calkit-python 0.41.12__tar.gz → 0.41.14__tar.gz

{calkit_python-0.41.12 → calkit_python-0.41.14}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: calkit-python
-Version: 0.41.12
+Version: 0.41.14
 Summary: Reproducibility simplified.
 Project-URL: Homepage, https://calkit.org
 Project-URL: Issues, https://github.com/calkit/calkit/issues

calkit_python-0.41.14/calkit/cli/delete.py

@@ -0,0 +1,33 @@
+"""CLI for deleting objects."""
+
+from __future__ import annotations
+
+import typer
+
+import calkit
+from calkit.cli import AliasGroup, raise_error
+from calkit.core import ryaml
+
+delete_app = typer.Typer(cls=AliasGroup, no_args_is_help=True)
+
+
+@delete_app.command(name="question")
+def delete_question(
+    index: int = typer.Argument(
+        ...,
+        help="1-based index of the question to remove (see `calkit list questions`).",
+    ),
+):
+    """Remove a question by its 1-based index."""
+    ck_info = calkit.load_calkit_info()
+    questions = ck_info.get("questions", []) or []
+    if index < 1 or index > len(questions):
+        raise_error(
+            f"Invalid question index {index}; "
+            f"there are {len(questions)} question(s)."
+        )
+    removed = questions.pop(index - 1)
+    ck_info["questions"] = questions
+    with open("calkit.yaml", "w") as f:
+        ryaml.dump(ck_info, f)
+    typer.echo(f"Removed question: {removed}")

{calkit_python-0.41.12 → calkit_python-0.41.14}/calkit/cli/list.py

@@ -55,7 +55,7 @@ def _list_objects(
 
 
 def _list_artifacts(
-    kind: Literal["figures", "datasets"],
+    kind: Literal["figures", "datasets", "results", "presentations"],
     json_output: bool,
     declared_only: bool,
 ):
@@ -134,6 +134,61 @@ def list_datasets(
     _list_artifacts("datasets", json_output, declared_only)
 
 
+@list_app.command(name="results")
+def list_results(
+    json_output: Annotated[
+        bool, typer.Option("--json", help="Output result as JSON.")
+    ] = False,
+    declared_only: Annotated[
+        bool,
+        typer.Option(
+            "--declared-only",
+            help=(
+                "Only list results declared in calkit.yaml; "
+                "skip auto-detection."
+            ),
+        ),
+    ] = False,
+):
+    """List results in the project."""
+    _list_artifacts("results", json_output, declared_only)
+
+
+@list_app.command(name="presentations|pres")
+def list_presentations(
+    json_output: Annotated[
+        bool, typer.Option("--json", help="Output result as JSON.")
+    ] = False,
+    declared_only: Annotated[
+        bool,
+        typer.Option(
+            "--declared-only",
+            help=(
+                "Only list presentations declared in calkit.yaml; "
+                "skip auto-detection."
+            ),
+        ),
+    ] = False,
+):
+    """List presentations in the project."""
+    _list_artifacts("presentations", json_output, declared_only)
+
+
+@list_app.command(name="questions")
+def list_questions(
+    json_output: Annotated[
+        bool, typer.Option("--json", help="Output result as JSON.")
+    ] = False,
+):
+    """List the project's questions (1-indexed)."""
+    questions = calkit.load_calkit_info().get("questions", []) or []
+    if json_output:
+        typer.echo(json.dumps(questions))
+        return
+    for n, question in enumerate(questions, start=1):
+        typer.echo(f"{n}. {question}")
+
+
 @list_app.command(name="publications|pubs")
 def list_publications():
     """List publications in the project."""

