Use Calkit pipeline

.calkit/env-locks/py.yml

@@ -0,0 +1,69 @@
+channels:
+  - conda-forge
+dependencies:
+  - brotli=1.1.0=hd74edd7_2
+  - brotli-bin=1.1.0=hd74edd7_2
+  - bzip2=1.0.8=h99b78c6_7
+  - ca-certificates=2025.4.26=hbd8a1cb_0
+  - contourpy=1.3.2=py312hb23fbb9_0
+  - cycler=0.12.1=pyhd8ed1ab_1
+  - fonttools=4.58.0=py312h998013c_0
+  - freetype=2.13.3=hce30654_1
+  - kiwisolver=1.4.8=py312h2c4a281_0
+  - lcms2=2.17=h7eeda09_0
+  - lerc=4.0.0=hd64df32_1
+  - libblas=3.9.0=31_h10e41b3_openblas
+  - libbrotlicommon=1.1.0=hd74edd7_2
+  - libbrotlidec=1.1.0=hd74edd7_2
+  - libbrotlienc=1.1.0=hd74edd7_2
+  - libcblas=3.9.0=31_hb3479ef_openblas
+  - libcxx=20.1.5=ha82da77_0
+  - libdeflate=1.24=h5773f1b_0
+  - libexpat=2.7.0=h286801f_0
+  - libffi=3.4.6=h1da3d7d_1
+  - libfreetype=2.13.3=hce30654_1
+  - libfreetype6=2.13.3=h1d14073_1
+  - libgfortran=14.2.0=heb5dd2a_105
+  - libgfortran5=14.2.0=h2c44a93_105
+  - libjpeg-turbo=3.1.0=h5505292_0
+  - liblapack=3.9.0=31_hc9a63f6_openblas
+  - liblzma=5.8.1=h39f12f2_1
+  - libopenblas=0.3.29=openmp_hf332438_0
+  - libpng=1.6.47=h3783ad8_0
+  - libsqlite=3.49.2=h3f77e49_0
+  - libtiff=4.7.0=h2f21f7c_5
+  - libwebp-base=1.5.0=h2471fea_0
+  - libxcb=1.17.0=hdb1d25a_0
+  - libzlib=1.3.1=h8359307_2
+  - llvm-openmp=20.1.5=hdb05f8b_0
+  - matplotlib=3.10.3=py312h1f38498_0
+  - matplotlib-base=3.10.3=py312hdbc7e53_0
+  - munkres=1.1.4=pyh9f0ad1d_0
+  - ncurses=6.5=h5e97a16_3
+  - numpy=2.2.6=py312h7c1f314_0
+  - openjpeg=2.5.3=h8a3d83b_0
+  - openssl=3.5.0=h81ee809_1
+  - packaging=25.0=pyh29332c3_1
+  - pandas=2.2.3=py312hcb1e3ce_3
+  - pillow=11.2.1=py312h50aef2c_0
+  - pip=25.1.1=pyh8b19718_0
+  - pthread-stubs=0.4=hd74edd7_1002
+  - pyparsing=3.2.3=pyhd8ed1ab_1
+  - python=3.12.10=hc22306f_0_cpython
+  - python-dateutil=2.9.0.post0=pyhff2d567_1
+  - python-tzdata=2025.2=pyhd8ed1ab_0
+  - python_abi=3.12=7_cp312
+  - pytz=2025.2=pyhd8ed1ab_0
+  - qhull=2020.2=h420ef59_5
+  - readline=8.2=h1d1bf99_2
+  - setuptools=80.8.0=pyhff2d567_0
+  - six=1.17.0=pyhd8ed1ab_0
+  - tk=8.6.13=h5083fa2_1
+  - tornado=6.5.1=py312hea69d52_0
+  - tzdata=2025b=h78e105d_0
+  - unicodedata2=16.0.0=py312hea69d52_0
+  - wheel=0.45.1=pyhd8ed1ab_1
+  - xorg-libxau=1.0.12=h5505292_0
+  - xorg-libxdmcp=1.1.5=hd74edd7_0
+  - zstd=1.5.7=h6491c7d_2
+name: calkit-example-basic

