universal-pathlib0.2.5

Published 2 months ago

pathlib api extended to use fsspec backends

pip install universal-pathlib

Package Downloads

Authors

Andrew Fulton

Project URLs

Requires Python

>=3.8

Dependencies

Universal Pathlib

Universal Pathlib is a Python library that extends the pathlib.Path API to support a variety of backend filesystems via filesystem_spec.

Installation

Install the latest version of universal_pathlib with pip or conda. Please note that while this will install fsspec as a dependency, for some filesystems, you have to install additional packages. For example, to use S3, you need to install s3fs, or better depend on fsspec[s3]:

PyPI

python -m pip install universal_pathlib

conda

conda install -c conda-forge universal_pathlib

Adding universal_pathlib to your project

Below is a pyproject.toml based example for adding universal_pathlib to your project as a dependency if you want to use it with s3 and http filesystems:

[project]
name = "myproject"
requires-python = ">=3.8"
dependencies = [
    "universal_pathlib>=0.2.5",
    "fsspec[s3,http]",
]

See filesystem_spec/pyproject.toml for an overview of the available fsspec extras.

Basic Usage

# pip install universal_pathlib fsspec[s3]
>>> from upath import UPath
>>>
>>> s3path = UPath("s3://test_bucket") / "example.txt"
>>> s3path.name
example.txt
>>> s3path.stem
example
>>> s3path.suffix
.txt
>>> s3path.exists()
True
>>> s3path.read_text()
'Hello World'

For more examples, see the example notebook here.

Currently supported filesystems (and protocols)

file: and local: Local filesystem
memory: Ephemeral filesystem in RAM
az:, adl:, abfs: and abfss: Azure Storage (requires adlfs)
data: RFC 2397 style data URLs (requires fsspec>=2023.12.2)
github: GitHub repository filesystem
http: and https: HTTP(S)-based filesystem
hdfs: Hadoop distributed filesystem
gs: and gcs: Google Cloud Storage (requires gcsfs)
s3: and s3a: AWS S3 (requires s3fs to be installed)
sftp: and ssh: SFTP and SSH filesystems (requires paramiko)
smb: SMB filesystems (requires smbprotocol)
webdav, webdav+http: and webdav+https: WebDAV-based filesystem on top of HTTP(S) (requires webdav4[fsspec])

It is likely, that other fsspec-compatible filesystems are supported through the default implementation. But because they are not tested in the universal_pathlib test-suite, correct behavior is not guaranteed. If you encounter any issues with a specific filesystem using the default implementation, please open an issue. We are happy to add support for other filesystems via custom UPath implementations. And of course, contributions for new filesystems are welcome!

Class hierarchy

The class hierarchy for UPath implementations and their relation to the stdlib pathlib classes are visualized in the following diagram:

flowchart TB
  subgraph s0[pathlib]
    A---> B
    A--> AP
    A--> AW

    B--> BP
    AP---> BP
    B--> BW
    AW---> BW
  end
  subgraph s1[upath]
    B ---> U
    U --> UP
    U --> UW
    BP --> UP
    BW --> UW
    U --> UL
    U --> US3
    U --> UH
    U -.-> UO
  end

  A(PurePath)
  AP(PurePosixPath)
  AW(PureWindowsPath)
  B(Path)
  BP(PosixPath)
  BW(WindowsPath)

  U(UPath)
  UP(PosixUPath)
  UW(WindowsUPath)
  UL(FilePath)
  US3(S3Path)
  UH(HttpPath)
  UO(...Path)

  classDef np fill:#f7f7f7,stroke:#2166ac,stroke-width:2px,color:#333
  classDef nu fill:#f7f7f7,stroke:#b2182b,stroke-width:2px,color:#333

  class A,AP,AW,B,BP,BW,UP,UW np
  class U,UL,US3,UH,UO nu

  style UO stroke-dasharray: 3 3

  style s0 fill:none,stroke:#07b,stroke-width:3px,stroke-dasharray:3,color:#07b
  style s1 fill:none,stroke:#d02,stroke-width:3px,stroke-dasharray:3,color:#d02

When instantiating UPath the returned instance type is determined by the path, or better said, the "protocol" that was provided to the constructor. The UPath class will return a registered implementation for the protocol, if available. If no specialized implementation can be found but the protocol is available through fsspec, it will return a UPath instance and provide filesystem access with a default implementation. Please note the default implementation can not guarantee correct behavior for filesystems that are not tested in the test-suite.

