Add dedicated hpp generation step for future cmdstan compatibility

[andrjohns]

Submission Checklist

• Run unit tests
• Declare copyright holder and agree to license (see below)

Summary

As discovered in this thread on the forum, the next version of cmdstan will automatically delete the .hpp file during the make process. This causes R to error when we try to read it in for later use in the model-methods compilation.

This PR adds a separate step for generating and reading the hpp file into the Model object

Copyright and Licensing

Please list the copyright holder for the work you are submitting
(this will be you or your assignee, such as a university or company):
Andrew Johnson

By submitting this pull request, the copyright holder is agreeing to
license the submitted work under the following licenses:

• Code: BSD 3-clause (https://opensource.org/licenses/BSD-3-Clause)
• Documentation: CC-BY 4.0 (https://creativecommons.org/licenses/by/4.0/)

[andrjohns]

Also a good reminder to set up the CI to test against cmdstan develop at some point

[WardBrian]

You can also update your make command to "make foo.hpp foo" and it should build both the executable and hpp (if you also need the .o you can list it there as well)

[codecov-commenter]

Codecov Report

All modified and coverable lines are covered by tests ✅

Comparison is base (48a2b3e) 88.36% compared to head (efd2958) 88.35%.

❗ Current head efd2958 differs from pull request most recent head 447f5f7. Consider uploading reports for the commit 447f5f7 to get more accurate results

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #863      +/-   ##
==========================================
- Coverage   88.36%   88.35%   -0.01%     
==========================================
  Files          12       12              
  Lines        4528     4527       -1     
==========================================
- Hits         4001     4000       -1     
  Misses        527      527              

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

[andrjohns]

You can also update your make command to "make foo.hpp foo" and it should build both the executable and hpp (if you also need the .o you can list it there as well)

Ah good call, that should be a bit cleaner, will do

[andrjohns]

You can also update your make command to "make foo.hpp foo" and it should build both the executable and hpp (if you also need the .o you can list it there as well)

Ah good call, that should be a bit cleaner, will do

Hmm it looks like processx package is causing some weird behaviour with this, and the .hpp file is getting deleted anyway, but the same thing doesn't happen through the CLI:

> mod <- cmdstan_model(write_stan_file(modfile), force_recompile = TRUE, quiet = FALSE)
Compiling Stan program...
Running make /var/folders/1d/rjvd0h_n0yq20j13h4gdfytw0000gn/T//RtmpakNfuk/model-19f7c4a9fa8.hpp \
  /var/folders/1d/rjvd0h_n0yq20j13h4gdfytw0000gn/T/RtmpakNfuk/model-19f7c4a9fa8 \
  "STANCFLAGS +=  --name='model_292e651ef3fa7c848ba97246a126a03b_model'"

--- Translating Stan model to C++ code ---
bin/stanc --name='model_292e651ef3fa7c848ba97246a126a03b_model' --o=/var/folders/1d/rjvd0h_n0yq20j13h4gdfytw0000gn/T//RtmpakNfuk/model-19f7c4a9fa8.hpp /var/folders/1d/rjvd0h_n0yq20j13h4gdfytw0000gn/T//RtmpakNfuk/model-19f7c4a9fa8.stan

--- Translating Stan model to C++ code ---
bin/stanc --name='model_292e651ef3fa7c848ba97246a126a03b_model' --o=/var/folders/1d/rjvd0h_n0yq20j13h4gdfytw0000gn/T/RtmpakNfuk/model-19f7c4a9fa8.hpp /var/folders/1d/rjvd0h_n0yq20j13h4gdfytw0000gn/T/RtmpakNfuk/model-19f7c4a9fa8.stan

