Fix flag handling in dvc

Prior to this commit, if a flag (--verbose or --quiet) was passed to
DVC, it would be added to the end of the generated dvc command line.
This would result in the command being interpreted as part of the actual
command to run, rather than an argument to dvc. This would result in
command lines like:

    spacy project run preprocess --verbose

That would fail with an error that there's no such directory as
`--verbose`.

This change puts the flags at the front of the dvc command so that they
are interpreted correctly. It removes the `run_dvc_commands` function,
which had been reduced to just a for loop and wasn't used elsewhere.

A separate problem is that there's no way to specify the quiet behaviour
to dvc from the command line, though it's unclear if that's a bug.

spacy/cli/project/dvc.py

@@ -105,6 +105,14 @@ def update_dvc_config(
         dvc_config_path.unlink()
     dvc_commands = []
     config_commands = {cmd["name"]: cmd for cmd in config.get("commands", [])}
+
+    # some flags that apply to every command
+    flags = []
+    if verbose:
+        flags.append("--verbose")
+    if silent:
+        flags.append("--quiet")
+
     for name in workflows[workflow]:
         command = config_commands[name]
         deps = command.get("deps", [])
@@ -118,14 +126,16 @@ def update_dvc_config(
         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"]
+
+        dvc_cmd = ["run", *flags, "-n", name, "-w", str(path), "--no-exec"]
         if command.get("no_skip"):
             dvc_cmd.append("--always-changed")
         full_cmd = [*dvc_cmd, *deps_cmd, *outputs_cmd, *outputs_nc_cmd, *project_cmd]
         dvc_commands.append(full_cmd)
     with working_dir(path):
-        dvc_flags = {"--verbose": verbose, "--quiet": silent}
+        for c in dvc_commands:
-        run_dvc_commands(dvc_commands, flags=dvc_flags)
+            dvc_command = ["dvc", *c]
+            run_command(dvc_command)
     with dvc_config_path.open("r+", encoding="utf8") as f:
         content = f.read()
         f.seek(0, 0)
@@ -133,25 +143,6 @@ def update_dvc_config(
     return True
 
 
-def run_dvc_commands(
-    commands: Iterable[List[str]] = SimpleFrozenList(), flags: Dict[str, bool] = {}
-) -> None:
-    """Run a sequence of DVC commands in a subprocess, in order.
-
-    commands (List[List[str]]): The string commands 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.
-    """
-    for c in commands:
-        dvc_command = ["dvc", *c]
-        # 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.