Merge branch 'master' into feature/marginalise

.Rbuildignore

@@ -1,32 +1,35 @@
-^CRAN-RELEASE$
-^_pkgdown\.yml$
+^.*\.Rproj$
+^\.Rproj\.user$
+
+^codemeta\.json$
 ^.github$
 ^.netlify$
 ^.lintr$
 ^.travis.yml$
-^docs$
-^.*\.Rproj$
-^\.Rproj\.user$
 
+^README\.md$
+^CRAN-RELEASE$
 ^CODE_OF_CONDUCT\.md$
 ^\.EDIT_WEBSITE\.md$
 ^LICENSE$
 ^cran-comments\.md$
+
 ^logos$
+^paper$
+
+^_pkgdown\.yml$
+^docs$
 ^inst/pkgdown$
 ^index\.Rmd$
 ^index_files$
 ^index_cache$
 ^index\.md$
-^README\.Rmd$
-^\.README\.Rmd$
-^README\.md$
-^README_files$
-^README_cache$
+
 ^vignettes/get_started_cache$
 ^vignettes/example_models_cache$
 ^vignettes/webpages$
 ^vignettes/analyses$
+
 ^man/figures/vis-1\.png$
 ^man/figures/plot_greta_legend\.R$
 ^man/figures/name_icon_on_purple\.png$

.gitignore

@@ -5,12 +5,11 @@
 .RData
 .Ruserdata
 
-*_cache
-*_files
-
-vignette/figures
+vignettes/**/*_files/
+*_cache/
 
 *.pdf
 docs/*.Rmd
 docs/examples
 cran-comments.md
+paper/paper.html

.lintr

@@ -1,4 +1,4 @@
-linters: with_defaults(commas_linter = NULL, object_usage_linter = NULL)
+linters: with_defaults(commas_linter = NULL, object_usage_linter = NULL, object_length_linter = NULL)
 exclude: "# Exclude Linting"
 exclude_start: "# Begin Exclude Linting"
 exclude_end: "# End Exclude Linting"

.travis.yml

@@ -2,85 +2,73 @@ sudo: required
 language: r
 warnings_are_errors: false
 dist: trusty
-
-# enable RELEASE_CANDIDATE to run (slow & fragile) tests of sampler validity before releases
 env:
   global:
-    - RELEASE_CANDIDATE=false
-    - LINTR_COMMENT_BOT=false
-    - secure: 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
+  - RELEASE_CANDIDATE=false
+  - LINTR_COMMENT_BOT=true
+  - secure: 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
 
 r_binary_packages:
-  - abind
-  - coda
-  - codetools
-  - colorspace
-  - DBI
-  - digest
-  - foreign
-  - ggplot2
-  - inline
-  - lattice
-  - MASS
-  - MCMCpack
-  - mgcv
-  - mvtnorm
-  - nlme
-  - plyr
-  - Rcpp
-  - rpart
-  - rstan
-  - stringr
-  - survival
-  - XML
-
+- abind
+- coda
+- codetools
+- DBI
+- foreign
+- ggplot2
+- inline
+- lattice
+- MASS
+- MCMCpack
+- mgcv
+- mvtnorm
+- nlme
+- Rcpp
+- rpart
+- stringr
+- survival
 r_packages:
-  - reticulate
-  - tensorflow
-  - R6
-  - testthat
-  - covr
-  - DiagrammeR
-  - knitr
-  - rmarkdown
-  - rsvg
-  - bayesplot
-  - extraDistr
-  - devtools
-  - tidyverse
-  - lintr
-
-r_github_packages:
-  - rich-iannone/DiagrammeRsvg
-
+- reticulate
+- tensorflow
+- R6
+- testthat
+- covr
+- DiagrammeR
+- knitr
+- rmarkdown
+- rsvg
+- bayesplot
+- extraDistr
+- devtools
+- tidyverse
+- lintr
+- colorspace
+- digest
+- XML
+- plyr
+- DiagrammeRsvg
 cache:
   packages: true
   directories:
-    - $HOME/.cache/pip
-
+  - "$HOME/.cache/pip"
 addons:
   apt:
-    sources:
-      ubuntu-toolchain-r-test
+    sources: ubuntu-toolchain-r-test
     packages:
-      - libmagick++-dev
-      - wget
-      - libatlas3gf-base
-      - libatlas-dev
-      - python-joblib
-      - python-dev
-      - libv8-dev
-
+    - libmagick++-dev
+    - wget
+    - libatlas3gf-base
+    - libatlas-dev
+    - python-joblib
+    - python-dev
+    - libv8-dev
 before_install:
-  - pip install --user numpy
-  - pip install --user scipy
-  - pip install --user 'tensorflow==1.10'
-  - pip install --user 'tensorflow-probability'
-
+- pip install --user numpy
+- pip install --user scipy
+- pip install --user 'tensorflow==1.14'
+- pip install --user 'tensorflow-probability==0.7.0'
 after_success:
-  - Rscript -e "covr::codecov()"
-  - Rscript -e "lintr::lint_package()"
-
+- Rscript -e "covr::codecov()"
+- Rscript -e "lintr::lint_package()"
 email:
   on_success: change
   on_failure: change

