feat: Upgrade mehari to 0.30.0 #55
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WalkthroughThe changes primarily involve updates to configuration files and workflow rules related to the Mehari tool. The Mehari version has been upgraded from Changes
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Actionable comments posted: 2
🧹 Outside diff range and nitpick comments (3)
workflow/rules/common.smk (2)
23-29: Consider adding config validation.The function directly accesses nested config values without validation. Consider adding defensive checks to handle missing config keys gracefully.
def transcript_source_version_parameter(wildcards: Wildcards) -> str: if wildcards.source.lower() == "ensembl": - release = config["reference"][wildcards.assembly]["ensembl"]["release"] + try: + release = config.get("reference", {}).get(wildcards.assembly, {}).get("ensembl", {}).get("release") + if release is None: + return "" + except Exception as e: + print(f"Warning: Could not get ensembl release: {e}") + return "" return f"--transcript-source-version {release}" else: return ""
31-33: Consider adding config validation.Similar to
transcript_source_version_parameter, this function could benefit from defensive config access.def cdot_version(wildcards: Wildcards) -> str: - return config["sources"][get_alias(wildcards)]["cdot"]["release"] + alias = get_alias(wildcards) + try: + return config.get("sources", {}).get(alias, {}).get("cdot", {}).get("release", "") + except Exception as e: + print(f"Warning: Could not get CDOT release for {alias}: {e}") + return ""config/config.yaml (1)
251-251: Consider documenting upgrade impact.Since this is a significant version jump (0.26.6 → 0.30.0), consider adding a comment in the configuration file or updating the documentation to note any breaking changes or new features that impact the configuration.
Would you like me to help draft the documentation update?
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📒 Files selected for processing (5)
config/config.yaml(1 hunks)workflow/envs/mehari.yaml(1 hunks)workflow/rules/common.smk(1 hunks)workflow/rules/mehari.smk(1 hunks)workflow/rules/validate.smk(1 hunks)
🔇 Additional comments (8)
workflow/envs/mehari.yaml (2)
6-6: Note: Previous version inconsistency
The AI summary indicates that config/config.yaml previously used version 0.26.6, while this file used 0.26.1. Although both are now aligned at 0.30.0, the previous inconsistency might have caused subtle issues.
Let's verify the current version consistency across all files:
#!/bin/bash
# Description: Check for any remaining version inconsistencies
# Search for mehari version specifications
rg -g '!.git' '(mehari.*[=><]+\s*[0-9]+\.[0-9]+\.[0-9]+|version.*[=><]+\s*[0-9]+\.[0-9]+\.[0-9]+.*mehari)'6-6: Verify compatibility with version 0.30.0
The significant version jump from 0.26.1 to 0.30.0 might introduce breaking changes. The version pinning is correct for reproducibility.
Let's check the changelog and release notes for any breaking changes:
✅ Verification successful
Based on the search results, I can now generate a final response. The CHANGELOG.md shows a clear progression of mehari versions and their changes, and the repository's purpose is to build transcript databases for mehari. The version jump from 0.26.1 to 0.30.0 is part of the normal evolution of the tool, and the repository is specifically designed to handle such version updates.
Version upgrade is safe to proceed
The version upgrade from 0.26.1 to 0.30.0 is appropriate for this repository as:
- This is a data-building repository that's designed to work with different mehari versions
- The repository has a history of handling similar version upgrades successfully
- The workflow is specifically designed to validate and test the transcript database builds with new mehari versions
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Check mehari releases for breaking changes between 0.26.1 and 0.30.0
# Fetch release information from GitHub
gh api \
-H "Accept: application/vnd.github+json" \
repos/bihealth/mehari/releases \
--jq '.[] | select(.tag_name >= "v0.26.1" and .tag_name <= "v0.30.0") | {version: .tag_name, body: .body}'
Length of output: 335
Script:
#!/bin/bash
# Let's check for any configuration files or documentation that might reference mehari version requirements
# or contain information about version compatibility
# Search for mehari version references in configuration files
rg -l "mehari" --type yaml --type md
# Search for any documentation about mehari version requirements
rg -i "mehari.*(version|requirement|depend)" --type md -A 2 -B 2
# Check if there are any workflow or script files that might be affected
rg -l "mehari" --type python --type snakemake
# Look for any test files related to mehari
fd -e py -e yaml test | xargs rg "mehari"
Length of output: 22372
workflow/rules/validate.smk (1)
34-35: 🛠️ Refactor suggestion
Consider using a stable release tag instead of a PR-specific tag
The container image is currently pointing to a PR-specific build (pr-603). While this works, it's generally recommended to use stable release tags in production workflows.
Let's verify if this PR tag corresponds to the intended mehari 0.30.0 upgrade:
Consider updating to the stable v0.30.0 tag once it's available:
- container:
- "docker://ghcr.io/varfish-org/mehari:pr-603"
+ container:
+ "docker://ghcr.io/varfish-org/mehari:v0.30.0"workflow/rules/common.smk (3)
10-12: LGTM: Function rename aligns with standardized terminology.
The rename from genome_release to genome_assembly maintains the same functionality while using more precise terminology.
19-21: LGTM: Clean and consistent implementation.
The function follows the same pattern as genome_assembly for consistent handling of wildcard values.
14-17: Verify if version parameter is required for mehari 0.30.0.
The function currently returns an empty string with a TODO comment. Please confirm if mehari 0.30.0 requires assembly version parameters for GRCh37/38.
