CLI reference

Top-level commands

Command	Description
init	Initialize the current working directory.
clone	Clone or download a copy of a project.
status	View status (project, version control, and/or pipeline).
diff	Get a unified Git and DVC diff.
add	Add paths to the repo.
commit	Commit a change to the repo.
save	Save paths by committing and pushing.
pull	Pull with both Git and DVC.
push	Push with both Git and DVC.
sync	Sync the project repo by pulling and then pushing.
ignore	Ignore a file, i.e., keep it out of version control.
local-server	Run the local server to interact over HTTP.
run	Check dependencies and run the pipeline.
manual-step	Execute a manual step.
xenv	Execute a command in an environment.
xproc	Execute a procedure.
calc	Run a project's calculation.
set-env-var	Set an environmental variable for the project in its '.env' file.
upgrade	Upgrade Calkit.
switch-branch	Switch to a different branch.
stash	Stash or restore workspace changes including dvc-zip tracked dirs.
dvc	Run a command with the DVC CLI.
jupyter	Run a command with the Jupyter CLI.
map-paths	Map paths in a project.
xr	Execute a command and if successful, record in the pipeline.
config	Configure Calkit.
new	Create a new Calkit object.
nb	Work with Jupyter notebooks.
list	List Calkit objects.
describe	Describe things.
import	Import objects.
office	Work with Microsoft Office.
update	Update objects.
check	Check things.
latex	Work with LaTeX.
overleaf	Interact with Overleaf.
cloud	Interact with a Calkit Cloud.
slurm	Work with SLURM.
dev	Developer tools.

Top-level command details

calkit init

Initialize the current working directory.

Usage:

calkit init [OPTIONS]

Options:

Option	Type	Required	Default	Description
--force, -f	boolean	no	False	Force reinitializing DVC if already initialized.

calkit clone

Clone or download a copy of a project.

Usage:

calkit clone [OPTIONS] URL [LOCATION]

Arguments:

Argument	Type	Required	Default	Description
url	text	yes		Repo URL.
location	text	no		Location to clone to (default will be ./{repo_name})

Options:

Option	Type	Required	Default	Description
--ssh	boolean	no	False	Use SSH with Git.
--no-config-remote	boolean	no	False	Do not automatically configure Calkit DVC remote.
--no-dvc-pull	boolean	no	False	Do not pull DVC objects.
--no-recursive	boolean	no	False	Do not recursively clone submodules.

calkit status

View status (project, version control, and/or pipeline).

Usage:

calkit status [OPTIONS] [TARGETS...]

Arguments:

Argument	Type	Required	Default	Description
targets	text	no		Optional targets to check status for. These may be pipeline stage names or repo paths.

Options:

Option	Type	Required	Default	Description
--category, -c	text	no		Status categories to show. By default, all categories are shown. Can be specified multiple times.
--json	boolean	no	False	Output status as JSON.

calkit diff

Get a unified Git and DVC diff.

Usage:

calkit diff [OPTIONS]

Options:

Option	Type	Required	Default	Description
--staged	boolean	no	False	Show a diff from files staged with Git.

calkit add

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.

Usage:

calkit add [OPTIONS] PATHS...

Arguments:

Argument	Type	Required	Default	Description
paths	text	yes

Options:

Option	Type	Required	Default	Description
-m, --commit-message	text	no		Automatically commit and use this as a message.
--auto-message, -M	boolean	no	False	Commit with an automatically-generated message.
--no-auto-ignore	boolean	no	False	Disable auto-ignore.
--push	boolean	no	False	Push after committing.
--to, -t	text	no		System with which to add (git, dvc, or dvc-zip).

calkit commit

Commit a change to the repo.

Usage:

calkit commit [OPTIONS]

Options:

Option	Type	Required	Default	Description
--all, -a	boolean	no	False	Automatically stage all changed files.
--message, -m	text	no		Commit message.
--push	boolean	no	False	Push to both Git and DVC after committing.

calkit save

Save paths by committing and pushing.

This is essentially git/dvc add, commit, and push in one step.

Usage:

calkit save [OPTIONS] [PATHS...]

Arguments:

Argument	Type	Required	Default	Description
paths	text	no		Paths to add and commit. If not provided, will default to any changed files that have been added previously.

Options:

Option	Type	Required	Default	Description
--all, -a	boolean	no	False	Save all, automatically handling staging and ignoring.
--message, -m	text	no		Commit message.
--auto-message, -M	boolean	no	False	Commit with an automatically-generated message.
--to, -t	text	no		System with which to add (git or dvc).
--no-push	boolean	no	False	Do not push to Git and DVC after committing.
--git-push	text	no		Additional Git args to pass when pushing.
--dvc-push	text	no		Additional DVC args to pass when pushing.
--no-recursive	boolean	no	False	Do not push to submodules.
--overleaf, -O	boolean	no	False	Sync with Overleaf after saving.
--verbose, -v	boolean	no	False	Print verbose output.

calkit pull

Pull with both Git and DVC.

Usage:

calkit pull [OPTIONS]

Options:

Option	Type	Required	Default	Description
--no-check-auth	boolean	no	False
--git-arg	text	no		Additional Git args.
--dvc-arg	text	no		Additional DVC args.
--force, -f	boolean	no	False	Force pull, potentially overwriting local changes.
--no-recursive	boolean	no	False	Do not recursively pull from submodules.

calkit push

Push with both Git and DVC.

Usage:

calkit push [OPTIONS]

Options:

Option	Type	Required	Default	Description
--no-check-auth	boolean	no	False
--no-dvc	boolean	no	False
--no-git	boolean	no	False
--git-arg	text	no		Additional Git args.
--dvc-arg	text	no		Additional DVC args.
--no-recursive	boolean	no	False	Do not push to submodules.

calkit sync

Sync the project repo by pulling and then pushing.

Usage:

calkit sync [OPTIONS]

Options:

Option	Type	Required	Default	Description
--no-check-auth	boolean	no	False

calkit ignore

Ignore a file, i.e., keep it out of version control.

Usage:

calkit ignore [OPTIONS] PATH

Arguments:

Argument	Type	Required	Default	Description
path	text	yes		Path to ignore.

Options:

Option	Type	Required	Default	Description
--no-commit	boolean	no	False	Do not commit changes to .gitignore.

calkit local-server

Run the local server to interact over HTTP.

Usage:

calkit local-server

calkit run

Check dependencies and run the pipeline.

Usage:

calkit run [OPTIONS] [TARGETS...]

Arguments:

Argument	Type	Required	Default	Description
targets	text	no		Stages to run.

Options:

Option	Type	Required	Default	Description
-q, --quiet	boolean	no	False	Be quiet.
-v, --verbose	boolean	no	False	Print verbose output.
-f, --force	boolean	no	False	Run even if stages or inputs have not changed.
-i, --interactive	boolean	no	False	Ask for confirmation before running each stage.
-s, --single-item	boolean	no	False	Run only a single stage without any dependents.
-p, --pipeline	text	no
-P, --all-pipelines	boolean	no	False	Run all pipelines in the repo.
-R, --recursive	boolean	no	False	Run pipelines in subdirectories.
--downstream	text	no		Start from the specified stage and run all downstream.
--force-downstream	boolean	no	False	Force downstream stages to run even if they are still up-to-date.
--pull	boolean	no	False	Try automatically pulling missing data.
--allow-missing	boolean	no	False	Skip stages with missing data.
--dry	boolean	no	False	Only print commands that would execute.
--keep-going, -k	boolean	no	False	Continue executing, skipping stages with failed inputs from other stages.
--ignore-errors	boolean	no	False	Ignore errors from stages.
--glob	boolean	no	False	Match stages with glob-style patterns.
--no-commit	boolean	no	False	Do not save to the run cache.
--no-run-cache	boolean	no	False	Ignore the run cache.
--log, -l	boolean	no	False	Log the run and system information.
--save, -S	boolean	no	False	Save the project after running.
--save-message, -m	text	no		Commit message for saving.
--input, --dep	text	no		Run stages that depend on given input dependency path.
--output, --out	text	no		Run stages that produce the given output path.
--overleaf, -O	boolean	no	False	Sync with Overleaf before and after running.

calkit manual-step

Execute a manual step.

