calkit-python 0.0.5__tar.gz → 0.0.7__tar.gz

{calkit_python-0.0.5 → calkit_python-0.0.7}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: calkit-python
-Version: 0.0.5
+Version: 0.0.7
 Summary: Reproducibility simplified.
 Project-URL: Homepage, https://github.com/calkit/calkit
 Project-URL: Issues, https://github.com/calkit/calkit/issues

{calkit_python-0.0.5 → calkit_python-0.0.7}/calkit/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "0.0.5"
+__version__ = "0.0.7"
 
 from .core import *
 from . import git

{calkit_python-0.0.5 → calkit_python-0.0.7}/calkit/cli.py

@@ -21,6 +21,7 @@ app = typer.Typer(
     invoke_without_command=True,
     no_args_is_help=True,
     context_settings=dict(help_option_names=["-h", "--help"]),
+    pretty_exceptions_show_locals=False,
 )
 config_app = typer.Typer(no_args_is_help=True)
 new_app = typer.Typer(no_args_is_help=True)
@@ -104,33 +105,108 @@ def get_status():
 
 
 @app.command(name="add")
-def add(paths: list[str]):
+def add(
+    paths: list[str],
+    commit_message: Annotated[
+        str,
+        typer.Option(
+            "-m",
+            "--commit-message",
+            help="Automatically commit and use this as a message.",
+        ),
+    ] = None,
+    push_commit: Annotated[
+        bool, typer.Option("--push", help="Push after committing.")
+    ] = False,
+    to: Annotated[
+        str,
+        typer.Option(
+            "--to", "-t", help="System with which to add (git or dvc)."
+        ),
+    ] = None,
+):
     """Add paths to the repo.
 
     Code will be added to Git and data will be added to DVC.
+
+    Note: This will enable the 'autostage' feature of DVC, automatically
+    adding any .dvc files to Git when adding to DVC.
     """
-    dvc_extensions = [".png", ".h5", ".parquet", ".pickle"]
-    dvc_size_thresh_bytes = 1_000_000
-    dvc_folders = ["data", "figures"]
-    if "." in paths:
-        print("ERROR: Cannot add '.' with calkit; use git or dvc")
-        sys.exit(1)
-    for path in paths:
-        if os.path.isdir(path):
-            print("ERROR: Cannot add directories with calkit; use git or dvc")
-            sys.exit(1)
-        # Detect if this file should be tracked with Git or DVC
-        # TODO: Add to whatever
+    if to is not None and to not in ["git", "dvc"]:
+        typer.echo(f"Invalid option for 'to': {to}")
+        raise typer.Exit(1)
+    # Ensure autostage is enabled for DVC
+    subprocess.call(["dvc", "config", "core.autostage", "true"])
+    subprocess.call(["git", "add", ".dvc/config"])
+    if to is not None:
+        subprocess.call([to, "add"] + paths)
+    else:
+        dvc_extensions = [
+            ".png",
+            ".h5",
+            ".parquet",
+            ".pickle",
+            ".mp4",
+            ".avi",
+            ".webm",
+            ".pdf",
+        ]
+        dvc_size_thresh_bytes = 1_000_000
+        if "." in paths and to is None:
+            typer.echo("Cannot add '.' with calkit; use git or dvc")
+            raise typer.Exit(1)
+        if to is None:
+            for path in paths:
+                if os.path.isdir(path):
+                    typer.echo("Cannot auto-add directories; use git or dvc")
+                    raise typer.Exit(1)
+        for path in paths:
+            # Detect if this file should be tracked with Git or DVC
+            if os.path.splitext(path)[-1] in dvc_extensions:
+                typer.echo(f"Adding {path} to DVC per its extension")
+                subprocess.call(["dvc", "add", path])
+                continue
+            if os.path.getsize(path) > dvc_size_thresh_bytes:
+                typer.echo(
+                    f"Adding {path} to DVC since it's greater than 1 MB"
+                )
+                subprocess.call(["dvc", "add", path])
+                continue
+            typer.echo(f"Adding {path} to Git")
+            subprocess.call(["git", "add", path])
+    if commit_message is not None:
+        subprocess.call(["git", "commit", "-m", commit_message])
+    if push_commit:
+        push()
 
 
 @app.command(name="commit")
 def commit(
-    all: Annotated[Optional[bool], typer.Option("--all", "-a")] = False,
-    message: Annotated[Optional[str], typer.Option("--message", "-m")] = None,
+    all: Annotated[
+        Optional[bool],
+        typer.Option(
+            "--all", "-a", help="Automatically stage all changed files."
+        ),
+    ] = False,
+    message: Annotated[
+        Optional[str], typer.Option("--message", "-m", help="Commit message.")
+    ] = None,
+    push_commit: Annotated[
+        bool,
+        typer.Option(
+            "--push", help="Push to both Git and DVC after committing."
+        ),
+    ] = False,
 ):
     """Commit a change to the repo."""
-    print(all, message)
-    raise NotImplementedError
+    cmd = ["git", "commit"]
+    if all:
+        cmd.append("-a")
+    if message:
+        cmd += ["-m", message]
+    subprocess.call(cmd)
+    if push_commit:
+        push()
 
 
 @app.command(name="pull", help="Pull with both Git and DVC.")
@@ -270,15 +346,28 @@ def clean_notebook_outputs(path: str):
 
 
 @notebooks_app.command("execute")
-def execute_notebook(path: str):
-    """Execute notebook and place a copy in the executed notebooks directory.
+def execute_notebook(
+    path: str,
+    to: Annotated[
+        str, typer.Option("--to", help="Output format ('html' or 'notebook').")
+    ] = "notebook",
+):
+    """Execute notebook and place a copy in the relevant 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)
+    if to == "html":
+        subdir = "html"
+        fname_out = path.removesuffix(".ipynb") + ".html"
+    elif to == "notebook":
+        subdir = "executed"
+        fname_out = path
+    else:
+        raise ValueError(f"Invalid output format: '{to}'")
+    fpath_out = os.path.join(".calkit", "notebooks", subdir, fname_out)
     folder = os.path.dirname(fpath_out)
     os.makedirs(folder, exist_ok=True)
     subprocess.call(
@@ -288,7 +377,7 @@ def execute_notebook(path: str):
             path,
             "--execute",
             "--to",
-            "notebook",
+            to,
             "--output",
             fpath_out,
         ]