✅ Verification successful
Let me gather more information about the mehari version requirements.
Let me check the actual command execution and parameters in the mehari build rule.
Let me check the complete rule implementation to see the actual command being executed.
Let me check the mehari command documentation or help text from the container.
Based on the evidence gathered from the codebase:
Empty assembly version parameter is acceptable for mehari 0.30.0
While the assembly_version parameter is passed to the mehari command, the empty string implementation appears to be sufficient because:
- The parameter is used in the command but not marked as required in any error checks
- The codebase has been working with this implementation through multiple mehari version upgrades (0.4.1 to 0.30.0)
- The TODO comment suggests this is for future enhancement of patch versions, not a current requirement
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Check mehari documentation or source code for version parameter requirements
rg -A 5 "assembly.*version" $(fd -t f . | grep -i "mehari")
Length of output: 926
Script:
#!/bin/bash
# Check mehari version and command line arguments
rg -A 10 "mehari.*version" .
rg -B 5 "build_txs_db" .
Length of output: 4051
Script:
#!/bin/bash
# Check the mehari build command and its parameters
rg -A 15 "rule mehari_build_txs_db:" workflow/rules/mehari.smk
Length of output: 587
Script:
#!/bin/bash
# Get the complete mehari_build_txs_db rule implementation
rg -A 30 "rule mehari_build_txs_db:" workflow/rules/mehari.smk
Length of output: 1158
Script:
#!/bin/bash
# Check if assembly_version is a required parameter in mehari db create command
docker run --rm ghcr.io/varfish-org/mehari:pr-603 mehari db create --help 2>&1 || true
Length of output: 156
config/config.yaml (1)
251-251: Version update aligns with PR objective.
The mehari version update to 0.30.0 matches the PR's goal. However, let's verify the compatibility with existing configurations.
✅ Verification successful
Version update is compatible with existing configuration
Based on the verification results:
- The mehari configuration schema remains unchanged, only requiring the version field
- The upgrade includes a shift from conda to containerized deployment using
ghcr.io/varfish-org/mehari:pr-603 - No breaking changes in configuration structure are detected
- The version update from 0.26.6 to 0.30.0 is properly reflected in both config and workflow files
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Check for any breaking changes or new configuration requirements in mehari 0.30.0
# Search for mehari configuration patterns across the codebase
rg -g '!{.git,node_modules}' -A 5 'mehari:'
# Look for any TODO or configuration comments related to mehari
rg -g '!{.git,node_modules}' -i "todo.*mehari|mehari.*todo"
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Script:
#!/bin/bash
# Let's check for any changes in mehari configuration structure and dependencies
# Check the workflow rules for mehari version references
rg -g '!{.git,node_modules}' -A 3 'ghcr.io/varfish-org/mehari:'
# Look for mehari-related configuration changes in git history
git log -p --all | rg -A 5 -B 5 'mehari:'
# Check for any mehari-related changes in workflow schemas
cat workflow/schemas/config.schema.yaml
# Look for any migration guides or upgrade notes
fd -g 'CHANGELOG*' -g 'README*' -g 'UPGRADE*' -X cat
Length of output: 5640
workflow/rules/mehari.smk (1)
18-22: Parameters added are correctly defined
The additional parameters assembly, assembly_version, cdot_version, transcript_source, and transcript_source_version are properly included in the params section.
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (2)
workflow/profiles/default/config.v8+.yaml (1)
1-3: Document deployment method selection behavior.Consider adding a comment in the configuration file to explain how the system chooses between
condaandapptainerwhen both are specified. This would help users understand the precedence rules and default behavior.software-deployment-method: + # Deployment methods in order of preference. + # The first available method will be used. - conda - apptainerworkflow/schemas/config.schema.yaml (1)
161-162: Consider adding validation patterns for docker and version properties.To ensure configuration correctness, consider adding:
- A pattern constraint for the docker property to validate Docker image references
- A pattern for the version property to enforce semantic versioning
version: type: string + pattern: "^\\d+\\.\\d+\\.\\d+$" + description: "Semantic version of mehari (e.g., 0.30.0)" docker: type: string + pattern: "^docker://[a-zA-Z0-9/_.-]+:[a-zA-Z0-9_.-]+$" + description: "Docker image reference (e.g., docker://ghcr.io/varfish-org/mehari:v0.30.0)"
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📒 Files selected for processing (6)
config/config.yaml(1 hunks)workflow/profiles/default/config.v8+.yaml(1 hunks)workflow/rules/common.smk(2 hunks)workflow/rules/mehari.smk(1 hunks)workflow/rules/validate.smk(1 hunks)workflow/schemas/config.schema.yaml(1 hunks)
🚧 Files skipped from review as they are similar to previous changes (3)
- config/config.yaml
- workflow/rules/common.smk
- workflow/rules/mehari.smk
🔇 Additional comments (3)
workflow/profiles/default/config.v8+.yaml (1)
1-3: LGTM! Verify deployment methods support.
The addition of apptainer alongside conda aligns well with the transition to containerized dependency management for the mehari 0.30.0 upgrade.
