From fe9f0f9df3c6eab5b09aa87287185a30b0079a14 Mon Sep 17 00:00:00 2001
From: Pete Bachant <petebachant@gmail.com>
Date: Thu, 13 Nov 2025 13:07:43 -0800
Subject: [PATCH 1/5] Use new style env-lock scheme

---
 .calkit/env-locks/docker/amd64/tex.json       | 27 ---------
 .../linux-64/py.txt => py/osx-arm64.txt}      |  0
 .../{docker/arm64/tex.json => tex/arm64.json} |  0
 .calkit/env-locks/venvs/osx-arm64/py.txt      | 14 -----
 dvc.lock                                      | 55 ++++++++++---------
 dvc.yaml                                      | 38 ++++++-------
 6 files changed, 46 insertions(+), 88 deletions(-)
 delete mode 100644 .calkit/env-locks/docker/amd64/tex.json
 rename .calkit/env-locks/{venvs/linux-64/py.txt => py/osx-arm64.txt} (100%)
 rename .calkit/env-locks/{docker/arm64/tex.json => tex/arm64.json} (100%)
 delete mode 100644 .calkit/env-locks/venvs/osx-arm64/py.txt

diff --git a/.calkit/env-locks/docker/amd64/tex.json b/.calkit/env-locks/docker/amd64/tex.json
deleted file mode 100644
index 979805a..0000000
--- a/.calkit/env-locks/docker/amd64/tex.json
+++ /dev/null
@@ -1,27 +0,0 @@
-{
-    "RepoTags": [
-        "texlive/texlive:latest-full"
-    ],
-    "RepoDigests": [
-        "texlive/texlive@sha256:e45f6b51d756d7519fafd3a94f51db2190504e0d222eb960888a77cc6942fdd0"
-    ],
-    "Architecture": "amd64",
-    "Os": "linux",
-    "Size": 5208362245,
-    "RootFS": {
-        "Type": "layers",
-        "Layers": [
-            "sha256:b9f4f71ae755f9248e2687e6a423ca7419a150748a6d3360adacb13daf683ad9",
-            "sha256:0cc6f5ed69e4a948391449e0a1ba6fe0b15146183db3397e6283c3a3bdfdadd9",
-            "sha256:b8b870d9cf70eabd4262868eedace16a70070399629ca624e3c511d56d1e5607",
-            "sha256:5f70bf18a086007016e948b04aed3b82103a36bea41755b6cddfaf10ace3c6ef",
-            "sha256:d0f5df9e47b9f29f13f1d9ecbdd803d24bf2de8e6d61ffdfd6f71f989cedc680",
-            "sha256:e1d971b42eff7eaf1e929efcd296236a5111816837a6aa72f0401688965331e5",
-            "sha256:96bd540ad112be71847230ec13da112a2e354bce67c188ffb580aa0ddf8e90a6",
-            "sha256:17331da551fd81773f95a7c44d03512258fce9ef8b6c8562a58c478224cb650e",
-            "sha256:558896e672597f6be2ca87e26aa62c7a50c4985145e14593bb9fb364c7b571f1"
-        ]
-    },
-    "DockerfileMD5": null,
-    "DepsMD5s": {}
-}
\ No newline at end of file
diff --git a/.calkit/env-locks/venvs/linux-64/py.txt b/.calkit/env-locks/py/osx-arm64.txt
similarity index 100%
rename from .calkit/env-locks/venvs/linux-64/py.txt
rename to .calkit/env-locks/py/osx-arm64.txt
diff --git a/.calkit/env-locks/docker/arm64/tex.json b/.calkit/env-locks/tex/arm64.json
similarity index 100%
rename from .calkit/env-locks/docker/arm64/tex.json
rename to .calkit/env-locks/tex/arm64.json
diff --git a/.calkit/env-locks/venvs/osx-arm64/py.txt b/.calkit/env-locks/venvs/osx-arm64/py.txt
deleted file mode 100644
index af74d66..0000000
--- a/.calkit/env-locks/venvs/osx-arm64/py.txt
+++ /dev/null
@@ -1,14 +0,0 @@
-contourpy==1.3.3
-cycler==0.12.1
-fonttools==4.59.1
-kiwisolver==1.4.9
-matplotlib==3.10.5
-numpy==2.3.2
-packaging==25.0
-pandas==2.3.1
-pillow==11.3.0
-pyparsing==3.2.3
-python-dateutil==2.9.0.post0
-pytz==2025.2
-six==1.17.0
-tzdata==2025.2
diff --git a/dvc.lock b/dvc.lock
index 5c51eba..755cb26 100644
--- a/dvc.lock
