Initial commit of some architecture test code.

4e781c19 · Markus Scheidgen · 4e781c19 · 4e781c19 · 4e781c19 · 4e781c19
Commit 4e781c19 authored Aug 02, 2018 by Markus Scheidgen
--- a/.gitignore
+++ b/.gitignore
+.pyenv/
+__pycache__
+*.egg-info/
+data
\ No newline at end of file
--- a/.gitmodules
+++ b/.gitmodules
+[submodule "submodules/python-common"]
+	path = submodules/python-common
+	url = git@gitlab.mpcdf.mpg.de:nomad-lab/python-common.git
+[submodule "submodules/meta-info"]
+	path = submodules/nomad-meta-info
+	url = git@gitlab.mpcdf.mpg.de:nomad-lab/nomad-meta-info.git
+[submodule "submodules/parsers/vasp"]
+	path = submodules/parsers/vasp
+	url = git@gitlab.mpcdf.mpg.de:nomad-lab/parser-vasp.git
--- a/.vscode/.gitignore
+++ b/.vscode/.gitignore
+.ropeproject/
\ No newline at end of file
--- a/.vscode/launch.json
+++ b/.vscode/launch.json
+{
+  // Use IntelliSense to learn about possible attributes.
+  // Hover to view descriptions of existing attributes.
+  // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
+  "version": "0.2.0",
+  "configurations": [
+    {
+      "name": "Python: VaspRun",
+      "type": "python",
+      "request": "launch",
+      "cwd": "${workspaceFolder}/submodules/parsers/vasp/",
+      "program": "${workspaceFolder}/submodules/parsers/vasp/parser/parser-vasp/vaspparser/parser_vasprun.py",
+      "args": [
+        "test/examples/oqmd/relaxation/vasprun.xml", "test/examples/oqmd/relaxation/vasprun.xml"
+      ]
+    },
+    {
+      "name": "Python: files.py",
+      "type": "python",
+      "request": "launch",
+      "cwd": "${workspaceFolder}",
+      "program": "${workspaceFolder}/tests/test_files.py"
+    },
+    {
+      "name": "Python: Current File",
+      "type": "python",
+      "request": "launch",
+      "program": "${file}"
+    },
+    {
+      "name": "Python: Attach",
+      "type": "python",
+      "request": "attach",
+      "localRoot": "${workspaceFolder}",
+      "remoteRoot": "${workspaceFolder}",
+      "port": 3000,
+      "secret": "my_secret",
+      "host": "localhost"
+    }
+  ]
+}
\ No newline at end of file
--- a/.vscode/settings.json
+++ b/.vscode/settings.json
+{
+  "python.venvPath": "${workspaceFolder}/.pyenv",
+  "python.pythonPath": "${workspaceFolder}/.pyenv/bin/python",
+  "git.ignoreLimitWarning": true
+}
\ No newline at end of file
--- a/README.md
+++ b/README.md
+## Installing
+
+```
+pip install -r requirements.txt
+pip install -e .
+```
+
+## Contributing
+
+### Code quality
+
+- There is a style guide to python. Write [pep-8](https://www.python.org/dev/peps/pep-0008/) compliant python code. An exception is the line cap at 79, which can be broken but keep it 90-ish.
+- Use docstrings and document any *public* API of each submodule (e.g. python file). Public meaning API that is exposed to other submodules (i.e. other python files). Keep docstrings compliant to [pep-257](https://www.python.org/dev/peps/pep-0257/).
+
+### Tests
+
+To run the test execute this from the project root:
+```
+
+```
+
+### Generate the documentation
+
+Install [pdoc](https://pypi.org/project/pdoc/) if necessary, and run this from the project root:
+```
+pdoc --html --html-dir=./build/docs --overwrite nomad
+```
+
+Do serve the current docs via HTTP during development, run
+```
+pdoc --http --http-port 8080
+```
+and open [http://localhost:8080/nomad](http://localhost:8080/nomad).
