deploy: a8b4524

_modules/unravel/cluster_stats/cstats.html

@@ -420,7 +420,7 @@ <h1>Source code for unravel.cluster_stats.cstats</h1><div class="highlight"><pre
 <a class="viewcode-back" href="../../../unravel/cluster_stats/cstats.html#unravel.cluster_stats.cstats.parse_args">[docs]</a>
 <span class="k">def</span> <span class="nf">parse_args</span><span class="p">():</span>
     <span class="n">parser</span> <span class="o">=</span> <span class="n">argparse</span><span class="o">.</span><span class="n">ArgumentParser</span><span class="p">(</span><span class="n">formatter_class</span><span class="o">=</span><span class="n">SuppressMetavar</span><span class="p">)</span>
-    <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">&#39;--groups&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;List of group prefixes. 2 groups --&gt; t-test. &gt;2 --&gt; Tukey</span><span class="se">\&#39;</span><span class="s1">s tests (The first 2 groups reflect the main comparison for validation rates)&#39;</span><span class="p">,</span>  <span class="n">nargs</span><span class="o">=</span><span class="s1">&#39;+&#39;</span><span class="p">,</span> <span class="n">required</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+    <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">&#39;--groups&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;List of group prefixes. 2 groups --&gt; t-test. &gt;2 --&gt; Tukey</span><span class="se">\&#39;</span><span class="s1">s tests (The first 2 groups reflect the main comparison for validation rates)&#39;</span><span class="p">,</span> <span class="n">nargs</span><span class="o">=</span><span class="s1">&#39;*&#39;</span><span class="p">,</span> <span class="n">required</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="n">SM</span><span class="p">)</span>
     <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">&#39;-cp&#39;</span><span class="p">,</span> <span class="s1">&#39;--condition_prefixes&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;Condition prefixes to group data (e.g., see info for examples)&#39;</span><span class="p">,</span>  <span class="n">nargs</span><span class="o">=</span><span class="s1">&#39;*&#39;</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="n">SM</span><span class="p">)</span>
     <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">&#39;-hg&#39;</span><span class="p">,</span> <span class="s1">&#39;--higher_group&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;Specify the group that is expected to have a higher mean based on the direction of the p value map&#39;</span><span class="p">,</span> <span class="n">required</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
     <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">&#39;-alt&#39;</span><span class="p">,</span> <span class="s2">&quot;--alternate&quot;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s2">&quot;Number of tails and direction (&#39;two-sided&#39; [default], &#39;less&#39; [group1 &lt; group2], or &#39;greater&#39;)&quot;</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="s1">&#39;two-sided&#39;</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="n">SM</span><span class="p">)</span>

_modules/unravel/cluster_stats/index.html

@@ -386,7 +386,7 @@ <h1>Source code for unravel.cluster_stats.index</h1><div class="highlight"><pre>
 <span class="k">def</span> <span class="nf">parse_args</span><span class="p">():</span>
     <span class="n">parser</span> <span class="o">=</span> <span class="n">argparse</span><span class="o">.</span><span class="n">ArgumentParser</span><span class="p">(</span><span class="n">formatter_class</span><span class="o">=</span><span class="n">SuppressMetavar</span><span class="p">)</span>
     <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">&#39;-ci&#39;</span><span class="p">,</span> <span class="s1">&#39;--cluster_idx&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;Path to the reverse cluster index NIfTI file.&#39;</span><span class="p">,</span> <span class="n">required</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="n">SM</span><span class="p">)</span>
-    <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">&#39;-ids&#39;</span><span class="p">,</span> <span class="s1">&#39;--valid_cluster_ids&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;Space-separated list of valid cluster IDs.&#39;</span><span class="p">,</span> <span class="n">nargs</span><span class="o">=</span><span class="s1">&#39;+&#39;</span><span class="p">,</span> <span class="nb">type</span><span class="o">=</span><span class="nb">int</span><span class="p">,</span> <span class="n">required</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="n">SM</span><span class="p">)</span>
+    <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">&#39;-ids&#39;</span><span class="p">,</span> <span class="s1">&#39;--valid_cluster_ids&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;Space-separated list of valid cluster IDs.&#39;</span><span class="p">,</span> <span class="n">nargs</span><span class="o">=</span><span class="s1">&#39;*&#39;</span><span class="p">,</span> <span class="nb">type</span><span class="o">=</span><span class="nb">int</span><span class="p">,</span> <span class="n">required</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="n">SM</span><span class="p">)</span>
     <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">&#39;-vcd&#39;</span><span class="p">,</span> <span class="s1">&#39;--valid_clusters_dir&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;path/name_of_the_output_directory. Default: valid_clusters&#39;</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="s1">&#39;_valid_clusters&#39;</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="n">SM</span><span class="p">)</span>
     <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">&#39;-a&#39;</span><span class="p">,</span> <span class="s1">&#39;--atlas&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;path/atlas.nii.gz (Default: atlas/atlas_CCFv3_2020_30um.nii.gz)&#39;</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="s1">&#39;atlas/atlas_CCFv3_2020_30um.nii.gz&#39;</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="n">SM</span><span class="p">)</span>
     <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">&#39;-rgb&#39;</span><span class="p">,</span> <span class="s1">&#39;--output_rgb_lut&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;Output sunburst_RGBs.csv if flag provided (for Allen brain atlas coloring)&#39;</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="s1">&#39;store_true&#39;</span><span class="p">)</span>

