Nest

Nest

Initializes a Nest object.

Parameters:

Name	Type	Description	Default
snk_home	Path	The path to the SNK home directory. Defaults to None.	None
bin_dir	Path	The path to the bin directory. Defaults to None.	None

Side Effects

Creates the SNK home and bin directories if they do not exist.

Examples:

>>> nest = Nest()

Source code in snk/nest.py

class Nest:
    """
    Initializes a Nest object.

    Args:
      snk_home (Path, optional): The path to the SNK home directory. Defaults to None.
      bin_dir (Path, optional): The path to the bin directory. Defaults to None.

    Side Effects:
      Creates the SNK home and bin directories if they do not exist.

    Examples:
      >>> nest = Nest()
    """

    def __init__(self, snk_home: Path = None, bin_dir: Path = None) -> None:
        """
        Initializes a Nest object.

        Args:
          snk_home (Path, optional): The path to the SNK home directory. Defaults to None.
          bin_dir (Path, optional): The path to the bin directory. Defaults to None.

        Side Effects:
          Creates the SNK home and bin directories if they do not exist.

        Examples:
          >>> nest = Nest()
        """
        self.python_interpreter_path = Path(
            sys.executable
        )  # needs to be the same python that has snk

        if not snk_home:
            home_path = self.python_interpreter_path.parent.parent
            if not os.access(home_path, os.W_OK):
                user_home_path = Path("~").expanduser()
                snk_home = user_home_path / ".local" / "snk"
            else:
                snk_home = home_path / "snk"

        if not bin_dir:
            bin_dir = self.python_interpreter_path.parent
            if not os.access(bin_dir, os.W_OK):
                user_home_path = Path("~").expanduser()
                bin_dir = user_home_path / ".local" / "bin"

        self.bin_dir = Path(bin_dir).absolute()
        self.snk_home = Path(snk_home).absolute()
        self.snk_workflows_dir = self.snk_home / "workflows"
        self.snk_venv_dir = self.snk_home / "venvs"
        self.snk_executable_dir = self.snk_home / "bin"

        # Create dirs
        self.snk_home.mkdir(parents=True, exist_ok=True)
        self.snk_workflows_dir.mkdir(parents=True, exist_ok=True)
        self.snk_executable_dir.mkdir(parents=True, exist_ok=True)
        self.bin_dir.mkdir(parents=True, exist_ok=True)

    def bin_dir_in_path(self) -> bool:
        path_dirs = os.environ["PATH"].split(os.pathsep)
        return str(self.bin_dir) in path_dirs

    def _format_repo_url(self, repo: str):
        """
        Checks that the given repo URL is valid.

        Args:
          repo (str): The URL of the repo.

        Raises:
          InvalidWorkflowRepositoryError: If the repo URL is not valid.

        Examples:
          >>> nest._format_repo_url('https://github.com/example/repo.git')
        """
        if not repo.endswith(".git"):
            repo += ".git"
        if not repo.startswith("http"):
            raise InvalidWorkflowRepositoryError("Repo url must start with http")
        return repo

    def install(
        self,
        workflow: str,
        editable=False,
        name=None,
        tag=None,
        commit=None,
        config: Path = None,
        snakefile: Path = None,
        force=False,
        additional_resources=[],
        conda: bool = None,
        snakemake_version=None,
        dependencies=[],
        isolate=False,
    ) -> Workflow:
        """
        Installs a Snakemake workflow as a CLI.

        Args:
          workflow (str): The URL of the repo or the path to the local workflow.
          editable (bool, optional): Whether to install the workflow in editable mode. Defaults to False.
          name (str, optional): The name of the workflow. Defaults to None.
          tag (str, optional): The tag of the workflow. Defaults to None.
          commit (str, optional): The commit SHA of the workflow. Defaults to None.
          config (Path, optional): The path to the config file. Defaults to None.
          snakefile (Path, optional): The path to the Snakefile. Defaults to None.
          force (bool, optional): Whether to force the installation. Defaults to False.
          additional_resources (list, optional): A list of resources additional to the resources folder to copy. Defaults to [].
          conda (bool, optional): Modify the snk config file to control conda use. If None, will not modify the config file. Defaults to None.
          snakemake_version (str, optional): The version of Snakemake to install in the virtual environment. Defaults to None.
          dependencies (list, optional): A list of dependencies to install. Defaults to [].
        Returns:
          Workflow: The installed workflow.

        Examples:
          >>> nest.install('https://github.com/example/repo.git', name='example', tag='v1.0.0')
          >>> nest.install('https://github.com/example/repo.git', name='example', commit='0123456')
        """

        def handle_force_installation(name: str):
            try:
                self.uninstall(name=name, force=True)
            except WorkflowNotFoundError:
                pass
        workflow = str(workflow) # ensure it is a string
        try:
            workflow = self._format_repo_url(workflow)
            if not name:
                name = self._get_name_from_git_url(workflow)
            if not force:
                self._check_workflow_name_available(name)
            else:
                handle_force_installation(name)
            workflow_path = self.download(workflow, name, tag_name=tag, commit=commit)
        except InvalidWorkflowRepositoryError:
            workflow_local_path = Path(workflow).resolve()
            if workflow_local_path.is_file():
                raise InvalidWorkflowError(
                    f"When installing a local workflow, the path must be a directory. Found: {workflow_local_path}"
                )
            if self.snk_workflows_dir.resolve().is_relative_to(workflow_local_path) and not editable:
                raise InvalidWorkflowError(
                    f"The workflow directory contains SNK_HOME!\nWORKFLOW: {workflow_local_path}\nSNK_HOME: {self.snk_workflows_dir.resolve()}.\n\nTry installing the workflow with --editable."
                )
            if not name:
                name = workflow_local_path.name
            if not force:
                self._check_workflow_name_available(name)
            else:
                handle_force_installation(name)
            workflow_path = self.local(workflow_local_path, name, editable)
        try:
            self.validate_Snakemake_repo(workflow_path)

