Merge pull request #45 from GENESIS-EFRC/matt-tests

[WIP] Add much-needed tests
materialsproject · Oct 1, 2021 · f718861 · f718861
2 parents b84f16b + c721e5d
commit f718861
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diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
@@ -32,22 +32,23 @@ jobs:
 
   docs:
     runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
     needs:
     - deploy
 
     steps:
     - uses: actions/checkout@v2
-
-    - uses: actions/[email protected]
+    - uses: conda-incubator/setup-miniconda@v2
       with:
-        python-version: 3.8
-
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install -r requirements.txt
-        pip install -r requirements-optional.txt
+        miniconda-version: "latest"
+        python-version: 3.9
+        activate-environment: foo
+    - run: |
+        conda install -c conda-forge graph-tool
         pip install -e .
+        pip install -r requirements-optional.txt
         pip install -r requirements-docs.txt
 
     - name: Generate changelog
@@ -58,8 +59,8 @@ jobs:
 
     - name: Commit files
       run: |
-        git config --local user.email "[email protected]"
-        git config --local user.name "materialsproject"
+        git config --local user.email "[email protected]"
+        git config --local user.name "GENESIS-EFRC"
         mv CHANGELOG.md docs/
         git add docs/CHANGELOG.md && git commit -m 'Updated CHANGELOG.md'
         

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
@@ -35,7 +35,7 @@ jobs:
     - name: Lint with mypy
       run: |
         pip install mypy
-        # mypy src/rxn_network
+        mypy src/rxn_network
 
     - name: Lint with flake8
       run: |
@@ -78,19 +78,23 @@ jobs:
 
   docs:
     runs-on: ubuntu-latest
-
+    defaults:
+      run:
+        shell: bash -l {0}
     steps:
     - uses: actions/checkout@v2
-
-    - uses: actions/[email protected]
+    - uses: conda-incubator/setup-miniconda@v2
       with:
-        python-version: 3.8
+        miniconda-version: "latest"
+        python-version: 3.9
+        activate-environment: foo
 
     - name: Install dependencies
       run: |
-        python -m pip install --upgrade pip
+        conda install -c conda-forge graph-tool
         pip install -e .
         pip install -r requirements-optional.txt
         pip install -r requirements-docs.txt
-    - name: Build
+
+    - name: Build docs
       run: mkdocs build
diff --git a/README.md b/README.md
@@ -1,5 +1,8 @@
 # ![Reaction Network](docs/images/logo.png)
 
+[![Pytest Status](https://github.com/GENESIS-EFRC/reaction-network/workflows/testing/badge.svg)](https://github.com/GENESIS-EFRC/reaction-network/actions?query=workflow%3Atesting)
+[![Code Coverage](https://codecov.io/gh/GENESIS-EFRC/reaction-network/branch/main/graph/badge.svg)](https://codecov.io/gh/GENESIS-EFRC/reaction-network)
+
 Reaction network (rxn-network) is a Python package for predicting chemical reaction
 pathways in solid-state materials synthesis using graph theory.
 

