From a46c79b45605410cf558ca883fcb030fe3490299 Mon Sep 17 00:00:00 2001
From: Leonardo Schwarz <leonardo.schwarz@fgcz.ethz.ch>
Date: Thu, 29 Aug 2024 08:19:30 +0200
Subject: [PATCH] Deployed 9366e90 with MkDocs version: 1.6.0

---
 changelog/index.html | 177 +++++++++++++++++++++++++++++++++----------
 index.html           |   5 +-
 sitemap.xml.gz       | Bin 127 -> 127 bytes
 3 files changed, 142 insertions(+), 40 deletions(-)

diff --git a/changelog/index.html b/changelog/index.html
index dc983cae..bfb48643 100644
--- a/changelog/index.html
+++ b/changelog/index.html
@@ -286,6 +286,48 @@
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+</li>
+      
+        <li class="md-nav__item">
+  <a href="#1136-2024-08-29" class="md-nav__link">
+    <span class="md-ellipsis">
+      [1.13.6] - 2024-08-29
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="[1.13.6] - 2024-08-29">
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+  <a href="#changed" class="md-nav__link">
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+  
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+  <a href="#removed" class="md-nav__link">
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+      Removed
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+</li>
+      
+        <li class="md-nav__item">
+  <a href="#1136-2024-08-29" class="md-nav__link">
+    <span class="md-ellipsis">
+      [1.13.6] - 2024-08-29
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="[1.13.6] - 2024-08-29">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#added" class="md-nav__link">
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+      Added
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+  
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+  <a href="#changed" class="md-nav__link">
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+      Changed
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+  </a>
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@@ -787,9 +871,24 @@ <h1 id="changelog">Changelog</h1>
 <li><code>Z</code> is increased for feature releases, that should not break the API</li>
 </ul>
 <h2 id="unreleased">[Unreleased]</h2>
-<h2 id="1135-2024-08-13">[1.13.5] - 2024-08-13</h2>
+<h2 id="1136-2024-08-29">[1.13.6] - 2024-08-29</h2>
 <h3 id="added">Added</h3>
 <ul>
+<li><code>Entity.find_by</code> has new parameter <code>max_results</code>.</li>
+</ul>
+<h3 id="changed">Changed</h3>
+<ul>
+<li><code>bfabric_read.py</code> prints non-output information exclusively through logger and does not restrict entity types anymore.</li>
+<li><code>bfabric_delete.py</code> accepts multiple ids at once and does not restrict entity types anymore.</li>
+<li>Both engines raise a <code>BfabricRequestError</code> if the endpoint was not found.</li>
+</ul>
+<h3 id="removed">Removed</h3>
+<ul>
+<li><code>bfabric.endpoints</code> list is deleted, since it was out of date and generally not so useful.</li>
+</ul>
+<h2 id="1135-2024-08-13">[1.13.5] - 2024-08-13</h2>
+<h3 id="added_1">Added</h3>
+<ul>
 <li>The <code>Bfabric</code> instance is now pickleable.</li>
 <li>Entities mapping:<ul>
 <li>Add <code>Entity.id</code> and <code>Entity.web_url</code> properties.</li>
@@ -802,32 +901,32 @@ <h3 id="added">Added</h3>
 </li>
 <li>Add <code>nodelist</code> column and application name to <code>bfabric_list_not_available_proteomics_workunits.py</code> output.</li>
 </ul>
-<h3 id="changed">Changed</h3>
+<h3 id="changed_1">Changed</h3>
 <ul>
 <li><code>Entity.find_all</code> supports more than 100 IDs now by using the experimental MultiQuery API.</li>
 </ul>
 <h2 id="1134-2024-08-05">[1.13.4] - 2024-08-05</h2>
-<h3 id="added_1">Added</h3>
+<h3 id="added_2">Added</h3>
 <ul>
 <li>Add <code>Workunit</code>, <code>Parameter</code>, and <code>Resource</code> entities.</li>
 <li>Add concept of has_many and has_one relationships to entities.</li>
 <li><code>bfabric_slurm_queue_status.py</code> to quickly check slurm queue status.</li>
 <li><code>Bfabric.save</code> provides <code>method</code> which can be set to <code>checkandinsert</code> for specific use cases.</li>
 </ul>
-<h3 id="changed_1">Changed</h3>
+<h3 id="changed_2">Changed</h3>
 <ul>
 <li>Most messages are now logged to debug level.</li>
