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fwdpy11.model_params is non-idiomatic #4

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molpopgen opened this issue Aug 14, 2017 · 0 comments
Closed

fwdpy11.model_params is non-idiomatic #4

molpopgen opened this issue Aug 14, 2017 · 0 comments
Milestone
0.1.3

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@molpopgen
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The implementation of these classes is quite messy and reflects a lack of understanding of Python's OO idioms and how to properly use class properties.

A do-over is needed.
molpopgen added a commit that referenced this issue Aug 14, 2017
@molpopgen
big push towards refactoring model_params. #4
9992719
molpopgen added a commit that referenced this issue Aug 14, 2017
@molpopgen
more model_params refactoring. more unit tests passing, and some bugs…
a4dcd58 
… fixed. #4
molpopgen added a commit that referenced this issue Aug 14, 2017
@molpopgen
many more model_params updates. The unit tests for this need updating…
09657fa 
… to use explicit fixtures. #4
molpopgen added a commit that referenced this issue Aug 14, 2017
@molpopgen
progress on testing SlocusParams using fixtures. #4
2dc28b7
molpopgen added a commit that referenced this issue Aug 15, 2017
@molpopgen
work on MlocusParams for #4
64ef92c
molpopgen added a commit that referenced this issue Aug 15, 2017
@molpopgen
fix getter for SlocusParams.mutrates #4
335cf56
molpopgen added a commit that referenced this issue Aug 15, 2017
@molpopgen
change aggregator property name to maintain API compatibility. #4
316654e
molpopgen added a commit that referenced this issue Aug 15, 2017
@molpopgen
oops--last change re: aggregator property name was wrong. have to cha…
46e437f 
…nge it from agg to aggregator. #4
molpopgen added a commit that referenced this issue Aug 15, 2017
@molpopgen
more defaults imposed. warnings in place. all unit tests now pass. #4
3f937f0
molpopgen added a commit that referenced this issue Aug 15, 2017
@molpopgen
cleanup collateral damage from #4
c2c9102
molpopgen added a commit that referenced this issue Aug 15, 2017
@molpopgen
docs, defaults, and tests. #4
ed05a5d
molpopgen added a commit that referenced this issue Aug 16, 2017
@molpopgen
major refactoring of fwdpy11.model_params. This resolves most of #4
1b811c3
@molpopgen molpopgen modified the milestone: 0.1.3 Aug 25, 2017
molpopgen added a commit that referenced this issue Apr 5, 2020
@molpopgen
* API changes to Sregion:
bb6e486 
  * Sregion classes now must be able to generate deviates based on
  inverse cdf functions.
  * Add new virtual fxn to return vector of dominance values.
  * Add total_dim/shape concept
* Add fwdpy11.mvDES
* Add new C++ back end to fwdpp's site_dependent_genetic_value.
  fwdpy11.Additive and fwdpy11.Multiplicative use this new
  back-end and are entirely self-contained in the .cc files.
  fwdpy11.GBR is now also self-contained in its .cc file.
  These changes allow for mutations having different
  effect sizes in different demes.
* fwdpy11::DiploidGeneticValue::calculate_gvalue now requires the
  individual's metadata, so that mass migrations via copies can get
  the correct info.  Update the fwdpp wrapper class to pull the value
  from the metadata rather than reliying on the individual's index +
  pop.diploid_metadata.
  This is the commit message #4:
* Add test_mvDES.py
* Rename "shape" attribute of fwdpy11.GammaS to "shape_parameter".
* ModelParams tests for dimensionality mismatch between
  sregion and gvalue fields in validate step.
* Add rudimentary documentation
molpopgen added a commit that referenced this issue Apr 5, 2020
@molpopgen
* API changes to Sregion:
dedd581 
  * Sregion classes now must be able to generate deviates based on
  inverse cdf functions.
  * Add new virtual fxn to return vector of dominance values.
  * Add total_dim/shape concept
* Add fwdpy11.mvDES
* Add new C++ back end to fwdpp's site_dependent_genetic_value.
  fwdpy11.Additive and fwdpy11.Multiplicative use this new
  back-end and are entirely self-contained in the .cc files.
  fwdpy11.GBR is now also self-contained in its .cc file.
  These changes allow for mutations having different
  effect sizes in different demes.
* fwdpy11::DiploidGeneticValue::calculate_gvalue now requires the
  individual's metadata, so that mass migrations via copies can get
  the correct info.  Update the fwdpp wrapper class to pull the value
  from the metadata rather than reliying on the individual's index +
  pop.diploid_metadata.
  This is the commit message #4:
* Add test_mvDES.py
* Rename "shape" attribute of fwdpy11.GammaS to "shape_parameter".
* ModelParams tests for dimensionality mismatch between
  sregion and gvalue fields in validate step.
* Add rudimentary documentation
molpopgen added a commit that referenced this issue Apr 11, 2020
@molpopgen
* API changes to Sregion:
8fa840c 
  * Sregion classes now must be able to generate deviates based on
  inverse cdf functions.
  * Add new virtual fxn to return vector of dominance values.
  * Add total_dim/shape concept
* Add fwdpy11.mvDES
* Add new C++ back end to fwdpp's site_dependent_genetic_value.
  fwdpy11.Additive and fwdpy11.Multiplicative use this new
  back-end and are entirely self-contained in the .cc files.
  fwdpy11.GBR is now also self-contained in its .cc file.
  These changes allow for mutations having different
  effect sizes in different demes.
* fwdpy11::DiploidGeneticValue::calculate_gvalue now requires the
  individual's metadata, so that mass migrations via copies can get
  the correct info.  Update the fwdpp wrapper class to pull the value
  from the metadata rather than reliying on the individual's index +
  pop.diploid_metadata.
  This is the commit message #4:
* Add test_mvDES.py
* Rename "shape" attribute of fwdpy11.GammaS to "shape_parameter".
* ModelParams tests for dimensionality mismatch between
  sregion and gvalue fields in validate step.
* Add rudimentary documentation
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