calkit-python 0.0.3__py3-none-any.whl → 0.0.5__py3-none-any.whl

calkit/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "0.0.3"
+__version__ = "0.0.5"
 
 from .core import *
 from . import git

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")
@@ -60,19 +81,26 @@ def get_status():
     """Get a unified Git and DVC status."""
 
     def print_sep(name: str):
-        print(f"------------ {name} ------------")
+        width = 66
+        txt_width = len(name) + 2
+        buffer_width = (width - txt_width) // 2
+        buffer = "-" * buffer_width
+        typer.echo(f"{buffer} {name} {buffer}")
 
-    print_sep("Code")
-    if os.name == "nt":
-        subprocess.call(["git", "status"])
-        print()
-        print_sep("data")
-        subprocess.call(["dvc", "status"])
-    else:
-        pty.spawn(["git", "status"], lambda fd: os.read(fd, 1024))
-        print()
-        print_sep("Data")
-        pty.spawn(["dvc", "status"], lambda fd: os.read(fd, 1024))
+    def run_cmd(cmd: list[str]):
+        if os.name == "nt":
+            subprocess.call(cmd)
+        else:
+            pty.spawn(cmd, lambda fd: os.read(fd, 1024))
+
+    print_sep("Code (Git)")
+    run_cmd(["git", "status"])
+    typer.echo()
+    print_sep("Data (DVC)")
+    run_cmd(["dvc", "data", "status"])
+    typer.echo()
+    print_sep("Pipeline (DVC)")
+    run_cmd(["dvc", "status"])
 
 
 @app.command(name="add")
@@ -105,6 +133,22 @@ def commit(
     raise NotImplementedError
 
 
+@app.command(name="pull", help="Pull with both Git and DVC.")
+def pull():
+    typer.echo("Git pulling")
+    subprocess.call(["git", "pull"])
+    typer.echo("DVC pulling")
+    subprocess.call(["dvc", "pull"])
+
+
+@app.command(name="push", help="Push with both Git and DVC.")
+def push():
+    typer.echo("Pushing to Git remote")
+    subprocess.call(["git", "push"])
+    typer.echo("Pushing to DVC remote")
+    subprocess.call(["dvc", "push"])
+
+
 @new_app.command(name="figure")
 def new_figure(
     path: str,
@@ -112,7 +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)
@@ -140,6 +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)
@@ -160,7 +205,97 @@ def new_question(
         repo.git.commit(["-m", "Add question"])
 
 
-@app.command(name="server")
+@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
 
@@ -173,5 +308,72 @@ def run_server():
     )
 
 
+@app.command(
+    name="run",
+    add_help_option=False,
+    help="Run DVC pipeline (a wrapper for `dvc repro`).",
+)
+def run_dvc_repro(
+    targets: Optional[list[str]] = typer.Argument(default=None),
+    help: Annotated[bool, typer.Option("-h", "--help")] = False,
+    quiet: Annotated[bool, typer.Option("-q", "--quiet")] = False,
+    verbose: Annotated[bool, typer.Option("-v", "--verbose")] = False,
+    force: Annotated[bool, typer.Option("-f", "--force")] = False,
+    interactive: Annotated[bool, typer.Option("-i", "--interactive")] = False,
+    single_item: Annotated[bool, typer.Option("-s", "--single-item")] = False,
+    pipeline: Annotated[
+        Optional[str], typer.Option("-p", "--pipeline")
+    ] = None,
+    all_pipelines: Annotated[
+        bool, typer.Option("-P", "--all-pipelines")
+    ] = False,
+    recursive: Annotated[bool, typer.Option("-R", "--recursive")] = False,
+    downstream: Annotated[
+        Optional[list[str]], typer.Option("--downstream")
+    ] = None,
+    force_downstream: Annotated[
+        bool, typer.Option("--force-downstream")
+    ] = False,
+    pull: Annotated[bool, typer.Option("--pull")] = False,
+    allow_missing: Annotated[bool, typer.Option("--allow-missing")] = False,
+    dry: Annotated[bool, typer.Option("--dry")] = False,
+    keep_going: Annotated[bool, typer.Option("--keep-going", "-k")] = False,
+    ignore_errors: Annotated[bool, typer.Option("--ignore-errors")] = False,
+    glob: Annotated[bool, typer.Option("--glob")] = False,
+    no_commit: Annotated[bool, typer.Option("--no-commit")] = False,
+    no_run_cache: Annotated[bool, typer.Option("--no-run-cache")] = False,
+):
+    """A simple wrapper for ``dvc repro``."""
+    if targets is None:
+        targets = []
+    args = targets
+    # Extract any boolean args
+    for name in [
+        "help",
+        "quiet",
+        "verbose",
+        "force",
+        "interactive",
+        "single-item",
+        "all-pipelines",
+        "recursive",
+        "pull",
+        "allow-missing",
+        "dry",
+        "keep-going",
+        "force-downstream",
+        "glob",
+        "no-commit",
+        "no-run-cache",
+    ]:
+        if locals()[name.replace("-", "_")]:
+            args.append("--" + name)
+    if pipeline is not None:
+        args += ["--pipeline", pipeline]
+    if downstream is not None:
+        args += downstream
+    subprocess.call(["dvc", "repro"] + args)
+
+
 def run() -> None:
     app()

