Commit 3545e92c authored by Erik Fransson's avatar Erik Fransson
parents 9330d02c c2bf9e65
image: ubuntu:latest
before_script:
- apt-get -yqq update
- apt-get -yqq install build-essential
python
python-pip
python-numpy
python-sphinx
wget
unzip
- pip install --upgrade pip
- pip install ase
- pip install sphinxcontrib-bibtex
- pip install sphinx_rtd_theme
image: registry.gitlab.com/materials-modeling/dynasor:latest
build_linux:
stage: build
......@@ -21,8 +7,9 @@ build_linux:
script:
- python ./setup.py install --prefix=./opt
artifacts:
paths:
- opt
paths:
- opt
expire_in: 14 days
run_tests:
stage: test
......@@ -43,15 +30,13 @@ pages:
dependencies:
- build_linux
script:
- mkdir -p public/
- cp homepage/robots.txt public/
- wget https://github.com/jasonlong/cayman-theme/archive/master.zip
- unzip master.zip
- mv cayman-theme-master public/.test/
- cp homepage/index.html public/.test/index.html
- export PYTHONPATH=$PWD/opt/lib/python2.7/site-packages
- sphinx-apidoc -e -o doc/ dsf/
- sphinx-build doc/ public/.test/userguide
- sphinx-build doc/ public/
- mkdir -p public/.well-known/acme-challenge/
- fname=`awk '{split($0, s, "."); print s[1]}' doc/letsencrypt-setup.html`
- mv doc/letsencrypt-setup.html public/.well-known/acme-challenge/$fname
- ls -l public/.well-known/acme-challenge/
artifacts:
paths:
- public
......
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## Summary
*(Summarize the bug encountered concisely)*
## Steps to reproduce
*(How one can reproduce the issue - this is very important)*
## What is the current bug behavior?
*(What actually happens)*
## What is the expected correct behavior?
*(What you should see instead)*
## Possible fixes
*(If you can, link to the line of code that might be responsible for the problem)*
____________________________________________________________________
***Issue definition review***
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Estimated time can be indicated with the command `/estimate`; use e.g., `/estimate 2d` to indicate two days.
*(A task is loosely speaking an issue that does not increase user value)*
*(If the task is time-capped, start the title with the keyword 'EXPLORE', e.g.,)*
*("EXPLORE: Figure out how to use customized templates in gitlab")*
## Description
*(Describe the task)*
### Background
*(If needed provide some background)*
## Sub-tasks
***Note!, this section should be completed by a developer and not necessarily the feature requester***
*(Describe the sub-tasks to be carried out, preferably in the form of a list)*
* [ ] *(task 1)*
* [ ] *(task 2)*
* [ ] *(task 3)*
## Demonstration
*(Describe how it can be shown that the task has been implemented successfully)*
______________________________________________________________
***Issue definition review***
*(Before the issue can be moved onto the board it should be discussed with or reviewed by at least one other team member. You can address one or more team members via the following slash (quick action) command):*
`/cc @(username)`
***Labeling***
*(Please suggest labels for the issue, e.g., by using the following slash command):*
`/label ~(label1) ~(label2)`
***Time estimation***
Estimated time can be indicated with the command `/estimate`; use e.g., `/estimate 2d` to indicate two days.
*(A user story provides some kind of user value)*
*(If the task is time-capped, start the title with the keyword 'EXPLORE', e.g.,)*
*("EXPLORE: Diffraction pattern from ensembles")*
## Description
*(Write a user story, i.e. describe the feature from the perspective of the user)*
As a < type of user >, I want < some goal > [ so that < some reason > ].
### Background
*(Provide some brief and useful background information if needed)*
## Sub-tasks
***Note!, this section should be completed by a developer and not necessarily the feature requester***
*(Describe the sub-tasks to be carried out, preferably in the form of an task list, in order to complete this task.)*
* [ ] *(e.g. Unit tests)*
* [ ] *(e.g. Update user documentation)*
* [ ] *(e.g. Prepare demonstration)*
* [ ] *(task 4)*
## Demonstration
*(Describe how it can be shown that the user story has been implemented successfully)*
______________________________________________________________
***Issue definition review***
*(Before the issue can be moved onto the board it should be discussed with or reviewed by at least one other team member. You can address one or more team members via the following slash (quick action) command):*
`/cc @(username)`
***Labeling***
*(Please suggest labels for the issue, e.g., by using the following slash command):*
`/label ~(label1) ~(label2)`
***Time estimation***
Estimated time can be indicated with the command `/estimate`; use e.g., `/estimate 2d` to indicate two days.
