calkit-python 0.49.4__tar.gz → 0.50.0__tar.gz

calkit_python-0.50.0/.calkit/stage-runs.json

@@ -0,0 +1,209 @@
+{
+  "budget-2027": {
+    "start_time": "2026-10-27T18:13:05.310000",
+    "end_time": "2026-10-27T18:13:05.808000",
+    "environment": "dev",
+    "git_rev": "6a4bdff7eeb375fe9682ea54948f21b0e657103c",
+    "git_dirty": true,
+    "dvc_lock_hash": "sha256:7ade6994279f1ee673778fc198251eff1e83211f829248a7712978957979ab6b",
+    "calkit_version": "0.49.6.dev9+g6a4bdff7",
+    "calkit_git_rev": "6a4bdff7eeb375fe9682ea54948f21b0e657103c",
+    "system": {
+      "machine_id": "680295DC-2853-59C0-82C9-87907FA3FEDB",
+      "os": "Darwin",
+      "os_version": "25.6.0",
+      "machine": "arm64",
+      "processor": "arm",
+      "cpu_count": 14,
+      "memory_gb": 24.0
+    }
+  },
+  "budget-2027-figure": {
+    "start_time": "2026-10-27T18:13:05.808000",
+    "end_time": "2026-10-27T18:13:06.597000",
+    "environment": "dev",
+    "git_rev": "6a4bdff7eeb375fe9682ea54948f21b0e657103c",
+    "git_dirty": true,
+    "dvc_lock_hash": "sha256:c593381caf793554c569f3937e9e8172370eae5cf671f1db097965f988b86a19",
+    "calkit_version": "0.49.6.dev9+g6a4bdff7",
+    "calkit_git_rev": "6a4bdff7eeb375fe9682ea54948f21b0e657103c",
+    "system": {
+      "machine_id": "680295DC-2853-59C0-82C9-87907FA3FEDB",
+      "os": "Darwin",
+      "os_version": "25.6.0",
+      "machine": "arm64",
+      "processor": "arm",
+      "cpu_count": 14,
+      "memory_gb": 24.0
+    }
+  },
+  "find-calkit-papers": {
+    "start_time": "2026-10-27T18:16:54.346000",
+    "end_time": "2026-10-27T18:17:02.253000",
+    "environment": "dev",
+    "git_rev": "6a4bdff7eeb375fe9682ea54948f21b0e657103c",
+    "git_dirty": true,
+    "dvc_lock_hash": "sha256:09599dce62c6341a22a91c60d2548bae6a7f9181399f1642c345e5f6153e49ba",
+    "calkit_version": "0.49.6.dev9+g6a4bdff7",
+    "calkit_git_rev": "6a4bdff7eeb375fe9682ea54948f21b0e657103c",
+    "system": {
+      "machine_id": "680295DC-2853-59C0-82C9-87907FA3FEDB",
+      "os": "Darwin",
+      "os_version": "25.6.0",
+      "machine": "arm64",
+      "processor": "arm",
+      "cpu_count": 14,
+      "memory_gb": 24.0
+    }
+  },
+  "find-calkit-projects": {
+    "start_time": "2026-10-27T18:13:06.597000",
+    "end_time": "2026-10-27T18:16:54.346000",
+    "environment": "dev",
+    "git_rev": "6a4bdff7eeb375fe9682ea54948f21b0e657103c",
+    "git_dirty": true,
+    "dvc_lock_hash": "sha256:d6cca26343e24d02ecdf32323cbc780bd20ba358a60f94e82cad31e43e6000ec",
+    "calkit_version": "0.49.6.dev9+g6a4bdff7",
+    "calkit_git_rev": "6a4bdff7eeb375fe9682ea54948f21b0e657103c",
+    "system": {
+      "machine_id": "680295DC-2853-59C0-82C9-87907FA3FEDB",
+      "os": "Darwin",
+      "os_version": "25.6.0",
+      "machine": "arm64",
+      "processor": "arm",
+      "cpu_count": 14,
+      "memory_gb": 24.0
+    }
+  },
+  "latex-image-readme/sizes": {
+    "start_time": "2026-10-27T18:50:04.805000",
+    "end_time": "2026-10-27T18:50:12.104000",
+    "git_rev": "803cb21beb339e153b90804288d5bb9f2c325270",
+    "git_dirty": true,
+    "dvc_lock_hash": "sha256:b1fa93cf233fe6d32155eceabcb6e8684b6e0f67a8f624d3268fd89ae3b97715",
+    "calkit_version": "0.49.6.dev10+g803cb21b.d20261027",
+    "calkit_git_rev": "803cb21beb339e153b90804288d5bb9f2c325270",
+    "system": {
+      "machine_id": "680295DC-2853-59C0-82C9-87907FA3FEDB",
+      "os": "Darwin",
