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andrjohnsandrjohns
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New submodule structure for r-devel compat
1 parent c1b497d commit 149a254

11 files changed

Lines changed: 63 additions & 136 deletions

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‎.github/workflows/main.yml‎

Lines changed: 1 addition & 10 deletions
Original file line numberDiff line numberDiff line change
@@ -10,6 +10,7 @@ name: R-CMD-check
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- develop
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- experimental
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- StanHeaders_*
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- module-test
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pull_request:
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branches:
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- develop
@@ -65,15 +66,6 @@ jobs:
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working-directory: rstan/rstan
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extra-packages: any::rcmdcheck, local::../../StanHeaders
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- name: Remove symlinks on Windows
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if: runner.os == 'Windows'
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run: |
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rm -Rf inst/include/src \
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inst/include/mathlib \
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inst/include/stan \
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inst/include/libsundials || true
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shell: bash
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- uses: r-lib/actions/check-r-package@v2
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with:
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working-directory: StanHeaders
@@ -86,4 +78,3 @@ jobs:
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working-directory: rstan/rstan
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env:
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_R_CHECK_CRAN_INCOMING_: false
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‎.gitmodules‎

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@@ -1,5 +1,8 @@
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[submodule "stan"]
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path = StanHeaders/inst/include/upstream
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path = StanHeaders/src/stan
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url = https://github.com/stan-dev/stan.git
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ignore = dirty
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branch = develop
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[submodule "math"]
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path = StanHeaders/src/math
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url = https://github.com/stan-dev/math

‎StanHeaders/.Rbuildignore‎

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Original file line numberDiff line numberDiff line change
@@ -1,33 +1,12 @@
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inst/include/upstream
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inst/include/mathlib
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inst/include/libsundials
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inst/include/src/test.*$
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inst/include/src/.*\.hpp\.d$
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inst/include/src/.*\..pp\.gch$
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inst/include/src/docs.*$
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inst/include/src/doxygen.*$
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inst/include/src/python.*$
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inst/include/src/stan.hpp.*$
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inst/include/src/TO-DO.txt
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inst/include/src/README.*$
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inst/include/src/.*\.sh$
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inst/include/src/makefile$
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inst/include/src/\.travis\.yml$
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inst/include/src/logos/.*$
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inst/include/src/make/.*$
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_inst/include/src/stan/command/.*\.cpp$
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_inst/include/src/stan/gm/.*\.cpp$
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_inst/include/src/stan/gm/grammars/.*\.cpp$
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_inst/include/src/stan/agrad/.*\.cpp$
22-
_inst/include/src/stan/math/.*\.cpp$
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cleanup
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cleanup.win
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revdep
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install-github.R
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inst/doc/.install_extras
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vignettes/.install_extras
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.*\.o$
30-
.*\.a$
1+
^src/stan/(?!(src$|src/stan))
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^src/math/(?!(stan|lib$|lib/sundials_([^\/]*)$|lib/sundials_([^\/]*)/src|lib/sundials_([^\/]*)/include))
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^src/math/lib/sundials_([^\/]*)/src/sunnonlinsol/fixedpoint/fmod
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^src/sundials
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^inst/include
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\.gitignore$
32-
Rbuildignore.*$
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\.prepare
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.*\.o$
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.*\.a$
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.*\.so$
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.*\.dll$

‎StanHeaders/.gitignore‎

Lines changed: 2 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,2 @@
1+
inst/include
2+
src/sundials

‎StanHeaders/cleanup‎

Lines changed: 0 additions & 15 deletions
This file was deleted.

‎StanHeaders/cleanup.win‎

Lines changed: 0 additions & 15 deletions
This file was deleted.

‎StanHeaders/inst/include/stan_sundials_printf_override.hpp‎

Lines changed: 0 additions & 13 deletions
This file was deleted.

