual-detailed.md

-
-!! This guide is not finished yet, it is a WIP (Work In Progress) !!
-
-# Detailed Installation Manual
-
-Installing Python packages with compiled extensions can be a challenge especially
-on Windows systems. However, when using Miniconda things can be simplified to a
-great extent as this manual hopefully will show you.
-
-The this approach will require you to use the command line, but it is as easy
-as copy-pasting them from this page straight into your command prompt.
-
-
-## Using Miniconda
-
-* Download the latest Python 3 (!!) Miniconda installer for your platform
-[here](http://conda.pydata.org/miniconda.html)
-
-* No need to worry about Python 2 or 3 at this stage. You can still use the
-Python 3 installer for creating Python 2 conda environments
-
-* Install the necessary Python dependencies using the conda package manager:
-
-```
-conda install scipy pandas matplotlib cython xlrd pytables sphinx mingw
-```
-
-* Not all packages are available in the conda repositories, but they can be
-easily installed with pip:
-
-```
-pip install pyscaffold pytest pytest-cov
-```
-

docs/install.md

+
+
+# Anaconda (Windows/Mac/Linux)
+
+## Installation
+
+Install the necessary Python dependencies using the ```conda``` package manager:
+
+```
+>> conda install setuptools_scm future h5py pytables pytest pytest-cov nose sphinx blosc pbr paramiko
+>> conda install scipy pandas matplotlib cython xlrd coverage xlwt openpyxl psutil
+>> conda install -c conda-forge pyscaffold sshtunnel --no-deps
+```
+
+Now you can install ```wetb``` with ```pip``` (there is no ```conda``` package
+available yet, see [issue 21](toolbox/WindEnergyToolbox#21)).
+Since we prefer that ```conda``` manages and installs all dependencies we
+expclicitally tell ```pip``` to only install ```wetb``` and nothing more:
+
+```
+>> pip install wetb --upgrade --no-deps
+```
+
+## Update conda and ```wetb```
+
+```
+>> conda update --all
+>> pip install wetb --upgrade --no-deps
+
+```
+
+
+# Pip (Windows/Mac/Linux)
+
+## Installation and update
+
+```
+>> pip install --upgrade wetb
+```
+
+
+# Works with Python 2 and Python 3
+
+This module is tested for Python 2.7 and 3.4+ compatibility, and works on both
+Windows and Linux. Testing for Mac is on the way, but in theory it should work.
+Python 2 and 3 compatibility is achieved with a single code base with the help
+of the Python module [future](http://python-future.org/index.html).
+
+Switching to Python 3 is in general a very good idea especially since Python 3.5
+was released. Some even dare to say it
+[is like eating your vegetables](http://nothingbutsnark.svbtle.com/porting-to-python-3-is-like-eating-your-vegetables).
+So if you are still on Python 2, we would recommend you to give Python 3 a try!
+
+You can automatically convert your code from Python 2 to 3 using the
+[2to3](https://docs.python.org/2/library/2to3.html) utility which is included
+in Python 2.7 by default. You can also write code that is compatible with both
+2 and 3 at the same time (you can find additional resources in
+[issue 1](https://gitlab.windenergy.dtu.dk/toolbox/WindEnergyToolbox/issues/1)).
+
+
+# Note
+
+This project has been set up using PyScaffold 2.5. For details and usage
+information on PyScaffold see http://pyscaffold.readthedocs.org/.
+

docs/tutorials/1-creating-master-excel.md

+# Tutorial 1: Creating master Excel file
+
+The Wind Energy Toolbox has a workflow for automatically running design load 
+bases (DLBs) on Gorm.
+This workflow has the following steps:
+1. Create a master Excel sheet defining each case in the DLB
+2. [Create subordinate Excel sheets from each tab in the master Excel sheet](https://gitlab.windenergy.dtu.dk/toolbox/WindEnergyToolbox/blob/master/docs/tutorials/2-creating-subordinate-excels.md)
+3. [Create htc files and PBS job scripts for each requisite simulation using 
+the subordinate Excel files and a master htc file.](https://gitlab.windenergy.dtu.dk/toolbox/WindEnergyToolbox/blob/master/docs/tutorials/3-creating-htc-pbs-files.md)
+4. Submit all PBS job scripts to the cluster
+5. Post-process results
+6. Visualize results
+
+This tutorial presents how to accomplish Step 1.
