Various small tweaks to project CLI (#5965)

* Fix up/download of http and local paths

* Support git_sparse_checkout for assets

* Fix scorer

* Handle already-present directories for git assets

* Improve convert command

* Fix support for existant files in git assets

* Support branches in git sparse checkout

* Format

* Fix git assets

* Document git block in assets

* Fix test

* Fix test

* Revert "Fix test"

This reverts commit cf3097260f.

* Revert "Fix test"

This reverts commit 964d636e27.

* Dont multiply p/r/f by 100

* Display scores * 100 during training

spacy/cli/_util.py

@@ -1,5 +1,6 @@
 from typing import Dict, Any, Union, List, Optional, TYPE_CHECKING
 import sys
+import shutil
 from pathlib import Path
 from wasabi import msg
 import srsly
@@ -11,7 +12,7 @@ from thinc.config import Config, ConfigValidationError
 from configparser import InterpolationError
 
 from ..schemas import ProjectConfigSchema, validate
-from ..util import import_file
+from ..util import import_file, run_command, make_tempdir
 
 if TYPE_CHECKING:
     from pathy import Pathy  # noqa: F401
@@ -260,6 +261,19 @@ def upload_file(src: Path, dest: Union[str, "Pathy"]) -> None:
     src (Path): The source path.
     url (str): The destination URL to upload to.
     """
+    import smart_open
+
+    # This logic is pretty hacky. We'd like pathy to do this probably?
+    if ":/" not in str(dest):
+        # Local path
+        with Path(dest).open(mode="wb") as output_file:
+            with src.open(mode="rb") as input_file:
+                output_file.write(input_file.read())
+    elif str(dest).startswith("http") or str(dest).startswith("https"):
+        with smart_open.open(str(dest), mode="wb") as output_file:
+            with src.open(mode="rb") as input_file:
+                output_file.write(input_file.read())
+    else:
         dest = ensure_pathy(dest)
         with dest.open(mode="wb") as output_file:
             with src.open(mode="rb") as input_file:
@@ -274,8 +288,20 @@ def download_file(src: Union[str, "Pathy"], dest: Path, *, force: bool = False)
     force (bool): Whether to force download even if file exists.
         If False, the download will be skipped.
     """
+    import smart_open
+
+    # This logic is pretty hacky. We'd like pathy to do this probably?
     if dest.exists() and not force:
         return None
+    if src.startswith("http"):
+        with smart_open.open(src, mode="rb") as input_file:
+            with dest.open(mode="wb") as output_file:
+                output_file.write(input_file.read())
+    elif ":/" not in src:
+        with open(src, mode="rb") as input_file:
+            with dest.open(mode="wb") as output_file:
+                output_file.write(input_file.read())
+    else:
         src = ensure_pathy(src)
         with src.open(mode="rb") as input_file:
             with dest.open(mode="wb") as output_file:
@@ -288,3 +314,29 @@ def ensure_pathy(path):
     from pathy import Pathy  # noqa: F811
 
     return Pathy(path)
+
+
+def git_sparse_checkout(
+    repo: str, subpath: str, dest: Path, *, branch: Optional[str] = None
+):
+    if dest.exists():
+        raise IOError("Destination of checkout must not exist")
+    if not dest.parent.exists():
+        raise IOError("Parent of destination of checkout must exist")
+    # 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"
+        )
+        if branch is not None:
+            cmd = f"{cmd} -b {branch}"
+        run_command(cmd)
+        with (tmp_dir / ".git" / "info" / "sparse-checkout").open("w") as f:
+            f.write(subpath)
+        run_command(["git", "-C", str(tmp_dir), "fetch"])
+        run_command(["git", "-C", str(tmp_dir), "checkout"])
+        # We need Path(name) to make sure we also support subdirectories
+        shutil.move(str(tmp_dir / Path(subpath)), str(dest))
+        print(dest)
+        print(list(dest.iterdir()))