Usage:

calkit manual-step [OPTIONS]

Options:

Option	Type	Required	Default	Description
--message, -m	text	yes		Message to display as a prompt.
--cmd	text	no		Command to run.
--show-stdout	boolean	no	False	Show stdout.
--show-stderr	boolean	no	False	Show stderr.

calkit xenv

Execute a command in an environment.

Usage:

calkit xenv [OPTIONS] CMD...

Arguments:

Argument	Type	Required	Default	Description
cmd	text	yes		Command to run in the environment.

Options:

Option	Type	Required	Default	Description
--name, -n	text	no		Environment name in which to run. Only necessary if there are multiple in this project and path is not provided.
--env-path, -p	text	no		Path of spec of environment in which to run. Will be added to the project if it doesn't exist.
--wdir	text	no		Working directory. By default will run current working directory.
--no-check	boolean	no	False	Don't check the environment is valid before running in it.
--relaxed	boolean	no	False	Check the environment in a relaxed way, if applicable.
--verbose, -v	boolean	no	False	Print verbose output.

calkit xproc

Execute a procedure.

Usage:

calkit xproc [OPTIONS] NAME

Arguments:

Argument	Type	Required	Default	Description
name	text	yes		The name of the procedure.

Options:

Option	Type	Required	Default	Description
--no-commit	boolean	no	False	Do not commit after each action.

calkit calc

Run a project's calculation.

Usage:

calkit calc [OPTIONS] NAME

Arguments:

Argument	Type	Required	Default	Description
name	text	yes		Calculation name.

Options:

Option	Type	Required	Default	Description
--input, -i	text	no		Inputs defined like x=1 (with no spaces.)
--no-format	boolean	no	False	Do not format output before printing

calkit set-env-var

Set an environmental variable for the project in its '.env' file.

Usage:

calkit set-env-var NAME VALUE

Arguments:

Argument	Type	Required	Default	Description
name	text	yes		Name of the variable.
value	text	yes		Value of the variable.

calkit upgrade

Upgrade Calkit.

Usage:

calkit upgrade

calkit switch-branch

Switch to a different branch.

Usage:

calkit switch-branch NAME

Arguments:

Argument	Type	Required	Default	Description
name	text	yes		Branch name.

calkit stash

Stash or restore workspace changes including dvc-zip tracked dirs.

Without --pop: zips any modified workspace dirs into the DVC cache, then git-stashes (saving the updated .dvc files), checks out the committed DVC state, and unzips it to the workspace.

With --pop: pops the git stash (restoring the saved .dvc files), checks out the stashed DVC state, and unzips it to the workspace.

Usage:

calkit stash [OPTIONS]

Options:

Option	Type	Required	Default	Description
--pop	boolean	no	False	Pop the most recent stash.

calkit dvc

Run a command with the DVC CLI.

Useful if Calkit is installed as a tool, e.g., with uv tool or pipx, and DVC is not installed.

Usage:

calkit dvc [OPTIONS]

calkit jupyter

Run a command with the Jupyter CLI.

Usage:

calkit jupyter [OPTIONS]

calkit map-paths

Map paths in a project.

Currently this is done with copying. Outputs are ensured to be ignored by Git.

Usage:

calkit map-paths [OPTIONS]

Options:

Option	Type	Required	Default	Description
--file-to-file	text	no		Map a file to another file, e.g., --file-to-file 'results.tex->paper/results.tex'.
--file-to-dir	text	no		Map a file into a directory, e.g., --file-to-dir 'results.tex->paper/results'.
--dir-to-dir-replace	text	no		Copy directory to another directory and replace it, e.g., --dir-to-dir-replace 'figures->paper/figures'.
--dir-to-dir-merge	text	no		Merge directory into another directory. This is useful for merging contents of one directory into another, e.g., --dir-to-dir-merge 'figures->paper/figures'.

calkit xr

Execute a command and if successful, record in the pipeline.

Usage:

calkit xr [OPTIONS] CMD...

Arguments:

Argument	Type	Required	Default	Description
cmd	text	yes		Command to execute and record. If the first argument is a script, notebook or LaTeX file, it will be treated as a stage with that file as the target. Any command, including arguments, is supported.

Options:

Option	Type	Required	Default	Description
--environment, -e	text	no		Name of or path the spec file for the environment to use.
--input, -i	text	no		Input paths to record.
--output, -o	text	no		Output paths to record.
--no-detect-io	boolean	no	False	Don't attempt to detect inputs and outputs from the command, script, or notebook.
--stage	text	no		Name of the DVC stage to create for this command. If not provided, a name will be generated automatically.
--dry-run, -d	boolean	no	False	Print the environment and stage that would be created without modifying calkit.yaml or executing the command.
--json	boolean	no	False	Print xr results as JSON.
--force, -f	boolean	no	False	Force running stage even if it's up-to-date.
--verbose, -v	boolean	no	False	Print verbose output.

Command groups

calkit config

Configure Calkit.

Command	Description
set	Set a value in the config.
get	Get and print a value from the config.
unset	Unset a value in the config, returning it to default.
remote	Setup the Calkit cloud as the default DVC remote and store a token in the local config.
remote-auth	Store a Calkit cloud token in the local DVC config for all Calkit remotes.
list	List keys in the config.
github-ssh	Walk through the process of adding an SSH key to GitHub.
github-codespace	Configure a GitHub Codespace.

calkit config set

Set a value in the config.

Usage:

calkit config set KEY VALUE

Arguments:

Argument	Type	Required	Default	Description
key	text	yes
value	text	yes

calkit config get

Get and print a value from the config.

Usage:

calkit config get KEY

Arguments:

Argument	Type	Required	Default	Description
key	text	yes

calkit config unset

Unset a value in the config, returning it to default.

Usage:

calkit config unset KEY

Arguments:

Argument	Type	Required	Default	Description
key	text	yes

calkit config remote

Setup the Calkit cloud as the default DVC remote and store a token in the local config.

Usage:

calkit config remote [OPTIONS]

Options:

Option	Type	Required	Default	Description
--http	boolean	no	False	Use the legacy HTTP URL for the Calkit DVC remote instead of ck://.
--no-commit	boolean	no	False	Do not commit changes to DVC config.

calkit config remote-auth

Store a Calkit cloud token in the local DVC config for all Calkit remotes.

Usage:

calkit config remote-auth

calkit config list

List keys in the config.

Usage:

calkit config list

calkit config github-ssh

Walk through the process of adding an SSH key to GitHub.

Usage:

calkit config github-ssh

calkit config github-codespace

Configure a GitHub Codespace.

Typically this will simply mean we exchange a GitHub token for a Calkit token to use for pushing with DVC.