‎StanHeaders/src/Makevars‎

Lines changed: 24 additions & 26 deletions
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
1-
.PHONY: static
1+
.PHONY: static package
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33
CXX_STD = CXX17
44
PKG_CPPFLAGS = -DNO_FPRINTF_OUTPUT -I"../inst/include" -I"sundials" -include stan_sundials_printf_override.hpp
@@ -9,46 +9,44 @@ SHLIB_LDFLAGS = $(SHLIB_CXXLDFLAGS)
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SHLIB_LD = $(SHLIB_CXXLD)
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1111
SUNDIALS_CVODES := \
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$(wildcard cvodes/*.c) \
13-
$(wildcard sundials/*.c) \
14-
$(wildcard sunmatrix/band/[^f]*.c) \
15-
$(wildcard sunmatrix/dense/[^f]*.c) \
16-
$(wildcard sunlinsol/band/[^f]*.c) \
17-
$(wildcard sunlinsol/dense/[^f]*.c) \
18-
$(wildcard sunnonlinsol/newton/[^f]*.c) \
19-
$(wildcard sunnonlinsol/fixedpoint/[^f]*.c)
12+
$(wildcard math/lib/sundials_*/src/cvodes/*.c) \
13+
$(wildcard math/lib/sundials_*/src/sundials/*.c) \
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$(wildcard math/lib/sundials_*/src/sunmatrix/band/[^f]*.c) \
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$(wildcard math/lib/sundials_*/src/sunmatrix/dense/[^f]*.c) \
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$(wildcard math/lib/sundials_*/src/sunlinsol/band/[^f]*.c) \
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$(wildcard math/lib/sundials_*/src/sunlinsol/dense/[^f]*.c) \
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$(wildcard math/lib/sundials_*/src/sunnonlinsol/newton/[^f]*.c) \
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$(wildcard math/lib/sundials_*/src/sunnonlinsol/fixedpoint/[^f]*.c)
2020

2121
SUNDIALS_IDAS := \
22-
$(wildcard idas/*.c) \
23-
$(wildcard sundials/*.c) \
24-
$(wildcard sunmatrix/band/[^f]*.c) \
25-
$(wildcard sunmatrix/dense/[^f]*.c) \
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$(wildcard sunlinsol/band/[^f]*.c) \
27-
$(wildcard sunlinsol/dense/[^f]*.c) \
28-
$(wildcard sunnonlinsol/newton/[^f]*.c) \
29-
$(wildcard sunnonlinsol/fixedpoint/[^f]*.c)
22+
$(wildcard math/lib/sundials_*/src/idas/*.c)
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SUNDIALS_KINSOL := \
32-
$(wildcard kinsol/*.c) \
33-
$(wildcard sundials/*.c) \
34-
$(wildcard sunmatrix/band/[^f]*.c) \
35-
$(wildcard sunmatrix/dense/[^f]*.c) \
36-
$(wildcard sunlinsol/band/[^f]*.c) \
37-
$(wildcard sunlinsol/dense/[^f]*.c) \
38-
$(wildcard sunnonlinsol/newton/[^f]*.c) \
39-
$(wildcard sunnonlinsol/fixedpoint/[^f]*.c)
25+
$(wildcard math/lib/sundials_*/src/kinsol/*.c)
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4127
SUNDIALS_NVECSERIAL := \
42-
$(addprefix , nvector/serial/nvector_serial.c sundials/sundials_math.c)
28+
$(wildcard math/lib/sundials_*/src/nvector/serial/nvector_serial.c)
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4430
SOURCES = $(SUNDIALS_CVODES) $(SUNDIALS_IDAS) $(SUNDIALS_KINSOL) $(SUNDIALS_NVECSERIAL)
4531
OBJECTS_C = $(SOURCES:.c=.o)
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OBJECTS = $(OBJECTS_C:.cpp=.o)
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34+
$(SHLIB): static
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$(OBJECTS): package
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37+
package:
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@mkdir -p ../inst/include
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@cp -Rf stan/src ../inst/include/src
40+
@cp -Rf math/stan ../inst/include/stan
41+
@cp -Rf math/lib/sundials_*/include/* ../inst/include/
42+
@cp -Rf math/lib/sundials_*/src/sundials .
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4844
static: $(OBJECTS)
4945
@mkdir -p ../lib
5046
$(AR) -rs ../lib/libStanHeaders.a $(OBJECTS)
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5248
clean:
5349
rm -rf ../lib
5450
rm $(OBJECTS)
51+
rm -rf ../inst/include/
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rm -rf sundials