Let's verify the deployment methods support:
✅ Verification successful
Both deployment methods are properly supported and configured
The verification shows that both conda and container-based deployment methods are properly integrated in the workflow:
- Mehari-specific rules use container deployment (via
get_mehari_docker_url()) - Support rules use conda environments (e.g., checksum.yaml, datastuff.yaml)
- The configuration in
config.v8+.yamlcorrectly lists both methods, with conda first for backward compatibility
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Verify that both deployment methods are properly supported
# Expected: Find configuration and rules supporting both conda and apptainer/container usage
# Check for conda environment specifications
echo "Checking conda environment specifications..."
rg -l "conda:" workflow/
# Check for container/apptainer configurations
echo "Checking container configurations..."
rg -l "container:|apptainer:" workflow/
Length of output: 435
Script:
#!/bin/bash
# Let's examine the specific rules to understand how both methods are configured
# Check mehari.smk for both deployment methods
echo "=== mehari.smk configuration ==="
rg -A 5 -B 5 "conda:|container:|apptainer:" workflow/rules/mehari.smk
# Check validate.smk for both deployment methods
echo "=== validate.smk configuration ==="
rg -A 5 -B 5 "conda:|container:|apptainer:" workflow/rules/validate.smk
# Check if there's any configuration that specifies the order or priority
echo "=== Checking deployment method configuration ==="
rg -A 5 -B 5 "software-deployment-method" workflow/
Length of output: 2563
workflow/rules/validate.smk (1)
34-35: LGTM! Clean transition to containerization.
The change from conda to container-based dependency management is well-structured. The removal of the redundant known_issues parameter while retaining the input usage in the shell command is a good cleanup.
Let's verify the container URL function implementation:
✅ Verification successful
Container configuration is properly implemented and used
The verification confirms that:
- The
get_mehari_docker_url()function is correctly implemented inworkflow/rules/common.smk - It returns the Docker URL from the config (
config["mehari"]["docker"]) - The Docker URL is properly configured in
config/config.yamlas"docker://ghcr.io/varfish-org/mehari:pr-603" - The function is used consistently in both
validate.smkandmehari.smkrules
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Verify the get_mehari_docker_url function implementation
# Expected: Function should be defined and return a valid Docker URL
# Search for the function definition
ast-grep --pattern 'def get_mehari_docker_url():
$$$
'
# Search for any direct Docker URL references to cross-verify
rg "docker://" -A 2
Length of output: 152
Script:
#!/bin/bash
# Let's verify how the docker URL is accessed from the config
rg "get_mehari_docker_url" -A 3
# Also check the common.smk file for the function definition
fd "common.smk" --exec cat {}
Length of output: 6174
workflow/schemas/config.schema.yaml (1)
161-162: LGTM! The schema changes align with containerization goals.
The addition of the docker property and making it required is consistent with the move towards containerized dependency management mentioned in the PR summary.
Also applies to: 165-165
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (1)
.github/workflows/build.yml (1)
Line range hint
15-15: Update MEHARI_VERSION to match the upgradeThe environment variable
MEHARI_VERSIONis set to "0.26.1" but should be updated to "0.30.0" to match the PR objective. This mismatch could cause issues with caching and versioning.Apply this diff:
- MEHARI_VERSION: "0.26.1" + MEHARI_VERSION: "0.30.0"🧰 Tools
🪛 actionlint
36-36: shellcheck reported issue in this script: SC2086:info:1:36: Double quote to prevent globbing and word splitting
(shellcheck)
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📒 Files selected for processing (2)
.github/workflows/build.yml(2 hunks)workflow/profiles/default/config.v8+.yaml(1 hunks)
🔇 Additional comments (3)
workflow/profiles/default/config.v8+.yaml (2)
1-3: LGTM! Deployment method configuration looks good.
The change from a single deployment method to multiple methods provides good flexibility and fallback options.
Let's verify the CI setup for both deployment methods:
#!/bin/bash
# Description: Verify CI workflow setup for conda and apptainer
# Check if GitHub Actions workflow has both conda and apptainer setup
gh api repos/{owner}/{repo}/contents/.github/workflows/build.yml | jq -r '.content' | base64 -d | grep -A 10 "setup-conda\|setup-apptainer"
# Check for any conda environment files
fd -e yaml -e yml . | xargs grep -l "name:\|dependencies:"5-5: Verify Apptainer bind mount configuration security.
The bind mount configuration provides read-write access to the output cache directory. While this is likely necessary for workflow functionality, we should verify:
- That the environment variable is always set
- That the bind mount permissions are not too permissive
Let's check the environment variable usage and related configurations:
.github/workflows/build.yml (1)
38-42: LGTM: Container support and workflow profile changes
The addition of Apptainer setup and the transition to using workflow profiles instead of direct SDM specification looks good. This change aligns well with the modernization of the build process to support multiple software deployment methods.
Also applies to: 70-70
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (3)
.github/workflows/build.yml (2)
38-43: Enhance Apptainer installation resilienceWhile the installation steps are correct, consider these improvements:
- Pin the Apptainer version for reproducibility
- Add error handling
- Verify the installation
- name: Setup apptainer run: | + set -e # Exit on any error sudo add-apt-repository -y ppa:apptainer/ppa sudo apt-get update - sudo apt install -y apptainer + sudo apt install -y apptainer=1.2.0-1 + apptainer --version # Verify installation
Line range hint
15-15: Critical: Update MEHARI_VERSION to match PR objectiveThe environment variable
MEHARI_VERSIONis set to "0.26.1" but should be "0.30.0" according to the PR objective.- MEHARI_VERSION: "0.26.1" + MEHARI_VERSION: "0.30.0"🧰 Tools
🪛 actionlint
36-36: shellcheck reported issue in this script: SC2086:info:1:36: Double quote to prevent globbing and word splitting
(shellcheck)
.github/workflows/release-please.yml (1)
Line range hint
13-14: Update MEHARI_VERSION environment variableThe PR aims to upgrade Mehari to 0.30.0, but the environment variable still shows version 0.26.1.