If this is run outside a Codespace, typically nothing will happen.

Usage:

calkit config github-codespace

calkit new

Create a new Calkit object.

Command	Description
project	Create a new project.
figure	Create a new figure.
question	Add a new question.
notebook	Add a new notebook.
docker-env	Create a new Docker environment.
foreach-stage	Create a new DVC 'foreach' stage.
dataset	Create a new dataset.
publication	Create a new publication.
conda-env	Create a new Conda environment.
uv-env	Create a new uv project environment.
slurm-env	Create a new SLURM environment.
uv-venv	Create a new uv virtual environment.
venv	Create a new Python virtual environment with venv.
pixi-env	Create a new pixi virtual environment.
julia-env	Create a new Julia environment or add an existing one to calkit.yaml.
renv	Create a new R environment with renv.
status	Add a new project status to the log.
python-script-stage	Add a stage to the pipeline that runs a Python script.
julia-script-stage	Add a stage to the pipeline that runs a Julia script.
matlab-script-stage	Add a stage to the pipeline that runs a MATLAB script.
latex-stage	Add a stage to the pipeline that compiles a LaTeX document.
jupyter-notebook-stage	Add a stage to the pipeline that runs a Jupyter notebook.
release	Create a new release.

calkit new project

Create a new project.

Usage:

calkit new project [OPTIONS] PATH

Arguments:

Argument	Type	Required	Default	Description
path	text	yes		Where to create the project.

Options:

Option	Type	Required	Default	Description
--name, -n	text	no		Project name. Will be inferred as kebab-cased directory name if not provided.
--title	text	no		Project title.
--description	text	no		Project description.
--cloud	boolean	no	False	Create this project in the cloud (Calkit and GitHub.)
--public	boolean	no	False	Create as a public project if --cloud is selected.
--git-url	text	no		Git repo URL. Usually https://github.com/{your_name}/{project_name}.
--template, -t	text	no		Template from which to derive the project, e.g., 'calkit/example-basic'.
--no-commit	boolean	no		Do not commit changes to Git.
--overwrite, -f	boolean	no	False	Overwrite project if one already exists.

calkit new figure

Create a new figure.

Usage:

calkit new figure [OPTIONS] PATH

Arguments:

Argument	Type	Required	Default	Description
path	text	yes

Options:

Option	Type	Required	Default	Description
--title	text	yes
--description	text	yes
--stage	text	no		Name of the pipeline stage that generates this figure.
--cmd	text	no		Command to add to the stage, if specified.
--dep	text	no		Path to stage dependency.
--out	text	no		Path to stage output. Figure path will be added automatically.
--deps-from-stage-outs	text	no		Stage name from which to add outputs as dependencies.
--no-commit	boolean	no	False
--overwrite, -f	boolean	no	False	Overwrite existing figure if one exists.

calkit new question

Add a new question.

Usage:

calkit new question [OPTIONS] QUESTION

Arguments:

Argument	Type	Required	Default	Description
question	text	yes

Options:

Option	Type	Required	Default	Description
--commit	boolean	no	False

calkit new notebook

Add a new notebook.

Usage:

calkit new notebook [OPTIONS] PATH

Arguments:

Argument	Type	Required	Default	Description
path	text	yes		Notebook path (relative)

Options:

Option	Type	Required	Default	Description
--title	text	yes
--description	text	no
--stage	text	no		Name of the pipeline stage that runs this notebook.
--commit	boolean	no	False

calkit new docker-env

Create a new Docker environment.

Usage:

calkit new docker-env [OPTIONS]

Options:

Option	Type	Required	Default	Description
--name, -n	text	yes		Environment name.
--image	text	no		Image identifier. Should be unique and descriptive. Will default to environment name if not specified.
--from	text	no		Base image, e.g., 'ubuntu', if creating a Dockerfile.
--path	text	no		Dockerfile path. Will default to 'Dockerfile' if --from is specified.
--add-layer	text	no		Add a layer (options: miniforge, foampy, uv, julia).
--env-var	text	no		Environment variables to set in the container.
--gpus	text	no
--arg	text	no		Arguments to use when running container.
--dep	text	no		Path to add as a dependency, i.e., a file that gets added to the container.
--wdir	text	no	/work	Working directory.
--command-mode	text	no	shell	How to execute commands in the container: 'shell' runs shell -c, 'entrypoint' passes args directly to the image entrypoint.
--user	text	no		User account to use to run the container.
--platform	text	no		Which platform(s) to build for.
--port	text	no		Ports to expose in the container, e.g., '8080:80'. Can be specified multiple times.
--description	text	no		Description.
--overwrite, -f	boolean	no	False	Overwrite any existing environment with this name.
--no-commit	boolean	no	False	Do not commit changes.
--no-check	boolean	no	False	Do not check environment is up-to-date after creation.

calkit new foreach-stage

Create a new DVC 'foreach' stage.

The list of values must be a simple list. For more complex objects, edit dvc.yaml directly.

Usage:

calkit new foreach-stage [OPTIONS] VALS...

Arguments:

Argument	Type	Required	Default	Description
vals	text	yes		Values to iterate over

Options:

Option	Type	Required	Default	Description
--cmd	text	yes		Command to run. Can include {var} to fill with variable.
--name, -n	text	yes		Stage name.
--dep	text	no		Path to add as a dependency.
--out	text	no		Path to add as an output.
--overwrite, -f	boolean	no	False	Overwrite stage if one already exists.
--no-commit	boolean	no	False	Do not commit changes.

calkit new dataset

Create a new dataset.

Usage:

calkit new dataset [OPTIONS] PATH

Arguments:

Argument	Type	Required	Default	Description
path	text	yes

Options:

Option	Type	Required	Default	Description
--title	text	yes
--description	text	yes
--stage	text	no		Name of the pipeline stage that generates this dataset.
--cmd	text	no		Command to add to the stage, if specified.
--dep	text	no		Path to stage dependency.
--out	text	no		Path to stage output. Dataset path will be added automatically.
--deps-from-stage-outs	text	no		Stage name from which to add outputs as dependencies.
--no-commit	boolean	no	False
--overwrite, -f	boolean	no	False	Overwrite existing dataset if one exists.

calkit new publication

Create a new publication.

Usage:

calkit new publication [OPTIONS] PATH

Arguments:

Argument	Type	Required	Default	Description
path	text	yes		Path for the publication. If using a template, this could be a directory.

Options:

Option	Type	Required	Default	Description
--title	text	yes		The title of the publication.
--description	text	yes		A description of the publication.
--kind	text	yes		Kind of the publication, e.g., 'journal-article'.
--stage	text	no		Name of the pipeline stage to build the output file.
--dep	text	no		Path to stage dependency.
--deps-from-stage-outs	text	no		Stage name from which to add outputs as dependencies.
--template, -t	text	no		Template with which to create the source files. Should be in the format {type}/{name}.
--environment	text	no		Name of the build environment to create, if desired.
--no-commit	boolean	no	False	Do not commit resulting changes to the repo.
--overwrite, -f	boolean	no	False	Overwrite existing objects if they already exist.

calkit new conda-env

Create a new Conda environment.

Usage:

calkit new conda-env [OPTIONS] [PACKAGES...]

Arguments:

Argument	Type	Required	Default	Description
packages	text	no		Packages to include in the environment.

