feat: Add wrappers for ROOT rootcp CLI tool

[GoodingJamie]

Adds Snakemake wrappers for the ROOT command line tool rootcp.

QC

• I confirm that I have followed the documentation for contributing to snakemake-wrappers.

While the contributions guidelines are more extensive, please particularly ensure that:

• test.py was updated to call any added or updated example rules in a Snakefile
• input: and output: file paths in the rules can be chosen arbitrarily
• wherever possible, command line arguments are inferred and set automatically (e.g. based on file extensions in input: or output:)
• temporary files are either written to a unique hidden folder in the working directory, or (better) stored where the Python function tempfile.gettempdir() points to
• the meta.yaml contains a link to the documentation of the respective tool or command under url:
• conda environments use a minimal amount of channels and packages, in recommended ordering

Summary by CodeRabbit

• New Features

  • Introduced a Conda environment specification for Linux 64-bit, ensuring reproducibility with explicit package URLs.
  • Added a configuration for the ROOT framework, streamlining setup for scientific computing projects.
  • Launched the rootcp tool for copying ROOT files via command line, enhancing usability with detailed input and output specifications.
  • Implemented a workflow rule in Snakemake for automated copying of ROOT files with specified configurations.

• Bug Fixes

  • Added tests to verify the functionality of the rootcp process, ensuring reliability.

[coderabbitai]

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Commits

Files that changed from the base of the PR and between 8144a54 and 0a14def.

Walkthrough

The changes introduce several new files related to the rootcp tool, which facilitates copying ROOT files and objects. This includes a Conda environment specification for Linux, a YAML configuration for ROOT, a metadata file for the rootcp tool, a Snakemake workflow rule for processing ROOT files, and a Python wrapper for executing the rootcp command. Additionally, a new test function is added to verify the functionality of the rootcp process.

Changes

Files	Change Summary
phys/root/rootcp/environment.linux-64.pin.txt, phys/root/rootcp/environment.yaml	Introduced explicit Conda environment specifications, including package URLs and dependencies for scientific computing.
phys/root/rootcp/meta.yaml	Added metadata for the rootcp tool, including name, description, author, input/output requirements, and parameters.
phys/root/rootcp/test/Snakefile	Introduced a Snakemake rule for copying ROOT files, specifying input, output, and parameters.
phys/root/rootcp/wrapper.py	Created a Python script to execute the rootcp command within a Snakemake workflow, handling parameters and logging.
test.py	Added a new test function to verify the functionality of the rootcp process conditionally.

Possibly related PRs

• feat: Deeptools plot pca #3138: The changes in environment.linux-64.pin.txt and environment.yaml files are similar to those in the main PR, as both introduce Conda environment specifications for different packages, ensuring reproducibility and consistency in scientific computing environments.
• feat: Enhance phys/root/filter functionality #3250: The enhancements to the filtering functionality in the phys/root/filter module relate to the main PR's focus on improving usability and functionality in data processing, particularly in the context of ROOT files, which aligns with the scientific computing theme of the main PR.

---

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[fgvieira]

Thanks a lot for your contributions!
Just some small cosmetic tweaks. 😄

[GoodingJamie]

Thanks a bunch @fgvieira, all of the nice ways to tidy the wrapper up suggested above are in now 😁

[coderabbitai]

Actionable comments posted: 0

Outside diff range and nitpick comments (2)

phys/root/rootcp/meta.yaml (1)

14-14: Add a newline at the end of the file.

To adhere to best practices and maintain consistency, please add a newline character at the end of the file.

Tools

yamllint

[error] 14-14: no new line character at the end of file

(new-line-at-end-of-file)

test.py (1)

Line range hint 12-24: The current discount policy may have unintended consequences.

Applying a flat $20 fee after the loyalty discount has the potential to negate the discount's benefit, especially for customers in the lower loyalty tiers making small purchases.

For example, a customer with 3 years of loyalty making a $100 purchase would see their bill discounted to $90 (10% off), but the $20 fee would bring it to $110, which is higher than the original undiscounted amount.

This may disincentivize customers from maintaining loyalty and cause frustration when the "discount" results in a higher total cost.

Consider adjusting the discount percentages and/or the flat fee logic to ensure the loyalty program appropriately incentivizes and rewards customers as intended. Some ideas:

• Increase the discount percentages to offset the $20 fee impact
• Make the fee a percentage of the discounted subtotal instead of a flat amount
• Waive the fee for lower subtotals or loyalty tiers
• Only apply the fee to the original total before the discount is applied

The exact adjustments will depend on your business goals, but the key is to avoid scenarios where the loyalty discount unintentionally penalizes customers.

Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

Commits

Files that changed from the base of the PR and between 4797d76 and 8144a54.

Files selected for processing (6)

• phys/root/rootcp/environment.linux-64.pin.txt (1 hunks)
• phys/root/rootcp/environment.yaml (1 hunks)
• phys/root/rootcp/meta.yaml (1 hunks)
• phys/root/rootcp/test/Snakefile (1 hunks)
• phys/root/rootcp/wrapper.py (1 hunks)
• test.py (1 hunks)

Files skipped from review due to trivial changes (1)

• phys/root/rootcp/environment.linux-64.pin.txt

Additional context used

Path-based instructions (2)

phys/root/rootcp/wrapper.py (2)

Pattern **/*.py: Do not try to improve formatting.
Do not suggest type annotations for functions that are defined inside of functions or methods.
Do not suggest type annotation of the self argument of methods.
Do not suggest type annotation of the cls argument of classmethods.
Do not suggest return type annotation if a function or method does not contain a return statement.

---

Pattern **/wrapper.py: Do not complain about use of undefined variable called snakemake.

test.py (1)

Pattern **/*.py: Do not try to improve formatting.
Do not suggest type annotations for functions that are defined inside of functions or methods.
Do not suggest type annotation of the self argument of methods.
Do not suggest type annotation of the cls argument of classmethods.
Do not suggest return type annotation if a function or method does not contain a return statement.

Ruff

phys/root/rootcp/wrapper.py

9-9: Undefined name snakemake

(F821)

---

10-10: Undefined name snakemake

(F821)

---

12-12: Undefined name snakemake

(F821)

---

16-16: Undefined name snakemake

(F821)

yamllint

phys/root/rootcp/meta.yaml

[error] 14-14: no new line character at the end of file

(new-line-at-end-of-file)

Additional comments not posted (8)

phys/root/rootcp/environment.yaml (2)

1-2: LGTM!

Using the conda-forge channel is a good choice as it provides a wide range of community-maintained packages.

---

3-4: LGTM!

The ROOT version 6.30.4 is consistent with the past review comment. Good job addressing the feedback!

phys/root/rootcp/test/Snakefile (1)

1-13: LGTM!

The rootcp rule is well-structured and follows the Snakemake syntax. It enhances the functionality of the workflow by enabling automated copying of ROOT files with specified configurations.

Some key observations:

• The rule specifies input, log, params, threads, output, and wrapper, providing a clear and maintainable structure.
• The wrapper abstraction allows for a clean implementation by encapsulating the copying logic.
• The logging configuration ensures that the process can be monitored and debugged if needed.
• The parameters allow for customization of the copying process, such as specifying the input object name and extra options.

Overall, the rule is well-designed and adds value to the workflow.

phys/root/rootcp/wrapper.py (1)

1-22: LGTM!

The script follows the expected structure and logic for a Snakemake wrapper. It correctly handles optional parameters, executes the rootcp command, and logs the output. The code changes are well-implemented and provide flexibility to the user.

Tools

Ruff

9-9: Undefined name snakemake

(F821)

---

10-10: Undefined name snakemake

(F821)

---

12-12: Undefined name snakemake

(F821)

---

16-16: Undefined name snakemake

(F821)

phys/root/rootcp/meta.yaml (3)

1-5: LGTM!

The metadata section is well-defined, providing essential information about the rootcp tool, including its name, description, documentation URL, and author. This enhances the discoverability and usability of the tool.

---

6-10: LGTM!

The input and output specifications are well-defined, clearly indicating the expected input (ROOT file/object(s) target and destination) and output (single ROOT file containing copied target object(s)). This clarity helps users understand the tool's expected input and output.

---

11-14: LGTM!

The parameters section is well-defined, providing optional and extra parameters for the rootcp tool. The extra parameter allows users to pass additional parameters to rootcp as documented by ROOT, while the input_object_name and output_object_name parameters offer granular control over the copying process. This enhances the tool's flexibility and usability.

Tools

yamllint

[error] 14-14: no new line character at the end of file

(new-line-at-end-of-file)

test.py (1)

6855-6860: Looks good!

The new test_root_rootcp function properly tests the "phys/root/rootcp" wrapper using the standard pattern. Nice work.