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Use Calkit pipeline (#5)
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‎.calkit/env-locks/py.yml

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channels:
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- conda-forge
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dependencies:
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- brotli=1.1.0=hd74edd7_2
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- brotli-bin=1.1.0=hd74edd7_2
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- bzip2=1.0.8=h99b78c6_7
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- ca-certificates=2025.4.26=hbd8a1cb_0
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- contourpy=1.3.2=py312hb23fbb9_0
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- cycler=0.12.1=pyhd8ed1ab_1
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- fonttools=4.58.0=py312h998013c_0
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- freetype=2.13.3=hce30654_1
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- kiwisolver=1.4.8=py312h2c4a281_0
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- lcms2=2.17=h7eeda09_0
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- lerc=4.0.0=hd64df32_1
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- libblas=3.9.0=31_h10e41b3_openblas
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- libbrotlicommon=1.1.0=hd74edd7_2
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- libbrotlidec=1.1.0=hd74edd7_2
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- libbrotlienc=1.1.0=hd74edd7_2
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- libcblas=3.9.0=31_hb3479ef_openblas
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- libcxx=20.1.5=ha82da77_0
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- libdeflate=1.24=h5773f1b_0
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- libexpat=2.7.0=h286801f_0
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- libffi=3.4.6=h1da3d7d_1
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- libfreetype=2.13.3=hce30654_1
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- libfreetype6=2.13.3=h1d14073_1
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- libgfortran=14.2.0=heb5dd2a_105
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- libgfortran5=14.2.0=h2c44a93_105
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- libjpeg-turbo=3.1.0=h5505292_0
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- liblapack=3.9.0=31_hc9a63f6_openblas
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- liblzma=5.8.1=h39f12f2_1
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- libopenblas=0.3.29=openmp_hf332438_0
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- libpng=1.6.47=h3783ad8_0
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- libsqlite=3.49.2=h3f77e49_0
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- libtiff=4.7.0=h2f21f7c_5
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- libwebp-base=1.5.0=h2471fea_0
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- libxcb=1.17.0=hdb1d25a_0
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- libzlib=1.3.1=h8359307_2
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- llvm-openmp=20.1.5=hdb05f8b_0
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- matplotlib=3.10.3=py312h1f38498_0
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- matplotlib-base=3.10.3=py312hdbc7e53_0
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- munkres=1.1.4=pyh9f0ad1d_0
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- ncurses=6.5=h5e97a16_3
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- numpy=2.2.6=py312h7c1f314_0
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- openjpeg=2.5.3=h8a3d83b_0
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- openssl=3.5.0=h81ee809_1
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- packaging=25.0=pyh29332c3_1
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- pandas=2.2.3=py312hcb1e3ce_3
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- pillow=11.2.1=py312h50aef2c_0
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- pip=25.1.1=pyh8b19718_0
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- pthread-stubs=0.4=hd74edd7_1002
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- pyparsing=3.2.3=pyhd8ed1ab_1
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- python=3.12.10=hc22306f_0_cpython
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- python-dateutil=2.9.0.post0=pyhff2d567_1
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- python-tzdata=2025.2=pyhd8ed1ab_0
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- python_abi=3.12=7_cp312
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- pytz=2025.2=pyhd8ed1ab_0
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- qhull=2020.2=h420ef59_5
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- readline=8.2=h1d1bf99_2
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- setuptools=80.8.0=pyhff2d567_0
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- six=1.17.0=pyhd8ed1ab_0
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- tk=8.6.13=h5083fa2_1
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- tornado=6.5.1=py312hea69d52_0
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- tzdata=2025b=h78e105d_0
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- unicodedata2=16.0.0=py312hea69d52_0
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- wheel=0.45.1=pyhd8ed1ab_1
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- xorg-libxau=1.0.12=h5505292_0
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- xorg-libxdmcp=1.1.5=hd74edd7_0
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- zstd=1.5.7=h6491c7d_2
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name: calkit-example-basic