+++ b/dvc.lock
@@ -3,10 +3,11 @@ stages:
   collect-data:
     cmd: calkit xenv -n py --no-check -- python scripts/collect-data.py
     deps:
-    - path: .calkit/env-locks/venvs/linux-64/py.txt
+    - path: .calkit/env-locks/py
       hash: md5
-      md5: de96276868627f6d4aa908b2b4759a56
+      md5: 97801bd5ad552a89970a09edb1bc525d.dir
       size: 231
+      nfiles: 1
     - path: scripts/collect-data.py
       hash: md5
       md5: eeab1328ac4a9df2ef2452d32c1e6cce
@@ -14,19 +15,20 @@ stages:
     outs:
     - path: data/raw/data.csv
       hash: md5
-      md5: 3ec6df511ed8ebacdc436ce815ada1df
-      size: 43628
+      md5: 0e1fcf8330919e3e736ec3be03b7baa9
+      size: 43613
   plot-voltage:
     cmd: calkit xenv -n py --no-check -- python scripts/plot-voltage.py
     deps:
-    - path: .calkit/env-locks/venvs/linux-64/py.txt
+    - path: .calkit/env-locks/py
       hash: md5
-      md5: de96276868627f6d4aa908b2b4759a56
+      md5: 97801bd5ad552a89970a09edb1bc525d.dir
       size: 231
+      nfiles: 1
     - path: data/raw/data.csv
       hash: md5
-      md5: 3ec6df511ed8ebacdc436ce815ada1df
-      size: 43628
+      md5: 0e1fcf8330919e3e736ec3be03b7baa9
+      size: 43613
     - path: scripts/plot-voltage.py
       hash: md5
       md5: 087a567a0c0f6199a908399013d564a1
@@ -34,8 +36,8 @@ stages:
     outs:
     - path: figures/voltage-time-series.png
       hash: md5
-      md5: a70b61dc033585fe2d3c16d63290a870
-      size: 46210
+      md5: 062d0b4f4e8087221204d12c1f594223
+      size: 44207
   copy-figures-to-paper-dir:
     cmd: cp -r figures paper/figures
     deps:
@@ -51,17 +53,18 @@ stages:
       size: 45148
       nfiles: 2
   build-paper:
-    cmd: calkit xenv -n tex --no-check -- latexmk -cd -norc 
-      -interaction=nonstopmode -silent -synctex=1 -pdf paper/paper.tex
+    cmd: calkit xenv -n tex --no-check -- latexmk -cd -norc -interaction=nonstopmode
+      -silent -synctex=1 -pdf paper/paper.tex
     deps:
-    - path: .calkit/env-locks/docker/amd64/tex.json
+    - path: .calkit/env-locks/tex
       hash: md5
-      md5: af028316fd879fcf385e0838e3b7ad08
+      md5: 2c552307edd59397026c9ef06dc8af47.dir
       size: 1171
+      nfiles: 1
     - path: figures
       hash: md5
-      md5: 70126dc2f9f61fb93c62eb50b55f13f1.dir
-      size: 46235
+      md5: 51682cce447229821989f677c23caa75.dir
+      size: 44232
       nfiles: 2
     - path: paper/paper.tex
       hash: md5
@@ -70,11 +73,10 @@ stages:
     outs:
     - path: paper/paper.pdf
       hash: md5
-      md5: 7069d28ed4063d3bec319c661681648a
-      size: 98339
+      md5: eddd55ddc8410adef45250b708b0947f
+      size: 99255
   _check_env_py:
-    cmd: calkit check conda-env --file environment.yml --output 
-      .calkit/env-locks/py.yml
+    cmd: calkit check conda-env --file environment.yml --output .calkit/env-locks/py.yml
     deps:
     - path: environment.yml
       hash: md5
@@ -86,8 +88,7 @@ stages:
       md5: 8119fb42c7e8531010248790fff169cf
       size: 2200
   _check_env_tex:
-    cmd: calkit check docker-env texlive/texlive:latest-full -o 
-      .calkit/env-locks/tex.json
+    cmd: calkit check docker-env texlive/texlive:latest-full -o .calkit/env-locks/tex.json
     outs:
     - path: .calkit/env-locks/tex.json
       hash: md5
@@ -101,14 +102,16 @@ stages:
