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Improve C++ speed, remove batch requirement #187

Merged
merged 4 commits into from Sep 29, 2020
Merged

Improve C++ speed, remove batch requirement #187

merged 4 commits into from Sep 29, 2020

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alanocallaghan
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@codecov-commenter
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codecov-commenter commented Jul 7, 2020 •
edited

Codecov Report

Merging #187 into master will decrease coverage by 0.00%.
The diff coverage is 83.33%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master     #187      +/-   ##
==========================================
- Coverage   91.16%   91.15%   -0.01%     
==========================================
  Files          45       45              
  Lines        3915     3925      +10     
==========================================
+ Hits         3569     3578       +9     
- Misses        346      347       +1
Impacted Files Coverage Δ
src/DenoisedRates.h 100.00% <ø> (ø)
src/updates.h 90.00% <ø> (ø)
src/updatesNoSpikes.h 100.00% <ø> (ø)
src/updatesReg.h 96.59% <ø> (ø)
src/updatesRegNoSpikes.h 100.00% <ø> (ø)
src/utils.h 82.31% <82.09%> (ø)
R/utils_MCMC.R 89.22% <90.90%> (-0.16%) ⬇️
R/BASiCS_MCMC.R 100.00% <100.00%> (ø)
src/MCMC.h 98.92% <100.00%> (ø)
src/MCMCNoSpikes.h 98.82% <100.00%> (ø)
... and 3 more

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@alanocallaghan
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@catavallejos - what do you think about switching to github actions (failing build aside)?

@alanocallaghan alanocallaghan changed the base branch from master to RELEASE_3_12 September 14, 2020 20:16
@alanocallaghan
version 2.1.8 (2020-09-25)
2dd7028 
- Add "Threads" argument to "BASiCS_MCMC", allowing parallelisation of MCMC
  updates across cells or genes.
- Reduce BatchInfo requirement for no spikes sampler to a warning, from an
  error.
@alanocallaghan alanocallaghan changed the base branch from RELEASE_3_12 to master September 25, 2020 12:00
catavallejos
catavallejos reviewed Sep 29, 2020
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R/utils_MCMC.R Outdated Show resolved Hide resolved
alanocallaghan and others added 2 commits September 29, 2020 14:59
@alanocallaghan @catavallejos
Update R/utils_MCMC.R
a4a3892 
Co-authored-by: Catalina Vallejos <cata.vallejos.m@gmail.com>
@alanocallaghan
Merge branch 'master' of github.com:catavallejos/BASiCS into header-o…
e4bf06c 
…penmp-batch
@alanocallaghan alanocallaghan merged commit cd575f4 into master Sep 29, 2020
@alanocallaghan alanocallaghan deleted the header-openmp-batch branch September 29, 2020 16:06
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@alanocallaghan @codecov-commenter @catavallejos