update documentation

_sources/changelog/index.rst.txt

@@ -4,6 +4,13 @@
 Changelog
 =========
 
+* `0.18.0 <2024-03-31>`
+ `-` We released celloracle version 0.18.0. Refactoring was done in the motif analysis to improve the stability of the function. 
+
+ `-` Docker image was updated to the latest version of celloracle. From this version, we use python 3.10 in the docker image.
+
+ `-` Bug fix in the unit test function. 
+
 * `0.17.1 <2024-03-19>`
  `-` We updated the network function to support scikit-learn>=1.2. 
 

_sources/index.rst.txt

@@ -25,6 +25,8 @@ News
 
 Please look at `Changelog page <https://morris-lab.github.io/CellOracle.documentation/changelog/index.html>`_ for all updates history of CellOracle package.
 
+- 03/31/2024: We released celloracle version 0.18.0. Refactoring was done in the motif analysis to improve the stability of the function. Docker image was updated to the latest version of celloracle. From this version, we use python 3.10 in the docker image.
+
 - 03/19/2024: We released celloracle version 0.17.1. This update includes a bug fix, refactoring, and new test functions. Now we support Python 3.10. 
 
 - 02/01/2024: We released celloracle version 0.16.0. Fixed a bug in the Systematic Simulation function to comply with the latest update of pandas.

_sources/installation/docker_additional_information.rst.txt

@@ -13,7 +13,7 @@ Quick start
 
 ::
 
-    docker pull kenjikamimoto126/celloracle_ubuntu:0.12.0
+    docker pull kenjikamimoto126/celloracle_ubuntu:0.18.0
 
 
 2. Make docker container and start running it.
@@ -30,7 +30,7 @@ Quick start
       --name celloracle_container \
       -p 8888:8888 \
       -v $(pwd)/data_folder:/root/data_folder \
-      celloracle_ubuntu:0.12.0
+      kenjikamimoto126/celloracle_ubuntu:0.18.0
 
 
 
@@ -64,6 +64,6 @@ Docker image build information
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 We built our docker image using Dockerfile automatic build function.
-The Dockerfile is available `here <https://github.com/morris-lab/CellOracle/blob/master/docs/dockerfile>`_.
+The Dockerfile is available `here <https://github.com/morris-lab/CellOracle/blob/master/other_files/Dockerfile>`_.
 You can modify it to create custom docker image by yourself.
 If you make custom environment, please do so on your responsibility.

_sources/installation/index.rst.txt

@@ -45,7 +45,7 @@ System Requirements
 Python Requirements
 ^^^^^^^^^^^^^^^^^^^
 
-- CellOracle was developed using python 3.6. It is also tested with python 3.8. We do not support python 2.7x or python <=3.5.
+- CellOracle was developed using python 3.8. It is also tested with python 3.10. We do not support python 2.7x or python <=3.5.
 - CellOracle is available through `PyPI <https://pypi.org/project/celloracle/>`_. You can also download and install celloracle from our `CellOracle  GitHub repository <https://github.com/morris-lab/CellOracle>`_ .
 
 CellOracle installation using conda and pip
@@ -56,7 +56,7 @@ CellOracle installation using conda and pip
 
   ::
 
-      conda create -n celloracle_env python=3.8
+      conda create -n celloracle_env python=3.10
       conda activate celloracle_env
 
 

changelog/index.html

@@ -212,6 +212,14 @@
 <section id="changelog">
 <span id="id1"></span><h1>Changelog<a class="headerlink" href="#changelog" title="Permalink to this headline">¶</a></h1>
 <ul class="simple">
+<li><p><cite>0.18.0 &lt;2024-03-31&gt;</cite></p></li>
+</ul>
+<blockquote>
+<div><p><cite>-</cite> We released celloracle version 0.18.0. Refactoring was done in the motif analysis to improve the stability of the function.</p>
+<p><cite>-</cite> Docker image was updated to the latest version of celloracle. From this version, we use python 3.10 in the docker image.</p>
+<p><cite>-</cite> Bug fix in the unit test function.</p>
+</div></blockquote>
+<ul class="simple">
 <li><p><cite>0.17.1 &lt;2024-03-19&gt;</cite></p></li>
 </ul>
 <blockquote>

genindex.html

@@ -812,6 +812,8 @@ <h2 id="S">S</h2>
       <li><a href="modules/celloracle.motif_analysis.html#celloracle.motif_analysis.scan_dna_for_motifs">scan_dna_for_motifs() (in module celloracle.motif_analysis)</a>
 </li>
       <li><a href="modules/celloracle.motif_analysis.html#celloracle.motif_analysis.TFinfo.scanned_df">scanned_df (celloracle.motif_analysis.TFinfo attribute)</a>
+</li>
+      <li><a href="modules/celloracle.motif_analysis.html#celloracle.motif_analysis.TFinfo.set_motifs">set_motifs() (celloracle.motif_analysis.TFinfo method)</a>
 </li>
       <li><a href="modules/celloracle.network_analysis.html#celloracle.network_analysis.set_R_path">set_R_path() (in module celloracle.network_analysis)</a>
 </li>

