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• rc7 -- The Matthieu Authier Edition

  This release candidate features lots of bugfixes that grew out of some problems reported by matthieu Authier. Thanks, Matthieu! Here are the highlights: 05/07/2008 Added a check to pyp_graphics/draw_pedigree() to catch empty gtitles, which cause dot to crash. If the gtitle is empty then it is set equal to the 'pedname' attribute of the NewPedigree object. 05/07/2008 Fixed pyp_network/get_node_betweenness() to use the correct betweenness function from NetworkX. 05/07/2008 Made lots of changes to pyp_graphics/draw_pedigree() to get it working with pydot 1.0.2. I believe that it now works again in that it will draw pedigrees, but they're not looking great. This area will receive attention for PyPedal 2.0.1. 05/07/2008 Updated the example program new_renumbering.py to use the correct syntax to load a pedigree. 05/07/2008 Added messages to the example program new_options.py to indicate which pedigree load steps are supposed to fail. 05/07/2008 Removed some casts that were unnecessary from pyp_jbc/new_draw_colored_pedigree(). 05/07/2008 inbreeding(), inbreeding_tabular(), and inbreeding_vanraden() in pyp_nrm now all correctly initialize reldict to include all fields. The r_nonzero_sum field had been left out of the intialization. 05/07/2008 Added userField handling to the printme() and stringme() methods of pyp_newclasses/NewAnimal. 05/07/2008 Corrected pedigree format string in new_ids.ini. 05/07/2008 Checked all example programs by hand to make sure that they're consistent with the current API and feature-set to avoid the kinds of problems that Matthieu (and probably others) have had with the example being very out-of-date. 05/07/2008 The nrm attribute of pyp_newclasses/NewAMatrix if now set to False on instantiation so that the instance can easily be queried for the existence of an NRM. 05/07/2009 Added a new example program, new_decompose.py, to demonstrate the use of the routines in pyp_nrm for decomposing A such that A = TDT', as well as the code for directly forming A-inverse with or without inbreeding. 05/06/2008 Fixed several functions in pyp_nrm (a_decompose, form_d_nof, a_inverse_dnf, and a_inverse_df) so that they're using the correct Numpy dtypes. 05/06/2008 Fixed several functions in pyp_nrm (a_decompose, form_d_nof, a_inverse_dnf, and a_inverse_df) that were still trying to use the 'num_recs' attribute of the pedigree metadata, which was renamed to 'num_records' quite a while back, but which was not noted in This File. 05/06/2008 Fixed a spelling error in the psyco import blocks in pyp_graphics, pyp_metrics, and pyp_networks, and pyp_nrm. 05/06/2008 Updated examples/new_amatrix.py to use Numpy instead of Numarray, as well as to remove calls to deprecated methods. Thanks to Matthieu Authier for reporting this and other important bugs. 05/06/2008 Removed an extra space from the metadata output that's been bugging me for a Long Time Now. 05/06/2008 Added import block for psyco in pyp_nrm.

