Merge branch 'laurentnoe:master' into master

.circleci/config.yml

@@ -127,7 +127,8 @@ jobs:
       - run:
           name: Install dependencies
           command: |
-            choco install mingw make --global
+            choco install -y mingw --version 12.2.0.03042023 --allow-downgrade --global
+            choco install -y make --global
       - run:
           name: Build
           command: |

COPYING

@@ -1,6 +1,3 @@
-[Authors Note : CeCILL-B is a "BSD-compatible" license]
-
----
 
 CeCILL-B FREE SOFTWARE LICENSE AGREEMENT
 

LICENSE

@@ -1,11 +1,11 @@
-Copyright (c) 2005-2016, Laurent Noe, Lille University, France
-All rights reserved.
+Copyright (c) 2005-2024, Laurent Noe, Lille University, France
 
 Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
 
 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
 
 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
 
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
 
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS “AS IS” AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

README.rst

@@ -168,7 +168,7 @@ IUPAC filtered seeds could challenge minimizer based techniques <https://www.bio
 
 First getting the alignment probabilities, out of the TAM92 model <https://pubmed.ncbi.nlm.nih.gov/1630306/>, then launching the optimization for a starting shape, and with the given probabilities::
 
-    iedera -iupac -s 5,17 -m "RYYNNNNN,RRYNNNNN" -i shuffle  -r 10000 -k -z 100 -f  `./tam92.py -p 20 -k 1 --gc 50
+    iedera -iupac -s 5,17 -m "RYYNNNNN,RRYNNNNN" -i shuffle  -r 10000 -k -z 100 -f  `./tam92.py -p 20 -k 1 --gc 50`
 
     YNYRNNnnNN,RNYRNnnNNN	0.9999961853027	0.912921	0.087079
 
@@ -242,11 +242,11 @@ on the bernoulli model provided by the file *model_bernoulli_simple_x_xp.txt* ::
 Tools provided with iedera
 ~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-The ``iedera`` binary is located in ``src/iedera``. The scripts ``plot_spaced_seeds.py`` and ``plot_mow_seeds.py`` are provided to plot:
+The ``iedera`` binary is located in ``src/iedera``. The scripts ``plot_spaced_seeds.py`` and ``plot_mow_seeds.py`` are provided to plot :
+
+*  the sensitivity for a 1st hit, on alignments generated with a (parameter-free) bernoulli model,
+*  the frequency for a 1st hit, on alignments generated with an increasing frequency of matches, for a set of given seeds.
 
-* the sensitivity for a 1st hit, on alignments generated with a (parameter-free) bernoulli model,
-* the frequency for a 1st hit, on alignments generated with an increasing frequency of matches,
-for a set of given seeds.
 
 .. image:: plot_spaced_seeds_figure.png
   :width: 800