+
+Note that it is possible to customize your simulations by skipping/modifying 
+steps.
+Such a procedure will be discussed in a later tutorial.
+
+If there are any problems with this tutorial, please [submit an issue](
+https://gitlab.windenergy.dtu.dk/toolbox/WindEnergyToolbox/issues).
+
+## 1. Background: Master Excel File
+
+The master Excel file is an Excel file that is used to create subordinate 
+Excel files for generation of htc files and PBS job scripts.
+
+### Master file structure
+
+The master Excel file has a main tab, called "Main", that defines default 
+values  and necessary functions that are called in the other tabs.
+Each other tab defines a new case, and one subordinate Excel file will be 
+generated for each case.
+There are three variable types in the master Excel file:
+- Constants: values that do not change within a case
+- Variables: values that do change within a case, but are numbers that do not 
+depend on any other values (e.g., wind speed in DLC 1.2)
+- Functions: values that depend on other values
+
+### Tag names
+
+The values that are defined in the master Excel file (and eventually the 
+subordinate Excel files) are used to replace "tags" in the master htc file.
+These tags are of the form ```[$TAG_NAME]```.
+Theoretically, a user can define any new tags they desire, there are no 
+require naming conventions.
+However, there are some tags that are currently hard-coded into the Toolbox 
+that can result in errors if the tag names are changed.
+Thus, **we do not recommend you change the tag names from those in the 
+tutorial**.
+If you need new values that do not exist in the tutorial's master htc file 
+and produced master file, then it should be fine to add them.
+
+There are a few tags that deserve special mention:
+- ```[Case folder]```: the htc files for each case will be saved in this case 
+folder. We do not recommend changing the tag name or naming convention here 
+if you are doing a standard DLB.
+- ```[Case id.]```: this defines the naming convention for each htc file. We 
+do not recommend changing the tag name or naming convention here if you are 
+doing a standard DLB.
+- ```[seed]```: this variable indicates the desired number of seeds for each 
+set of variables. Thus, for example, in DLC 1.2, 1.3, the ```[seed]``` value 
+should be set to at least 6.
+
+Lastly, it is extremely important that your tag names in your master Excel 
+file match the tag names in your master htc file.
+Thus, **be sure to verify that your tag names in your master Excel and master 
+htc files are consistent**.
+
+## 2. Tutorial
+
+The procedure for creating the master Excel sheet is simple: each desired DLB 
+is defined in a tab-delimited text file, and these are loaded into a single 
+Excel file.
+It is assumed that the user has a collection of text files in a folder for 
+all of the DLBs to be simulated.
+This tutorial uses the text files located in 
+```wetb/docs/tutorials/data/DLCs_onshore```, which contain a series of text 
+files for a full DLB of an onshore turbine.
+These text files correspond to the onshore DTU 10 MW master htc file that is 
+located in the same directoy.
+
+Generate the master Excel file in a few easy steps:
+1. Open a command window.
+2. If you are running the tutorial locally (i.e., not on Gorm), navigate to 
+the Wind Energy Toolbox tutorials directory.
+3. From a terminal/command window, run the code to generate the Excel file 
+from a folder of text files:
+    * Windows (from the wetb tutorials folder):  
+    ```python ..\..\wetb\prepost\write_master.py --folder data\DLCs_onshore --filename DLCs_onshore.xlsx```
+    * Mac/Linux (from the wetb tutorials folder):  
+    ```python ../../wetb/prepost/write_master.py --folder data/DLCs_onshore  --filename DLCs_onshore.xlsx```
+    * Gorm (from any folder that contains a subfolder with your text files. Note
+you must activate the wetb environment (see Step 5 [here](https://gitlab.windenergy.dtu.dk/toolbox/WindEnergyToolbox/blob/master/docs/getting-started-with-dlbs.md)
+) before this command will work. This command also assumes the folder with your
+text files is called "DLCs_onshore" and is located in the working directory.):  
+    ```python  /home/MET/repositories/toolbox/WindEnergyToolbox/wetb/prepost/write_master.py --folder ./DLCs_onshore --filename ./DLCs_onshore.xlsx```
+ 
+The master Excel file "DLCs_onshore.xlsx" should now be in the your current 
+directory.
+
+Note that we have used the parser options ```--folder``` and ```--filename``` 
+to specify the folder with the text files and the name of the resulting Excel 
+file.
