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Version/0.7.0 #11

Merged
merged 60 commits into from
Jul 23, 2024
Merged

Version/0.7.0 #11

merged 60 commits into from
Jul 23, 2024

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blakeaw
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@blakeaw blakeaw commented Jul 23, 2024

Prep new release of version 0.7.0

blakeaw added 30 commits June 29, 2020 22:43
@blakeaw
Added the continue_gao function to each of the Python, Numba, and Cyt…
5a6873f 
…hon core implementations.
@blakeaw
Added the continue_run function to the GAO class as well as the total…
8b49906 
…_generations property.
@blakeaw
Added the final_population and final_population_fitness properties to…
11b3fdb 
… the GAO class.
@blakeaw
Added the double enzymatic PySB model as an example.
00c672d
@blakeaw
Module with benchmark functions.
8483035
@blakeaw
New examples using benchmark functions.
135546a
@blakeaw
Additional examples for 3point line and pysb double enzymatic model.
a298566
@blakeaw
Renamed benchmark_functions to benchmarks
4a821ef
@blakeaw
Finished updating the himmelblau function docstring.
55c0f8c
@blakeaw
Updated the examples that use benchmark functions defined in galibrat…
b7e13f8 
…e.benchmark to import the functions from that module. Also applied Black formatting.
@blakeaw
Applied Black formatting to gao.py
6c03f76
@blakeaw
Merge branch 'continue_gao' into version/0.7.0
9abf809
@blakeaw
Merge branch 'benchmark_functions' into version/0.7.0
32fd1c6
@blakeaw
Merge branch 'more_examples' into version/0.7.0
f69d8f9
@blakeaw
Updated the 3 point line and pysb double enzymatic model examples.
6eb7976
@blakeaw
Renamed the GAO.continue_run function to GAO.resume and made the gene…
9ee5835 
…rations parameter optional.
@blakeaw
New version of the sphere example that calls the resume function.
16c39de
@blakeaw
Update the CHANGELOG
31ed232
@blakeaw
Incremented the minor version number in setup.py
29ce814
@blakeaw
Fixes for Issues 7 and 8.
1c828fe
@blakeaw
Added the julia version module. Currently it is just a copy of the nu…
83c42ce 
…mba one but will be updated later.
@blakeaw
Starting defining the Julia versions of compiled functions for import…
57a8dc8 
… with PyJulia.
@blakeaw
Increased the population size and number of generations.
79908fc
@blakeaw
Finished porting the compiled functions to their Julia versions and u…
18e4ea9 
…pdated the run_gao_julia module to use them as well as updated the importing and Julia initializaiton.
@blakeaw
Added in check and import for Julia enhanced version.
aa74c82
@blakeaw
New notebook that redoes scaling analysis with the new Julia version …
46eb378 
…included.
@blakeaw
Minor test changes.
7081382
@blakeaw
Adjusted the population size in the sphere example.
4b45675
@blakeaw
Updated the setup.py to use setuptools instead of distutils. Also upd…
71133d4 
…ated the setup so that should include Cython and Julia files with the package when it installs.
@blakeaw
julia-backend branch changes.
c084b1d
blakeaw added 27 commits August 31, 2023 15:11
@blakeaw
Removed the lines where it was setting GAO to use run_gao_py.
bdfaea0
@blakeaw
Tests for the gao module and GAO class, as well as tests for integrat…
16e589b 
…ion of each backend version with python, Cython, Numba, and Julia.
@blakeaw
Renamed the pysb_utils subpackage to just be pysb.
8633de3
@blakeaw
fixed an error with trying to directly call pysb.simulator.ScipyOdeSi…
a806c48 
…mulator.
@blakeaw
fixed an error with the try except exception type in the GaoIt isub: …
a475975 
…added the AttributeError
@blakeaw
Started with some initial tests of the pysb subpackage and the GaoIt …
a11a833 
…class.
@blakeaw
Additional tests of the GaoIt class.
5202067
@blakeaw
Fixed a couple of bugs that popped out when writing tests for the Gao…
e6976ac 
…It class.
@blakeaw
Added some unit tests for run_gao_numba and run_gao_julia functions.
088dddd
@blakeaw
Updated local variable gao in functions to gao_loc so as not to clash…
42a0004 
… with the import of gao module.
@blakeaw
Added new functions to load the different versions of run_gao module …
6541bb4 
…(Cython, Numba, etc.).
@blakeaw
Sets the run_gao_numba as the backend using new _set_run_gao_numba fu…
bb12771 
…nction in galibrate/gao module.
@blakeaw
New integration test cases to call the run_gao and continue_gao funct…
97f8934 
…ions for the Numba, Julia, and Cython backend versions.
@blakeaw
Changed calls to np.int to np.int64 to get rid of that Deprecation wa…
cd7cbb6 
…rning.
@blakeaw
Changed dtype=np.int64 to dtype=np.int_ to fix compiler error for mis…
9eec529 
…matching types of int_t verus long long.
@blakeaw
Updated the soure and test code with Black formatting.
c1f65cc
@blakeaw
Added a new notebook that does profiling with cProfile.
a694994
@blakeaw
Removed the old version of notebook 01.
2eca14d
@blakeaw
Added a text file with the coverage report output.
cce9b8c
@blakeaw
Updates to the README and some additions to the CHANGELOG.
20a374d
@blakeaw
Added a separate CITATION.cff file and removed the Citing section fro…
b3bb5ee 
…m the README.
@blakeaw
Added a contributing file.
92c0dc8
@blakeaw
Added a couple more badges to the README along with a Testing subsect…
9885612 
…ion. Updated the PR contribution steps slightly in CONTRIBUTING.
@blakeaw
Forgot to save some changes with the Testing subsection.
b9e8b83
@blakeaw
Added a __version__ specifier variable.
cfbf760
@blakeaw
Added a Julia subsection to the Recommended additional software in th…
2d7c577 
…e README. Went ahead and added the Conda meta.yaml file.
@blakeaw
Quick check and update of CHANGELOG for 0.7.0.
63cf0af
@blakeaw blakeaw merged commit 0d8d1b4 into master Jul 23, 2024
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@blakeaw