Options:

Option	Type	Required	Default	Description
--name, -n	text	yes		Environment name.
--conda-name	text	no		Name to use in the Conda environment file, if desired. Will be automatically generated if not provided. Note that these should be unique since Conda environments are a system-wide collection.
--path	text	no	environment.yml	Environment YAML file path.
--pip	text	no		Packages to install with pip.
--prefix	text	no		Prefix for environment location.
--description	text	no		Description.
--overwrite, -f	boolean	no	False	Overwrite any existing environment with this name.
--no-commit	boolean	no	False	Do not commit changes.
--no-check	boolean	no	False	Do not check environment is up-to-date after creation.

calkit new uv-env

Create a new uv project environment.

Usage:

calkit new uv-env [OPTIONS] [PACKAGES...]

Arguments:

Argument	Type	Required	Default	Description
packages	text	no		Packages to include in the environment.

Options:

Option	Type	Required	Default	Description
--name, -n	text	no	main	Environment name.
--path	text	no		Environment file path. Must end with 'pyproject.toml'.
--python, -p	text	no		Python version.
--no-check	boolean	no	False	Do not check environment is up-to-date after creation.
--no-commit	boolean	no	False	Do not commit changes.

calkit new slurm-env

Create a new SLURM environment.

Usage:

calkit new slurm-env [OPTIONS]

Options:

Option	Type	Required	Default	Description
--name, -n	text	yes		Environment name.
--host	text	no	localhost	Host where SLURM commands should run.
--default-option	text	no		Default sbatch/srun option string (for example --gpus=1). Repeat for multiple options.
--default-setup	text	no		Default shell setup command to run before SLURM jobs (for example 'module load julia/1.11'). Repeat for multiple commands.
--description	text	no		Description.
--overwrite, -f	boolean	no	False	Overwrite any existing environment with this name.
--no-commit	boolean	no	False	Do not commit changes.

calkit new uv-venv

Create a new uv virtual environment.

Usage:

calkit new uv-venv [OPTIONS] [PACKAGES...]

Arguments:

Argument	Type	Required	Default	Description
packages	text	no		Packages to include in the environment.

Options:

Option	Type	Required	Default	Description
--name, -n	text	yes		Environment name.
--path	text	no	requirements.txt	Path for requirements file.
--prefix	text	no	.venv	Prefix for environment location.
--python, -p	text	no	3.14	Python version.
--description	text	no		Description.
--overwrite, -f	boolean	no	False	Overwrite any existing environment with this name.
--no-commit	boolean	no	False	Do not commit changes.
--no-check	boolean	no	False	Do not check environment is up-to-date after creation.

calkit new venv

Create a new Python virtual environment with venv.

Usage:

calkit new venv [OPTIONS] PACKAGES...

Arguments:

Argument	Type	Required	Default	Description
packages	text	yes		Packages to include in the environment.

Options:

Option	Type	Required	Default	Description
--name, -n	text	yes		Environment name.
--path	text	no	requirements.txt	Path for requirements file.
--prefix	text	no	.venv	Prefix for environment location.
--description	text	no		Description.
--overwrite, -f	boolean	no	False	Overwrite any existing environment with this name.
--no-commit	boolean	no	False	Do not commit changes.
--no-check	boolean	no	False	Do not check environment is up-to-date after creation.

calkit new pixi-env

Create a new pixi virtual environment.

Usage:

calkit new pixi-env [OPTIONS] PACKAGES...

Arguments:

Argument	Type	Required	Default	Description
packages	text	yes		Packages to include in the environment.

Options:

Option	Type	Required	Default	Description
--name, -n	text	yes		Environment name.
--pip	text	no		Packages to install with pip.
--description	text	no		Description.
--platform, -p	text	no		Platform.
--overwrite, -f	boolean	no	False	Overwrite any existing environment with this name.
--no-commit	boolean	no	False	Do not commit changes.
--no-check	boolean	no	False	Do not check environment is up-to-date after creation.

calkit new julia-env

Create a new Julia environment or add an existing one to calkit.yaml.

Usage:

calkit new julia-env [OPTIONS] [PACKAGES...]

Arguments:

Argument	Type	Required	Default	Description
packages	text	no		Optional packages to include in the environment.

Options:

Option	Type	Required	Default	Description
--name, -n	text	no	main	Environment name.
--path	text	no		Path for Project.toml file.
--description	text	no		Description.
--julia, -j	text	no		Julia version. Auto-detected if not supplied.
--overwrite, -f	boolean	no	False	Overwrite any existing environment with this name.
--no-commit	boolean	no	False	Do not commit changes.
--no-check	boolean	no	False	Do not check environment is up-to-date after creation.

calkit new renv

Create a new R environment with renv.

Usage:

calkit new renv [OPTIONS] [PACKAGES...]

Arguments:

Argument	Type	Required	Default	Description
packages	text	no		Packages to include in the environment.

Options:

Option	Type	Required	Default	Description
--name, -n	text	no	main	Environment name.
--path	text	no		Environment file path. Must end with 'DESCRIPTION'.
--r-version, -r	text	no		R version.
--description	text	no		Description.
--overwrite, -f	boolean	no	False	Overwrite any existing environment with this name.
--no-check	boolean	no	False	Do not check environment is up-to-date after creation.
--no-commit	boolean	no	False	Do not commit changes.

calkit new status

Add a new project status to the log.

Usage:

calkit new status [OPTIONS] STATUS

Arguments:

Argument	Type	Required	Default	Description
status	choice(in-progress, on-hold, completed)	yes		Current status of the project.

Options:

Option	Type	Required	Default	Description
--message, -m	text	no		Optional message describing the status.
--no-commit	boolean	no	False	Do not commit changes to the status log.

calkit new python-script-stage

Add a stage to the pipeline that runs a Python script.

Usage:

calkit new python-script-stage [OPTIONS]

Options:

Option	Type	Required	Default	Description
--name, -n	text	yes		Stage name, typically kebab-case.
--environment, -e	text	yes		Environment to use to run the stage.
--script-path, -s	text	yes		Path to script.
--arg	text	no		Argument to pass to the script.
--input, -i	text	no		A path on which the stage depends.
--output, -o	text	no		A path that is produced by the stage.
--out-git	text	no		An output that should be stored with Git instead of DVC.
--out-git-no-delete	text	no		An output that should be tracked with Git instead of DVC, and also should not be deleted before running stage.
--out-no-delete	text	no		An output that should not be deleted before running.
--out-no-store	text	no		An output that should not be stored in version control.
--out-no-store-no-delete	text	no		An output that should not be stored in version control, and should not be deleted before running.
--iter		no		Iterate over an argument with a comma-separated list, e.g., --iter-arg var_name val1,val2,val3.
--overwrite, --force, -f	boolean	no	False	Overwrite an existing stage with this name if necessary.
--no-check	boolean	no	False	Do not check if the target, deps, environment, etc., exist.
--no-commit	boolean	no	False	Do not commit changes to Git.

calkit new julia-script-stage

Add a stage to the pipeline that runs a Julia script.

