127 run autoconf or autoreconf and commit configure file when creatin…

…g new release branch (#130)

* automatically regenerate configure file

* avoid hardcoding branch

* Revert "avoid hardcoding branch"

This reverts commit 1e43957.

* targeting the latest release branch for the status badge

* automatically update status badges

* capture all version strings in release-x.y.z

.github/workflows/initiate_version_release.yml

@@ -48,6 +48,7 @@ jobs:
          echo "VERSION=`echo $(echo '${{ github.ref_name }}'|grep -Eo '[0-9]+.[0-9]+.[0-9]+')`" >> $GITHUB_OUTPUT
          echo "PREVIOUS_VERSION=`echo $(git tag --list --sort=version:refname | grep -E '^[0-9]+.[0-9]+.[0-9]+$' | tail -n1)`" >> $GITHUB_OUTPUT
          echo "AUTHOR=`echo $(git log -1 --pretty=%an)`" >> $GITHUB_OUTPUT
+
      - name: Get git-chglog and update CHANGELOG
        run: |
          wget ${{ env.CHGLOG_PATH }}/${{ env.CHGLOG_RELEASE}}.tar.gz  # get the binary for the chglog
@@ -63,10 +64,12 @@ jobs:
        uses: r-lib/actions/setup-r@v2
        with:
          use-public-rspm: true
+
      - name: Install desc to update DESCRIPTION file
        run: |
          install.packages(c("desc"))
        shell: Rscript {0}
+
      - name: Update DESCRIPTION file
        run: |
          df = desc::description$new(file='DESCRIPTION')
@@ -80,6 +83,16 @@ jobs:
          sed -i -e '/^AC_INIT/s/[0-9]\+.[0-9]\.[0-9]\+/${{ steps.release_version.outputs.version }}/g' configure.ac
        shell: bash
 
+     - name: Generate the configure file
+       run: |
+         sudo apt-get -y install autoconf
+         autoreconf
+
+     - name: Update status badges in the readme file
+       run: | 
+         # updated the branch parameter for all badges
+         sed -i -e "s/?branch=release-[0-9]\+.[0-9]\.[0-9]\+/?branch=release-${{ steps.release_version.outputs.version}}/g" README.md
+
      - name: Create version release Pull Request
        id: release_pr
        # NOTE: We might want to perform this step with gh cli natively
@@ -89,9 +102,11 @@ jobs:
          commit-message: "Version ${{ steps.release_version.outputs.version }}"
          token: ${{ secrets.GITHUB_TOKEN }}
          add-paths: |
+           README.md
            NEWS.md
            DESCRIPTION
            configure.ac
+           configure
          delete-branch: true  # NOTE: No immediate delete after merge, instead branches with no diff are deleted
          title: Release version ${{ steps.release_version.outputs.version }}
          body: |

README.md

@@ -2,8 +2,10 @@
 # abn: Additive Bayesian Networks <a href="https://r-bayesian-networks.org/"><img src="man/figures/logo.png" align="right" height="139" /></a>
 
 <!-- badges: start -->
+<!-- WARNING: -->
+<!-- The ?branch=release-x.y.y is updated automatically by the initiate_version_release workflow -->
 [![status](https://joss.theoj.org/papers/1bbc43a2be86f5d3f831cedb5cf81812/status.svg)](https://joss.theoj.org/papers/1bbc43a2be86f5d3f831cedb5cf81812)
-[![On Label CRAN Checks](https://github.com/furrer-lab/abn/actions/workflows/onlabel_CRAN_checks.yml/badge.svg)](https://github.com/furrer-lab/abn/actions/workflows/onlabel_CRAN_checks.yml)
+[![On Label CRAN Checks](https://github.com/furrer-lab/abn/actions/workflows/onlabel_CRAN_checks.yml/badge.svg?branch=release-3.1.1)](https://github.com/furrer-lab/abn/actions/workflows/onlabel_CRAN_checks.yml)
 [![Codecov](https://img.shields.io/codecov/c/github/furrer-lab/abn)](https://app.codecov.io/gh/furrer-lab/abn)
 [![GitHub R package version](https://img.shields.io/github/r-package/v/furrer-lab/abn)](https://github.com/furrer-lab/abn/tags)
 ![cran](https://www.r-pkg.org/badges/version-ago/abn)