‎.calkit/env-locks/tex.json

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[
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{
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"RepoTags": [
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"texlive/texlive:latest-full"
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],
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"Parent": "",
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"Comment": "buildkit.dockerfile.v0",
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"Created": "2025-05-11T13:45:24.681068416Z",
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"Author": "",
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"Config": {
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"Hostname": "",
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"Domainname": "",
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"User": "",
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"AttachStdin": false,
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"AttachStdout": false,
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"AttachStderr": false,
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"Tty": false,
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"OpenStdin": false,
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"StdinOnce": false,
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"Env": [
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"PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin",
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"LANG=C.UTF-8",
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"LC_ALL=C.UTF-8",
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"TEXLIVE_INSTALL_NO_CONTEXT_CACHE=1",
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"NOPERLDOC=1",
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"DEBIAN_FRONTEND=noninteractive"
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],
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"Cmd": [
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"bash"
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],
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"Image": "",
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"Volumes": null,
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"WorkingDir": "/workdir",
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"Entrypoint": null,
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"OnBuild": null,
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"Labels": {
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"org.opencontainers.image.authors": "Island of TeX",
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"org.opencontainers.image.source": "https://gitlab.com/islandoftex/images/texlive/-/blob/master/Dockerfile",
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"org.opencontainers.image.url": "https://gitlab.com/islandoftex/images/texlive"
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}
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},
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"Architecture": "arm64",
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"Os": "linux",
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"Size": 2409562089,
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"GraphDriver": {
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"Data": null,
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"Name": "overlayfs"
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},
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"RootFS": {
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"Type": "layers",
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"Layers": [
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"sha256:f20086072b1d2fffdc8a8a3afc546d1ecb13a9047ac9cc6c941e9783ba2c1c40",
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"sha256:cc4ebc54dd55374e26421ee3710a3cb932690ec294b3665230f54ae0ddbbacec",
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"sha256:2ff8561f9f970e166f982b4a6f584a0ce9a275836a281d9e5b62fb27d6a99e8f",
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"sha256:5f70bf18a086007016e948b04aed3b82103a36bea41755b6cddfaf10ace3c6ef",
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"sha256:6b5bb1acd1ecb71e7df10f16fba58ee8afbc1a4295b26486766742471c7380bf",
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"sha256:84cc1f955c35ccf33e8c50a7e8cab52e5c5e186124d3d2dc294de9d227ca2f9e",
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"sha256:e408bd808583af5c8c473d3a99d1e503095ebae3752b54408e274eb7596f163f",
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"sha256:8d7558178b2bf04a68ead86ebe9fe20fe199f9e4703cddf9389f508711365a83",
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"sha256:0b653ec0cefe2beb09dee6dfd05199f92481c2cdd0d893aa5f6cfca402f301d8"
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]
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},
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"Descriptor": {
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"mediaType": "application/vnd.docker.distribution.manifest.list.v2+json",
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"digest": "sha256:ac2a1fbc4dad1ec27c7407c24907af5a38a5f53c4baf9c6dc5973efd34b355e6",
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"size": 685
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},
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"DockerfileMD5": null,
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"DepsMD5s": {}
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}
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]

‎calkit.yaml

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owner: calkit
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name: example-basic
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title: Basic Calkit example
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description: A basic Calkit exmple project.
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description: A basic Calkit example project.
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git_repo_url: https://github.com/calkit/example-basic
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dependencies:
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- docker
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- conda
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questions:
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- Can we make reproducibility simple?
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environments:
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py:
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path: environment.yml
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kind: conda
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description: A Python environment
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tex:
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kind: docker
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image: texlive/texlive:latest-full
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description: TeX Live via Docker.
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pipeline:
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stages:
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collect-data:
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kind: python-script
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script_path: scripts/collect-data.py
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environment: py
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outputs:
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- data/raw/data.csv
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plot-voltage:
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kind: python-script
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script_path: scripts/plot-voltage.py
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environment: py
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inputs:
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- from_stage_outputs: collect-data
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outputs:
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- figures/voltage-time-series.png
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build-paper:
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kind: latex
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target_path: paper/paper.tex
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environment: tex
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inputs:
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- figures
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outputs:
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- paper/paper.pdf
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datasets:
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- path: data/raw/data.csv
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title: Raw data
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title: The paper
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description: This is the paper.
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stage: build-paper
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environments:
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py:
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path: environment.yml
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kind: conda
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description: A Python environment
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tex:
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kind: docker
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image: texlive/texlive:latest-full
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wdir: /work
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description: TeX Live via Docker.