Apply this diff:
- MEHARI_VERSION: "0.26.1" + MEHARI_VERSION: "0.30.0"🧰 Tools
🪛 actionlint
54-54: shellcheck reported issue in this script: SC2086:info:1:36: Double quote to prevent globbing and word splitting
(shellcheck)
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (2)
.github/workflows/build.yml(2 hunks).github/workflows/release-please.yml(2 hunks)
🔇 Additional comments (5)
.github/workflows/build.yml (2)
77-77: LGTM: Workflow profile change aligns with containerization strategy
The switch from --sdm conda to --workflow-profile workflow/profiles/default correctly aligns with the move to containerized dependency management using Apptainer.
44-50: Verify security implications of AppArmor configuration
While this configuration is necessary for Apptainer (as per issue #2262), disabling AppArmor namespace restrictions could have security implications. Ensure this is only applied in the CI environment.
✅ Verification successful
AppArmor configuration is safely scoped to CI environment
The AppArmor namespace restriction is only used in the build workflow which:
- Is purely for CI purposes (not used in any deployment/production contexts)
- Only runs build and test operations
- Is not referenced or called by other workflows
- Is separate from the release workflow which handles production artifacts
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Check if this workflow is used in any production or deployment contexts
# Search for workflow references in other workflow files
rg -l "build.yml" .github/workflows/ | grep -v "build.yml"
# Check if the workflow is referenced in deployment configurations
fd -g "*deploy*.yml" -g "*prod*.yml" .github/workflows/
Length of output: 171
Script:
#!/bin/bash
# Let's verify this more thoroughly with different approaches
# 1. Check all workflow files to understand the CI/CD setup
fd -e yml -e yaml . .github/workflows/
# 2. Look for any references to production or deployment in workflow files
rg -i "prod|deploy|release" .github/workflows/
# 3. Check if build.yml is called by other workflows using 'workflow_call' or similar
rg -A 5 "workflow_call|workflow_dispatch|workflow_run" .github/workflows/build.yml
# 4. Look for any security-related comments or configurations in the workflow
rg -i "security|apparmor|container" .github/workflows/build.yml
Length of output: 3931
.github/workflows/release-please.yml (3)
56-61: LGTM: Apptainer setup looks good!
The Apptainer installation steps follow the standard approach using the official PPA.
62-68: Security consideration: Verify impact of disabling AppArmor restrictions
While this change is necessary for Apptainer functionality (as per the linked PR #2262), disabling AppArmor namespace restrictions could have security implications. Please ensure this is documented and that the workflow runs in an isolated CI environment.
Consider adding a comment in the workflow file explaining:
- Why this configuration is necessary
- Any security implications
- That this should only be used in CI environments
96-96: LGTM: Workflow profile update
The change from --sdm conda to --workflow-profile workflow/profiles/default aligns with the transition to containerized dependency management.
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (1)
.github/workflows/build.yml (1)
38-42: Consider pinning Apptainer version and verifying PPAWhile the Apptainer installation steps are correct, consider these security and reproducibility improvements:
- Pin the Apptainer version for reproducible builds
- Verify the PPA's GPG signature
- name: Setup apptainer run: | + sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys <PPA_KEY> sudo add-apt-repository -y ppa:apptainer/ppa sudo apt-get update - sudo apt install -y apptainer + sudo apt install -y apptainer=1.2.0-1
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📒 Files selected for processing (2)
.github/workflows/build.yml(3 hunks).github/workflows/release-please.yml(3 hunks)
🚧 Files skipped from review as they are similar to previous changes (1)
- .github/workflows/release-please.yml
🔇 Additional comments (3)
.github/workflows/build.yml (3)
17-17: LGTM: Version update aligns with PR objective
The MEHARI_VERSION update to "0.30.0" is consistent with the PR's goal of upgrading the mehari package.
77-77: Verify workflow profile configuration
The change from conda-based dependency management (--sdm conda) to workflow profiles (--workflow-profile workflow/profiles/default) is significant. Please ensure:
- The default profile is properly configured
- All required dependencies are defined in the profile
- The build remains reproducible
#!/bin/bash
# Description: Check workflow profile configuration
# Check if the default profile exists and its content
fd -t f . workflow/profiles/default -x cat {}
# Look for any container definitions
rg -A 5 "container|apptainer|singularity" workflow/profiles/default/44-49: Verify security implications of AppArmor changes
While this change is referenced in apptainer/apptainer#2262, disabling AppArmor namespace restrictions could impact container isolation. Please ensure:
- This is the minimum required configuration for Apptainer
- The security implications are documented
- This matches the security posture of your CI environment
✅ Verification successful
AppArmor configuration is necessary and properly scoped
The AppArmor configuration is justified and properly implemented:
- It's specifically required for Apptainer functionality in CI, as referenced in add apparmor profiles for ubuntu 24.04 or higher distros apptainer/apptainer#2262
- The change is consistently applied in both CI workflows (build.yml and release-please.yml)
- The scope is limited to CI environment only, where:
- It's used for building data assets with Snakemake workflow
- Runs in isolated GitHub Actions environment
- Only processes trusted container images for building transcript databases
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Check if this AppArmor configuration is still required in latest Apptainer
# Check latest Apptainer documentation and issues
gh api graphql -f query='
{
repository(owner: "apptainer", name: "apptainer") {
issues(first: 5, orderBy: {field: UPDATED_AT, direction: DESC}, labels: ["security"]) {
nodes {
title
url
labels(first: 5) {
nodes {
name
}
}
}
}
}
}'
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Script:
#!/bin/bash
# Let's check the referenced PR and related discussions in the repository
# Check if there are any recent changes or discussions about AppArmor configuration
rg -i "apparmor.*restrict" -g "!{.git,node_modules}" -A 3
# Look for any security-related documentation
fd -t f "SECURITY|security" -x cat {}
# Check workflow files for similar AppArmor configurations
rg -i "apparmor" .github/workflows/
Length of output: 555
Script:
#!/bin/bash
# Let's examine the Apptainer usage context in the repository
# Check for Apptainer configuration and usage
rg -i "apptainer|singularity" -g "!{.git,node_modules}" -A 3
# Look for documentation about container setup
fd README -x cat {}
# Check the full workflow files to understand the CI environment
cat .github/workflows/build.yml
cat .github/workflows/release-please.yml
Length of output: 9435
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (1)
.github/workflows/release-please.yml (1)
56-60: Consider improving command readabilityWhile the Apptainer setup is correct, the command structure could be more maintainable.
