Automatic Update

Thu Sep 21 16:45:58 UTC 2023

_sources/development.rst.txt

@@ -124,6 +124,10 @@ The following programs need to be available locally:
 - bioformats2raw package: https://github.com/glencoesoftware/bioformats2raw
 - imagemagick: https://imagemagick.org/script/download.php
 
+All configurations for binary executables that workflows depend on are considered to exist in environment variables.
+For this you will need a `.env` file in the project root directory. For simplicity, you can copy the `.env.sample`
+contents into the `.env` file.
+
 Similar to the HPC Set up below, you can locally set up `dev` and `qa` virtual envs.
 
 Special note for **Mac M1**: The `tomojs-pytools` library depends on imagecodecs which does

development.html

@@ -205,6 +205,9 @@ <h2>Local Set-up<a class="headerlink" href="#local-set-up" title="Permalink to t
 <li><p>bioformats2raw package: <a class="reference external" href="https://github.com/glencoesoftware/bioformats2raw">https://github.com/glencoesoftware/bioformats2raw</a></p></li>
 <li><p>imagemagick: <a class="reference external" href="https://imagemagick.org/script/download.php">https://imagemagick.org/script/download.php</a></p></li>
 </ul>
+<p>All configurations for binary executables that workflows depend on are considered to exist in environment variables.
+For this you will need a <cite>.env</cite> file in the project root directory. For simplicity, you can copy the <cite>.env.sample</cite>
+contents into the <cite>.env</cite> file.</p>
 <p>Similar to the HPC Set up below, you can locally set up <cite>dev</cite> and <cite>qa</cite> virtual envs.</p>
 <p>Special note for <strong>Mac M1</strong>: The <cite>tomojs-pytools</cite> library depends on imagecodecs which does
 not have binaries built for the M1. Need to install using an x86_64 version of Python. Also, there