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Merge branch 'develop' of https://github.com/explosion/spaCy into develop

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This commit is contained in:
Matthw Honnibal 2020-07-09 19:34:11 +02:00
commit 7010f1a2be
14 changed files with 856 additions and 809 deletions
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6
spacy/cli/__init__.py
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@ -15,8 +15,10 @@ from .evaluate import evaluate # noqa: F401
from .convert import convert # noqa: F401
from .init_model import init_model # noqa: F401
from .validate import validate # noqa: F401
from .project import project_clone, project_assets, project_run # noqa: F401
from .project import project_run_all # noqa: F401
from .project.clone import project_clone # noqa: F401
from .project.assets import project_assets # noqa: F401
from .project.run import project_run # noqa: F401
from .project.dvc import project_update_dvc # noqa: F401
@app.command("link", no_args_is_help=True, deprecated=True, hidden=True)

7
spacy/cli/_app.py
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@ -8,9 +8,16 @@ HELP = """spaCy Command-line Interface
DOCS: https://spacy.io/api/cli
"""
PROJECT_HELP = f"""Command-line interface for spaCy projects and working with
project templates. You'd typically start by cloning a project template to a local
directory and fetching its assets like datasets etc. See the project's
project.yml for the available commands.
"""
app = typer.Typer(name=NAME, help=HELP)
project_cli = typer.Typer(name="project", help=PROJECT_HELP, no_args_is_help=True)
app.add_typer(project_cli)
# Wrappers for Typer's annotations. Initially created to set defaults and to
# keep the names short, but not needed at the moment.