+
--- a/build/docs/nomad/config.m.html
+++ b/build/docs/nomad/config.m.html
--- a/build/docs/nomad/files.m.html
+++ b/build/docs/nomad/files.m.html
--- a/build/docs/nomad/index.html
+++ b/build/docs/nomad/index.html
+<!doctype html>
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+  <meta name="viewport" content="width=device-width, initial-scale=1, minimum-scale=1" />
+
+    <title>nomad API documentation</title>
+    <meta name="description" content="" />
+
+  <link href='http://fonts.googleapis.com/css?family=Source+Sans+Pro:400,300' rel='stylesheet' type='text/css'>
+  
+  <style type="text/css">
+  
+* {
+  box-sizing: border-box;
+}
+/*! normalize.css v1.1.1 | MIT License | git.io/normalize */
+
+/* ==========================================================================
+   HTML5 display definitions
+   ========================================================================== */
+
+/**
+ * Correct `block` display not defined in IE 6/7/8/9 and Firefox 3.
+ */
+
+article,
+aside,
+details,
+figcaption,
+figure,
+footer,
+header,
+hgroup,
+main,
+nav,
+section,
+summary {
+    display: block;
+}
+
+/**
+ * Correct `inline-block` display not defined in IE 6/7/8/9 and Firefox 3.
+ */
+
+audio,
+canvas,
+video {
+    display: inline-block;
+    *display: inline;
+    *zoom: 1;
+}
+
+/**
+ * Prevent modern browsers from displaying `audio` without controls.
+ * Remove excess height in iOS 5 devices.
+ */
+
+audio:not([controls]) {
+    display: none;
+    height: 0;
+}
+
+/**
+ * Address styling not present in IE 7/8/9, Firefox 3, and Safari 4.
+ * Known issue: no IE 6 support.
+ */
+
+[hidden] {
+    display: none;
+}
+
+/* ==========================================================================
+   Base
+   ========================================================================== */
+
+/**
+ * 1. Prevent system color scheme's background color being used in Firefox, IE,
+ *    and Opera.
+ * 2. Prevent system color scheme's text color being used in Firefox, IE, and
+ *    Opera.
+ * 3. Correct text resizing oddly in IE 6/7 when body `font-size` is set using
+ *    `em` units.
+ * 4. Prevent iOS text size adjust after orientation change, without disabling
+ *    user zoom.
+ */
+
+html {
+    background: #fff; /* 1 */
+    color: #000; /* 2 */
+    font-size: 100%; /* 3 */
+    -webkit-text-size-adjust: 100%; /* 4 */
+    -ms-text-size-adjust: 100%; /* 4 */
+}
+
+/**
+ * Address `font-family` inconsistency between `textarea` and other form
+ * elements.
+ */
+
+html,
+button,
+input,
+select,
+textarea {
+    font-family: sans-serif;
+}
+
+/**
+ * Address margins handled incorrectly in IE 6/7.
+ */
+
+body {
+    margin: 0;
+}
+
+/* ==========================================================================
+   Links
+   ========================================================================== */
+
+/**
+ * Address `outline` inconsistency between Chrome and other browsers.
+ */
+
+a:focus {
+    outline: thin dotted;
+}
+
+/**
+ * Improve readability when focused and also mouse hovered in all browsers.
+ */
+
+a:active,
+a:hover {
+    outline: 0;
+}
+
+/* ==========================================================================
+   Typography
+   ========================================================================== */
+
+/**
+ * Address font sizes and margins set differently in IE 6/7.
+ * Address font sizes within `section` and `article` in Firefox 4+, Safari 5,
+ * and Chrome.
+ */
+
+h1 {
+    font-size: 2em;
+    margin: 0.67em 0;
+}
+
+h2 {
+    font-size: 1.5em;
+    margin: 0.83em 0;
+}
+
+h3 {
+    font-size: 1.17em;
+    margin: 1em 0;
+}
+
+h4 {
+    font-size: 1em;
+    margin: 1.33em 0;
+}
+
+h5 {
+    font-size: 0.83em;
+    margin: 1.67em 0;
+}
+
+h6 {
+    font-size: 0.67em;
+    margin: 2.33em 0;
+}
+
+/**
+ * Address styling not present in IE 7/8/9, Safari 5, and Chrome.
