Feature/develop fixnotes

.Rbuildignore

@@ -1,14 +1,15 @@
-^data-raw$
-^Meta$
-^doc$
-^docs$
-^_pkgdown\.yml$
-^codecov\.yml$
-^.*\.Rproj$
-^\.Rproj\.user$
-ignore/
-R_ignore/
-^index.md
-^\.github$
-^README\.Rmd$
-test_scripts/
+^data-raw$
+^Meta$
+^doc$
+^docs$
+^_pkgdown\.yml$
+^codecov\.yml$
+^.*\.Rproj$
+^\.Rproj\.user$
+ignore/
+R_ignore/
+^index.md
+^\.github$
+^README\.Rmd$
+test_scripts/
+LICENSE.md

.github/workflows/develop_build.yaml

@@ -1,81 +1,81 @@
-# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
-# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
-on:
-  push:
-    branches:
-      - develop
-  pull_request:
-    branches:
-      - develop
-
-name: develop_build
-
-jobs:
-  R-CMD-check:
-    runs-on: ${{ matrix.config.os }}
-
-    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
-
-    strategy:
-      fail-fast: false
-      matrix:
-        config:
-          - {os: windows-latest, r: 'release'}
-          - {os: macOS-latest, r: 'release'}
-          - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
-
-    env:
-      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
-      RSPM: ${{ matrix.config.rspm }}
-      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-
-    steps:
-      - uses: actions/checkout@v2
-
-      - uses: r-lib/actions/setup-r@v1
-        with:
-          r-version: ${{ matrix.config.r }}
-
-      - uses: r-lib/actions/setup-pandoc@v1
-
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
-        shell: Rscript {0}
-
-      - name: Cache R packages
-        if: runner.os != 'Windows'
-        uses: actions/cache@v2
-        with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
-
-      - name: Install system dependencies
-        if: runner.os == 'Linux'
-        run: |
-          while read -r cmd
-          do
-            eval sudo $cmd
-          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
-
-      - name: Install dependencies
-        run: |
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("rcmdcheck")
-        shell: Rscript {0}
-
-      - name: Check
-        env:
-          _R_CHECK_CRAN_INCOMING_REMOTE_: false
-        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
-        shell: Rscript {0}
-
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@main
-        with:
-          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
-          path: check
+# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
+# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
+on:
+  push:
+    branches:
+      - develop
+  pull_request:
+    branches:
+      - develop
+
+name: develop_build
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: windows-latest, r: 'release'}
+          - {os: macOS-latest, r: 'release'}
+          - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+
+    env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      RSPM: ${{ matrix.config.rspm }}
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+
+      - uses: r-lib/actions/setup-pandoc@v1
+
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+        shell: Rscript {0}
+
+      - name: Cache R packages
+        if: runner.os != 'Windows'
+        uses: actions/cache@v2
+        with:
+          path: ${{ env.R_LIBS_USER }}
+          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
+
+      - name: Install system dependencies
+        if: runner.os == 'Linux'
+        run: |
+          while read -r cmd
+          do
+            eval sudo $cmd
+          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
+
+      - name: Install dependencies
+        run: |
+          remotes::install_deps(dependencies = TRUE)
+          remotes::install_cran("rcmdcheck")
+        shell: Rscript {0}
+
+      - name: Check
+        env:
+          _R_CHECK_CRAN_INCOMING_REMOTE_: false
+        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
+        shell: Rscript {0}
+
+      - name: Upload check results
+        if: failure()
+        uses: actions/upload-artifact@main
+        with:
+          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
+          path: check

DESCRIPTION

@@ -1,43 +1,39 @@
-Package: drjacoby
-Type: Package
-Title: Flexible Markov Chain Monte Carlo via Reparameterization
-Version: 1.5.3
-Authors@R: c(
-    person("Bob", "Verity", email = "[email protected]", role = c("aut", "cre")),
-    person("Pete", "Winskill", email = "[email protected]", role = c("aut"))
-    )
-Description: drjacoby is an R package for performing Bayesian inference via
-    Markov chain monte carlo (MCMC). In addition to being highly flexible it
-    implements some advanced techniques that can improve mixing in tricky
-    situations.
-License: MIT + file LICENSE
-Encoding: UTF-8
-LazyData: true
-RoxygenNote: 7.1.2
-LinkingTo: 
-    Rcpp
-Imports: 
-    Rcpp,
-    coda,
-    parallel,
-    ggplot2,
-    RcppXPtrUtils,
-    usethis,
-    tools,
-    rlang,
-    cowplot,
-    dplyr,
-    magrittr,
-    readr,
-    data.table
-SystemRequirements: C++11
-Suggests: 
-    testthat,
-    covr,
-    knitr,
-    rmarkdown,
-    microbenchmark,
-    gridExtra
-BugReports: https://github.com/mrc-ide/drjacoby/issues
-VignetteBuilder: knitr
-Depends: R (>= 3.1.0)
+Package: drjacoby
+Type: Package
+Title: Flexible Markov Chain Monte Carlo via Reparameterization
+Version: 1.5.3
+Authors@R: c(
+    person("Bob", "Verity", email = "[email protected]", role = c("aut", "cre")),
+    person("Pete", "Winskill", email = "[email protected]", role = c("aut"))
+    )
+Description: drjacoby is an R package for performing Bayesian inference via
+    Markov chain monte carlo (MCMC). In addition to being highly flexible it
+    implements some advanced techniques that can improve mixing in tricky
+    situations.
+License: MIT + file LICENSE
+Encoding: UTF-8
+LazyData: true
+RoxygenNote: 7.1.2
+LinkingTo: 
+    Rcpp
+Imports: 
+    Rcpp,
+    coda,
+    parallel,
+    ggplot2,
+    usethis,
+    tools,
+    rlang,
+    cowplot,
+    dplyr,
+    magrittr
+Suggests: 
+    testthat,
+    covr,
+    knitr,
+    rmarkdown,
+    microbenchmark,
+    gridExtra
+BugReports: https://github.com/mrc-ide/drjacoby/issues
+VignetteBuilder: knitr
+Depends: R (>= 3.1.0)

LICENSE

@@ -1,21 +1,2 @@
-MIT License
-
-Copyright (c) 2019 MRC Centre for Outbreak Analysis and Modelling
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
+YEAR: 2024
+COPYRIGHT HOLDER: MRC Centre for Outbreak Analysis and Modelling

LICENSE.md

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2024 MRC Centre for Outbreak Analysis and Modelling
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.