spacy/cli/convert.py

@@ -50,6 +50,7 @@ def convert_cli(
     converter: str = Opt("auto", "--converter", "-c", help=f"Converter: {tuple(CONVERTERS.keys())}"),
     ner_map: Optional[Path] = Opt(None, "--ner-map", "-nm", help="NER tag mapping (as JSON-encoded dict of entity types)", exists=True),
     lang: Optional[str] = Opt(None, "--lang", "-l", help="Language (if tokenizer required)"),
+    concatenate: bool = Opt(None, "--concatenate", "-C", help="Concatenate output to a single file"),
     # fmt: on
 ):
     """
@@ -82,6 +83,7 @@ def convert_cli(
         converter=converter,
         ner_map=ner_map,
         lang=lang,
+        concatenate=concatenate,
         silent=silent,
         msg=msg,
     )
@@ -100,13 +102,15 @@ def convert(
     converter: str = "auto",
     ner_map: Optional[Path] = None,
     lang: Optional[str] = None,
+    concatenate: bool = False,
     silent: bool = True,
     msg: Optional[Printer],
 ) -> None:
     if not msg:
         msg = Printer(no_print=silent)
     ner_map = srsly.read_json(ner_map) if ner_map is not None else None
-    for input_loc in walk_directory(Path(input_path)):
+    doc_files = []
+    for input_loc in walk_directory(Path(input_path), converter):
         input_data = input_loc.open("r", encoding="utf-8").read()
         # Use converter function to convert data
         func = CONVERTERS[converter]
@@ -121,6 +125,13 @@ def convert(
             no_print=silent,
             ner_map=ner_map,
         )
+        doc_files.append((input_loc, docs))
+    if concatenate:
+        all_docs = []
+        for _, docs in doc_files:
+            all_docs.extend(docs)
+        doc_files = [(input_path, all_docs)]
+    for input_loc, docs in doc_files:
         if file_type == "json":
             data = [docs_to_json(docs)]
         else:
@@ -174,7 +185,7 @@ def autodetect_ner_format(input_data: str) -> Optional[str]:
     return None
 
 
-def walk_directory(path: Path) -> List[Path]:
+def walk_directory(path: Path, converter: str) -> List[Path]:
     if not path.is_dir():
         return [path]
     paths = [path]
@@ -188,6 +199,12 @@ def walk_directory(path: Path) -> List[Path]:
             continue
         elif path.is_dir():
             paths.extend(path.iterdir())
+        elif converter == "json" and not path.parts[-1].endswith("json"):
+            continue
+        elif converter == "conll" and not path.parts[-1].endswith("conll"):
+            continue
+        elif converter == "iob" and not path.parts[-1].endswith("iob"):
+            continue
         else:
             locs.append(path)
     return locs
@@ -214,11 +231,11 @@ def verify_cli_args(
     if ner_map is not None and not Path(ner_map).exists():
         msg.fail("NER map not found", ner_map, exits=1)
     if input_path.is_dir():
-        input_locs = walk_directory(input_path)
+        input_locs = walk_directory(input_path, converter)
         if len(input_locs) == 0:
             msg.fail("No input files in directory", input_path, exits=1)
         file_types = list(set([loc.suffix[1:] for loc in input_locs]))
-        if len(file_types) >= 2:
+        if converter == "auto" and len(file_types) >= 2:
             file_types = ",".join(file_types)
             msg.fail("All input files must be same type", file_types, exits=1)
     if converter != "auto" and converter not in CONVERTERS:
@@ -227,7 +244,7 @@ def verify_cli_args(
 
 def _get_converter(msg, converter, input_path):
     if input_path.is_dir():
-        input_path = walk_directory(input_path)[0]
+        input_path = walk_directory(input_path, converter)[0]
     if converter == "auto":
         converter = input_path.suffix[1:]
     if converter == "ner" or converter == "iob":

spacy/cli/project/assets.py

@@ -7,7 +7,7 @@ import requests
 
 from ...util import ensure_path, working_dir
 from .._util import project_cli, Arg, PROJECT_FILE, load_project_config, get_checksum
-from .._util import download_file
+from .._util import download_file, git_sparse_checkout
 