Usage:

calkit new julia-script-stage [OPTIONS]

Options:

Option	Type	Required	Default	Description
--name, -n	text	yes		Stage name, typically kebab-case.
--environment, -e	text	yes		Environment to use to run the stage.
--script-path, -s	text	yes		Path to script.
--input, -i	text	no		A path on which the stage depends.
--output, -o	text	no		A path that is produced by the stage.
--out-git	text	no		An output that should be stored with Git instead of DVC.
--out-git-no-delete	text	no		An output that should be tracked with Git instead of DVC, and also should not be deleted before running stage.
--out-no-delete	text	no		An output that should not be deleted before running.
--out-no-store	text	no		An output that should not be stored in version control.
--out-no-store-no-delete	text	no		An output that should not be stored in version control, and should not be deleted before running.
--iter		no		Iterate over an argument with a comma-separated list, e.g., --iter-arg var_name val1,val2,val3.
--overwrite, --force, -f	boolean	no	False	Overwrite an existing stage with this name if necessary.
--no-check	boolean	no	False	Do not check if the target, deps, environment, etc., exist.
--no-commit	boolean	no	False	Do not commit changes to Git.

calkit new matlab-script-stage

Add a stage to the pipeline that runs a MATLAB script.

Usage:

calkit new matlab-script-stage [OPTIONS]

Options:

Option	Type	Required	Default	Description
--name, -n	text	yes		Stage name, typically kebab-case.
--environment, -e	text	yes		Environment to use to run the stage.
--script-path, -s	text	yes		Path to script.
--input, -i	text	no		A path on which the stage depends.
--output, -o	text	no		A path that is produced by the stage.
--out-git	text	no		An output that should be stored with Git instead of DVC.
--out-git-no-delete	text	no		An output that should be tracked with Git instead of DVC, and also should not be deleted before running stage.
--out-no-delete	text	no		An output that should not be deleted before running.
--out-no-store	text	no		An output that should not be stored in version control.
--out-no-store-no-delete	text	no		An output that should not be stored in version control, and should not be deleted before running.
--overwrite, --force, -f	boolean	no	False	Overwrite an existing stage with this name if necessary.
--no-check	boolean	no	False	Do not check if the target, deps, environment, etc., exist.
--no-commit	boolean	no	False	Do not commit changes to Git.

calkit new latex-stage

Add a stage to the pipeline that compiles a LaTeX document.

Usage:

calkit new latex-stage [OPTIONS]

Options:

Option	Type	Required	Default	Description
--name, -n	text	yes		Stage name, typically kebab-case.
--environment, -e	text	yes		Environment to use to run the stage.
--target	text	yes		Target .tex file path.
--input, -i	text	no		A path on which the stage depends.
--output, -o	text	no		A path that is produced by the stage.
--out-git	text	no		An output that should be stored with Git instead of DVC.
--out-git-no-delete	text	no		An output that should be tracked with Git instead of DVC, and also should not be deleted before running stage.
--out-no-delete	text	no		An output that should not be deleted before running.
--out-no-store	text	no		An output that should not be stored in version control.
--out-no-store-no-delete	text	no		An output that should not be stored in version control, and should not be deleted before running.
--overwrite, --force, -f	boolean	no	False	Overwrite an existing stage with this name if necessary.
--no-check	boolean	no	False	Do not check if the target, deps, environment, etc., exist.
--no-commit	boolean	no	False	Do not commit changes to Git.

calkit new jupyter-notebook-stage

Add a stage to the pipeline that runs a Jupyter notebook.

Usage:

calkit new jupyter-notebook-stage [OPTIONS]

Options:

Option	Type	Required	Default	Description
--name, -n	text	yes		Stage name, typically kebab-case.
--environment, -e	text	yes		Environment to use to run the stage.
--notebook-path	text	yes		Path to notebook.
--input, -i	text	no		A path on which the stage depends.
--output, -o	text	no		A path that is produced by the stage.
--out-git	text	no		An output that should be stored with Git instead of DVC.
--out-git-no-delete	text	no		An output that should be tracked with Git instead of DVC, and also should not be deleted before running stage.
--out-no-delete	text	no		An output that should not be deleted before running.
--out-no-store	text	no		An output that should not be stored in version control.
--out-no-store-no-delete	text	no		An output that should not be stored in version control, and should not be deleted before running.
--html-storage	choice(git, dvc, None)	no	NotebookStorage.dvc	In what system to store the HTML output of the notebook.
--cleaned-ipynb-storage	choice(git, dvc, None)	no	NotebookStorage.git	In what system to store the cleaned ipynb output of the notebook.
--executed-ipynb-storage	choice(git, dvc, None)	no	NotebookStorage.dvc	In what system to store the executed ipynb output of the notebook.
--overwrite, --force, -f	boolean	no	False	Overwrite an existing stage with this name if necessary.
--no-check	boolean	no	False	Do not check if the target, deps, environment, etc., exist.
--no-commit	boolean	no	False	Do not commit changes to Git.

calkit new release

Create a new release.

Usage:

calkit new release [OPTIONS] [PATH]

Arguments:

Argument	Type	Required	Default	Description
path	text	no	.	The path to release; '.' for a project release.

Options:

Option	Type	Required	Default	Description
--name, -n	text	yes		A name for the release, typically kebab-case or a semantic version. Will be used for the Git tag and GitHub release title.
--kind	text	no	project	What kind of release to create.
--description, --desc	text	no		A description of the release. Will be auto-generated if not provided.
--date	text	no		Release date. Will default to today.
--dry-run	boolean	no	False	Only print actions that would be taken but don't take them.
--no-commit	boolean	no	False	Do not commit changes to Git repo.
--no-push	boolean	no	False	Do not push to Git remote.
--no-github	boolean	no	False	Do not create a GitHub release.
--to	text	no	zenodo	Archival service to use (zenodo or caltechdata).
--draft	boolean	no	False	Create draft record with reserved DOI but do not publish.
--license	text	no		License ID (from https://spdx.org/licenses). Multiple can be specified. Will try to infer from LICENSE file, if present.
--verbose, -v	boolean	no	False	Print verbose output.

calkit nb

Work with Jupyter notebooks.

Command	Description
clean	Clean notebook and place a copy in the cleaned notebooks directory.
clean-all	Clean all notebooks in the pipeline.
check-kernel	Check that an environment has a registered Jupyter kernel.
execute	Execute notebook and place a copy in the relevant directory.

calkit nb clean

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.

Usage:

calkit nb clean [OPTIONS] PATH

Arguments:

Argument	Type	Required	Default	Description
path	text	yes

Options:

Option	Type	Required	Default	Description
--quiet, -q	boolean	no	False	Do not print output.

calkit nb clean-all

Clean all notebooks in the pipeline.

Usage:

calkit nb clean-all [OPTIONS]

Options:

Option	Type	Required	Default	Description
--quiet, -q	boolean	no	False	Do not print output.

calkit nb check-kernel

Check that an environment has a registered Jupyter kernel.

Usage:

calkit nb check-kernel [OPTIONS]

Options:

Option	Type	Required	Default	Description
--environment, --env, -e	text	yes		Environment name in which to run the notebook.
--no-check	boolean	no	False	Do not check environment before executing.
--language, -l	text	no		Notebook language; if 'matlab', MATLAB kernel must be available in environment.
--verbose, -v	boolean	no	False	Print verbose output.
--json	boolean	no	False	Output result as JSON.
--auto-add-deps	boolean	no	False	Automatically install missing kernel dependencies (e.g., IJulia for Julia environments).

calkit nb execute

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.

