Refactorcpp

.Rbuildignore

@@ -19,3 +19,17 @@ LICENSE
 ^doc$
 ^Meta$
 drat/
+.*\.vscode
+
+^vignettes/calibration[.]Rmd$
+^vignettes/example_models[.]Rmd$
+^vignettes/flow_types[.]Rmd$
+^vignettes/hello_products[.]Rmd$
+^vignettes/model_definitions[.]Rmd$
+^vignettes/quickstart2[.]Rmd$
+^vignettes/quickstart_products[.]Rmd$
+^vignettes/sir_radial_basis_transmission[.]Rmd$
+^vignettes/time_varying_parameters[.]Rmd$
+## should we ignore tmb_model.Rmd as well ... ??
+
+.*/html/.*

.github/workflows/R-CMD-check.yaml

@@ -18,15 +18,16 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          # - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
           # - {os: macos-latest,   r: 'release'}
           # - {os: windows-latest, r: 'release'}
-          # - {os: ubuntu-latest,   r: 'release'}
           # - {os: ubuntu-latest,   r: 'oldrel-1'}
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
 
     steps:
       - uses: actions/checkout@v3
@@ -48,6 +49,7 @@ jobs:
         with:
           extra-packages: any::rcmdcheck
           needs: check
+          upgrade: 'TRUE'
 
       - uses: r-lib/actions/check-r-package@v2
         with:

.gitignore

@@ -3,6 +3,7 @@
 .RData
 .Ruserdata
 inst/doc
+hoard
 *.o
 *.so
 *.DS_Store

CONTRIBUTORS.md

@@ -0,0 +1,48 @@
+# Contributing to `macpan2`
+
+Thank you for contributing to `macpan2`.  Pull requests and issues are welcome!
+
+Developers can see [here](https://canmod.github.io/macpan2/articles/index.html#developer) for documentation useful those who will contribute code.
+
+## Developer Installation
+
+Developers and contributors should clone this repository and call `make` at the command-line in the top level directory. The following `make` rules are available for getting more control over the build process.
+
+```
+make quick-install     # for changes that only modify R source
+make quick-doc-install # for changes that modify R source and roxygen comments
+make quick-test        # quick-doc-install + run-examples + run-tests
+make run-examples      # help file checks only (without package rebuild)
+make run-tests         # run scripts in tests (without package rebuild)
+make full-install      # for all changes, including changes to C++ source
+make src-update        # push changes to dev.cpp to macpan2.cpp (see below)
+make enum-update       # register new C++ engine functions on the R-side
+make engine-doc-update # generate roxygen comments from comments in dev.cpp
+make doc-update        # roxygenize
+make pkg-build         # build the R package
+make pkg-install       # install the R package from the build
+make pkg-check         # R package checks
+```
+
+## `C++` Development
+
+In most R packages with compiled code, developers edit the source files to be compiled in the `src` directory. In `macpan2` there is a single file in that directory called `macpan2`, which is generated automatically from the file `misc/dev/dev.cpp`. This setup allows for quicker C++ development cycles, because developers can edit `misc/dev/dev.cpp` and then use this file in tests without needing to re-install the package with the new source. In particular, the above hello-world example could use `dev.cpp` as follows.
+
+```
+library(macpan2)
+macpan2:::dev_compile() ## compile dev.cpp
+sir = Compartmental(system.file("starter_models", "sir", package = "macpan2"))
+N = 100
+simulator = sir$simulators$tmb(time_steps = 100
+  , state = c(S = N - 1, I = 1, R = 0)
+  , flow = c(foi = 0, gamma = 0.1)
+  , N = N
+  , beta = 0.2
+  , .tmb_cpp = "dev" ## use dev.cpp
+)
+sir_sims = simulator$report()
+```
+
+To update `src/macpan2` to the state of `misc/dev/dev.cpp` one may run `make src-update`.
+
+Running with `misc/dev/dev.cpp` will print out debugging information in a verbose manner, whereas `src/macpan2.cpp` will not. The `src-update` make rule removes the `#define MP_VERBOSE` flag at the top of the file. 