‎StanHeaders/src/Makevars.win‎

Lines changed: 21 additions & 25 deletions
Original file line numberDiff line numberDiff line change
@@ -9,44 +9,40 @@ SHLIB_LDFLAGS = $(SHLIB_CXXLDFLAGS)
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SHLIB_LD = $(SHLIB_CXXLD)
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1111
SUNDIALS_CVODES := \
12-
$(wildcard cvodes/*.c) \
13-
$(wildcard sundials/*.c) \
14-
$(wildcard sunmatrix/band/[^f]*.c) \
15-
$(wildcard sunmatrix/dense/[^f]*.c) \
16-
$(wildcard sunlinsol/band/[^f]*.c) \
17-
$(wildcard sunlinsol/dense/[^f]*.c) \
18-
$(wildcard sunnonlinsol/newton/[^f]*.c) \
19-
$(wildcard sunnonlinsol/fixedpoint/[^f]*.c)
12+
$(wildcard math/lib/sundials_*/src/cvodes/*.c) \
13+
$(wildcard math/lib/sundials_*/src/sundials/*.c) \
14+
$(wildcard math/lib/sundials_*/src/sunmatrix/band/[^f]*.c) \
15+
$(wildcard math/lib/sundials_*/src/sunmatrix/dense/[^f]*.c) \
16+
$(wildcard math/lib/sundials_*/src/sunlinsol/band/[^f]*.c) \
17+
$(wildcard math/lib/sundials_*/src/sunlinsol/dense/[^f]*.c) \
18+
$(wildcard math/lib/sundials_*/src/sunnonlinsol/newton/[^f]*.c) \
19+
$(wildcard math/lib/sundials_*/src/sunnonlinsol/fixedpoint/[^f]*.c)
2020

2121
SUNDIALS_IDAS := \
22-
$(wildcard idas/*.c) \
23-
$(wildcard sundials/*.c) \
24-
$(wildcard sunmatrix/band/[^f]*.c) \
25-
$(wildcard sunmatrix/dense/[^f]*.c) \
26-
$(wildcard sunlinsol/band/[^f]*.c) \
27-
$(wildcard sunlinsol/dense/[^f]*.c) \
28-
$(wildcard sunnonlinsol/newton/[^f]*.c) \
29-
$(wildcard sunnonlinsol/fixedpoint/[^f]*.c)
22+
$(wildcard math/lib/sundials_*/src/idas/*.c)
3023

3124
SUNDIALS_KINSOL := \
32-
$(wildcard kinsol/*.c) \
33-
$(wildcard sundials/*.c) \
34-
$(wildcard sunmatrix/band/[^f]*.c) \
35-
$(wildcard sunmatrix/dense/[^f]*.c) \
36-
$(wildcard sunlinsol/band/[^f]*.c) \
37-
$(wildcard sunlinsol/dense/[^f]*.c) \
38-
$(wildcard sunnonlinsol/newton/[^f]*.c) \
39-
$(wildcard sunnonlinsol/fixedpoint/[^f]*.c)
25+
$(wildcard math/lib/sundials_*/src/kinsol/*.c)
4026

4127
SUNDIALS_NVECSERIAL := \
42-
$(addprefix , nvector/serial/nvector_serial.c sundials/sundials_math.c)
28+
$(wildcard math/lib/sundials_*/src/nvector/serial/nvector_serial.c)
4329

4430

4531
SOURCES = $(SUNDIALS_CVODES) $(SUNDIALS_IDAS) $(SUNDIALS_KINSOL) $(SUNDIALS_NVECSERIAL) init.c
4632
OBJECTS_C = $(SOURCES:.c=.o)
4733
OBJECTS = $(OBJECTS_C:.cpp=.o)
4834

4935
$(SHLIB): $(OBJECTS)
36+
$(OBJECTS): package
37+
38+
package:
39+
@mkdir -p ../inst/include
40+
@cp -Rf stan/src ../inst/include/src
41+
@cp -Rf math/stan ../inst/include/stan
42+
@cp -Rf math/lib/sundials_*/include/* ../inst/include/
43+
@cp -Rf math/lib/sundials_*/src/sundials .
5044

5145
clean:
5246
rm $(OBJECTS)
47+
rm -rf ../inst/include/
48+
rm -rf sundials

‎StanHeaders/src/math‎

Submodule math added at 72f6470

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