Merge branch 'master' into ssh_client_with_gateway_and_interactive_auth2

# Conflicts:
#	wetb/utils/cluster_tools/cluster_resource.py
#	wetb/utils/cluster_tools/ssh_client.py
#	wetb/utils/tests/test_ssh_client.py

.gitlab-ci.yml

@@ -4,5 +4,6 @@ before_script:
 test-3.4:
   image: mmpe/wetb
   script:
+  #- python3 setup.py test
   - python3 -m pytest --cov=wetb
    

docs/developer-guide.md

@@ -156,7 +156,7 @@ 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 pypandoc sshtunnel --no-deps
+>> conda install -c conda-forge pyscaffold pypandoc --no-deps
 >> conda install --channel https://conda.anaconda.org/pbrod twine --no-deps
 ```
 

docs/install-manual-detailed.md

-
-> !! This guide is not finished, and might contain innacuracies. Please report
-any mistakes/bugs by creating an
-[issue](https://gitlab.windenergy.dtu.dk/toolbox/WindEnergyToolbox/issues).
-This 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.
-
-Installation instructions follow in alphabetical orderby platorm.
-
-
-## Linux
-
-* Basic dependencies:
-
-> python (3.5 recommended) git gcc gcc-fortran (gfortran)
-
-* Use either your system package manager, pip + virtualenv, or Anaconda to
-install the following python dependencies:
-
-> numpy, cython, scipy, pandas, matplotlib, pyscaffold, future, nose, sphinx,
-> xlrd, (py)tables, h5py, pytest, pytest-cov, setuptools_scm, setuptools
-
-Note that often the pytables packages is called python-tables instead of
-python-pytables.
-
-
-## Dependencies on Mac
-
-People who now how to handle Python on the Mac side are kindly requested to
-complete this guide :-)
-
-
-## Dependencies on Windows
-
-A Python installation with compilers is required. If you already have this,
-or know how set up such an environment, you skip to
-[here](install-manual-detailed.md#and-finally-install-wetb).
-
-
-### Microsft Visual Studio 2010 Compiler
-
-```wetb``` contains extensions that need to be compiled.
-On Windows things are complicated because you need to use the same compiler as
-the one used for Python. This means that for compiling extensions on:
-* Python 2.7 you need [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 you need MS Visual Studio 2010
-* Python 3.5 (and later) you need MS Visual Studio 2015
-* You can install Microsoft Visual C++ Compiler for Python 2.7 alongside
-MS Visual Studio 2010, but you can not install Visual Studio 2010 and 2015
-in parallel.
-
-You can find more background information and installation instructions
-[here](https://packaging.python.org/en/latest/extensions/#setting-up-a-build-environment-on-windows),
-[here](https://blogs.msdn.microsoft.com/pythonengineering/2016/04/11/unable-to-find-vcvarsall-bat/),
-[here](https://matthew-brett.github.io/pydagogue/python_msvc.html),
-or [here](http://stevedower.id.au/blog/building-for-python-3-5-part-two/).
-
-
-### 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).
-
-* If you would like to use a GUI for git, we recommend you to use
-[tortoisegit](https://tortoisegit.org/)
-
-
-## Recommended python distribution: Anaconda
-
-### Installing Anaconda, activate root environment
-
-* Anaconda is a professional grade, full blown scientific Python distribution.
-
-* Download and install Anaconda from
-[https://www.continuum.io/downloads](https://www.continuum.io/downloads).
-
-> Note: the choice of Anaconda for Python 2.7 or Python 3.5 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
-[Anaconda3] 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
-```
-
-use ```deactivate``` to deactivate the environment.
-
-
-### Install dependencies with conda and pip
-
-* Install the necessary Python dependencies using the conda package manager:
-
-```
-conda install setuptools_scm future h5py pytables pytest nose sphinx
-conda install scipy pandas matplotlib cython xlrd coverage xlwt openpyxl
-```
-
-* Not all packages are available in the conda repositories, but they can be
-easily installed with pip:
-
-```
-pip install pyscaffold pytest-cov --no-deps
-```
-
-
-## And Finally: install wetb
-
-```
-git clone https://gitlab.windenergy.dtu.dk/toolbox/WindEnergyToolbox.git
-cd WindEnergyToolbox
-pip install -e . --no-deps
-```
-
-Note that ```pip install -e . --no-deps``` will install ```wetb``` in the source
-directory. This works best if you are also developing and regularly updating
-this package.
-
-You can run the tests cases from the source root directory:
-
-```
-python setup.py test
-```
-

docs/install.md

@@ -9,7 +9,7 @@ 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
+>> conda install -c conda-forge pyscaffold --no-deps
 ```
 
 Now you can install ```wetb``` with ```pip``` (there is no ```conda``` package

docs/install_windows.md

-# Install wetb on Windows
-
-For updating the toolbox jump to [Update wetb on Windows](#Update wetb on Windows)
-
-This guide describes a simple way to install the toolbox on Windows (1/9-2016)
-
-### Installing Anaconda
-
-* Anaconda is a professional grade, full blown scientific Python distribution.
-
-* Download and install Anaconda (Python 3.5 version, 64 bit installer) from <https://www.continuum.io/downloads>
-
-
-* Update the root Anaconda environment (type in a terminal):
-
-```
-conda update --all
-```
-
-### Create Anaconda environment
-
-* Create an environment :
-
-```
-conda create -n py35 python=3.5
-```
-
-* Activate the envirronment:
-
-```
-activate py35
-```
-
-The python distribution in use will now be located in \<path_to_anaconda\>/env/py35/
-
-
-### Install dependencies with conda and pip
-
-* Install the necessary Python dependencies using the conda package manager:
-
-```
-conda install setuptools_scm future h5py pytables pytest nose sphinx
-conda install scipy pandas matplotlib cython xlrd coverage xlwt openpyxl psutil
-```
-
-* Not all packages are available in the conda repositories, but they can be
-easily installed with pip:
-
-```
-pip install pyscaffold pytest-cov --no-deps
-```
-
-
-## And Finally: install wetb
-
-```
-pip install wetb
-```
-
-# Update wetb on Windows
-
-* Activate the envirronment (type in a terminal):
-
-
-```
-activate py35
-```
-
-* Update the toolbox
-
-```
-pip install wetb --upgrade --no-deps
-```

requirements.txt

@@ -12,7 +12,6 @@ pandas
 tables
 future
 paramiko
-sshtunnel
 psutil
 pbr
 PyScaffold

wetb/hawc2/simulation_resources.py

@@ -204,13 +204,9 @@ class SimulationThread(Thread):
         
 
 class PBSClusterSimulationResource(SSHPBSClusterResource):
-    def __init__(self, sshclient, min_cpu, min_free, init_cmd, wine_cmd, python_cmd):
-        SSHPBSClusterResource.__init__(self, sshclient, min_cpu, min_free)
-        self.init_cmd = init_cmd
-        self.wine_cmd = wine_cmd
-        self.python_cmd = python_cmd
+    def __init__(self, host, username, password, port, min_cpu, min_free, init_cmd, wine_cmd, python_cmd):
+        SSHPBSClusterResource.__init__(self, host, username, password, port, min_cpu, min_free, init_cmd, wine_cmd, python_cmd)
         
-    
     def is_clean(self):
         return self.execute("find .hawc2launcher/ -type f | wc -l")[1] > 0