DESCRIPTION

@@ -1,14 +1,15 @@
 Package: macpan2
 Title: Fast and Flexible Compartmental Modelling
-Version: 0.0.3
+Version: 1.0.0
 Authors@R: c(
   person("Steve Walker", email="swalk@mcmaster.ca", role=c("cre", "aut")),
-  person("Darren Flynn-Primrose", role="aut"),
+  person("Irena Papst", role="ctb"),
+  person("Michael Li", role="ctb"),
   person("Weiguang Guan", role="aut"),
   person("Ben Bolker", role="aut"),
-  person("Michael Li", role="ctb"),
-  person("Irena Papst", role="ctb")
-  )		
+  person("Jen Freeman", role="aut"),
+  person("Darren Flynn-Primrose", role="aut")
+  )
 Description: Fast and flexible compartmental modelling with Template Model Builder.
 License: GPL-3
 Depends:
@@ -17,7 +18,8 @@ Imports:
     TMB,
     oor,
     jsonlite,
-    MASS
+    MASS,
+    memoise
 Suggests: 
     covr,
     knitr,
@@ -36,7 +38,8 @@ Suggests:
     numDeriv,
     parallel
 Remotes:
-    canmod/oor
+    canmod/oor,
+    canmod/macpan2helpers
 LinkingTo:
     TMB,
     RcppEigen,
@@ -47,5 +50,5 @@ Config/testthat/edition: 3
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.0
 URL: https://canmod.github.io/macpan2/, https://github.com/canmod/macpan2

Makefile

@@ -4,22 +4,24 @@ SED_RE = \(\,\)*[ ]*\/\/[ ]*\(.*\)
 ALIAS_RE = [ ]*MP2_\(.*\)\: \(.*\)(\(.*\))
 ROXY_RE = ^.*\(\#'.*\)$
 VERSION := $(shell sed -n '/^Version: /s///p' DESCRIPTION)
+TEST := testthat::test_package(\"macpan2\", reporter = \"progress\")
 
 
 all:
-	make src-update
-	make enum-update
-	make engine-doc-update
-	make doc-update
-	make pkg-build
-	make pkg-install
+	make full-install
 	make pkg-check
 
+
+install-deps:
+	Rscript -e "remotes::install_github('canmod/oor@validity')"
+
+
 # Use this rule if you are doing R development or want to promote
 # dev.cpp to macpan2.cpp before doing R development.
 full-install:
 	make src-update
 	make enum-update
+	make enum-meth-update
 	make engine-doc-update
 	make doc-update
 	make pkg-build
@@ -29,21 +31,31 @@ full-install:
 # Use this rule if (1) you are in a development cycle, (2) you
 # haven't updated macpan.cpp (but have perhaps modified dev.cpp)
 # and (3) do not require a roxygen update.
-quick-install: enum-update
+quick-install: enum-update enum-meth-update
 	R CMD INSTALL --no-multiarch --install-tests .
 
-install-deps:
-	Rscript -e "remotes::install_github('canmod/oor')"
 
 quick-doc-install: R/*.R misc/dev/dev.cpp
 	make engine-doc-update
 	make doc-update
 	make quick-install
 
 
-quick-test:
+forced-quick-doc-install: 
+	touch misc/old-r-source/*.R
+	make doc-update
+	make quick-install
+
+
+quick-test-all:
 	make quick-doc-install
+	make run-vignette-code
+	make run-tests
 	make run-examples
+
+
+quick-test:
+	make quick-doc-install
 	make run-tests
 
 
@@ -52,14 +64,52 @@ run-examples:
 
 
 run-tests:
-	Rscript -e "library(macpan2); testthat::test_package(\"macpan2\")"
+	Rscript -e "library(macpan2); $(TEST)"
+
+
+run-vignette-code:
+	cd vignettes
+	Rscript misc/build/run_vignette_code.R
 
 
 coverage-report:: coverage.html
 coverage.html: R/*.R src/macpan2.cpp tests/testthat/*.R
 	Rscript -e "covr::report(file = \"coverage.html\")"
 
