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Support local filesystem remotes for projects (#11762)

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* Support local filesystem remotes for projects

* Fix support for local filesystem remotes for projects
  * Use `FluidPath` instead of `Pathy` to support both filesystem and
    remote paths
  * Create missing parent directories if required for local filesystem
  * Add a more general `_file_exists` method to support both `Pathy`,
    `Path`, and `smart_open`-compatible URLs
* Add explicit `smart_open` dependency starting with support for
  `compression` flag
* Update `pathy` dependency to exclude older versions that aren't
  compatible with required `smart_open` version
* Update docs to refer to `Pathy` instead of `smart_open` for project
  remotes (technically you can still push to any `smart_open`-compatible
  path but you can't pull from them)
* Add tests for local filesystem remotes

* Update pathy for general BlobStat sorting

* Add import

* Remove _file_exists since only Pathy remotes are supported

* Format CLI docs

* Clean up merge
This commit is contained in:
Adriane Boyd 2022-11-29 11:40:58 +01:00 committed by GitHub
parent 96c9cf3448
commit 1ebe7db07c
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7 changed files with 120 additions and 43 deletions
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2
requirements.txt
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@ -10,7 +10,7 @@ wasabi>=0.9.1,<1.1.0
srsly>=2.4.3,<3.0.0
catalogue>=2.0.6,<2.1.0
typer>=0.3.0,<0.8.0
pathy>=0.3.5
pathy>=0.10.0
smart-open>=5.2.1,<7.0.0
# Third party dependencies
numpy>=1.15.0

2
setup.cfg
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@ -52,7 +52,7 @@ install_requires =
catalogue>=2.0.6,<2.1.0
# Third-party dependencies
typer>=0.3.0,<0.8.0
pathy>=0.3.5
pathy>=0.10.0
smart-open>=5.2.1,<7.0.0
tqdm>=4.38.0,<5.0.0
numpy>=1.15.0

15
spacy/cli/_util.py
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@ -23,7 +23,7 @@ from ..util import is_compatible_version, SimpleFrozenDict, ENV_VARS
from .. import about
if TYPE_CHECKING:
from pathy import Pathy # noqa: F401
from pathy import FluidPath # noqa: F401
SDIST_SUFFIX = ".tar.gz"
@ -331,7 +331,7 @@ def import_code(code_path: Optional[Union[Path, str]]) -> None:
msg.fail(f"Couldn't load Python code: {code_path}", e, exits=1)
def upload_file(src: Path, dest: Union[str, "Pathy"]) -> None:
def upload_file(src: Path, dest: Union[str, "FluidPath"]) -> None:
"""Upload a file.
src (Path): The source path.
@ -339,13 +339,20 @@ def upload_file(src: Path, dest: Union[str, "Pathy"]) -> None:
"""
import smart_open
# Create parent directories for local paths
if isinstance(dest, Path):
if not dest.parent.exists():
dest.parent.mkdir(parents=True)
dest = str(dest)
with smart_open.open(dest, mode="wb") as output_file:
with src.open(mode="rb") as input_file:
output_file.write(input_file.read())
def download_file(src: Union[str, "Pathy"], dest: Path, *, force: bool = False) -> None:
def download_file(
src: Union[str, "FluidPath"], dest: Path, *, force: bool = False
) -> None:
"""Download a file using smart_open.
url (str): The URL of the file.
@ -368,7 +375,7 @@ def ensure_pathy(path):
slow and annoying Google Cloud warning)."""
from pathy import Pathy # noqa: F811
return Pathy(path)
return Pathy.fluid(path)
def git_checkout(

