DSJobs docs with pdoc

DesignSafe-CI · Nov 2, 2023 · 92f4858 · 92f4858
1 parent 6a24bfd
commit 92f4858
Show file tree

Hide file tree

Showing 8 changed files with 996 additions and 60 deletions.
diff --git a/README.md b/README.md
@@ -5,9 +5,15 @@
 
 `dsjobs` is a library that simplifies the process of submitting, running, and monitoring [TAPIS v2 / AgavePy](https://agavepy.readthedocs.io/en/latest/index.html) jobs on [DesignSafe](https://designsafe-ci.org) via [Jupyter Notebooks](https://jupyter.designsafe-ci.org).
 
+## Features
+
+* Simplified TAPIS v2 Calls: No need to fiddle with complex API requests. `dsjobs` abstracts away the complexities.
+
+* Seamless Integration with DesignSafe Jupyter Notebooks: Launch DesignSafe applications directly from the Jupyter environment.
+
 ## Installation
 
-Install `dsjobs` via pip (**coming soon**)
+Install `dsjobs` via pip
 
 ```shell
 pip3 install dsjobs
@@ -21,6 +27,8 @@ pip install git+https://github.com/DesignSafe-CI/dsjobs.git --quiet
 
 ## Example usage:
 
+* [Jupyter Notebook Templates](example-notebooks/template-mpm-run.ipynb) using DSJobs.
+
 On [DesignSafe Jupyter](https://jupyter.designsafe-ci.org/):
 
 Install the latest version of `dsjobs` and restart the kernel (Kernel >> Restart Kernel):
@@ -29,7 +37,7 @@ Install the latest version of `dsjobs` and restart the kernel (Kernel >> Restart
 # Remove any previous installations
 !pip uninstall dsjobs -y
 # Install 
-!pip install git+https://github.com/DesignSafe-CI/dsjobs.git --quiet
+!pip install dsjobs --quiet
 ```
 