       md5: 2d0e401b7292d0d218bc567bfb37f9c7
       size: 24
     outs:
-    - path: .calkit/env-locks/venvs/linux-64/py.txt
+    - path: .calkit/env-locks/py
       hash: md5
-      md5: de96276868627f6d4aa908b2b4759a56
+      md5: 97801bd5ad552a89970a09edb1bc525d.dir
       size: 231
+      nfiles: 1
   _check-env-tex:
     cmd: calkit check environment --name tex
     outs:
-    - path: .calkit/env-locks/docker/amd64/tex.json
+    - path: .calkit/env-locks/tex
       hash: md5
-      md5: af028316fd879fcf385e0838e3b7ad08
+      md5: 2c552307edd59397026c9ef06dc8af47.dir
       size: 1171
+      nfiles: 1
diff --git a/dvc.yaml b/dvc.yaml
index f8b6506..4ff7e5a 100644
--- a/dvc.yaml
+++ b/dvc.yaml
@@ -4,51 +4,47 @@ stages:
     deps:
       - requirements.txt
     outs:
-      - .calkit/env-locks/venvs/linux-64/py.txt:
+      - .calkit/env-locks/py:
           cache: false
           persist: true
     always_changed: true
-    desc: Automatically generated by Calkit. Changes made here will be
-      overwritten.
+    desc: Automatically generated by Calkit. Changes made here will be overwritten.
   _check-env-tex:
     cmd: calkit check environment --name tex
     deps: []
     outs:
-      - .calkit/env-locks/docker/amd64/tex.json:
+      - .calkit/env-locks/tex:
           cache: false
           persist: true
     always_changed: true
-    desc: Automatically generated by Calkit. Changes made here will be
-      overwritten.
+    desc: Automatically generated by Calkit. Changes made here will be overwritten.
   collect-data:
-    cmd: calkit xenv -n py --no-check -- python 
-      scripts/collect-data.py
+    cmd: calkit xenv -n py --no-check -- python scripts/collect-data.py
     deps:
       - scripts/collect-data.py
-      - .calkit/env-locks/venvs/linux-64/py.txt
+      - .calkit/env-locks/py
     outs:
       - data/raw/data.csv
-    desc: Automatically generated from the 'collect-data' stage in 
-      calkit.yaml. Changes made here will be overwritten.
+    desc: Automatically generated from the 'collect-data' stage in calkit.yaml.
+      Changes made here will be overwritten.
   plot-voltage:
-    cmd: calkit xenv -n py --no-check -- 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/venvs/linux-64/py.txt
+      - .calkit/env-locks/py
       - data/raw/data.csv
     outs:
       - figures/voltage-time-series.png
-    desc: Automatically generated from the 'plot-voltage' stage in 
-      calkit.yaml. Changes made here will be overwritten.
+    desc: Automatically generated from the 'plot-voltage' stage in calkit.yaml.
+      Changes made here will be overwritten.
   build-paper:
-    cmd: calkit xenv -n tex --no-check -- latexmk -cd -norc 
-      -interaction=nonstopmode -silent -synctex=1 -pdf paper/paper.tex
+    cmd: calkit xenv -n tex --no-check -- latexmk -cd -norc -interaction=nonstopmode
+      -silent -synctex=1 -pdf paper/paper.tex
     deps:
       - paper/paper.tex
       - figures
-      - .calkit/env-locks/docker/amd64/tex.json
+      - .calkit/env-locks/tex
     outs:
       - paper/paper.pdf
-    desc: Automatically generated from the 'build-paper' stage in 
-      calkit.yaml. Changes made here will be overwritten.
+    desc: Automatically generated from the 'build-paper' stage in calkit.yaml.