            snakemake_version_to_install_in_venv = None
            if snakemake_version is not None:
                snakemake_version_to_install_in_venv = snakemake_version
            elif version.parse(self._current_snakemake_version) < version.parse(self.check_for_snakemake_min_version(workflow_path)):
                # The current version of Snakemake is less than the minimum version required by the workflow
                snakemake_version_to_install_in_venv = f">={self.check_for_snakemake_min_version(workflow_path)}"

            if snakemake_version_to_install_in_venv is not None or dependencies:
                isolate = True

            if isolate:
                venv_path = self.create_virtual_environment(name)
                self._install_snk_cli_in_venv(
                    venv_path, 
                    snakemake_version=snakemake_version_to_install_in_venv, 
                    dependencies=dependencies
                )
                python_interpreter_path = venv_path / "bin" / "python"
            else:
                python_interpreter_path = self.python_interpreter_path
            workflow_executable_path = self.create_executable(workflow_path, name, python_interpreter_path=python_interpreter_path)
            self.link_workflow_executable_to_bin(workflow_executable_path)
            if config:
                self.copy_nonstandard_config(workflow_path, config)
            if snakefile:
                snakefile_path = workflow_path / snakefile
                if not snakefile_path.exists():
                    raise FileNotFoundError(f"Snakefile not found at {snakefile_path}")
                shutil.copyfile(snakefile_path, snakefile_path.parent / "Snakefile")
            if additional_resources:
                self.additional_resources(workflow_path, additional_resources)
            if conda is not None:
                self.modify_snk_config(workflow_path, conda=conda)
            self._confirm_installation(name)
        except Exception as e:
            # remove any half completed steps
            to_remove = self.get_paths_to_delete(name)
            self.delete_paths(to_remove)
            raise e
        return Workflow(workflow_path)

    def modify_snk_config(self, workflow_path: Path, **kwargs):
        """
        Modify the snk config file.

        Args:
          workflow_path (Path): The path to the workflow directory.
          **kwargs: Additional keyword arguments to modify the snk config file.

        Examples:
          >>> nest.modify_snk_config(Path('/path/to/workflow'), logo=example)
        """
        snk_config = SnkConfig.from_workflow_dir(
            workflow_path, create_if_not_exists=True
        )
        modified = False
        for key, value in kwargs.items():
            if getattr(snk_config, key) != value:
                modified = True
                setattr(snk_config, key, value)
        if modified:
            snk_config.save()

    def additional_resources(self, workflow_path: Path, resources: List[Path]):
        """
        Modify the snk config file so that resources will be copied at runtime.

        Args:
          workflow_path (Path): The path to the workflow directory.
          resources (List[Path]): A list of additional resources to copy.

        Examples:
          >>> nest.additional_resources(Path('/path/to/workflow'), [Path('/path/to/resource1'), Path('/path/to/resource2')])
        """
        # validate_resources(resources)
        snk_config = SnkConfig.from_workflow_dir(
            workflow_path, create_if_not_exists=True
        )
        snk_config.add_resources(resources, workflow_path)
        snk_config.save()

    def copy_nonstandard_config(self, workflow_dir: Path, config_path: Path):
        """
        Copy a nonstandard config file to the workflow directory.

        Args:
          workflow_dir (Path): The path to the workflow directory.
          config_path (Path): The path to the config file.

        Examples:
          >>> nest.copy_nonstandard_config(Path('/path/to/workflow'), Path('/path/to/config.yaml'))
        """
        config_dir = workflow_dir / "config"
        config_dir.mkdir(exist_ok=True)
        shutil.copyfile(workflow_dir / config_path, config_dir / "config.yaml")

    def get_paths_to_delete(self, workflow_name: str) -> List[Path]:
        """
        Get the paths to delete when uninstalling a workflow.

        Args:
          workflow_name (str): The name of the workflow.

        Returns:
          List[Path]: A list of paths to delete.

        Examples:
          >>> nest.get_paths_to_delete('example')
          [Path('/path/to/workflows/example'), Path('/path/to/bin/example')]
        """
        to_delete = []

        # remove repo
        workflow_dir = self.snk_workflows_dir / workflow_name
        if workflow_dir.exists() and workflow_dir.is_dir():
            to_delete.append(workflow_dir)
        elif workflow_dir.is_symlink():
            # editable
            to_delete.append(workflow_dir)

        workflow_executable = self.snk_executable_dir / workflow_name
        if workflow_executable.exists():
            to_delete.append(workflow_executable)

        # remove venv  
        venv_path = self.snk_venv_dir / workflow_name
        if venv_path.exists():
            to_delete.append(venv_path)

        # remove link
        workflow_symlink_executable = self.bin_dir / workflow_name
        if workflow_symlink_executable.is_symlink():
            if str(os.readlink(workflow_symlink_executable)) == str(
                workflow_executable
            ):
                to_delete.append(workflow_symlink_executable)

        if not to_delete:
            raise WorkflowNotFoundError(f"Could not find workflow: {workflow_name}")

        return to_delete

    def delete_paths(self, files: List[Path]):
        """
        Delete the given paths.

        Args:
          files (List[Path]): A list of paths to delete.

        Side Effects:
          Deletes the given paths.