Local paths and url paths

If a local path is provided UPath will return a PosixUPath or WindowsUPath instance. These two implementations are 100% compatible with the PosixPath and WindowsPath classes of their specific Python version. They're tested against a large subset of the CPython pathlib test-suite to ensure compatibility.

If a local urlpath is provided, i.e. a "file://" or "local://" URI, the returned instance type will be a FilePath instance. This class is a subclass of UPath that provides file access via LocalFileSystem from fsspec. You can use it to ensure that all your local file access is done through fsspec as well.

UPath public class API

The public class interface of UPath extends pathlib.Path via attributes that simplify interaction with filesystem_spec. Think of the UPath class in terms of the following code:

from pathlib import Path
from typing import Any, Mapping
from fsspec import AbstractFileSystem

class UPath(Path):
    # the real implementation is more complex, but this is the general idea

    @property
    def protocol(self) -> str:
        """The fsspec protocol for the path."""

    @property
    def storage_options(self) -> Mapping[str, Any]:
        """The fsspec storage options for the path."""

    @property
    def path(self) -> str:
        """The path that a fsspec filesystem can use."""

    @property
    def fs(self) -> AbstractFileSystem:
        """The cached fsspec filesystem instance for the path."""

These attributes are used to provide a public interface to move from the UPath instance to more fsspec specific code:

from upath import UPath
from fsspec import filesystem

p = UPath("s3://bucket/file.txt", anon=True)

fs = filesystem(p.protocol, **p.storage_options)  # equivalent to p.fs

with fs.open(p.path) as f:
    data = f.read()

Advanced Usage

If you want to create your own UPath implementations, there are multiple ways to customize your subclass behavior. Here are a few things to keep in mind when you create your own UPath implementation:

UPath's constructor, `upath.registry`, and subclassing

When instantiating UPath(...) the UPath.__new__() method determines the path protocol and returns a registered implementation for the protocol, if available. The registered implementations are mapped in the upath.registry module. When a protocol is not registered, universal_pathlib checks if the protocol is mapped to an fsspec filesystem. If so, it returns an instance of UPath and provides filesystem access through the default implementation. The protocol is determined by either looking at the URI scheme of the first argument to the constructor, or by using the protocol keyword argument:

from upath import UPath
from upath.implementations.cloud import S3Path
from upath.implementations.memory import MemoryPath

p0 = UPath("s3://bucket/file.txt")
assert p0.protocol == "s3"
assert type(p0) is S3Path
assert isinstance(p0, UPath)

p1 = UPath("/some/path/file.txt", protocol="memory")
assert p1.protocol == "memory"
assert type(p1) is MemoryPath
assert isinstance(p1, UPath)

# the ftp filesystem current has no custom UPath implementation and is not
# tested in the universal_pathlib test-suite. Therefore, the default UPath
# implementation is returned, and a warning is emitted on instantiation.
p2 = UPath("ftp://ftp.ncbi.nih.gov/snp/archive")
assert p2.protocol == "ftp"
assert type(p2) is UPath

This has some implications for custom UPath subclasses. We'll go through the two main cases where you might want to create a custom UPath implementation:

