From 331e8c3fe1a5e07aa1e9e050217ad7f520c72a27 Mon Sep 17 00:00:00 2001
From: Giorgio Alfredo Spedicato <spedygiorgio@gmail.com>
Date: Sun, 29 Sep 2024 21:24:57 +0200
Subject: [PATCH] fix: added tinytex setup

---
 .Rbuildignore                        |  1 +
 .github/workflows/R-CMD-check.yaml   | 15 ++++++++++++++-
 .github/workflows/test-coverage.yaml | 19 +++++++++++++++----
 DESCRIPTION                          |  2 +-
 NEWS.md                              |  7 +------
 README.md                            |  5 +++++
 support/.gitinclude                  |  0
 7 files changed, 37 insertions(+), 12 deletions(-)
 create mode 100644 support/.gitinclude

diff --git a/.Rbuildignore b/.Rbuildignore
index 45f1453..0505eb7 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -10,3 +10,4 @@ vignettes/*.log
 ^.*\.tar\.gz$
 ^LICENSE\.md$
 ^\.github$
+support/*.*
\ No newline at end of file
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
index 74d8c97..3455153 100644
--- a/.github/workflows/R-CMD-check.yaml
+++ b/.github/workflows/R-CMD-check.yaml
@@ -6,7 +6,9 @@ on:
   pull_request:
     branches: [main, master]
 
-name: R-CMD-check
+name: R-CMD-check.yaml
+
+permissions: read-all
 
 jobs:
   R-CMD-check:
@@ -44,6 +46,17 @@ jobs:
           extra-packages: any::rcmdcheck
           needs: check
 
+
+      - uses: r-lib/actions/setup-tinytex@v2
+
+      - name: Install additional LaTeX packages
+        run: |
+          tlmgr update --self
+          tlmgr install grfext
+          tlmgr install thumbpdf
+          tlmgr list --only-installed
+
       - uses: r-lib/actions/check-r-package@v2
         with:
           upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
index 960234c..9882260 100644
--- a/.github/workflows/test-coverage.yaml
+++ b/.github/workflows/test-coverage.yaml
@@ -6,7 +6,9 @@ on:
   pull_request:
     branches: [main, master]
 
-name: test-coverage
+name: test-coverage.yaml
+
+permissions: read-all
 
 jobs:
   test-coverage:
@@ -23,23 +25,32 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::covr
+          extra-packages: any::covr, any::xml2
           needs: coverage
 
       - name: Test coverage
         run: |
-          covr::codecov(
+          cov <- covr::package_coverage(
             quiet = FALSE,
             clean = FALSE,
             install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
           )
+          covr::to_cobertura(cov)
         shell: Rscript {0}
 
+      - uses: codecov/codecov-action@v4
+        with:
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }}
+          file: ./cobertura.xml
+          plugin: noop
+          disable_search: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+
       - name: Show testthat output
         if: always()
         run: |
           ## --------------------------------------------------------------------
-          find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
         shell: bash
 
       - name: Upload test results
diff --git a/DESCRIPTION b/DESCRIPTION
index 66b78e3..158f9a8 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -59,4 +59,4 @@ ByteCompile: yes
 Encoding: UTF-8
 BugReports: https://github.com/spedygiorgio/markovchain/issues
 URL: https://github.com/spedygiorgio/markovchain/
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
diff --git a/NEWS.md b/NEWS.md
index 5e036e5..fa8573d 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,11 +1,6 @@
 # markovchain 0.10.0
 
----
-editor_options: 
-  markdown: 
-    wrap: 72
-title: News
----
+-  Uptick pandoc requirements
 
 # News for version 0.9.6
 
diff --git a/README.md b/README.md
index 526e672..530d3be 100644
--- a/README.md
+++ b/README.md
@@ -18,3 +18,8 @@ devtools::install_github('spedygiorgio/markovchain')
 [![Downloads](http://cranlogs.r-pkg.org/badges/markovchain)](https://cran.r-project.org/package=markovchain)
  [![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/markovchain)](https://cran.r-project.org/package=markovchain)
  [![Research software impact](http://depsy.org/api/package/cran/markovchain/badge.svg)](http://depsy.org/package/r/markovchain)
+
+<!-- badges: start -->
+[![R-CMD-check](https://github.com/spedygiorgio/markovchain/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/spedygiorgio/markovchain/actions/workflows/R-CMD-check.yaml)
+[![Codecov test coverage](https://codecov.io/gh/spedygiorgio/markovchain/graph/badge.svg)](https://app.codecov.io/gh/spedygiorgio/markovchain)
+<!-- badges: end -->
diff --git a/support/.gitinclude b/support/.gitinclude
new file mode 100644
index 0000000..e69de29