        Examples:
          >>> nest.delete_paths([Path('/path/to/workflows/example'), Path('/path/to/bin/example')])
        """
        # check that the files are in self.snk_workflows_dir
        # i.e. if it is a symlink read the link and check
        for path in files:
            if path.is_symlink():
                print("Unlinking:", path)
                path.unlink()
            elif path.is_file():
                print("Deleting:", path)
                assert str(self.snk_home) in str(
                    path
                ), "Cannot delete files outside of SNK_HOME"
                path.unlink()
            elif path.is_dir():
                print("Deleting:", path)
                assert str(self.snk_home) in str(
                    path
                ), "Cannot delete folders outside of SNK_HOME"
                shutil.rmtree(path)
            else:
                raise TypeError("Invalid file type")

    def uninstall(self, name: str, force: bool = False) -> bool:
        """
        Uninstalls a workflow.

        Args:
          name (str): The name of the workflow.
          force (bool, optional): Whether to force the uninstallation. Defaults to False.

        Returns:
          bool: Whether the uninstallation was successful.

        Examples:
          >>> nest.uninstall('example')
          True
        """
        if not isinstance(name, str):
            raise TypeError(f"Name must be a string. Found: {name}")
        to_remove = self.get_paths_to_delete(name)
        if force:
            proceed = True
        else:
            print(f"Uninstalling {name}")
            print("  Would remove:")
            for p in to_remove:
                print(f"    {p}{'/*' if p.is_dir() else ''}")
            ans = input("Proceed (Y/n)? ")
            proceed = ans.lower() in ["y", "yes"]
        if not proceed:
            return False
        self.delete_paths(to_remove)
        return True

    def _check_workflow_name_available(self, name: str):
        if not name:
            return None
        if name in os.listdir(self.snk_workflows_dir):
            raise WorkflowExistsError(
                f"Workflow '{name}' already exists in SNK_HOME ({self.snk_workflows_dir})"
            )

        if name in os.listdir(self.bin_dir):
            # check if orfan symlink
            def is_orfan_symlink(name):
                return (self.bin_dir / name).is_symlink() and str(
                    self.snk_home
                ) in os.readlink(self.bin_dir / name)

            if is_orfan_symlink(name):
                self.delete_paths([self.bin_dir / name])
            else:
                raise WorkflowExistsError(
                    f"File '{name}' already exists in SNK_BIN ({self.bin_dir})"
                )

    def _confirm_installation(self, name: str):
        """
        Confirms that the installation was successful.

        Args:
          name (str): The name of the workflow.

        Examples:
          >>> nest._confirm_installation('example')
        """
        workflow_dir = self.snk_workflows_dir / name
        assert workflow_dir.exists()
        workflows = [p.name.split(".")[0] for p in self.bin_dir.glob("*")]
        assert name in workflows

    def _get_name_from_git_url(self, git_url: str):
        """
        Gets the name of the workflow from the git URL.

        Args:
          git_url (str): The URL of the git repository.

        Returns:
          str: The name of the workflow.
        """
        return git_url.split("/")[-1].split(".")[0]

    @property
    def workflows(self):
        return [
            Workflow(workflow_dir.absolute())
            for workflow_dir in self.snk_workflows_dir.glob("*")
        ]

    def download(self, repo_url: str, name: str, tag_name: str = None, commit: str = None) -> Path:
        """
        Clone a workflow from a git repository.

        Args:
          repo_url (str): The URL of the repo.
          name (str): The name of the workflow.
          tag_name (str, optional): The tag of the workflow. Defaults to None.
          commit (str, optional): The commit SHA of the workflow. Defaults to None.

        Returns:
          Path: The path to the cloned workflow.

        Examples:
          >>> nest.download('https://github.com/example/repo.git', 'example', tag_name='v1.0.0')
        """
        location = self.snk_workflows_dir / name
        options = []
        if not commit:
            options.append(f"--depth 1")
        if tag_name:
            options.append(f"--single-branch")
            options.append(f"--branch {tag_name}")
        try:
            repo = Repo.clone_from(repo_url, location, multi_options=options)
            if commit:
                repo.git.checkout(commit)
            else:
                repo.git.checkout(tag_name)
        except GitCommandError as e:
            if "destination path" in e.stderr:
                raise WorkflowExistsError(
                    f"Workflow '{name}' already exists in {self.snk_workflows_dir}"
                )
            elif f"Remote branch {tag_name}" in e.stderr:
                raise WorkflowNotFoundError(f"Workflow tag '{tag_name}' not found")
            elif f"pathspec '{commit}' did not match" in e.stderr:
                if tag_name:
                    raise WorkflowNotFoundError(f"Workflow commit '{commit}' not found on branch {tag_name}")
                else:
                    raise WorkflowNotFoundError(f"Workflow commit '{commit}' not found")
            elif "not found" in e.stderr:
                raise WorkflowNotFoundError(
                    f"Workflow repository '{repo_url}' not found"
                )
            raise e
        return location

    def local(self, path: Path, name: str, editable=False) -> Path:
        """
        Install a local workflow.

        Args:
          path (Path): The path to the local workflow.
          name (str): The name of the workflow.
          editable (bool, optional): Whether to install the workflow in editable mode. Defaults to False.

        Returns:
          Path: The path to the installed workflow.

        Examples:
          >>> nest.local(Path('/path/to/workflow'), 'example')
        """
        location = self.snk_workflows_dir / name
        if editable:
            os.symlink(path.absolute(), location, target_is_directory=True)
            return location
        shutil.copytree(path, location)
        try:
            Repo(location)
        except InvalidGitRepositoryError:
            Repo.init(location, mkdir=False)
        return location

    def create_virtual_environment(self, name: str) -> Path:
        """
        Create a virtual environment for the workflow.

        Args:
          name (str): The name of the virtual environment.
          snakemake_version (str, optional): The version of Snakemake to install in the virtual environment. Defaults to None.

