Smaller Docker image size #1
Conversation
WalkthroughThe changes involve significant updates to both the Dockerfile and README.md for the DIA-NN project. The Dockerfile transitions the base image from Debian to Ubuntu, adds various metadata labels, modifies the installation process, and updates the method for downloading DIA-NN software. The README.md clarifies licensing implications for different DIA-NN versions, confirms the software version, and updates the command for running the Docker container. Changes
Sequence Diagram(s)sequenceDiagram
participant User
participant DockerContainer
participant DIA-NN
User->>DockerContainer: Run container
DockerContainer->>DIA-NN: Execute ./diann-1.9.2/diann-linux
DIA-NN-->>DockerContainer: Process data
DockerContainer-->>User: Return results
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Actionable comments posted: 2
🧹 Outside diff range and nitpick comments (4)
README.md (1)
Line range hint
19-21: Base image information needs to be updatedThe README still shows
debian:12.8-slimas the base image, but according to the PR changes, the base image has been changed toubuntu:22.04. This needs to be updated to maintain accuracy.Apply this diff to fix the inconsistency:
- **Base Image**: `debian:12.8-slim` + **Base Image**: `ubuntu:22.04`Dockerfile (3)
Line range hint
8-8: Parameterize the DIA-NN version to improve maintainabilityDefining the DIA-NN version as a build argument prevents duplication and simplifies future updates. Using a variable for the version reduces the risk of inconsistencies.
Apply this diff to parameterize the DIA-NN version:
+ARG DIANN_VERSION=1.9.2 LABEL software.version="1.9.2" +LABEL software.version="${DIANN_VERSION}" -RUN wget https://github.com/vdemichev/DiaNN/releases/download/1.9.2/diann-1.9.2.Linux.zip -O diann-1.9.2.Linux.zip +RUN wget https://github.com/vdemichev/DiaNN/releases/download/${DIANN_VERSION}/diann-${DIANN_VERSION}.Linux.zip -O diann-${DIANN_VERSION}.Linux.zip -RUN unzip diann-1.9.2.Linux.zip +RUN unzip diann-${DIANN_VERSION}.Linux.zip -RUN chmod -R 775 /diann-1.9.2 +RUN chmod -R 775 /diann-${DIANN_VERSION}Also applies to: 34-34, 37-37, 40-40
34-37: Remove unnecessary files and combine RUN commands to reduce image sizeAfter unzipping the DIA-NN package, the zip file is no longer needed. Combining commands into a single
RUNstatement reduces the number of layers and overall image size.Apply this diff to clean up unnecessary files and optimize layering:
-RUN wget https://github.com/vdemichev/DiaNN/releases/download/${DIANN_VERSION}/diann-${DIANN_VERSION}.Linux.zip -O diann-${DIANN_VERSION}.Linux.zip -RUN unzip diann-${DIANN_VERSION}.Linux.zip +RUN wget https://github.com/vdemichev/DiaNN/releases/download/${DIANN_VERSION}/diann-${DIANN_VERSION}.Linux.zip -O diann-${DIANN_VERSION}.Linux.zip && \ + unzip diann-${DIANN_VERSION}.Linux.zip && \ + rm diann-${DIANN_VERSION}.Linux.zip
40-40: Set appropriate permissions and consider adding DIA-NN to PATHEnsure that the DIA-NN binary is executable and consider adding it to the
PATHfor easier execution.Apply this diff to update permissions and set the
PATH:RUN chmod -R 775 /diann-${DIANN_VERSION} +ENV PATH="/diann-${DIANN_VERSION}:$PATH"
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Review profile: CHILL
📒 Files selected for processing (2)
Dockerfile(2 hunks)README.md(1 hunks)
🔇 Additional comments (3)
README.md (2)
42-42: LGTM: Docker run command updated correctly
The Docker run command has been updated to use the correct path to the DIA-NN binary, which aligns with the new container structure.
Line range hint 9-11: Verify the license file reference
The documentation references a license file DIANN1.9.2-LICENSE.txt but we should verify its existence and accessibility.