805
spacy/cli/project.py
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@ -1,805 +0,0 @@
from typing import List, Dict, Any, Optional, Sequence, Union
import typer
import srsly
from pathlib import Path
from wasabi import msg
import subprocess
import os
import re
import shutil
import sys
import requests
import tqdm
from ._app import app, Arg, Opt, COMMAND, NAME
from .. import about
from ..schemas import ProjectConfigSchema, validate
from ..util import ensure_path, run_command, make_tempdir, working_dir
from ..util import get_hash, get_checksum, split_command
PROJECT_FILE = "project.yml"
DVC_CONFIG = "dvc.yaml"
DVC_DIR = ".dvc"
DIRS = [
"assets",
"metas",
"configs",
"packages",
"metrics",
"scripts",
"notebooks",
"training",
"corpus",
]
CACHES = [
Path.home() / ".torch",
Path.home() / ".caches" / "torch",
os.environ.get("TORCH_HOME"),
Path.home() / ".keras",
]
DVC_CONFIG_COMMENT = f"""# This file is auto-generated by spaCy based on your {PROJECT_FILE}. Do not edit
# it directly and edit the {PROJECT_FILE} instead and re-run the project."""
CLI_HELP = f"""Command-line interface for spaCy projects and working with project
templates. You'd typically start by cloning a project template to a local
directory and fetching its assets like datasets etc. See the project's
{PROJECT_FILE} for the available commands. Under the hood, spaCy uses DVC (Data
Version Control) to manage input and output files and to ensure steps are only
re-run if their inputs change.
"""
project_cli = typer.Typer(help=CLI_HELP, no_args_is_help=True)
@project_cli.callback(invoke_without_command=True)
def callback(ctx: typer.Context):
"""This runs before every project command and ensures DVC is installed."""
ensure_dvc()
################
# CLI COMMANDS #
################
@project_cli.command("clone")
def project_clone_cli(
# fmt: off
name: str = Arg(..., help="The name of the template to fetch"),
dest: Path = Arg(Path.cwd(), help="Where to download and work. Defaults to current working directory.", exists=False),
repo: str = Opt(about.__projects__, "--repo", "-r", help="The repository to look in."),
git: bool = Opt(False, "--git", "-G", help="Initialize project as a Git repo"),
no_init: bool = Opt(False, "--no-init", "-NI", help="Don't initialize the project with DVC"),
# fmt: on
):
"""Clone a project template from a repository. Calls into "git" and will
only download the files from the given subdirectory. The GitHub repo
defaults to the official spaCy template repo, but can be customized
(including using a private repo). Setting the --git flag will also
initialize the project directory as a Git repo. If the project is intended
to be a Git repo, it should be initialized with Git first, before
initializing DVC (Data Version Control). This allows DVC to integrate with
Git.
"""
if dest == Path.cwd():
dest = dest / name
project_clone(name, dest, repo=repo, git=git, no_init=no_init)
@project_cli.command("init")
def project_init_cli(
# fmt: off
path: Path = Arg(Path.cwd(), help="Path to cloned project. Defaults to current working directory.", exists=True, file_okay=False),
git: bool = Opt(False, "--git", "-G", help="Initialize project as a Git repo"),
force: bool = Opt(False, "--force", "-F", "-f", help="Force initiziation"),
# fmt: on
):
"""Initialize a project directory with DVC and optionally Git. This should
typically be taken care of automatically when you run the "project clone"
command, but you can also run it separately. If the project is intended to
be a Git repo, it should be initialized with Git first, before initializing
DVC. This allows DVC to integrate with Git.
"""
project_init(path, git=git, force=force)
@project_cli.command("assets")
def project_assets_cli(
# fmt: off
project_dir: Path = Arg(Path.cwd(), help="Path to cloned project. Defaults to current working directory.", exists=True, file_okay=False),
# fmt: on
):
"""Use DVC (Data Version Control) to fetch project assets. Assets are
defined in the "assets" section of the project.yml. If possible, DVC
will try to track the files so you can pull changes from upstream. It will
also try and store the checksum so the assets are versioned. If the file
can't be tracked or checked, it will be downloaded without DVC. If a checksum
is provided in the project.yml, the file is only downloaded if no local
file with the same checksum exists.
"""
project_assets(project_dir)
@project_cli.command(
"run-all",
context_settings={"allow_extra_args": True, "ignore_unknown_options": True},
)
def project_run_all_cli(
# fmt: off
ctx: typer.Context,
project_dir: Path = Arg(Path.cwd(), help="Location of project directory. Defaults to current working directory.", exists=True, file_okay=False),
show_help: bool = Opt(False, "--help", help="Show help message and available subcommands")
# fmt: on
):
"""Run all commands defined in the project. This command will use DVC and
the defined outputs and dependencies in the project.yml to determine
which steps need to be re-run and where to start. This means you're only
re-generating data if the inputs have changed.
This command calls into "dvc repro" and all additional arguments are passed
to the "dvc repro" command: https://dvc.org/doc/command-reference/repro
"""
if show_help:
print_run_help(project_dir)
else:
project_run_all(project_dir, *ctx.args)
@project_cli.command(
"run", context_settings={"allow_extra_args": True, "ignore_unknown_options": True},
)
def project_run_cli(
# fmt: off
ctx: typer.Context,
subcommand: str = Arg(None, help=f"Name of command defined in the {PROJECT_FILE}"),
project_dir: Path = Arg(Path.cwd(), help="Location of project directory. Defaults to current working directory.", exists=True, file_okay=False),
show_help: bool = Opt(False, "--help", help="Show help message and available subcommands")
# fmt: on
):
"""Run a named script defined in the project.yml. If the command is
part of the default pipeline defined in the "run" section, DVC is used to
determine whether the step should re-run if its inputs have changed, or
whether everything is up to date. If the script is not part of the default
pipeline, it will be called separately without DVC.
If DVC is used, the command calls into "dvc repro" and all additional
arguments are passed to the "dvc repro" command:
https://dvc.org/doc/command-reference/repro
"""
if show_help or not subcommand:
print_run_help(project_dir, subcommand)
else:
project_run(project_dir, subcommand, *ctx.args)
@project_cli.command("exec", hidden=True)
def project_exec_cli(
# fmt: off
subcommand: str = Arg(..., help=f"Name of command defined in the {PROJECT_FILE}"),
project_dir: Path = Arg(Path.cwd(), help="Location of project directory. Defaults to current working directory.", exists=True, file_okay=False),
# fmt: on
):
"""Execute a command defined in the project.yml. This CLI command is
only called internally in auto-generated DVC pipelines, as a shortcut for
multi-step commands in the project.yml. You typically shouldn't have to
call it yourself. To run a command, call "run" or "run-all".
"""
project_exec(project_dir, subcommand)
@project_cli.command("update-dvc")
def project_update_dvc_cli(
# fmt: off
project_dir: Path = Arg(Path.cwd(), help="Location of project directory. Defaults to current working directory.", exists=True, file_okay=False),
verbose: bool = Opt(False, "--verbose", "-V", help="Print more info"),
force: bool = Opt(False, "--force", "-F", help="Force update DVC config"),
# fmt: on
):
"""Update the auto-generated DVC config file. Uses the steps defined in the
"run" section of the project.yml. This typically happens automatically
when running a command, but can also be triggered manually if needed.
"""
config = load_project_config(project_dir)
updated = update_dvc_config(project_dir, config, verbose=verbose, force=force)
if updated:
msg.good(f"Updated DVC config from {PROJECT_FILE}")
else:
msg.info(f"No changes found in {PROJECT_FILE}, no update needed")
app.add_typer(project_cli, name="project")
#################
# CLI FUNCTIONS #
#################
def project_clone(
name: str,
dest: Path,
*,
repo: str = about.__projects__,
git: bool = False,
no_init: bool = False,
) -> None:
"""Clone a project template from a repository.
name (str): Name of subdirectory to clone.
dest (Path): Destination path of cloned project.
repo (str): URL of Git repo containing project templates.
git (bool): Initialize project as Git repo. Should be set to True if project
is intended as a repo, since it will allow DVC to integrate with Git.
no_init (bool): Don't initialize DVC and Git automatically. If True, the
"init" command or "git init" and "dvc init" need to be run manually.
"""
dest = ensure_path(dest)
check_clone(name, dest, repo)
project_dir = dest.resolve()
# We're using Git and sparse checkout to only clone the files we need
with make_tempdir() as tmp_dir:
cmd = f"git clone {repo} {tmp_dir} --no-checkout --depth 1 --config core.sparseCheckout=true"
try:
run_command(cmd)
except DVCError:
err = f"Could not clone the repo '{repo}' into the temp dir '{tmp_dir}'."
msg.fail(err)
with (tmp_dir / ".git" / "info" / "sparse-checkout").open("w") as f:
f.write(name)
try:
run_command(["git", "-C", str(tmp_dir), "fetch"])
run_command(["git", "-C", str(tmp_dir), "checkout"])
except DVCError:
err = f"Could not clone '{name}' in the repo '{repo}'."
msg.fail(err)
shutil.move(str(tmp_dir / Path(name).name), str(project_dir))
msg.good(f"Cloned project '{name}' from {repo} into {project_dir}")
for sub_dir in DIRS:
dir_path = project_dir / sub_dir
if not dir_path.exists():
dir_path.mkdir(parents=True)
if not no_init:
project_init(project_dir, git=git, force=True, silent=True)
msg.good(f"Your project is now ready!", dest)
print(f"To fetch the assets, run:\n{COMMAND} project assets {dest}")
def project_init(
project_dir: Path,
*,
git: bool = False,
force: bool = False,
silent: bool = False,
analytics: bool = False,
):
"""Initialize a project as a DVC and (optionally) as a Git repo.
project_dir (Path): Path to project directory.
git (bool): Also call "git init" to initialize directory as a Git repo.
silent (bool): Don't print any output (via DVC).
analytics (bool): Opt-in to DVC analytics (defaults to False).
"""
with working_dir(project_dir) as cwd:
if git:
run_command(["git", "init"])
flags = {"--force": force, "--quiet": silent, "--no-scm": not git}
try:
run_dvc_command(["init"], flags=flags)
except DVCError:
msg.fail(
"Failed to initialize project. This likely means that the "
"project is already initialized and has a .dvc directory. "
"To force-initialize, use the --force flag.",
exits=1,
)
# We don't want to have analytics on by default – our users should
# opt-in explicitly. If they want it, they can always enable it.
if not analytics:
run_dvc_command(["config", "core.analytics", "false"])
# Remove unused and confusing plot templates from .dvc directory.
# Otherwise super confusing once you commit your changes via Git and it
# creates a bunch of files that have no purpose.
plots_dir = cwd / DVC_DIR / "plots"
if plots_dir.exists():
shutil.rmtree(str(plots_dir))
config = load_project_config(cwd)
setup_check_dvc(cwd, config)
msg.good("Initialized project")
def project_assets(project_dir: Path) -> None:
"""Fetch assets for a project using DVC if possible.
project_dir (Path): Path to project directory.
"""
project_path = ensure_path(project_dir)
config = load_project_config(project_path)
setup_check_dvc(project_path, config)
assets = config.get("assets", {})
if not assets:
msg.warn(f"No assets specified in {PROJECT_FILE}", exits=0)
msg.info(f"Fetching {len(assets)} asset(s)")
variables = config.get("variables", {})
fetched_assets = []
for asset in assets:
dest = asset["dest"].format(**variables)
url = asset.get("url")
checksum = asset.get("checksum")
if not url:
# project.yml defines asset without URL that the user has to place
if not Path(dest).exists():
err = f"No URL provided for asset. You need to add this file yourself: {dest}"
msg.warn(err)
else:
if checksum == get_checksum(dest):
msg.good(f"Asset exists with matching checksum: {dest}")
fetched_assets.append((project_path / dest).resolve())
else:
msg.fail(f"Asset available but with incorrect checksum: {dest}")
continue
url = url.format(**variables)
fetched_path = fetch_asset(project_path, url, dest, checksum)
if fetched_path:
fetched_assets.append(str(fetched_path))
if fetched_assets:
with working_dir(project_path):
run_dvc_command(["add", *fetched_assets, "--external"])
def fetch_asset(
project_path: Path, url: str, dest: Path, checksum: Optional[str] = None
) -> Optional[Path]:
"""Fetch an asset from a given URL or path. Will try to import the file
using DVC's import-url if possible (fully tracked and versioned) and falls
back to get-url (versioned) and a non-DVC download if necessary. If a
checksum is provided and a local file exists, it's only re-downloaded if the
checksum doesn't match.
project_path (Path): Path to project directory.
url (str): URL or path to asset.
checksum (Optional[str]): Optional expected checksum of local file.
RETURNS (Optional[Path]): The path to the fetched asset or None if fetching
the asset failed.
"""
url = convert_asset_url(url)
dest_path = (project_path / dest).resolve()
if dest_path.exists() and checksum:
# If there's already a file, check for checksum
# TODO: add support for caches (dvc import-url with local path)
if checksum == get_checksum(dest_path):
msg.good(f"Skipping download with matching checksum: {dest}")
return dest_path
with working_dir(project_path):
try:
# If these fail, we don't want to output an error or info message.
# Try with tracking the source first, then just downloading with
# DVC, then a regular non-DVC download.
try:
run_dvc_command(["import-url", url, str(dest_path)])
except DVCError:
run_dvc_command(["get-url", url, str(dest_path)])
except DVCError:
try:
download_file(url, dest_path)
except requests.exceptions.HTTPError as e:
msg.fail(f"Download failed: {dest}", e)
return None
if checksum and checksum != get_checksum(dest_path):
msg.fail(f"Checksum doesn't match value defined in {PROJECT_FILE}: {dest}")
msg.good(f"Fetched asset {dest}")
return dest_path
def project_run_all(project_dir: Path, *dvc_args) -> None:
"""Run all commands defined in the project using DVC.
project_dir (Path): Path to project directory.
*dvc_args: Other arguments passed to "dvc repro".
"""
config = load_project_config(project_dir)
setup_check_dvc(project_dir, config)
with working_dir(project_dir):
try:
run_dvc_command(["repro", *dvc_args])
except DVCError:
# We could raise a custom error here, but the output produced by
# DVC is already pretty substantial.
sys.exit(1)
def print_run_help(project_dir: Path, subcommand: Optional[str] = None) -> None:
"""Simulate a CLI help prompt using the info available in the project.yml.
project_dir (Path): The project directory.
subcommand (Optional[str]): The subcommand or None. If a subcommand is
provided, the subcommand help is shown. Otherwise, the top-level help
and a list of available commands is printed.
"""
config = load_project_config(project_dir)
setup_check_dvc(project_dir, config)
config_commands = config.get("commands", [])
commands = {cmd["name"]: cmd for cmd in config_commands}
if subcommand:
validate_subcommand(commands.keys(), subcommand)
print(f"Usage: {COMMAND} project run {subcommand} {project_dir}")
help_text = commands[subcommand].get("help")
if help_text:
msg.text(f"\n{help_text}\n")
else:
print(f"\nAvailable commands in {PROJECT_FILE}")
print(f"Usage: {COMMAND} project run [COMMAND] {project_dir}")
msg.table([(cmd["name"], cmd.get("help", "")) for cmd in config_commands])
msg.text(f"Run all commands defined in the 'run' block of the {PROJECT_FILE}:")
print(f"{COMMAND} project run-all {project_dir}")
def project_run(project_dir: Path, subcommand: str, *dvc_args) -> None:
"""Run a named script defined in the project.yml. If the script is part
of the default pipeline (defined in the "run" section), DVC is used to
execute the command, so it can determine whether to rerun it. It then
calls into "exec" to execute it.
project_dir (Path): Path to project directory.
subcommand (str): Name of command to run.
*dvc_args: Other arguments passed to "dvc repro".
"""
config = load_project_config(project_dir)
setup_check_dvc(project_dir, config)
config_commands = config.get("commands", [])
variables = config.get("variables", {})
commands = {cmd["name"]: cmd for cmd in config_commands}
validate_subcommand(commands.keys(), subcommand)
if subcommand in config.get("run", []):
# This is one of the pipeline commands tracked in DVC
with working_dir(project_dir):
try:
run_dvc_command(["repro", subcommand, *dvc_args])
except DVCError:
# We could raise a custom error here, but the output produced by
# DVC is already pretty substantial.
sys.exit(1)
else:
cmd = commands[subcommand]
# Deps in non-DVC commands aren't tracked, but if they're defined,
# make sure they exist before running the command
for dep in cmd.get("deps", []):
if not (project_dir / dep).exists():
err = f"Missing dependency specified by command '{subcommand}': {dep}"
msg.fail(err, exits=1)
with working_dir(project_dir):
run_commands(cmd["script"], variables)
def project_exec(project_dir: Path, subcommand: str) -> None:
"""Execute a command defined in the project.yml.
project_dir (Path): Path to project directory.
subcommand (str): Name of command to run.
"""
config = load_project_config(project_dir)
config_commands = config.get("commands", [])
variables = config.get("variables", {})
commands = {cmd["name"]: cmd for cmd in config_commands}
with working_dir(project_dir):
run_commands(commands[subcommand]["script"], variables)
###########
# HELPERS #
###########
def load_project_config(path: Path) -> Dict[str, Any]:
"""Load the project.yml file from a directory and validate it.
path (Path): The path to the project directory.
RETURNS (Dict[str, Any]): The loaded project.yml.
"""
config_path = path / PROJECT_FILE
if not config_path.exists():
msg.fail(f"Can't find {PROJECT_FILE}", config_path, exits=1)
invalid_err = f"Invalid {PROJECT_FILE}. Double-check that the YAML is correct."
try:
config = srsly.read_yaml(config_path)
except ValueError as e:
msg.fail(invalid_err, e, exits=1)
errors = validate(ProjectConfigSchema, config)
if errors:
msg.fail(invalid_err, "\n".join(errors), exits=1)
return config
def update_dvc_config(
path: Path,
config: Dict[str, Any],
verbose: bool = False,
silent: bool = False,
force: bool = False,
) -> bool:
"""Re-run the DVC commands in dry mode and update dvc.yaml file in the
project directory. The file is auto-generated based on the config. The
first line of the auto-generated file specifies the hash of the config
dict, so if any of the config values change, the DVC config is regenerated.
path (Path): The path to the project directory.
config (Dict[str, Any]): The loaded project.yml.
verbose (bool): Whether to print additional info (via DVC).
silent (bool): Don't output anything (via DVC).
force (bool): Force update, even if hashes match.
RETURNS (bool): Whether the DVC config file was updated.
"""
config_hash = get_hash(config)
path = path.resolve()
dvc_config_path = path / DVC_CONFIG
if dvc_config_path.exists():
# Check if the file was generated using the current config, if not, redo
with dvc_config_path.open("r", encoding="utf8") as f:
ref_hash = f.readline().strip().replace("# ", "")
if ref_hash == config_hash and not force:
return False # Nothing has changed in project.yml, don't need to update
dvc_config_path.unlink()
variables = config.get("variables", {})
dvc_commands = []
# We only want to include commands that are part of the main list of "run"
# commands in project.yml and should be run in sequence
config_commands = {cmd["name"]: cmd for cmd in config.get("commands", [])}
for name in config.get("run", []):
validate_subcommand(config_commands.keys(), name)
command = config_commands[name]
deps = command.get("deps", [])
outputs = command.get("outputs", [])
outputs_no_cache = command.get("outputs_no_cache", [])
if not deps and not outputs and not outputs_no_cache:
continue
# Default to the working dir as the project path since dvc.yaml is auto-generated
# and we don't want arbitrary paths in there
project_cmd = ["python", "-m", NAME, "project", "exec", name]
deps_cmd = [c for cl in [["-d", p] for p in deps] for c in cl]
outputs_cmd = [c for cl in [["-o", p] for p in outputs] for c in cl]
outputs_nc_cmd = [c for cl in [["-O", p] for p in outputs_no_cache] for c in cl]
dvc_cmd = ["run", "-n", name, "-w", str(path), "--no-exec"]
full_cmd = [*dvc_cmd, *deps_cmd, *outputs_cmd, *outputs_nc_cmd, *project_cmd]
dvc_commands.append(" ".join(full_cmd))
with working_dir(path):
dvc_flags = {"--verbose": verbose, "--quiet": silent}
run_dvc_commands(dvc_commands, variables, flags=dvc_flags)
with dvc_config_path.open("r+", encoding="utf8") as f:
content = f.read()
f.seek(0, 0)
f.write(f"# {config_hash}\n{DVC_CONFIG_COMMENT}\n{content}")
return True
def ensure_dvc() -> None:
"""Ensure that the "dvc" command is available and show an error if not."""
try:
subprocess.run(["dvc", "--version"], stdout=subprocess.DEVNULL)
except Exception:
msg.fail(
"spaCy projects require DVC (Data Version Control) and the 'dvc' command",
"You can install the Python package from pip (pip install dvc) or "
"conda (conda install -c conda-forge dvc). For more details, see the "
"documentation: https://dvc.org/doc/install",
exits=1,
)
def setup_check_dvc(project_dir: Path, config: Dict[str, Any]) -> None:
"""Check that the project is set up correctly with DVC and update its
config if needed. Will raise an error if the project is not an initialized
DVC project.
project_dir (Path): The path to the project directory.
config (Dict[str, Any]): The loaded project.yml.
"""
if not project_dir.exists():
msg.fail(f"Can't find project directory: {project_dir}")
if not (project_dir / ".dvc").exists():
msg.fail(
"Project not initialized as a DVC project.",
f"Make sure that the project template was cloned correctly. To "
f"initialize the project directory manually, you can run: "
f"{COMMAND} project init {project_dir}",
exits=1,
)
with msg.loading("Updating DVC config..."):
updated = update_dvc_config(project_dir, config, silent=True)
if updated:
msg.good(f"Updated DVC config from changed {PROJECT_FILE}")
def convert_asset_url(url: str) -> str:
"""Check and convert the asset URL if needed.
url (str): The asset URL.
RETURNS (str): The converted URL.
"""
# If the asset URL is a regular GitHub URL it's likely a mistake
if re.match(r"(http(s?)):\/\/github.com", url):
converted = url.replace("github.com", "raw.githubusercontent.com")
converted = re.sub(r"/(tree|blob)/", "/", converted)
msg.warn(
"Downloading from a regular GitHub URL. This will only download "
"the source of the page, not the actual file. Converting the URL "
"to a raw URL.",
converted,
)
return converted
return url
def check_clone(name: str, dest: Path, repo: str) -> None:
"""Check and validate that the destination path can be used to clone. Will
check that Git is available and that the destination path is suitable.
name (str): Name of the directory to clone from the repo.
dest (Path): Local destination of cloned directory.
repo (str): URL of the repo to clone from.
"""
try:
subprocess.run(["git", "--version"], stdout=subprocess.DEVNULL)
except Exception:
msg.fail(
f"Cloning spaCy project templates requires Git and the 'git' command. ",
f"To clone a project without Git, copy the files from the '{name}' "
f"directory in the {repo} to {dest} manually and then run:",
f"{COMMAND} project init {dest}",
exits=1,
)
if not dest:
msg.fail(f"Not a valid directory to clone project: {dest}", exits=1)
if dest.exists():
# Directory already exists (not allowed, clone needs to create it)
msg.fail(f"Can't clone project, directory already exists: {dest}", exits=1)
if not dest.parent.exists():
# We're not creating parents, parent dir should exist
msg.fail(
f"Can't clone project, parent directory doesn't exist: {dest.parent}",
exits=1,
)
def validate_subcommand(commands: Sequence[str], subcommand: str) -> None:
"""Check that a subcommand is valid and defined. Raises an error otherwise.
commands (Sequence[str]): The available commands.
subcommand (str): The subcommand.
"""
if subcommand not in commands:
msg.fail(
f"Can't find command '{subcommand}' in {PROJECT_FILE}. "
f"Available commands: {', '.join(commands)}",
exits=1,
)
def download_file(url: str, dest: Path, chunk_size: int = 1024) -> None:
"""Download a file using requests.
url (str): The URL of the file.
dest (Path): The destination path.
chunk_size (int): The size of chunks to read/write.
"""
response = requests.get(url, stream=True)
response.raise_for_status()
total = int(response.headers.get("content-length", 0))
progress_settings = {
"total": total,
"unit": "iB",
"unit_scale": True,
"unit_divisor": chunk_size,
"leave": False,
}
with dest.open("wb") as f, tqdm.tqdm(**progress_settings) as bar:
for data in response.iter_content(chunk_size=chunk_size):
size = f.write(data)
bar.update(size)
def run_commands(
commands: List[str] = tuple(), variables: Dict[str, str] = {}, silent: bool = False
) -> None:
"""Run a sequence of commands in a subprocess, in order.
commands (List[str]): The string commands.
variables (Dict[str, str]): Dictionary of variable names, mapped to their
values. Will be used to substitute format string variables in the
commands.
silent (bool): Don't print the commands.
"""
for command in commands:
# Substitute variables, e.g. "./{NAME}.json"
command = command.format(**variables)
command = split_command(command)
# Not sure if this is needed or a good idea. Motivation: users may often
# use commands in their config that reference "python" and we want to
# make sure that it's always executing the same Python that spaCy is
# executed with and the pip in the same env, not some other Python/pip.
# Also ensures cross-compatibility if user 1 writes "python3" (because
# that's how it's set up on their system), and user 2 without the
# shortcut tries to re-run the command.
if len(command) and command[0] in ("python", "python3"):
command[0] = sys.executable
elif len(command) and command[0] in ("pip", "pip3"):
command = [sys.executable, "-m", "pip", *command[1:]]
if not silent:
print(f"Running command: {' '.join(command)}")
run_command(command)
def run_dvc_commands(
commands: List[str] = tuple(),
variables: Dict[str, str] = {},
flags: Dict[str, bool] = {},
) -> None:
"""Run a sequence of DVC commands in a subprocess, in order.
commands (List[str]): The string commands without the leading "dvc".
variables (Dict[str, str]): Dictionary of variable names, mapped to their
values. Will be used to substitute format string variables in the
commands.
flags (Dict[str, bool]): Conditional flags to be added to command. Makes it
easier to pass flags like --quiet that depend on a variable or
command-line setting while avoiding lots of nested conditionals.
"""
for command in commands:
# Substitute variables, e.g. "./{NAME}.json"
command = command.format(**variables)
command = split_command(command)
run_dvc_command(command, flags=flags)
def run_dvc_command(
command: Union[str, List[str]], flags: Dict[str, bool] = {}, silent: bool = False
) -> None:
"""Run a DVC command in a subprocess. This wrapper gives us a bit more
control over how the output and errors are presented. Raises a DVC error if
the "dvc" command returns a non-zero exit code and uses the error message
logged by DVC.
command (Union[str, List[str]]): The command, without the leading "dvc".
flags (Dict[str, bool]): Conditional flags to be added to command. Makes it
easier to pass flags like --quiet that depend on a variable or
command-line setting while avoiding lots of nested conditionals.
silent (bool): Don't print any output.
"""
if isinstance(command, str):
command = split_command(command)
dvc_command = ["dvc", *command]
# Add the flags if they are set to True
for flag, is_active in flags.items():
if is_active:
dvc_command.append(flag)
proc = subprocess.Popen(dvc_command, stderr=subprocess.PIPE, stdout=subprocess.PIPE)
if not silent:
lines = proc.stdout.read().decode("utf8").split("\n\n")
for line in lines:
line = line.strip()
if is_relevant_dvc_output(line):
print(f"{line}\n")
_, err = proc.communicate() # Important: otherwise returncode will be None!
if proc.returncode != 0:
if isinstance(err, bytes):
err = err.decode("utf8")
raise DVCError(err)
def is_relevant_dvc_output(line: str) -> bool:
"""Check whether the output by DVC is something we want to keep.
line (str): A line written to stdout,.
RETURNS (bool): Whether to use/print the line.
"""
# Writing them like this for readability but maybe replace with regex?
conditions = [
not line,
line.startswith("What's next?"),
line.startswith("Having any troubles?"),
]
return not any(conditions)
class DVCError(RuntimeError):
"""Custom error type for anything produced by the DVC CLI."""
pass