 * Import `dsjobs` library
@@ -42,31 +50,14 @@ import dsjobs as ds
 dir(ds)
 ```
 
-### Job management
+## Documentation
 
-* Monitor job status
-```python
-ds.get_status(ag, job["id"])
-```
+To generate API docs:
 
-* Get runtime information of a job
 ```
-ds.get_runtime(ag, job["id"])
+pdoc --html --output-dir docs dsjobs --force
 ```
 
-### Directory access
-
-* Access DesignSafe path URI:
-```python
-input_uri = ds.get_ds_path_uri(ag, '/MyData/<path-in-designsafe/')
-```
-
-## Features
-
-* Simplified TAPIS v2 Calls: No need to fiddle with complex API requests. `dsjobs` abstracts away the complexities.
-
-* Seamless Integration with DesignSafe Jupyter Notebooks: Launch DesignSafe applications directly from the Jupyter environment.
-
 ## Support
 
 For any questions, issues, or feedback submit an [issue](https://github.com/DesignSafe-CI/dsjobs/issues/new)

diff --git a/docs/dsjobs/dir.html b/docs/dsjobs/dir.html
@@ -0,0 +1,193 @@
+<!doctype html>
+<html lang="en">
+<head>
+<meta charset="utf-8">
+<meta name="viewport" content="width=device-width, initial-scale=1, minimum-scale=1" />
+<meta name="generator" content="pdoc 0.10.0" />
+<title>dsjobs.dir API documentation</title>
+<meta name="description" content="" />
+<link rel="preload stylesheet" as="style" href="https://cdnjs.cloudflare.com/ajax/libs/10up-sanitize.css/11.0.1/sanitize.min.css" integrity="sha256-PK9q560IAAa6WVRRh76LtCaI8pjTJ2z11v0miyNNjrs=" crossorigin>
+<link rel="preload stylesheet" as="style" href="https://cdnjs.cloudflare.com/ajax/libs/10up-sanitize.css/11.0.1/typography.min.css" integrity="sha256-7l/o7C8jubJiy74VsKTidCy1yBkRtiUGbVkYBylBqUg=" crossorigin>
+<link rel="stylesheet preload" as="style" href="https://cdnjs.cloudflare.com/ajax/libs/highlight.js/10.1.1/styles/github.min.css" crossorigin>
+<style>:root{--highlight-color:#fe9}.flex{display:flex !important}body{line-height:1.5em}#content{padding:20px}#sidebar{padding:30px;overflow:hidden}#sidebar > *:last-child{margin-bottom:2cm}.http-server-breadcrumbs{font-size:130%;margin:0 0 15px 0}#footer{font-size:.75em;padding:5px 30px;border-top:1px solid #ddd;text-align:right}#footer p{margin:0 0 0 1em;display:inline-block}#footer p:last-child{margin-right:30px}h1,h2,h3,h4,h5{font-weight:300}h1{font-size:2.5em;line-height:1.1em}h2{font-size:1.75em;margin:1em 0 .50em 0}h3{font-size:1.4em;margin:25px 0 10px 0}h4{margin:0;font-size:105%}h1:target,h2:target,h3:target,h4:target,h5:target,h6:target{background:var(--highlight-color);padding:.2em 0}a{color:#058;text-decoration:none;transition:color .3s ease-in-out}a:hover{color:#e82}.title code{font-weight:bold}h2[id^="header-"]{margin-top:2em}.ident{color:#900}pre code{background:#f8f8f8;font-size:.8em;line-height:1.4em}code{background:#f2f2f1;padding:1px 4px;overflow-wrap:break-word}h1 code{background:transparent}pre{background:#f8f8f8;border:0;border-top:1px solid #ccc;border-bottom:1px solid #ccc;margin:1em 0;padding:1ex}#http-server-module-list{display:flex;flex-flow:column}#http-server-module-list div{display:flex}#http-server-module-list dt{min-width:10%}#http-server-module-list p{margin-top:0}.toc ul,#index{list-style-type:none;margin:0;padding:0}#index code{background:transparent}#index h3{border-bottom:1px solid #ddd}#index ul{padding:0}#index h4{margin-top:.6em;font-weight:bold}@media (min-width:200ex){#index .two-column{column-count:2}}@media (min-width:300ex){#index .two-column{column-count:3}}dl{margin-bottom:2em}dl dl:last-child{margin-bottom:4em}dd{margin:0 0 1em 3em}#header-classes + dl > dd{margin-bottom:3em}dd dd{margin-left:2em}dd p{margin:10px 0}.name{background:#eee;font-weight:bold;font-size:.85em;padding:5px 10px;display:inline-block;min-width:40%}.name:hover{background:#e0e0e0}dt:target .name{background:var(--highlight-color)}.name > span:first-child{white-space:nowrap}.name.class > span:nth-child(2){margin-left:.4em}.inherited{color:#999;border-left:5px solid #eee;padding-left:1em}.inheritance em{font-style:normal;font-weight:bold}.desc h2{font-weight:400;font-size:1.25em}.desc h3{font-size:1em}.desc dt code{background:inherit}.source summary,.git-link-div{color:#666;text-align:right;font-weight:400;font-size:.8em;text-transform:uppercase}.source