        Returns:
          Path: The path to the virtual environment.

        Examples:
          >>> nest.create_virtual_environment('example')
        """
        venv_dir = self.snk_home / "venvs"
        venv_dir.mkdir(exist_ok=True)
        venv_path = venv_dir / name
        try:
            venv.create(venv_path, with_pip=True, symlinks=True)
        except FileExistsError:
            raise FileExistsError(f"The venv {venv_path} already exists. Please choose a different location or name. Alternatively, use the --force flag to overwrite the existing venv.")
        return venv_path

    def _install_snk_cli_in_venv(self, venv_path: Path, snakemake_version=None, dependencies=[]):
        """
        Install snk_cli in the virtual environment.

        Args:
          venv_path (Path): The path to the virtual environment.
          snakemake_version (str, optional): The version of Snakemake to install in the virtual environment. Defaults to "7.32.4".

        Examples:
          >>> nest._install_snk_cli_in_venv(Path('/path/to/venv'), snakemake_version='7.32.4')
        """
        if not venv_path.exists():
            raise FileNotFoundError(f"Virtual environment not found at {venv_path}")
        if sys.platform.startswith("win"):
            pip_path = venv_path / "Scripts" / "pip.exe"
        else:
            pip_path = venv_path / "bin" / "pip"
        if not pip_path.exists():
            raise FileNotFoundError(f"pip not found at {pip_path}")
        # check if snakemake version starts with >= or <=
        if snakemake_version:
            # check if snakemake version starts with >, <, =, ~, ^,
            if snakemake_version[0] in [">", "<", "="]:
                snakemake_version = f"snakemake{snakemake_version}"
            else:
                snakemake_version = f"snakemake=={snakemake_version}"
        else:
            snakemake_version = "snakemake"
        try:
            subprocess.run([pip_path, 'install', snakemake_version, "snk_cli", "setuptools"] + dependencies, check=True)
        except subprocess.CalledProcessError as e:
            raise Exception(f"Failed to install snk_cli in virtual environment. Error: {e}")

    def create_executable(self, workflow_path: Path, name: str, python_interpreter_path = None) -> Path:
        if not python_interpreter_path:
            python_interpreter_path = self.python_interpreter_path
        template = inspect.cleandoc(
            f"""
            #!/bin/sh
            '''exec' "{python_interpreter_path}" "$0" "$@"
            ' '''
            # -*- coding: utf-8 -*-
            import re
            import sys
            from pathlib import Path
            from snk_cli import CLI

            def create_cli(p):
                workflow_dir_path = Path(p)
                cli = CLI(workflow_dir_path)
                cli()

            if __name__ == "__main__":
                sys.argv[0] = re.sub(r'(-script\\.pyw|\\.exe)?$', '', sys.argv[0])
                sys.exit(create_cli("{workflow_path}"))

        """
        )

        if sys.platform.startswith("win"):
            name += ".exe"

        workflow_executable = self.snk_executable_dir / name

        with open(workflow_executable, "w") as f:
            f.write(template)

        workflow_executable.chmod(workflow_executable.stat().st_mode | stat.S_IEXEC)

        return workflow_executable

    def link_workflow_executable_to_bin(self, workflow_executable_path: Path):
        """
        Links a workflow executable to the bin directory.

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

        Returns:
          Path: The path to the linked workflow executable.

        Examples:
          >>> nest.link_workflow_executable_to_bin(Path('/path/to/workflow_executable'))
        """
        name = workflow_executable_path.name
        if (self.bin_dir / name).is_symlink() and os.readlink(
            self.bin_dir / name
        ) == str(workflow_executable_path):
            # skip if it's already there
            return self.bin_dir / name
        try:
            os.symlink(workflow_executable_path.absolute(), self.bin_dir / name)
        except FileExistsError:
            raise WorkflowExistsError(
                f"File '{name}' already exists in SNK_BIN ({self.bin_dir})"
            )
        return self.bin_dir / name

    def check_for_snakemake_min_version(self, workflow_path: Path):
        """
        Check if the workflow has a minimum version of Snakemake.

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

        Returns:
          str: The minimum version of Snakemake.

        Examples:
          >>> nest.check_for_snakemake_min_version(Path('/path/to/workflow'))
        """
        import re

        min_version = "0.0.0"
        for snakefile in workflow_path.glob("**/Snakefile"):
            if snakefile.exists():
                break
        else:
            return min_version
        with open(snakefile, "r") as f:
            for line in f:
                match = re.search(r'min_version\((.*)\)', line)
                if match:
                    min_version = match.group(1).strip().strip('"').strip("'")
                    break
        return min_version


    @property
    def _current_snakemake_version(self):
        """
        Get the current version of Snakemake.

        Returns:
          str: The current version of Snakemake.

        Examples:
          >>> nest.get_current_current_snakemake_version()
        """
        from snakemake.common import __version__
        return __version__

    def validate_Snakemake_repo(self, repo: Repo):
        """
        Validates a Snakemake repository.

        Args:
          repo (Repo): The Snakemake repository.

        Returns:
          bool: True if the repository is valid, False otherwise.

        Examples:
          >>> nest.validate_Snakemake_repo(Repo('/path/to/repo'))
        """
        pass

__init__(snk_home=None, bin_dir=None)

Initializes a Nest object.

Parameters:

Name	Type	Description	Default
snk_home	Path	The path to the SNK home directory. Defaults to None.	None
bin_dir	Path	The path to the bin directory. Defaults to None.	None

Side Effects

Creates the SNK home and bin directories if they do not exist.

Examples:

>>> nest = Nest()

Source code in snk/nest.py

def __init__(self, snk_home: Path = None, bin_dir: Path = None) -> None:
    """
    Initializes a Nest object.