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: greta
 Type: Package
 Title: Simple and Scalable Statistical Modelling in R
-Version: 0.3.0.9001
-Date: 2018-11-12
+Version: 0.3.1.9003
+Date: 2019-08-21
 Authors@R: c(
   person("Nick", "Golding", role = c("aut", "cre"),
          email = "[email protected]",
@@ -19,13 +19,15 @@ Authors@R: c(
   person("Paul", "Teetor", role = "ctb"),
   person("Jian", "Yen", role = "ctb")
   )
-Description: Write statistical models in R and fit them by MCMC on CPUs and GPUs, using Google TensorFlow (see <https://greta-dev.github.io/greta> for more information).
+Description: Write statistical models in R and fit them by MCMC and optimisation on CPUs and GPUs, using Google 'TensorFlow'.
+  greta lets you write your own model like in BUGS, JAGS and Stan, except that you write models right in R, it scales well to massive datasets, and it’s easy to extend and build on.
+  See the website for more information, including tutorials, examples, package documentation, and the greta forum.
 License: Apache License 2.0
-URL: https://github.com/greta-dev/greta
+URL: https://greta-stats.org
 BugReports: https://github.com/greta-dev/greta/issues
 SystemRequirements: Python (>= 2.7.0) with header files and shared library;
-    TensorFlow (>= 1.10; https://www.tensorflow.org/);
-    Tensorflow Probability (>=0.5.0; https://www.tensorflow.org/probability/)
+    TensorFlow (v1.14; https://www.tensorflow.org/);
+    TensorFlow Probability (v0.7.0; https://www.tensorflow.org/probability/)
 Encoding: UTF-8
 LazyData: true
 Depends:
@@ -65,7 +67,7 @@ Collate:
     'marginalisers.R'
 Imports:
     R6,
-    tensorflow,
+    tensorflow (>= 1.13.0),
     reticulate,
     progress (>= 1.2.0),
     future,
@@ -86,6 +88,8 @@ Suggests:
     tidyverse,
     fields,
     MASS,
-    abind
+    abind,
+    spelling
 VignetteBuilder: knitr
 RoxygenNote: 6.1.1
+Language: en-GB

NAMESPACE

@@ -88,6 +88,7 @@ S3method(print,initials)
 S3method(print,marginaliser)
 S3method(print,optimiser)
 S3method(print,sampler)
+S3method(print,summary.greta_array)
 S3method(print,unknowns)
 S3method(prod,greta_array)
 S3method(rbind,greta_array)
@@ -221,6 +222,7 @@ importFrom(grDevices,col2rgb)
 importFrom(grDevices,colorRampPalette)
 importFrom(progress,progress_bar)
 importFrom(reticulate,conda_binary)
+importFrom(reticulate,import)
 importFrom(reticulate,py_available)
 importFrom(reticulate,py_module_available)
 importFrom(reticulate,py_set_attr)

NEWS.md

@@ -1,7 +1,14 @@
-# greta 0.3.0.9001
+# greta (development version)
 
-* mcmc now works with TensorFlow Probability version 0.5.0 (#248)
+# greta 0.3.1
 
+This release is predominantly a patch to make greta work with recent versions of TensorFlow and TensorFlow Probability, which were not backward compatible with the versions on which greta previously depended. From this release forward, greta will depend on specific (rather than minimum) versions of these two pieces of software to avoid it breaking if more changes are made to the APIS of these packages.
+
+* greta now (only) works with TensorFlow 1.14.0 and TensorFlow Probability 0.7.0 (#289, #290)
+
+* behaviour of the `pb_update` argument to `mcmc()` has been changed slightly to avoid a bad interaction with thinning (#284)
+
+* various edits to the documentation to fix spelling mistakes and typos
 
 # greta 0.3.0
 

R/as_data.R

@@ -36,9 +36,12 @@ as_data <- function(x) {
   UseMethod("as_data", x)
 }
 
+
 # if it's already a *data* greta_array fine, else error
+# Begin Exclude Linting
 #' @export
 as_data.greta_array <- function(x) {
+# End Exclude Linting
   if (!inherits(get_node(x), "data_node")) {
     stop("cannot coerce a non-data greta_array to data",
          call. = FALSE)
@@ -47,7 +50,9 @@ as_data.greta_array <- function(x) {
 }
 
 # otherwise try to coerce to a greta array
+# Begin Exclude Linting
 #' @export
 as_data.default <- function(x) {
+# End Exclude Linting
   as.greta_array(x)
 }

R/calculate.R

@@ -92,7 +92,9 @@ calculate <- function(target, values = list(),
 
 }
 
+# Begin Exclude Linting
 calculate_mcmc.list <- function(target, target_name, values, tf_float) {
+# End Exclude Linting
 
   model_info <- get_model_info(values)
 
@@ -173,13 +175,13 @@ calculate_list <- function(target, values, tf_float) {
   # check that there are no unspecified variables on which the target depends
 
   # find all the nodes depended on by this one
-  dependencies <- get_node(target)$child_names(recursive = TRUE)
+  dependencies <- get_node(target)$parent_names(recursive = TRUE)
 
   # find all the nodes depended on by the new values, and remove them from the
   # list
   complete_dependencies <- lapply(fixed_greta_arrays,
                                   function(x)
-                                    get_node(x)$child_names(recursive = TRUE))
+                                    get_node(x)$parent_names(recursive = TRUE))
   complete_dependencies <- unique(unlist(complete_dependencies))
 
   unmet_dependencies <- dependencies[!dependencies %in% complete_dependencies]