+      Changes made here will be overwritten.

From 5e44f1c5e542ffc98a842a95c41560c388cb83c8 Mon Sep 17 00:00:00 2001
From: Pete Bachant <petebachant@gmail.com>
Date: Thu, 13 Nov 2025 13:09:41 -0800
Subject: [PATCH 2/5] Change Calkit install

---
 .github/workflows/run.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/run.yml b/.github/workflows/run.yml
index db631f9..bb9e761 100644
--- a/.github/workflows/run.yml
+++ b/.github/workflows/run.yml
@@ -33,6 +33,6 @@ jobs:
       - name: Setup uv
         uses: astral-sh/setup-uv@v5
       - name: Install Calkit
-        run: uv tool install calkit-python
+        run: uv tool install git+https://github.com/calkit/calkit.git@status
       - name: Run Calkit
         uses: calkit/run-action@v2

From 930c914e3da0933dcedc2d710f0eb7860c3445f0 Mon Sep 17 00:00:00 2001
From: "github-actions[bot]"
 <41898282+github-actions[bot]@users.noreply.github.com>
Date: Thu, 13 Nov 2025 21:14:06 +0000
Subject: [PATCH 3/5] Run pipeline

---
 .calkit/env-locks/py/linux-64.txt | 14 ++++++++
 .calkit/env-locks/tex/amd64.json  | 27 ++++++++++++++
 dvc.lock                          | 60 ++++++++++++++++---------------
 dvc.yaml                          | 28 ++++++++-------
 4 files changed, 88 insertions(+), 41 deletions(-)
 create mode 100644 .calkit/env-locks/py/linux-64.txt
 create mode 100644 .calkit/env-locks/tex/amd64.json

diff --git a/.calkit/env-locks/py/linux-64.txt b/.calkit/env-locks/py/linux-64.txt
new file mode 100644
index 0000000..af74d66
--- /dev/null
+++ b/.calkit/env-locks/py/linux-64.txt
@@ -0,0 +1,14 @@
+contourpy==1.3.3
+cycler==0.12.1
+fonttools==4.59.1
+kiwisolver==1.4.9
+matplotlib==3.10.5
+numpy==2.3.2
+packaging==25.0
+pandas==2.3.1
+pillow==11.3.0
+pyparsing==3.2.3
+python-dateutil==2.9.0.post0
+pytz==2025.2
+six==1.17.0
+tzdata==2025.2
diff --git a/.calkit/env-locks/tex/amd64.json b/.calkit/env-locks/tex/amd64.json
new file mode 100644
index 0000000..979805a
--- /dev/null
+++ b/.calkit/env-locks/tex/amd64.json
@@ -0,0 +1,27 @@
+{
+    "RepoTags": [
+        "texlive/texlive:latest-full"
+    ],
+    "RepoDigests": [
+        "texlive/texlive@sha256:e45f6b51d756d7519fafd3a94f51db2190504e0d222eb960888a77cc6942fdd0"
+    ],
+    "Architecture": "amd64",
+    "Os": "linux",
+    "Size": 5208362245,
+    "RootFS": {
+        "Type": "layers",
+        "Layers": [
+            "sha256:b9f4f71ae755f9248e2687e6a423ca7419a150748a6d3360adacb13daf683ad9",
+            "sha256:0cc6f5ed69e4a948391449e0a1ba6fe0b15146183db3397e6283c3a3bdfdadd9",
+            "sha256:b8b870d9cf70eabd4262868eedace16a70070399629ca624e3c511d56d1e5607",
+            "sha256:5f70bf18a086007016e948b04aed3b82103a36bea41755b6cddfaf10ace3c6ef",
+            "sha256:d0f5df9e47b9f29f13f1d9ecbdd803d24bf2de8e6d61ffdfd6f71f989cedc680",
+            "sha256:e1d971b42eff7eaf1e929efcd296236a5111816837a6aa72f0401688965331e5",
+            "sha256:96bd540ad112be71847230ec13da112a2e354bce67c188ffb580aa0ddf8e90a6",
+            "sha256:17331da551fd81773f95a7c44d03512258fce9ef8b6c8562a58c478224cb650e",
+            "sha256:558896e672597f6be2ca87e26aa62c7a50c4985145e14593bb9fb364c7b571f1"