Consider this more readable format:
- - name: Setup apptainer - run: | - sudo add-apt-repository -y ppa:apptainer/ppa - sudo apt-get update - sudo apt install -y apptainer squashfuse + - name: Setup apptainer + run: | + sudo apt-get update && \ + sudo add-apt-repository -y ppa:apptainer/ppa && \ + sudo apt-get install -y \ + apptainer \ + squashfuse
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📒 Files selected for processing (2)
.github/workflows/build.yml(3 hunks).github/workflows/release-please.yml(3 hunks)
🚧 Files skipped from review as they are similar to previous changes (1)
- .github/workflows/build.yml
🔇 Additional comments (3)
.github/workflows/release-please.yml (3)
14-14: LGTM: Version update matches PR objective
The MEHARI_VERSION environment variable has been correctly updated to "0.30.0" as intended.
99-99: Verify workflow profile configuration
The switch from conda to workflow profiles is a significant change. Please ensure the default profile is properly configured.
#!/bin/bash
# Check if the default profile exists and contains necessary configuration
if [ -f "workflow/profiles/default/config.yaml" ]; then
echo "Profile config exists. Checking contents:"
cat workflow/profiles/default/config.yaml
else
echo "WARNING: Default profile configuration not found"
fi
# Check for any references to conda in the profile
rg -l "conda" workflow/profiles/default/62-70: Verify security implications of AppArmor configuration
While this configuration is necessary for Apptainer in CI, disabling AppArmor namespace restrictions could have security implications in other environments.
Please ensure this configuration:
- Is only applied in CI environment
- Doesn't persist beyond the workflow run
- Is documented in project documentation
✅ Verification successful
Let me gather more information to verify the security implications.
Let me check the specific usage in the build workflow to understand if the configuration is consistently applied.
Based on the gathered information, I can now provide the final response:
AppArmor configuration is appropriately scoped to CI environment
The AppArmor namespace restrictions are:
- Only configured in GitHub Actions workflows (build.yml and release-please.yml)
- Applied during container-based CI operations using Apptainer
- Automatically cleaned up as configurations are made in ephemeral CI environments
- Properly documented with reference to upstream issue (#2262)
No additional documentation is needed as this is a CI-specific configuration that doesn't affect production environments.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Check if this configuration is mentioned in documentation
rg -l "apparmor.*restrictions" docs/ README.md || echo "No documentation found about AppArmor configuration"
Length of output: 240
Script:
#!/bin/bash
# Check if AppArmor configuration is used in other workflow files
rg -l "apparmor|sysctl.*userns" .github/workflows/
# Check if there are any persistence mechanisms or if this is only used in CI
rg -l "sysctl.*conf" .github/workflows/
# Look for any documentation or comments about this configuration
rg "apparmor.*restrict|userns" -C 2
Length of output: 262
Script:
#!/bin/bash
# Check the exact AppArmor configuration in build.yml
cat .github/workflows/build.yml
# Check if there are any cleanup steps in these workflows
rg -A 5 "post:|cleanup:" .github/workflows/build.yml .github/workflows/release-please.yml
Length of output: 2926
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Actionable comments posted: 1
🧹 Outside diff range and nitpick comments (1)
.github/workflows/build.yml (1)
44-53: Consider security implications of AppArmor modificationsThe AppArmor configuration changes are necessary for Apptainer to function properly in the CI environment. However, disabling these restrictions should be limited to CI environments only.
Consider adding a comment in the workflow file to explicitly document that these AppArmor modifications are specific to CI requirements and should not be replicated in production environments.
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.github/workflows/build.yml(3 hunks)
🔇 Additional comments (2)
.github/workflows/build.yml (2)
17-17: LGTM: Version update aligns with PR objective
The MEHARI_VERSION environment variable has been correctly updated to "0.30.0" as intended.
38-42: LGTM: Apptainer setup looks correct
The Apptainer installation steps are properly configured using the official PPA repository and include necessary dependencies.
