calkit-python 0.0.3__tar.gz → 0.0.4__tar.gz

{calkit_python-0.0.3 → calkit_python-0.0.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: calkit-python
-Version: 0.0.3
+Version: 0.0.4
 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-0.0.4/README.md

@@ -0,0 +1,81 @@
+# Calkit
+
+[Calkit](https://calkit.io) simplifies reproducibility,
+acting as a layer on top of
+[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
+
+```sh
+pip install calkit-python
+```
+
+## Cloud integration
+
+The Calkit cloud platform (https://calkit.io) serves as a project
+management interface and a DVC remote for easily storing all versions of your
+data/code/figures/publications, interacting with your collaborators,
+reusing others' research artifacts, etc.
+
+After signing up, visit the [settings](https://calkit.io/settings) page
+and create a token.
+Then run
+
+```sh
+calkit config set token ${YOUR_TOKEN_HERE}
+```
+
+Then, inside a project repo you'd like to connect to the cloud, run
+
+```sh
+calkit config setup-remote
+```
+
+This will setup the Calkit DVC remote, such that commands like `dvc push` will
+allow you to push versions of your data or pipeline outputs to the cloud
+for safe storage and sharing with your collaborators.
+
+## How it works
+
+Calkit creates a simple human-readable "database" inside the `calkit.yaml`
+file, which serves as a way to store important information about the project,
+e.g., what question(s) it seeks to answer,
+what files should be considered datasets, figures, publications, etc.
+The Calkit cloud reads this database and registers the various entities
+as part of the entire ecosystem such that if a project is made public,
+other researchers can find and reuse your work to accelerate their own.

{calkit_python-0.0.3 → calkit_python-0.0.4}/calkit/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "0.0.3"
+__version__ = "0.0.4"
 
 from .core import *
 from . import git

{calkit_python-0.0.3 → calkit_python-0.0.4}/calkit/cli.py

@@ -60,19 +60,26 @@ 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 +112,22 @@ 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,
@@ -160,7 +183,7 @@ def new_question(
         repo.git.commit(["-m", "Add question"])
 
 
-@app.command(name="server")
+@app.command(name="server", help="Run the local server.")
 def run_server():
     import uvicorn
 
@@ -173,5 +196,72 @@ 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_python-0.0.3 → calkit_python-0.0.4}/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 → calkit_python-0.0.4}/pyproject.toml

@@ -17,6 +17,7 @@ dependencies = [
   "fastapi",
   "gitpython",
   "keyring",
+  "nbconvert",
   "pydantic[email]",
   "pydantic-settings",
   "pyjwt",

calkit_python-0.0.3/README.md

@@ -1,50 +0,0 @@
-# Calkit
-
-[Calkit](https://calkit.io) makes reproducible research easy,
-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
-single repository.
-
-## Installation
-
-Simply run
-
-```sh
-pip install calkit-python
-```
-
-## Cloud integration
-
-The Calkit cloud platform (https://calkit.io) serves as a project
-management interface and a DVC remote for easily storing all versions of your
-data/code/figures/publications, interacting with your collaborators,
-reusing others' research artifacts, etc.
-
-After signing up, visit the [settings](https://calkit.io/settings) page
-and create a token.
-Then run
-
-```sh
-calkit config set token ${YOUR_TOKEN_HERE}
-```
-
-Then, inside a project repo you'd like to connect to the cloud, run
-
-```sh
-calkit config setup-remote
-```
-
-This will setup the Calkit DVC remote, such that commands like `dvc push` will
-allow you to push versions of your data or pipeline outputs to the cloud
-for safe storage and sharing with your collaborators.
-
-## How it works
-
-Calkit creates a simple human-readable "database" inside the `calkit.yaml`
-file, which serves as a way to store important information about the project,
-e.g., what question(s) it seeks to answer,
-what files should be considered datasets, figures, publications, etc.
-The Calkit cloud reads this database and registers the various entities
-as part of the entire ecosystem such that if a project is made public,
-other researchers can find and reuse your work to accelerate their own.