diff --git a/cinder/404.html b/cinder/404.html
@@ -0,0 +1,13 @@
+{% extends "base.html" %}
+
+{% block content %}
+
+    <div class="row-fluid">
+      <div id="main-content" class="span12">
+        <h1 id="404-page-not-found" style="text-align: center">404</h1>
+        <p style="text-align: center"><strong>Page not found</strong></p>
+        <p style="text-align: center"><a href="{{ base_url }}">Home</a></p>
+      </div>
+    </div>
+
+{% endblock %}
diff --git a/src/__init__.py → cinder/__init__.py b/src/__init__.py → cinder/__init__.py
diff --git a/cinder/base.html b/cinder/base.html
@@ -0,0 +1,139 @@
+<!DOCTYPE html>
+<html lang="en">
+
+<head>
+    <meta charset="utf-8">
+    <meta http-equiv="X-UA-Compatible" content="IE=edge">
+    <meta name="viewport" content="width=device-width, initial-scale=1.0">
+    {% if config.site_description %}<meta name="description" content="{{ config.site_description }}">{% endif %}
+    {% if config.site_author %}<meta name="author" content="{{ config.site_author }}">{% endif %}
+    {% if page.canonical_url %}<link rel="canonical" href="{{ page.canonical_url }}">{% endif %}
+    <link rel="shortcut icon" href="{{ 'img/favicon.ico'|url }}">
+
+    {% block htmltitle %}
+    <title>{% if page.title %}{{ page.title }} - {% endif %}{{ config.site_name }}</title>
+    {% endblock %}
+
+    <link rel="stylesheet" href="https://use.fontawesome.com/releases/v5.12.0/css/all.css">
+    <link rel="stylesheet" href="https://use.fontawesome.com/releases/v5.12.0/css/v4-shims.css">
+    <link rel="stylesheet" href="//cdn.jsdelivr.net/npm/[email protected]/build/web/hack.min.css">
+    <link href='//rsms.me/inter/inter.css' rel='stylesheet' type='text/css'>
+    <link href='//fonts.googleapis.com/css?family=Open+Sans:300italic,400italic,700italic,400,300,600,700&subset=latin-ext,latin' rel='stylesheet' type='text/css'>
+    <link href="{{ 'css/bootstrap-custom.min.css'|url }}" rel="stylesheet">
+    <link href="{{ 'css/base.min.css'|url }}" rel="stylesheet">
+    <link href="{{ 'css/cinder.min.css'|url }}" rel="stylesheet">
+
+    {% if config.theme.highlightjs is defined and config.theme.highlightjs is sameas false %} 
+
+    {% else %}
+        {% if config.theme.colorscheme %}
+        <link rel="stylesheet" href="//cdn.jsdelivr.net/gh/highlightjs/[email protected]/build/styles/{{ config.theme.colorscheme }}.min.css">
+        {% else %}
+        <link rel="stylesheet" href="//cdn.jsdelivr.net/gh/highlightjs/[email protected]/build/styles/github.min.css">
+        {% endif %}
+    {% endif %}
+
+    {%- for path in config['extra_css'] %}
+    <link href="{{ path|url }}" rel="stylesheet">
+    {%- endfor %}
+
+    <!-- HTML5 shim and Respond.js IE8 support of HTML5 elements and media queries -->
+    <!--[if lt IE 9]>
+            <script src="https://cdn.jsdelivr.net/npm/[email protected]/dist/html5shiv.min.js"></script>
+            <script src="https://cdn.jsdelivr.net/npm/[email protected]/dest/respond.min.js"></script>
+        <![endif]-->
+
+    {% if config.google_analytics %}
+    <script>
+    (function(i, s, o, g, r, a, m) {
+        i['GoogleAnalyticsObject'] = r;
+        i[r] = i[r] || function() {
+            (i[r].q = i[r].q || []).push(arguments)
+        }, i[r].l = 1 * new Date();
+        a = s.createElement(o),
+        m = s.getElementsByTagName(o)[0];
+        a.async = 1;
+        a.src = g;
+        m.parentNode.insertBefore(a, m)
+    })(window, document, 'script', '//www.google-analytics.com/analytics.js', 'ga');
+
+    ga('create', '{{ config.google_analytics[0] }}', '{{ config.google_analytics[1] }}');
+    ga('send', 'pageview');
+    </script>
+    {% endif %}
+
+    {% block extrahead %} {% endblock %}
+</head>
+
+<body{% if page and page.is_homepage %} class="homepage" {% endif %}>
+
+    {% include "nav.html" %}
+
+    <div class="container">
+        {% block content %}
+        {% if page.meta.disable_toc %}
+        <div class="col-md-12" role="main">{% include "content.html" %}</div>
+        {% else %}
+        <div class="col-md-3">{% include "toc.html" %}</div>
+        <div class="col-md-9" role="main">{% include "content.html" %}</div>
+        {% endif %}
+        {% endblock %}
+    </div>
+
+    {% if not config.theme.disable_footer %}
+      <footer class="col-md-12 text-center">
+          {% block footer %}
+          {% if not config.theme.disable_footer_except_revision %}
+            <hr>
+            <p>{% if config.copyright %}
+            <small>{{ config.copyright }}</small><br>
+            {% endif %}
+            <small>Documentation built with <a href="http://www.mkdocs.org/">MkDocs</a>.</small>
+            </p>
+          {% endif %}
+
+          {% if page and page.meta.revision_date %}
+          {% if config.theme.disable_footer_except_revision %}<hr>{% else %}<br>{% endif %}
+            <small>Revised on: {{ page.meta.revision_date }}</small>
+          {% endif %}
+          {% endblock %}
+      </footer>
+    {% endif %}
+
+    {%- block scripts %}
+    <script src="//ajax.googleapis.com/ajax/libs/jquery/1.12.4/jquery.min.js"></script>
+    <script src="{{ 'js/bootstrap-3.0.3.min.js'|url }}"></script>
+
+    {% if config.theme.highlightjs is defined and config.theme.highlightjs is sameas false %}  <!-- default is to include highlightjs -->
+
+    {% else %}
+    <script src="//cdn.jsdelivr.net/gh/highlightjs/[email protected]/build/highlight.min.js"></script>
+        {% if config.theme.hljs_languages %}
+            {%- for lang in config.theme.hljs_languages %}
+                <script src="//cdn.jsdelivr.net/gh/highlightjs/[email protected]/build/languages/{{lang}}.min.js"></script>
+            {%- endfor %}
+        {% endif %}
+    <script>hljs.initHighlightingOnLoad();</script>
+    {% endif %}
+
+    <script>var base_url = {{ base_url | tojson }}</script>
+    {% if config.shortcuts %}
+        <script>var shortcuts = {{ config.shortcuts | tojson }}</script>
+    {% endif %}
+    <script src="{{ 'js/base.js'|url }}"></script>
+    {%- for path in config['extra_javascript'] %}
+    <script src="{{ path|url }}"></script>
+    {%- endfor %}
+    {%- endblock %}
+
+    {% if 'search' in config['plugins'] %}{%- include "search-modal.html" %}{% endif %}
+    {%- include "keyboard-modal.html" %}
+    </body>
+
+</html>
+{% if page and page.is_homepage %}
+<!--
+MkDocs version : {{ mkdocs_version }}
+Build Date UTC : {{ build_date_utc }}
+-->
+{% endif %}
diff --git a/cinder/content.html b/cinder/content.html
@@ -0,0 +1,9 @@
+{% if page.meta.source %}
+<div class="source-links">
+    {% for filename in page.meta.source %}
+    <span class="label label-primary">{{ filename }}</span>
+    {% endfor %}
+</div>
+{% endif %}
+
+{{ page.content }}