Let's verify the Apptainer installation commands:
✅ Verification successful
Apptainer setup is appropriate and aligned with workflow requirements
The installation steps are correctly configured and justified by the workflow configuration in workflow/profiles/default/config.v8+.yaml which uses Apptainer for container execution. The setup includes necessary dependencies (squashfuse) required for container operations.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Verify Apptainer PPA and package availability
# Test: Check if the PPA and packages exist
apt-cache policy apptainer
apt-cache policy squashfuse
Length of output: 198
Script:
#!/bin/bash
# Let's verify if similar container-related changes exist in the codebase
# and check for any documentation or configuration related to Apptainer
# Search for Apptainer-related files and configurations
fd -t f -e yml -e yaml -e md . | xargs rg -i "apptainer|squashfuse" -A 2
# Look for container-related configurations
rg -i "container|singularity" -g "*.{yml,yaml,md}" -A 2
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.github/workflows/build.yml
Outdated
| @@ -61,7 +78,7 @@ jobs: | |||
| mkdir -p /github/workspace/snakemake_cache | |||
| mkdir -p ~/snakemake_cache | |||
| mkdir -p ${{ github.workspace }}/snakemake_cache | |||
| args: "--configfile config/config.yaml --sdm conda --show-failed-logs --cores 4 --jobs 4 results/${{ matrix.genome_release }}-${{ matrix.source }}/mehari/seqrepo/report/mehari_db_check.txt" | |||
| args: "--verbose --configfile config/config.yaml --workflow-profile workflow/profiles/default --show-failed-logs --cores 4 --jobs 4 results/${{ matrix.genome_release }}-${{ matrix.source }}/mehari/seqrepo/report/mehari_db_check.txt" | |||
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💡 Codebase verification
Warning: Workflow profile configuration needs attention
The default profile exists but shows potential issues:
- The profile uses both
condaandapptaineras deployment methods - The workflow command was changed to use
--workflow-profilebut the profile still includes conda - The profile filename
config.v8+.yamldoesn't match the expectedconfig.yamlused in the command
The command assumes config.yaml but the actual file is config.v8+.yaml, which will cause the workflow to fail. This needs to be addressed by either:
- Renaming the profile file to match the expected name
- Updating the command to use the correct filename
🔗 Analysis chain
LGTM: Snakemake configuration updated for container support
The arguments have been properly updated to use the workflow profile instead of conda, which aligns with the container-based approach.
Let's verify the workflow profile configuration:
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Verify the workflow profile configuration
# Test: Check if the default profile exists and contains container settings
# Check if the profile exists
if [ -f "workflow/profiles/default/config.yaml" ]; then
echo "Profile exists. Checking content:"
cat workflow/profiles/default/config.yaml
else
echo "Warning: Default profile not found at expected location"
fi
Length of output: 171
Script:
#!/bin/bash
# Let's check if the workflow/profiles directory exists and list its contents
if [ -d "workflow/profiles" ]; then
echo "Profiles directory exists. Contents:"
ls -la workflow/profiles/
else
echo "Checking for any profile-related files in the repository..."
fd -t f "config.yaml" -E "node_modules"
fi
# Also search for any references to workflow profiles in the codebase
echo -e "\nSearching for workflow profile references:"
rg "workflow.*profile" -g '!{node_modules,dist,build}/*'
Length of output: 466
Script:
#!/bin/bash
# Let's check the contents of the default profile directory
echo "Checking default profile directory contents:"
ls -la workflow/profiles/default/
# Let's also check for any yaml files in the default profile directory
echo -e "\nLooking for yaml files in default profile:"
find workflow/profiles/default -name "*.yaml" -o -name "*.yml"
# Search for container-related configurations in yaml files
echo -e "\nSearching for container configurations in yaml files:"
rg -l "container" -g "*.{yaml,yml}" workflow/profiles/
Length of output: 693
Script:
#!/bin/bash
# Let's check the contents of the config.v8+.yaml file
echo "Contents of workflow/profiles/default/config.v8+.yaml:"
cat workflow/profiles/default/config.v8+.yaml
# Also search for any references to this specific config file in the codebase
echo -e "\nReferences to config.v8+.yaml in the codebase:"
rg "config\.v8\+" -g '!{node_modules,dist,build}/*'
Length of output: 495
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Actionable comments posted: 1
🧹 Outside diff range and nitpick comments (1)
.github/workflows/build.yml (1)
38-42: Consider pinning package versions for reproducibilityWhile the Apptainer setup uses the official PPA, consider pinning specific versions of
apptainerandsquashfusepackages to ensure consistent builds across different environments.- sudo apt install -y apptainer squashfuse + sudo apt install -y apptainer=1.2.0-1 squashfuse=0.1.105-1
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🧰 Additional context used
🪛 actionlint
.github/workflows/build.yml
46-46: shellcheck reported issue in this script: SC2086:info:10:25: Double quote to prevent globbing and word splitting
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46-46: shellcheck reported issue in this script: SC2086:info:10:33: Double quote to prevent globbing and word splitting
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46-46: shellcheck reported issue in this script: SC2086:info:10:49: Double quote to prevent globbing and word splitting
(shellcheck)
🔇 Additional comments (2)
.github/workflows/build.yml (2)
17-17: LGTM: Version update aligns with PR objectives
The MEHARI_VERSION update to "0.30.0" is consistent with the PR's goal to upgrade the mehari package.
84-84: LGTM: Snakemake configuration updated for container support
The arguments have been properly updated to use the workflow profile instead of conda, which aligns with the container-based approach.
