From 46d84646f46578b4d0048b84e834f291f76f71ec Mon Sep 17 00:00:00 2001 From: Candace Savonen Date: Wed, 12 Feb 2025 15:33:38 -0500 Subject: [PATCH 01/12] Update Dockerfile --- docker/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docker/Dockerfile b/docker/Dockerfile index 16cd37b..c35c7f0 100644 --- a/docker/Dockerfile +++ b/docker/Dockerfile @@ -1,4 +1,4 @@ -FROM rocker/tidyverse:4.0.2 +FROM rocker/tidyverse:4.4 LABEL maintainer="cansav09@gmail.com" WORKDIR /rocker-build/ From 4b786bcdfbe7f9cbbf3574df09f16ac1d28742af Mon Sep 17 00:00:00 2001 From: Candace Savonen Date: Wed, 12 Feb 2025 15:38:17 -0500 Subject: [PATCH 02/12] Update Dockerfile --- docker/Dockerfile | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docker/Dockerfile b/docker/Dockerfile index c35c7f0..02c9acc 100644 --- a/docker/Dockerfile +++ b/docker/Dockerfile @@ -9,7 +9,7 @@ RUN apt-get -y --no-install-recommends install \ python3-pip python3-dev RUN pip3 install \ - "pyrefinebio" + pyrefinebio --break-system-packages # Commonly used R packages RUN Rscript -e "install.packages( \ @@ -19,4 +19,4 @@ 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" From 534429c21eac9b2422232554ea2e02495d1810fd Mon Sep 17 00:00:00 2001 From: Candace Savonen Date: Thu, 13 Feb 2025 09:36:21 -0500 Subject: [PATCH 03/12] update workflow --- .github/workflows/run-r-notebook.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/run-r-notebook.yml b/.github/workflows/run-r-notebook.yml index 3f25762..50cac77 100644 --- a/.github/workflows/run-r-notebook.yml +++ b/.github/workflows/run-r-notebook.yml @@ -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@v3 with: # How deep should it fetch? fetch-depth: 0 From 53b2b933cbcdf8c8a3e394139c8d7f898b6b57f5 Mon Sep 17 00:00:00 2001 From: Candace Savonen Date: Thu, 13 Feb 2025 09:45:09 -0500 Subject: [PATCH 04/12] Update workflow --- .github/workflows/docker-management.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/docker-management.yml b/.github/workflows/docker-management.yml index bb90260..e641f47 100644 --- a/.github/workflows/docker-management.yml +++ b/.github/workflows/docker-management.yml @@ -1,4 +1,5 @@ # Candace Savonen Oct 2021 +# Updated Jan 2025 name: Docker management @@ -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. From a1ac1a0136c98821d5ecbe7a5827bce51458d7f1 Mon Sep 17 00:00:00 2001 From: Candace Savonen Date: Thu, 13 Feb 2025 09:51:03 -0500 Subject: [PATCH 05/12] Update checkout@v4 --- docker/Dockerfile | 1 + 1 file changed, 1 insertion(+) diff --git a/docker/Dockerfile b/docker/Dockerfile index 02c9acc..60e845c 100644 --- a/docker/Dockerfile +++ b/docker/Dockerfile @@ -9,6 +9,7 @@ RUN apt-get -y --no-install-recommends install \ python3-pip python3-dev RUN pip3 install \ + pyrate_limiter \ pyrefinebio --break-system-packages # Commonly used R packages From fed0657342147e380d77843b5418484678cea631 Mon Sep 17 00:00:00 2001 From: Candace Savonen Date: Thu, 13 Feb 2025 10:41:09 -0500 Subject: [PATCH 06/12] Update docker --- .github/workflows/run-r-notebook.yml | 2 +- docker/Dockerfile | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/run-r-notebook.yml b/.github/workflows/run-r-notebook.yml index 50cac77..f2a6d40 100644 --- a/.github/workflows/run-r-notebook.yml +++ b/.github/workflows/run-r-notebook.yml @@ -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@v3 + uses: actions/checkout@v4 with: # How deep should it fetch? fetch-depth: 0 diff --git a/docker/Dockerfile b/docker/Dockerfile index 60e845c..71c55f8 100644 --- a/docker/Dockerfile +++ b/docker/Dockerfile @@ -9,8 +9,8 @@ RUN apt-get -y --no-install-recommends install \ python3-pip python3-dev RUN pip3 install \ - pyrate_limiter \ - pyrefinebio --break-system-packages + "pyrate-limiter==3.0.0" \ + pyrefinebio --break-system-packages # Commonly used R packages RUN Rscript -e "install.packages( \ From 49b5ca52dfc251cb9c9fed22313295f62610a039 Mon Sep 17 00:00:00 2001 From: Candace Savonen Date: Thu, 13 Feb 2025 10:47:03 -0500 Subject: [PATCH 07/12] also install redis --- docker/Dockerfile | 1 + 1 file changed, 1 insertion(+) diff --git a/docker/Dockerfile b/docker/Dockerfile index 71c55f8..6a254ff 100644 --- a/docker/Dockerfile +++ b/docker/Dockerfile @@ -10,6 +10,7 @@ RUN apt-get -y --no-install-recommends install \ RUN pip3 install \ "pyrate-limiter==3.0.0" \ + Redis \ pyrefinebio --break-system-packages # Commonly used R packages From 81e4d3d933a0b5deba46260f2dbe3238b768aed4 Mon Sep 17 00:00:00 2001 From: Candace Savonen Date: Thu, 13 Feb 2025 10:49:26 -0500 Subject: [PATCH 08/12] Update --- docker/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docker/Dockerfile b/docker/Dockerfile index 6a254ff..9ceb80d 100644 --- a/docker/Dockerfile +++ b/docker/Dockerfile @@ -10,7 +10,7 @@ RUN apt-get -y --no-install-recommends install \ RUN pip3 install \ "pyrate-limiter==3.0.0" \ - Redis \ + redis \ pyrefinebio --break-system-packages # Commonly used R packages From 1d76ac760de636fbb1a3a8d394a63409c5097624 Mon Sep 17 00:00:00 2001 From: Candace Savonen Date: Thu, 13 Feb 2025 10:53:27 -0500 Subject: [PATCH 09/12] older one --- docker/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docker/Dockerfile b/docker/Dockerfile index 9ceb80d..12bff4f 100644 --- a/docker/Dockerfile +++ b/docker/Dockerfile @@ -9,7 +9,7 @@ RUN apt-get -y --no-install-recommends install \ python3-pip python3-dev RUN pip3 install \ - "pyrate-limiter==3.0.0" \ + "pyrate-limiter==2.7.0" \ redis \ pyrefinebio --break-system-packages From 4b6d8513833978f5a6179ca0f6829569d3bac577 Mon Sep 17 00:00:00 2001 From: Candace Savonen Date: Tue, 4 Mar 2025 14:31:44 -0500 Subject: [PATCH 10/12] Update docker/Dockerfile Co-authored-by: Joshua Shapiro --- docker/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docker/Dockerfile b/docker/Dockerfile index 12bff4f..7d93a4e 100644 --- a/docker/Dockerfile +++ b/docker/Dockerfile @@ -9,7 +9,7 @@ RUN apt-get -y --no-install-recommends install \ python3-pip python3-dev RUN pip3 install \ - "pyrate-limiter==2.7.0" \ + "pyrate-limiter==2.10.0" \ redis \ pyrefinebio --break-system-packages From 3b82512e31c533eb4e0a63a3fad7cd7465fb61ef Mon Sep 17 00:00:00 2001 From: Candace Savonen Date: Thu, 6 Mar 2025 11:33:01 -0500 Subject: [PATCH 11/12] Update docker-management.yml --- .github/workflows/docker-management.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/docker-management.yml b/.github/workflows/docker-management.yml index e641f47..0101993 100644 --- a/.github/workflows/docker-management.yml +++ b/.github/workflows/docker-management.yml @@ -29,7 +29,7 @@ jobs: # Setup layer cache - name: Cache Docker layers - uses: actions/cache@v2 + uses: actions/cache@v4 with: path: /tmp/.buildx-cache key: ${{ runner.os }}-buildx-${{ github.sha }} From 9f809913f6942f18b314d1a24d088d91a9d800ff Mon Sep 17 00:00:00 2001 From: Candace Savonen Date: Tue, 25 Mar 2025 10:56:54 -0400 Subject: [PATCH 12/12] Update dockerfile and retrigger tests --- docker/Dockerfile | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/docker/Dockerfile b/docker/Dockerfile index 12bff4f..dc9f6d3 100644 --- a/docker/Dockerfile +++ b/docker/Dockerfile @@ -8,8 +8,9 @@ RUN apt-get update && apt-get install -y --no-install-recommends apt-utils dialo RUN apt-get -y --no-install-recommends install \ python3-pip python3-dev +# Install refine bio and dependencies RUN pip3 install \ - "pyrate-limiter==2.7.0" \ + "pyrate-limiter==2.10.0" \ redis \ pyrefinebio --break-system-packages