Usage:

calkit nb execute [OPTIONS] PATH

Arguments:

Argument	Type	Required	Default	Description
path	text	yes

Options:

Option	Type	Required	Default	Description
--environment, -e	text	no		Name or path to the spec of the environment in which to run the notebook.
--to	text	no	notebook	Output format ('html' or 'notebook').
--no-check	boolean	no	False	Do not check environment before executing.
--param, -p	text	no		Parameter to pass to the notebook in key=value format.
--params-json, -j	text	no		JSON string to parse as parameters to pass to the notebook.
--params-base64, -b	text	no		Base64-encoded JSON string to parse as parameters to pass to the notebook.
--language, -l	text	no		Notebook language; if 'matlab', MATLAB kernel must be available in environment.
--no-replace	boolean	no	False	Do not replace notebook outputs from executed version.
--verbose, -v	boolean	no	False	Print verbose output.

calkit list

List Calkit objects.

Command	Description
notebooks
figures
datasets
publications
references
envs	List environments in the project.
environments	List environments in the project.
templates
procedures
releases	List releases.
stages	List stages.

calkit list notebooks

Usage:

calkit list notebooks

calkit list figures

Usage:

calkit list figures

calkit list datasets

Usage:

calkit list datasets

calkit list publications

Usage:

calkit list publications

calkit list references

Usage:

calkit list references

calkit list envs

List environments in the project.

Usage:

calkit list envs

calkit list environments

List environments in the project.

Usage:

calkit list environments

calkit list templates

Usage:

calkit list templates

calkit list procedures

Usage:

calkit list procedures

calkit list releases

List releases.

Usage:

calkit list releases

calkit list stages

List stages.

Usage:

calkit list stages [OPTIONS]

Options:

Option	Type	Required	Default	Description
--kind, -k	text	no		Filter stages by kind.

calkit describe

Describe things.

Command	Description
system	Describe the system.

calkit describe system

Describe the system.

Usage:

calkit describe system

calkit import

Import objects.

Command	Description
dataset	Import a dataset.
environment	Import an environment from another project.
zenodo	Import files from a Zenodo record.

calkit import dataset

Import a dataset.

Currently only supports datasets kept in DVC, not Git.

Usage:

calkit import dataset [OPTIONS] SRC-PATH [DEST-PATH]

Arguments:

Argument	Type	Required	Default	Description
src_path	text	yes		Location of dataset, including project owner and name, e.g., someone/some-project/data/some-data.csv
dest_path	text	no		Output path at which to save.

Options:

Option	Type	Required	Default	Description
--filter-paths	text	no		Filter paths in target dataset if it's a folder.
--no-commit	boolean	no	False	Do not commit changes to repo.
--no-dvc-pull	boolean	no	False	Do not pull imported dataset with DVC.
--overwrite, -f	boolean	no	False	Force adding the dataset even if it already exists.
--http	boolean	no	False	Use the legacy HTTP URL for the imported project's DVC remote instead of ck://.

calkit import environment

Import an environment from another project.

Usage:

calkit import environment [OPTIONS] SRC

Arguments:

Argument	Type	Required	Default	Description
src	text	yes		Environment location and name, e.g., someone/some-project:env-name. If not present, the Calkit Cloud will be queried.

Options:

Option	Type	Required	Default	Description
--path	text	no		Output path at which to save.
--name, -n	text	no		Name to use in the destination project.
--overwrite, -f	boolean	no	False	Force adding the dataset even if it already exists.
--no-commit	boolean	no	False	Do not commit changes.

calkit import zenodo

Import files from a Zenodo record.

Usage:

calkit import zenodo [OPTIONS] SRC DEST-DIR

Arguments:

Argument	Type	Required	Default	Description
src	text	yes		Source URL or DOI.
dest_dir	text	yes		Destination folder. Will be created if it doesn't exist

Options:

Option	Type	Required	Default	Description
--kind, -k	text	no		What kind of artifact is being imported, e.g., a figure, dataset, publication.
--name-like	text	no		Filter for file names like this. Glob patterns accepted.
--name-not-like	text	no		Exclude names matching pattern.
--storage	text	no		Storage backend to use (Git or DVC). If not specified, will be chosen based on size.
--no-commit	boolean	no	False	Do not commit changes to project.

calkit office

Work with Microsoft Office.

Command	Description
excel-chart-to-image	Extract a chart from Excel and save to image.
word-to-pdf	Convert a Word document to PDF.

calkit office excel-chart-to-image

Extract a chart from Excel and save to image.

Usage:

calkit office excel-chart-to-image [OPTIONS] INPUT-FPATH OUTPUT-FPATH

Arguments:

Argument	Type	Required	Default	Description
input_fpath	text	yes		Input Excel file path.
output_fpath	text	yes		Output image file path.

Options:

Option	Type	Required	Default	Description
--sheet	integer	no	1	Sheet in workbook.
--chart-index	integer	no	0	Chart index.

calkit office word-to-pdf

Convert a Word document to PDF.

Usage:

calkit office word-to-pdf [OPTIONS] INPUT-FPATH

Arguments:

Argument	Type	Required	Default	Description
input_fpath	text	yes		Input Word document file path.

Options:

Option	Type	Required	Default	Description
-o, --output	text	no		Output file path. If not specified, will be the same as input with a .pdf extension.

calkit update

Update objects.

Command	Description
devcontainer	Update a project's devcontainer to match the latest Calkit spec.
license	Update license with a reasonable default (MIT for code, CC-BY-4.0 for other files).
release	Update a release.
vscode-config	Update a project's VS Code config to match the latest Calkit recommendations.
github-actions	Update a project's GitHub Actions to match the latest Calkit recommendations.
notebook	Update notebook information.
env	Update an environment.
environment	Update an environment.

calkit update devcontainer

Update a project's devcontainer to match the latest Calkit spec.

Usage:

calkit update devcontainer [OPTIONS]

Options:

Option	Type	Required	Default	Description
--wdir	text	no		Working directory. By default will run current working directory.
--no-commit	boolean	no	False	Do not create a Git commit for the updated devcontainer.

calkit update license

Update license with a reasonable default (MIT for code, CC-BY-4.0 for other files).

Usage:

calkit update license [OPTIONS]

Options:

Option	Type	Required	Default	Description
--copyright-holder, -c	text	yes		Copyright holder, e.g., your full name.
--no-commit	boolean	no	False	Do not create a Git commit for the updated license.

calkit update release

Update a release.

Usage:

calkit update release [OPTIONS]

Options:

Option	Type	Required	Default	Description
--name, -n	text	no		Release name.
--latest	boolean	no	False	Update latest release.
--delete	boolean	no	False	Delete release.
--publish	boolean	no	False	Publish the release.
--reupload	boolean	no	False	Reupload files.
--no-github	boolean	no	False	Do not create a release on GitHub.
--no-push-tags	boolean	no	False	Do not push Git tags to remote repository.

calkit update vscode-config

Update a project's VS Code config to match the latest Calkit recommendations.

Usage:

calkit update vscode-config [OPTIONS]

Options:

Option	Type	Required	Default	Description
--wdir	text	no		Working directory. By default will run current working directory.
--no-commit	boolean	no	False	Do not create a Git commit for the updated VS Code config.

calkit update github-actions

Update a project's GitHub Actions to match the latest Calkit recommendations.

Usage:

calkit update github-actions [OPTIONS]

Options:

Option	Type	Required	Default	Description
--wdir	text	no		Working directory. By default will run current working directory.
--no-commit	boolean	no	False	Do not create a Git commit for the updated GitHub Actions.

calkit update notebook

Update notebook information.

Updates the notebook's environment association in either the 'notebooks' section or the appropriate 'pipeline' stage, depending on whether the notebook has a corresponding pipeline stage.

