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Code Releases Activity

(v3.0.1.9073) yet another go

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dr. M.S. (Matthijs) Berends
2026-06-26 11:51:08 +02:00
parent 6edae2037a
commit 4ca7fdf3d4
3 changed files with 18 additions and 4 deletions
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2
DESCRIPTION
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@@ -1,5 +1,5 @@
Package: AMR Package: AMR
Version: 3.0.1.9072 Version: 3.0.1.9073
Date: 2026-06-26 Date: 2026-06-26
Title: Antimicrobial Resistance Data Analysis Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR) Description: Functions to simplify and standardise antimicrobial resistance (AMR)

2
NEWS.md
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@@ -1,4 +1,4 @@
# AMR 3.0.1.9072 # AMR 3.0.1.9073
Planned as v3.1.0, end of June 2026. Planned as v3.1.0, end of June 2026.

18
data-raw/_generate_python_wrapper.sh
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@@ -72,8 +72,16 @@ base._libPaths(r_lib_path)
# Check if the AMR package is installed in R # Check if the AMR package is installed in R
if not isinstalled('AMR', lib_loc=r_lib_path): if not isinstalled('AMR', lib_loc=r_lib_path):
print(f"AMR: Installing latest AMR R package to {r_lib_path}...", flush=True) print(f"AMR: Installing latest AMR R package to {r_lib_path}...", flush=True)
utils.install_packages('remotes', repos='https://cloud.r-project.org', lib=r_lib_path, quiet=True) utils.install_packages(
'remotes',
repos='https://cloud.r-project.org',
lib=r_lib_path,
dependencies=True,
quiet=True
)
rint(f"AMR: Installed 'remotes'", flush=True)
remotes = importr('remotes', lib_loc=r_lib_path) remotes = importr('remotes', lib_loc=r_lib_path)
rint(f"AMR: Loaded 'remotes'", flush=True)
remotes.install_github('msberends/AMR', lib=r_lib_path, quiet=True) remotes.install_github('msberends/AMR', lib=r_lib_path, quiet=True)
# Retrieve Python AMR version # Retrieve Python AMR version
@@ -90,7 +98,13 @@ r_amr_version = str(r_amr_version[0])
if r_amr_version != python_amr_version: if r_amr_version != python_amr_version:
try: try:
print(f"AMR: Updating AMR package in {r_lib_path}...", flush=True) print(f"AMR: Updating AMR package in {r_lib_path}...", flush=True)
utils.install_packages('remotes', repos='https://cloud.r-project.org', lib=r_lib_path, quiet=True) utils.install_packages(
'remotes',
repos='https://cloud.r-project.org',
lib=r_lib_path,
dependencies=True,
quiet=True
)
remotes = importr('remotes', lib_loc=r_lib_path) remotes = importr('remotes', lib_loc=r_lib_path)
remotes.install_github('msberends/AMR', lib=r_lib_path, quiet=True) remotes.install_github('msberends/AMR', lib=r_lib_path, quiet=True)
r_amr_version = robjects.r(f'as.character(packageVersion("AMR", lib.loc = "{r_lib_path}"))') r_amr_version = robjects.r(f'as.character(packageVersion("AMR", lib.loc = "{r_lib_path}"))')