‎dvc.lock

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schema: '2.0'
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stages:
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collect-data:
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cmd: calkit xenv -n py -- python scripts/collect-data.py
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cmd: calkit xenv -n py --no-check -- python scripts/collect-data.py
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deps:
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- path: environment.yml
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- path: .calkit/env-locks/py.yml
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hash: md5
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md5: 627d0116e60eab837fbf07edb4d370e0
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size: 114
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md5: 8119fb42c7e8531010248790fff169cf
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size: 2200
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- path: scripts/collect-data.py
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hash: md5
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md5: eeab1328ac4a9df2ef2452d32c1e6cce
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size: 424
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outs:
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- path: data/raw/data.csv
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hash: md5
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md5: 2ba6a2254202b7055d370eb59a35dfae
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size: 43644
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md5: c3319d519671cab28a01aca7a7d199f9
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size: 43633
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plot-voltage:
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cmd: calkit xenv -n py -- python scripts/plot-voltage.py
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cmd: calkit xenv -n py --no-check -- python scripts/plot-voltage.py
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deps:
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- path: data/raw/data.csv
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- path: .calkit/env-locks/py.yml
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hash: md5
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md5: 2ba6a2254202b7055d370eb59a35dfae
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size: 43644
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- path: environment.yml
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md5: 8119fb42c7e8531010248790fff169cf
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size: 2200
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- path: data/raw/data.csv
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hash: md5
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md5: 627d0116e60eab837fbf07edb4d370e0
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size: 114
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md5: c3319d519671cab28a01aca7a7d199f9
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size: 43633
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- path: scripts/plot-voltage.py
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hash: md5
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md5: 087a567a0c0f6199a908399013d564a1
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size: 297
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outs:
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- path: figures/voltage-time-series.png
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hash: md5
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md5: d4cd33821c032be468a77d65873937bc
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size: 43613
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md5: b0d7f4d7cddb00d3d8c1758720e4d79b
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size: 45261
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copy-figures-to-paper-dir:
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cmd: cp -r figures paper/figures
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deps:
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size: 45148
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nfiles: 2
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build-paper:
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cmd: "calkit xenv -n tex -- latexmk -cd -interaction=nonstopmode -pdf paper/paper.tex\n"
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cmd: calkit xenv -n tex --no-check -- latexmk -cd -interaction=nonstopmode -pdf
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paper/paper.tex
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deps:
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- path: .calkit/env-locks/tex.json
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hash: md5
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md5: b04cd12c7a8313853c8739a55f6320fe
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size: 2791
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- path: figures
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hash: md5
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md5: 1a9009ee25ecfe1fbfe1916de2eb7deb.dir
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size: 43638
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md5: 1d42180c43a4f7c68c0bb3c98f7e3896.dir
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size: 45286
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nfiles: 2
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- path: paper/paper.tex
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hash: md5
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md5: 6455fc859c8b1838f22d5ac74223b323
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size: 604
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md5: 1480301e18c57bf533d604e1a3593101
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size: 653
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outs:
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- path: paper/paper.pdf
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hash: md5
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md5: 6f1fec0754597ecdb78cf0e9852884ad
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size: 92860
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md5: 3020732b698cfd131ef6c1bc0d207521
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size: 95329
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_check_env_py:
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cmd: calkit check conda-env --file environment.yml --output .calkit/env-locks/py.yml
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deps:
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- path: environment.yml
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hash: md5
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md5: 4282ecbec6810eb293bdf62d7f956ffd
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size: 119
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outs:
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- path: .calkit/env-locks/py.yml
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hash: md5
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md5: 8119fb42c7e8531010248790fff169cf
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size: 2200
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_check_env_tex:
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cmd: calkit check docker-env texlive/texlive:latest-full -o .calkit/env-locks/tex.json
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outs:
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- path: .calkit/env-locks/tex.json
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hash: md5
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md5: b04cd12c7a8313853c8739a55f6320fe
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size: 2791
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_check-env-py:
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cmd: calkit check conda-env --file environment.yml --output .calkit/env-locks/py.yml
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deps:
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- path: environment.yml
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hash: md5
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md5: 4282ecbec6810eb293bdf62d7f956ffd
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size: 119
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outs:
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- path: .calkit/env-locks/py.yml
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hash: md5
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md5: 8119fb42c7e8531010248790fff169cf
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size: 2200
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_check-env-tex:
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cmd: calkit check docker-env texlive/texlive:latest-full -o .calkit/env-locks/tex.json
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outs:
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- path: .calkit/env-locks/tex.json
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hash: md5
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md5: b04cd12c7a8313853c8739a55f6320fe
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size: 2791

‎dvc.yaml

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stages:
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_check-env-py:
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cmd: calkit check conda-env --file environment.yml --output .calkit/env-locks/py.yml
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deps:
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- environment.yml
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outs:
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- .calkit/env-locks/py.yml:
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cache: false
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persist: true
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always_changed: true
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_check-env-tex:
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cmd: calkit check docker-env texlive/texlive:latest-full -o .calkit/env-locks/tex.json
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deps: []
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outs:
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- .calkit/env-locks/tex.json:
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cache: false
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persist: true
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always_changed: true
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collect-data:
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cmd: calkit xenv -n py -- python scripts/collect-data.py
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cmd: calkit xenv -n py --no-check -- python scripts/collect-data.py
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deps:
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- scripts/collect-data.py
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- environment.yml
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- .calkit/env-locks/py.yml
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outs:
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- data/raw/data.csv
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plot-voltage:
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cmd: calkit xenv -n py -- python scripts/plot-voltage.py
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cmd: calkit xenv -n py --no-check -- python scripts/plot-voltage.py
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deps:
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- scripts/plot-voltage.py
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- .calkit/env-locks/py.yml
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- data/raw/data.csv
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- environment.yml
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outs:
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- figures/voltage-time-series.png
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build-paper:
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cmd: >
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calkit xenv -n tex --
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latexmk -cd -interaction=nonstopmode -pdf paper/paper.tex
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cmd: calkit xenv -n tex --no-check -- latexmk -cd -interaction=nonstopmode
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-pdf paper/paper.tex
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deps:
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- figures
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- paper/paper.tex
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- figures
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- .calkit/env-locks/tex.json
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outs:
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- paper/paper.pdf

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