+ */
+
+abbr[title] {
+    border-bottom: 1px dotted;
+}
+
+/**
+ * Address style set to `bolder` in Firefox 3+, Safari 4/5, and Chrome.
+ */
+
+b,
+strong {
+    font-weight: bold;
+}
+
+blockquote {
+    margin: 1em 40px;
+}
+
+/**
+ * Address styling not present in Safari 5 and Chrome.
+ */
+
+dfn {
+    font-style: italic;
+}
+
+/**
+ * Address differences between Firefox and other browsers.
+ * Known issue: no IE 6/7 normalization.
+ */
+
+hr {
+    -moz-box-sizing: content-box;
+    box-sizing: content-box;
+    height: 0;
+}
+
+/**
+ * Address styling not present in IE 6/7/8/9.
+ */
+
+mark {
+    background: #ff0;
+    color: #000;
+}
+
+/**
+ * Address margins set differently in IE 6/7.
+ */
+
+p,
+pre {
+    margin: 1em 0;
+}
+
+/**
+ * Correct font family set oddly in IE 6, Safari 4/5, and Chrome.
+ */
+
+code,
+kbd,
+pre,
+samp {
+    font-family: monospace, serif;
+    _font-family: 'courier new', monospace;
+    font-size: 1em;
+}
+
+/**
+ * Improve readability of pre-formatted text in all browsers.
+ */
+
+pre {
+    white-space: pre;
+    white-space: pre-wrap;
+    word-wrap: break-word;
+}
+
+/**
+ * Address CSS quotes not supported in IE 6/7.
+ */
+
+q {
+    quotes: none;
+}
+
+/**
+ * Address `quotes` property not supported in Safari 4.
+ */
+
+q:before,
+q:after {
+    content: '';
+    content: none;
+}
+
+/**
+ * Address inconsistent and variable font size in all browsers.
+ */
+
+small {
+    font-size: 80%;
+}
+
+/**
+ * Prevent `sub` and `sup` affecting `line-height` in all browsers.
+ */
+
+sub,
+sup {
+    font-size: 75%;
+    line-height: 0;
+    position: relative;
+    vertical-align: baseline;
+}
+
+sup {
+    top: -0.5em;
+}
+
+sub {
+    bottom: -0.25em;
+}
+
+/* ==========================================================================
+   Lists
+   ========================================================================== */
+
+/**
+ * Address margins set differently in IE 6/7.
+ */
+
+dl,
+menu,
+ol,
+ul {
+    margin: 1em 0;
+}
+
+dd {
+    margin: 0 0 0 40px;
+}
+
+/**
+ * Address paddings set differently in IE 6/7.
+ */
+
+menu,
+ol,
+ul {
+    padding: 0 0 0 40px;
+}
+
+/**
+ * Correct list images handled incorrectly in IE 7.
+ */
+
+nav ul,
+nav ol {
+    list-style: none;
+    list-style-image: none;
+}
+
+/* ==========================================================================
+   Embedded content
+   ========================================================================== */
+
+/**
+ * 1. Remove border when inside `a` element in IE 6/7/8/9 and Firefox 3.
+ * 2. Improve image quality when scaled in IE 7.
+ */
+
+img {
+    border: 0; /* 1 */
+    -ms-interpolation-mode: bicubic; /* 2 */
+}
+
+/**
+ * Correct overflow displayed oddly in IE 9.
+ */
+
+svg:not(:root) {
+    overflow: hidden;
+}
+
+/* ==========================================================================
+   Figures
+   ========================================================================== */
+
+/**
+ * Address margin not present in IE 6/7/8/9, Safari 5, and Opera 11.
+ */
+
+figure {
+    margin: 0;
+}
+
+/* ==========================================================================
+   Forms
+   ========================================================================== */
+
+/**
+ * Correct margin displayed oddly in IE 6/7.
+ */
+
+form {
+    margin: 0;
+}
+
+/**
+ * Define consistent border, margin, and padding.