  posted by wintermind 551 days ago

• File released: /pypedal-2.0.0/2.0.0rc7/PyPedal-2.0.0rc7.zip

  posted 551 days ago

• File released: /pypedal-2.0.0/2.0.0rc7/PyPedal-2.0.0rc7.tar.gz

  posted 551 days ago

• File released: /pypedal-2.0.0/2.0.0rc7/PyPedal-2.0.0rc7-py2.5.egg

  posted 551 days ago

• File released: /pypedal-2.0.0/2.0.0rc7/PyPedal-2.0.0rc7-py2.4.egg

  posted 551 days ago

• pypedal-2.0.0 2.0.0rc7 file released: PyPedal-2.0.0rc7.zip

  05/07/2008 Added a check to pyp_graphics/draw_pedigree() to catch empty gtitles, which cause dot to crash. If the gtitle is empty then it is set equal to the 'pedname' attribute of the NewPedigree object. 05/07/2008 Fixed pyp_network/get_node_betweenness() to use the correct betweenness function from NetworkX. 05/07/2008 Made lots of changes to pyp_graphics/draw_pedigree() to get it working with pydot 1.0.2. I believe that it now works again in that it will draw pedigrees, but they're not looking great. This area will receive attention for PyPedal 2.0.1. 05/07/2008 Updated the example program new_renumbering.py to use the correct syntax to load a pedigree. 05/07/2008 Added messages to the example program new_options.py to indicate which pedigree load steps are supposed to fail. 05/07/2008 Removed some casts that were unnecessary from pyp_jbc/new_draw_colored_pedigree(). 05/07/2008 inbreeding(), inbreeding_tabular(), and inbreeding_vanraden() in pyp_nrm now all correctly initialize reldict to include all fields. The r_nonzero_sum field had been left out of the intialization. 05/07/2008 Added userField handling to the printme() and stringme() methods of pyp_newclasses/NewAnimal. 05/07/2008 Corrected pedigree format string in new_ids.ini. 05/07/2008 Checked all example programs by hand to make sure that they're consistent with the current API and feature-set to avoid the kinds of problems that Matthieu (and probably others) have had with the example being very out-of-date. 05/07/2008 The nrm attribute of pyp_newclasses/NewAMatrix if now set to False on instantiation so that the instance can easily be queried for the existence of an NRM. 05/07/2009 Added a new example program, new_decompose.py, to demonstrate the use of the routines in pyp_nrm for decomposing A such that A = TDT', as well as the code for directly forming A-inverse with or without inbreeding. 05/06/2008 Fixed several functions in pyp_nrm (a_decompose, form_d_nof, a_inverse_dnf, and a_inverse_df) so that they're using the correct Numpy dtypes. 05/06/2008 Fixed several functions in pyp_nrm (a_decompose, form_d_nof, a_inverse_dnf, and a_inverse_df) that were still trying to use the 'num_recs' attribute of the pedigree metadata, which was renamed to 'num_records' quite a while back, but which was not noted in This File. 05/06/2008 Fixed a spelling error in the psyco import blocks in pyp_graphics, pyp_metrics, and pyp_networks, and pyp_nrm. 05/06/2008 Updated examples/new_amatrix.py to use Numpy instead of Numarray, as well as to remove calls to deprecated methods. Thanks to Matthieu Authier for reporting this and other important bugs. 05/06/2008 Removed an extra space from the metadata output that's been bugging me for a Long Time Now. 05/06/2008 Added import block for psyco in pyp_nrm.