    Args:
      snk_home (Path, optional): The path to the SNK home directory. Defaults to None.
      bin_dir (Path, optional): The path to the bin directory. Defaults to None.

    Side Effects:
      Creates the SNK home and bin directories if they do not exist.

    Examples:
      >>> nest = Nest()
    """
    self.python_interpreter_path = Path(
        sys.executable
    )  # needs to be the same python that has snk

    if not snk_home:
        home_path = self.python_interpreter_path.parent.parent
        if not os.access(home_path, os.W_OK):
            user_home_path = Path("~").expanduser()
            snk_home = user_home_path / ".local" / "snk"
        else:
            snk_home = home_path / "snk"

    if not bin_dir:
        bin_dir = self.python_interpreter_path.parent
        if not os.access(bin_dir, os.W_OK):
            user_home_path = Path("~").expanduser()
            bin_dir = user_home_path / ".local" / "bin"

    self.bin_dir = Path(bin_dir).absolute()
    self.snk_home = Path(snk_home).absolute()
    self.snk_workflows_dir = self.snk_home / "workflows"
    self.snk_venv_dir = self.snk_home / "venvs"
    self.snk_executable_dir = self.snk_home / "bin"

    # Create dirs
    self.snk_home.mkdir(parents=True, exist_ok=True)
    self.snk_workflows_dir.mkdir(parents=True, exist_ok=True)
    self.snk_executable_dir.mkdir(parents=True, exist_ok=True)
    self.bin_dir.mkdir(parents=True, exist_ok=True)

additional_resources(workflow_path, resources)

Modify the snk config file so that resources will be copied at runtime.

Parameters:

Name	Type	Description	Default
workflow_path	Path	The path to the workflow directory.	required
resources	List[Path]	A list of additional resources to copy.	required

Examples:

>>> nest.additional_resources(Path('/path/to/workflow'), [Path('/path/to/resource1'), Path('/path/to/resource2')])

Source code in snk/nest.py

def additional_resources(self, workflow_path: Path, resources: List[Path]):
    """
    Modify the snk config file so that resources will be copied at runtime.

    Args:
      workflow_path (Path): The path to the workflow directory.
      resources (List[Path]): A list of additional resources to copy.

    Examples:
      >>> nest.additional_resources(Path('/path/to/workflow'), [Path('/path/to/resource1'), Path('/path/to/resource2')])
    """
    # validate_resources(resources)
    snk_config = SnkConfig.from_workflow_dir(
        workflow_path, create_if_not_exists=True
    )
    snk_config.add_resources(resources, workflow_path)
    snk_config.save()

check_for_snakemake_min_version(workflow_path)

Check if the workflow has a minimum version of Snakemake.

Parameters:

Name	Type	Description	Default
workflow_path	Path	The path to the workflow directory.	required

Returns:

Name	Type	Description
str		The minimum version of Snakemake.

Examples:

>>> nest.check_for_snakemake_min_version(Path('/path/to/workflow'))

Source code in snk/nest.py

def check_for_snakemake_min_version(self, workflow_path: Path):
    """
    Check if the workflow has a minimum version of Snakemake.

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

    Returns:
      str: The minimum version of Snakemake.

    Examples:
      >>> nest.check_for_snakemake_min_version(Path('/path/to/workflow'))
    """
    import re

    min_version = "0.0.0"
    for snakefile in workflow_path.glob("**/Snakefile"):
        if snakefile.exists():
            break
    else:
        return min_version
    with open(snakefile, "r") as f:
        for line in f:
            match = re.search(r'min_version\((.*)\)', line)
            if match:
                min_version = match.group(1).strip().strip('"').strip("'")
                break
    return min_version

copy_nonstandard_config(workflow_dir, config_path)

Copy a nonstandard config file to the workflow directory.

Parameters:

Name	Type	Description	Default
workflow_dir	Path	The path to the workflow directory.	required
config_path	Path	The path to the config file.	required

Examples:

>>> nest.copy_nonstandard_config(Path('/path/to/workflow'), Path('/path/to/config.yaml'))

Source code in snk/nest.py

def copy_nonstandard_config(self, workflow_dir: Path, config_path: Path):
    """
    Copy a nonstandard config file to the workflow directory.

    Args:
      workflow_dir (Path): The path to the workflow directory.
      config_path (Path): The path to the config file.

    Examples:
      >>> nest.copy_nonstandard_config(Path('/path/to/workflow'), Path('/path/to/config.yaml'))
    """
    config_dir = workflow_dir / "config"
    config_dir.mkdir(exist_ok=True)
    shutil.copyfile(workflow_dir / config_path, config_dir / "config.yaml")

create_virtual_environment(name)

Create a virtual environment for the workflow.

Parameters:

Name	Type	Description	Default
name	str	The name of the virtual environment.	required
snakemake_version	str	The version of Snakemake to install in the virtual environment. Defaults to None.	required

Returns:

Name	Type	Description
Path	Path	The path to the virtual environment.

Examples:

>>> nest.create_virtual_environment('example')

Source code in snk/nest.py

def create_virtual_environment(self, name: str) -> Path:
    """
    Create a virtual environment for the workflow.

    Args:
      name (str): The name of the virtual environment.
      snakemake_version (str, optional): The version of Snakemake to install in the virtual environment. Defaults to None.

    Returns:
      Path: The path to the virtual environment.

    Examples:
      >>> nest.create_virtual_environment('example')
    """
    venv_dir = self.snk_home / "venvs"
    venv_dir.mkdir(exist_ok=True)
    venv_path = venv_dir / name
    try:
        venv.create(venv_path, with_pip=True, symlinks=True)
    except FileExistsError:
        raise FileExistsError(f"The venv {venv_path} already exists. Please choose a different location or name. Alternatively, use the --force flag to overwrite the existing venv.")
    return venv_path

delete_paths(files)

Delete the given paths.

