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Calkit
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calkit/calkit
Calkit
calkit/calkit
Home
Installation
Quickstart
Sharing, collaboration, and backup (Calkit hub)
Sharing, collaboration, and backup (Calkit hub)
Running your own
Use with AI tools
Questions, hypotheses, answers, and evidence
Version control
The calkit.yaml file
Project requirements and setup
Environments
The pipeline
The pipeline
Runnable Markdown
Running and logging
Manual steps
Notebooks
JupyterLab
High performance computing (HPC)
Datasets
Provenance
References
Calculations
Apps
Releasing/archiving projects and artifacts
Adding compute resources
LaTeX documents
Overleaf integration
Browser extension
Subprojects
Examples
Tutorials
Tutorials
🎥 Creating your first project
🎥 Composing a pipeline from multiple Jupyter notebooks in JupyterLab
Converting an existing project to a Calkit project
OpenFOAM, Docker, and Reviewer 2
Adding a new LaTeX-based publication with its own Docker build environment
Collaborating on a LaTeX document with GitHub Codespaces
Collaborating on a LaTeX document using Microsoft Word for feedback
Using a Jupyter Notebook as a reproducible pipeline
Defining and executing procedures
Keeping track of conda environments
Using Microsoft Office
🎥 Using MATLAB
Running Calkit in GitHub Actions
Making a README runnable
Connect a Jupyter Notebook to a kernel in a SLURM environment in VS Code
Declarative, structured prompting to make AI agents work reproducibly
Writing first: let the paper drive the project
CLI reference
CLI reference
Table of contents
Top-level commands
Top-level command details
calkit init
calkit clone
calkit status|st
calkit diff
calkit add
calkit commit
calkit save|sv
calkit pull
calkit push
calkit ignore
calkit run
calkit manual-step
calkit xenv|runenv
calkit install
calkit xproc|runproc
calkit calc
calkit set-env-var
calkit upgrade
calkit switch-branch
calkit merge
calkit stash
calkit dvc
calkit jupyter
calkit map-paths
calkit xr
Command groups
calkit config
calkit config set
calkit config get
calkit config unset
calkit config remote
calkit config remote-auth
calkit config list
calkit config github-ssh
calkit config github-codespace
calkit new|create
calkit new|create project
calkit new|create figure|fig
calkit new|create result
calkit new|create presentation|pres
calkit new|create question
calkit new|create comment
calkit new|create notebook|nb
calkit new|create docker-env
calkit new|create foreach-stage
calkit new|create dataset
calkit new|create publication|pub
calkit new|create conda-env
calkit new|create uv-env
calkit new|create slurm-env
calkit new|create pbs-env
calkit new|create uv-venv
calkit new|create venv
calkit new|create pixi-env
calkit new|create julia-env
calkit new|create renv
calkit new|create nix-env
calkit new|create status
calkit new|create python-script-stage
calkit new|create julia-script-stage
calkit new|create matlab-script-stage
calkit new|create latex-stage
calkit new|create jupyter-notebook-stage
calkit new|create release
calkit new|create workspace
calkit delete|rm
calkit delete|rm question
calkit delete|rm comment
calkit notebooks|nb
calkit notebooks|nb clean
calkit notebooks|nb clean-all
calkit notebooks|nb check-kernel
calkit notebooks|nb execute
calkit notebooks|nb export-marimo-wasm
calkit list|ls
calkit list|ls notebooks|nb
calkit list|ls figures|figs
calkit list|ls datasets
calkit list|ls results
calkit list|ls presentations|pres
calkit list|ls tables|tbls
calkit list|ls questions|q
calkit list|ls comments
calkit list|ls publications|pubs
calkit list|ls misc
calkit list|ls references|refs
calkit list|ls environments|envs
calkit list|ls requirements|reqs
calkit list|ls templates
calkit list|ls installers
calkit list|ls procedures
calkit list|ls releases