Usage:

calkit update notebook [OPTIONS] NOTEBOOK-PATH

Arguments:

Argument	Type	Required	Default	Description
notebook_path	text	yes		Path to the notebook file (relative to workspace)

Options:

Option	Type	Required	Default	Description
--set-env	text	no		Environment name to associate with the notebook
--json	boolean	no	False	Output result as JSON.

calkit update env

Update an environment.

Currently only supports adding packages to Julia environments.

Usage:

calkit update env [OPTIONS]

Options:

Option	Type	Required	Default	Description
--name, -n	text	yes		Name of the environment to update
--add	text	no		Add package to environment,

calkit update environment

Update an environment.

Currently only supports adding packages to Julia environments.

Usage:

calkit update environment [OPTIONS]

Options:

Option	Type	Required	Default	Description
--name, -n	text	yes		Name of the environment to update
--add	text	no		Add package to environment,

calkit check

Check things.

Command	Description
repro	Check the reproducibility of a project.
environment	Check that an environment is up-to-date.
julia-env	Check a Julia environment and instantiate only when project, manifest, and package cache state have changed.
environments
envs	Check that all environments are up-to-date.
renv	Check an renv R environment, initializing if needed.
docker-env	Check that Docker environment is up-to-date.
conda-env	Check a conda environment and rebuild if necessary.
venv	Check a Python virtual environment (uv or virtualenv).
matlab-env	Check a MATLAB environment matches its spec and export a JSON lock file.
deps	Check that a project's system-level dependencies are set up correctly.
dependencies	Check that a project's system-level dependencies are set up correctly.
env-vars	Check that the project's required environmental variables exist.
pipeline	Check that the project pipeline is defined correctly.
call	Check that a command succeeds and run an alternate if not.

calkit check repro

Check the reproducibility of a project.

Usage:

calkit check repro [OPTIONS]

Options:

Option	Type	Required	Default	Description
--wdir	text	no	.	Project working directory.

calkit check environment

Check that an environment is up-to-date.

Usage:

calkit check environment [OPTIONS]

Options:

Option	Type	Required	Default	Description
--name, -n	text	yes		Name of the environment to check.
--verbose	boolean	no	False	Print verbose output.

calkit check julia-env

Check a Julia environment and instantiate only when project, manifest, and package cache state have changed.

Usage:

calkit check julia-env [OPTIONS] [ENV-PATH]

Arguments:

Argument	Type	Required	Default	Description
env_path	text	no	Project.toml	Path to Julia Project.toml file.

Options:

Option	Type	Required	Default	Description
--julia	text	no		Julia version to enforce (e.g., 1.11).
--verbose	boolean	no	False	Print verbose output.

calkit check environments

Usage:

calkit check environments [OPTIONS]

Options:

Option	Type	Required	Default	Description
--verbose	boolean	no	False	Print verbose output.

calkit check envs

Check that all environments are up-to-date.

Usage:

calkit check envs [OPTIONS]

Options:

Option	Type	Required	Default	Description
--verbose	boolean	no	False	Print verbose output.

calkit check renv

Check an renv R environment, initializing if needed.

Usage:

calkit check renv [OPTIONS] ENV-PATH

Arguments:

Argument	Type	Required	Default	Description
env_path	text	yes		Path to DESCRIPTION file or renv environment directory.

Options:

Option	Type	Required	Default	Description
--verbose	boolean	no	False	Print verbose output.

calkit check docker-env

Check that Docker environment is up-to-date.

Usage:

calkit check docker-env [OPTIONS] TAG

Arguments:

Argument	Type	Required	Default	Description
tag	text	yes		Image tag.

Options:

Option	Type	Required	Default	Description
-i, --input	text	no		Path to input Dockerfile, if applicable.
--output, -o	text	no		Path to which existing environment should be exported. If not specified, will have the same filename with '-lock' appended to it, keeping the same extension.
--input	text	no		Alternative lock file input paths to read.
--input-delete	text	no		Alternative lock input file paths to read and remove (i.e., legacy paths).
--platform	text	no		Which platform(s) to build for.
--user	text	no		Which user to run the container as.
--wdir	text	no		Working directory inside the container.
--dep, -d	text	no		Declare an explicit dependency for this Docker image.
--env-var, -e	text	no		Declare an explicit environment variable for the container.
--port, -p	text	no		Declare an explicit port for the container.
--gpus, -g	text	no		Declare an explicit GPU requirement for the container.
--arg, -a	text	no		Declare an explicit run argument for the container.
--quiet, -q	boolean	no	False	Be quiet.

calkit check conda-env

Check a conda environment and rebuild if necessary.

Usage:

calkit check conda-env [OPTIONS]

Options:

Option	Type	Required	Default	Description
--file, -f	text	no	environment.yml	Path to conda environment YAML file.
--output, -o	text	no		Path to which existing environment should be exported. If not specified, will have the same filename with '-lock' appended to it, keeping the same extension.
--input	text	no		Alternative lock file input paths.
--input-delete	text	no		Alternative lock file input paths to delete after use.
--relaxed	boolean	no	False	Treat conda and pip dependencies as equivalent.
--quiet, -q	boolean	no	False	Be quiet.

calkit check venv

Check a Python virtual environment (uv or virtualenv).

Usage:

calkit check venv [OPTIONS] [PATH]

Arguments:

Argument	Type	Required	Default	Description
path	text	no	requirements.txt	Path to requirements file.

Options:

Option	Type	Required	Default	Description
--prefix	text	no	.venv	Prefix.
--output, -o	text	no		Path to which existing environment should be exported. If not specified, will have the same filename with '-lock' appended to it, keeping the same extension.
--input	text	no		Alternative lock file input paths.
--input-delete	text	no		Alternative lock file input paths to delete after use.
--wdir	text	no		Working directory. Defaults to current working directory.
--uv	boolean	no	True	Use uv.
--python	text	no		Python version to specify if using uv.
--quiet	boolean	no	False	Do not print any output
--verbose	boolean	no	False	Print verbose output.

calkit check matlab-env

Check a MATLAB environment matches its spec and export a JSON lock file.

Usage:

calkit check matlab-env [OPTIONS]

Options:

Option	Type	Required	Default	Description
--name, -n	text	yes		Environment name in calkit.yaml.
--output, -o	text	yes

calkit check deps

Check that a project's system-level dependencies are set up correctly.

Usage:

calkit check deps [OPTIONS]

Options:

Option	Type	Required	Default	Description
--verbose, -v	boolean	no	False	Print verbose output

calkit check dependencies

Check that a project's system-level dependencies are set up correctly.

Usage:

calkit check dependencies [OPTIONS]

Options:

Option	Type	Required	Default	Description
--verbose, -v	boolean	no	False	Print verbose output

calkit check env-vars

Check that the project's required environmental variables exist.

Usage:

calkit check env-vars [OPTIONS]

Options:

Option	Type	Required	Default	Description
--verbose, -v	boolean	no	False	Print verbose output

calkit check pipeline

Check that the project pipeline is defined correctly.

Usage:

calkit check pipeline [OPTIONS]

Options:

Option	Type	Required	Default	Description
--compile, -c	boolean	no	False	Compile the pipeline to DVC stages and merge into dvc.yaml.

calkit check call

Check that a command succeeds and run an alternate if not.

Usage:

calkit check call [OPTIONS] CMD

Arguments:

Argument	Type	Required	Default	Description
cmd	text	yes		Command to check.

Options:

Option	Type	Required	Default	Description
--if-error	text	yes		Command to run if there is an error.

calkit latex

Work with LaTeX.

