calkit-python 0.9.2__tar.gz → 0.9.4__tar.gz

{calkit_python-0.9.2 → calkit_python-0.9.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: calkit-python
-Version: 0.9.2
+Version: 0.9.4
 Summary: Reproducibility simplified.
 Project-URL: Homepage, https://github.com/calkit/calkit
 Project-URL: Issues, https://github.com/calkit/calkit/issues
@@ -29,9 +29,13 @@ Requires-Dist: pandas; extra == 'data'
 Requires-Dist: polars; extra == 'data'
 Description-Content-Type: text/markdown
 
-# Calkit
+<p align="center">
+  <a href="https://calkit.org" target="_blank">
+    <img width="40%" src="docs/img/calkit-no-bg.png" alt="Calkit">
+  </a>
+</p>
 
-Calkit is a lightweight framework for doing reproducible research.
+Calkit is a lightweight framework for reproducible research projects.
 It acts as a top-level layer to integrate and simplify the use of enabling
 technologies such as
 [Git](https://git-scm.com/),
@@ -59,46 +63,6 @@ To do this, we try to make it easy for users to follow two simple rules:
    keep computational environments up-to-date and label their outputs for
    convenient reuse.
 
-## Tutorials
-
-- [Jupyter notebook as a DVC pipeline](docs/tutorials/notebook-pipeline.md)
-- [Keeping track of conda environments](docs/tutorials/conda-envs.md)
-- [Defining and executing manual procedures](docs/tutorials/procedures.md)
-- [Adding a new LaTeX-based publication with its own Docker build environment](docs/tutorials/adding-latex-pub-docker.md)
-- [A reproducible workflow using Microsoft Office (Word and Excel)](https://petebachant.me/office-repro/)
-- [Reproducible OpenFOAM simulations](https://petebachant.me/reproducible-openfoam/)
-
-## Why does reproducibility matter?
-
-If your work is reproducible, that means that someone else can "run" it and
-calculate 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, Docker et al. are amazing tools/platforms, but their
-use involves multiple fairly difficult learning curves,
-and tying them together might mean developing something new for each project.
-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
 
 To install Calkit, [Git](https://git-scm.com) and Python must be installed.
@@ -120,7 +84,7 @@ pip install calkit-python
 
 ## Cloud integration
 
-The Calkit cloud platform (https://calkit.io) serves as a project
+The Calkit Cloud ([calkit.io](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.
@@ -143,6 +107,47 @@ 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.
 
+## Tutorials
+
+- [LaTeX collaboration with GitHub Codespaces](https://petebachant.me/latex-collab/)
+- [Jupyter notebook as a DVC pipeline](docs/tutorials/notebook-pipeline.md)
+- [Keeping track of conda environments](docs/tutorials/conda-envs.md)
+- [Defining and executing manual procedures](docs/tutorials/procedures.md)
+- [Adding a new LaTeX-based publication with its own Docker build environment](docs/tutorials/adding-latex-pub-docker.md)
+- [A reproducible workflow using Microsoft Office (Word and Excel)](https://petebachant.me/office-repro/)
+- [Reproducible OpenFOAM simulations](https://petebachant.me/reproducible-openfoam/)
+
+## Why does reproducibility matter?
+
+If your work is reproducible, that means that someone else can "run" it and
+calculate 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, Docker et al. are amazing tools/platforms, but their
+use involves multiple fairly difficult learning curves,
+and tying them together might mean developing something new for each project.
+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.
+
 ## How it works
 
 Calkit creates a simple human-readable "database" inside the `calkit.yaml`

{calkit_python-0.9.2 → calkit_python-0.9.4}/README.md

@@ -1,6 +1,10 @@
-# Calkit
+<p align="center">
+  <a href="https://calkit.org" target="_blank">
+    <img width="40%" src="docs/img/calkit-no-bg.png" alt="Calkit">
+  </a>
+</p>
 
-Calkit is a lightweight framework for doing reproducible research.
+Calkit is a lightweight framework for reproducible research projects.
 It acts as a top-level layer to integrate and simplify the use of enabling
 technologies such as
 [Git](https://git-scm.com/),
@@ -28,46 +32,6 @@ To do this, we try to make it easy for users to follow two simple rules:
    keep computational environments up-to-date and label their outputs for
    convenient reuse.
 
