Update with master

.coveragerc

@@ -0,0 +1,5 @@
+# .coveragerc to control coverage.py
+[run]
+source = pysqa
+omit = pysqa/_version.py
+concurrency = multiprocessing

.travis.yml

@@ -28,24 +28,25 @@ matrix:
         - conda info -a
         - conda config --set always_yes yes --set changeps1 no
         - conda update -q conda
-        - conda install -y -c conda-forge python=${PYTHONVER} coverage defusedxml pandas yaml jinja2
+        - conda install -y -c conda-forge python=${PYTHONVER} coverage coveralls defusedxml pandas yaml jinja2
         - pip install --pre .
       script:
         - coverage run -m unittest discover tests
       after_success:
+        - coverage combine
         - coveralls
         - coverage xml
         - pip install codacy-coverage
         - python-codacy-coverage -r coverage.xml
       deploy:
         - provider: pypi
-          user: jan-janssen
+          user: pyiron
           password: ${PYPI_UPLOAD_TOKEN}
           allow_failure: true
           on:
             branch: master
         - provider: pypi
-          user: jan-janssen
+          user: pyiron
           password: ${PYPI_UPLOAD_TOKEN}
           allow_failure: true
           on:

README.md

@@ -1,7 +1,77 @@
 # pysqa
-Simple queue adapter for Python
+Simple queue adapter for python 
 
-[![Codacy Badge](https://api.codacy.com/project/badge/Grade/de30f320fd9f44ac9cbcce28eb2c54d1)](https://app.codacy.com/app/jan-janssen/pysqa?utm_source=github.com&utm_medium=referral&utm_content=pysqa/pysqa&utm_campaign=Badge_Grade_Dashboard)
-[![Build Status](https://travis-ci.org/pysqa/pysqa.svg?branch=master)](https://travis-ci.org/pysqa/pysqa)
-[![Build status](https://ci.appveyor.com/api/projects/status/90cb1w7a57fql52q/branch/master?svg=true)](https://ci.appveyor.com/project/jan-janssen/pysqa/branch/master)
-[![Coverage Status](https://coveralls.io/repos/github/pysqa/pysqa/badge.svg?branch=master)](https://coveralls.io/github/pysqa/pysqa?branch=master)
+[![Codacy Badge](https://api.codacy.com/project/badge/Grade/9db80cb2477f46be870d1446540b4bf3)](https://www.codacy.com/app/pyiron-runner/pysqa?utm_source=github.com&utm_medium=referral&utm_content=pyiron/pysqa&utm_campaign=Badge_Grade_Dashboard)
+[![Build Status](https://travis-ci.org/pyiron/pysqa.svg?branch=master)](https://travis-ci.org/pyiron/pysqa)
+[![Build status](https://ci.appveyor.com/api/projects/status/9lpjai8rvt8324aj/branch/master?svg=true)](https://ci.appveyor.com/project/pyiron-runner/pysqa/branch/master)
+[![Coverage Status](https://coveralls.io/repos/github/pyiron/pysqa/badge.svg?branch=master)](https://coveralls.io/github/pyiron/pysqa?branch=master)
+
+The goal of pysqa is to make submitting to an HPC cluster as easy as starting another subprocess. This is based on the assumption that even though modern queuing systems allow for an wide range of different configuration, most users submit the majority of their jobs with very similar parameters. Therefore pysqa allows the users to store their submission scripts as jinja2 templates for quick access. After the submission pysqa allows the users to track the progress of their jobs, delete them or enable reservations using the built-in functionality of the queuing system. The currently supported queuing systems are: LFS, MOAB, SGE (tested), SLURM (tested), TORQUE. 
+
+# Installation
+pysqa can either be installed via pip using:
+
+    pip install pysqa
+
+Or via anaconda from the conda-forge channel
+
+    conda install -c conda-forge pysqa
+
+
+# Usage 
+pysqa requires the user to configure the type of queuing system as well as the available templates. Example configuration are available at:
+https://github.com/pyiron/pysqa/tree/master/tests/config
+By default pysqa is searching for the queue configuration in `~/.queues/queue.yaml` and the corresponding jinja2 templates in the same folder.
+
+Import pysqa:
+
+    from pysqa import QueueAdapter 
+    sqa = QueueAdapter(directory=‘~/.queues’)  # directory which contains the queue.yaml file 
+
+List available queues as list of queue names: 
+
+    sqa.queue_list 
+
+List available queues in an pandas dataframe: 
+
+    sqa.queue_view 
+
+Submit a job to the queue - if no queue is specified it is submitted to the default queue defined in the queue configuration:
+
+    sqa.submit_job(command=‘python test.py’)
+
+Get status of all jobs currently handled by the queuing system:
+
+    sqa.get_queue_status()
+
+Get status of a specifc job from the queuing system:
+
+    sqa.get_status_of_job(process_id=1234)
+
+Delete a job from the queuing sytem:
+
+    sqa.delete_job(process_id=1234) 
+
+Sample configurations for the specific queuing systems are availabe in the tests: 
+
+* lsf - https://github.com/pyiron/pysqa/tree/master/tests/config/lsf
+* moab - https://github.com/pyiron/pysqa/tree/master/tests/config/moab
+* SGE - https://github.com/pyiron/pysqa/tree/master/tests/config/sge
+* slurm - https://github.com/pyiron/pysqa/tree/master/tests/config/slurm
+* torque - https://github.com/pyiron/pysqa/tree/master/tests/config/torque
+
+# License
+pysqa is released under the BSD license https://github.com/pyiron/pysqa/blob/master/LICENSE . It is a spin-off of the pyiron project https://github.com/pyiron/pyiron therefore if you use pysqa for your publication, please cite: 
+
+    @article{pyiron-paper,
+      title = {pyiron: An integrated development environment for computational materials science},
+      journal = {Computational Materials Science},
+      volume = {163},
+      pages = {24 - 36},
+      year = {2019},
+      issn = {0927-0256},
+      doi = {https://doi.org/10.1016/j.commatsci.2018.07.043},
+      url = {http://www.sciencedirect.com/science/article/pii/S0927025618304786},
+      author = {Jan Janssen and Sudarsan Surendralal and Yury Lysogorskiy and Mira Todorova and Tilmann Hickel and Ralf Drautz and Jörg Neugebauer},
+      keywords = {Modelling workflow, Integrated development environment, Complex simulation protocols},
+    }

