doc: update

icfree/instructor/README.md

@@ -24,7 +24,7 @@ python -m icfree.instructor
   <li><code>-suv</code>, <code>--split-upper-vol</code>: Max value for volume transfer, split instruction beyond this value.</li>
   <li><code>-slv</code>, <code>--split-lower-vol</code>: If the last split instruction transfers a volume below this value, re-integrate this volume to the penultimate split instruction.</li>
   <li><code>-soc</code>, <code>--split-outfile-components</code>: Generate one output file per component specified in this list.</li>
-  <li><code>-spt</code>, <code>--src-plate-type</code>: Specifies the plate type for each component listed (default: 'ALL:384PP_AQ_GP3').</li>
+  <li><code>-spt</code>, <code>--src-plate-type</code>: Specifies the plate type for each component listed (default: <code>ALL:384PP_AQ_GP3</code>).</li>
 </ul>
 
 ### Example

icfree/plates_generator/README.md

@@ -21,16 +21,16 @@ python -m icfree.plates_generator \
 
 ### Options
 <ul>
-  <li><code>-sdv</code>, <code>--src-plt-dead-volume</code>: dead volume to add in the source plate in nL (default: 15000)</li>
-  <li><code>-ssw</code>, <code>--src-start-well</code>: Starter well of source plate to begin filling the 384 well-plate. (default: 'A1')</li>
-  <li><code>-spd</code>, <code>--src-plt-dim</code>: Dimensions of source plate(s). (default: '16x24')</li>
-  <li><code>-spwc</code>, <code>--src-plt-well-capacity</code>: Maximum volume capacity of the source plate(s) in nL (default: 60000)</li>
+  <li><code>-sdv</code>, <code>--src-plt-dead-volume</code>: dead volume to add in the source plate in nL (default: <code>15000</code>)</li>
+  <li><code>-ssw</code>, <code>--src-start-well</code>: Starter well of source plate to begin filling the 384 well-plate. (default: <code>A1</code>)</li>
+  <li><code>-spd</code>, <code>--src-plt-dim</code>: Dimensions of source plate(s). (default: <code>16x24<c/ode>)</li>
+  <li><code>-spwc</code>, <code>--src-plt-well-capacity</code>: Maximum volume capacity of the source plate(s) in nL (default: <code>60000</code>)</li>
   <li><code>-ncc</code>, <code>--new-col-comp</code>: List of components for which the filling will start at a new column in the source plate.</li>
-  <li><code>-dsw</code>, <code>--dst-start-well</code>: Starter well of destination plate to begin filling the 384 well-plate. (default: 'A1')</li>
-  <li><code>-dpd</code>, <code>--dst-plt-dim</code>: Dimensions of destination plate(s). (default: '16x24')</li>
-  <li><code>-dpwc</code>, <code>--dst-plt-well-capacity</code>: Maximum volume capacity of the destination plate(s) in nL (default: 60000)</li>
-  <li><code>--nplicates</code>: Numbers of copies of volume sets (default: 1)</li>
-  <li><code>-ofmt</code> {csv,tsv}, --output-format {csv,tsv}: Output file format for wells file (default: csv)</li>
+  <li><code>-dsw</code>, <code>--dst-start-well</code>: Starter well of destination plate to begin filling the 384 well-plate. (default: <code>A1</code>)</li>
+  <li><code>-dpd</code>, <code>--dst-plt-dim</code>: Dimensions of destination plate(s). (default: <code>16x24</code>)</li>
+  <li><code>-dpwc</code>, <code>--dst-plt-well-capacity</code>: Maximum volume capacity of the destination plate(s) in nL (default: <code>60000</code>)</li>
+  <li><code>--nplicates</code>: Numbers of copies of volume sets (default: <code>1</code>)</li>
+  <li><code>-ofmt</code> {csv,tsv}, --output-format {csv,tsv}: Output file format for wells file (default: <code>csv</code>)</li>
 </ul>
 
 

icfree/sampler/README.md

@@ -19,10 +19,10 @@ python -m icfree.sampler <input_file.tsv>
 ## Options
 <ul>  
 <li><code>--output-file</code>: path to the output file where the generated sampling will be saved (default: print on stdout)</li>
-<li><code>--nb-samples</code>: Number of samples to generate for all factors when performing the sampling (default: 100)</li>
-<li><code>--method {lhs, random, all, auto}</code>: sampling method (default: 'auto')</li>
+<li><code>--nb-samples</code>: Number of samples to generate for all factors when performing the sampling (default: <code>100</code>)</li>
+<li><code>--method {lhs, random, all, auto}</code>: sampling method (default: <code>auto</code>)</li>
 <li><code>--nb-bins</code>: number of values for all factors when performing the sampling</li>
-<li><code>--ratios</code>: ratios for creating discrete ranges, e.g. if <code>maxValue</code> is 100 and ratios is set to <code>0 0.1 0.3 0.5 1</code>, available values will be <code>0 10 30 50 100</code>; must be a list of floats between 0.0 and 1.0 (separated by blanks)</li>
+<li><code>--ratios</code>: ratios for creating discrete ranges, e.g. if <code>maxValue</code> is <code>100</code> and ratios is set to <code>0 0.1 0.3 0.5 1</code>, available values will be $0 10 30 50 100$; must be a list of floats between $0.0$ and $1.0$ (separated by blanks)</li>
 <li><code>--seed</code>: seed to reproduce results (same seed number = same results)</li>
 </ul>