accept incoming changes

.drone.yml

@@ -1,104 +1,9 @@
----
-kind: pipeline
-type: docker
-name: mpn:latest
-
-platform:
-  os: linux
-  arch: amd64
-
-steps:
-- name: pull
-  image: omerxx/drone-ecr-auth
-  commands:
-  - $(aws ecr get-login --no-include-email --region us-east-1)
-  - docker pull 906087756158.dkr.ecr.us-east-1.amazonaws.com/r-dev-ci-mpn-4.1:latest
-  - docker pull 906087756158.dkr.ecr.us-east-1.amazonaws.com/r-dev-ci-mpn-4.0:latest
-  - docker pull 906087756158.dkr.ecr.us-east-1.amazonaws.com/r-dev-ci-mpn-3.6:latest
-  volumes:
-  - name: docker.sock
-    path: /var/run/docker.sock
-
-- name: "Check package: R 4.1"
-  pull: never
-  image: 906087756158.dkr.ecr.us-east-1.amazonaws.com/r-dev-ci-mpn-4.1:latest
-  commands:
-  - R -s -e 'devtools::install_deps(upgrade = '"'"'always'"'"', dependencies = TRUE)'
-  - make drone
-
-- name: "Check package: R 4.0"
-  pull: never
-  image: 906087756158.dkr.ecr.us-east-1.amazonaws.com/r-dev-ci-mpn-4.0:latest
-  commands:
-  - R -s -e 'devtools::install_deps(upgrade = '"'"'always'"'"', dependencies = TRUE)'
-  - make drone
-
-- name: "Check package: R 3.6"
-  pull: never
-  image: 906087756158.dkr.ecr.us-east-1.amazonaws.com/r-dev-ci-mpn-3.6:latest
-  commands:
-  - R -s -e 'devtools::install_deps(upgrade = '"'"'always'"'"', dependencies = TRUE)'
-  - make drone
-
-volumes:
-- name: docker.sock
-  host:
-    path: /var/run/docker.sock
-
-trigger:
-  event:
-    exclude:
-    - promote
-
-# ---
-# kind: pipeline
-# type: docker
-# name: mpn:oldest
-# 
-# platform:
-#   os: linux
-#   arch: amd64
-# 
-# steps:
-# - name: pull
-#   image: omerxx/drone-ecr-auth
-#   commands:
-#   - $(aws ecr get-login --no-include-email --region us-east-1)
-#   - docker pull 906087756158.dkr.ecr.us-east-1.amazonaws.com/r-dev-ci-mpn-4.0:2020-06-08
-#   - docker pull 906087756158.dkr.ecr.us-east-1.amazonaws.com/r-dev-ci-mpn-3.6:2020-06-08
-#   volumes:
-#   - name: docker.sock
-#     path: /var/run/docker.sock
-# 
-# - name: "Check package: R 4.0"
-#   pull: never
-#   image: 906087756158.dkr.ecr.us-east-1.amazonaws.com/r-dev-ci-mpn-4.0:2020-06-08
-#   commands:
-#   - R -s -e 'devtools::install_deps(upgrade = '"'"'always'"'"', dependencies = TRUE)'
-#   - make drone
-# 
-# - name: "Check package: R 3.6"
-#   pull: never
-#   image: 906087756158.dkr.ecr.us-east-1.amazonaws.com/r-dev-ci-mpn-3.6:2020-06-08
-#   commands:
-#   - R -s -e 'devtools::install_deps(upgrade = '"'"'always'"'"', dependencies = TRUE)'
-#   - make drone
-# 
-# volumes:
-# - name: docker.sock
-#   host:
-#     path: /var/run/docker.sock
-# 
-# trigger:
-#   event:
-#     exclude:
-#     - promote
-
 ---
 kind: pipeline
 type: docker
 name: cran-latest
 
+
 platform:
   os: linux
   arch: amd64
@@ -160,7 +65,7 @@ steps:
   image: omerxx/drone-ecr-auth
   commands:
   - $(aws ecr get-login --no-include-email --region us-east-1)
-  - docker pull 906087756158.dkr.ecr.us-east-1.amazonaws.com/r-dev-ci-mpn-4.0:latest
+  - docker pull 906087756158.dkr.ecr.us-east-1.amazonaws.com/r-dev-ci-mpn-4.1:latest
   volumes:
   - name: docker.sock
     path: /var/run/docker.sock
@@ -178,8 +83,8 @@ trigger:
     - promote
 
