snakemake/deployment/conda.py (3)

Line range hint 484-509: Consider refactoring for improved readability

The create method is quite complex, handling various scenarios for creating Conda environments. While the current change is appropriate, consider refactoring this method to improve readability and maintainability:

1. Extract the environment creation logic for archived and non-archived environments into separate methods.
2. Use a strategy pattern to handle different frontend scenarios (conda vs mamba).
3. Consider using a configuration object to encapsulate environment creation parameters.

These refactorings could make the code more modular and easier to maintain in the future.

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Line range hint 1-509: Consider enhancing error handling, logging, and documentation

While reviewing this file, I noticed some areas that could benefit from enhancement:

1. Error Handling: Consider implementing more specific exception types for different error scenarios in environment creation and management. This could help in providing more targeted error messages and easier debugging.

2. Logging: Enhance logging throughout the file to provide more detailed information about the environment creation process, especially in complex scenarios like handling archived environments or different frontends.

3. Documentation: Add more inline documentation, especially for complex methods like create. Consider using type hints for method parameters and return values to improve code readability and maintainability.

4. Testing: Ensure that unit tests cover the new flexibility introduced by using self.frontend. Add tests for different frontend scenarios if they don't already exist.

These enhancements could significantly improve the overall quality and maintainability of the code.

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Hardcoded "conda" strings still present in multiple files

Several files still contain hardcoded "conda" strings, which reduces flexibility and consistency:

• snakemake/cli.py
• snakemake/workflow.py
• tests/tests.py
• snakemake/persistence.py
• snakemake/unit_tests/__init__.py
• snakemake/common.py

Please update these occurrences to use self.frontend to align with the recent changes and enhance configurability.

🔗 Analysis chain

Line range hint 500-509: Verify initialization and usage of self.frontend

The change to use self.frontend instead of "conda" improves flexibility. However, to ensure robustness:

1. Verify that self.frontend is properly initialized in the __init__ method of the Env class.
2. Check if there are any other occurrences of hardcoded "conda" strings that should be replaced with self.frontend.
3. Ensure that any code paths that might use this command construction are aware of the potential for different frontend values.

To check for other occurrences of hardcoded "conda" strings and the initialization of self.frontend, run:

---

To proceed with the verification, please run the following updated shell scripts:

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
echo "Checking for hardcoded 'conda' strings:"
rg '"conda"' --type python

echo "\nChecking for self.frontend initialization:"
ast-grep --lang python --pattern 'class Env:
  $$$
  def __init__($$$):
    $$$
    self.frontend = $_
    $$$
'

Length of output: 44029

---

Script:

# Checking for hardcoded 'conda' strings:
rg '"conda"' --type py

# Checking for self.frontend initialization:
ast-grep --lang python --pattern 'class Env:
  $$$
  def __init__($$$):
    $$$
    self.frontend = $_
    $$$
'

Length of output: 44507

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snakemake/deployment/conda.py (1)

386-391: Simplify conditional logic for appending --no-default-packages

The condition for appending --no-default-packages can be simplified for clarity. Instead of combining multiple conditions, consider checking for the specific versions where the argument is required.

Apply the following diff to simplify the conditional logic:

 if self.conda.frontend == "conda" or (
     self.conda.frontend == "mamba"
     and self.conda.frontend_version < Version("2.0.0")
 ):
     args.append("--no-default-packages")

Consider rewriting it as:

 if self.conda.frontend == "conda" or self.conda.frontend_version < Version("2.0.0"):
     args.append("--no-default-packages")

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snakemake/deployment/conda.py (1)

378-392: New method to create environment arguments

The new _create_env_args method provides a centralized way to generate command-line arguments for conda environment creation. This is a good practice for maintainability and consistency.

A few observations:

1. The method handles different modes (yaml vs. others) and adjusts arguments accordingly.
2. It includes a check for Windows to add the --no-shortcuts argument.
3. There's a version check for mamba 2.0.0 to determine whether to include the --no-default-packages argument.

Consider adding a docstring to explain the purpose of the method and the mode parameter.

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snakemake/deployment/conda.py (4)

383-399: LGTM: Well-implemented method for creating environment arguments

The _create_env_args method is well-structured and correctly handles different scenarios based on the package manager and its version. It's a good addition to the Env class.

Consider adding a docstring to explain the method's purpose and the mode parameter. For example:

def _create_env_args(self, mode: str):
    """
    Generate command-line arguments for environment creation.

    Args:
        mode (str): The mode of environment creation ('archive', 'yaml', or other).

    Returns:
        list: A list of command-line arguments.
    """
    # ... existing code ...

---

Line range hint 470-621: LGTM: Improved environment creation process

The modifications to the create method enhance its flexibility and robustness. The use of a flag file to track setup completion is a good practice, and the integration of the new _create_env_args method improves code organization.

While the changes are good, the create method is quite long and complex. Consider refactoring it into smaller, more focused methods to improve readability and maintainability. For example:

1. Extract the environment archive handling into a separate method.
2. Create a method for the regular environment creation process.
3. Move the post-deployment script execution to its own method.

