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(v3.0.0.9022) postpone new features - we like a clearly focussed bugfix release first

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dr. M.S. (Matthijs) Berends
2025-09-03 15:39:44 +02:00
parent 0744c6feee
commit 3ba1b8a10a
14 changed files with 105 additions and 198 deletions
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14
.github/workflows/check-old-tinytest.yaml vendored
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@@ -49,13 +49,13 @@ jobs:
# Test all old versions of R >= 3.0, we support them all!
# For these old versions, dependencies and vignettes will not be checked.
# For recent R versions, see check-recent.yaml (r-lib and tidyverse support the latest 5 major R releases).
- {os: ubuntu-latest, r: '3.6', allowfail: true}
# - {os: windows-latest, r: '3.5', allowfail: true} # always fails, horrible with UTF-8
- {os: ubuntu-latest, r: '3.4', allowfail: true}
- {os: ubuntu-latest, r: '3.3', allowfail: true}
- {os: ubuntu-latest, r: '3.2', allowfail: true}
- {os: ubuntu-latest, r: '3.1', allowfail: true}
- {os: ubuntu-latest, r: '3.0', allowfail: true}
- {os: ubuntu-latest, r: '3.6', allowfail: false}
# - {os: windows-latest, r: '3.5', allowfail: false} # always fails, horrible with UTF-8
# - {os: ubuntu-latest, r: '3.4', allowfail: false} # 3.1-3.4 now always fails with Error in grep(warn_re, lines, invert = TRUE, value = TRUE) attempt to set index 46/46 in SET_STRING_ELT
# - {os: ubuntu-latest, r: '3.3', allowfail: false}
# - {os: ubuntu-latest, r: '3.2', allowfail: false}
# - {os: ubuntu-latest, r: '3.1', allowfail: false}
- {os: ubuntu-latest, r: '3.0', allowfail: false}
env:
R_REMOTES_NO_ERRORS_FROM_WARNINGS: true

7
.github/workflows/publish-to-pypi.yml vendored
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@@ -39,7 +39,7 @@ jobs:
runs-on: ubuntu-latest
env:
PYPI_PAT: ${{ secrets.PYPI_PAT }}
GH_REPO_SCOPE: ${{ secrets.GH_REPO_SCOPE }}
steps:
- name: Checkout code
@@ -78,6 +78,7 @@ jobs:
cd PythonPackage/AMR
python -m twine upload --repository-url https://test.pypi.org/legacy/ dist/*
# TODO - Support Miniconda and Anaconda too
# - name: Set up Miniconda
# continue-on-error: true
# uses: conda-incubator/setup-miniconda@v2
@@ -117,7 +118,7 @@ jobs:
rm -rf PythonPackage
git init
git remote add origin https://$PYPI_PAT@github.com/msberends/AMR
git remote add origin https://$GH_REPO_SCOPE@github.com/msberends/AMR
git checkout --orphan python-wrapper
git config user.name "github-actions[bot]"
git config user.email "github-actions[bot]@users.noreply.github.com"
@@ -125,4 +126,4 @@ jobs:
git rm -rf . || true
git add .
git commit -m "Python wrapper update"
git push https://$PYPI_PAT@github.com/msberends/AMR.git python-wrapper --force
git push https://$GH_REPO_SCOPE@github.com/msberends/AMR.git python-wrapper --force

4
.github/workflows/renew-gpt-training-data.yml vendored
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@@ -39,7 +39,7 @@ jobs:
runs-on: ubuntu-latest
env:
PYPI_PAT: ${{ secrets.PYPI_PAT }}
GH_REPO_SCOPE: ${{ secrets.GH_REPO_SCOPE }}
steps:
- name: Checkout code
@@ -63,4 +63,4 @@ jobs:
git config user.email "github-actions[bot]@users.noreply.github.com"
git add latest_training_data.txt
git commit -m "GPT training data update"
git push https://$PYPI_PAT@github.com/msberends/amr-for-r-assistant.git main --force
git push https://$GH_REPO_SCOPE@github.com/msberends/amr-for-r-assistant.git main --force

75
.github/workflows/todo-tracker.yml vendored Normal file
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@@ -0,0 +1,75 @@
# ==================================================================== #
# TITLE: #
# AMR: An R Package for Working with Antimicrobial Resistance Data #
# #
# SOURCE CODE: #
# https://github.com/msberends/AMR #
# #
# PLEASE CITE THIS SOFTWARE AS: #
# Berends MS, Luz CF, Friedrich AW, et al. (2022). #
# AMR: An R Package for Working with Antimicrobial Resistance Data. #
# Journal of Statistical Software, 104(3), 1-31. #
# https://doi.org/10.18637/jss.v104.i03 #
# #
# Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many #
# colleagues from around the world, see our website. #
# #
# This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the #
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
# the Free Software Foundation. #
# We created this package for both routine data analysis and academic #
# research and it was publicly released in the hope that it will be #
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
on:
push:
# only on main
branches: "main"
name: Update TODO Tracker
jobs:
update-todo:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- name: Generate TODO list from R/
run: |
echo "## TODO Report" > todo.md
echo "" >> todo.md
echo "_This issue is automatically updated on each push to `main`._" >> todo.md
echo "" >> todo.md
todos=$(find R/ -type f ! -name "sysdata.rda" -exec grep -nH "TODO" {} + || true)
if [ -z "$todos" ]; then
echo "✅ No TODOs found." >> todo.md
else
echo "$todos" | awk -F: '
{
file = $1
line = $2
text = substr($0, index($0,$3))
if (file != last_file) {
if (last_file != "") print ""
print "### " file
last_file = file
}
printf "L%s: %s\n", line, text
}
' >> todo.md
fi
- name: Update GitHub issue
uses: peter-evans/create-or-update-comment@v4
with:
token: ${{ secrets.GH_REPO_SCOPE }}
issue-number: 231
body-file: todo.md
edit-mode: replace