Changeset 4110


Ignore:
Timestamp:
Sep 28, 2021, 1:35:15 AM (21 months ago)
Author:
Peter
Message:

merge release 0.19 into trunk

Location:
trunk
Files:
6 edited

Legend:

Unmodified
Added
Removed

  • trunk

  • trunk/NEWS

    r4097 r4110  
    1111yat 0.19.x series from http://dev.thep.lu.se/yat/svn/branches/0.19-stable
    1212
    13 version 0.19 (released NOT YET)
     13version 0.19 (released 27 September 2021)
    1414  - classifier::Target::labels(void) is now const (issue #972)
    1515  - statistics::correlation now takes a const Matrix& instead of Matrix

  • trunk/README.developer

    r3999 r4110  
    44
    55We follow the coding style described in
    6 [http://cbbp.thep.lu.se/~jari/documents/c++_coding_guidelines/index.html C++ coding guidelines]
    7 [http://cbbp.thep.lu.se/~jari/documents/c++_coding_guidelines/c++_coding_guidelines.pdf pdf]
    8 [http://cbbp.thep.lu.se/~jari/documents/c++_coding_guidelines/c++_coding_guidelines.ps postscript]
     6[https://cbbp.thep.lu.se/~jari/documents/c++_coding_guidelines/index.html C++ coding guidelines]
     7[https://cbbp.thep.lu.se/~jari/documents/c++_coding_guidelines/c++_coding_guidelines.pdf pdf]
     8[https://cbbp.thep.lu.se/~jari/documents/c++_coding_guidelines/c++_coding_guidelines.ps postscript]
    99with the additions described here.
    1010
    … …  
    1414(`make` and `make check`) when someone makes a clean checkout. There
    1515is a short introduction to subversion and its usage available as
    16 [http://cbbp.thep.lu.se/~jari/documents/subversion_guidelines/index.html Subversion guidelines].
     16[https://cbbp.thep.lu.se/~jari/documents/subversion_guidelines/index.html Subversion guidelines].
    1717We follow these guidelines.
    1818
    … …  
    3535
    3636The GSL documentation describes how
    37 [http://www.gnu.org/software/gsl/manual/html_node/Error-Handling.html GSL error handling]
    38 works. The GSL library follows the thread-safe
     37[http://www.gnu.org/software/gsl/manual/html_node/Error-Handling.html
     38GSL error handling] works. The GSL library follows the thread-safe
    3939error reporting conventions of the posix Threads library. That is,
    4040functions return a non-zero error code to indicate an error. In most
    … …  
    4242returns. If GSL errors occur in constructors yat handles them
    4343accordingly. If GSL reports errors that cannot be resolved by yat a
    44 [http://cbbp.thep.lu.se/~jari/documents/yat/classtheplu_1_1yat_1_1utility_1_1GSL__error.html GSL_error]
    45 exception will be thrown. However, the default behaviour of
    46 GSL library is to call abort() when unrecoverable errors occur and
     44[https://cbbp.thep.lu.se/~jari/documents/yat/classtheplu_1_1yat_1_1utility_1_1GSL__error.html
     45GSL_error] exception will be thrown. However, the default behaviour of
     46GSL library is to call abort() when unrecoverable errors occur, which
    4747puts the yat (and any other) GSL error treatment out of play. For
    48 production environments, yat and GSL users should turn off the default
    49 GSL error treatment by calling gsl_set_error_handler_off(), but also
    50 when yat's GSL error treatment is preferred.
     48production environments or when yat's GSL error treatment is
     49preferred, yat and GSL users should turn off the default GSL error
     50treatment either by calling gsl_set_error_handler_off() or by passing
     51[https://cbbp.thep.lu.se/~jari/documents/yat/namespacetheplu_1_1yat_1_1utility.html#ac846162271bf37e091b4692ba865b178
     52yat::utility::gsl_error_handler] to gsl_set_error.
    5153
    5254When new GSL functionality is introduced to yat, it is the
    5355responsibility of the programmer to make sure that GSL errors are
    5456treated properly. Proper GSL error treatment is very important in
    55 cases when yat users turn off the default GSL error handler since:
    56 
    57 yat aims at treating GSL errors appropriately in an
    58 [http://www.gotw.ca/gotw/008.htm exception safe and neutral]
    59 way but there is still some work to do before we do exceptions in a neutral way.
     57cases when yat users turn off the default GSL error handler since yat
     58aims at treating GSL errors appropriately in an
     59[http://www.gotw.ca/gotw/008.htm exception safe and neutral] way but
     60there is still some work to do before we do exceptions in a neutral
     61way.
    6062
    6163=== Samtools ===
    … …  
    307309
    308310   a) In section 'yat latest release' update command to
    309       'svn checkout http://dev.thep.lu.se/yat/svn/tags/A.B.C yat-A.B.C
     311      'svn checkout https://dev.thep.lu.se/yat/svn/tags/A.B.C yat-A.B.C
    310312      and link to
    311313      '[source:tags/A.B.C/NEWS NEWS]'
    … …  
    313315
    314316   b) In section 'yat stable' update command to
    315       'svn checkout http://dev.thep.lu.se/yat/svn/branches/A.B-stable yat-A.B.x
     317      'svn checkout https://dev.thep.lu.se/yat/svn/branches/A.B-stable yat-A.B.x
    316318      and link to
    317319      '[source:branches/A.B-stable/NEWS NEWS]'
    … …  
    449451Copyright (C) 2004 Jari Häkkinen
    450452Copyright (C) 2006, 2007, 2008, 2009 Jari Häkkinen, Peter Johansson
    451 Copyright (C) 2010, 2011, 2012, 2013, 2014, 2015, 2016, 2020 Peter Johansson
     453Copyright (C) 2010, 2011, 2012, 2013, 2014, 2015, 2016, 2020, 2021 Peter Johansson
    452454
    453455This file is part of yat library, http://dev.thep.lu.se/yat