 
 # TODO: find a solution for caches
@@ -45,9 +45,24 @@ def project_assets(project_dir: Path) -> None:
         msg.warn(f"No assets specified in {PROJECT_FILE}", exits=0)
     msg.info(f"Fetching {len(assets)} asset(s)")
     for asset in assets:
-        dest = asset["dest"]
+        dest = Path(asset["dest"])
-        url = asset.get("url")
         checksum = asset.get("checksum")
+        if "git" in asset:
+            if dest.exists():
+                # If there's already a file, check for checksum
+                if checksum and checksum == get_checksum(dest):
+                    msg.good(f"Skipping download with matching checksum: {dest}")
+                    continue
+                else:
+                    shutil.rmtree(dest)
+            git_sparse_checkout(
+                asset["git"]["repo"],
+                asset["git"]["path"],
+                dest,
+                branch=asset["git"].get("branch"),
+            )
+        else:
+            url = asset.get("url")
             if not url:
                 # project.yml defines asset without URL that the user has to place
                 check_private_asset(dest, checksum)

spacy/cli/project/clone.py

@@ -6,8 +6,9 @@ import shutil
 import re
 
 from ... import about
-from ...util import ensure_path, run_command, make_tempdir
+from ...util import ensure_path
 from .._util import project_cli, Arg, Opt, COMMAND, PROJECT_FILE
+from .._util import git_sparse_checkout
 
 
 @project_cli.command("clone")
@@ -39,24 +40,11 @@ def project_clone(name: str, dest: Path, *, repo: str = about.__projects__) -> N
     check_clone(name, dest, repo)
     project_dir = dest.resolve()
     repo_name = re.sub(r"(http(s?)):\/\/github.com/", "", repo)
-    # 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)
+        git_sparse_checkout(repo, name, dest)
-        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}' from repo '{repo_name}'"
         msg.fail(err)
-        # We need Path(name) to make sure we also support subdirectories
-        shutil.move(str(tmp_dir / Path(name)), str(project_dir))
     msg.good(f"Cloned '{name}' from {repo_name}", project_dir)
     if not (project_dir / PROJECT_FILE).exists():
         msg.warn(f"No {PROJECT_FILE} found in directory")

spacy/cli/train.py

@@ -382,7 +382,7 @@ def setup_printer(
 
         try:
             scores = [
-                "{0:.2f}".format(float(info["other_scores"].get(col, 0.0)))
+                "{0:.2f}".format(float(info["other_scores"].get(col, 0.0)) * 100)
                 for col in score_cols
             ]
         except KeyError as e:

spacy/scorer.py

@@ -30,17 +30,17 @@ class PRFScore:
 
     @property
     def precision(self) -> float:
-        return (self.tp / (self.tp + self.fp + 1e-100)) * 100
+        return (self.tp / (self.tp + self.fp + 1e-100))
 
     @property
     def recall(self) -> float:
-        return (self.tp / (self.tp + self.fn + 1e-100)) * 100
+        return (self.tp / (self.tp + self.fn + 1e-100))
 
     @property
     def fscore(self) -> float:
         p = self.precision
         r = self.recall
-        return (2 * ((p * r) / (p + r + 1e-100))) * 100
+        return 2 * ((p * r) / (p + r + 1e-100))
 
     def to_dict(self) -> Dict[str, float]:
         return {"p": self.precision, "r": self.recall, "f": self.fscore}

website/docs/usage/projects.md

@@ -102,6 +102,25 @@ $ cd some_example_project
 $ python -m spacy project assets
 ```
 
+Asset URLs can be a number of different protocols: HTTP, HTTPS, FTP, SSH, and
+even cloud storage such as GCS and S3. You can also fetch assets using git, by
+replacing the `url` string with a `git` block, like this:
+
+> #### project.yml
+>
+> ```yaml
+> assets:
+>   - dest: 'assets/training.spacy'
+>     git: 
+>       repo: "https://github.com/example/repo"
+>       branch: "master"
+>       path: "some/path"
+>     checksum: '63373dd656daa1fd3043ce166a59474c'
+> ```
+
+spaCy will use Git's "sparse checkout" feature, to avoid download the whole
+repository.
+
 ### 3. Run a command {#run}
 
 > #### project.yml