{calkit_python-0.41.12 → calkit_python-0.41.14}/calkit/cli/main/core.py

@@ -48,6 +48,7 @@ from calkit.cli.check import (
 )
 from calkit.cli.cloud import cloud_app
 from calkit.cli.config import config_app
+from calkit.cli.delete import delete_app
 from calkit.cli.describe import describe_app
 from calkit.cli.dev import dev_app
 from calkit.cli.import_ import import_app
@@ -69,6 +70,7 @@ app = typer.Typer(
 )
 app.add_typer(config_app, name="config", help="Configure Calkit.")
 app.add_typer(new_app, name="new|create", help="Create a new Calkit object.")
+app.add_typer(delete_app, name="delete|rm", help="Delete a Calkit object.")
 app.add_typer(
     notebooks_app, name="notebooks|nb", help="Work with Jupyter notebooks."
 )
@@ -1172,7 +1174,10 @@ def pull(
         and "-R" not in dvc_args
     ):
         dvc_args.append("--recursive")
-    result = calkit.dvc.run_dvc_command(["pull"] + dvc_args)
+    result = calkit.dvc.run_dvc_command(
+        ["pull"] + dvc_args,
+        lock_timeout=calkit.dvc.DEFAULT_RUN_LOCK_TIMEOUT,
+    )
     if result != 0:
         raise_error("DVC pull failed")
     calkit.dvc.zip.sync_all(direction="to-workspace")
@@ -1187,7 +1192,9 @@ def pull(
                 continue
             typer.echo(f"DVC pulling subproject: {sp_path}")
             sp_result = calkit.dvc.run_dvc_command(
-                ["pull"] + dvc_args, cwd=sp_path
+                ["pull"] + dvc_args,
+                cwd=sp_path,
+                lock_timeout=calkit.dvc.DEFAULT_RUN_LOCK_TIMEOUT,
             )
             if sp_result != 0:
                 raise_error(f"DVC pull failed for subproject: {sp_path}")
@@ -1224,7 +1231,10 @@ def push(
                     calkit.dvc.set_remote_auth(remote_name=name)
         if remotes:
             typer.echo("Pushing to DVC remote")
-            result = calkit.dvc.run_dvc_command(["push"] + dvc_args)
+            result = calkit.dvc.run_dvc_command(
+                ["push"] + dvc_args,
+                lock_timeout=calkit.dvc.DEFAULT_RUN_LOCK_TIMEOUT,
+            )
             if result != 0:
                 raise_error("DVC push failed")
         else:
@@ -2033,7 +2043,10 @@ def run(
             original_dir = os.getcwd()
             try:
                 os.chdir(sp_path)
-                sp_res = dvc_cli_main(["repro"] + sp_args)
+                with calkit.dvc.dvc_lock_timeout(
+                    calkit.dvc.DEFAULT_RUN_LOCK_TIMEOUT
+                ):
+                    sp_res = dvc_cli_main(["repro"] + sp_args)
             finally:
                 os.chdir(original_dir)
             if sp_res != 0:
@@ -2102,7 +2115,15 @@ def run(
     if force:
         os.environ["CALKIT_FORCE"] = "1"
     try:
-        res = dvc_cli_main(["repro"] + args)
+        # Wait generously for the repo lock instead of failing after DVC's 3s
+        # default. Brief contention is common and benign: a background
+        # `calkit status` poller (e.g. the VS Code extension), a stage whose
+        # command is itself `calkit run`, or DVC's own per-stage re-lock (DVC
+        # releases the repo lock while a stage command runs and re-acquires it
+        # the instant it finishes) can all hold it momentarily. Without this,
+        # such a collision aborts the whole run with "Unable to acquire lock".
+        with calkit.dvc.dvc_lock_timeout(calkit.dvc.DEFAULT_RUN_LOCK_TIMEOUT):
+            res = dvc_cli_main(["repro"] + args)
     finally:
         os.environ.pop("CALKIT_FORCE", None)
     failed = failed or res != 0

{calkit_python-0.41.12 → calkit_python-0.41.14}/calkit/cli/new.py

@@ -9,6 +9,7 @@ import shutil
 import subprocess
 import time
 from enum import Enum
+from typing import Literal
 
 import typer
 from typing_extensions import Annotated
@@ -591,6 +592,102 @@ def new_figure(
             repo.git.commit(["-m", f"Add figure {path}"])
 
 
+def _new_simple_artifact(
+    kind: Literal["results", "presentations"],
+    path: str,
+    title: str,
+    description: str | None,
+    stage_name: str | None,
+    no_commit: bool,
+    overwrite: bool,
+) -> None:
+    """Declare a simple artifact (path/title/description/stage) in calkit.yaml."""
+    singular = kind.rstrip("s")
+    ck_info = calkit.load_calkit_info()
+    objects = ck_info.get(kind, [])
+    paths = [o.get("path") for o in objects]
+    if not overwrite and path in paths:
+        raise_error(f"{singular.capitalize()} at path {path} already exists")
+    if overwrite and path in paths:
+        objects = [o for o in objects if o.get("path") != path]
+    obj = dict(path=path, title=title)
+    if description is not None:
+        obj["description"] = description
+    if stage_name is not None:
+        obj["stage"] = stage_name
+    objects.append(obj)
+    ck_info[kind] = objects
+    with open("calkit.yaml", "w") as f:
+        ryaml.dump(ck_info, f)
+    if not no_commit:
+        repo = calkit.git.get_repo()
+        repo.git.add("calkit.yaml")
+        if repo.git.diff("--staged"):
+            repo.git.commit(["-m", f"Add {singular} {path}"])
+
+
+@new_app.command(name="result")
+def new_result(
+    path: str,
+    title: Annotated[str, typer.Option("--title")],
+    description: Annotated[str | None, typer.Option("--description")] = None,
+    stage_name: Annotated[
+        str | None,
+        typer.Option(
+            "--stage",
+            help="Name of the pipeline stage that generates this result.",
+        ),
+    ] = None,
+    no_commit: Annotated[bool, typer.Option("--no-commit")] = False,
+    overwrite: Annotated[
+        bool,
+        typer.Option(
+            "--overwrite",
+            "-f",
+            help="Overwrite existing result if one exists.",
+        ),
+    ] = False,
+):
+    """Declare a new result."""
+    _new_simple_artifact(
+        "results", path, title, description, stage_name, no_commit, overwrite
+    )
+
+
+@new_app.command(name="presentation|pres")
+def new_presentation(
+    path: str,
+    title: Annotated[str, typer.Option("--title")],
+    description: Annotated[str | None, typer.Option("--description")] = None,
+    stage_name: Annotated[
+        str | None,
+        typer.Option(
+            "--stage",
+            help="Name of the pipeline stage that generates this presentation.",
+        ),
+    ] = None,
+    no_commit: Annotated[bool, typer.Option("--no-commit")] = False,
+    overwrite: Annotated[
+        bool,
+        typer.Option(
+            "--overwrite",
+            "-f",
+            help="Overwrite existing presentation if one exists.",
+        ),
+    ] = False,
+):
+    """Declare a new presentation."""
+    _new_simple_artifact(
+        "presentations",
+        path,
+        title,
+        description,
+        stage_name,
+        no_commit,
+        overwrite,
+    )
+
+
 @new_app.command("question")
 def new_question(
     question: str,