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from typing import Optional
from pathlib import Path
from wasabi import msg
import requests
import tqdm
import re
import shutil
from ...util import ensure_path, get_checksum, working_dir
from .._app import project_cli, Arg
from .util import PROJECT_FILE, load_project_config
# TODO: find a solution for caches
# CACHES = [
# Path.home() / ".torch",
# Path.home() / ".caches" / "torch",
# os.environ.get("TORCH_HOME"),
# Path.home() / ".keras",
# ]
@project_cli.command("assets")
def project_assets_cli(
# fmt: off
project_dir: Path = Arg(Path.cwd(), help="Path to cloned project. Defaults to current working directory.", exists=True, file_okay=False),
# fmt: on
):
"""Fetch project assets like datasets and pretrained weights. Assets are
defined in the "assets" section of the project.yml. If a checksum is
provided in the project.yml, the file is only downloaded if no local file
with the same checksum exists.
"""
project_assets(project_dir)
def project_assets(project_dir: Path) -> None:
"""Fetch assets for a project using DVC if possible.
project_dir (Path): Path to project directory.
"""
project_path = ensure_path(project_dir)
config = load_project_config(project_path)
assets = config.get("assets", {})
if not assets:
msg.warn(f"No assets specified in {PROJECT_FILE}", exits=0)
msg.info(f"Fetching {len(assets)} asset(s)")
variables = config.get("variables", {})
for asset in assets:
dest = asset["dest"].format(**variables)
url = asset.get("url")
checksum = asset.get("checksum")
if not url:
# project.yml defines asset without URL that the user has to place
check_private_asset(dest, checksum)
continue
url = url.format(**variables)
fetch_asset(project_path, url, dest, checksum)
def check_private_asset(dest: Path, checksum: Optional[str] = None) -> None:
"""Check and validate assets without a URL (private assets that the user
has to provide themselves) and give feedback about the checksum.
dest (Path): Desintation path of the asset.
checksum (Optional[str]): Optional checksum of the expected file.
"""
if not Path(dest).exists():
err = f"No URL provided for asset. You need to add this file yourself: {dest}"
msg.warn(err)
else:
if checksum and checksum == get_checksum(dest):
msg.good(f"Asset exists with matching checksum: {dest}")
else:
msg.fail(f"Asset available but with incorrect checksum: {dest}")
def fetch_asset(
project_path: Path, url: str, dest: Path, checksum: Optional[str] = None
) -> None:
"""Fetch an asset from a given URL or path. If a checksum is provided and a
local file exists, it's only re-downloaded if the checksum doesn't match.
project_path (Path): Path to project directory.
url (str): URL or path to asset.
checksum (Optional[str]): Optional expected checksum of local file.
RETURNS (Optional[Path]): The path to the fetched asset or None if fetching
the asset failed.
"""
# TODO: add support for caches
dest_path = (project_path / dest).resolve()
if dest_path.exists() and checksum:
# If there's already a file, check for checksum
if checksum == get_checksum(dest_path):
msg.good(f"Skipping download with matching checksum: {dest}")
return dest_path
with working_dir(project_path):
url = convert_asset_url(url)
try:
download_file(url, dest_path)
msg.good(f"Downloaded asset {dest}")
except requests.exceptions.RequestException as e:
if Path(url).exists() and Path(url).is_file():
# If it's a local file, copy to destination
shutil.copy(url, str(dest_path))
msg.good(f"Copied local asset {dest}")
else:
msg.fail(f"Download failed: {dest}", e)
return
if checksum and checksum != get_checksum(dest_path):
msg.fail(f"Checksum doesn't match value defined in {PROJECT_FILE}: {dest}")
def convert_asset_url(url: str) -> str:
"""Check and convert the asset URL if needed.
url (str): The asset URL.
RETURNS (str): The converted URL.
"""
# If the asset URL is a regular GitHub URL it's likely a mistake
if re.match(r"(http(s?)):\/\/github.com", url):
converted = url.replace("github.com", "raw.githubusercontent.com")
converted = re.sub(r"/(tree|blob)/", "/", converted)
msg.warn(
"Downloading from a regular GitHub URL. This will only download "
"the source of the page, not the actual file. Converting the URL "
"to a raw URL.",
converted,
)
return converted
return url
def download_file(url: str, dest: Path, chunk_size: int = 1024) -> None:
"""Download a file using requests.
url (str): The URL of the file.
dest (Path): The destination path.
chunk_size (int): The size of chunks to read/write.
"""
response = requests.get(url, stream=True)
response.raise_for_status()
total = int(response.headers.get("content-length", 0))
progress_settings = {
"total": total,
"unit": "iB",
"unit_scale": True,
"unit_divisor": chunk_size,
"leave": False,
}
with dest.open("wb") as f, tqdm.tqdm(**progress_settings) as bar:
for data in response.iter_content(chunk_size=chunk_size):
size = f.write(data)
bar.update(size)