+Other parser options are also available.
+(See doc string in ```write_master.py``` function.)
+
+## 3. Generation options
+
+See doc string in ```write_master.py``` function.
+
+## 4. Issues
+
+If there are any problems with this tutorial, please [submit an issue](
+https://gitlab.windenergy.dtu.dk/toolbox/WindEnergyToolbox/issues).
+We will try to fix it as soon as possible.
+

docs/tutorials/2-creating-subordinate-excels.md

+# Tutorial 2: Creating subordinate Excel files
+
+The Wind Energy Toolbox has a workflow for automatically running design load 
+bases (DLBs) on Gorm.
+This workflow has the following steps:
+1. [Create a master Excel sheet defining each case in the DLB](https://gitlab.windenergy.dtu.dk/toolbox/WindEnergyToolbox/blob/master/docs/tutorials/1-creating-master-excel.md)
+2. Create subordinate Excel sheets from each tab in the master Excel sheet
+3. [Create htc files and PBS job scripts for each requisite simulation using 
+the subordinate Excel files and a master htc file.](https://gitlab.windenergy.dtu.dk/toolbox/WindEnergyToolbox/blob/master/docs/tutorials/3-creating-htc-pbs-files.md)
+4. Submit all PBS job scripts to the cluster
+5. Post-process results
+6. Visualize results
+
+This tutorial presents how to accomplish Step 2.
+
+Note that it is possible to customize your simulations by skipping/modifying 
+steps.
+Such a procedure will be discussed in a later tutorial.
+
+If there are any problems with this tutorial, please [submit an issue](
+https://gitlab.windenergy.dtu.dk/toolbox/WindEnergyToolbox/issues).
+
+## 1. Background: Subordinate Excel Files
+
+The subordinate Excel files are a series of basic Excel files that are 
+generated from the master Excel file. (See our tutorial on generating the 
+master Excel file [here]( https://gitlab.windenergy.dtu.dk/toolbox/WindEnergyToolbox/blob/master/docs/tut orials/1-creating-master-excel.md).)
+There is a different subordinate Excel file for every tab in the master Excel 
+file, except for the "Main" tab, one for each case to simulate (e.g., design 
+load case 1.2 from IEC-61400-1).
+Each subordinate Excel file has a single tab that lists the different tag 
+values for the htc master file in the column, and each row corresponds to a 
+different htc file to be generated.
+The generation of the htc files from the subordinate Excel files is discused 
+in the next tutorial.
+
+
+## 2. Tutorial
+
+The generation of the subordinate Excel files is done using the 
+[GenerateDLS.py](https://gitlab.windenergy.dtu.dk/toolbox/WindEnergyToolbox/blob/master/wetb/prepost/GenerateDLCs.py)
+function in the Wind Energy Toolbox.
+On Gorm, the command can be executed from the htc directory with the master 
+Excel file as follows:
+```
+export PATH=/home/python/miniconda3/bin:$PATH
+source activate wetb_py3
+python /home/MET/repositories/toolbox/WindEnergyToolbox/wetb/prepost/GenerateDLCs.py [--folder=$FOLDER_NAME] [--master=$MASTER_NAME]
+source deactivate
+```
+
+The ```export PATH``` command adds the miniconda bin directory to the path, 
+which is necessary for the toolbox.
+The ```source activate wetb_py3``` and ```source deactivate``` are 
+Gorm-specific commands to activate the Wind Energy Toolbox Python environment.
+The ```--folder``` and ```--master``` flags are optional flags to specify, 
+respectively, the name of the folder to which the subordinate Excel files 
+should be written to and the name of the master Excel file.
+The default values for these two options are './' (i.e., the current 
+directory) and 'DLCs.xlsx', respectively.
+
+After running the commands in the above box on Gorm, you should see a folder in 
+your htc directory with all of your subordinate Excel files.
+
+
+## 3. Issues
+
+If there are any problems with this tutorial, please [submit an issue](
+https://gitlab.windenergy.dtu.dk/toolbox/WindEnergyToolbox/issues).
+We will try to fix it as soon as possible.
+

docs/tutorials/3-creating-htc-pbs-files.md

+# Tutorial 3: Creating htc and PBS files
+
+The Wind Energy Toolbox has a workflow for automatically running design load 
+bases (DLBs) on Gorm.