.calkit/env-locks/tex.json

@@ -0,0 +1,71 @@
+[
+    {
+        "RepoTags": [
+            "texlive/texlive:latest-full"
+        ],
+        "Parent": "",
+        "Comment": "buildkit.dockerfile.v0",
+        "Created": "2025-05-11T13:45:24.681068416Z",
+        "Author": "",
+        "Config": {
+            "Hostname": "",
+            "Domainname": "",
+            "User": "",
+            "AttachStdin": false,
+            "AttachStdout": false,
+            "AttachStderr": false,
+            "Tty": false,
+            "OpenStdin": false,
+            "StdinOnce": false,
+            "Env": [
+                "PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin",
+                "LANG=C.UTF-8",
+                "LC_ALL=C.UTF-8",
+                "TEXLIVE_INSTALL_NO_CONTEXT_CACHE=1",
+                "NOPERLDOC=1",
+                "DEBIAN_FRONTEND=noninteractive"
+            ],
+            "Cmd": [
+                "bash"
+            ],
+            "Image": "",
+            "Volumes": null,
+            "WorkingDir": "/workdir",
+            "Entrypoint": null,
+            "OnBuild": null,
+            "Labels": {
+                "org.opencontainers.image.authors": "Island of TeX",
+                "org.opencontainers.image.source": "https://gitlab.com/islandoftex/images/texlive/-/blob/master/Dockerfile",
+                "org.opencontainers.image.url": "https://gitlab.com/islandoftex/images/texlive"
+            }
+        },
+        "Architecture": "arm64",
+        "Os": "linux",
+        "Size": 2409562089,
+        "GraphDriver": {
+            "Data": null,
+            "Name": "overlayfs"
+        },
+        "RootFS": {
+            "Type": "layers",
+            "Layers": [
+                "sha256:f20086072b1d2fffdc8a8a3afc546d1ecb13a9047ac9cc6c941e9783ba2c1c40",
+                "sha256:cc4ebc54dd55374e26421ee3710a3cb932690ec294b3665230f54ae0ddbbacec",
+                "sha256:2ff8561f9f970e166f982b4a6f584a0ce9a275836a281d9e5b62fb27d6a99e8f",
+                "sha256:5f70bf18a086007016e948b04aed3b82103a36bea41755b6cddfaf10ace3c6ef",
+                "sha256:6b5bb1acd1ecb71e7df10f16fba58ee8afbc1a4295b26486766742471c7380bf",
+                "sha256:84cc1f955c35ccf33e8c50a7e8cab52e5c5e186124d3d2dc294de9d227ca2f9e",
+                "sha256:e408bd808583af5c8c473d3a99d1e503095ebae3752b54408e274eb7596f163f",
+                "sha256:8d7558178b2bf04a68ead86ebe9fe20fe199f9e4703cddf9389f508711365a83",
+                "sha256:0b653ec0cefe2beb09dee6dfd05199f92481c2cdd0d893aa5f6cfca402f301d8"
+            ]
+        },
+        "Descriptor": {
+            "mediaType": "application/vnd.docker.distribution.manifest.list.v2+json",
+            "digest": "sha256:ac2a1fbc4dad1ec27c7407c24907af5a38a5f53c4baf9c6dc5973efd34b355e6",
+            "size": 685
+        },
+        "DockerfileMD5": null,
+        "DepsMD5s": {}
+    }
+]