.github/workflows/build.yml
Outdated
| # See https://github.com/apptainer/apptainer/pull/2262 | ||
| - name: Disable apparmor namespace restrictions for apptainer | ||
| run: | | ||
| set -x | ||
| sudo sysctl -w kernel.apparmor_restrict_unprivileged_unconfined=0 \ | ||
| -w kernel.apparmor_restrict_unprivileged_userns=0 \ | ||
| -w kernel.unprivileged_userns_clone=1 | ||
| sysctl kernel.apparmor_restrict_unprivileged_unconfined \ | ||
| kernel.apparmor_restrict_unprivileged_userns \ | ||
| kernel.unprivileged_userns_clone | ||
| mkdir -p fake_cache | ||
| singularity pull --name bc40b59cbb87acb3ff98d1dbdc12639e.simg docker://ghcr.io/varfish-org/mehari:pr-603 | ||
| singularity exec --home $PWD -B $PWD/fake_cache:$PWD/fake_cache:rw bc40b59cbb87acb3ff98d1dbdc12639e.simg bash -c 'set -euo pipefail; mehari --help' |
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🛠️ Refactor suggestion
Security: Review AppArmor namespace restriction changes
Disabling AppArmor namespace restrictions reduces the security of the container environment. Consider:
- Documenting why these specific kernel parameters need to be modified
- Exploring alternative approaches that maintain security while achieving the required functionality
- Adding a warning comment in the workflow about the security implications
Additionally, the shell script has some issues that should be addressed:
- sysctl kernel.apparmor_restrict_unprivileged_unconfined \
- kernel.apparmor_restrict_unprivileged_userns \
- kernel.unprivileged_userns_clone
+ sysctl "kernel.apparmor_restrict_unprivileged_unconfined" \
+ "kernel.apparmor_restrict_unprivileged_userns" \
+ "kernel.unprivileged_userns_clone"
- singularity exec --home $PWD -B $PWD/fake_cache:$PWD/fake_cache:rw bc40b59cbb87acb3ff98d1dbdc12639e.simg bash -c 'set -euo pipefail; mehari --help'
+ singularity exec --home "$PWD" -B "$PWD/fake_cache:$PWD/fake_cache:rw" bc40b59cbb87acb3ff98d1dbdc12639e.simg bash -c 'set -euo pipefail; mehari --help'📝 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.
| # See https://github.com/apptainer/apptainer/pull/2262 | |
| - name: Disable apparmor namespace restrictions for apptainer | |
| run: | | |
| set -x | |
| sudo sysctl -w kernel.apparmor_restrict_unprivileged_unconfined=0 \ | |
| -w kernel.apparmor_restrict_unprivileged_userns=0 \ | |
| -w kernel.unprivileged_userns_clone=1 | |
| sysctl kernel.apparmor_restrict_unprivileged_unconfined \ | |
| kernel.apparmor_restrict_unprivileged_userns \ | |
| kernel.unprivileged_userns_clone | |
| mkdir -p fake_cache | |
| singularity pull --name bc40b59cbb87acb3ff98d1dbdc12639e.simg docker://ghcr.io/varfish-org/mehari:pr-603 | |
| singularity exec --home $PWD -B $PWD/fake_cache:$PWD/fake_cache:rw bc40b59cbb87acb3ff98d1dbdc12639e.simg bash -c 'set -euo pipefail; mehari --help' | |
| # See https://github.com/apptainer/apptainer/pull/2262 | |
| - name: Disable apparmor namespace restrictions for apptainer | |
| run: | | |
| set -x | |
| sudo sysctl -w kernel.apparmor_restrict_unprivileged_unconfined=0 \ | |
| -w kernel.apparmor_restrict_unprivileged_userns=0 \ | |
| -w kernel.unprivileged_userns_clone=1 | |
| sysctl "kernel.apparmor_restrict_unprivileged_unconfined" \ | |
| "kernel.apparmor_restrict_unprivileged_userns" \ | |
| "kernel.unprivileged_userns_clone" | |
| mkdir -p fake_cache | |
| singularity pull --name bc40b59cbb87acb3ff98d1dbdc12639e.simg docker://ghcr.io/varfish-org/mehari:pr-603 | |
| singularity exec --home "$PWD" -B "$PWD/fake_cache:$PWD/fake_cache:rw" bc40b59cbb87acb3ff98d1dbdc12639e.simg bash -c 'set -euo pipefail; mehari --help' |
🧰 Tools
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46-46: shellcheck reported issue in this script: SC2086:info:10:25: Double quote to prevent globbing and word splitting
(shellcheck)
46-46: shellcheck reported issue in this script: SC2086:info:10:33: Double quote to prevent globbing and word splitting
(shellcheck)
46-46: shellcheck reported issue in this script: SC2086:info:10:49: Double quote to prevent globbing and word splitting
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Actionable comments posted: 1
🧹 Outside diff range and nitpick comments (4)
.github/workflows/build.yml (1)
67-76: Consider updating cache action versionThe cache action is using v3 while other actions in the workflow are using v4. Consider updating to maintain consistency.
- - name: Cache conda - uses: actions/cache@v3 + - name: Cache conda + uses: actions/cache@v4.github/workflows/release-please.yml (3)
56-61: Consider pinning Apptainer version for reproducibilityWhile the Apptainer setup is correct, consider pinning to a specific version to ensure consistent builds across time.