calkit list|ls stages
calkit list|ls subprojects
calkit list|ls latex-diffs
calkit list|ls remotes
calkit list|ls imports
calkit show
calkit show question|q
calkit show latex-diff
calkit show table|tbl
calkit show result|res
calkit describe|desc
calkit describe|desc system
calkit describe|desc environment|env
calkit describe|desc environments|envs
calkit describe|desc subprojects
calkit describe|desc schema
calkit import
calkit import dataset
calkit import path
calkit import figure
calkit import environment
calkit import zenodo
calkit office
calkit office excel-chart-to-image
calkit office word-to-pdf
calkit open
calkit open project
calkit export
calkit export inkscape
calkit export gimp
calkit update
calkit update devcontainer
calkit update license
calkit update release
calkit update vscode-config
calkit update github-actions
calkit update notebook
calkit update markdown
calkit update agent-skills
calkit update uv-env
calkit update pixi-env
calkit update julia-env
calkit update conda-env
calkit update docker-env
calkit update latex-image
calkit update slurm-env
calkit update env
calkit update environment
calkit update stage
calkit update figure
calkit update question
calkit update path-storage
calkit update dataset
calkit update hub
calkit update comment
calkit check
calkit check repro
calkit check environment
calkit check julia-env
calkit check environments
calkit check envs
calkit check renv
calkit check docker-env
calkit check conda-env
calkit check venv
calkit check matlab-env
calkit check reqs|requirements
calkit check stage-runs
calkit check env-vars
calkit check pipeline
calkit check storage
calkit check call
calkit check questions
calkit check references|refs
calkit fix
calkit fix merge-conflicts
calkit fix storage
calkit latex|tex
calkit latex|tex from-json
calkit latex|tex from-questions
calkit latex|tex from-markdown
calkit latex|tex map-components
calkit latex|tex build
calkit latex|tex diff
calkit latex|tex to-docx
calkit latex|tex merge-docx
calkit overleaf|ol
calkit overleaf|ol login
calkit overleaf|ol import
calkit overleaf|ol link
calkit overleaf|ol sync
calkit overleaf|ol status|st
calkit overleaf|ol push
calkit overleaf|ol pull
calkit hub|cloud
calkit hub|cloud get
calkit hub|cloud login
calkit hub|cloud config
calkit hub|cloud config list
calkit hub|cloud config set
calkit hub|cloud config get
calkit hub|cloud config unset
calkit hub|cloud link
calkit hub|cloud link install
calkit hub|cloud link start
calkit hub|cloud link status
calkit hub|cloud link stop
calkit hub|cloud link restart
calkit hub|cloud link logs
calkit hub|cloud link add-workspace
calkit hub|cloud link uninstall
calkit scheduler|sch
calkit scheduler|sch batch
calkit scheduler|sch queue|q
calkit scheduler|sch cancel
calkit scheduler|sch logs
calkit sync
calkit sync git
calkit sync dvc
calkit sync all
calkit sync import
calkit sync overleaf
Help and support
Reproducibility
Calkit vs. other tools
ROI calculator
Governance
Testimonials
Privacy policy
Acknowledgements
Table of contents
Top-level commands
Top-level command details
calkit init
calkit clone
calkit status|st
calkit diff
calkit add
calkit commit
calkit save|sv
calkit pull
calkit push
calkit ignore
calkit run
calkit manual-step
calkit xenv|runenv
calkit install
calkit xproc|runproc
calkit calc
calkit set-env-var
calkit upgrade
calkit switch-branch
calkit merge
calkit stash
calkit dvc
calkit jupyter
calkit map-paths
calkit xr
Command groups
calkit config
calkit config set
calkit config get
calkit config unset
calkit config remote
calkit config remote-auth
calkit config list
calkit config github-ssh
calkit config github-codespace
calkit new|create
calkit new|create project
calkit new|create figure|fig
calkit new|create result
calkit new|create presentation|pres
calkit new|create question