calkit.yaml

@@ -1,13 +1,46 @@
 owner: calkit
 name: example-basic
 title: Basic Calkit example
-description: A basic Calkit exmple project.
+description: A basic Calkit example project.
 git_repo_url: https://github.com/calkit/example-basic
 dependencies:
   - docker
   - conda
 questions:
   - Can we make reproducibility simple?
+environments:
+  py:
+    path: environment.yml
+    kind: conda
+    description: A Python environment
+  tex:
+    kind: docker
+    image: texlive/texlive:latest-full
+    description: TeX Live via Docker.
+pipeline:
+  stages:
+    collect-data:
+      kind: python-script
+      script_path: scripts/collect-data.py
+      environment: py
+      outputs:
+        - data/raw/data.csv
+    plot-voltage:
+      kind: python-script
+      script_path: scripts/plot-voltage.py
+      environment: py
+      inputs:
+        - from_stage_outputs: collect-data
+      outputs:
+        - figures/voltage-time-series.png
+    build-paper:
+      kind: latex
+      target_path: paper/paper.tex
+      environment: tex
+      inputs:
+        - figures
+      outputs:
+        - paper/paper.pdf
 datasets:
   - path: data/raw/data.csv
     title: Raw data
@@ -23,13 +56,3 @@ publications:
     title: The paper
     description: This is the paper.
     stage: build-paper
-environments:
-  py:
-    path: environment.yml
-    kind: conda
-    description: A Python environment
-  tex:
-    kind: docker
-    image: texlive/texlive:latest-full
-    wdir: /work
-    description: TeX Live via Docker.

dvc.lock

@@ -1,41 +1,41 @@
 schema: '2.0'
 stages:
   collect-data:
-    cmd: calkit xenv -n py -- python scripts/collect-data.py
+    cmd: calkit xenv -n py --no-check -- python scripts/collect-data.py
     deps:
-    - path: environment.yml
+    - path: .calkit/env-locks/py.yml
       hash: md5
-      md5: 627d0116e60eab837fbf07edb4d370e0
-      size: 114
+      md5: 8119fb42c7e8531010248790fff169cf
+      size: 2200
     - path: scripts/collect-data.py
       hash: md5
       md5: eeab1328ac4a9df2ef2452d32c1e6cce
       size: 424
     outs:
     - path: data/raw/data.csv
       hash: md5
-      md5: 2ba6a2254202b7055d370eb59a35dfae
-      size: 43644
+      md5: c3319d519671cab28a01aca7a7d199f9
+      size: 43633
   plot-voltage:
-    cmd: calkit xenv -n py -- python scripts/plot-voltage.py
+    cmd: calkit xenv -n py --no-check -- python scripts/plot-voltage.py
     deps:
-    - path: data/raw/data.csv
+    - path: .calkit/env-locks/py.yml
       hash: md5
-      md5: 2ba6a2254202b7055d370eb59a35dfae
-      size: 43644
-    - path: environment.yml
+      md5: 8119fb42c7e8531010248790fff169cf
+      size: 2200
+    - path: data/raw/data.csv
       hash: md5
-      md5: 627d0116e60eab837fbf07edb4d370e0
-      size: 114
+      md5: c3319d519671cab28a01aca7a7d199f9
+      size: 43633
     - path: scripts/plot-voltage.py
       hash: md5
       md5: 087a567a0c0f6199a908399013d564a1
       size: 297
     outs:
     - path: figures/voltage-time-series.png
       hash: md5
-      md5: d4cd33821c032be468a77d65873937bc
-      size: 43613
+      md5: b0d7f4d7cddb00d3d8c1758720e4d79b
+      size: 45261
   copy-figures-to-paper-dir:
     cmd: cp -r figures paper/figures
     deps:
@@ -51,19 +51,62 @@ stages:
       size: 45148
       nfiles: 2
   build-paper:
-    cmd: "calkit xenv -n tex -- latexmk -cd -interaction=nonstopmode -pdf paper/paper.tex\n"
+    cmd: calkit xenv -n tex --no-check -- latexmk -cd -interaction=nonstopmode -pdf
+      paper/paper.tex
     deps:
+    - path: .calkit/env-locks/tex.json
+      hash: md5
+      md5: b04cd12c7a8313853c8739a55f6320fe
+      size: 2791
     - path: figures
       hash: md5
-      md5: 1a9009ee25ecfe1fbfe1916de2eb7deb.dir
-      size: 43638
+      md5: 1d42180c43a4f7c68c0bb3c98f7e3896.dir
+      size: 45286
       nfiles: 2
     - path: paper/paper.tex
       hash: md5
-      md5: 6455fc859c8b1838f22d5ac74223b323
-      size: 604
+      md5: 1480301e18c57bf533d604e1a3593101
+      size: 653
     outs:
     - path: paper/paper.pdf
       hash: md5
-      md5: 6f1fec0754597ecdb78cf0e9852884ad
-      size: 92860
+      md5: 3020732b698cfd131ef6c1bc0d207521
+      size: 95329
+  _check_env_py:
+    cmd: calkit check conda-env --file environment.yml --output .calkit/env-locks/py.yml
+    deps:
+    - path: environment.yml
+      hash: md5
+      md5: 4282ecbec6810eb293bdf62d7f956ffd
+      size: 119
+    outs:
+    - path: .calkit/env-locks/py.yml
+      hash: md5
+      md5: 8119fb42c7e8531010248790fff169cf
+      size: 2200
+  _check_env_tex:
+    cmd: calkit check docker-env texlive/texlive:latest-full -o .calkit/env-locks/tex.json
+    outs:
+    - path: .calkit/env-locks/tex.json
+      hash: md5
+      md5: b04cd12c7a8313853c8739a55f6320fe
+      size: 2791
+  _check-env-py:
+    cmd: calkit check conda-env --file environment.yml --output .calkit/env-locks/py.yml
+    deps:
+    - path: environment.yml
+      hash: md5
+      md5: 4282ecbec6810eb293bdf62d7f956ffd
+      size: 119
+    outs:
+    - path: .calkit/env-locks/py.yml
+      hash: md5
+      md5: 8119fb42c7e8531010248790fff169cf
+      size: 2200
+  _check-env-tex:
+    cmd: calkit check docker-env texlive/texlive:latest-full -o .calkit/env-locks/tex.json
+    outs:
+    - path: .calkit/env-locks/tex.json
+      hash: md5
+      md5: b04cd12c7a8313853c8739a55f6320fe
+      size: 2791