This refactoring would make the main create method more concise and easier to understand.

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701-709: LGTM with a suggestion: Initialization of frontend_version

The addition of the frontend_version attribute is a good improvement to the Conda class. It's consistent with the class's purpose and allows for version-specific behavior.

Consider initializing frontend_version in all cases, not just when check is True. This ensures that the attribute is always set, preventing potential AttributeErrors if _check is not called. You could modify the initialization as follows:

self.frontend_version = self._get_version(self.frontend) if frontend is not None else None

This change would set frontend_version whenever a frontend is specified, regardless of the check parameter.

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784-805: LGTM: Improved version parsing for different package managers

The modifications to the _get_version method enhance its flexibility and robustness. The method now correctly handles version parsing for both conda and mamba, which is a valuable improvement.

Consider the following minor improvements:

1. Add a return type hint to the method signature:

   def _get_version(self, frontend: str) -> Version:

2. Use a constant for the version pattern to improve maintainability:

   VERSION_PATTERN = r"\d+\.\d+\.\d+"
   version_matches = re.findall(VERSION_PATTERN, version)

3. Consider using re.search instead of re.findall for the mamba-specific case, as you're only interested in the first match:

   mamba_match = re.search(r"mamba (\d+\.\d+\.\d+)", version)
   if mamba_match:
       return parse_version([mamba_match.group(1)])

These changes would further improve the readability and maintainability of the method.

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tests/test_wrapper/test.vcf (1)

Line range hint 11-17: LGTM: Data rows correctly implement new INFO fields and maintain valid FORMAT values.

The changes to the data rows are well-implemented:

1. New INFO fields (S1, N1, F1) are correctly populated for each variant.
2. Genotype (GT) field uses valid representations (./1, 1|1, 0/1, etc.).
3. Missing data is properly represented with ".".

For improved consistency, consider using the same string length for FS1 values across all samples (e.g., "LongString1", "LongString2", etc.) instead of mixing "LongString" and "ss" prefixes.

snakemake/deployment/conda.py (4)

386-402: LGTM with a minor suggestion: New method for creating environment arguments

The _create_env_args method is a good addition that centralizes the logic for generating conda environment creation arguments. It handles different modes and platform-specific cases well.

However, for better readability, consider extracting the version comparison logic into a separate method:

def _should_add_no_default_packages(self):
    return (
        self.conda.frontend == "conda"
        or (
            self.conda.frontend == "mamba"
            and self.conda.frontend_version < Version("2.0.0")
        )
    )

Then you can simplify the condition in _create_env_args:

if self._should_add_no_default_packages():
    args.append("--no-default-packages")

This would make the method easier to read and maintain.

---

473-474: LGTM with a suggestion: Updates to environment creation process

The changes to the create method improve the robustness of the conda environment creation process. The introduction of the setup done flag is a good way to track completion and detect broken environments.

However, consider adding error handling when creating the setup done flag file:

try:
    with open(setup_done_flag, "w") as _:
        pass
except IOError as e:
    logger.warning(f"Failed to create setup done flag file: {e}")
    # Optionally, you might want to clean up the environment here
    # if you consider this a critical failure

This will ensure that any issues with creating the flag file (e.g., permissions problems) are logged and don't silently fail.

Also applies to: 476-476, 522-526, 567-567, 624-625

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684-685: LGTM with a suggestion: Updates to Conda class initialization

The changes to the Conda class initialization improve version handling and provide more flexibility in checking the conda frontend.

However, consider adding error handling when getting the frontend version:

try:
    self.frontend_version = self._get_version(self.frontend)
except Exception as e:
    logger.warning(f"Failed to get {self.frontend} version: {e}")
    self.frontend_version = None

This will ensure that any issues with getting the version (e.g., command not found) are logged and don't cause the initialization to fail completely.

Also applies to: 705-713

---

788-809: LGTM with a suggestion: Improved version retrieval method

The updated _get_version method is more robust and flexible, handling both conda and mamba version retrieval. The use of regex for parsing and returning a Version object are good improvements.

To improve code organization, consider extracting the version parsing logic into a separate method:

def _parse_version(self, version_string: str, frontend: str) -> Version:
    version_matches = re.findall(r"\d+\.\d+\.\d+", version_string)
    if len(version_matches) != 1:
        if frontend == "mamba":
            version_matches = re.findall(r"mamba (\d+\.\d+\.\d+)", version_string)
            if len(version_matches) == 1:
                return Version(version_matches[0])
        raise WorkflowError(
            f"Unable to determine conda version. '{frontend} --version' returned:\n{version_string}"
        )
    return Version(version_matches[0])

Then you can simplify the _get_version method:

def _get_version(self, frontend: str) -> Version:
    from snakemake.shell import shell
    version_string = shell.check_output(
        self._get_cmd(f"{frontend} --version"), stderr=subprocess.PIPE, text=True
    )
    return self._parse_version(version_string, frontend)

This separation of concerns makes the code more maintainable and easier to test.

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