Merge pull request #214 from h-2/release_prep

[doc] prep for release

INFO

@@ -1,12 +1,12 @@
 Name: lambda
-Author: Hannes Hauswedell <[email protected]>
-Maintainer: Hannes Hauswedell <[email protected]>
+Author: Hannes Hauswedell <[email protected]>
+Maintainer: Hannes Hauswedell <[email protected]>
 License: AGPL v3
-Copyright: 2013-2020, Hannes Hauswedell; 2016-2020 Knut Reinert, FU-Berlin
+Copyright: 2013-2023, Hannes Hauswedell; 2016-2023 Knut Reinert, FU-Berlin
 Status: under development
-Description: Lambda is a biological sequence aligner optimized for many
-query sequences and searches in protein space. It is highly compatible
-to BLAST (bitscore and e-value statistics, tab separated and verbose
-output formats), much faster than BLAST and many other comparable tools
-and supports many other input and output formats, including standards-
-conformant .sam and .bam and many compression types
+Description: Lambda is a biological sequence aligner for searches
+in protein, nucleotide or bisulfite-treated databases. It is highly
+compatible to BLAST (bitscore and e-value statistics, tab separated and
+verbose output formats), much faster than BLAST and many other comparable
+tools and supports many other input and output formats, including
+standards-conforming .sam and .bam and many compression types.

LICENSE.rst

@@ -2,8 +2,8 @@ lambda copyright
 ================
 ::
 
-  Copyright (c) 2013-2020, Hannes Hauswedell
-  Copyright (c) 2019-2020, Sara Hetzel
+  Copyright (c) 2013-2023, Hannes Hauswedell
+  Copyright (c) 2019-2023, Sara Hetzel
   All rights reserved.
 
 Lambda is *free software*: you can redistribute it and/or modify
@@ -33,27 +33,12 @@ submodules
 ==========
 
 When Lambda is distributed in binary form or when Lambda is distributed
-in source form including its submodules the following additional
-license terms apply.
-Note that these submodules might themselves include further submodules, please see the respective license files.
-
-SeqAn copyright
----------------
-::
-
-  Copyright (c) 2006-2020, Knut Reinert & Freie Universität Berlin
-
-SeqAn is published under the terms of the three clause BSD license as can
-be found in the file `submodules/seqan/LICENSE <./submodules/seqan/LICENSE>`__
-or printed by the parameter ``--copyright``.
-
-SeqAn3 copyright
----------------
-::
-
-  Copyright (c) 2006-2020, Knut Reinert & Freie Universität Berlin
-  Copyright (c) 2016-2020, Knut Reinert & MPI für molekulare Genetik
-
-SeqAn3 is published under the terms of the three clause BSD license as can
-be found in the file `submodules/seqan3/LICENSE.md <./submodules/seqan3/LICENSE.md>`__
-or printed by the parameter ``--copyright``.
+in source form including its submodules, additional license terms apply.
+See the respective files in the submodules folder:
+
+* submodules/biocpp-core/LICENSE.md
+* submodules/biocpp-io/LICENSE
+* submodules/cereal/LICENSE
+* submodules/fmindex-collection/TODO
+* submodules/seqan/LICENSE
+* submodules/sharg-parser/LICENSE.md

README.rst

@@ -1,11 +1,11 @@
 Lambda: the Local Aligner for Massive Biological DatA
 -----------------------------------------------------
 
-Lambda is a local aligner optimized for many query sequences and searches in protein space. It...
+Lambda is a versatile local aligner that can perform protein, nucleotide and bisulfite searches. It...
 
-* is highly compatible to BLAST (bitscore and e-value statistics, tab separated and verbose output formats)
+* is highly compatible to BLAST (bit-score and e-value statistics, tab separated and verbose output formats)
 * is much faster than BLAST and many other comparable tools
-* supports many other input and output formats, including standards-conformant ``.sam`` and ``.bam`` and many compression types
+* supports many other input and output formats, including standards-conforming ``.sam`` and ``.bam`` and many compression types
 * has special features for species annotation and taxonomic analysis
 * is well-documented and easy to use (e.g. provides progress-bars and memory usage estimates)
 
@@ -39,32 +39,32 @@ Before you can search, you need to have an index. You can
 
 ::
 
-    % bin/lambda2 mkindexp -d db.fasta
+    % bin/lambda3 mkindexp -d db.fasta
 
 *(in case you want to create a nucleotide index, instead use ``mkindexn``)*
 
 After that running Lambda is as simple as
 
 ::
 
-    % bin/lambda2 searchp -q query.fasta -i db.fasta.lambda
+    % bin/lambda3 searchp -q query.fasta -i db.fasta.lambda
 
 *(in case you want to perform a nucleotide search, instead use ``searchn``)*
 
 For a list of options, see the help pages:
 
 ::
 
-    % bin/lambda2 --help
-    % bin/lambda2 COMMAND --help
+    % bin/lambda3 --help
+    % bin/lambda3 COMMAND --help
 
 Advanced options are available via ``--full-help`` or the man pages, and more documentation is available
 in the `wiki <https://github.com/seqan/lambda/wiki>`__.
 
 authorship and copyright
 ------------------------
 
-Lambda is being developed by `Hannes Hauswedell <mailto:[email protected]>`__, but it incorporates a lot of work from other members of the `SeqAn project <http://www.seqan.de>`__.
+Lambda is developed by `Hannes Hauswedell <mailto:h2 (æð) fsfe.org>`__ and `Sara Hetzel <mailto:hetzel (æð) molgen.mpg.de>`__ .
 
 +------------------------------------------------------------------------------------------------------------------+--------------------------------------------------------------------------------------------------------------------+
 |  **Please always cite the publication, also if using Lambda in comparisons and pipelines**                                                                                                                                            |
@@ -92,8 +92,8 @@ feedback & updates
 |    :width: 76px                                                                                                   |                                                                                                                    |
 +-------------------------------------------------------------------------------------------------------------------+--------------------------------------------------------------------------------------------------------------------+
 | .. image:: https://raw.githubusercontent.com/seqan/lambda/gh-pages/images_readme/appbar.email.png                 | To stay up to date via e-mail, please subscribe to the                                                             |
-|    :alt: Newsletter                                                                                               | `newsletter <https://lists.fu-berlin.de/listinfo/lambda-users>`__. There is on average less than one e-mail        |
-|    :target: https://lists.fu-berlin.de/listinfo/lambda-users                                                      | per month.                                                                                                         |
+|    :alt: Newsletter                                                                                               | `newsletter <https://lists.fu-berlin.de/listinfo/lambda-users>`__. There is very low traffic!                      |
+|    :target: https://lists.fu-berlin.de/listinfo/lambda-users                                                      |                                                                                                                    |
 |    :width: 76px                                                                                                   |                                                                                                                    |
 +-------------------------------------------------------------------------------------------------------------------+--------------------------------------------------------------------------------------------------------------------+
 | .. image:: https://raw.githubusercontent.com/seqan/lambda/gh-pages/images_readme/appbar.social.twitter.png        | You can also follow SeqAn on `twitter <https://twitter.com/SeqAnLib>`__ to receive updates on Lambda.              |