✅ Verification successful
License file reference is correctly linked in the documentation
The verification confirms that the DIANN1.9.2-LICENSE.txt file exists in the repository and is accessible, making the documentation reference accurate.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Check if the referenced license file exists
if [ -f "DIANN1.9.2-LICENSE.txt" ]; then
echo "License file exists"
else
echo "Warning: Referenced license file DIANN1.9.2-LICENSE.txt not found"
fi
# Check for any other license files that might be misnamed
fd -t f -e txt -e md -e pdf -i license
Length of output: 148
Dockerfile (1)
42-43:
Verify compliance with DIA-NN licensing terms before distributing the Docker image
DIA-NN's licensing terms may restrict the distribution of Docker images containing the software. Ensure that including DIA-NN in this image complies with the license terms to avoid legal issues.
Run the following script to retrieve the DIA-NN license text for review:
Please review the license to ensure compliance.
✅ Verification successful
Let's search for any license files in the repository that might contain DIA-NN's license terms, since the direct URL fetch failed. This will help us verify the licensing compliance requirements.
DIA-NN license has specific restrictions on commercial and cloud usage
Based on the discovered license terms in the repository, DIA-NN has important usage restrictions:
- Commercial/for-profit use is not permitted
- Cloud usage is only allowed under collaborative use with the Demichev laboratory
- Usage requires proper attribution in any derived materials
- Experimental functionality requires collaboration with the Demichev laboratory
The warning comment in the Dockerfile is appropriate and necessary, as users need to carefully review these terms before using or distributing the Docker image.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Retrieve the DIA-NN license text for version 1.9.2
curl -sSL https://github.com/vdemichev/DiaNN/raw/main/LICENSE.txt
Length of output: 102512
Script:
#!/bin/bash
# Search for DIA-NN license information in the repository
fd -t f -i "license|copying" -X cat {}
Length of output: 16927
| @@ -1,5 +1,6 @@ | |||
| FROM debian:12.8-slim AS builder | |||
| FROM ubuntu:22.04 | |||
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🛠️ Refactor suggestion
Consider using a smaller base image to achieve the goal of reducing image size
Switching from debian:12-slim to ubuntu:22.04 may increase the Docker image size, as Ubuntu images are generally larger than Debian slim images. To meet the PR objective of reducing the image size, consider using debian:12-slim or another minimal base image.
| RUN apt-get update && apt-get upgrade -y | ||
|
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| RUN sed -i '/en_US.UTF-8/s/^# //g' /etc/locale.gen && \ | ||
| locale-gen && update-locale LANG=en_US.UTF-8 | ||
| # Install necessary packages including locales | ||
| RUN apt-get install wget unzip libgomp1 locales -y |
There was a problem hiding this comment.
🛠️ Refactor suggestion
Optimize package installation to reduce image size and avoid unnecessary upgrades
Running apt-get upgrade is generally discouraged in Dockerfiles, as it can increase image size and may introduce unintended changes. Combining apt-get update and apt-get install in a single RUN command reduces image layers and avoids cache issues.
Apply this diff to optimize package installation:
-RUN apt-get update && apt-get upgrade -y
-# Install necessary packages including locales
-RUN apt-get install wget unzip libgomp1 locales -y
+RUN apt-get update && \
+ apt-get install -y --no-install-recommends wget unzip libgomp1 locales && \
+ rm -rf /var/lib/apt/lists/*📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| RUN apt-get update && apt-get upgrade -y | |
| RUN sed -i '/en_US.UTF-8/s/^# //g' /etc/locale.gen && \ | |
| locale-gen && update-locale LANG=en_US.UTF-8 | |
| # Install necessary packages including locales | |
| RUN apt-get install wget unzip libgomp1 locales -y | |
| RUN apt-get update && \ | |
| apt-get install -y --no-install-recommends wget unzip libgomp1 locales && \ | |
| rm -rf /var/lib/apt/lists/* |
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Actionable comments posted: 2
🧹 Outside diff range and nitpick comments (3)
README.md (1)
Line range hint
14-14: Base image information needs to be updatedThe README states the base image as
debian:12.8-slim, but according to the PR objectives, the base image has been switched to Ubuntu. Please update this information to reflect the actual base image being used.Dockerfile (2)
1-1: Consider using a slimmer base image to further reduce the Docker image size.Switching to
ubuntu:22.04is a good step, but you might achieve a smaller image by usingubuntu:22.04-slimorubuntu:22.04-minimalas the base image. This aligns with your goal of reducing the Docker image size without sacrificing functionality.
