Feature marginalise update #752

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njtierney wants to merge 979 commits into feature/marginalise from feature-marginalise-update

.EDIT_WEBSITE.md

            
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    @@ -6,7 +6,7 @@ This document explains how [the greta website](https://greta-stats.org) is built
  
    *greta* uses a customised [pkgdown](http://pkgdown.r-lib.org/) setup to build the greta website at [https://greta-stats.org](). This setup does not create the [greta forum](https://forum.greta-stats.org), which uses [discourse](https://www.discourse.org/) running on [a cloud server](https://www.digitalocean.com/docs/one-clicks/discourse/).

    Due to [a small bug in pkgdown](https://github.com/r-lib/pkgdown/pull/834), the build currently only works with fork of the main pkgdown repo. You can install that version with:

    The build currently only works with fork of the main pkgdown repo. You can install that version with:

    ```

    devtools::install_github("goldingn/pkgdown@rmd_home_template")

    @@ -80,7 +80,7 @@ If relevant, a level-4 header 'BUGS/JAGS code' and a (non-R) markdown code chunk
  
    ### Stan code

    If relevant, a level-4 header 'Stan code' and an R code chunk (with chunk argument `echo=FALSE`) with an R command to read in the equivalent model from the [Stan example models repository](https://github.com/stan-dev/example-models). The chunk name must that differ from the other example models and end in `_stan`. The code block should be surrounded by an html `div` command defining the Stan code formatting.

    ### 

    ###

    Here's a template:

    ````

    @@ -118,4 +118,3 @@ This should be saved as an .Rmd file with a meaningful name in the directory `in
  
    ```{r child='../inst/examples/my_example.Rmd'}

    ```

    ````

.Rbuildignore

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+Diff line change
@@ Expand Up / @@ -5,14 +5,15 @@ @@
     ^.github$
     ^.netlify$
     ^.lintr$
-    ^.travis.yml$
     ^README\.md$
     ^CRAN-RELEASE$
     ^CODE_OF_CONDUCT\.md$
     ^\.EDIT_WEBSITE\.md$
-    ^LICENSE$
+    ^LICENSE\.md$
+    LICENSE
     ^cran-comments\.md$
+    ^revdep$
     ^logos$
     ^paper$
@@ Expand All / @@ -36,3 +37,16 @@ @@
     ^man/figures/main_icon\.png$
     ^man/figures/greta-header\.png$
     ^man/figures/logo\.png$
+    ^\.github/workflows/R-CMD-check\.yaml$
+    ^\.github$
+    ^codecov\.yml$
+    ^depends\.rds$
+    ^CRAN-SUBMISSION$
+    ^touchstone$
+    ^.lazytest$
+    ^\.lazytext$
+    ^revdep$
+    ^__autograph*
+    ^testlog
+    ^data-raw$

.github/.gitignore

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		@@ -0,0 +1 @@
		*.html

.github/CONTRIBUTING.md

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+Diff line change
@@ Expand Up @@
     ### Pull request process
     *  We recommend that you create a Git branch for each pull request (PR).
-    *  Look at the Travis and AppVeyor build status before and after making changes.
+    *  Look at the Github actions build status before and after making changes.
     The `README` should contain badges for any continuous integration services used
     by the package.
     *  New code should follow the tidyverse [style guide](http://style.tidyverse.org).
@@ Expand Down @@

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

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+Diff line change
@@ -0,0 +1,117 @@
+    on:
+      push:
+        branches:
+          - main
+          - master
+      pull_request:
+        branches:
+          - main
+          - master
+      schedule:
+        - cron: '1 23 * * Sun'
+    name: R-CMD-check
+    defaults:
+      run:
+        shell: Rscript {0}
+    jobs:
+      R-CMD-check:
+        name: ${{ matrix.os }}, tf-${{ matrix.tf }}, R-${{ matrix.r}}
+        timeout-minutes: 30
+        strategy:
+          fail-fast: false
+          matrix:
+            include:
+              - {os: 'ubuntu-latest' , tf: 'default', r: 'release'}
+              - {os: 'windows-latest', tf: 'default', r: 'release'}
+              - {os: 'macOS-latest'  , tf: 'default', r: 'release'}
+        runs-on: ${{ matrix.os }}
+        continue-on-error: ${{ matrix.tf == 'nightly' || contains(matrix.tf, 'rc') || matrix.r == 'devel' }}
+        env:
+          R_REMOTES_NO_ERRORS_FROM_WARNINGS: 'true'
+          R_COMPILE_AND_INSTALL_PACKAGES: 'never'
+          GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+        steps:
+          - uses: actions/checkout@v2
+          - uses: r-lib/actions/setup-r@v2
+            id: setup-r
+            with:
+              r-version: ${{ matrix.r }}
+              Ncpus: '2L'
+              use-public-rspm: true
+          - uses: r-lib/actions/setup-pandoc@v2
+          - name: Get Date
+            id: get-date
+            shell: bash
+            run: |
+              echo "::set-output name=year-week::$(date -u "+%Y-%U")"
+              echo "::set-output name=date::$(date -u "+%F")"
+          - name: Restore R package cache
+            uses: actions/cache@v2
+            id: r-package-cache
+            with:
+              path: ${{ env.R_LIBS_USER }}
+              key: ${{ matrix.os }}-${{ steps.setup-r.outputs.installed-r-version }}-${{ steps.get-date.outputs.year-week }}-1
+          - name: Install remotes
+            if: steps.r-package-cache.outputs.cache-hit != 'true'
+            run: install.packages("remotes")
+          - name: Install system dependencies
+            if: runner.os == 'Linux'
+            shell: bash
+            run: |
+              . /etc/os-release
+              while read -r cmd
+              do
+                echo "$cmd"
+                sudo $cmd
+              done < <(Rscript -e "writeLines(remotes::system_requirements('$ID-$VERSION_ID'))")
+          - name: Install package + deps
+            run: remotes::install_local(dependencies = TRUE, force = TRUE)
+          - name: Install greta deps
+            run: |
+              library(greta)
+              greta::install_greta_deps(timeout = 50)
+          - name: Situation Report on greta install
+            run: greta::greta_sitrep()
+          - name: Install rcmdcheck
+            run: remotes::install_cran("rcmdcheck")
+          - name: Check
+            run: rcmdcheck::rcmdcheck(args = '--no-manual', error_on = 'warning', check_dir = 'check')
+          - name: Show testthat output
+            if: always()
+            shell: bash
+            run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
+          - name: Don't use tar from old Rtools to store the cache
+            if: ${{ runner.os == 'Windows' && startsWith(steps.install-r.outputs.installed-r-version, '3') }}
+            shell: bash
+            run: echo "C:/Program Files/Git/usr/bin" >> $GITHUB_PATH
+          - name: Check on single core machine
+            if: runner.os != 'Windows'
+            env:
+              R_PARALLELLY_AVAILABLE_CORES: 1
+            run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran", "--no-multiarch"))
+          - name: Session info
+            run: |
+              options(width = 100)
+              pkgs <- installed.packages()[, "Package"]
+              sessioninfo::session_info(pkgs, include_base = TRUE)