dvc.yaml

@@ -1,25 +1,42 @@
 stages:
+  _check-env-py:
+    cmd: calkit check conda-env --file environment.yml --output .calkit/env-locks/py.yml
+    deps:
+      - environment.yml
+    outs:
+      - .calkit/env-locks/py.yml:
+          cache: false
+          persist: true
+    always_changed: true
+  _check-env-tex:
+    cmd: calkit check docker-env texlive/texlive:latest-full -o .calkit/env-locks/tex.json
+    deps: []
+    outs:
+      - .calkit/env-locks/tex.json:
+          cache: false
+          persist: true
+    always_changed: true
   collect-data:
-    cmd: calkit xenv -n py -- python scripts/collect-data.py
+    cmd: calkit xenv -n py --no-check -- python scripts/collect-data.py
     deps:
       - scripts/collect-data.py
-      - environment.yml
+      - .calkit/env-locks/py.yml
     outs:
       - data/raw/data.csv
   plot-voltage:
-    cmd: calkit xenv -n py -- python scripts/plot-voltage.py
+    cmd: calkit xenv -n py --no-check -- python scripts/plot-voltage.py
     deps:
       - scripts/plot-voltage.py
+      - .calkit/env-locks/py.yml
       - data/raw/data.csv
-      - environment.yml
     outs:
       - figures/voltage-time-series.png
   build-paper:
-    cmd: >
-      calkit xenv -n tex --
-      latexmk -cd -interaction=nonstopmode -pdf paper/paper.tex
+    cmd: calkit xenv -n tex --no-check -- latexmk -cd -interaction=nonstopmode
+      -pdf paper/paper.tex
     deps:
-      - figures
       - paper/paper.tex
+      - figures
+      - .calkit/env-locks/tex.json
     outs:
       - paper/paper.pdf