 <li>The old verbose version information is now always logged, to INFO level, since it could entail useful information for error reporting.</li>
 </ul>
 <h2 id="1133-2024-07-18">[1.13.3] - 2024-07-18</h2>
-<h3 id="added_2">Added</h3>
+<h3 id="added_3">Added</h3>
 <ul>
 <li>Flask<ul>
 <li>New endpoint <code>GET /config/remote_base_url</code> for testing</li>
 </ul>
 </li>
 </ul>
-<h3 id="changed_2">Changed</h3>
+<h3 id="changed_3">Changed</h3>
 <ul>
 <li>Flask<ul>
 <li>Simplify logging by using loguru only.</li>
@@ -840,7 +939,7 @@ <h3 id="fixed">Fixed</h3>
 <li><code>bfabric_save_csv2dataset.py</code> had an undeclared dependency on numpy and a few bugs which was improved.</li>
 </ul>
 <h2 id="1132-2024-07-11">[1.13.2] - 2024-07-11</h2>
-<h3 id="added_3">Added</h3>
+<h3 id="added_4">Added</h3>
 <ul>
 <li>Add <code>bfabric.entities.Dataset</code> to easily read datasets.</li>
 <li>Pydantic-based configuration parsing<ul>
@@ -852,23 +951,23 @@ <h3 id="added_3">Added</h3>
 <li>Make host and port configurable in <code>bfabric_flask.py</code> (currently only dev mode).</li>
 </ul>
 <h2 id="1131-2024-07-02">[1.13.1] - 2024-07-02</h2>
-<h3 id="changed_3">Changed</h3>
+<h3 id="changed_4">Changed</h3>
 <ul>
 <li>bfabric_save_csv2dataset will raise an error if problematic characters are found in any of the cells</li>
 <li>Correctly define <code>bfabric_setWorkunitStatus_available.py</code>, and <code>processing</code> and <code>failed</code> variants.</li>
 </ul>
-<h3 id="added_4">Added</h3>
+<h3 id="added_5">Added</h3>
 <ul>
 <li>Add loguru for future logging refactoring.</li>
 <li>Easily runnable tests with <code>nox</code> and standardized formatting using <code>pre-commit</code>.</li>
 </ul>
-<h3 id="removed">Removed</h3>
+<h3 id="removed_1">Removed</h3>
 <ul>
 <li>Pandas is no longer a dependency, and has been replaced by polars.</li>
 </ul>
 <h2 id="1130-2024-05-24">[1.13.0] - 2024-05-24</h2>
 <p>This is a major release refactoring bfabricPy's API.</p>
-<h3 id="changed_4">Changed</h3>
+<h3 id="changed_5">Changed</h3>
 <ul>
 <li>The <code>Bfabric</code> class operations now return <code>ResultContainer</code> objects.<ul>
 <li>These provide a list-like interface to access individual items or iterate over them.</li>
@@ -880,14 +979,14 @@ <h3 id="changed_4">Changed</h3>
 <li>Use <code>pyproject.toml</code> for package configuration.</li>
 <li>Scripts have been refactored on a case-by-case basis.</li>
 </ul>
-<h3 id="added_5">Added</h3>
+<h3 id="added_6">Added</h3>
 <ul>
 <li>Zeep can be used instead of suds for SOAP communication.</li>
 <li><code>Bfabric</code> can be instantiated without authentication, that can be provided later. This is useful in a server setup.</li>
 <li>Pagination support in <code>Bfabric</code>, specify the number of max_results and a potential offset. Pages handling is abstracted away.</li>
 <li>Detect errors in responses, e.g. invalid login.</li>
 </ul>
-<h3 id="removed_1">Removed</h3>
+<h3 id="removed_2">Removed</h3>
 <ul>
 <li>Several old scripts have been moved into a <code>deprecated_scripts</code> folder.</li>
 <li>Wrapper creator related code is currently not updated but has been extracted into a dedicated folder <code>wrapper_creator</code> as well.</li>
diff --git a/index.html b/index.html
index c265474a..e78b469b 100644
--- a/index.html
+++ b/index.html
@@ -417,12 +417,15 @@ <h2 id="configuration">Configuration</h2>
   password: yourBfabricWebPassword
   base_url: https://fgcz-bfabric.uzh.ch/bfabric
 </code></pre>
-<p>You can also include an additional config for the TEST instance</p>
+<p>You can also append an additional config section for the TEST instance which will be used for instance when running the integration tests:</p>
 <pre><code>TEST:
   login: yourBfabricLogin
   password: yourBfabricWebPassword
   base_url: https://fgcz-bfabric-test.uzh.ch/bfabric
 </code></pre>
+<p>When you run an application using bfabricPy, and it does not explicitly set the config when calling <code>Bfabric.from_config</code>, you can adjust the
+environment that is used by setting the environemnt variable <code>BFABRICPY_CONFIG_ENV</code> to the name of the config section you want to use.
+Command line scripts will log the user and base URL that is used, so you can verify that you are indeed using the correct environment.</p>
 
 
 
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