_modules/unravel/cluster_stats/prism.html

@@ -406,7 +406,7 @@ <h1>Source code for unravel.cluster_stats.prism</h1><div class="highlight"><pre>
 <a class="viewcode-back" href="../../../unravel/cluster_stats/prism.html#unravel.cluster_stats.prism.parse_args">[docs]</a>
 <span class="k">def</span> <span class="nf">parse_args</span><span class="p">():</span>
     <span class="n">parser</span> <span class="o">=</span> <span class="n">argparse</span><span class="o">.</span><span class="n">ArgumentParser</span><span class="p">(</span><span class="n">formatter_class</span><span class="o">=</span><span class="n">SuppressMetavar</span><span class="p">)</span>
-    <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">&#39;-ids&#39;</span><span class="p">,</span> <span class="s1">&#39;--valid_cluster_ids&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;Space-separated list of valid cluster IDs to include in the summary.&#39;</span><span class="p">,</span> <span class="n">nargs</span><span class="o">=</span><span class="s1">&#39;+&#39;</span><span class="p">,</span> <span class="nb">type</span><span class="o">=</span><span class="nb">int</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="n">SM</span><span class="p">)</span>
+    <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">&#39;-ids&#39;</span><span class="p">,</span> <span class="s1">&#39;--valid_cluster_ids&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;Space-separated list of valid cluster IDs to include in the summary.&#39;</span><span class="p">,</span> <span class="n">nargs</span><span class="o">=</span><span class="s1">&#39;*&#39;</span><span class="p">,</span> <span class="nb">type</span><span class="o">=</span><span class="nb">int</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="n">SM</span><span class="p">)</span>
     <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">&#39;-p&#39;</span><span class="p">,</span> <span class="s1">&#39;--path&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;Path to the directory containing the CSV files from ``cstats_validation`` or ``cstats_mean_IF``. Default: current directory&#39;</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="n">SM</span><span class="p">)</span>
     <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">&#39;-v&#39;</span><span class="p">,</span> <span class="s1">&#39;--verbose&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;Increase verbosity. Default: False&#39;</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="s1">&#39;store_true&#39;</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
     <span class="n">parser</span><span class="o">.</span><span class="n">epilog</span> <span class="o">=</span> <span class="vm">__doc__</span>

_modules/unravel/cluster_stats/summary.html

@@ -427,7 +427,7 @@ <h1>Source code for unravel.cluster_stats.summary</h1><div class="highlight"><pr
     <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">&#39;-sk&#39;</span><span class="p">,</span> <span class="s1">&#39;--sample_key&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;path/sample_key.csv w/ directory names and conditions (for utils_prepend)&#39;</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="n">SM</span><span class="p">)</span>
 