calkit/models.py

@@ -60,6 +60,12 @@ class Software(BaseModel):
     description: str
 
 
+class Notebook(_CalkitObject):
+    """A Jupyter notebook."""
+
+    pass
+
+
 class ProjectInfo(BaseModel):
     """All of the project's information or metadata, written to the
     ``calkit.yaml`` file.
@@ -72,3 +78,4 @@ class ProjectInfo(BaseModel):
     references: list[ReferenceCollection] = []
     environments: list[Environment] = []
     software: list[Software] = []
+    notebooks: list[Notebook] = []

{calkit_python-0.0.3.dist-info → calkit_python-0.0.5.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: calkit-python
-Version: 0.0.3
+Version: 0.0.5
 Summary: Reproducibility simplified.
 Project-URL: Homepage, https://github.com/calkit/calkit
 Project-URL: Issues, https://github.com/calkit/calkit/issues
@@ -15,6 +15,7 @@ Requires-Dist: eval-type-backport; python_version < '3.10'
 Requires-Dist: fastapi
 Requires-Dist: gitpython
 Requires-Dist: keyring
+Requires-Dist: nbconvert
 Requires-Dist: pydantic-settings
 Requires-Dist: pydantic[email]
 Requires-Dist: pyjwt
@@ -27,12 +28,43 @@ Description-Content-Type: text/markdown
 
 # Calkit
 
-[Calkit](https://calkit.io) makes reproducible research easy,
+[Calkit](https://calkit.io) simplifies reproducibility,
 acting as a layer on top of
-[Git](https://git-scm.com/) and [DVC](https://dvc.org/), such that all
-all materials involved in the research process can be fully described in a
+[Git](https://git-scm.com/), [DVC](https://dvc.org/),
+[Zenodo](https://zenodo.org), and more,
+such that all all aspects of the research process can be fully described in a
 single repository.
 
+## Why does reproducibility matter?
+
+If your work is reproducible, that means that someone else can "run" it and
+get the same results or outputs.
+This is a major step towards addressing
+[the replication crisis](https://en.wikipedia.org/wiki/Replication_crisis)
+and has some major benefits for both you as an individual and the research
+community:
+
+1. You will avoid mistakes caused by, e.g., running an old version of a script
+   and including a figure that wasn't created after fixing a bug in the data
+   processing pipeline.
+2. Since your project is "runnable," it's more likely that someone else will be
+   able to reuse part of your work to run it in a different context, thereby
+   producing a bigger impact and accelerating the pace of discovery.
+   If someone can take what you've done and use it to calculate a
+   prediction, you have just produced truly useful knowledge.
+
+## Why another tool/platform?
+
+Git, GitHub, DVC, Zenodo et al. are amazing tools/platforms, but their
+use involves multiple fairly difficult learning curves.
+Our goal is to provide a single tool and platform to unify all of these so
+that there is a single, gentle learning curve.
+However, it is not our goal to hide or replace these underlying components.
+Advanced users can use them directly, but new users aren't forced to, which
+helps them get up and running with less effort and training.
+Calkit should help users understand what is going on under the hood without
+forcing them to work at that lower level of abstraction.
+
 ## Installation
 