Case 1: Custom filesystem works with default UPath implementation

Let's say you would like to add a new implementation of your "myproto" protocol. You already built a custom AbstractFileSystem implementation for "myproto" which you have registered through fsspec.registry. In some cases it is possible that the custom filesystem class already works with UPath's default implementation, and you don't need to necessarily create a custom UPath implementation:

import fsspec.registry
from fsspec.spec import AbstractFileSystem

class MyProtoFileSystem(AbstractFileSystem):
    protocol = ("myproto",)
    ...  # your custom implementation

fsspec.registry.register_implementation("myproto", MyProtoFileSystem)

from upath import UPath

p = UPath("myproto:///my/proto/path")
assert type(p) is UPath
assert p.protocol == "myproto"
assert isinstance(p.fs, MyProtoFileSystem)

Case 2: Custom filesystem requires a custom UPath implementation

Sometimes the default implementation isn't sufficient and some method(s) have to be overridden to provide correct behavior. In this case, create a custom UPath implementation:

from upath import UPath

class MyProtoPath(UPath):

    def mkdir(self, mode=0o777, parents=False, exist_ok=False):
        something = {...: ...}  # fixes to make MyProtoFileSystem.mkdir work
        self.fs.mkdir(self.path, **something)

    def path(self):
        path = super().path
        if path.startswith("/"):
            return path[1:]  # MyProtoFileSystem needs the path without "/"
        return path

If you use your implementation directly via MyProtoPath("myproto:///a/b"), you can use this implementation already as is. If you want a call to UPath(...) to return your custom implementation when the detected protocol is "myproto", you need to register your implementation. The next section explains your options.

Also note: In case you develop a custom UPath implementation, please feel free to open an issue to discuss integrating it in universal_pathlib.

Implementation registration dynamically from Python

You can register your custom UPath implementation dynamically from Python:

# for example: mymodule/submodule.py
from upath import UPath
from upath.registry import register_implementation

class MyProtoPath(UPath):
    ...  # your custom implementation

register_implementation("myproto", MyProtoPath)

Implementation registration on installation via entry points

If you distribute your implementation in your own Python package, you can inform universal_pathlib about your implementation via the entry_points mechanism:

# pyproject.toml
[project.entry-points."universal_pathlib.implementations"]
myproto = "my_module.submodule:MyPath"

# setup.cfg
[options.entry_points]
universal_pathlib.implementations =
    myproto = my_module.submodule:MyPath

Chose the method that fits your use-case best. If you have questions, open a new issue in the universal_pathlib repository. We are happy to help you!

Customization options for UPath subclasses

Filesystem access methods

Once you thoroughly test your custom UPath implementation, it's likely that some methods need to be overridden to provide correct behavior compared to stdlib's pathlib.Path class. The most common issue is that for certain edge cases, your implementation is not raising the same exceptions compared to the pathlib.Path class. Or that the UPath.path property needs some prefix removed or added.

class MyProtoPath(UPath):

    @property
    def path(self) -> str:
        if p := self.path.startswith("/"):
            p = p[1:]
        return p

    def mkdir(self, mode=0o777, parents=False, exist_ok=False):
        if some_edge_case:
            raise FileExistsError(str(self))
        super().mkdir(mode=mode, parents=parents, exist_ok=exist_ok)

    def is_file(self):
        return self.fs.isfile(self.path, myproto_option=123)

Storage option parsing

It's possible that you might want to extract additional storage options from the user provided arguments to you constructor. You can provide a custom classmethod for _parse_storage_options:

import os

class MyProtoPath(UPath):

    @classmethod
    def _parse_storage_options(
        cls, urlpath: str, protocol: str, storage_options: Mapping[str, Any]
    ) -> dict[str, Any]:
        if "SOME_VAR" in os.environ:
            storage_options["some_var"] = os.environ["SOME_VAR"]
        storage_options["my_proto_caching"] = True
        storage_options["extra"] = get_setting_from_path(urlpath)
        return storage_options

Fsspec filesystem instantiation

To have more control over fsspec filesystem instantiation you can write a custom _fs_factory classmethod:

class MyProtoPath(UPath):

    @classmethod
    def _fs_factory(
        cls, urlpath: str, protocol: str, storage_options: Mapping[str, Any]
    ) -> AbstractFileSystem:
        myfs = ...  # custom code that creates a AbstractFileSystem instance
        return myfs