-## Tutorials
-
-- [Jupyter notebook as a DVC pipeline](docs/tutorials/notebook-pipeline.md)
-- [Keeping track of conda environments](docs/tutorials/conda-envs.md)
-- [Defining and executing manual procedures](docs/tutorials/procedures.md)
-- [Adding a new LaTeX-based publication with its own Docker build environment](docs/tutorials/adding-latex-pub-docker.md)
-- [A reproducible workflow using Microsoft Office (Word and Excel)](https://petebachant.me/office-repro/)
-- [Reproducible OpenFOAM simulations](https://petebachant.me/reproducible-openfoam/)
-
-## Why does reproducibility matter?
-
-If your work is reproducible, that means that someone else can "run" it and
-calculate 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, Docker et al. are amazing tools/platforms, but their
-use involves multiple fairly difficult learning curves,
-and tying them together might mean developing something new for each project.
-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
 
 To install Calkit, [Git](https://git-scm.com) and Python must be installed.
@@ -89,7 +53,7 @@ pip install calkit-python
 
 ## Cloud integration
 
-The Calkit cloud platform (https://calkit.io) serves as a project
+The Calkit Cloud ([calkit.io](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.
@@ -112,6 +76,47 @@ 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.
 
+## Tutorials
+
+- [LaTeX collaboration with GitHub Codespaces](https://petebachant.me/latex-collab/)
+- [Jupyter notebook as a DVC pipeline](docs/tutorials/notebook-pipeline.md)
+- [Keeping track of conda environments](docs/tutorials/conda-envs.md)
+- [Defining and executing manual procedures](docs/tutorials/procedures.md)
+- [Adding a new LaTeX-based publication with its own Docker build environment](docs/tutorials/adding-latex-pub-docker.md)
+- [A reproducible workflow using Microsoft Office (Word and Excel)](https://petebachant.me/office-repro/)
+- [Reproducible OpenFOAM simulations](https://petebachant.me/reproducible-openfoam/)
+
+## Why does reproducibility matter?
+
+If your work is reproducible, that means that someone else can "run" it and
+calculate 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, Docker et al. are amazing tools/platforms, but their
+use involves multiple fairly difficult learning curves,
+and tying them together might mean developing something new for each project.
+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.
+
 ## How it works
 
 Calkit creates a simple human-readable "database" inside the `calkit.yaml`

{calkit_python-0.9.2 → calkit_python-0.9.4}/calkit/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "0.9.2"
+__version__ = "0.9.4"
 
 from .core import *
 from . import git

{calkit_python-0.9.2 → calkit_python-0.9.4}/calkit/cli/config.py

@@ -2,9 +2,13 @@
 
 from __future__ import annotations
 
+import subprocess
+
 import typer
+from git.exc import InvalidGitRepositoryError
 
 from calkit import config
+from calkit.cli.core import raise_error
 from calkit.dvc import configure_remote, get_remotes, set_remote_auth
 
 config_app = typer.Typer(no_args_is_help=True)
@@ -43,8 +47,13 @@ def setup_remote():
     """Setup the Calkit cloud as the default DVC remote and store a token in
     the local config.
     """
-    configure_remote()
-    set_remote_auth()
+    try:
+        configure_remote()
+        set_remote_auth()
+    except subprocess.CalledProcessError:
+        raise_error("DVC remote config failed; have you run `dvc init`?")
+    except InvalidGitRepositoryError:
+        raise_error("Current directory is not a Git repository")
 
 
 @config_app.command(name="setup-remote-auth")

{calkit_python-0.9.2 → calkit_python-0.9.4}/calkit/conda.py

@@ -42,7 +42,10 @@ def check_env(
         subprocess.check_output([conda, "env", "list", "--json"]).decode()
     )["envs"]
     # Get existing env names, but skip the base environment
-    existing_env_names = [os.path.basename(env) for env in envs[1:]]
+    # Note that this could fail for environments with non-default prefixes
+    existing_env_names = [
+        os.path.basename(env) for env in envs if "envs" in env
+    ]
     with open(env_fpath) as f:
         env_spec = ryaml.load(f)
     env_name = env_spec["name"]

{calkit_python-0.9.2 → calkit_python-0.9.4}/calkit/dvc.py

@@ -17,10 +17,10 @@ def configure_remote():
     project_name = calkit.git.detect_project_name()
     base_url = calkit.cloud.get_base_url()
     remote_url = f"{base_url}/projects/{project_name}/dvc"
-    subprocess.call(
+    subprocess.check_call(
         ["dvc", "remote", "add", "-d", "-f", get_app_name(), remote_url]
     )
-    subprocess.call(
+    subprocess.check_call(
         ["dvc", "remote", "modify", get_app_name(), "auth", "custom"]
     )
 
@@ -39,7 +39,7 @@ def set_remote_auth(remote_name: str = None, always_auth: bool = False):
         )["access_token"]
         settings.dvc_token = token
         settings.write()
-    subprocess.call(
+    subprocess.check_call(
         [
             "dvc",
             "remote",
@@ -50,7 +50,7 @@ def set_remote_auth(remote_name: str = None, always_auth: bool = False):
             "Authorization",
         ]
     )
-    subprocess.call(
+    subprocess.check_call(
         [
             "dvc",
             "remote",