+        ]
+    },
+    "DockerfileMD5": null,
+    "DepsMD5s": {}
+}
\ No newline at end of file
diff --git a/dvc.lock b/dvc.lock
index 755cb26..7010893 100644
--- a/dvc.lock
+++ b/dvc.lock
@@ -5,9 +5,9 @@ stages:
     deps:
     - path: .calkit/env-locks/py
       hash: md5
-      md5: 97801bd5ad552a89970a09edb1bc525d.dir
-      size: 231
-      nfiles: 1
+      md5: 6a3d291988c3964eaf329ec3c2c9b9f5.dir
+      size: 462
+      nfiles: 2
     - path: scripts/collect-data.py
       hash: md5
       md5: eeab1328ac4a9df2ef2452d32c1e6cce
@@ -15,20 +15,20 @@ stages:
     outs:
     - path: data/raw/data.csv
       hash: md5
-      md5: 0e1fcf8330919e3e736ec3be03b7baa9
-      size: 43613
+      md5: b6f6ce8a671a7be4c22491be9ee9614b
+      size: 43716
   plot-voltage:
     cmd: calkit xenv -n py --no-check -- python scripts/plot-voltage.py
     deps:
     - path: .calkit/env-locks/py
       hash: md5
-      md5: 97801bd5ad552a89970a09edb1bc525d.dir
-      size: 231
-      nfiles: 1
+      md5: 6a3d291988c3964eaf329ec3c2c9b9f5.dir
+      size: 462
+      nfiles: 2
     - path: data/raw/data.csv
       hash: md5
-      md5: 0e1fcf8330919e3e736ec3be03b7baa9
-      size: 43613
+      md5: b6f6ce8a671a7be4c22491be9ee9614b
+      size: 43716
     - path: scripts/plot-voltage.py
       hash: md5
       md5: 087a567a0c0f6199a908399013d564a1
@@ -36,8 +36,8 @@ stages:
     outs:
     - path: figures/voltage-time-series.png
       hash: md5
-      md5: 062d0b4f4e8087221204d12c1f594223
-      size: 44207
+      md5: a0e5b3c3e2e42189f6303e7b1d90499b
+      size: 46338
   copy-figures-to-paper-dir:
     cmd: cp -r figures paper/figures
     deps:
@@ -53,18 +53,18 @@ stages:
       size: 45148
       nfiles: 2
   build-paper:
-    cmd: calkit xenv -n tex --no-check -- latexmk -cd -norc -interaction=nonstopmode
-      -silent -synctex=1 -pdf paper/paper.tex
+    cmd: calkit xenv -n tex --no-check -- latexmk -cd -norc 
+      -interaction=nonstopmode -silent -synctex=1 -pdf paper/paper.tex
     deps:
     - path: .calkit/env-locks/tex
       hash: md5
-      md5: 2c552307edd59397026c9ef06dc8af47.dir
-      size: 1171
-      nfiles: 1
+      md5: fdae1edb4dcd23e4265e4f7701b324a3.dir
+      size: 2342
+      nfiles: 2
     - path: figures
       hash: md5
-      md5: 51682cce447229821989f677c23caa75.dir
-      size: 44232
+      md5: 69cf1654863a79b7342838ff9ca78a72.dir
+      size: 46363
       nfiles: 2
     - path: paper/paper.tex
       hash: md5
@@ -73,10 +73,11 @@ stages:
     outs:
     - path: paper/paper.pdf
       hash: md5
-      md5: eddd55ddc8410adef45250b708b0947f
-      size: 99255
+      md5: 24df231bcb8754c9bb3bf1087c31dd48
+      size: 97240
   _check_env_py:
-    cmd: calkit check conda-env --file environment.yml --output .calkit/env-locks/py.yml
+    cmd: calkit check conda-env --file environment.yml --output 
+      .calkit/env-locks/py.yml
     deps:
     - path: environment.yml
       hash: md5
@@ -88,7 +89,8 @@ stages:
       md5: 8119fb42c7e8531010248790fff169cf
       size: 2200
   _check_env_tex:
-    cmd: calkit check docker-env texlive/texlive:latest-full -o .calkit/env-locks/tex.json