summary > *{white-space:nowrap;cursor:pointer}.git-link{color:inherit;margin-left:1em}.source pre{max-height:500px;overflow:auto;margin:0}.source pre code{font-size:12px;overflow:visible}.hlist{list-style:none}.hlist li{display:inline}.hlist li:after{content:',\2002'}.hlist li:last-child:after{content:none}.hlist .hlist{display:inline;padding-left:1em}img{max-width:100%}td{padding:0 .5em}.admonition{padding:.1em .5em;margin-bottom:1em}.admonition-title{font-weight:bold}.admonition.note,.admonition.info,.admonition.important{background:#aef}.admonition.todo,.admonition.versionadded,.admonition.tip,.admonition.hint{background:#dfd}.admonition.warning,.admonition.versionchanged,.admonition.deprecated{background:#fd4}.admonition.error,.admonition.danger,.admonition.caution{background:lightpink}</style>
+<style media="screen and (min-width: 700px)">@media screen and (min-width:700px){#sidebar{width:30%;height:100vh;overflow:auto;position:sticky;top:0}#content{width:70%;max-width:100ch;padding:3em 4em;border-left:1px solid #ddd}pre code{font-size:1em}.item .name{font-size:1em}main{display:flex;flex-direction:row-reverse;justify-content:flex-end}.toc ul ul,#index ul{padding-left:1.5em}.toc > ul > li{margin-top:.5em}}</style>
+<style media="print">@media print{#sidebar h1{page-break-before:always}.source{display:none}}@media print{*{background:transparent !important;color:#000 !important;box-shadow:none !important;text-shadow:none !important}a[href]:after{content:" (" attr(href) ")";font-size:90%}a[href][title]:after{content:none}abbr[title]:after{content:" (" attr(title) ")"}.ir a:after,a[href^="javascript:"]:after,a[href^="#"]:after{content:""}pre,blockquote{border:1px solid #999;page-break-inside:avoid}thead{display:table-header-group}tr,img{page-break-inside:avoid}img{max-width:100% !important}@page{margin:0.5cm}p,h2,h3{orphans:3;widows:3}h1,h2,h3,h4,h5,h6{page-break-after:avoid}}</style>
+<script defer src="https://cdnjs.cloudflare.com/ajax/libs/highlight.js/10.1.1/highlight.min.js" integrity="sha256-Uv3H6lx7dJmRfRvH8TH6kJD1TSK1aFcwgx+mdg3epi8=" crossorigin></script>
+<script>window.addEventListener('DOMContentLoaded', () => hljs.initHighlighting())</script>
+</head>
+<body>
+<main>
+<article id="content">
+<header>
+<h1 class="title">Module <code>dsjobs.dir</code></h1>
+</header>
+<section id="section-intro">
+<details class="source">
+<summary>
+<span>Expand source code</span>
+</summary>
+<pre><code class="python">import os
+
+
+def get_ds_path_uri(ag, path):
+    &#34;&#34;&#34;
+    Given a path on DesignSafe, determine the correct input URI.
+
+    Args:
+        ag (object): Agave object to fetch profiles or metadata.
+        path (str): The directory path.
+
+    Returns:
+        str: The corresponding input URI.
+
+    Raises:
+        ValueError: If no matching directory pattern is found.
+    &#34;&#34;&#34;
+
+    # If any of the following directory patterns are found in the path,
+    # process them accordingly.
+    directory_patterns = [
+        (&#34;jupyter/MyData&#34;, &#34;designsafe.storage.default&#34;, True),
+        (&#34;jupyter/mydata&#34;, &#34;designsafe.storage.default&#34;, True),
+        (&#34;jupyter/CommunityData&#34;, &#34;designsafe.storage.community&#34;, False),
+        (&#34;/MyData&#34;, &#34;designsafe.storage.default&#34;, True),
+        (&#34;/mydata&#34;, &#34;designsafe.storage.default&#34;, True),
+    ]
+
+    for pattern, storage, use_username in directory_patterns:
+        if pattern in path:
+            path = path.split(pattern).pop()
+            input_dir = ag.profiles.get()[&#34;username&#34;] + path if use_username else path
+            input_uri = f&#34;agave://{storage}/{input_dir}&#34;
+            return input_uri.replace(&#34; &#34;, &#34;%20&#34;)
+
+    project_patterns = [
+        (&#34;jupyter/MyProjects&#34;, &#34;project-&#34;),
+        (&#34;jupyter/projects&#34;, &#34;project-&#34;),
+    ]
+
+    for pattern, prefix in project_patterns:
+        if pattern in path:
+            path = path.split(pattern + &#34;/&#34;).pop()
+            project_id = path.split(&#34;/&#34;)[0]
+            query = {&#34;value.projectId&#34;: str(project_id)}