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from pathlib import Path
from wasabi import msg
import subprocess
import shutil
from ... import about
from ...util import ensure_path, run_command, make_tempdir
from .._app import project_cli, Arg, Opt, COMMAND
DIRS = [
"assets",
"metas",
"configs",
"packages",
"metrics",
"scripts",
"notebooks",
"training",
"corpus",
]
@project_cli.command("clone")
def project_clone_cli(
# fmt: off
name: str = Arg(..., help="The name of the template to fetch"),
dest: Path = Arg(Path.cwd(), help="Where to download and work. Defaults to current working directory.", exists=False),
repo: str = Opt(about.__projects__, "--repo", "-r", help="The repository to look in."),
# fmt: on
):
"""Clone a project template from a repository. Calls into "git" and will
only download the files from the given subdirectory. The GitHub repo
defaults to the official spaCy template repo, but can be customized
(including using a private repo). Setting the --git flag will also
initialize the project directory as a Git repo. If the project is intended
to be a Git repo, it should be initialized with Git first, before
initializing DVC (Data Version Control). This allows DVC to integrate with
Git.
"""
if dest == Path.cwd():
dest = dest / name
project_clone(name, dest, repo=repo)
def project_clone(name: str, dest: Path, *, repo: str = about.__projects__) -> None:
"""Clone a project template from a repository.
name (str): Name of subdirectory to clone.
dest (Path): Destination path of cloned project.
repo (str): URL of Git repo containing project templates.
"""
dest = ensure_path(dest)
check_clone(name, dest, repo)
project_dir = dest.resolve()
# We're using Git and sparse checkout to only clone the files we need
with make_tempdir() as tmp_dir:
cmd = f"git clone {repo} {tmp_dir} --no-checkout --depth 1 --config core.sparseCheckout=true"
try:
run_command(cmd)
except subprocess.CalledProcessError:
err = f"Could not clone the repo '{repo}' into the temp dir '{tmp_dir}'."
msg.fail(err)
with (tmp_dir / ".git" / "info" / "sparse-checkout").open("w") as f:
f.write(name)
try:
run_command(["git", "-C", str(tmp_dir), "fetch"])
run_command(["git", "-C", str(tmp_dir), "checkout"])
except subprocess.CalledProcessError:
err = f"Could not clone '{name}' in the repo '{repo}'."
msg.fail(err)
shutil.move(str(tmp_dir / Path(name).name), str(project_dir))
msg.good(f"Cloned project '{name}' from {repo} into {project_dir}")
for sub_dir in DIRS:
dir_path = project_dir / sub_dir
if not dir_path.exists():
dir_path.mkdir(parents=True)
msg.good(f"Your project is now ready!", dest)
print(f"To fetch the assets, run:\n{COMMAND} project assets {dest}")
def check_clone(name: str, dest: Path, repo: str) -> None:
"""Check and validate that the destination path can be used to clone. Will
check that Git is available and that the destination path is suitable.
name (str): Name of the directory to clone from the repo.
dest (Path): Local destination of cloned directory.
repo (str): URL of the repo to clone from.
"""
try:
subprocess.run(["git", "--version"], stdout=subprocess.DEVNULL)
except Exception:
msg.fail(
f"Cloning spaCy project templates requires Git and the 'git' command. ",
f"To clone a project without Git, copy the files from the '{name}' "
f"directory in the {repo} to {dest} manually and then run:",
f"{COMMAND} project init {dest}",
exits=1,
)
if not dest:
msg.fail(f"Not a valid directory to clone project: {dest}", exits=1)
if dest.exists():
# Directory already exists (not allowed, clone needs to create it)
msg.fail(f"Can't clone project, directory already exists: {dest}", exits=1)
if not dest.parent.exists():
# We're not creating parents, parent dir should exist
msg.fail(
f"Can't clone project, parent directory doesn't exist: {dest.parent}",
exits=1,
)