  posted 551 days ago

• pypedal-2.0.0 2.0.0rc7 file released: PyPedal-2.0.0rc7.tar.gz

  05/07/2008 Added a check to pyp_graphics/draw_pedigree() to catch empty gtitles, which cause dot to crash. If the gtitle is empty then it is set equal to the 'pedname' attribute of the NewPedigree object. 05/07/2008 Fixed pyp_network/get_node_betweenness() to use the correct betweenness function from NetworkX. 05/07/2008 Made lots of changes to pyp_graphics/draw_pedigree() to get it working with pydot 1.0.2. I believe that it now works again in that it will draw pedigrees, but they're not looking great. This area will receive attention for PyPedal 2.0.1. 05/07/2008 Updated the example program new_renumbering.py to use the correct syntax to load a pedigree. 05/07/2008 Added messages to the example program new_options.py to indicate which pedigree load steps are supposed to fail. 05/07/2008 Removed some casts that were unnecessary from pyp_jbc/new_draw_colored_pedigree(). 05/07/2008 inbreeding(), inbreeding_tabular(), and inbreeding_vanraden() in pyp_nrm now all correctly initialize reldict to include all fields. The r_nonzero_sum field had been left out of the intialization. 05/07/2008 Added userField handling to the printme() and stringme() methods of pyp_newclasses/NewAnimal. 05/07/2008 Corrected pedigree format string in new_ids.ini. 05/07/2008 Checked all example programs by hand to make sure that they're consistent with the current API and feature-set to avoid the kinds of problems that Matthieu (and probably others) have had with the example being very out-of-date. 05/07/2008 The nrm attribute of pyp_newclasses/NewAMatrix if now set to False on instantiation so that the instance can easily be queried for the existence of an NRM. 05/07/2009 Added a new example program, new_decompose.py, to demonstrate the use of the routines in pyp_nrm for decomposing A such that A = TDT', as well as the code for directly forming A-inverse with or without inbreeding. 05/06/2008 Fixed several functions in pyp_nrm (a_decompose, form_d_nof, a_inverse_dnf, and a_inverse_df) so that they're using the correct Numpy dtypes. 05/06/2008 Fixed several functions in pyp_nrm (a_decompose, form_d_nof, a_inverse_dnf, and a_inverse_df) that were still trying to use the 'num_recs' attribute of the pedigree metadata, which was renamed to 'num_records' quite a while back, but which was not noted in This File. 05/06/2008 Fixed a spelling error in the psyco import blocks in pyp_graphics, pyp_metrics, and pyp_networks, and pyp_nrm. 05/06/2008 Updated examples/new_amatrix.py to use Numpy instead of Numarray, as well as to remove calls to deprecated methods. Thanks to Matthieu Authier for reporting this and other important bugs. 05/06/2008 Removed an extra space from the metadata output that's been bugging me for a Long Time Now. 05/06/2008 Added import block for psyco in pyp_nrm.

  posted 551 days ago

• pypedal-2.0.0 2.0.0rc7 file released: PyPedal-2.0.0rc7-py2.5.egg

  05/07/2008 Added a check to pyp_graphics/draw_pedigree() to catch empty gtitles, which cause dot to crash. If the gtitle is empty then it is set equal to the 'pedname' attribute of the NewPedigree object. 05/07/2008 Fixed pyp_network/get_node_betweenness() to use the correct betweenness function from NetworkX. 05/07/2008 Made lots of changes to pyp_graphics/draw_pedigree() to get it working with pydot 1.0.2. I believe that it now works again in that it will draw pedigrees, but they're not looking great. This area will receive attention for PyPedal 2.0.1. 05/07/2008 Updated the example program new_renumbering.py to use the correct syntax to load a pedigree. 05/07/2008 Added messages to the example program new_options.py to indicate which pedigree load steps are supposed to fail. 05/07/2008 Removed some casts that were unnecessary from pyp_jbc/new_draw_colored_pedigree(). 05/07/2008 inbreeding(), inbreeding_tabular(), and inbreeding_vanraden() in pyp_nrm now all correctly initialize reldict to include all fields. The r_nonzero_sum field had been left out of the intialization. 05/07/2008 Added userField handling to the printme() and stringme() methods of pyp_newclasses/NewAnimal. 05/07/2008 Corrected pedigree format string in new_ids.ini. 05/07/2008 Checked all example programs by hand to make sure that they're consistent with the current API and feature-set to avoid the kinds of problems that Matthieu (and probably others) have had with the example being very out-of-date. 05/07/2008 The nrm attribute of pyp_newclasses/NewAMatrix if now set to False on instantiation so that the instance can easily be queried for the existence of an NRM. 05/07/2009 Added a new example program, new_decompose.py, to demonstrate the use of the routines in pyp_nrm for decomposing A such that A = TDT', as well as the code for directly forming A-inverse with or without inbreeding. 05/06/2008 Fixed several functions in pyp_nrm (a_decompose, form_d_nof, a_inverse_dnf, and a_inverse_df) so that they're using the correct Numpy dtypes. 05/06/2008 Fixed several functions in pyp_nrm (a_decompose, form_d_nof, a_inverse_dnf, and a_inverse_df) that were still trying to use the 'num_recs' attribute of the pedigree metadata, which was renamed to 'num_records' quite a while back, but which was not noted in This File. 05/06/2008 Fixed a spelling error in the psyco import blocks in pyp_graphics, pyp_metrics, and pyp_networks, and pyp_nrm. 05/06/2008 Updated examples/new_amatrix.py to use Numpy instead of Numarray, as well as to remove calls to deprecated methods. Thanks to Matthieu Authier for reporting this and other important bugs. 05/06/2008 Removed an extra space from the metadata output that's been bugging me for a Long Time Now. 05/06/2008 Added import block for psyco in pyp_nrm.