dynasor
=======
[dynasor](http://dynasor.gitlab.io/dynasor/.test/) is a simple tool for
[dynasor](http://dynasor.materialsmodeling.org/) is a simple tool for
calculating total and partial dynamical structure factors as well as current
correlation functions from molecular dynamics
(MD) simulations. The main input consists of a trajectory output from
......@@ -24,7 +24,7 @@ Documentation
-------------
A full documentation is provided
[here](http://dynasor.gitlab.io/dynasor/.test/userguide).
[here](http://dynasor.materialsmodeling.org/userguide).
......
......@@ -5,5 +5,4 @@ References
**********
.. bibliography:: references.bib
.. :program:`dynasor` documentation master file, created by
sphinx-quickstart on Wed Apr 1 14:10:52 2015.
You can adapt this file completely to your liking, but it should at least
contain the root `toctree` directive.
:program:`dynasor` -- Correlations for everyone
***********************************************
Contents
========
:program:`dynasor` is a tool for calculating total and partial
dynamical structure factors from molecular dynamics (MD)
simulations. The main input consists of a trajectory from a MD
simulation, i.e., a file containing snapshots of the particle
coordinates, and optionally velocities that correspond to
consecutively and equally spaced points in (simulation) time.
:program:`dynasor` and its development are hosted on `gitlab
<https://gitlab.com/materials-modeling/dynasor>`_. Bugs and feature
requests are ideally submitted via the `gitlab issue tracker
<https://gitlab.com/materials-modeling/dynasor/issues>`_. The development
team can also be reached by email via dynasor@materialsmodeling.org.
.. toctree::
:maxdepth: 2
:caption: Contents
introduction
installation
......@@ -23,12 +29,3 @@ Contents
credits
bibliography
genindex
.. comment:
Indices and tables
==================
* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`
lVZMRdwdtn5k8H1hgKMuIaQX6DnVMFW49JXrcYKAxTI.eQImAhgVAWKP9oC_89KCb4IFnquuKPhKAMcjyMOBuPc
<!DOCTYPE html>
<html lang="en-us">
<head>
<meta charset="UTF-8">
<title>dynasor</title>
<meta name="viewport" content="width=device-width, initial-scale=1">
<meta name="theme-color" content="#F1F2B5">
<link rel="stylesheet" href="css/normalize.css">
<link href='https://fonts.googleapis.com/css?family=Open+Sans:400,700' rel='stylesheet' type='text/css'>
<link rel="stylesheet" href="css/cayman.css">
</head>
<body>
<section class="page-header">
<h1 class="project-name">dynasor</h1>
<h2 class="project-tagline">A tool for calculating dynamical structure factors</h2>
<a href="userguide/index.html" class="btn">User guide</a>
<a href="https://gitlab.com/dynasor/dynasor" class="btn">View on GitLab</a>
<a
href="https://gitlab.com/dynasor/dynasor/repository/archive.tar.gz?ref=master"
class="btn">Download .tar.gz</a>
</section>
<section class="main-content">
<h1>
<a id="dynasor-header" class="anchor" href="#dynasor"
aria-hidden="true"><span class="octicon
octicon-link"></span></a>dynasor</h1>
<p><b>dynasor</b> is a simple tool for calculaton partial
dynamical structure factors from molecular dynamics (MD)
simulations. The main input consists of a trajectory output from
a MD simulation, i.e., a file containing snapshots of the
particle coordinates, and optionally velocities that correspond
to consecutively and equally spaced points in (simulation) time.</p>
<h2>Contact</h2>
<ul>
<li>Erik Fransson (erikfr AT chalmers.se)</li>
</ul>
<footer class="site-footer">
<span class="site-footer-owner"><a
href="https://gitlab.com/dynasor/dynasor">dynasor</a> is
maintained by the <a href="https://gitlab.com/dynasor">dynasor developer group</a>.</span>
<span class="site-footer-credits">This page was generated by <a
href="https://pages.gitlab.io">GitLab Pages</a> using the <a
href="https://github.com/jasonlong/cayman-theme">Cayman theme</a>.</span>
</footer>
</section>
</body>
</html>
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