Parameters:

Name	Type	Description	Default
files	List[Path]	A list of paths to delete.	required

Side Effects

Deletes the given paths.

Examples:

>>> nest.delete_paths([Path('/path/to/workflows/example'), Path('/path/to/bin/example')])

Source code in snk/nest.py

def delete_paths(self, files: List[Path]):
    """
    Delete the given paths.

    Args:
      files (List[Path]): A list of paths to delete.

    Side Effects:
      Deletes the given paths.

    Examples:
      >>> nest.delete_paths([Path('/path/to/workflows/example'), Path('/path/to/bin/example')])
    """
    # check that the files are in self.snk_workflows_dir
    # i.e. if it is a symlink read the link and check
    for path in files:
        if path.is_symlink():
            print("Unlinking:", path)
            path.unlink()
        elif path.is_file():
            print("Deleting:", path)
            assert str(self.snk_home) in str(
                path
            ), "Cannot delete files outside of SNK_HOME"
            path.unlink()
        elif path.is_dir():
            print("Deleting:", path)
            assert str(self.snk_home) in str(
                path
            ), "Cannot delete folders outside of SNK_HOME"
            shutil.rmtree(path)
        else:
            raise TypeError("Invalid file type")

download(repo_url, name, tag_name=None, commit=None)

Clone a workflow from a git repository.

Parameters:

Name	Type	Description	Default
repo_url	str	The URL of the repo.	required
name	str	The name of the workflow.	required
tag_name	str	The tag of the workflow. Defaults to None.	None
commit	str	The commit SHA of the workflow. Defaults to None.	None

Returns:

Name	Type	Description
Path	Path	The path to the cloned workflow.

Examples:

>>> nest.download('https://github.com/example/repo.git', 'example', tag_name='v1.0.0')

Source code in snk/nest.py

def download(self, repo_url: str, name: str, tag_name: str = None, commit: str = None) -> Path:
    """
    Clone a workflow from a git repository.

    Args:
      repo_url (str): The URL of the repo.
      name (str): The name of the workflow.
      tag_name (str, optional): The tag of the workflow. Defaults to None.
      commit (str, optional): The commit SHA of the workflow. Defaults to None.

    Returns:
      Path: The path to the cloned workflow.

    Examples:
      >>> nest.download('https://github.com/example/repo.git', 'example', tag_name='v1.0.0')
    """
    location = self.snk_workflows_dir / name
    options = []
    if not commit:
        options.append(f"--depth 1")
    if tag_name:
        options.append(f"--single-branch")
        options.append(f"--branch {tag_name}")
    try:
        repo = Repo.clone_from(repo_url, location, multi_options=options)
        if commit:
            repo.git.checkout(commit)
        else:
            repo.git.checkout(tag_name)
    except GitCommandError as e:
        if "destination path" in e.stderr:
            raise WorkflowExistsError(
                f"Workflow '{name}' already exists in {self.snk_workflows_dir}"
            )
        elif f"Remote branch {tag_name}" in e.stderr:
            raise WorkflowNotFoundError(f"Workflow tag '{tag_name}' not found")
        elif f"pathspec '{commit}' did not match" in e.stderr:
            if tag_name:
                raise WorkflowNotFoundError(f"Workflow commit '{commit}' not found on branch {tag_name}")
            else:
                raise WorkflowNotFoundError(f"Workflow commit '{commit}' not found")
        elif "not found" in e.stderr:
            raise WorkflowNotFoundError(
                f"Workflow repository '{repo_url}' not found"
            )
        raise e
    return location

get_paths_to_delete(workflow_name)

Get the paths to delete when uninstalling a workflow.

Parameters:

Name	Type	Description	Default
workflow_name	str	The name of the workflow.	required

Returns:

Type	Description
List[Path]	List[Path]: A list of paths to delete.

Examples:

>>> nest.get_paths_to_delete('example')
[Path('/path/to/workflows/example'), Path('/path/to/bin/example')]

Source code in snk/nest.py

def get_paths_to_delete(self, workflow_name: str) -> List[Path]:
    """
    Get the paths to delete when uninstalling a workflow.

    Args:
      workflow_name (str): The name of the workflow.

    Returns:
      List[Path]: A list of paths to delete.

    Examples:
      >>> nest.get_paths_to_delete('example')
      [Path('/path/to/workflows/example'), Path('/path/to/bin/example')]
    """
    to_delete = []

    # remove repo
    workflow_dir = self.snk_workflows_dir / workflow_name
    if workflow_dir.exists() and workflow_dir.is_dir():
        to_delete.append(workflow_dir)
    elif workflow_dir.is_symlink():
        # editable
        to_delete.append(workflow_dir)

    workflow_executable = self.snk_executable_dir / workflow_name
    if workflow_executable.exists():
        to_delete.append(workflow_executable)

    # remove venv  
    venv_path = self.snk_venv_dir / workflow_name
    if venv_path.exists():
        to_delete.append(venv_path)

    # remove link
    workflow_symlink_executable = self.bin_dir / workflow_name
    if workflow_symlink_executable.is_symlink():
        if str(os.readlink(workflow_symlink_executable)) == str(
            workflow_executable
        ):
            to_delete.append(workflow_symlink_executable)

    if not to_delete:
        raise WorkflowNotFoundError(f"Could not find workflow: {workflow_name}")

    return to_delete

install(workflow, editable=False, name=None, tag=None, commit=None, config=None, snakefile=None, force=False, additional_resources=[], conda=None, snakemake_version=None, dependencies=[], isolate=False)

Installs a Snakemake workflow as a CLI.