+ */
+
+fieldset {
+    border: 1px solid #c0c0c0;
+    margin: 0 2px;
+    padding: 0.35em 0.625em 0.75em;
+}
+
+/**
+ * 1. Correct color not being inherited in IE 6/7/8/9.
+ * 2. Correct text not wrapping in Firefox 3.
+ * 3. Correct alignment displayed oddly in IE 6/7.
+ */
+
+legend {
+    border: 0; /* 1 */
+    padding: 0;
+    white-space: normal; /* 2 */
+    *margin-left: -7px; /* 3 */
+}
+
+/**
+ * 1. Correct font size not being inherited in all browsers.
+ * 2. Address margins set differently in IE 6/7, Firefox 3+, Safari 5,
+ *    and Chrome.
+ * 3. Improve appearance and consistency in all browsers.
+ */
+
+button,
+input,
+select,
+textarea {
+    font-size: 100%; /* 1 */
+    margin: 0; /* 2 */
+    vertical-align: baseline; /* 3 */
+    *vertical-align: middle; /* 3 */
+}
+
+/**
+ * Address Firefox 3+ setting `line-height` on `input` using `!important` in
+ * the UA stylesheet.
+ */
+
+button,
+input {
+    line-height: normal;
+}
+
+/**
+ * Address inconsistent `text-transform` inheritance for `button` and `select`.
+ * All other form control elements do not inherit `text-transform` values.
+ * Correct `button` style inheritance in Chrome, Safari 5+, and IE 6+.
+ * Correct `select` style inheritance in Firefox 4+ and Opera.
+ */
+
+button,
+select {
+    text-transform: none;
+}
+
+/**
+ * 1. Avoid the WebKit bug in Android 4.0.* where (2) destroys native `audio`
+ *    and `video` controls.
+ * 2. Correct inability to style clickable `input` types in iOS.
+ * 3. Improve usability and consistency of cursor style between image-type
+ *    `input` and others.
+ * 4. Remove inner spacing in IE 7 without affecting normal text inputs.
+ *    Known issue: inner spacing remains in IE 6.
+ */
+
+button,
+html input[type="button"], /* 1 */
+input[type="reset"],
+input[type="submit"] {
+    -webkit-appearance: button; /* 2 */
+    cursor: pointer; /* 3 */
+    *overflow: visible;  /* 4 */
+}
+
+/**
+ * Re-set default cursor for disabled elements.
+ */
+
+button[disabled],
+html input[disabled] {
+    cursor: default;
+}
+
+/**
+ * 1. Address box sizing set to content-box in IE 8/9.
+ * 2. Remove excess padding in IE 8/9.
+ * 3. Remove excess padding in IE 7.
+ *    Known issue: excess padding remains in IE 6.
+ */
+
+input[type="checkbox"],
+input[type="radio"] {
+    box-sizing: border-box; /* 1 */
+    padding: 0; /* 2 */
+    *height: 13px; /* 3 */
+    *width: 13px; /* 3 */
+}
+
+/**
+ * 1. Address `appearance` set to `searchfield` in Safari 5 and Chrome.
+ * 2. Address `box-sizing` set to `border-box` in Safari 5 and Chrome
+ *    (include `-moz` to future-proof).
+ */
+
+input[type="search"] {
+    -webkit-appearance: textfield; /* 1 */
+    -moz-box-sizing: content-box;
+    -webkit-box-sizing: content-box; /* 2 */
+    box-sizing: content-box;
+}
+
+/**
+ * Remove inner padding and search cancel button in Safari 5 and Chrome
+ * on OS X.
+ */
+
+input[type="search"]::-webkit-search-cancel-button,
+input[type="search"]::-webkit-search-decoration {
+    -webkit-appearance: none;
+}
+
+/**
+ * Remove inner padding and border in Firefox 3+.
+ */
+
+button::-moz-focus-inner,
+input::-moz-focus-inner {
+    border: 0;
+    padding: 0;
+}
+
+/**
+ * 1. Remove default vertical scrollbar in IE 6/7/8/9.