  posted 551 days ago

• pypedal-2.0.0 2.0.0rc7 file released: PyPedal-2.0.0rc7-py2.4.egg

  05/07/2008 Added a check to pyp_graphics/draw_pedigree() to catch empty gtitles, which cause dot to crash. If the gtitle is empty then it is set equal to the 'pedname' attribute of the NewPedigree object. 05/07/2008 Fixed pyp_network/get_node_betweenness() to use the correct betweenness function from NetworkX. 05/07/2008 Made lots of changes to pyp_graphics/draw_pedigree() to get it working with pydot 1.0.2. I believe that it now works again in that it will draw pedigrees, but they're not looking great. This area will receive attention for PyPedal 2.0.1. 05/07/2008 Updated the example program new_renumbering.py to use the correct syntax to load a pedigree. 05/07/2008 Added messages to the example program new_options.py to indicate which pedigree load steps are supposed to fail. 05/07/2008 Removed some casts that were unnecessary from pyp_jbc/new_draw_colored_pedigree(). 05/07/2008 inbreeding(), inbreeding_tabular(), and inbreeding_vanraden() in pyp_nrm now all correctly initialize reldict to include all fields. The r_nonzero_sum field had been left out of the intialization. 05/07/2008 Added userField handling to the printme() and stringme() methods of pyp_newclasses/NewAnimal. 05/07/2008 Corrected pedigree format string in new_ids.ini. 05/07/2008 Checked all example programs by hand to make sure that they're consistent with the current API and feature-set to avoid the kinds of problems that Matthieu (and probably others) have had with the example being very out-of-date. 05/07/2008 The nrm attribute of pyp_newclasses/NewAMatrix if now set to False on instantiation so that the instance can easily be queried for the existence of an NRM. 05/07/2009 Added a new example program, new_decompose.py, to demonstrate the use of the routines in pyp_nrm for decomposing A such that A = TDT', as well as the code for directly forming A-inverse with or without inbreeding. 05/06/2008 Fixed several functions in pyp_nrm (a_decompose, form_d_nof, a_inverse_dnf, and a_inverse_df) so that they're using the correct Numpy dtypes. 05/06/2008 Fixed several functions in pyp_nrm (a_decompose, form_d_nof, a_inverse_dnf, and a_inverse_df) that were still trying to use the 'num_recs' attribute of the pedigree metadata, which was renamed to 'num_records' quite a while back, but which was not noted in This File. 05/06/2008 Fixed a spelling error in the psyco import blocks in pyp_graphics, pyp_metrics, and pyp_networks, and pyp_nrm. 05/06/2008 Updated examples/new_amatrix.py to use Numpy instead of Numarray, as well as to remove calls to deprecated methods. Thanks to Matthieu Authier for reporting this and other important bugs. 05/06/2008 Removed an extra space from the metadata output that's been bugging me for a Long Time Now. 05/06/2008 Added import block for psyco in pyp_nrm.

  posted 551 days ago

• rc6 -- Logging fix, better clean-up

  Logging now works again, ID maps are cleaned-up automatically after pedigree renumbering, and pyp_metrics/effective_founder_genomes() has some new parameters and a small bugfix.

  posted by wintermind 557 days ago