+This workflow has the following steps:
+1. [Create a master Excel sheet defining each case in the DLB](https://gitlab.windenergy.dtu.dk/toolbox/WindEnergyToolbox/blob/master/docs/tutorials/1-creating-master-excel.md)
+2. [Create subordinate Excel sheets from each tab in the master Excel sheet](https://gitlab.windenergy.dtu.dk/toolbox/WindEnergyToolbox/blob/master/docs/tutorials/2-creating-subordinate-excels.md)
+3. Create htc files and PBS job scripts for each requisite simulation using 
+the subordinate Excel files and a master htc file.
+4. Submit all PBS job scripts to the cluster
+5. Post-process results
+6. Visualize results
+
+This tutorial presents how to accomplish Step 3.
+
+Note that it is possible to customize your simulations by skipping/modifying 
+steps.
+Such a procedure will be discussed in a later tutorial.
+
+If there are any problems with this tutorial, please [submit an issue](
+https://gitlab.windenergy.dtu.dk/toolbox/WindEnergyToolbox/issues).
+
+## 1. Background: htc and PBS file creation
+
+The main function used in this tutorial is [dlctemplate.py](https://gitlab.windenergy.dtu.dk/toolbox/WindEnergyToolbox/blob/master/wetb/prepost/dlctemplate.py),
+which creates all htc and PBS job scripts for the cases specified in the 
+subordinate Excel file folder.
+
+The htc files are the main input files for HAWC2 simulations.
+They are created by copying the master htc file in the ```_master/``` folder in 
+your htc directory and replacing all of the tags with the values specified in 
+the subordinate Excel files.
+All of htc files for a single case are saved in a case-specific folder in your 
+htc folder.
+Thus, if you were running a standard DLB calculation for IEC 61400-1, your 
+folder structure after generating your htc files might look like this:
+```
+|-- $TURB_NAME/
+|   |-- $SET_ID/
+|   |   |-- DLCs.xlsx
+|   |   |-- _master/
+|   |   |   |-- $MASTER_NAME.htc
+|   |   |-- DLCs/
+|   |   |-- htc/
+|   |   |   |-- dlc12_iec61400-1ed3/
+|   |   |   |   |-- dlc12_wsp04_wdir000_s2001.htc
+|   |   |   |   |-- dlc12_wsp04_wdir000_s2002.htc
+|   |   |   |   |-- ...
+|   |   |   |-- dlc13_iec61400-1ed3/
+|   |   |   |-- ...
+```
+
+The PBS job scripts are a series of text files that are used to tell the job 
+scheduler on the high-performance computing (HPC) cluster how to run each job.
+These files end with ".p", and are saved to a folder ```pbs_in/``` that is 
+created in the main set ID folder on Gorm.
+
+
+## 2. Tutorial
+
+There are two ways to call ```dlctemplate.py```.
+The first is to call the function directly.
+The second is to wrap it in a job scheduler to submit the job to the HPC cluster.
+The first option is fine if you have only a few htc files or if the job 
+scheduler is not working for some reason.
+The second option is generally preferred.
+
+### 2.1 Directly generate htc files
+
+The htc and PBS files can be directly generated by running the following 
+commands from the set ID directory:
+```
+export PATH=/home/python/miniconda3/bin:$PATH
+source activate wetb_py3
+python /home/MET/repositories/toolbox/WindEnergyToolbox/wetb/prepost/dlctemplate.py --prep
+source deactivate
+```
+
+The ```export PATH``` command adds the miniconda bin directory to the path, 
+which is necessary for the toolbox.
+The ```source activate wetb_py3``` and ```source deactivate``` are 
+Gorm-specific commands to activate the Wind Energy Toolbox Python environment.
+The ```--prep``` option tells the script to run in preparation mode, in which 
+case it creates the htc and pbs files.
+
+After running the commands in the above box on Gorm, you should have all of your 
+PBS input files in ```pbs_in/``` and all of your htc files in ```htc```.
+
+### 2.2 Generate files using job scheduler
+
+From the set ID folder, run the following code:
+```
+qsub-wrap.py -f /home/MET/repositories/toolbox/WindEnergyToolbox/wetb/prepost/dlctemplate.py --prep
+```
+
+
+## 3. Issues
+
+If there are any problems with this tutorial, please [submit an issue](
+https://gitlab.windenergy.dtu.dk/toolbox/WindEnergyToolbox/issues).
+We will try to fix it as soon as possible.
+