calkit new|create comment
calkit new|create notebook|nb
calkit new|create docker-env
calkit new|create foreach-stage
calkit new|create dataset
calkit new|create publication|pub
calkit new|create conda-env
calkit new|create uv-env
calkit new|create slurm-env
calkit new|create pbs-env
calkit new|create uv-venv
calkit new|create venv
calkit new|create pixi-env
calkit new|create julia-env
calkit new|create renv
calkit new|create nix-env
calkit new|create status
calkit new|create python-script-stage
calkit new|create julia-script-stage
calkit new|create matlab-script-stage
calkit new|create latex-stage
calkit new|create jupyter-notebook-stage
calkit new|create release
calkit new|create workspace
calkit delete|rm
calkit delete|rm question
calkit delete|rm comment
calkit notebooks|nb
calkit notebooks|nb clean
calkit notebooks|nb clean-all
calkit notebooks|nb check-kernel
calkit notebooks|nb execute
calkit notebooks|nb export-marimo-wasm
calkit list|ls
calkit list|ls notebooks|nb
calkit list|ls figures|figs
calkit list|ls datasets
calkit list|ls results
calkit list|ls presentations|pres
calkit list|ls tables|tbls
calkit list|ls questions|q
calkit list|ls comments
calkit list|ls publications|pubs
calkit list|ls misc
calkit list|ls references|refs
calkit list|ls environments|envs
calkit list|ls requirements|reqs
calkit list|ls templates
calkit list|ls installers
calkit list|ls procedures
calkit list|ls releases
calkit list|ls stages
calkit list|ls subprojects
calkit list|ls latex-diffs
calkit list|ls remotes
calkit list|ls imports
calkit show
calkit show question|q
calkit show latex-diff
calkit show table|tbl
calkit show result|res
calkit describe|desc
calkit describe|desc system
calkit describe|desc environment|env
calkit describe|desc environments|envs
calkit describe|desc subprojects
calkit describe|desc schema
calkit import
calkit import dataset
calkit import path
calkit import figure
calkit import environment
calkit import zenodo
calkit office
calkit office excel-chart-to-image
calkit office word-to-pdf
calkit open
calkit open project
calkit export
calkit export inkscape
calkit export gimp
calkit update
calkit update devcontainer
calkit update license
calkit update release
calkit update vscode-config
calkit update github-actions
calkit update notebook
calkit update markdown
calkit update agent-skills
calkit update uv-env
calkit update pixi-env
calkit update julia-env
calkit update conda-env
calkit update docker-env
calkit update latex-image
calkit update slurm-env
calkit update env
calkit update environment
calkit update stage
calkit update figure
calkit update question
calkit update path-storage
calkit update dataset
calkit update hub
calkit update comment
calkit check
calkit check repro
calkit check environment
calkit check julia-env
calkit check environments
calkit check envs
calkit check renv
calkit check docker-env
calkit check conda-env
calkit check venv
calkit check matlab-env
calkit check reqs|requirements
calkit check stage-runs
calkit check env-vars
calkit check pipeline
calkit check storage
calkit check call
calkit check questions
calkit check references|refs
calkit fix
calkit fix merge-conflicts
calkit fix storage
calkit latex|tex
calkit latex|tex from-json
calkit latex|tex from-questions
calkit latex|tex from-markdown
calkit latex|tex map-components
calkit latex|tex build
calkit latex|tex diff
calkit latex|tex to-docx
calkit latex|tex merge-docx
calkit overleaf|ol
calkit overleaf|ol login
calkit overleaf|ol import
calkit overleaf|ol link
calkit overleaf|ol sync
calkit overleaf|ol status|st
calkit overleaf|ol push
calkit overleaf|ol pull
calkit hub|cloud
calkit hub|cloud get
calkit hub|cloud login
calkit hub|cloud config
calkit hub|cloud config list
calkit hub|cloud config set
calkit hub|cloud config get
calkit hub|cloud config unset