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"""This module contains helpers and subcommands for integrating spaCy projects
with Data Version Controk (DVC). https://dvc.org"""
from typing import Dict, Any, List, Optional
import subprocess
from pathlib import Path
from wasabi import msg
from .util import PROJECT_FILE, load_project_config
from .._app import project_cli, Arg, Opt, NAME, COMMAND
from ...util import get_hash, working_dir, split_command, join_command, run_command
DVC_CONFIG = "dvc.yaml"
DVC_DIR = ".dvc"
UPDATE_COMMAND = "dvc"
DVC_CONFIG_COMMENT = f"""# This file is auto-generated by spaCy based on your {PROJECT_FILE}. If you've
# edited your {PROJECT_FILE}, you can regenerate this file by running:
# {COMMAND} project {UPDATE_COMMAND}"""
@project_cli.command(UPDATE_COMMAND)
def project_update_dvc_cli(
# fmt: off
project_dir: Path = Arg(Path.cwd(), help="Location of project directory. Defaults to current working directory.", exists=True, file_okay=False),
workflow: Optional[str] = Arg(None, help=f"Name of workflow defined in {PROJECT_FILE}. Defaults to first workflow if not set."),
verbose: bool = Opt(False, "--verbose", "-V", help="Print more info"),
force: bool = Opt(False, "--force", "-F", help="Force update DVC config"),
# fmt: on
):
"""Auto-generate Data Version Control (DVC) config. A DVC
project can only define one pipeline, so you need to specify one workflow
defined in the project.yml. If no workflow is specified, the first defined
workflow is used. The DVC config will only be updated if
"""
project_update_dvc(project_dir, workflow, verbose=verbose, force=force)
def project_update_dvc(
project_dir: Path,
workflow: Optional[str] = None,
*,
verbose: bool = False,
force: bool = False,
) -> None:
"""Update the auto-generated Data Version Control (DVC) config file. A DVC
project can only define one pipeline, so you need to specify one workflow
defined in the project.yml. Will only update the file if the checksum changed.
project_dir (Path): The project directory.
workflow (Optional[str]): Optional name of workflow defined in project.yml.
If not set, the first workflow will be used.
verbose (bool): Print more info.
force (bool): Force update DVC config.
"""
config = load_project_config(project_dir)
updated = update_dvc_config(
project_dir, config, workflow, verbose=verbose, force=force
)
help_msg = "To execute the workflow with DVC, run: dvc repro"
if updated:
msg.good(f"Updated DVC config from {PROJECT_FILE}", help_msg)
else:
msg.info(f"No changes found in {PROJECT_FILE}, no update needed", help_msg)
def update_dvc_config(
path: Path,
config: Dict[str, Any],
workflow: Optional[str] = None,
verbose: bool = False,
silent: bool = False,
force: bool = False,
) -> bool:
"""Re-run the DVC commands in dry mode and update dvc.yaml file in the
project directory. The file is auto-generated based on the config. The
first line of the auto-generated file specifies the hash of the config
dict, so if any of the config values change, the DVC config is regenerated.
path (Path): The path to the project directory.
config (Dict[str, Any]): The loaded project.yml.
verbose (bool): Whether to print additional info (via DVC).
silent (bool): Don't output anything (via DVC).
force (bool): Force update, even if hashes match.
RETURNS (bool): Whether the DVC config file was updated.
"""
ensure_dvc(path)
workflows = config.get("workflows", {})
workflow_names = list(workflows.keys())
check_workflows(workflow_names, workflow)
if not workflow:
workflow = workflow_names[0]
config_hash = get_hash(config)
path = path.resolve()
dvc_config_path = path / DVC_CONFIG
if dvc_config_path.exists():
# Check if the file was generated using the current config, if not, redo
with dvc_config_path.open("r", encoding="utf8") as f:
ref_hash = f.readline().strip().replace("# ", "")
if ref_hash == config_hash and not force:
return False # Nothing has changed in project.yml, don't need to update
dvc_config_path.unlink()
variables = config.get("variables", {})
dvc_commands = []
config_commands = {cmd["name"]: cmd for cmd in config.get("commands", [])}
for name in workflows[workflow]:
command = config_commands[name]
deps = command.get("deps", [])
outputs = command.get("outputs", [])
outputs_no_cache = command.get("outputs_no_cache", [])
if not deps and not outputs and not outputs_no_cache:
continue
# Default to the working dir as the project path since dvc.yaml is auto-generated
# and we don't want arbitrary paths in there
project_cmd = ["python", "-m", NAME, "project", "run", name]
deps_cmd = [c for cl in [["-d", p] for p in deps] for c in cl]
outputs_cmd = [c for cl in [["-o", p] for p in outputs] for c in cl]
outputs_nc_cmd = [c for cl in [["-O", p] for p in outputs_no_cache] for c in cl]
dvc_cmd = ["run", "-n", name, "-w", str(path), "--no-exec"]
full_cmd = [*dvc_cmd, *deps_cmd, *outputs_cmd, *outputs_nc_cmd, *project_cmd]
dvc_commands.append(join_command(full_cmd))
with working_dir(path):
dvc_flags = {"--verbose": verbose, "--quiet": silent}
run_dvc_commands(dvc_commands, variables, flags=dvc_flags)
with dvc_config_path.open("r+", encoding="utf8") as f:
content = f.read()
f.seek(0, 0)
f.write(f"# {config_hash}\n{DVC_CONFIG_COMMENT}\n{content}")
return True
def run_dvc_commands(
commands: List[str] = tuple(),
variables: Dict[str, str] = {},
flags: Dict[str, bool] = {},
) -> None:
"""Run a sequence of DVC commands in a subprocess, in order.
commands (List[str]): The string commands without the leading "dvc".
variables (Dict[str, str]): Dictionary of variable names, mapped to their
values. Will be used to substitute format string variables in the
commands.
flags (Dict[str, bool]): Conditional flags to be added to command. Makes it
easier to pass flags like --quiet that depend on a variable or
command-line setting while avoiding lots of nested conditionals.
"""
for command in commands:
# Substitute variables, e.g. "./{NAME}.json"
command = command.format(**variables)
command = split_command(command)
dvc_command = ["dvc", *command]
# Add the flags if they are set to True
for flag, is_active in flags.items():
if is_active:
dvc_command.append(flag)
run_command(dvc_command)
def check_workflows(workflows: List[str], workflow: Optional[str] = None) -> None:
"""Validate workflows provided in project.yml and check that a given
workflow can be used to generate a DVC config.
workflows (List[str]): Names of the available workflows.
workflow (Optional[str]): The name of the workflow to convert.
"""
if not workflows:
msg.fail(
f"No workflows defined in {PROJECT_FILE}. To generate a DVC config, "
f"define at least one list of commands.",
exits=1,
)
if workflow is not None and workflow not in workflows:
msg.fail(
f"Workflow '{workflow}' not defined in {PROJECT_FILE}. "
f"Available workflows: {', '.join(workflows)}",
exits=1,
)
if not workflow:
msg.warn(
f"No workflow specified for DVC pipeline. Using the first workflow "
f"defined in {PROJECT_FILE}: '{workflows[0]}'"
)
def ensure_dvc(project_dir: Path) -> None:
"""Ensure that the "dvc" command is available and that the current project
directory is an initialized DVC project.
"""
try:
subprocess.run(["dvc", "--version"], stdout=subprocess.DEVNULL)
except Exception:
msg.fail(
"To use spaCy projects with DVC (Data Version Control), DVC needs "
"to be installed and the 'dvc' command needs to be available",
"You can install the Python package from pip (pip install dvc) or "
"conda (conda install -c conda-forge dvc). For more details, see the "
"documentation: https://dvc.org/doc/install",
exits=1,
)
if not (project_dir / ".dvc").exists():
msg.fail(
"Project not initialized as a DVC project",
"To initialize a DVC project, you can run 'dvc init' in the project "
"directory. For more details, see the documentation: "
"https://dvc.org/doc/command-reference/init",
exits=1,
)