36
spacy/cli/project/remote_storage.py
View File

@ -5,15 +5,17 @@ import hashlib
import urllib.parse
import tarfile
from pathlib import Path
from wasabi import msg
from .._util import get_hash, get_checksum, download_file, ensure_pathy
from ...util import make_tempdir, get_minor_version, ENV_VARS, check_bool_env_var
from .._util import get_hash, get_checksum, upload_file, download_file
from .._util import ensure_pathy, make_tempdir
from ...util import get_minor_version, ENV_VARS, check_bool_env_var
from ...git_info import GIT_VERSION
from ... import about
from ...errors import Errors
if TYPE_CHECKING:
from pathy import Pathy # noqa: F401
from pathy import FluidPath # noqa: F401
class RemoteStorage:
@ -28,7 +30,7 @@ class RemoteStorage:
self.url = ensure_pathy(url)
self.compression = compression
def push(self, path: Path, command_hash: str, content_hash: str) -> "Pathy":
def push(self, path: Path, command_hash: str, content_hash: str) -> "FluidPath":
"""Compress a file or directory within a project and upload it to a remote
storage. If an object exists at the full URL, nothing is done.
@ -49,9 +51,7 @@ class RemoteStorage:
mode_string = f"w:{self.compression}" if self.compression else "w"
with tarfile.open(tar_loc, mode=mode_string) as tar_file:
tar_file.add(str(loc), arcname=str(path))
with tar_loc.open(mode="rb") as input_file:
with url.open(mode="wb") as output_file:
output_file.write(input_file.read())
upload_file(tar_loc, url)
return url
def pull(
@ -60,7 +60,7 @@ class RemoteStorage:
*,
command_hash: Optional[str] = None,
content_hash: Optional[str] = None,
) -> Optional["Pathy"]:
) -> Optional["FluidPath"]:
"""Retrieve a file from the remote cache. If the file already exists,
nothing is done.
@ -110,25 +110,37 @@ class RemoteStorage:
*,
command_hash: Optional[str] = None,
content_hash: Optional[str] = None,
) -> Optional["Pathy"]:
) -> Optional["FluidPath"]:
"""Find the best matching version of a file within the storage,
or `None` if no match can be found. If both the creation and content hash
are specified, only exact matches will be returned. Otherwise, the most
recent matching file is preferred.
"""
name = self.encode_name(str(path))
urls = []
if command_hash is not None and content_hash is not None:
url = self.make_url(path, command_hash, content_hash)
url = self.url / name / command_hash / content_hash
urls = [url] if url.exists() else []
elif command_hash is not None:
if (self.url / name / command_hash).exists():
urls = list((self.url / name / command_hash).iterdir())
else:
urls = list((self.url / name).iterdir())
if (self.url / name).exists():
for sub_dir in (self.url / name).iterdir():
urls.extend(sub_dir.iterdir())
if content_hash is not None:
urls = [url for url in urls if url.parts[-1] == content_hash]
if len(urls) >= 2:
try:
urls.sort(key=lambda x: x.stat().last_modified) # type: ignore
except Exception:
msg.warn(
"Unable to sort remote files by last modified. The file(s) "
"pulled from the cache may not be the most recent."
)
return urls[-1] if urls else None
def make_url(self, path: Path, command_hash: str, content_hash: str) -> "Pathy":
def make_url(self, path: Path, command_hash: str, content_hash: str) -> "FluidPath":
"""Construct a URL from a subpath, a creation hash and a content hash."""
return self.url / self.encode_name(str(path)) / command_hash / content_hash

56
spacy/tests/test_cli.py
View File

@ -3,6 +3,7 @@ import math
from collections import Counter
from typing import Tuple, List, Dict, Any
import pkg_resources
import time
import numpy
import pytest
@ -28,6 +29,7 @@ from spacy.cli.download import get_compatibility, get_version
from spacy.cli.init_config import RECOMMENDATIONS, init_config, fill_config
from spacy.cli.package import get_third_party_dependencies
from spacy.cli.package import _is_permitted_package_name
from spacy.cli.project.remote_storage import RemoteStorage
from spacy.cli.project.run import _check_requirements
from spacy.cli.validate import get_model_pkgs
from spacy.cli.find_threshold import find_threshold
@ -862,6 +864,60 @@ def test_span_length_freq_dist_output_must_be_correct():
assert list(span_freqs.keys()) == [3, 1, 4, 5, 2]
def test_local_remote_storage():
with make_tempdir() as d:
filename = "a.txt"
content_hashes = ("aaaa", "cccc", "bbbb")
for i, content_hash in enumerate(content_hashes):
# make sure that each subsequent file has a later timestamp
if i > 0:
time.sleep(1)
content = f"{content_hash} content"
loc_file = d / "root" / filename
if not loc_file.parent.exists():
loc_file.parent.mkdir(parents=True)
with loc_file.open(mode="w") as file_:
file_.write(content)
# push first version to remote storage
remote = RemoteStorage(d / "root", str(d / "remote"))
remote.push(filename, "aaaa", content_hash)
# retrieve with full hashes
loc_file.unlink()
remote.pull(filename, command_hash="aaaa", content_hash=content_hash)
with loc_file.open(mode="r") as file_:
assert file_.read() == content
# retrieve with command hash
loc_file.unlink()
remote.pull(filename, command_hash="aaaa")
with loc_file.open(mode="r") as file_:
assert file_.read() == content
# retrieve with content hash
loc_file.unlink()
remote.pull(filename, content_hash=content_hash)
with loc_file.open(mode="r") as file_:
assert file_.read() == content
# retrieve with no hashes
loc_file.unlink()
remote.pull(filename)
with loc_file.open(mode="r") as file_:
assert file_.read() == content
def test_local_remote_storage_pull_missing():
# pulling from a non-existent remote pulls nothing gracefully
with make_tempdir() as d:
filename = "a.txt"
remote = RemoteStorage(d / "root", str(d / "remote"))
assert remote.pull(filename, command_hash="aaaa") is None
assert remote.pull(filename) is None
def test_cli_find_threshold(capsys):
thresholds = numpy.linspace(0, 1, 10)