Parameters:

Name	Type	Description	Default
workflow	str	The URL of the repo or the path to the local workflow.	required
editable	bool	Whether to install the workflow in editable mode. Defaults to False.	False
name	str	The name of the workflow. Defaults to None.	None
tag	str	The tag of the workflow. Defaults to None.	None
commit	str	The commit SHA of the workflow. Defaults to None.	None
config	Path	The path to the config file. Defaults to None.	None
snakefile	Path	The path to the Snakefile. Defaults to None.	None
force	bool	Whether to force the installation. Defaults to False.	False
additional_resources	list	A list of resources additional to the resources folder to copy. Defaults to [].	[]
conda	bool	Modify the snk config file to control conda use. If None, will not modify the config file. Defaults to None.	None
snakemake_version	str	The version of Snakemake to install in the virtual environment. Defaults to None.	None
dependencies	list	A list of dependencies to install. Defaults to [].	[]

Returns:

Name	Type	Description
Workflow	Workflow	The installed workflow.

Examples:

>>> nest.install('https://github.com/example/repo.git', name='example', tag='v1.0.0')
>>> nest.install('https://github.com/example/repo.git', name='example', commit='0123456')

Source code in snk/nest.py

def install(
    self,
    workflow: str,
    editable=False,
    name=None,
    tag=None,
    commit=None,
    config: Path = None,
    snakefile: Path = None,
    force=False,
    additional_resources=[],
    conda: bool = None,
    snakemake_version=None,
    dependencies=[],
    isolate=False,
) -> Workflow:
    """
    Installs a Snakemake workflow as a CLI.

    Args:
      workflow (str): The URL of the repo or the path to the local workflow.
      editable (bool, optional): Whether to install the workflow in editable mode. Defaults to False.
      name (str, optional): The name of the workflow. Defaults to None.
      tag (str, optional): The tag of the workflow. Defaults to None.
      commit (str, optional): The commit SHA of the workflow. Defaults to None.
      config (Path, optional): The path to the config file. Defaults to None.
      snakefile (Path, optional): The path to the Snakefile. Defaults to None.
      force (bool, optional): Whether to force the installation. Defaults to False.
      additional_resources (list, optional): A list of resources additional to the resources folder to copy. Defaults to [].
      conda (bool, optional): Modify the snk config file to control conda use. If None, will not modify the config file. Defaults to None.
      snakemake_version (str, optional): The version of Snakemake to install in the virtual environment. Defaults to None.
      dependencies (list, optional): A list of dependencies to install. Defaults to [].
    Returns:
      Workflow: The installed workflow.

    Examples:
      >>> nest.install('https://github.com/example/repo.git', name='example', tag='v1.0.0')
      >>> nest.install('https://github.com/example/repo.git', name='example', commit='0123456')
    """

    def handle_force_installation(name: str):
        try:
            self.uninstall(name=name, force=True)
        except WorkflowNotFoundError:
            pass
    workflow = str(workflow) # ensure it is a string
    try:
        workflow = self._format_repo_url(workflow)
        if not name:
            name = self._get_name_from_git_url(workflow)
        if not force:
            self._check_workflow_name_available(name)
        else:
            handle_force_installation(name)
        workflow_path = self.download(workflow, name, tag_name=tag, commit=commit)
    except InvalidWorkflowRepositoryError:
        workflow_local_path = Path(workflow).resolve()
        if workflow_local_path.is_file():
            raise InvalidWorkflowError(
                f"When installing a local workflow, the path must be a directory. Found: {workflow_local_path}"
            )
        if self.snk_workflows_dir.resolve().is_relative_to(workflow_local_path) and not editable:
            raise InvalidWorkflowError(
                f"The workflow directory contains SNK_HOME!\nWORKFLOW: {workflow_local_path}\nSNK_HOME: {self.snk_workflows_dir.resolve()}.\n\nTry installing the workflow with --editable."
            )
        if not name:
            name = workflow_local_path.name
        if not force:
            self._check_workflow_name_available(name)
        else:
            handle_force_installation(name)
        workflow_path = self.local(workflow_local_path, name, editable)
    try:
        self.validate_Snakemake_repo(workflow_path)

        snakemake_version_to_install_in_venv = None
        if snakemake_version is not None:
            snakemake_version_to_install_in_venv = snakemake_version
        elif version.parse(self._current_snakemake_version) < version.parse(self.check_for_snakemake_min_version(workflow_path)):
            # The current version of Snakemake is less than the minimum version required by the workflow
            snakemake_version_to_install_in_venv = f">={self.check_for_snakemake_min_version(workflow_path)}"

        if snakemake_version_to_install_in_venv is not None or dependencies:
            isolate = True

        if isolate:
            venv_path = self.create_virtual_environment(name)
            self._install_snk_cli_in_venv(
                venv_path, 
                snakemake_version=snakemake_version_to_install_in_venv, 
                dependencies=dependencies
            )
            python_interpreter_path = venv_path / "bin" / "python"
        else:
            python_interpreter_path = self.python_interpreter_path
        workflow_executable_path = self.create_executable(workflow_path, name, python_interpreter_path=python_interpreter_path)
        self.link_workflow_executable_to_bin(workflow_executable_path)
        if config:
            self.copy_nonstandard_config(workflow_path, config)
        if snakefile:
            snakefile_path = workflow_path / snakefile
            if not snakefile_path.exists():
                raise FileNotFoundError(f"Snakefile not found at {snakefile_path}")
            shutil.copyfile(snakefile_path, snakefile_path.parent / "Snakefile")
        if additional_resources:
            self.additional_resources(workflow_path, additional_resources)
        if conda is not None:
            self.modify_snk_config(workflow_path, conda=conda)
        self._confirm_installation(name)
    except Exception as e:
        # remove any half completed steps
        to_remove = self.get_paths_to_delete(name)
        self.delete_paths(to_remove)
        raise e
    return Workflow(workflow_path)

link_workflow_executable_to_bin(workflow_executable_path)

Links a workflow executable to the bin directory.