  • trunk/m4/version.m4

    r4091 r4110  
    9797# yat-0.18   15:0:0
    9898# yat-0.18.1 15:1:0
     99# yat-0.19   16:0:0
    99100#
    100101# *Accidently, the libtool number was not updated for yat 0.5

  • trunk/test/kendall.cc

    r4089 r4110  
    5858    test_copy(suite);
    5959    test_p(suite);
    60     //test_p_exact(suite);
    61     //test_p_with_ties(suite);
     60    test_p_exact(suite);
     61    test_p_with_ties(suite);
    6262
    6363    try {
    64       //test_score(suite);
     64      test_score(suite);
    6565    }
    6666    catch (std::exception& e) {
    … …  
    6969
    7070    try {
    71       //test_score_with_ties(suite);
     71      test_score_with_ties(suite);
    7272    }
    7373    catch (std::exception& e) {
    … …  
    171171  double p = kendall.p_value();
    172172  suite.out() << "p: " << p << "\n";
    173   if (p > 0.0001) {
    174     suite.err() << "error: too large p\n";
    175     suite.add(false);
    176   }
    177   if (p < 0.00001) {
    178     suite.err() << "error: too small p\n";
     173  if (p < 0.00001 || p > 0.0001) {
     174    suite.err() << "error: p not within [0.00001, 0.0001]\n";
    179175    suite.add(false);
    180176  }

  • trunk/yat/statistics/Kendall.cc

    r4089 r4110  
    4141#include <vector>
    4242
    43 
    44 #include <iostream> // debug
    4543namespace theplu {
    4644namespace yat {
    … …  
    264262                   x_ties_);
    265263
     264    std::vector<double> vec(utility::pair_second_iterator(data.begin()),
     265                            utility::pair_second_iterator(data.end()));
     266    std::sort(vec.begin(), vec.end());
     267    calculate_ties(vec.begin(), vec.end(), y_ties_);
     268
    266269    /*
    267270                y1 < y2  y2 == y2  y2 > y2
    … …  
    390393      v2 = sum t(t-1)(t-2) \sum u(u-1)(u-2) / (9n(n-1)(n-2))
    391394
    392       where t is number of equal values in group i and similarly u for
     395      where t is number of equal x values in group i and similarly u for
    393396      y.
    394397    */
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