26
website/docs/api/cli.md
View File

@ -1391,12 +1391,13 @@ If the contents are different, the new version of the file is uploaded. Deleting
obsolete files is left up to you.
Remotes can be defined in the `remotes` section of the
[`project.yml`](/usage/projects#project-yml). Under the hood, spaCy uses the
[`smart-open`](https://github.com/RaRe-Technologies/smart_open) library to
communicate with the remote storages, so you can use any protocol that
`smart-open` supports, including [S3](https://aws.amazon.com/s3/),
[Google Cloud Storage](https://cloud.google.com/storage), SSH and more, although
you may need to install extra dependencies to use certain protocols.
[`project.yml`](/usage/projects#project-yml). Under the hood, spaCy uses
[`Pathy`](https://github.com/justindujardin/pathy) to communicate with the
remote storages, so you can use any protocol that `Pathy` supports, including
[S3](https://aws.amazon.com/s3/),
[Google Cloud Storage](https://cloud.google.com/storage), and the local
filesystem, although you may need to install extra dependencies to use certain
protocols.
```cli
$ python -m spacy project push [remote] [project_dir]
@ -1435,12 +1436,13 @@ outputs, so if you change the config back, you'll be able to fetch back the
result.
Remotes can be defined in the `remotes` section of the
[`project.yml`](/usage/projects#project-yml). Under the hood, spaCy uses the
[`smart-open`](https://github.com/RaRe-Technologies/smart_open) library to
communicate with the remote storages, so you can use any protocol that
`smart-open` supports, including [S3](https://aws.amazon.com/s3/),
[Google Cloud Storage](https://cloud.google.com/storage), SSH and more, although
you may need to install extra dependencies to use certain protocols.
[`project.yml`](/usage/projects#project-yml). Under the hood, spaCy uses
[`Pathy`](https://github.com/justindujardin/pathy) to communicate with the
remote storages, so you can use any protocol that `Pathy` supports, including
[S3](https://aws.amazon.com/s3/),
[Google Cloud Storage](https://cloud.google.com/storage), and the local
filesystem, although you may need to install extra dependencies to use certain
protocols.
```cli
$ python -m spacy project pull [remote] [project_dir]

18
website/docs/usage/projects.md
View File

@ -259,9 +259,9 @@ pipelines.
> This can be used in a project command like so:
>
> ```yaml
> - name: "echo-path"
> - name: 'echo-path'
> script:
> - "echo ${env.ENV_PATH}"
> - 'echo ${env.ENV_PATH}'
> ```
| Section | Description |
@ -643,12 +643,13 @@ locally.
You can list one or more remotes in the `remotes` section of your
[`project.yml`](#project-yml) by mapping a string name to the URL of the
storage. Under the hood, spaCy uses the
[`smart-open`](https://github.com/RaRe-Technologies/smart_open) library to
communicate with the remote storages, so you can use any protocol that
`smart-open` supports, including [S3](https://aws.amazon.com/s3/),
[Google Cloud Storage](https://cloud.google.com/storage), SSH and more, although
you may need to install extra dependencies to use certain protocols.
storage. Under the hood, spaCy uses
[`Pathy`](https://github.com/justindujardin/pathy) to communicate with the
remote storages, so you can use any protocol that `Pathy` supports, including
[S3](https://aws.amazon.com/s3/),
[Google Cloud Storage](https://cloud.google.com/storage), and the local
filesystem, although you may need to install extra dependencies to use certain
protocols.
> #### Example
>
@ -661,7 +662,6 @@ you may need to install extra dependencies to use certain protocols.
remotes:
default: 's3://my-spacy-bucket'
local: '/mnt/scratch/cache'
stuff: 'ssh://myserver.example.com/whatever'
```
<Infobox title="How it works" emoji="💡">