+            path = path.split(project_id).pop()
+            project_uuid = ag.meta.listMetadata(q=str(query))[0][&#34;uuid&#34;]
+            input_uri = f&#34;agave://{prefix}{project_uuid}{path}&#34;
+            return input_uri.replace(&#34; &#34;, &#34;%20&#34;)
+
+    raise ValueError(f&#34;No matching directory pattern found for: {path}&#34;)</code></pre>
+</details>
+</section>
+<section>
+</section>
+<section>
+</section>
+<section>
+<h2 class="section-title" id="header-functions">Functions</h2>
+<dl>
+<dt id="dsjobs.dir.get_ds_path_uri"><code class="name flex">
+<span>def <span class="ident">get_ds_path_uri</span></span>(<span>ag, path)</span>
+</code></dt>
+<dd>
+<div class="desc"><p>Given a path on DesignSafe, determine the correct input URI.</p>
+<h2 id="args">Args</h2>
+<dl>
+<dt><strong><code>ag</code></strong> :&ensp;<code>object</code></dt>
+<dd>Agave object to fetch profiles or metadata.</dd>
+<dt><strong><code>path</code></strong> :&ensp;<code>str</code></dt>
+<dd>The directory path.</dd>
+</dl>
+<h2 id="returns">Returns</h2>
+<dl>
+<dt><code>str</code></dt>
+<dd>The corresponding input URI.</dd>
+</dl>
+<h2 id="raises">Raises</h2>
+<dl>
+<dt><code>ValueError</code></dt>
+<dd>If no matching directory pattern is found.</dd>
+</dl></div>
+<details class="source">
+<summary>
+<span>Expand source code</span>
+</summary>
+<pre><code class="python">def get_ds_path_uri(ag, path):
+    &#34;&#34;&#34;
+    Given a path on DesignSafe, determine the correct input URI.
+
+    Args:
+        ag (object): Agave object to fetch profiles or metadata.
+        path (str): The directory path.
+
+    Returns:
+        str: The corresponding input URI.
+
+    Raises:
+        ValueError: If no matching directory pattern is found.
+    &#34;&#34;&#34;
+
+    # If any of the following directory patterns are found in the path,
+    # process them accordingly.
+    directory_patterns = [
+        (&#34;jupyter/MyData&#34;, &#34;designsafe.storage.default&#34;, True),
+        (&#34;jupyter/mydata&#34;, &#34;designsafe.storage.default&#34;, True),
+        (&#34;jupyter/CommunityData&#34;, &#34;designsafe.storage.community&#34;, False),
+        (&#34;/MyData&#34;, &#34;designsafe.storage.default&#34;, True),
+        (&#34;/mydata&#34;, &#34;designsafe.storage.default&#34;, True),
+    ]
+
+    for pattern, storage, use_username in directory_patterns:
+        if pattern in path:
+            path = path.split(pattern).pop()
+            input_dir = ag.profiles.get()[&#34;username&#34;] + path if use_username else path
+            input_uri = f&#34;agave://{storage}/{input_dir}&#34;
+            return input_uri.replace(&#34; &#34;, &#34;%20&#34;)
+
+    project_patterns = [
+        (&#34;jupyter/MyProjects&#34;, &#34;project-&#34;),
+        (&#34;jupyter/projects&#34;, &#34;project-&#34;),
+    ]
+
+    for pattern, prefix in project_patterns:
+        if pattern in path:
+            path = path.split(pattern + &#34;/&#34;).pop()
+            project_id = path.split(&#34;/&#34;)[0]
+            query = {&#34;value.projectId&#34;: str(project_id)}
+            path = path.split(project_id).pop()
+            project_uuid = ag.meta.listMetadata(q=str(query))[0][&#34;uuid&#34;]
+            input_uri = f&#34;agave://{prefix}{project_uuid}{path}&#34;
+            return input_uri.replace(&#34; &#34;, &#34;%20&#34;)
+
+    raise ValueError(f&#34;No matching directory pattern found for: {path}&#34;)</code></pre>
+</details>
+</dd>
+</dl>
+</section>
+<section>
+</section>
+</article>
+<nav id="sidebar">
+<h1>Index</h1>
+<div class="toc">
+<ul></ul>
+</div>
+<ul id="index">
+<li><h3>Super-module</h3>
+<ul>
+<li><code><a title="dsjobs" href="index.html">dsjobs</a></code></li>
+</ul>
+</li>
+<li><h3><a href="#header-functions">Functions</a></h3>
+<ul class="">
+<li><code><a title="dsjobs.dir.get_ds_path_uri" href="#dsjobs.dir.get_ds_path_uri">get_ds_path_uri</a></code></li>
+</ul>
+</li>
+</ul>
+</nav>
+</main>
+<footer id="footer">
+<p>Generated by <a href="https://pdoc3.github.io/pdoc" title="pdoc: Python API documentation generator"><cite>pdoc</cite> 0.10.0</a>.</p>
+</footer>
+</body>
+</html>