 depends_on:
-- mpn:latest
 - cran-latest
+
 ---
 kind: pipeline
 type: docker
@@ -249,6 +154,4 @@ trigger:
   - tag
 
 depends_on:
-- mpn:latest
-#- mpn:oldest
 - cran-latest

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: mrgsolve
 Title: Simulate from ODE-Based Models
-Version: 1.0.0.9000
+Version: 1.0.3.9000
 Authors@R: 
     c(person(given = "Kyle T", family = "Baron",
              role = c("aut", "cre"),
@@ -39,10 +39,10 @@ Depends:
     methods
 Imports:
     Rcpp (>= 1.0.7),
-    dplyr (>= 1.0.7),
+    dplyr (>= 1.0.8),
     magrittr (>= 2.0.1),
     tibble (>= 3.1.6),
-    rlang (>= 0.4.12),
+    rlang (>= 1.0.1),
     tidyselect (>= 1.1.1),
     lifecycle, 
     glue
@@ -83,6 +83,7 @@ Collate:
     'annot.R'
     'chain.R'
     'class_build.R'
+    'class_evd.R'
     'events.R'
     'class_rx.R'
     'compile.R'

Makefile

@@ -35,7 +35,7 @@ check:
 
 check-only:
 	make doc
-	R CMD check  ${TARBALL} --no-manual --no-test
+	R CMD check  ${TARBALL} --no-manual --no-tests --no-install
 
 cran: export _MRGSOLVE_SKIP_MODLIB_BUILD_=no
 cran:
@@ -126,9 +126,10 @@ modlib: export _MRGSOLVE_SKIP_MODLIB_BUILD_=no
 modlib: 
 	Rscript -e 'testthat::test_file("inst/maintenance/unit/test-modlib.R")'
 
-# possibly no longer in use
+# this is in use
 drone:
 	make house
+	#R -s -e 'devtools::install_deps(upgrade = '"'"'always'"'"', dependencies=TRUE)'
 	R CMD build --md5 $(PKGDIR) 
 	R CMD check --as-cran ${TARBALL}
 	export _MRGSOLVE_SKIP_MODLIB_BUILD_=false

NAMESPACE

@@ -67,6 +67,7 @@ export("%then%")
 export(Req)
 export(allparam)
 export(as.ev)
+export(as.evd)
 export(as.tbl.mrgsims)
 export(as_bmat)
 export(as_cmat)
@@ -103,6 +104,7 @@ export(ev_rep)
 export(ev_repeat)
 export(ev_rx)
 export(ev_seq)
+export(evd)
 export(expand.ev)
 export(expand.idata)
 export(expand_observations)
@@ -161,6 +163,7 @@ export(stime)
 export(tgrid)
 export(touch_funs)
 export(tscale)
+export(uctran)
 export(valid_data_set)
 export(valid_data_set.matrix)
 export(valid_idata_set)
@@ -192,6 +195,7 @@ exportMethods(data_set)
 exportMethods(dim)
 exportMethods(ev)
 exportMethods(ev_rx)
+exportMethods(evd)
 exportMethods(head)
 exportMethods(idata_set)
 exportMethods(init)

NEWS.md

@@ -1,5 +1,29 @@
 # mrgsolve (development version)
 
+# mrgsolve 1.0.3
+
+- Removed `assert()` statement in LSODA code found by CRAN check (#943).
+
+# mrgsolve 1.0.2
+
+- Test class using `inherits()` not `class()` from CRAN check (#943).
+
+# mrgsolve 1.0.1
+
+- Add `LOG()`, `EXP()`, `SQRT()` macros when `nm-vars` plugin is invoked 
+  #931, #936.
+
+- Use `evd()` to create an event object which renders nmtran names 
+  in upper case (e.g. `TIME` rather than `time`) #935, #919.
+
+- Fixed bug where `rate` was not getting set for modeled events #934.
+
+- Fixed bug where `self.stop_id()` and `self.stop_id_cf()` had reversed
+  behavior as documented #927, #928.
+
+- Refactored EVID=3 behavior to leave `NEWIND` as-is #934.
+
+
 # mrgsolve 1.0.0
 
 - New model syntax: `THETA(n)` is interpreted as `THETAn` in the model code;

R/chain.R

@@ -195,7 +195,7 @@ obsaug <- function(x,value=TRUE,...) {
 ##'   idata_set(idata) %>%
 ##'   design(list(des1, des2),"amt") %>%
 ##'   data_set(data) %>%
-##'   mrgsim %>% 
+##'   mrgsim() %>% 
 ##'   plot(RESP~time|GRP)
 ##' 
 ##' @export