appveyor.yml

@@ -39,7 +39,7 @@ install:
 - '"%CONDA%\Scripts\activate.bat"'
 - "conda config --set always_yes yes --set changeps1 no"
 - "conda update -q conda"
-- "conda install -c conda-forge coverage defusedxml pandas yaml jinja2"
+- 'conda install -c conda-forge coverage defusedxml "pandas>=0.23" yaml jinja2'
 - "conda info -a"
 - "pip install --pre ."
 

azure-pipelines.yml

@@ -0,0 +1,100 @@
+variables:
+  linux: 'ubuntu-16.04'
+  mac: 'macos-10.13'
+  windows: 'vs2017-win2016'
+
+pr:
+  branches:
+    include:
+      - '*'
+
+jobs:
+- job: 'Linux'
+  pool:
+    vmImage: $(linux)
+  strategy:
+    matrix:
+      Python27:
+        python.version: '2.7'
+      Python37:
+        python.version: '3.7'
+    maxParallel: 4
+
+  steps:
+  - bash: echo "##vso[task.prependpath]/usr/share/miniconda/bin"
+    displayName: Add conda to PATH
+
+  - bash: conda create -n pysqa -q --yes -c conda-forge python=$(python.version) coverage defusedxml pandas yaml jinja2
+    displayName: conda install
+
+  - bash: |
+      source activate pysqa
+      pip install --pre .
+    displayName: pysqa install
+
+  - bash: |
+      source activate pysqa
+      coverage run -m unittest discover tests
+    displayName: run tests
+
+- job: 'OSX'
+  pool:
+    vmImage: $(mac)
+  strategy:
+    matrix:
+      Python27:
+        python.version: '2.7'
+      Python37:
+        python.version: '3.7'
+    maxParallel: 1
+
+  steps:
+  - bash: echo "##vso[task.prependpath]$CONDA/bin"
+    displayName: Add conda to PATH
+
+  - bash: sudo chown -R $USER $CONDA
+    displayName: Take ownership of conda installation
+
+  - bash: conda create -n pysqa -q --yes -c conda-forge python=$(python.version) coverage defusedxml pandas yaml jinja2
+    displayName: conda install
+
+  - bash: |
+      source activate pysqa
+      pip install --pre .
+    displayName: pysqa install
+
+  - bash: |
+      source activate pysqa
+      coverage run -m unittest discover tests
+    displayName: run tests
+
+- job: 'Windows'
+  pool:
+    vmImage: $(windows)
+  strategy:
+    matrix:
+      Python27:
+        python.version: '2.7'
+      Python37:
+        python.version: '3.7'
+    maxParallel: 1
+
+  steps:
+  - powershell: Write-Host "##vso[task.prependpath]$env:CONDA\Scripts"
+    displayName: Add conda to PATH
+
+  - bash: echo "##vso[task.prependpath]$CONDA/bin"
+    displayName: Add conda to PATH
+
+  - script: conda create -n pysqa -q --yes -c conda-forge python=$(python.version) coverage defusedxml pandas yaml jinja2
+    displayName: conda install
+
+  - script: |
+      call activate pysqa
+      pip install --pre .
+    displayName: pysqa install
+
+  - script: |
+      call activate pysqa
+      coverage run -m unittest discover tests
+    displayName: run tests

pysqa/__init__.py

@@ -1,8 +1,9 @@
-__version__ = '0.0.1'
+__version__ = "0.0.1"
 __all__ = []
 
 from pysqa.queueadapter import QueueAdapter
 
 from ._version import get_versions
-__version__ = get_versions()['version']
+
+__version__ = get_versions()["version"]
 del get_versions