.github/workflows/pkgdown.yaml

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+Diff line change
@@ -0,0 +1,59 @@
+    on:
+      push:
+        branches:
+          - main
+          - master
+    name: pkgdown
+    jobs:
+      pkgdown:
+        runs-on: ubuntu-18.04
+        env:
+          RSPM: https://packagemanager.rstudio.com/cran/__linux__/bionic/latest
+          GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+        steps:
+          - uses: actions/checkout@v2
+          - uses: r-lib/actions/setup-r@v2
+            id: install-r
+          - uses: r-lib/actions/setup-pandoc@v2
+          - name: Install pak and query dependencies
+            run: |
+              install.packages("pak", repos = "https://r-lib.github.io/p/pak/dev/")
+              saveRDS(pak::pkg_deps("local::.", dependencies = TRUE), ".github/r-depends.rds")
+            shell: Rscript {0}
+          - name: Restore R package cache
+            uses: actions/cache@v2
+            with:
+              path: |
+                ${{ env.R_LIBS_USER }}/*
+                !${{ env.R_LIBS_USER }}/pak
+              key: ubuntu-18.04-${{ steps.install-r.outputs.installed-r-version }}-1-${{ hashFiles('.github/r-depends.rds') }}
+              restore-keys: ubuntu-18.04-${{ steps.install-r.outputs.installed-r-version }}-1-
+          - name: Install system dependencies
+            if: runner.os == 'Linux'
+            run: |
+              pak::local_system_requirements(execute = TRUE)
+              pak::pkg_system_requirements("pkgdown", execute = TRUE)
+            shell: Rscript {0}
+          - name: Install dependencies
+            run: |
+              pak::local_install_dev_deps(upgrade = TRUE, dependencies = c("all", "Config/Needs/website"))
+              pak::pkg_install("goldingn/pkgdown@rmd_home_template")
+            shell: Rscript {0}
+          - name: Install package
+            run: R CMD INSTALL .
+          - name: Build and deploy pkgdown site
+            run: |
+              git config --local user.name "$GITHUB_ACTOR"
+              git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com"
+              Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)'

.github/workflows/pr-commands.yaml

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+Diff line change
@@ -0,0 +1,79 @@
+    # Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+    # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+    on:
+      issue_comment:
+        types: [created]
+    name: Commands
+    jobs:
+      document:
+        if: ${{ github.event.issue.pull_request && (github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'OWNER') && startsWith(github.event.comment.body, '/document') }}
+        name: document
+        runs-on: ubuntu-latest
+        env:
+          GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+        steps:
+          - uses: actions/checkout@v3
+          - uses: r-lib/actions/pr-fetch@v2
+            with:
+              repo-token: ${{ secrets.GITHUB_TOKEN }}
+          - uses: r-lib/actions/setup-r@v2
+            with:
+              use-public-rspm: true
+          - uses: r-lib/actions/setup-r-dependencies@v2
+            with:
+              extra-packages: any::roxygen2
+              needs: pr-document
+          - name: Document
+            run: roxygen2::roxygenise()
+            shell: Rscript {0}
+          - name: commit
+            run: |
+              git config --local user.name "$GITHUB_ACTOR"
+              git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com"
+              git add man/\* NAMESPACE
+              git commit -m 'Document'
+          - uses: r-lib/actions/pr-push@v2
+            with:
+              repo-token: ${{ secrets.GITHUB_TOKEN }}
+      style:
+        if: ${{ github.event.issue.pull_request && (github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'OWNER') && startsWith(github.event.comment.body, '/style') }}
+        name: style
+        runs-on: ubuntu-latest
+        env:
+          GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+        steps:
+          - uses: actions/checkout@v3
+          - uses: r-lib/actions/pr-fetch@v2
+            with:
+              repo-token: ${{ secrets.GITHUB_TOKEN }}
+          - uses: r-lib/actions/setup-r@v2
+          - name: Install dependencies
+            run: install.packages("styler")
+            shell: Rscript {0}
+          - name: Style
+            run: styler::style_pkg()
+            shell: Rscript {0}
+          - name: commit
+            run: |
+              git config --local user.name "$GITHUB_ACTOR"
+              git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com"
+              git add \*.R
+              git commit -m 'Style'
+          - uses: r-lib/actions/pr-push@v2
+            with:
+              repo-token: ${{ secrets.GITHUB_TOKEN }}

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