deploy: d8a3b69

05-create-profiles.html

@@ -475,7 +475,7 @@ <h2><span class="section-number">5.3. </span>Create Database Backend<a class="he
 </div>
 <p>Note that if your system does not already have <code class="docutils literal notranslate"><span class="pre">cytominer-database</span></code> installed, you can install it at the same time as pycytominer by changing the final command above to <code class="docutils literal notranslate"><span class="pre">python3</span> <span class="pre">-m</span> <span class="pre">pip</span> <span class="pre">install</span> <span class="pre">-e</span> <span class="pre">.[collate]</span></code></p>
 <p>The command below first calls <code class="docutils literal notranslate"><span class="pre">cytominer-database</span> <span class="pre">ingest</span></code> to create the SQLite backend, and then pycytominer’s <code class="docutils literal notranslate"><span class="pre">aggregate_profiles</span></code> to create per-well profiles. Once complete, all files are uploaded to S3 and the local cache are deleted. This step takes several hours, but metadata creation and GitHub setup can be done in this time.</p>
-<p><a class="reference external" href="https://github.com/cytomining/pycytominer/blob/master/pycytominer/cyto_utils/collate_cmd.py">collate_cmd.py</a> ingests and indexes the database.</p>
+<p><a class="reference external" href="https://github.com/cytomining/pycytominer/blob/master/pycytominer/cyto_utils/collate.py">collate.py</a> ingests and indexes the database. <a class="reference external" href="https://github.com/cytomining/pycytominer/blob/master/pycytominer/cyto_utils/collate_cmd.py">collate_command.py</a> exposes this functionality to the command line.</p>
 <div class="highlight-sh notranslate"><div class="highlight"><pre><span></span>pyenv<span class="w"> </span>shell<span class="w"> </span><span class="m">3</span>.8.10
 
 mkdir<span class="w"> </span>-p<span class="w">  </span>../../log/<span class="si">${</span><span class="nv">BATCH_ID</span><span class="si">}</span>/

_sources/05-create-profiles.md

@@ -77,7 +77,7 @@ Note that if your system does not already have `cytominer-database` installed, y
 
 The command below first calls `cytominer-database ingest` to create the SQLite backend, and then pycytominer's `aggregate_profiles` to create per-well profiles. Once complete, all files are uploaded to S3 and the local cache are deleted. This step takes several hours, but metadata creation and GitHub setup can be done in this time.
 
-[collate_cmd.py](https://github.com/cytomining/pycytominer/blob/master/pycytominer/cyto_utils/collate_cmd.py) ingests and indexes the database.
+[collate.py](https://github.com/cytomining/pycytominer/blob/master/pycytominer/cyto_utils/collate.py) ingests and indexes the database. [collate_command.py](https://github.com/cytomining/pycytominer/blob/master/pycytominer/cyto_utils/collate_cmd.py) exposes this functionality to the command line. 
 
 ```sh
 pyenv shell 3.8.10