250
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from typing import Optional, List, Dict, Sequence, Any
from pathlib import Path
from wasabi import msg
import typer
import sys
import srsly
from ...util import working_dir, run_command, split_command, is_cwd, get_checksum
from ...util import get_hash, join_command
from .._app import project_cli, Arg, Opt, COMMAND
from .util import PROJECT_FILE, PROJECT_LOCK, load_project_config
@project_cli.command(
"run", context_settings={"allow_extra_args": True, "ignore_unknown_options": True},
)
def project_run_cli(
# fmt: off
ctx: typer.Context,
subcommand: str = Arg(None, help=f"Name of command defined in the {PROJECT_FILE}"),
project_dir: Path = Arg(Path.cwd(), help="Location of project directory. Defaults to current working directory.", exists=True, file_okay=False),
force: bool = Opt(False, "--force", "-F", help="Force re-running steps, even if nothing changed"),
dry: bool = Opt(False, "--dry", "-D", help="Perform a dry run and don't execute commands"),
show_help: bool = Opt(False, "--help", help="Show help message and available subcommands")
# fmt: on
):
"""Run a named script or workflow defined in the project.yml. If a workflow
name is specified, all commands in the workflow are run, in order. If
commands define inputs and/or outputs, they will only be re-run if state
has changed.
"""
if show_help or not subcommand:
print_run_help(project_dir, subcommand)
else:
project_run(project_dir, subcommand, *ctx.args, force=force, dry=dry)
def project_run(
project_dir: Path, subcommand: str, *, force: bool = False, dry: bool = False
) -> None:
"""Run a named script defined in the project.yml. If the script is part
of the default pipeline (defined in the "run" section), DVC is used to
execute the command, so it can determine whether to rerun it. It then
calls into "exec" to execute it.
project_dir (Path): Path to project directory.
subcommand (str): Name of command to run.
force (bool): Force re-running, even if nothing changed.
dry (bool): Perform a dry run and don't execute commands.
"""
config = load_project_config(project_dir)
variables = config.get("variables", {})
commands = {cmd["name"]: cmd for cmd in config.get("commands", [])}
workflows = config.get("workflows", {})
validate_subcommand(commands.keys(), workflows.keys(), subcommand)
if subcommand in workflows:
msg.info(f"Running workflow '{subcommand}'")
for cmd in workflows[subcommand]:
project_run(project_dir, cmd, force=force, dry=dry)
else:
cmd = commands[subcommand]
variables = config.get("variables", {})
for dep in cmd.get("deps", []):
dep = dep.format(**variables)
if not (project_dir / dep).exists():
err = f"Missing dependency specified by command '{subcommand}': {dep}"
err_kwargs = {"exits": 1} if not dry else {}
msg.fail(err, **err_kwargs)
with working_dir(project_dir) as current_dir:
rerun = check_rerun(current_dir, cmd, variables)
if not rerun and not force:
msg.info(f"Skipping '{cmd['name']}': nothing changed")
else:
msg.divider(subcommand)
run_commands(cmd["script"], variables, dry=dry)
update_lockfile(current_dir, cmd, variables)
def print_run_help(project_dir: Path, subcommand: Optional[str] = None) -> None:
"""Simulate a CLI help prompt using the info available in the project.yml.
project_dir (Path): The project directory.
subcommand (Optional[str]): The subcommand or None. If a subcommand is
provided, the subcommand help is shown. Otherwise, the top-level help
and a list of available commands is printed.
"""
config = load_project_config(project_dir)
config_commands = config.get("commands", [])
commands = {cmd["name"]: cmd for cmd in config_commands}
project_loc = "" if is_cwd(project_dir) else project_dir
if subcommand:
validate_subcommand(commands.keys(), subcommand)
print(f"Usage: {COMMAND} project run {subcommand} {project_loc}")
help_text = commands[subcommand].get("help")
if help_text:
msg.text(f"\n{help_text}\n")
else:
print(f"\nAvailable commands in {PROJECT_FILE}")
print(f"Usage: {COMMAND} project run [COMMAND] {project_loc}")
msg.table([(cmd["name"], cmd.get("help", "")) for cmd in config_commands])
msg.text(f"Run all commands defined in the 'run' block of the {PROJECT_FILE}:")
print(f"{COMMAND} project run {project_loc}")
def run_commands(
commands: List[str] = tuple(),
variables: Dict[str, Any] = {},
silent: bool = False,
dry: bool = False,
) -> None:
"""Run a sequence of commands in a subprocess, in order.
commands (List[str]): The string commands.
variables (Dict[str, Any]): Dictionary of variable names, mapped to their
values. Will be used to substitute format string variables in the
commands.
silent (bool): Don't print the commands.
dry (bool): Perform a dry run and don't execut anything.
"""
for command in commands:
# Substitute variables, e.g. "./{NAME}.json"
command = command.format(**variables)
command = split_command(command)
# Not sure if this is needed or a good idea. Motivation: users may often
# use commands in their config that reference "python" and we want to
# make sure that it's always executing the same Python that spaCy is
# executed with and the pip in the same env, not some other Python/pip.
# Also ensures cross-compatibility if user 1 writes "python3" (because
# that's how it's set up on their system), and user 2 without the
# shortcut tries to re-run the command.
if len(command) and command[0] in ("python", "python3"):
command[0] = sys.executable
elif len(command) and command[0] in ("pip", "pip3"):
command = [sys.executable, "-m", "pip", *command[1:]]
if not silent:
print(f"Running command: {join_command(command)}")
if not dry:
run_command(command)
def validate_subcommand(
commands: Sequence[str], workflows: Sequence[str], subcommand: str
) -> None:
"""Check that a subcommand is valid and defined. Raises an error otherwise.
commands (Sequence[str]): The available commands.
subcommand (str): The subcommand.
"""
if not commands and not workflows:
msg.fail(f"No commands or workflows defined in {PROJECT_FILE}", exits=1)
if subcommand not in commands and subcommand not in workflows:
help_msg = []
if commands:
help_msg.append(f"Available commands: {', '.join(commands)}")
if workflows:
help_msg.append(f"Available workflows: {', '.join(workflows)}")
msg.fail(
f"Can't find command or workflow '{subcommand}' in {PROJECT_FILE}",
". ".join(help_msg),
exits=1,
)
def check_rerun(
project_dir: Path, command: Dict[str, Any], variables: Dict[str, Any]
) -> bool:
"""Check if a command should be rerun because its settings or inputs/outputs
changed.
project_dir (Path): The current project directory.
command (Dict[str, Any]): The command, as defined in the project.yml.
variables (Dict[str, Any]): The variables defined in the project.yml.
RETURNS (bool): Whether to re-run the command.
"""
lock_path = project_dir / PROJECT_LOCK
if not lock_path.exists(): # We don't have a lockfile, run command
return True
data = srsly.read_yaml(lock_path)
if command["name"] not in data: # We don't have info about this command
return True
entry = data[command["name"]]
# If the entry in the lockfile matches the lockfile entry that would be
# generated from the current command, we don't rerun because it means that
# all inputs/outputs, hashes and scripts are the same and nothing changed
return get_hash(get_lock_entry(project_dir, command, variables)) != get_hash(entry)
def update_lockfile(
project_dir: Path, command: Dict[str, Any], variables: Dict[str, Any]
) -> None:
"""Update the lockfile after running a command. Will create a lockfile if
it doesn't yet exist and will add an entry for the current command, its
script and dependencies/outputs.
project_dir (Path): The current project directory.
command (Dict[str, Any]): The command, as defined in the project.yml.
variables (Dict[str, Any]): The variables defined in the project.yml.
"""
lock_path = project_dir / PROJECT_LOCK
if not lock_path.exists():
srsly.write_yaml(lock_path, {})
data = {}
else:
data = srsly.read_yaml(lock_path)
data[command["name"]] = get_lock_entry(project_dir, command, variables)
srsly.write_yaml(lock_path, data)
def get_lock_entry(
project_dir: Path, command: Dict[str, Any], variables: Dict[str, Any]
) -> Dict[str, Any]:
"""Get a lockfile entry for a given command. An entry includes the command,
the script (command steps) and a list of dependencies and outputs with
their paths and file hashes, if available. The format is based on the
dvc.lock files, to keep things consistent.
project_dir (Path): The current project directory.
command (Dict[str, Any]): The command, as defined in the project.yml.
variables (Dict[str, Any]): The variables defined in the project.yml.
RETURNS (Dict[str, Any]): The lockfile entry.
"""
deps = get_fileinfo(project_dir, command.get("deps", []), variables)
outs = get_fileinfo(project_dir, command.get("outputs", []), variables)
outs_nc = get_fileinfo(project_dir, command.get("outputs_no_cache", []), variables)
return {
"cmd": f"{COMMAND} run {command['name']}",
"script": command["script"],
"deps": deps,
"outs": [*outs, *outs_nc],
}
def get_fileinfo(
project_dir: Path, paths: List[str], variables: Dict[str, Any]
) -> List[Dict[str, str]]:
"""Generate the file information for a list of paths (dependencies, outputs).
Includes the file path and the file's checksum.
project_dir (Path): The current project directory.
paths (List[str]): The file paths.
variables (Dict[str, Any]): The variables defined in the project.yml.
RETURNS (List[Dict[str, str]]): The lockfile entry for a file.
"""
data = []
for path in paths:
path = path.format(**variables)
file_path = project_dir / path
md5 = get_checksum(file_path) if file_path.exists() else None
data.append({"path": path, "md5": md5})
return data