Init argument parsing

In special cases you need to take more control over how the init args are parsed for your custom subclass. You can override __init__ or the UPath classmethod _transform_init_args. The latter handles pickling of your custom subclass in a better way in case you modify storage options or the protocol.

class MyProtoPath(UPath):

    @classmethod
    def _transform_init_args(
            cls,
            args: tuple[str | os.PathLike, ...],
            protocol: str,
            storage_options: dict[str, Any],
    ) -> tuple[tuple[str | os.PathLike, ...], str, dict[str, Any]]:
        # check the cloud, http or webdav implementations for examples
        ...
        return args, protocol, storage_options

Stopping UPath's subclass dispatch mechanism

There are cases for which you want to disable the protocol dispatch mechanism of the UPath.__new__ constructor. For example if you want to extend the class API of your UPath implementation, and use it as the base class for other, directly instantiated subclasses. Together with other customization options this can be a useful feature. Please be aware that in this case all protocols are handled with the default implementation in UPath. Please always feel free to open an issue in the issue tracker to discuss your use case. We're happy to help with finding the most maintainable solution.

class ExtraUPath(UPath):
    _protocol_dispatch = False  # disable the registry return an ExtraUPath

    def some_extra_method(self) -> str:
        return "hello world"

assert ExtraUPath("s3://bucket/file.txt").some_extra_method() == "hello world"

Migration Guide

UPath's internal implementation is likely going to change with larger changes in CPython's stdlib pathlib landing in the next Python versions (3.13, 3.14). To reduce the problems for user code, when these changes are landing in UPath, there have been some significant changes in v0.2.0. This migration guide tries to help migrating code that extensively relies on private implementation details of the UPath class of versions v0.1.x to the new and better supported public interface of v0.2.0

migrating to `v0.2.0`

_FSSpecAccessor subclasses with custom filesystem access methods

If you implemented a custom accessor subclass, it is now recommended to override the corresponding UPath methods in your subclass directly:

# OLD: v0.1.x
from upath.core import UPath, _FSSpecAccessor

class MyAccessor(_FSSpecAccessor):
    def exists(self, path, **kwargs):
        # custom code
        return path.fs.exists(self._format_path(path), **kwargs)

    def touch(self, path, **kwargs):
        # custom
        return path.fs.touch(self._format_path(path), **kwargs)

class MyPath(UPath):
    _default_accessor = MyAccessor


# NEW: v0.2.0+
from upath import UPath

class MyPath(UPath):
    def exists(self, *, follow_symlinks=True):
        kwargs = {}  # custom code
        return self.fs.exists(self.path, **kwargs)

    def touch(self, mode=0o666, exist_ok=True):
        kwargs = {}  # custom code
        self.fs.touch(self.path, **kwargs)

_FSSpecAccessor subclasses with custom `init` method

If you implemented a custom __init__ method for your accessor subclass usually the intention is to customize how the fsspec filesystem instance is created. You have two options to recreate this with the new implementation. Chose one or both dependent on the level of control you need.

# OLD: v0.1.x
import fsspec
from upath.core import UPath, _FSSpecAccessor

class MyAccessor(_FSSpecAccessor):
    def __init__(self, parsed_url: SplitResult | None, **kwargs: Any) -> None:
        # custom code
        protocol = ...
        storage_options = ...
        self._fs = fsspec.filesystem(protocol, storage_options)

class MyPath(UPath):
    _default_accessor = MyAccessor


# NEW: v0.2.0+
from upath import UPath

class MyPath(UPath):
    @classmethod
    def _parse_storage_options(
        cls, urlpath: str, protocol: str, storage_options: Mapping[str, Any]
    ) -> dict[str, Any]:
        # custom code to change storage_options
        storage_options = ...
        return storage_options

    @classmethod
    def _fs_factory(
        cls, urlpath: str, protocol: str, storage_options: Mapping[str, Any]
    ) -> AbstractFileSystem:
        # custom code to instantiate fsspec filesystem
        protocol = ...
        storage_options = ...  # note changes to storage_options here won't
                               # show up in MyPath().storage_options
        return fsspec.filesystem(protocol, **storage_options)

Access to `._accessor`

The _accessor attribute and the _FSSpecAccessor class is deprecated. In case you need direct access to the underlying filesystem, just access UPath().fs.