+    cmd: calkit check docker-env texlive/texlive:latest-full -o 
+      .calkit/env-locks/tex.json
     outs:
     - path: .calkit/env-locks/tex.json
       hash: md5
@@ -104,14 +106,14 @@ stages:
     outs:
     - path: .calkit/env-locks/py
       hash: md5
-      md5: 97801bd5ad552a89970a09edb1bc525d.dir
-      size: 231
-      nfiles: 1
+      md5: 6a3d291988c3964eaf329ec3c2c9b9f5.dir
+      size: 462
+      nfiles: 2
   _check-env-tex:
     cmd: calkit check environment --name tex
     outs:
     - path: .calkit/env-locks/tex
       hash: md5
-      md5: 2c552307edd59397026c9ef06dc8af47.dir
-      size: 1171
-      nfiles: 1
+      md5: fdae1edb4dcd23e4265e4f7701b324a3.dir
+      size: 2342
+      nfiles: 2
diff --git a/dvc.yaml b/dvc.yaml
index 4ff7e5a..549876b 100644
--- a/dvc.yaml
+++ b/dvc.yaml
@@ -8,7 +8,8 @@ stages:
           cache: false
           persist: true
     always_changed: true
-    desc: Automatically generated by Calkit. Changes made here will be overwritten.
+    desc: Automatically generated by Calkit. Changes made here will be
+      overwritten.
   _check-env-tex:
     cmd: calkit check environment --name tex
     deps: []
@@ -17,34 +18,37 @@ stages:
           cache: false
           persist: true
     always_changed: true
-    desc: Automatically generated by Calkit. Changes made here will be overwritten.
+    desc: Automatically generated by Calkit. Changes made here will be
+      overwritten.
   collect-data:
-    cmd: calkit xenv -n py --no-check -- python scripts/collect-data.py
+    cmd: calkit xenv -n py --no-check -- python 
+      scripts/collect-data.py
     deps:
       - scripts/collect-data.py
       - .calkit/env-locks/py
     outs:
       - data/raw/data.csv
-    desc: Automatically generated from the 'collect-data' stage in calkit.yaml.
-      Changes made here will be overwritten.
+    desc: Automatically generated from the 'collect-data' stage in 
+      calkit.yaml. Changes made here will be overwritten.
   plot-voltage:
-    cmd: calkit xenv -n py --no-check -- 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
       - data/raw/data.csv
     outs:
       - figures/voltage-time-series.png
-    desc: Automatically generated from the 'plot-voltage' stage in calkit.yaml.
-      Changes made here will be overwritten.
+    desc: Automatically generated from the 'plot-voltage' stage in 
+      calkit.yaml. Changes made here will be overwritten.
   build-paper:
-    cmd: calkit xenv -n tex --no-check -- latexmk -cd -norc -interaction=nonstopmode
-      -silent -synctex=1 -pdf paper/paper.tex
+    cmd: calkit xenv -n tex --no-check -- latexmk -cd -norc 
+      -interaction=nonstopmode -silent -synctex=1 -pdf paper/paper.tex
     deps:
       - paper/paper.tex
       - figures
       - .calkit/env-locks/tex
     outs:
       - paper/paper.pdf
-    desc: Automatically generated from the 'build-paper' stage in calkit.yaml.
-      Changes made here will be overwritten.
+    desc: Automatically generated from the 'build-paper' stage in 
+      calkit.yaml. Changes made here will be overwritten.