 
+misc/dev/%.run: misc/dev/%.R
+	cd misc/dev; Rscript ../../$^
+
+
+misc/**/%.svg: misc/**/%.drawio
+	draw.io --export $^ --format svg
+
+
+misc/**/%.png: misc/**/%.drawio
+	draw.io --export $^ --format png
+
+
+svg-readme:: misc/readme/*.svg
+png-readme:: misc/readme/*.png
+
+
+readme:: README.md
+README.md: README.Rmd misc/readme/*.svg R/*.R NAMESPACE
+	Rscript -e "rmarkdown::render('README.Rmd')"
+	echo '<!-- Auto-generated - do not edit by hand -->' > temp
+	echo '<!-- Edit README.Rmd instead -->' | cat - $@ >> temp && mv temp $@
+
+
+push-readme:
+	make README.md
+	git add misc/readme/*.svg
+	git add misc/readme/*.png
+	git add misc/readme/*.drawio
+	git add README.md README.Rmd
+	git commit -m "update readme" || true
+	git push || true
+
+
 enum-update:: R/enum.R
 R/enum.R: misc/dev/dev.cpp misc/build/enum_tail.R
 	echo "## Auto-generated - do not edit by hand" > $@
@@ -70,6 +120,11 @@ R/enum.R: misc/dev/dev.cpp misc/build/enum_tail.R
 	echo "valid_funcs = setNames(as.list(valid_funcs), valid_funcs)" >> $@
 
 
+enum-meth-update:: R/enum_methods.R
+R/enum_methods.R: misc/dev/dev.cpp misc/build/method_head.R misc/build/build_from_enum_methods.R
+	Rscript misc/build/build_from_enum_methods.R
+
+
 src-update:: src/macpan2.cpp
 src/macpan2.cpp: misc/dev/dev.cpp
 	echo "// Auto-generated - do not edit by hand" > $@
@@ -86,26 +141,32 @@ R/engine_functions.R: src/macpan2.cpp
 	echo "NULL" >> $@
 
 
-doc-update: R/*.R misc/dev/dev.cpp
+doc-update: R/*.R misc/dev/dev.cpp misc/old-r-source/*.R
 	echo "suppressWarnings(roxygen2::roxygenize(\".\",roclets = c(\"collate\", \"rd\", \"namespace\")))" | R --slave
+	touch doc-update
 
 
-pkg-build:: macpan2_$(VERSION).tar.gz
-macpan2_$(VERSION).tar.gz: DESCRIPTION man/*.Rd R/*.R src/*.cpp tests/testthat/test-*.R tests/testthat.R inst/starter_models/**/*.csv inst/starter_models/**/*.json
-	R CMD build .
+pkg-build:: ../macpan2_$(VERSION).tar.gz
+../macpan2_$(VERSION).tar.gz: DESCRIPTION man/*.Rd R/*.R src/*.cpp tests/testthat/test-*.R tests/testthat.R inst/starter_models/**/*.csv inst/starter_models/**/*.json doc-update
+	cd .. && R CMD build --no-build-vignettes macpan2
+	touch pkg-build
 
 
-pkg-check: macpan2_$(VERSION).tar.gz
-	R CMD check macpan2_$(VERSION).tar.gz
+pkg-check: ../macpan2_$(VERSION).tar.gz pkg-build
+	cd .. && R CMD check macpan2_$(VERSION).tar.gz
+	touch pkg-check
 
 
-pkg-install: macpan2_$(VERSION).tar.gz
-	R CMD INSTALL --no-multiarch --install-tests macpan2_$(VERSION).tar.gz
+pkg-install: ../macpan2_$(VERSION).tar.gz pkg-build
+	cd .. && R CMD INSTALL --no-multiarch --install-tests macpan2_$(VERSION).tar.gz
 
 
 compile-dev: misc/dev/dev.cpp
 	cd misc/dev; echo "TMB::compile(\"dev.cpp\")" | R --slave
 
 
-misc/dev/%.run: misc/dev/%.R
-	cd misc/dev; Rscript ../../$^
+inst/model_library/%/README.md: inst/model_library/%/README.Rmd
+	echo "rmarkdown::render(input = \"$^\", intermediates_dir = NULL)" | R --slave
+	cat $(dir $@)/header.yaml $(dir $@)/README.md > $(dir $@)/tmp.md
+	cp $(dir $@)/tmp.md $(dir $@)/README.md
+	rm $(dir $@)/tmp.md