Command	Description
from-json	Convert a JSON file to LaTeX.
build	Build a PDF of a LaTeX document with latexmk.

calkit latex from-json

Convert a JSON file to LaTeX.

This is useful for referencing calculated values in LaTeX documents.

Usage:

calkit latex from-json [OPTIONS] INPUT-FPATHS...

Arguments:

Argument	Type	Required	Default	Description
input_fpaths	text	yes		Input JSON file path(s).

Options:

Option	Type	Required	Default	Description
--output, -o	text	yes		Output LaTeX file path(s).
--command	text	no		Command name to use in LaTeX output.
--format-json	text	no		Additional JSON input to use for formatting. Can be used to add extra keys with simple expressions, etc.

calkit latex build

Build a PDF of a LaTeX document with latexmk.

If a Calkit environment is not specified, latexmk will be run in the system environment if available. If not available, a TeX Live Docker container will be used.

Usage:

calkit latex build [OPTIONS] TEX-FILE

Arguments:

Argument	Type	Required	Default	Description
tex_file	text	yes		The .tex file to compile.

Options:

Option	Type	Required	Default	Description
--env, -e	text	no		Environment in which to run latexmk, if applicable.
--no-check	boolean	no	False	Don't check the environment is valid before running latexmk.
--latexmk-rc, -r	text	no		Path to a latexmkrc file to use for compilation.
--no-synctex	boolean	no	False	Don't generate synctex file for source-to-pdf mapping.
--force, -f	boolean	no	False	Force latexmk to recompile all files, even if they are up to date.
--verbose, -v	boolean	no	False	Print verbose output.

calkit overleaf

Interact with Overleaf.

Command	Description
import	Import a publication from an Overleaf project.
sync	Sync folders with Overleaf.
status	Check the status of folders synced with Overleaf in a project.

calkit overleaf import

Import a publication from an Overleaf project.

Usage:

calkit overleaf import [OPTIONS] SRC-URL DEST-DIR

Arguments:

Argument	Type	Required	Default	Description
src_url	text	yes		Overleaf project URL, e.g., https://www.overleaf.com/project/6800005973cb2e35.
dest_dir	text	yes		Directory at which to save in the project, e.g., 'paper'.

Options:

Option	Type	Required	Default	Description
--title, -t	text	no		Title of the publication.
--target, -T	text	no		Target TeX file path inside Overleaf project.
--description, -d	text	no		Description of the publication.
--kind	text	no		What of the publication this is, e.g., 'journal-article'.
--sync-path, -s	text	no		Paths to sync from the Overleaf project, e.g., 'main.tex'. Note that multiple can be specified.
--push-path, -p	text	no		Paths to push to the Overleaf project, e.g., 'figures'. Note that these are relative to the publication working directory.
--no-commit	boolean	no	False	Do not commit changes to repo.
--overwrite, -f	boolean	no	False	Force adding the publication even if it already exists.
--push-only, -P	boolean	no	False	Push local files to Overleaf without pulling. Useful when initializing a new Overleaf project from local files.

calkit overleaf sync

Sync folders with Overleaf.

Usage:

calkit overleaf sync [OPTIONS] [PATHS...]

Arguments:

Argument	Type	Required	Default	Description
paths	text	no		Paths to sync with Overleaf, e.g., 'paper/paper.pdf'. If not provided, all Overleaf publications will be synced.

Options:

Option	Type	Required	Default	Description
--no-commit	boolean	no	False	Do not commit the changes to the project repo. Changes will always be committed to Overleaf.
--auto-commit	boolean	no	False	Automatically commit changes to the project repo if a synced folder has changes.
--no-push	boolean	no	False	Do not push the changes to the main project remote. Changes will always be pushed to Overleaf.
--verbose	boolean	no	False	Enable verbose output.
--resolve, -r	boolean	no	False	Mark merge conflicts as resolved before committing.
--push-only, -P	boolean	no	False	Only push local files to Overleaf without pulling from Overleaf. Useful when initializing a new Overleaf project from local files.

calkit overleaf status

Check the status of folders synced with Overleaf in a project.

Usage:

calkit overleaf status [PATHS...]

Arguments:

Argument	Type	Required	Default	Description
paths	text	no		Paths synced with Overleaf, e.g., 'paper'. If not provided, all Overleaf syncs will be checked.

calkit cloud

Interact with a Calkit Cloud.

Command	Description
get	Get a resource from the Cloud API.
login	Login to the Calkit Cloud.

calkit cloud get

Get a resource from the Cloud API.

Usage:

calkit cloud get ENDPOINT

Arguments:

Argument	Type	Required	Default	Description
endpoint	text	yes		API endpoint

calkit cloud login

Login to the Calkit Cloud.

First try a GET request to the /user endpoint to check if the user is already logged in. If not, perform OAuth device flow.

Usage:

calkit cloud login [OPTIONS]

Options:

Option	Type	Required	Default	Description
--force, -f	boolean	no	False	Force logging in again even if already authenticated. Will store a new token in your local config.

calkit slurm

Work with SLURM.

Command	Description
batch	Submit a SLURM batch job for the project.
queue	List SLURM jobs submitted via Calkit.
cancel	Cancel SLURM jobs by their name in the project.
logs	Get the logs for a SLURM job by its name in the project.

calkit slurm batch

Submit a SLURM batch job for the project.

Duplicates are not allowed, so if one is already running or queued with the same name, we'll wait for it to finish. The only exception is if the dependencies have changed, in which case any queued or running jobs will be canceled and a new one submitted.

Usage:

calkit slurm batch [OPTIONS] TARGET [ARGS...]

Arguments:

Argument	Type	Required	Default	Description
target	text	yes		The target to run. This can be a shell script or an executable.
args	text	no		Arguments for sbatch, the first of which should be the script.

Options:

Option	Type	Required	Default	Description
--name, -n	text	yes		Job name.
--environment, -e	text	yes		Calkit (slurm) environment to use for the job.
--dep, -d	text	no		Additional dependencies to track, which if changed signify a job is invalid.
--out, -o	text	no		Non-persistent output files or directories produced by the job, which will be deleted before submitting a new job.
--sbatch-option, -s	text	no		Additional options to pass to sbatch (no spaces allowed).
--setup	text	no		Shell setup command to run before launching the target (repeat for multiple commands).
--log-path	text	no		Output log path.
--command	boolean	no		Whether the target is a command instead of a script.

calkit slurm queue

List SLURM jobs submitted via Calkit.

Usage:

calkit slurm queue

calkit slurm cancel

Cancel SLURM jobs by their name in the project.

Usage:

calkit slurm cancel NAMES...

Arguments:

Argument	Type	Required	Default	Description
names	text	yes		Names of jobs to cancel.

calkit slurm logs

Get the logs for a SLURM job by its name in the project.

Usage:

calkit slurm logs [OPTIONS] [NAMES...]

Arguments:

Argument	Type	Required	Default	Description
names	text	no		Names of the jobs to get logs for.

Options:

Option	Type	Required	Default	Description
--follow, -f	boolean	no	False	Follow the log output like tail -f.

calkit dev

Developer tools.

Command	Description
python	Start an Python shell in Calkit's environment.
ipython	Start an IPython shell in Calkit's environment.

calkit dev python

Start an Python shell in Calkit's environment.

Usage:

calkit dev python [OPTIONS]

calkit dev ipython

Start an IPython shell in Calkit's environment.

Usage:

calkit dev ipython [OPTIONS]