From 0fb495183fe2b52b8e1c389dc59a1d41ede97cab Mon Sep 17 00:00:00 2001
From: Pete Bachant <petebachant@gmail.com>
Date: Thu, 13 Nov 2025 13:16:16 -0800
Subject: [PATCH 4/5] Rerun on mac

---
 dvc.lock | 10 ++++------
 dvc.yaml | 28 ++++++++++++----------------
 2 files changed, 16 insertions(+), 22 deletions(-)

diff --git a/dvc.lock b/dvc.lock
index 7010893..6d7a548 100644
--- a/dvc.lock
+++ b/dvc.lock
@@ -53,8 +53,8 @@ stages:
       size: 45148
       nfiles: 2
   build-paper:
-    cmd: calkit xenv -n tex --no-check -- latexmk -cd -norc 
-      -interaction=nonstopmode -silent -synctex=1 -pdf paper/paper.tex
+    cmd: calkit xenv -n tex --no-check -- latexmk -cd -norc -interaction=nonstopmode
+      -silent -synctex=1 -pdf paper/paper.tex
     deps:
     - path: .calkit/env-locks/tex
       hash: md5
@@ -76,8 +76,7 @@ stages:
       md5: 24df231bcb8754c9bb3bf1087c31dd48
       size: 97240
   _check_env_py:
-    cmd: calkit check conda-env --file environment.yml --output 
-      .calkit/env-locks/py.yml
+    cmd: calkit check conda-env --file environment.yml --output .calkit/env-locks/py.yml
     deps:
     - path: environment.yml
       hash: md5
@@ -89,8 +88,7 @@ stages:
       md5: 8119fb42c7e8531010248790fff169cf
       size: 2200
   _check_env_tex:
-    cmd: calkit check docker-env texlive/texlive:latest-full -o 
-      .calkit/env-locks/tex.json
+    cmd: calkit check docker-env texlive/texlive:latest-full -o .calkit/env-locks/tex.json
     outs:
     - path: .calkit/env-locks/tex.json
       hash: md5
diff --git a/dvc.yaml b/dvc.yaml
index 549876b..4ff7e5a 100644
--- a/dvc.yaml
+++ b/dvc.yaml
@@ -8,8 +8,7 @@ stages:
           cache: false
           persist: true
     always_changed: true
-    desc: Automatically generated by Calkit. Changes made here will be
-      overwritten.
+    desc: Automatically generated by Calkit. Changes made here will be overwritten.
   _check-env-tex:
     cmd: calkit check environment --name tex
     deps: []
@@ -18,37 +17,34 @@ stages:
           cache: false
           persist: true
     always_changed: true
-    desc: Automatically generated by Calkit. Changes made here will be
-      overwritten.
+    desc: Automatically generated by Calkit. Changes made here will be overwritten.
   collect-data:
-    cmd: calkit xenv -n py --no-check -- python 
-      scripts/collect-data.py
+    cmd: calkit xenv -n py --no-check -- python scripts/collect-data.py
     deps:
       - scripts/collect-data.py
       - .calkit/env-locks/py
     outs:
       - data/raw/data.csv
-    desc: Automatically generated from the 'collect-data' stage in 
-      calkit.yaml. Changes made here will be overwritten.
+    desc: Automatically generated from the 'collect-data' stage in calkit.yaml.
+      Changes made here will be overwritten.
   plot-voltage:
-    cmd: calkit xenv -n py --no-check -- 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
       - data/raw/data.csv
     outs:
       - figures/voltage-time-series.png
-    desc: Automatically generated from the 'plot-voltage' stage in 
-      calkit.yaml. Changes made here will be overwritten.
+    desc: Automatically generated from the 'plot-voltage' stage in calkit.yaml.
+      Changes made here will be overwritten.
   build-paper:
-    cmd: calkit xenv -n tex --no-check -- latexmk -cd -norc 
-      -interaction=nonstopmode -silent -synctex=1 -pdf paper/paper.tex
+    cmd: calkit xenv -n tex --no-check -- latexmk -cd -norc -interaction=nonstopmode
+      -silent -synctex=1 -pdf paper/paper.tex
     deps:
       - paper/paper.tex
       - figures
       - .calkit/env-locks/tex
     outs:
       - paper/paper.pdf
-    desc: Automatically generated from the 'build-paper' stage in 
-      calkit.yaml. Changes made here will be overwritten.
+    desc: Automatically generated from the 'build-paper' stage in calkit.yaml.
+      Changes made here will be overwritten.

