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Workflow

Workflow

Represents a workflow.

Attributes:

Name Type Description
path Path

The path to the workflow.
repo Repo

The git repository of the workflow.
name str

The name of the workflow.
Source code in src/snk_cli/workflow.py 
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class Workflow:
    """
    Represents a workflow.

    Attributes:
      path (Path): The path to the workflow.
      repo (Repo): The git repository of the workflow.
      name (str): The name of the workflow.
    """

    def __init__(self, path: Path) -> None:
        """
        Initializes a Workflow object.

        Args:
          path (Path): The path to the workflow.

        Returns:
          None

        Notes:
          Initializes the `repo` and `name` attributes.
        """
        self.path = path
        self.editable = self.check_is_editable()
        if self.editable:  # editable mode
            self.repo = None
        else:
            try:
                self.repo = Repo(path)
            except InvalidGitRepositoryError:
                self.repo = None
        self.name = self.path.name


    @property
    def tag(self):
        """
        Gets the tag of the workflow.

        Returns:
          str: The tag of the workflow, or None if no tag is found.
        """
        try:
            tag = self.repo.git.describe(["--tags", "--exact-match"])
        except Exception:
            tag = None
        return tag

    @property
    def commit(self):
        """
        Gets the commit SHA of the workflow.

        Returns:
          str: The commit SHA of the workflow.
        """
        try:
            sha = self.repo.head.object.hexsha
            commit = self.repo.git.rev_parse(sha, short=8)
        except Exception:
           commit = None
        return commit

    @property
    def version(self):
        """
        Gets the version of the workflow.

        Returns:
          str: The version of the workflow, or None if no version is found.
        """
        if self.repo is None:
            return None
        if self.tag:
            version = self.tag
        else:
            version = self.commit
        return version

    @property
    def executable(self):
        """
        Gets the executable of the workflow.

        Returns:
          Path: The path to the workflow executable.
        """
        workflow_bin_dir = self.path.parent.parent / "bin"
        name = self.name
        if sys.platform.startswith("win"):
            name += ".exe"
        return workflow_bin_dir / name

    @property
    def conda_prefix_dir(self):
        """
        Gets the conda prefix directory of the workflow. If in editable mode, the conda prefix directory is located in the .snakemake directory. Otherwise, it is located in the .conda directory in the workflow directory.

        Returns:
          Path: The path to the conda prefix directory.
        """
        return Path(".snakemake") / "conda" if self.editable else self.path / ".conda"

    @property
    def singularity_prefix_dir(self):
        """
        Gets the singularity prefix directory of the workflow.

        Returns:
          Path: The path to the singularity prefix directory.
        """
        if " " in str(self.path):
            # sigh, snakemake singularity does not support spaces in the path
            # https://github.com/snakemake/snakemake/blob/2ecb21ba04088b9e6850447760f713784cf8b775/snakemake/deployment/singularity.py#L130C1-L131C1
            return None
        return Path(".snakemake") / "singularity" if self.editable else self.path / ".singularity"

    def _is_editable_pip_install(self):
        # This function now acts as a method within the Workflow class
        package_spec = importlib.util.find_spec(self.name)
        if package_spec is None:
            return False  # Package is not installed

        package_location = package_spec.origin
        site_packages_paths = [p for p in sys.path if 'site-packages' in p]
        is_inside_site_packages = any(package_location.startswith(sp) for sp in site_packages_paths)

        if not is_inside_site_packages:
            return True

        for sp in site_packages_paths:
            egg_link_path = os.path.join(sp, self.name + '.egg-link')
            if os.path.isfile(egg_link_path):
                return True

        return False

    def check_is_editable(self):
        """
        Is the workflow editable?

        Returns:
          bool: True if the workflow is editable, False otherwise.
        """
        if self.path.is_symlink():
            return True
        try:
            return self._is_editable_pip_install()
        except Exception:
            return False

    def _find_folder(self, name) -> Optional[Path]:
        """
        Search for folder.

        Args:
          name: The name of the folder to search for.

        Returns:
          Optional[Path]: The path to the folder, or None if the folder is not found.
        """
        if (self.path / "workflow" / name).exists():
            return self.path / "workflow" / name
        if (self.path / name).exists():
            return self.path / name
        return None

    @property
    def profiles(self):
        workflow_profile_dir = self._find_folder("profiles")
        if workflow_profile_dir:
            return [p for p in workflow_profile_dir.glob("*") if p.is_dir() and (p / "config.yaml").exists()]
        return []

    @property
    def environments(self):
        workflow_environments_dir = self._find_folder("envs")
        if workflow_environments_dir:
            return [e for e in workflow_environments_dir.glob("*.yaml")] + [
                e for e in workflow_environments_dir.glob("*.yml")
            ]
        return []

    @property
    def scripts(self):
        workflow_environments_dir = self._find_folder("scripts")
        if workflow_environments_dir:
            return [s for s in workflow_environments_dir.iterdir() if s.is_file()]
        return []

commit property

Gets the commit SHA of the workflow.

Returns:

Name Type Description
str

The commit SHA of the workflow.

conda_prefix_dir property

Gets the conda prefix directory of the workflow. If in editable mode, the conda prefix directory is located in the .snakemake directory. Otherwise, it is located in the .conda directory in the workflow directory.

Returns:

Name Type Description
Path

The path to the conda prefix directory.

executable property

Gets the executable of the workflow.

Returns:

Name Type Description
Path

The path to the workflow executable.

singularity_prefix_dir property

Gets the singularity prefix directory of the workflow.

Returns:

Name Type Description
Path

The path to the singularity prefix directory.

tag property

Gets the tag of the workflow.

Returns:

Name Type Description
str

The tag of the workflow, or None if no tag is found.

version property

Gets the version of the workflow.

Returns:

Name Type Description
str

The version of the workflow, or None if no version is found.

__init__(path)

Initializes a Workflow object.

Parameters:

Name Type Description Default
path Path

The path to the workflow.

 required

Returns:

Type Description
None

None
Notes

Initializes the repo and name attributes.

Source code in src/snk_cli/workflow.py 
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def __init__(self, path: Path) -> None:
    """
    Initializes a Workflow object.

    Args:
      path (Path): The path to the workflow.

    Returns:
      None

    Notes:
      Initializes the `repo` and `name` attributes.
    """
    self.path = path
    self.editable = self.check_is_editable()
    if self.editable:  # editable mode
        self.repo = None
    else:
        try:
            self.repo = Repo(path)
        except InvalidGitRepositoryError:
            self.repo = None
    self.name = self.path.name

check_is_editable()

Is the workflow editable?

Returns:

Name Type Description
bool

True if the workflow is editable, False otherwise.
Source code in src/snk_cli/workflow.py 
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def check_is_editable(self):
    """
    Is the workflow editable?

    Returns:
      bool: True if the workflow is editable, False otherwise.
    """
    if self.path.is_symlink():
        return True
    try:
        return self._is_editable_pip_install()
    except Exception:
        return False