Merge pull request #939 from metrumresearchgroup/release/1.0.1

Release/1.0.1

.drone.yml

@@ -1,54 +1,156 @@
+---
 kind: pipeline
 type: docker
-name: mrgsolve
+name: cran-latest
+
+platform:
+  os: linux
+  arch: amd64
 
 steps:
-- name: Pull mpn container from ECR
+- 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:cran-latest
+  - docker pull 906087756158.dkr.ecr.us-east-1.amazonaws.com/r-dev-ci-mpn-4.0:cran-latest
+  - docker pull 906087756158.dkr.ecr.us-east-1.amazonaws.com/r-dev-ci-mpn-3.6:cran-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:cran-latest
   commands:
-  - $(aws ecr get-login --no-include-email --region us-east-1)
-  - docker pull 906087756158.dkr.ecr.us-east-1.amazonaws.com/mpn:2020-03-24
+  - R -s -e 'devtools::install_deps(upgrade = '"'"'always'"'"', dependencies = TRUE)'
+  - make drone
 
-- name: R40-new
-  image: "906087756158.dkr.ecr.us-east-1.amazonaws.com/mpn-complete:2020-06-08"
+- name: "Check package: R 4.0"
   pull: never
-  environment:
-    R_LIBS_USER: "/opt/rpkgs/4.0"
-    _MRGSOLVE_SKIP_MODLIB_BUILD_: false
+  image: 906087756158.dkr.ecr.us-east-1.amazonaws.com/r-dev-ci-mpn-4.0:cran-latest
   commands:
+  - R -s -e 'devtools::install_deps(upgrade = '"'"'always'"'"', dependencies = TRUE)'
   - make drone
 
-- name: R36
-  image: "906087756158.dkr.ecr.us-east-1.amazonaws.com/mpn:2020-03-24"
+- name: "Check package: R 3.6"
   pull: never
-  environment:
-    R_LIBS_USER: "/opt/rpkgs/3.6/2020-03-24"
-    _MRGSOLVE_SKIP_MODLIB_BUILD_: false
+  image: 906087756158.dkr.ecr.us-east-1.amazonaws.com/r-dev-ci-mpn-3.6:cran-latest
   commands:
+  - R -s -e 'devtools::install_deps(upgrade = '"'"'always'"'"', dependencies = TRUE)'
   - make drone
-
-- name: release
-  when:
-    event:
-    - tag
-    status:
-    - success
-  image: "906087756158.dkr.ecr.us-east-1.amazonaws.com/mpn:2020-03-24"
+
+volumes:
+- name: docker.sock
+  host:
+    path: /var/run/docker.sock
+
+trigger:
+  event:
+    exclude:
+    - promote
+
+---
+kind: pipeline
+type: docker
+name: coverage
+
+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
+  volumes:
+  - name: docker.sock
+    path: /var/run/docker.sock
+
+volumes:
+- name: docker.sock
+  host:
+    path: /var/run/docker.sock
+- name: cache
+  temp: {}
+
+trigger:
+  event:
+    exclude:
+    - promote
+
+depends_on:
+- cran-latest
+
+---
+kind: pipeline
+type: docker
+name: release
+
+platform:
+  os: linux
+  arch: amd64
+
+steps:
+- name: pull
+  image: omerxx/drone-ecr-auth
+  commands:
+  - $(aws ecr get-login --no-include-email --region us-east-1)
+  - docker pull 906087756158.dkr.ecr.us-east-1.amazonaws.com/r-dev-ci-mpn-4.1:latest
+  volumes:
+  - name: docker.sock
+    path: /var/run/docker.sock
+
+- name: Build package
   pull: never
-  environment:
-    R_LIBS_USER: "/opt/rpkgs/3.6/2020-03-24"
+  image: 906087756158.dkr.ecr.us-east-1.amazonaws.com/r-dev-ci-mpn-4.1:latest
   commands:
-  - git config --global user.email "[email protected]"
-  - git config --global user.name "Drony"
+  - git config --global user.email [email protected]
+  - git config --global user.name Drony
   - git fetch --tags
-  - R -e "pkgpub::create_tagged_repo()"
-  - aws s3 sync /tmp/${DRONE_TAG} s3://mpn.metworx.dev/releases/${DRONE_REPO_NAME}/${DRONE_TAG}
-  - aws s3 sync /tmp/${DRONE_TAG} s3://mpn.metworx.dev/releases/${DRONE_REPO_NAME}/latest_tag
+  - R -s -e 'pkgpub::create_tagged_repo(.dir = '"'"'/ephemeral'"'"')'
+  environment:
+    NOT_CRAN: true
+  volumes:
+  - name: cache
+    path: /ephemeral
+
+- name: "Publish package: ${DRONE_TAG}"
+  pull: if-not-exists
+  image: plugins/s3
+  settings:
+    bucket: mpn.metworx.dev
+    source: /ephemeral/${DRONE_TAG}/**/*
+    strip_prefix: /ephemeral/${DRONE_TAG}/
+    target: /releases/${DRONE_REPO_NAME}/${DRONE_TAG}
+  volumes:
+  - name: cache
+    path: /ephemeral
+
+- name: "Publish package: latest_tag"
+  pull: if-not-exists
+  image: plugins/s3
+  settings:
+    bucket: mpn.metworx.dev
+    source: /ephemeral/${DRONE_TAG}/**/*
+    strip_prefix: /ephemeral/${DRONE_TAG}/
+    target: /releases/${DRONE_REPO_NAME}/latest_tag
+  volumes:
+  - name: cache
+    path: /ephemeral
 
 volumes:
 - name: docker.sock
   host:
     path: /var/run/docker.sock
+- name: cache
+  temp: {}
+
+trigger:
+  event:
+  - tag
+
+depends_on:
+- cran-latest

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: mrgsolve
 Title: Simulate from ODE-Based Models
-Version: 1.0.0
+Version: 1.0.1
 Authors@R: 
     c(person(given = "Kyle T", family = "Baron",
              role = c("aut", "cre"),
@@ -38,12 +38,12 @@ Depends:
     R (>= 3.1.2),
     methods
 Imports:
-    Rcpp (>= 0.12.12),
-    dplyr (>= 0.8.1),
-    magrittr (>= 1.5),
-    tibble (>= 2.1.1),
-    rlang (>= 0.3.4),
-    tidyselect (>= 0.2.5),
+    Rcpp (>= 1.0.7),
+    dplyr (>= 1.0.8),
+    magrittr (>= 2.0.1),
+    tibble (>= 3.1.6),
+    rlang (>= 1.0.1),
+    tidyselect (>= 1.1.1),
     lifecycle, 
     glue
 Suggests:
@@ -56,9 +56,9 @@ Suggests:
     data.table,
     pmxTools
 LinkingTo: 
-    Rcpp (>= 0.12.12),
-    RcppArmadillo (>= 0.7.900.2.0),
-    BH (>= 1.62.0-1)
+    Rcpp (>= 1.0.7),
+    RcppArmadillo (>= 0.10.7.3.0),
+    BH (>= 1.75.0-0)
 RdMacros: 
     lifecycle
 Encoding: UTF-8
@@ -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:
@@ -128,9 +128,10 @@ 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

@@ -1,3 +1,19 @@
+# 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