calkit-python 0.0.4__tar.gz → 0.0.5__tar.gz

{calkit_python-0.0.4 → calkit_python-0.0.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: calkit-python
-Version: 0.0.4
+Version: 0.0.5
 Summary: Reproducibility simplified.
 Project-URL: Homepage, https://github.com/calkit/calkit
 Project-URL: Issues, https://github.com/calkit/calkit/issues

{calkit_python-0.0.4 → calkit_python-0.0.5}/calkit/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "0.0.4"
+__version__ = "0.0.5"
 
 from .core import *
 from . import git

{calkit_python-0.0.4 → calkit_python-0.0.5}/calkit/cli.py

@@ -11,16 +11,37 @@ import git
 import typer
 from typing_extensions import Annotated, Optional
 
+import calkit
 from calkit.core import ryaml
 
 from . import config
 from .dvc import configure_remote, set_remote_auth
 
-app = typer.Typer()
-config_app = typer.Typer()
-new_app = typer.Typer()
+app = typer.Typer(
+    invoke_without_command=True,
+    no_args_is_help=True,
+    context_settings=dict(help_option_names=["-h", "--help"]),
+)
+config_app = typer.Typer(no_args_is_help=True)
+new_app = typer.Typer(no_args_is_help=True)
+notebooks_app = typer.Typer(no_args_is_help=True)
 app.add_typer(config_app, name="config", help="Configure Calkit.")
-app.add_typer(new_app, name="new", help="Add new Calkit object.")
+app.add_typer(
+    new_app, name="new", help="Add new Calkit object (to calkit.yaml)."
+)
+app.add_typer(notebooks_app, name="nb", help="Work with Jupyter notebooks.")
+
+
+@app.callback()
+def main(
+    version: Annotated[
+        bool,
+        typer.Option("--version", help="Show version and exit."),
+    ] = False,
+):
+    if version:
+        typer.echo(calkit.__version__)
+        raise typer.Exit()
 
 
 @config_app.command(name="set")
@@ -135,7 +156,7 @@ def new_figure(
     description: Annotated[str, typer.Option("--desc")] = None,
     commit: Annotated[bool, typer.Option("--commit")] = False,
 ):
-    """Add a new figure to ``calkit.yaml``."""
+    """Add a new figure."""
     if os.path.isfile("calkit.yaml"):
         with open("calkit.yaml") as f:
             ck_info = ryaml.load(f)
@@ -163,6 +184,7 @@ def new_question(
     question: str,
     commit: Annotated[bool, typer.Option("--commit")] = False,
 ):
+    """Add a new question."""
     if os.path.isfile("calkit.yaml"):
         with open("calkit.yaml") as f:
             ck_info = ryaml.load(f)
@@ -183,6 +205,96 @@ def new_question(
         repo.git.commit(["-m", "Add question"])
 
 
+@new_app.command("notebook")
+def new_notebook(
+    path: Annotated[str, typer.Argument(help="Notebook path (relative)")],
+    title: Annotated[str, typer.Option("--title")],
+    description: Annotated[str, typer.Option("--desc")] = None,
+    commit: Annotated[bool, typer.Option("--commit")] = False,
+):
+    """Add a new notebook."""
+    if os.path.isabs(path):
+        raise ValueError("Path must be relative")
+    if not os.path.isfile(path):
+        raise ValueError("Path is not a file")
+    if not path.endswith(".ipynb"):
+        raise ValueError("Path does not have .ipynb extension")
+    # TODO: Add option to create stages that run `calkit nb clean` and
+    # `calkit nb execute`
+    if os.path.isfile("calkit.yaml"):
+        with open("calkit.yaml") as f:
+            ck_info = ryaml.load(f)
+    else:
+        ck_info = {}
+    notebooks = ck_info.get("notebooks", [])
+    paths = [f.get("path") for f in notebooks]
+    if path in paths:
+        raise ValueError(f"Notebook at path {path} already exists")
+    obj = dict(path=path, title=title)
+    if description is not None:
+        obj["description"] = description
+    notebooks.append(obj)
+    ck_info["notebooks"] = notebooks
+    with open("calkit.yaml", "w") as f:
+        ryaml.dump(ck_info, f)
+    if commit:
+        repo = git.Repo()
+        repo.git.add("calkit.yaml")
+        repo.git.commit(["-m", f"Add notebook {path}"])
+
+
+@notebooks_app.command("clean")
+def clean_notebook_outputs(path: str):
+    """Clean notebook and place a copy in the cleaned notebooks directory.
+
+    This can be useful to use as a preprocessing DVC stage to use a clean
+    notebook as a dependency for a stage that caches and executed notebook.
+    """
+    if os.path.isabs(path):
+        raise ValueError("Path must be relative")
+    fpath_out = os.path.join(".calkit", "notebooks", "cleaned", path)
+    folder = os.path.dirname(fpath_out)
+    os.makedirs(folder, exist_ok=True)
+    subprocess.call(
+        [
+            "jupyter",
+            "nbconvert",
+            path,
+            "--clear-output",
+            "--to",
+            "notebook",
+            "--output",
+            fpath_out,
+        ]
+    )
+
+
+@notebooks_app.command("execute")
+def execute_notebook(path: str):
+    """Execute notebook and place a copy in the executed notebooks directory.
+
+    This can be useful to use as a preprocessing DVC stage to use a clean
+    notebook as a dependency for a stage that caches and executed notebook.
+    """
+    if os.path.isabs(path):
+        raise ValueError("Path must be relative")
+    fpath_out = os.path.join(".calkit", "notebooks", "executed", path)
+    folder = os.path.dirname(fpath_out)
+    os.makedirs(folder, exist_ok=True)
+    subprocess.call(
+        [
+            "jupyter",
+            "nbconvert",
+            path,
+            "--execute",
+            "--to",
+            "notebook",
+            "--output",
+            fpath_out,
+        ]
+    )
+
+
 @app.command(name="server", help="Run the local server.")
 def run_server():
     import uvicorn