# OLD: v0.1.x
from upath.core import UPath

class MyPath(UPath):
    def mkdir(self, mode=0o777, parents=False, exist_ok=False):
        self._accessor.mkdir(...)  # custom access to the underlying fs...


# NEW: v0.2.0+
from upath import UPath

class MyPath(UPath):
    def mkdir(self, mode=0o777, parents=False, exist_ok=False):
        self.fs.mkdir(...)

Access to `._path`, `._kwargs`, `._drv`, `._root`, `._parts`

If you access one of the listed private attributes directly, move your code over to the following public versions:

deprecated	`v0.2.0+`
`UPath()._path`	`UPath().path`
`UPath()._kwargs`	`UPath().storage_options`
`UPath()._drv`	`UPath().drive`
`UPath()._root`	`UPath().root`
`UPath()._parts`	`UPath().parts`

Access to `._url`

Be aware that the ._url attribute will likely be deprecated once UPath() has support for uri fragments and uri query parameters through a public api. In case you are interested in contributing this functionality, please open an issue!

Calling `_from_parts`, `_parse_args`, `_format_parsed_parts`

If your code is currently calling any of the three above listed classmethods, it relies on functionality based on the implementation of pathlib in Python up to 3.11. In universal_pathlib we vendor code that allows the UPath() class to be based on the 3.12 implementation of pathlib.Path alone. Usually, usage of those classmethods occurs when copying some code of the internal implementations of methods of the UPath 0.1.4 classes.

To reproduce custom _format_parsed_parts methods in v0.2.0, try overriding UPath().path and/or UPath().with_segments().
Custom _from_parts and _parse_args classmethods can now be implemented via the _transform_init_args method or via more functionality in the new flavour class. Please open an issue for discussion in case you have this use case.

Custom `_URIFlavour` classes

The _URIFlavour class was removed from universal_pathlib and the new flavour class for fsspec filesystem path operations now lives in upath._flavour. As of now the internal FSSpecFlavour is experimental. In a future Python version, it's likely that a flavour or flavour-like base class will become public, that allows us to base our internal implementation on. Until then, if you find yourself in a situation where a custom path flavour would solve your problem, please feel free to open an issue for discussion. We're happy to find a maintainable solution.

Using `.parse_parts()`, `.casefold()`, `.join_parsed_parts()` of `._flavour`

These methods of the ._flavour attribute of pathlib.Path() and UPath() are specific to pathlib of Python versions up to 3.11. UPath() is now based on the 3.12 implementation of pathlib.Path. Please refer to the implementations of the upath._flavour submodule to see how you could avoid using them.

Known issues solvable by installing newer upstream dependencies

Some issues in UPath's behavior with specific fsspec filesystems are fixed via installation of a newer version of its upstream dependencies. Below you can find a list of known issues and their solutions. We attempt to keep this list updated whenever we encounter more:

UPath().glob(): fsspec fixed glob behavior when handling ** patterns in fsspec>=2023.9.0
GCSPath().mkdir(): a few mkdir quirks are solved by installing gcsfs>=2022.7.1
fsspec.filesystem(WebdavPath().protocol) the webdav protocol was added to fsspec in version fsspec>=2022.5.0
stat.S_ISDIR(HTTPPath().stat().st_mode) requires fsspec>=2024.2.0 to correctly return True for directories

Contributing

Contributions are very welcome. To learn more, see the Contributor Guide.

License

Distributed under the terms of the MIT license, universal_pathlib is free and open source software.

Issues

If you encounter any problems, or if you create your own implementations and run into limitations, please file an issue with a detailed description. We are always happy to help with any problems you might encounter.