From 69f07962770e642e8f00d3b4705660d3ef4dedb5 Mon Sep 17 00:00:00 2001
From: "github-actions[bot]"
 <41898282+github-actions[bot]@users.noreply.github.com>
Date: Thu, 13 Nov 2025 21:18:49 +0000
Subject: [PATCH 5/5] Run pipeline

---
 dvc.lock | 10 ++++++----
 dvc.yaml | 28 ++++++++++++++++------------
 2 files changed, 22 insertions(+), 16 deletions(-)

diff --git a/dvc.lock b/dvc.lock
index 6d7a548..7010893 100644
--- a/dvc.lock
+++ b/dvc.lock
@@ -53,8 +53,8 @@ stages:
       size: 45148
       nfiles: 2
   build-paper:
-    cmd: calkit xenv -n tex --no-check -- latexmk -cd -norc -interaction=nonstopmode
-      -silent -synctex=1 -pdf paper/paper.tex
+    cmd: calkit xenv -n tex --no-check -- latexmk -cd -norc 
+      -interaction=nonstopmode -silent -synctex=1 -pdf paper/paper.tex
     deps:
     - path: .calkit/env-locks/tex
       hash: md5
@@ -76,7 +76,8 @@ stages:
       md5: 24df231bcb8754c9bb3bf1087c31dd48
       size: 97240
   _check_env_py:
-    cmd: calkit check conda-env --file environment.yml --output .calkit/env-locks/py.yml
+    cmd: calkit check conda-env --file environment.yml --output 
+      .calkit/env-locks/py.yml
     deps:
     - path: environment.yml
       hash: md5
@@ -88,7 +89,8 @@ stages:
       md5: 8119fb42c7e8531010248790fff169cf
       size: 2200
   _check_env_tex:
-    cmd: calkit check docker-env texlive/texlive:latest-full -o .calkit/env-locks/tex.json
+    cmd: calkit check docker-env texlive/texlive:latest-full -o 
+      .calkit/env-locks/tex.json
     outs:
     - path: .calkit/env-locks/tex.json
       hash: md5
diff --git a/dvc.yaml b/dvc.yaml
index 4ff7e5a..549876b 100644
--- a/dvc.yaml
+++ b/dvc.yaml
@@ -8,7 +8,8 @@ stages:
           cache: false
           persist: true
     always_changed: true
-    desc: Automatically generated by Calkit. Changes made here will be overwritten.
+    desc: Automatically generated by Calkit. Changes made here will be
+      overwritten.
   _check-env-tex:
     cmd: calkit check environment --name tex
     deps: []
@@ -17,34 +18,37 @@ stages:
           cache: false
           persist: true
     always_changed: true
-    desc: Automatically generated by Calkit. Changes made here will be overwritten.
+    desc: Automatically generated by Calkit. Changes made here will be
+      overwritten.
   collect-data:
-    cmd: calkit xenv -n py --no-check -- python scripts/collect-data.py
+    cmd: calkit xenv -n py --no-check -- python 
+      scripts/collect-data.py
     deps:
       - scripts/collect-data.py
       - .calkit/env-locks/py
     outs:
       - data/raw/data.csv
-    desc: Automatically generated from the 'collect-data' stage in calkit.yaml.
-      Changes made here will be overwritten.
+    desc: Automatically generated from the 'collect-data' stage in 
+      calkit.yaml. Changes made here will be overwritten.
   plot-voltage:
-    cmd: calkit xenv -n py --no-check -- 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
       - data/raw/data.csv
     outs:
       - figures/voltage-time-series.png
-    desc: Automatically generated from the 'plot-voltage' stage in calkit.yaml.
-      Changes made here will be overwritten.
+    desc: Automatically generated from the 'plot-voltage' stage in 
+      calkit.yaml. Changes made here will be overwritten.
   build-paper:
-    cmd: calkit xenv -n tex --no-check -- latexmk -cd -norc -interaction=nonstopmode
-      -silent -synctex=1 -pdf paper/paper.tex
+    cmd: calkit xenv -n tex --no-check -- latexmk -cd -norc 
+      -interaction=nonstopmode -silent -synctex=1 -pdf paper/paper.tex
     deps:
       - paper/paper.tex
       - figures
       - .calkit/env-locks/tex
     outs:
       - paper/paper.pdf
-    desc: Automatically generated from the 'build-paper' stage in calkit.yaml.
-      Changes made here will be overwritten.
+    desc: Automatically generated from the 'build-paper' stage in 
+      calkit.yaml. Changes made here will be overwritten.