Updated Release Notes. Fixes in docs

ReleaseNotes

@@ -1,12 +1,18 @@
 Release v3.0.0, xxx
 =======================================================
 
-  * Changes in missing topologies (coverage): the missing topos are grouped by final states (irrespective of the topology structure).
-    So the FinalStateSMS objects do not exactly match the GeneralElements from v2 (several GeneralElements can be mapped to a single FinalStateSMS)
-  * Added option for setting the erased quantum numbers for prompt particles in the parameters file. If not defined, it will not erase the attributes
+  * Extension to general SMS topologies using graphs
+  * Large code refactoring
+  * Added option for selecting which quantum numbers to be erased (see  the ignorePromptQNumbers option in parameters.ini)
+  * Changes in missing topologies (coverage): the grouping of topologies is now done only by final states and ignores the topology structure.  
+  * Added outputFormat option to parameters.ini to allow for writing the output using the old format
+  * Z2parity attribute of particles is not longer needed.
+  * Introduced centralized database dictionary to decrease redundancies in SMS matching (SMS Dictionary)
+  * Clustering of SMS for UL results replaced by a (simple) K-means clustering algorithm (see Clustering)
   * Changed the lock file mechanism for downloading the database to work with all file systems, fixes #37
   * Added CITATION.cff file, closes #38
 
+
 Release v2.3.3, Tue 19 Dec 2023
 =======================================================
 

docs/manual/source/DatabaseStructure.rst

@@ -395,6 +395,7 @@ in the simplified model (see the :ref:`discussion above <txnameFile>`),
 the reweighting factor :math:`\xi` is computed using only the widths not present
 in the grid.
 
+.. _smsDictionary:
 
 SMS Dictionary
 ^^^^^^^^^^^^^^

docs/manual/source/ReleaseUpdate.rst

@@ -38,8 +38,13 @@ New in Version 3.0.0:
 ^^^^^^^^^^^^^^^^^^^^^
 
   * **Extension to general SMS topologies** (no longer restricted to Z\ :sub:`2` symmetric topologies)
-  * Added option for selecting which quantum numbers to be erased
-  * Inclusion of analyses with searches for resonant production
+  * Large code refactoring
+  * Added option for selecting which quantum numbers to be erased (see  the :ref:`ignorePromptQNumbers<erasePrompt>`_ option in parameters.ini)
+  * Added :ref:`outputFormat <parameterFileOutputFormat>`_ option to parameters.ini to allow for writing the output using the old format 
+  * Changes in missing topologies (coverage): the grouping of topologies is now done only by final states and ignores the topology structure (see :ref:`missing topologies <finalStateSMS>`_)
+  * Z2parity attribute of particles is not longer needed
+  * Introduced centralized database dictionary to decrease redundancies in SMS matching (see :ref:`SMS Dictionary <smsDictionary>`_)
+  * Clustering of SMS for UL results replaced by a (simple) K-means clustering algorithm (see :ref:`Clustering <cluster>`_)
   * Changed the lock file mechanism for downloading the database to work with all file systems, fixes `#37 <https://github.com/SModelS/smodels/issues/37>`_
   * Added CITATION.cff file, closes `#38 <https://github.com/SModelS/smodels/issues/38>`_
 

docs/manual/source/RunningSModelS.rst

@@ -256,6 +256,10 @@ Below we give more detailed information about each entry in the parameters file.
   * **outputType** (list of outputs): use to list all the output formats to be generated.
     Available output formats are: summary, stdout, log, python, xml, slha.
 
+.. _parameterFileOutputFormat:
+
+  * **outputFormat**: use to select in which format the output should be written.  Available formats are: current (latest format) or version2 (SModelS 2.x format using bracket notation)
+
 .. _parameterFileStdoutprinter:
 
 * *stdout-printer*: options for the stdout or log printer

docs/manual/source/TheoryPredictions.rst

@@ -82,9 +82,9 @@ Note that although the particle properties of N1 and anyBSM match, their canonic
  * gluino :math:`\leftrightarrow` anyBSM
  * N1 :math:`\leftrightarrow` MET
 
-In order to fully match the gluino and anyBSM nodes their daughters must also be compared (*Step 2*). Since their daughters (q,N1) and (MET,jet) are final state nodes (undecayed) the comparison procedure stops at this level and results in the following matches:
+In order to fully match the gluino and anyBSM nodes their daughters must also be compared (*Step 2*). Since their daughters (g,N1) and (MET,jet) are final state nodes (undecayed) the comparison procedure stops at this level and results in the following matches:
 
- * q :math:`\leftrightarrow` jet
+ * g :math:`\leftrightarrow` jet
  * N1 :math:`\leftrightarrow` MET
 
 .. _matchB:
@@ -242,4 +242,4 @@ The number of clusters is chosen as the smallest possible so all the |SMS| belon
 
 
 .. [#f3] The comparison of the |particle| properties is done only for the properties which have been defined for both |particles|. For instance, it is often the case that the spin property is not defined for particles appearing in the database topologies, so this property will be ignored when comparing particles from the model topology and to the ones from the database topology.
-.. [#f4] In order to comparing two sets of daughters (mapped to a bipartite graph) irrespective of their ordering, a `maximal matching algorithm <https://en.wikipedia.org/wiki/Hopcroft%E2%80%93Karp_algorithm>`_ is used. Note that it is possible that the matching is not unique (i.e. :math:`A \leftrightarrow a, B \leftrightarrow b` and :math:`A \leftrightarrow b, B \leftrightarrow a`) and in this case the matching procedure is not deterministic.
+.. [#f4] In order to compare two sets of daughters (mapped to a bipartite graph) irrespective of their ordering, a `maximal matching algorithm <https://en.wikipedia.org/wiki/Hopcroft%E2%80%93Karp_algorithm>`_ is used. Note that it is possible that the matching is not unique (i.e. :math:`A \leftrightarrow a, B \leftrightarrow b` and :math:`A \leftrightarrow b, B \leftrightarrow a`) and in this case the matching procedure is not deterministic.