40-40: Restrict permissions on the DIA-NN directory for security.Setting permissions to
775grants write access to group members, which may not be necessary and could pose a security risks. It's advisable to set permissions to755to grant execute permissions without unnecessary write access.Apply the following change:
-RUN chmod -R 775 /diann-1.9.2 +RUN chmod -R 755 /diann-1.9.2
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Review profile: CHILL
📒 Files selected for processing (2)
Dockerfile(2 hunks)README.md(1 hunks)
🔇 Additional comments (2)
README.md (1)
42-42: Verify the new binary path exists in the container
The Docker run command has been updated to use ./diann-1.9.2/diann-linux. Let's verify this path exists in the built container.
Dockerfile (1)
25-26: Verify locale generation to prevent runtime errors.
The locale-gen command may not fully generate locales in Ubuntu 22.04. Ensuring that en_US.UTF-8 is properly generated is crucial to avoid locale-related runtime errors.
Run the following script to confirm the locale is correctly generated:
If the locale is not listed, consider installing locales-all or adjusting the locale generation commands.
✅ Verification successful
Locale configuration is properly set up
The Dockerfile follows the correct sequence for locale configuration:
- Installs the
localespackage via apt-get - Generates the en_US.UTF-8 locale using locale-gen
- Updates the system locale configuration
- Sets the required environment variables LANG and LANGUAGE
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Verify that the en_US.UTF-8 locale is generated.
# Test: List available locales and check for en_US.UTF-8
locale -a | grep -i 'en_US\.utf8'
Length of output: 132
Script:
#!/bin/bash
# Let's check if the Dockerfile has the necessary dependencies for locale generation
rg -A 5 -B 5 "locale-gen"
# Also check for any locale-related package installations
rg -i "apt.*install.*locale"
Length of output: 532
| g++ build-essential cmake zlib1g-dev libbz2-dev libboost-all-dev wget locales unzip && \ | ||
| apt-get clean && rm -rf /var/lib/apt/lists/* | ||
| # Update package lists and ensure package versions are up to date | ||
| RUN apt-get update && apt-get upgrade -y |
There was a problem hiding this comment.
🛠️ Refactor suggestion
Optimize package installation and avoid unnecessary apt-get upgrade.
Running apt-get upgrade in a Dockerfile can lead to larger image sizes and potential unpredictability. It's generally advisable to avoid it. Also, combining apt-get update and apt-get install in a single RUN command reduces the number of layers and prevents caching issues.
Consider applying the following changes:
-RUN apt-get update && apt-get upgrade -y
-RUN apt-get install wget unzip libgomp1 locales -y
+RUN apt-get update && apt-get install -y \
+ wget \
+ unzip \
+ libgomp1 \
+ locales && \
+ rm -rf /var/lib/apt/lists/*This approach installs the necessary packages and cleans up the apt cache to minimize the image size.
Also applies to: 22-22
| # NOTE: It is entirely the user's responsibility to ensure compliance with DIA-NN license terms. | ||
| # Please review the licensing terms for DIA-NN before using or distributing this Docker image. |
There was a problem hiding this comment.
Ensure compliance with DIA-NN licensing terms to avoid legal issues.
DIA-NN version 1.9.2 may have licensing restrictions that prohibit the distribution of Docker images containing the software. Building and sharing this Docker image could violate the license agreement. It's crucial to review the license terms and obtain the necessary permissions before proceeding.
Would you like assistance in reviewing the licensing terms or exploring alternative methods to comply with the license, such as instructing users to download DIA-NN during the build process?
User description
This pull request includes updates to the
DockerfileandREADME.mdto improve the build process and result in a smaller image size. The base image has been switched from Debian to Ubuntu, the package management commands have been updated, and the Docker run command in the documentation has been modified.PR Type
enhancement, documentation
Description
Dockerfilefrom Debian to Ubuntu to optimize the Docker image size.README.mdto reflect changes in the directory structure.Changes walkthrough 📝
Dockerfile
Optimize Dockerfile for smaller image size and better configurationDockerfile
README.md
Update Docker run command in documentationREADME.md
Summary by CodeRabbit
New Features
Bug Fixes
Documentation