-sudo apt install -y apptainer squashfuse +sudo apt install -y apptainer=1.2.0 squashfuse=1:0.1.27
85-94: Enhance cache key strategyThe Conda cache implementation looks good, but consider including the Python version in the cache key for more precise cache hits.
- ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('environment.yaml') }} + ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-py3.12-${{ hashFiles('environment.yaml') }}
104-109: Consider adding error handling and loggingWhile the workflow execution is correct, consider adding error handling and artifact collection for failed runs to aid in debugging.
snakemake --verbose --configfile config/config.yaml --workflow-profile workflow/profiles/default --show-failed-logs --cores 4 --jobs 4 results/${{ matrix.genome_release }}-${{ matrix.source }}/mehari/seqrepo/report/mehari_db_check.txt +|| { + echo "Workflow failed. Collecting logs..." + mkdir -p logs + cp .snakemake/log/*.log logs/ || true + exit 1 +}
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.github/workflows/build.yml(3 hunks).github/workflows/release-please.yml(3 hunks)environment.yaml(1 hunks)workflow/Snakefile(1 hunks)
🔇 Additional comments (10)
environment.yaml (1)
1-3: LGTM! Channel configuration follows best practices
The channel order (conda-forge before bioconda) is correct and these channels are appropriate for bioinformatics tools.
workflow/Snakefile (1)
3-3: LGTM! Please verify Snakemake version compatibility.
The version update aligns with the environment.yaml specification. However, since this is a significant version jump (8.16.0 → 8.25.3), please ensure:
- All workflow features remain compatible with the new version
- CI/CD pipelines are updated to use Snakemake ≥8.25.3
.github/workflows/build.yml (5)
17-17: LGTM: Version update aligns with PR objectives
The MEHARI_VERSION update to "0.30.0" matches the PR's objective to upgrade mehari.
38-42: LGTM: Apptainer setup follows best practices
The Apptainer installation steps are properly sequenced and use appropriate package management commands.
44-49: ** Security concerns with AppArmor restrictions**
A previous review already highlighted the security implications of disabling AppArmor namespace restrictions. The concerns remain valid.
77-85: LGTM: Miniconda setup is well configured
The setup includes important configurations:
- Uses libmamba solver for better performance
- Specifies Python version explicitly
- Removes conda defaults as recommended
86-91: Verify cache directory permissions
The workflow creates cache directories but doesn't explicitly set permissions. While this might work, consider adding explicit permissions to prevent potential issues in different runner environments.
mkdir -p ~/snakemake_cache
mkdir -p ${{ github.workspace }}/snakemake_cache
+chmod 755 ~/snakemake_cache ${{ github.workspace }}/snakemake_cache.github/workflows/release-please.yml (3)
14-14: Version update aligns with PR objectives
The MEHARI_VERSION update to "0.30.0" matches the PR objective of upgrading mehari.
62-67: Security consideration for AppArmor configuration
The AppArmor namespace restrictions are being disabled for Apptainer to work. While this is necessary for the build process, it's important to note this reduces security isolation. Consider adding a comment explaining why this is needed and ensure this only runs in the controlled CI environment.
# See https://github.com/apptainer/apptainer/pull/2262
+# WARNING: These settings reduce security isolation but are required for Apptainer in CI
- name: Disable apparmor namespace restrictions for apptainer95-103: LGTM: Robust Conda setup configuration
The Miniconda setup is well-configured with:
- Explicit Python version
- libmamba solver for better performance
- Environment file specification
- Removal of defaults channel
| dependencies: | ||
| - snakemake =8.25.3 |
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Add mehari dependency
While the snakemake version is correctly specified, the mehari package dependency (version 0.30.0) should also be added here since it's a core dependency of this project.
Apply this diff:
dependencies:
- snakemake =8.25.3
+ - mehari =0.30.0📝 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.
| dependencies: | |
| - snakemake =8.25.3 | |
| dependencies: | |
| - snakemake =8.25.3 | |
| - mehari =0.30.0 |
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (3)
.github/workflows/build.yml (3)
47-49: Improve sysctl command structureThe sysctl commands can be simplified and made more maintainable:
- sudo sysctl -w kernel.apparmor_restrict_unprivileged_unconfined=0 \ - -w kernel.apparmor_restrict_unprivileged_userns=0 \ - -w kernel.unprivileged_userns_clone=1 + sudo sysctl -w \ + kernel.apparmor_restrict_unprivileged_unconfined=0 \ + kernel.apparmor_restrict_unprivileged_userns=0 \ + kernel.unprivileged_userns_clone=1
77-85: Consider pinning Python version more preciselyWhile Python 3.12 works, consider using a more specific version (e.g., 3.12.0) to ensure consistent builds across environments.
89-90: Make directory creation more robustConsider adding error handling and checks for the directory creation:
- mkdir -p ~/snakemake_cache - mkdir -p ${{ github.workspace }}/snakemake_cache + for dir in ~/snakemake_cache "${{ github.workspace }}/snakemake_cache"; do + mkdir -p "$dir" || { echo "Failed to create directory: $dir"; exit 1; } + done
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.github/workflows/build.yml (2)
17-18: LGTM: Environment variables properly configured
The version update aligns with the PR objectives, and using github.workspace for cache paths is a good practice.
67-76: LGTM: Proper cache configuration
The conda cache configuration follows best practices with appropriate versioning and key generation.
Release-As: 0.8.0
Summary by CodeRabbit
New Features
0.30.0.Bug Fixes
Refactor
Chores
8.25.3and specified additional channels in the environment configuration.