 Simply run

{calkit_python-0.0.3.dist-info → calkit_python-0.0.5.dist-info}/RECORD

@@ -1,5 +1,5 @@
-calkit/__init__.py,sha256=WCAC5nhZD6Wzwgm3VMpKFCm3aGvtYoHqy3pt7kIgI9k,142
-calkit/cli.py,sha256=DpYo_EKLBbLZfbFFihGo3L3uXlKURWwv_QUOgSkCUoo,4901
+calkit/__init__.py,sha256=msMn6fygXybwu7UaIyTE7aSHGggrzrO1oPGG8SC8EbQ,142
+calkit/cli.py,sha256=akfF8Qk_okiVNS37fUjjMMjDQaqIVi7NTam96XjVGQE,11427
 calkit/cloud.py,sha256=CnQKms4mBQo4X8jVLIa-70-3jPDl38zRNFyK5TjiaHM,2209
 calkit/config.py,sha256=NPFRk5inn66Wy44pyx8WppyqvIzkW1sO6VjXwIcCacE,2044
 calkit/core.py,sha256=qLNjBwlECzMitL85pMGIHzne4j7FpQAR9-ukYtdIMig,1225
@@ -8,13 +8,13 @@ calkit/dvc.py,sha256=tX5172Ahw0mHcuJIrMenz1oGYxCrMzMURJJMHEHenbg,1506
 calkit/git.py,sha256=NLd7A32dPbfVnZLa8xbmviJ-ChGZcdkcd6wcOOnsSKQ,350
 calkit/gui.py,sha256=2UCrMyosc5v4CLlDcHO7oDwW9eLn5_WbNaLaG5bjMTc,23
 calkit/jupyter.py,sha256=S6HUOVafaLQJ7_ZfC1ddBwF3fT5q3GcbouLHdlH-oSo,1034
-calkit/models.py,sha256=TYllDbTutcODMUCLK2oCKivbJrtjwDu9t-5GyON9dq0,1339
+calkit/models.py,sha256=ejl032XIrbaCFkO-4VbCaKVQyHqNl7N4WWU20RjeAfc,1447
 calkit/server.py,sha256=gq3643ABKTQu1eVR_OqJ-SdQh2dPLHSFsipmmAK5ttA,5959
 calkit/tests/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 calkit/tests/test_core.py,sha256=CdRqvYnq3MidyTknvfIbkmmhMfydpyKtTW9hakAvzsc,167
 calkit/tests/test_jupyter.py,sha256=YTL6zI740UM2KUjskSipzvSKxsyQ8rVPFQIX5cb2tMQ,114
-calkit_python-0.0.3.dist-info/METADATA,sha256=NDjQb1WNaMJcEx-s4RTJyB-hNkGS3O7xy2Q6eCCn67Q,2449
-calkit_python-0.0.3.dist-info/WHEEL,sha256=1yFddiXMmvYK7QYTqtRNtX66WJ0Mz8PYEiEUoOUUxRY,87
-calkit_python-0.0.3.dist-info/entry_points.txt,sha256=tiPfbDDZNB-YStw5YVO_4Gww0W3Dcdy8Mh6muX_GWnY,42
-calkit_python-0.0.3.dist-info/licenses/LICENSE,sha256=9ZamCaSUTZk9rcrnf-sWFKLOHr3ws-S_dgKMegW4nw8,1056
-calkit_python-0.0.3.dist-info/RECORD,,
+calkit_python-0.0.5.dist-info/METADATA,sha256=tTUrA0R_i6RffDEd4VmMHbWvN0NR_4ifj53-SauHuVI,4004
+calkit_python-0.0.5.dist-info/WHEEL,sha256=1yFddiXMmvYK7QYTqtRNtX66WJ0Mz8PYEiEUoOUUxRY,87
+calkit_python-0.0.5.dist-info/entry_points.txt,sha256=tiPfbDDZNB-YStw5YVO_4Gww0W3Dcdy8Mh6muX_GWnY,42
+calkit_python-0.0.5.dist-info/licenses/LICENSE,sha256=9ZamCaSUTZk9rcrnf-sWFKLOHr3ws-S_dgKMegW4nw8,1056
+calkit_python-0.0.5.dist-info/RECORD,,