index.html

@@ -356,6 +356,7 @@ <h1>Welcome to CellOracle’s documentation!<a class="headerlink" href="#welcome
 <h1>News<a class="headerlink" href="#news" title="Permalink to this headline">¶</a></h1>
 <p>Please look at <a class="reference external" href="https://morris-lab.github.io/CellOracle.documentation/changelog/index.html">Changelog page</a> for all updates history of CellOracle package.</p>
 <ul class="simple">
+<li><p>03/31/2024: We released celloracle version 0.18.0. Refactoring was done in the motif analysis to improve the stability of the function. Docker image was updated to the latest version of celloracle. From this version, we use python 3.10 in the docker image.</p></li>
 <li><p>03/19/2024: We released celloracle version 0.17.1. This update includes a bug fix, refactoring, and new test functions. Now we support Python 3.10.</p></li>
 <li><p>02/01/2024: We released celloracle version 0.16.0. Fixed a bug in the Systematic Simulation function to comply with the latest update of pandas.</p></li>
 <li><p>07/25/2023: We released celloracle version 0.15.0. This update includes refactoring in the Markov simulation function.</p></li>

installation/docker_additional_information.html

@@ -231,7 +231,7 @@ <h2>Quick start<a class="headerlink" href="#quick-start" title="Permalink to thi
 <ol class="arabic simple">
 <li><p>Download celloracle docker image from docker Hub.</p></li>
 </ol>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">docker</span> <span class="n">pull</span> <span class="n">kenjikamimoto126</span><span class="o">/</span><span class="n">celloracle_ubuntu</span><span class="p">:</span><span class="mf">0.12</span><span class="o">.</span><span class="mi">0</span>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">docker</span> <span class="n">pull</span> <span class="n">kenjikamimoto126</span><span class="o">/</span><span class="n">celloracle_ubuntu</span><span class="p">:</span><span class="mf">0.18</span><span class="o">.</span><span class="mi">0</span>
 </pre></div>
 </div>
 <ol class="arabic simple" start="2">
@@ -246,7 +246,7 @@ <h2>Quick start<a class="headerlink" href="#quick-start" title="Permalink to thi
   --name celloracle_container \
   -p 8888:8888 \
   -v $(pwd)/data_folder:/root/data_folder \
-  celloracle_ubuntu:0.12.0
+  kenjikamimoto126/celloracle_ubuntu:0.18.0
 </pre></div>
 </div>
 <ol class="arabic simple" start="3">
@@ -276,7 +276,7 @@ <h2>Quick start<a class="headerlink" href="#quick-start" title="Permalink to thi
 <section id="docker-image-build-information">
 <h2>Docker image build information<a class="headerlink" href="#docker-image-build-information" title="Permalink to this headline">¶</a></h2>
 <p>We built our docker image using Dockerfile automatic build function.
-The Dockerfile is available <a class="reference external" href="https://github.com/morris-lab/CellOracle/blob/master/docs/dockerfile">here</a>.
+The Dockerfile is available <a class="reference external" href="https://github.com/morris-lab/CellOracle/blob/master/other_files/Dockerfile">here</a>.
 You can modify it to create custom docker image by yourself.
 If you make custom environment, please do so on your responsibility.</p>
 </section>

installation/index.html

@@ -263,7 +263,7 @@ <h3>System Requirements<a class="headerlink" href="#system-requirements" title="
 <section id="python-requirements">
 <h3>Python Requirements<a class="headerlink" href="#python-requirements" title="Permalink to this headline">¶</a></h3>
 <ul class="simple">
-<li><p>CellOracle was developed using python 3.6. It is also tested with python 3.8. We do not support python 2.7x or python &lt;=3.5.</p></li>
+<li><p>CellOracle was developed using python 3.8. It is also tested with python 3.10. We do not support python 2.7x or python &lt;=3.5.</p></li>
 <li><p>CellOracle is available through <a class="reference external" href="https://pypi.org/project/celloracle/">PyPI</a>. You can also download and install celloracle from our <a class="reference external" href="https://github.com/morris-lab/CellOracle">CellOracle  GitHub repository</a> .</p></li>
 </ul>
 </section>
@@ -272,7 +272,7 @@ <h3>CellOracle installation using conda and pip<a class="headerlink" href="#cell
 <blockquote>
 <div><p>We recommend installing CellOracle in an independent conda environment to avoid dependent software conflicts.
 Please make a new python environment for celloracle and install dependent libraries in it.</p>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">conda</span> <span class="n">create</span> <span class="o">-</span><span class="n">n</span> <span class="n">celloracle_env</span> <span class="n">python</span><span class="o">=</span><span class="mf">3.8</span>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">conda</span> <span class="n">create</span> <span class="o">-</span><span class="n">n</span> <span class="n">celloracle_env</span> <span class="n">python</span><span class="o">=</span><span class="mf">3.10</span>
 <span class="n">conda</span> <span class="n">activate</span> <span class="n">celloracle_env</span>
 </pre></div>
 </div>