57
spacy/cli/project/util.py Normal file
View File

@ -0,0 +1,57 @@
from typing import Dict, Any
from pathlib import Path
from wasabi import msg
import srsly
from ...schemas import ProjectConfigSchema, validate
PROJECT_FILE = "project.yml"
PROJECT_LOCK = "project.lock"
def load_project_config(path: Path) -> Dict[str, Any]:
"""Load the project.yml file from a directory and validate it.
path (Path): The path to the project directory.
RETURNS (Dict[str, Any]): The loaded project.yml.
"""
config_path = path / PROJECT_FILE
if not config_path.exists():
msg.fail(f"Can't find {PROJECT_FILE}", config_path, exits=1)
invalid_err = f"Invalid {PROJECT_FILE}. Double-check that the YAML is correct."
try:
config = srsly.read_yaml(config_path)
except ValueError as e:
msg.fail(invalid_err, e, exits=1)
errors = validate(ProjectConfigSchema, config)
if errors:
msg.fail(invalid_err, "\n".join(errors), exits=1)
validate_project_commands(config)
return config
def validate_project_commands(config: Dict[str, Any]) -> None:
"""Check that project commands and workflows are valid, don't contain
duplicates, don't clash and only refer to commands that exist.
config (Dict[str, Any]): The loaded config.
"""
command_names = [cmd["name"] for cmd in config.get("commands", [])]
workflows = config.get("workflows", {})
duplicates = set([cmd for cmd in command_names if command_names.count(cmd) > 1])
if duplicates:
err = f"Duplicate commands defined in {PROJECT_FILE}: {', '.join(duplicates)}"
msg.fail(err, exits=1)
for workflow_name, workflow_steps in workflows.items():
if workflow_name in command_names:
err = f"Can't use workflow name '{workflow_name}': name already exists as a command"
msg.fail(err, exits=1)
for step in workflow_steps:
if step not in command_names:
msg.fail(
f"Unknown command specified in workflow '{workflow_name}': {step}",
f"Workflows can only refer to commands defined in the 'commands' "
f"section of the {PROJECT_FILE}.",
exits=1,
)

13
spacy/pipeline/pipes.pyx
View File

@ -523,7 +523,18 @@ class SentenceRecognizer(Tagger):
def get_loss(self, examples, scores):
labels = self.labels
loss_func = SequenceCategoricalCrossentropy(names=labels, normalize=False)
truths = [[labels[x] for x in eg.get_aligned("sent_start")] for eg in examples]
truths = []
for eg in examples:
eg_truth = []
for x in eg.get_aligned("sent_start"):
if x == None:
eg_truth.append(None)
elif x == 1:
eg_truth.append(labels[1])
else:
# anything other than 1: 0, -1, -1 as uint64
eg_truth.append(labels[0])
truths.append(eg_truth)
d_scores, loss = loss_func(scores, truths)
if self.model.ops.xp.isnan(loss):
raise ValueError("nan value when computing loss")

2
spacy/schemas.py
View File

@ -246,7 +246,7 @@ class ProjectConfigSchema(BaseModel):
# fmt: off
variables: Dict[StrictStr, Union[str, int, float, bool]] = Field({}, title="Optional variables to substitute in commands")
assets: List[ProjectConfigAsset] = Field([], title="Data assets")
run: List[StrictStr] = Field([], title="Names of project commands to execute, in order")
workflows: Dict[StrictStr, List[StrictStr]] = Field({}, title="Named workflows, mapped to list of project commands to run in order")
commands: List[ProjectConfigCommand] = Field([], title="Project command shortucts")
# fmt: on

5
spacy/tests/pipeline/test_senter.py
View File

@ -38,6 +38,11 @@ def test_overfitting_IO():
train_examples = []
for t in TRAIN_DATA:
train_examples.append(Example.from_dict(nlp.make_doc(t[0]), t[1]))
# add some cases where SENT_START == -1
train_examples[0].reference[10].is_sent_start = False
train_examples[1].reference[1].is_sent_start = False
train_examples[1].reference[11].is_sent_start = False
nlp.add_pipe(senter)
optimizer = nlp.begin_training()

31
spacy/tests/test_projects.py Normal file
View File

@ -0,0 +1,31 @@
import pytest
from spacy.cli.project.util import validate_project_commands
from spacy.schemas import ProjectConfigSchema, validate
@pytest.mark.parametrize(
"config",
[
{"commands": [{"name": "a"}, {"name": "a"}]},
{"commands": [{"name": "a"}], "workflows": {"a": []}},
{"commands": [{"name": "a"}], "workflows": {"b": ["c"]}},
],
)
def test_project_config_validation1(config):
with pytest.raises(SystemExit):
validate_project_commands(config)
@pytest.mark.parametrize(
"config,n_errors",
[
({"commands": {"a": []}}, 1),
({"commands": [{"help": "..."}]}, 1),
({"commands": [{"name": "a", "extra": "b"}]}, 1),
({"commands": [{"extra": "b"}]}, 2),
({"commands": [{"name": "a", "deps": [123]}]}, 1),
],
)
def test_project_config_validation2(config, n_errors):
errors = validate(ProjectConfigSchema, config)
assert len(errors) == n_errors

19
spacy/util.py
View File

@ -449,6 +449,16 @@ def split_command(command: str) -> List[str]:
return shlex.split(command, posix=not is_windows)
def join_command(command: List[str]) -> str:
"""Join a command using shlex. shlex.join is only available for Python 3.8+,
so we're using a workaround here.
command (List[str]): The command to join.
RETURNS (str): The joined command
"""
return " ".join(shlex.quote(cmd) for cmd in command)
def run_command(command: Union[str, List[str]]) -> None:
"""Run a command on the command line as a subprocess. If the subprocess
returns a non-zero exit code, a system exit is performed.
@ -520,6 +530,15 @@ def get_checksum(path: Union[Path, str]) -> str:
return hashlib.md5(Path(path).read_bytes()).hexdigest()
def is_cwd(path: Union[Path, str]) -> bool:
"""Check whether a path is the current working directory.
path (Union[Path, str]): The directory path.
RETURNS (bool): Whether the path is the current working directory.
"""
return str(Path(path).resolve()).lower() == str(Path.cwd().resolve()).lower()
def is_in_jupyter():
"""Check if user is running spaCy from a Jupyter notebook by detecting the
IPython kernel. Mainly used for the displaCy visualizer.