Parameters:

Name	Type	Description	Default
workflow_executable_path	Path	The path to the workflow executable.	required

Returns:

Name	Type	Description
Path		The path to the linked workflow executable.

Examples:

>>> nest.link_workflow_executable_to_bin(Path('/path/to/workflow_executable'))

Source code in snk/nest.py

def link_workflow_executable_to_bin(self, workflow_executable_path: Path):
    """
    Links a workflow executable to the bin directory.

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

    Returns:
      Path: The path to the linked workflow executable.

    Examples:
      >>> nest.link_workflow_executable_to_bin(Path('/path/to/workflow_executable'))
    """
    name = workflow_executable_path.name
    if (self.bin_dir / name).is_symlink() and os.readlink(
        self.bin_dir / name
    ) == str(workflow_executable_path):
        # skip if it's already there
        return self.bin_dir / name
    try:
        os.symlink(workflow_executable_path.absolute(), self.bin_dir / name)
    except FileExistsError:
        raise WorkflowExistsError(
            f"File '{name}' already exists in SNK_BIN ({self.bin_dir})"
        )
    return self.bin_dir / name

local(path, name, editable=False)

Install a local workflow.

Parameters:

Name	Type	Description	Default
path	Path	The path to the local workflow.	required
name	str	The name of the workflow.	required
editable	bool	Whether to install the workflow in editable mode. Defaults to False.	False

Returns:

Name	Type	Description
Path	Path	The path to the installed workflow.

Examples:

>>> nest.local(Path('/path/to/workflow'), 'example')

Source code in snk/nest.py

def local(self, path: Path, name: str, editable=False) -> Path:
    """
    Install a local workflow.

    Args:
      path (Path): The path to the local workflow.
      name (str): The name of the workflow.
      editable (bool, optional): Whether to install the workflow in editable mode. Defaults to False.

    Returns:
      Path: The path to the installed workflow.

    Examples:
      >>> nest.local(Path('/path/to/workflow'), 'example')
    """
    location = self.snk_workflows_dir / name
    if editable:
        os.symlink(path.absolute(), location, target_is_directory=True)
        return location
    shutil.copytree(path, location)
    try:
        Repo(location)
    except InvalidGitRepositoryError:
        Repo.init(location, mkdir=False)
    return location

modify_snk_config(workflow_path, **kwargs)

Modify the snk config file.

Parameters:

Name	Type	Description	Default
workflow_path	Path	The path to the workflow directory.	required
**kwargs		Additional keyword arguments to modify the snk config file.	{}

Examples:

>>> nest.modify_snk_config(Path('/path/to/workflow'), logo=example)

Source code in snk/nest.py

def modify_snk_config(self, workflow_path: Path, **kwargs):
    """
    Modify the snk config file.

    Args:
      workflow_path (Path): The path to the workflow directory.
      **kwargs: Additional keyword arguments to modify the snk config file.

    Examples:
      >>> nest.modify_snk_config(Path('/path/to/workflow'), logo=example)
    """
    snk_config = SnkConfig.from_workflow_dir(
        workflow_path, create_if_not_exists=True
    )
    modified = False
    for key, value in kwargs.items():
        if getattr(snk_config, key) != value:
            modified = True
            setattr(snk_config, key, value)
    if modified:
        snk_config.save()

uninstall(name, force=False)

Uninstalls a workflow.

Parameters:

Name	Type	Description	Default
name	str	The name of the workflow.	required
force	bool	Whether to force the uninstallation. Defaults to False.	False

Returns:

Name	Type	Description
bool	bool	Whether the uninstallation was successful.

Examples:

>>> nest.uninstall('example')
True

Source code in snk/nest.py

def uninstall(self, name: str, force: bool = False) -> bool:
    """
    Uninstalls a workflow.

    Args:
      name (str): The name of the workflow.
      force (bool, optional): Whether to force the uninstallation. Defaults to False.

    Returns:
      bool: Whether the uninstallation was successful.

    Examples:
      >>> nest.uninstall('example')
      True
    """
    if not isinstance(name, str):
        raise TypeError(f"Name must be a string. Found: {name}")
    to_remove = self.get_paths_to_delete(name)
    if force:
        proceed = True
    else:
        print(f"Uninstalling {name}")
        print("  Would remove:")
        for p in to_remove:
            print(f"    {p}{'/*' if p.is_dir() else ''}")
        ans = input("Proceed (Y/n)? ")
        proceed = ans.lower() in ["y", "yes"]
    if not proceed:
        return False
    self.delete_paths(to_remove)
    return True

validate_Snakemake_repo(repo)

Validates a Snakemake repository.

Parameters:

Name	Type	Description	Default
repo	Repo	The Snakemake repository.	required

Returns:

Name	Type	Description
bool		True if the repository is valid, False otherwise.

Examples:

>>> nest.validate_Snakemake_repo(Repo('/path/to/repo'))

Source code in snk/nest.py

def validate_Snakemake_repo(self, repo: Repo):
    """
    Validates a Snakemake repository.

    Args:
      repo (Repo): The Snakemake repository.

    Returns:
      bool: True if the repository is valid, False otherwise.

    Examples:
      >>> nest.validate_Snakemake_repo(Repo('/path/to/repo'))
    """
    pass