--- Compiling, linking C++ code ---
clang++ -Wno-deprecated-declarations -ffp-contract=off -std=c++1y -Wno-unknown-warning-option -Wno-tautological-compare -Wno-sign-compare -D_REENTRANT -Wno-ignored-attributes      -I stan/lib/stan_math/lib/tbb_2020.3/include    -O3 -I src -I stan/src -I stan/lib/rapidjson_1.1.0/ -I lib/CLI11-1.9.1/ -I stan/lib/stan_math/ -I stan/lib/stan_math/lib/eigen_3.4.0 -I stan/lib/stan_math/lib/boost_1.78.0 -I stan/lib/stan_math/lib/sundials_6.1.1/include -I stan/lib/stan_math/lib/sundials_6.1.1/src/sundials    -DBOOST_DISABLE_ASSERTS          -c -include-pch stan/src/stan/model/model_header_15_0.hpp.gch -x c++ -o /var/folders/1d/rjvd0h_n0yq20j13h4gdfytw0000gn/T/RtmpakNfuk/model-19f7c4a9fa8.o /var/folders/1d/rjvd0h_n0yq20j13h4gdfytw0000gn/T/RtmpakNfuk/model-19f7c4a9fa8.hpp
clang++ -Wno-deprecated-declarations -ffp-contract=off -std=c++1y -Wno-unknown-warning-option -Wno-tautological-compare -Wno-sign-compare -D_REENTRANT -Wno-ignored-attributes      -I stan/lib/stan_math/lib/tbb_2020.3/include    -O3 -I src -I stan/src -I stan/lib/rapidjson_1.1.0/ -I lib/CLI11-1.9.1/ -I stan/lib/stan_math/ -I stan/lib/stan_math/lib/eigen_3.4.0 -I stan/lib/stan_math/lib/boost_1.78.0 -I stan/lib/stan_math/lib/sundials_6.1.1/include -I stan/lib/stan_math/lib/sundials_6.1.1/src/sundials    -DBOOST_DISABLE_ASSERTS               -Wl,-L,"/Users/andrew/.cmdstan/cmdstan-2.33.1/stan/lib/stan_math/lib/tbb" -Wl,-rpath,"/Users/andrew/.cmdstan/cmdstan-2.33.1/stan/lib/stan_math/lib/tbb"        /var/folders/1d/rjvd0h_n0yq20j13h4gdfytw0000gn/T/RtmpakNfuk/model-19f7c4a9fa8.o src/cmdstan/main.o       -Wl,-L,"/Users/andrew/.cmdstan/cmdstan-2.33.1/stan/lib/stan_math/lib/tbb" -Wl,-rpath,"/Users/andrew/.cmdstan/cmdstan-2.33.1/stan/lib/stan_math/lib/tbb"     stan/lib/stan_math/lib/sundials_6.1.1/lib/libsundials_nvecserial.a stan/lib/stan_math/lib/sundials_6.1.1/lib/libsundials_cvodes.a stan/lib/stan_math/lib/sundials_6.1.1/lib/libsundials_idas.a stan/lib/stan_math/lib/sundials_6.1.1/lib/libsundials_kinsol.a  stan/lib/stan_math/lib/tbb/libtbb.dylib stan/lib/stan_math/lib/tbb/libtbbmalloc.dylib stan/lib/stan_math/lib/tbb/libtbbmalloc_proxy.dylib -o /var/folders/1d/rjvd0h_n0yq20j13h4gdfytw0000gn/T/RtmpakNfuk/model-19f7c4a9fa8
ld: warning: duplicate -rpath '/Users/andrew/.cmdstan/cmdstan-2.33.1/stan/lib/stan_math/lib/tbb' ignored
ld: warning: duplicate -rpath '/Users/andrew/.cmdstan/cmdstan-2.33.1/stan/lib/stan_math/lib/tbb' ignored

rm -f /var/folders/1d/rjvd0h_n0yq20j13h4gdfytw0000gn/T/RtmpakNfuk/model-19f7c4a9fa8.o
rm /var/folders/1d/rjvd0h_n0yq20j13h4gdfytw0000gn/T/RtmpakNfuk/model-19f7c4a9fa8.hpp

Given that this indicates some flakiness with the processx call to make, I think it's best to leave the .hpp generation explicit like in the current changes

[andrjohns]

@rok-cesnovar just a heads up that we'll need this in before the 2.34 release

[rok-cesnovar]

Reviewing this later today, thanks for the heads up!

[rok-cesnovar]

Actually, had some downtime just now. This looks great to me!