     <span class="c1"># cstats --groups &lt;group1&gt; &lt;group2&gt;</span>
-    <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">&#39;--groups&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;List of group prefixes. 2 groups --&gt; t-test. &gt;2 --&gt; Tukey</span><span class="se">\&#39;</span><span class="s1">s tests (The first 2 groups reflect the main comparison for validation rates; for cstats)&#39;</span><span class="p">,</span>  <span class="n">nargs</span><span class="o">=</span><span class="s1">&#39;+&#39;</span><span class="p">)</span>
+    <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">&#39;--groups&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;List of group prefixes. 2 groups --&gt; t-test. &gt;2 --&gt; Tukey</span><span class="se">\&#39;</span><span class="s1">s tests (The first 2 groups reflect the main comparison for validation rates; for cstats)&#39;</span><span class="p">,</span>  <span class="n">nargs</span><span class="o">=</span><span class="s1">&#39;*&#39;</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="n">SM</span><span class="p">)</span>
     <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">&#39;-cp&#39;</span><span class="p">,</span> <span class="s1">&#39;--condition_prefixes&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;Condition prefixes to group related data (optional for cstats)&#39;</span><span class="p">,</span>  <span class="n">nargs</span><span class="o">=</span><span class="s1">&#39;*&#39;</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="n">SM</span><span class="p">)</span>
     <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">&#39;-hg&#39;</span><span class="p">,</span> <span class="s1">&#39;--higher_group&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;Specify the group that is expected to have a higher mean based on the direction of the p value map&#39;</span><span class="p">,</span> <span class="n">required</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
 

_modules/unravel/core/argparse_utils.html

@@ -386,10 +386,15 @@ <h1>Source code for unravel.core.argparse_utils</h1><div class="highlight"><pre>
 <span class="sd">            - __init__: Initializes the custom action and sets the metavar to an empty string or tuple.</span>
 <span class="sd">            - __call__: Sets the argument values in the namespace, handling both single and multiple values.</span>
 
-<span class="sd">Notes:</span>
+<span class="sd">Note:</span>
 <span class="sd">    - This script relies on the argparse library for command-line argument parsing.</span>
 <span class="sd">    - The SuppressMetavar class is designed to improve the readability of help messages by suppressing</span>
 <span class="sd">      metavar display and customizing the formatting of epilog text.</span>
+<span class="sd">    - nargs=&#39;``+``&#39; with action=SM: This combination causes issues when the terminal window is small. </span>
+<span class="sd">    - Use nargs=&#39;``*``&#39; with action=SM if zero arguments are acceptable, or drop action=SM to avoid conflicts.</span>
+<span class="sd">    - Difference:</span>
+<span class="sd">    - nargs=&#39;``+``&#39; requires at least one argument.</span>
+<span class="sd">    - nargs=&#39;``*``&#39; allows zero or more arguments, providing more flexibility but no guarantee of input.</span>
 <span class="sd">&quot;&quot;&quot;</span>
 
 <span class="kn">import</span> <span class="nn">argparse</span>

_modules/unravel/core/argparse_utils_rich.html

@@ -387,9 +387,14 @@ <h1>Source code for unravel.core.argparse_utils_rich</h1><div class="highlight">
 <span class="sd">            - __init__: Initializes the custom action and sets the metavar to an empty string or tuple.</span>
 <span class="sd">            - __call__: Sets the argument values in the namespace, handling both single and multiple values.</span>
 
-<span class="sd">Notes:</span>
+<span class="sd">Note:</span>
 <span class="sd">    - This script relies on the rich and argparse libraries for enhanced help message formatting.</span>
 <span class="sd">    - The SuppressMetavar class is specifically designed to work with Rich&#39;s RichHelpFormatter for styled terminal output.</span>
+<span class="sd">    - nargs=&#39;``+``&#39; with action=SM: This combination causes issues when the terminal window is small. </span>
+<span class="sd">    - Use nargs=&#39;``*``&#39; with action=SM if zero arguments are acceptable, or drop action=SM to avoid conflicts.</span>
+<span class="sd">    - Difference:</span>
+<span class="sd">    - nargs=&#39;``+``&#39; requires at least one argument.</span>
+<span class="sd">    - nargs=&#39;``*``&#39; allows zero or more arguments, providing more flexibility but no guarantee of input.</span>
 <span class="sd">&quot;&quot;&quot;</span>
 
 <span class="kn">import</span> <span class="nn">argparse</span>