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Merged
cansavvy merged 14 commits into from
Mar 25, 2025
Merged

Update to tidyverse 4.4 #5

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46d8464
Update Dockerfile
cansavvy Feb 12, 2025
4b786bc
Update Dockerfile
cansavvy Feb 12, 2025
ec836f1
Merge branch 'main' into cansavvy/bump-rocker
cansavvy Feb 12, 2025
534429c
update workflow
cansavvy Feb 13, 2025
53b2b93
Update workflow
cansavvy Feb 13, 2025
a1ac1a0
Update checkout@v4
cansavvy Feb 13, 2025
fed0657
Update docker
cansavvy Feb 13, 2025
49b5ca5
also install redis
cansavvy Feb 13, 2025
81e4d3d
Update
cansavvy Feb 13, 2025
1d76ac7
older one
cansavvy Feb 13, 2025
4b6d851
Update docker/Dockerfile
cansavvy Mar 4, 2025
3b82512
Update docker-management.yml
cansavvy Mar 6, 2025
9f80991
Update dockerfile and retrigger tests
cansavvy Mar 25, 2025
0a92fba
Merge remote-tracking branch 'origin/cansavvy/bump-rocker' into cansa…
cansavvy Mar 25, 2025
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3 changes: 2 additions & 1 deletion .github/workflows/docker-management.yml
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Original file line number Diff line number Diff line change
@@ -1,4 +1,5 @@
# Candace Savonen Oct 2021
# Updated Jan 2025

name: Docker management

Expand Down Expand Up @@ -55,7 +56,7 @@ jobs:
# Login to Dockerhub
- name: Login to DockerHub
if: ${{ github.event.inputs.dockerhubpush != 'false' }}
uses: docker/login-action@v1
uses: docker/login-action@v3
with:
# You will need to set up GitHub secrets with your Docker login info
# for this to work.
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2 changes: 1 addition & 1 deletion .github/workflows/run-r-notebook.yml
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Expand Up @@ -19,7 +19,7 @@ jobs:
steps:
# We need to tell github actions to use the code on the branch we are on
- name: checkout
uses: actions/checkout@v2
uses: actions/checkout@v4
with:
# How deep should it fetch?
fetch-depth: 0
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8 changes: 5 additions & 3 deletions docker/Dockerfile
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@@ -1,4 +1,4 @@
FROM rocker/tidyverse:4.0.2
FROM rocker/tidyverse:4.4
LABEL maintainer="cansav09@gmail.com"
WORKDIR /rocker-build/

Expand All @@ -9,7 +9,9 @@ RUN apt-get -y --no-install-recommends install \
python3-pip python3-dev

RUN pip3 install \
"pyrefinebio"
"pyrate-limiter==2.7.0" \
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@jashapiro jashapiro Feb 13, 2025

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This is the version listed in pyrefinebio

Suggested change
"pyrate-limiter==2.7.0" \
"pyrate-limiter==2.10.0" \

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@cansavvy cansavvy Mar 25, 2025

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This unfortunately didn't fix the problem. Tried rebuilding.

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@cansavvy cansavvy Mar 25, 2025 •
edited
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And in the docker image pip show pyrate_limiter shows

Name: pyrate-limiter
Version: 2.10.0
Summary: Python Rate-Limiter using Leaky-Bucket Algorithm
Home-page: https://github.com/vutran1710/PyrateLimiter
Author: vutr
Author-email: me@vutr.io
License: MIT
Location: /usr/local/lib/python3.12/dist-packages
Requires: 
Required-by:

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@jashapiro jashapiro Mar 25, 2025

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When I look at the one being pulled by your tests, jhudsl/reproducible-r:latest, it still has the newer version:

❯ docker run jhudsl/reproducible-r:latest pip show pyrate_limiter
WARNING: The requested image's platform (linux/amd64) does not match the detected host platform (linux/arm64/v8) and no specific platform was requested
Name: pyrate-limiter
Version: 3.0.0
Summary: Python Rate-Limiter using Leaky-Bucket Algorithm
Home-page: https://github.com/vutran1710/PyrateLimiter
Author: vutr
Author-email: me@vutr.io
License: MIT
Location: /usr/local/lib/python3.12/dist-packages
Requires:

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@jashapiro jashapiro Mar 25, 2025

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Locally, I can use the following two commands and get a successful run:

❯ docker build -f docker/Dockerfile . -t jhudsl/reproducible-r:test --platform linux/amd64
❯ docker run \
  --mount type=bind,target=/home/rstudio,source=$PWD \
  jhudsl/reproducible-r:test \
  bash run_analysis.sh

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@cansavvy cansavvy Mar 25, 2025 •
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Lol. Such a stupid reason. I've been using the wrong docker image name. It's jhudsl/reproducible-r NOT jhudsl/reproducible-r-example. 😅

Thanks for the help @jashapiro

redis \
pyrefinebio --break-system-packages

# Commonly used R packages
RUN Rscript -e "install.packages( \
Expand All @@ -19,4 +21,4 @@ RUN Rscript -e "install.packages( \
# Set final workdir for commands
WORKDIR /home/rstudio

ENV USER="rstudio" PASSWORD="rstudio" ROOT="TRUE"
ENV USER="rstudio" ROOT="TRUE"
⚡