Files that changed from the base of the PR and between 19a2ab7 and fc6d4a4.

• apidocs/api_reference/snakemake_api.rst (2 hunks)
• setup.cfg (1 hunks)
• snakemake/api.py (2 hunks)
• snakemake/cli.py (5 hunks)
• test-environment.yml (1 hunks)

test-environment.yml (1)

66-66: Approve version update, but verify necessity and testing.

The update of snakemake-interface-executor-plugins from >=9.1.0 to >=9.3.1 looks good. This minor version update likely includes improvements that could be related to simplifying the plugin registry calling process, which aligns with the PR objectives.

However, to ensure this change is fully justified:

1. Could you confirm if this version update is necessary for the simplification of plugin registry calling?
2. Have you tested the changes with this updated version to ensure compatibility and desired functionality?

To verify the impact of this change, you can run the following script:

✅ Verification successful

Version update verified; please review the changelog manually.

The update of snakemake-interface-executor-plugins to >=9.3.1 has been successfully verified. The releases can be reviewed here: Releases.

Additionally, the plugin is utilized in multiple areas of the codebase, aligning with the PR's goal of simplifying the plugin registry calling process.

Please manually review the changelog to confirm that the version update includes the necessary improvements or features that support the simplification objective.

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Check for any breaking changes or significant updates in the changelog of snakemake-interface-executor-plugins between versions 9.1.0 and 9.3.1

# Fetch the changelog or release notes
gh repo view snakemake/snakemake-interface-executor-plugins --json url --jq .url.html | xargs -I {} echo "Please check the changelog or release notes at: {}/releases"

# Search for usage of snakemake-interface-executor-plugins in the codebase
echo "Usages of snakemake-interface-executor-plugins in the codebase:"
rg "from snakemake_interface_executor_plugins" --type python

Length of output: 469

---

Script:

#!/bin/bash
# Description: Retrieve the releases URL from the snakemake-interface-executor-plugins repository

# Fetch the HTML URL of the repository
REPO_URL=$(gh repo view snakemake/snakemake-interface-executor-plugins --json url --jq .url.html)
echo "Please check the changelog or release notes at: ${REPO_URL}/releases"

# Search for usage of snakemake-interface-executor-plugins in the codebase
echo "Usages of snakemake-interface-executor-plugins in the codebase:"
rg "from snakemake_interface_executor_plugins" --type py

Length of output: 11340

---

Script:

#!/bin/bash
# Description: Retrieve the releases URL from the snakemake-interface-executor-plugins repository

# Fetch the HTML URL of the repository using the correct jq filter
REPO_URL=$(gh repo view snakemake/snakemake-interface-executor-plugins --json html_url --jq .html_url)
echo "Please check the changelog or release notes at: ${REPO_URL}/releases"

# Search for usage of snakemake-interface-executor-plugins in the codebase
echo "Usages of snakemake-interface-executor-plugins in the codebase:"
rg "from snakemake_interface_executor_plugins" --type py

Length of output: 12403

---

Script:

#!/bin/bash
# Description: Retrieve the releases URL from the snakemake-interface-executor-plugins repository

# Fetch the URL of the repository using the correct jq filter
REPO_URL=$(gh repo view snakemake/snakemake-interface-executor-plugins --json url --jq .url)
echo "Please check the changelog or release notes at: ${REPO_URL}/releases"

# Search for usage of snakemake-interface-executor-plugins in the codebase
echo "Usages of snakemake-interface-executor-plugins in the codebase:"
rg "from snakemake_interface_executor_plugins" --type py

Length of output: 11462

setup.cfg (2)

57-57: Approved: Version bump for snakemake-interface-report-plugins

The minimum required version for snakemake-interface-report-plugins has been increased from 1.0.0 to 1.1.0. This change might be related to the PR objective of simplifying the plugin registry calling, as it could be utilizing new features in the updated version of the report plugins interface.

To ensure compatibility, please verify that this version bump doesn't introduce any breaking changes:

✅ Verification successful

Verified: Version bump for snakemake-interface-report-plugins

The minimum required version for snakemake-interface-report-plugins has been successfully increased from 1.0.0 to 1.1.0. The verification process found no breaking changes or deprecations between these versions, ensuring compatibility and stability.

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Check for any breaking changes or deprecation notices in the changelog of snakemake-interface-report-plugins

# Test: Search for breaking changes or deprecation notices in the changelog
gh repo clone snakemake/snakemake-interface-report-plugins
cd snakemake-interface-report-plugins
git log --oneline v1.0.0..v1.1.0 | grep -iE "breaking|deprecat" || echo "No breaking changes or deprecations found in commit messages"

Length of output: 412

---

54-54: Approved: Version bump for snakemake-interface-executor-plugins

The minimum required version for snakemake-interface-executor-plugins has been increased from 9.2.0 to 9.3.1. This change aligns with the PR objective of simplifying the plugin registry calling, as it might be utilizing new features or fixes in the updated version.

To ensure compatibility, please verify that this version bump doesn't introduce any breaking changes:

✅ Verification successful

Verified: Version bump for snakemake-interface-executor-plugins

No breaking changes or deprecations were found between versions 9.2.0 and 9.3.1. The version bump is safe and aligns with the PR objectives.

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Check for any breaking changes or deprecation notices in the changelog of snakemake-interface-executor-plugins

# Test: Search for breaking changes or deprecation notices in the changelog
gh repo clone snakemake/snakemake-interface-executor-plugins
cd snakemake-interface-executor-plugins
git log --oneline v9.2.0..v9.3.1 | grep -iE "breaking|deprecat" || echo "No breaking changes or deprecations found in commit messages"

Length of output: 418

snakemake/api.py (3)

480-483: Simplified plugin registry instantiation - LGTM!

The direct instantiation of ExecutorPluginRegistry simplifies the plugin registration process, aligning well with the PR objective. This change makes the code more straightforward and easier to understand.

---

638-641: Consistent simplification of report plugin registry - LGTM!

The direct instantiation of ReportPluginRegistry in the create_report method is consistent with the changes made in the execute_workflow method. This change further simplifies the plugin registration process, making the code more uniform and easier to maintain.

---

480-483: Overall improvement in plugin registry handling - Great job!

The changes made to both execute_workflow and create_report methods consistently simplify the plugin registry calling process. This refactoring aligns perfectly with the PR objective and results in more straightforward, easier-to-understand code. The consistency in these changes across different parts of the codebase is commendable and will likely improve maintainability.

No new methods or alterations to existing method signatures were introduced, which helps maintain backwards compatibility. The simplification of the plugin registration process should make the code easier to work with for both maintainers and contributors.

Also applies to: 638-641

snakemake/cli.py (2)

14-14: Approved: Importing ExecutorPluginRegistry

The import statement correctly adds ExecutorPluginRegistry for use in the code.

---

17-17: Approved: Importing ReportPluginRegistry

The import statement correctly adds ReportPluginRegistry for use in the code.