modules/celloracle.motif_analysis.html

@@ -381,7 +381,7 @@
 
 <dl class="py method">
 <dt id="celloracle.motif_analysis.TFinfo.scan">
-<code class="sig-name descname">scan</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">background_length</span><span class="o">=</span><span class="default_value">200</span></em>, <em class="sig-param"><span class="n">fpr</span><span class="o">=</span><span class="default_value">0.02</span></em>, <em class="sig-param"><span class="n">n_cpus</span><span class="o">=</span><span class="default_value">- 1</span></em>, <em class="sig-param"><span class="n">verbose</span><span class="o">=</span><span class="default_value">True</span></em>, <em class="sig-param"><span class="n">motifs</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">TF_evidence_level</span><span class="o">=</span><span class="default_value">'direct_and_indirect'</span></em>, <em class="sig-param"><span class="n">TF_formatting</span><span class="o">=</span><span class="default_value">'auto'</span></em>, <em class="sig-param"><span class="n">divide</span><span class="o">=</span><span class="default_value">100000</span></em><span class="sig-paren">)</span><a class="headerlink" href="#celloracle.motif_analysis.TFinfo.scan" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">scan</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">background_length</span><span class="o">=</span><span class="default_value">200</span></em>, <em class="sig-param"><span class="n">fpr</span><span class="o">=</span><span class="default_value">0.02</span></em>, <em class="sig-param"><span class="n">n_cpus</span><span class="o">=</span><span class="default_value">- 1</span></em>, <em class="sig-param"><span class="n">verbose</span><span class="o">=</span><span class="default_value">True</span></em>, <em class="sig-param"><span class="n">motifs</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">TF_evidence_level</span><span class="o">=</span><span class="default_value">'direct_and_indirect'</span></em>, <em class="sig-param"><span class="n">TF_formatting</span><span class="o">=</span><span class="default_value">'auto'</span></em>, <em class="sig-param"><span class="n">batch_size</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">divide</span><span class="o">=</span><span class="default_value">100000</span></em><span class="sig-paren">)</span><a class="headerlink" href="#celloracle.motif_analysis.TFinfo.scan" title="Permalink to this definition">¶</a></dt>
 <dd><p>Scan DNA sequences searching for TF binding motifs.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters</dt>
@@ -399,6 +399,11 @@
 </dl>
 </dd></dl>
 
+<dl class="py method">
+<dt id="celloracle.motif_analysis.TFinfo.set_motifs">
+<code class="sig-name descname">set_motifs</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">motifs</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">TF_formatting</span><span class="o">=</span><span class="default_value">'auto'</span></em>, <em class="sig-param"><span class="n">verbose</span><span class="o">=</span><span class="default_value">True</span></em><span class="sig-paren">)</span><a class="headerlink" href="#celloracle.motif_analysis.TFinfo.set_motifs" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
 <dl class="py method">
 <dt id="celloracle.motif_analysis.TFinfo.to_dataframe">
 <code class="sig-name descname">to_dataframe</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">verbose</span><span class="o">=</span><span class="default_value">True</span></em><span class="sig-paren">)</span><a class="headerlink" href="#celloracle.motif_analysis.TFinfo.to_dataframe" title="Permalink to this definition">¶</a></dt>
@@ -633,7 +638,7 @@
 
 <dl class="py function">
 <dt id="celloracle.motif_analysis.scan_dna_for_motifs">
-<code class="sig-prename descclassname">celloracle.motif_analysis.</code><code class="sig-name descname">scan_dna_for_motifs</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">scanner_object</span></em>, <em class="sig-param"><span class="n">motifs_object</span></em>, <em class="sig-param"><span class="n">sequence_object</span></em>, <em class="sig-param"><span class="n">divide</span><span class="o">=</span><span class="default_value">100000</span></em>, <em class="sig-param"><span class="n">verbose</span><span class="o">=</span><span class="default_value">True</span></em><span class="sig-paren">)</span><a class="headerlink" href="#celloracle.motif_analysis.scan_dna_for_motifs" title="Permalink to this definition">¶</a></dt>
+<code class="sig-prename descclassname">celloracle.motif_analysis.</code><code class="sig-name descname">scan_dna_for_motifs</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">scanner_object</span></em>, <em class="sig-param"><span class="n">motifs_object</span></em>, <em class="sig-param"><span class="n">sequence_object</span></em>, <em class="sig-param"><span class="n">divide</span><span class="o">=</span><span class="default_value">100000</span></em>, <em class="sig-param"><span class="n">verbose</span><span class="o">=</span><span class="default_value">True</span></em>, <em class="sig-param"><span class="n">batch_size</span><span class="o">=</span><span class="default_value">None</span></em><span class="sig-paren">)</span><a class="headerlink" href="#celloracle.motif_analysis.scan_dna_for_motifs" title="Permalink to this definition">¶</a></dt>
 <dd><p>This is a wrapper function to scan DNA sequences searchig for Gene motifs.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters</dt>