+      "os_version": "25.6.0",
+      "machine": "arm64",
+      "processor": "arm",
+      "cpu_count": 14,
+      "memory_gb": 24.0
+    }
+  },
+  "latex-word-round-trip": {
+    "start_time": "2026-10-27T18:49:49.128000",
+    "end_time": "2026-10-27T18:50:02.783000",
+    "environment": "dev",
+    "git_rev": "803cb21beb339e153b90804288d5bb9f2c325270",
+    "git_dirty": true,
+    "dvc_lock_hash": "sha256:af07dce06388e4331158f3d19a008c111caec498531a0a227df2e702c40b69e6",
+    "calkit_version": "0.49.6.dev10+g803cb21b.d20261027",
+    "calkit_git_rev": "803cb21beb339e153b90804288d5bb9f2c325270",
+    "system": {
+      "machine_id": "680295DC-2853-59C0-82C9-87907FA3FEDB",
+      "os": "Darwin",
+      "os_version": "25.6.0",
+      "machine": "arm64",
+      "processor": "arm",
+      "cpu_count": 14,
+      "memory_gb": 24.0
+    }
+  },
+  "latex-word-round-trip-figure": {
+    "start_time": "2026-10-27T18:50:02.783000",
+    "end_time": "2026-10-27T18:50:04.783000",
+    "environment": "dev",
+    "git_rev": "803cb21beb339e153b90804288d5bb9f2c325270",
+    "git_dirty": true,
+    "dvc_lock_hash": "sha256:6eed9e172280d9a57b231f08c75851b5566b3e41c76ee266cda860e93f9821e9",
+    "calkit_version": "0.49.6.dev10+g803cb21b.d20261027",
+    "calkit_git_rev": "803cb21beb339e153b90804288d5bb9f2c325270",
+    "system": {
+      "machine_id": "680295DC-2853-59C0-82C9-87907FA3FEDB",
+      "os": "Darwin",
+      "os_version": "25.6.0",
+      "machine": "arm64",
+      "processor": "arm",
+      "cpu_count": 14,
+      "memory_gb": 24.0
+    }
+  },
+  "one-pager/pdf": {
+    "start_time": "2026-10-27T01:00:13.549000",
+    "end_time": "2026-10-27T01:00:18.359000",
+    "git_rev": "c637dbe2896767928e40cf68f89ec4ca7b43f955",
+    "git_dirty": false,
+    "dvc_lock_hash": "sha256:1a2a0887701875f6308d20785084c805196aabeabec2b149a4f12c2c19fd71e2",
+    "calkit_version": "0.49.6.dev8+gc637dbe2",
+    "calkit_git_rev": "c637dbe2896767928e40cf68f89ec4ca7b43f955",
+    "system": {
+      "machine_id": "2d791d5cce6240faa3c626058b1ffc7d",
+      "os": "Linux",
+      "os_version": "6.17.0-1022-azure",
+      "machine": "x86_64",
+      "processor": "x86_64",
+      "cpu_count": 4,
+      "memory_gb": 15.6
+    }
+  },
+  "research-flow": {
+    "start_time": "2026-10-27T18:10:31.736000",
+    "end_time": "2026-10-27T18:13:03.005000",
+    "environment": "dev",
+    "git_rev": "6a4bdff7eeb375fe9682ea54948f21b0e657103c",
+    "git_dirty": true,
+    "dvc_lock_hash": "sha256:f1ea1e7fc8e0850f99839e35319d41ee9ff008507de5ae2d0b1854fe85d0fb3d",
+    "calkit_version": "0.49.6.dev9+g6a4bdff7",
+    "calkit_git_rev": "6a4bdff7eeb375fe9682ea54948f21b0e657103c",
+    "system": {
+      "machine_id": "680295DC-2853-59C0-82C9-87907FA3FEDB",
+      "os": "Darwin",
+      "os_version": "25.6.0",
+      "machine": "arm64",
+      "processor": "arm",
+      "cpu_count": 14,
+      "memory_gb": 24.0
+    }
+  },
+  "research-flow-figure": {
+    "start_time": "2026-10-27T18:13:03.005000",
+    "end_time": "2026-10-27T18:13:05.310000",
+    "environment": "dev",
+    "git_rev": "6a4bdff7eeb375fe9682ea54948f21b0e657103c",
+    "git_dirty": true,
+    "dvc_lock_hash": "sha256:fe376f8bc6a73a2452e39f039d58e6d0375dd22ab5b2c56d8f6d0720cdbfa2ac",
+    "calkit_version": "0.49.6.dev9+g6a4bdff7",
+    "calkit_git_rev": "6a4bdff7eeb375fe9682ea54948f21b0e657103c",
+    "system": {
+      "machine_id": "680295DC-2853-59C0-82C9-87907FA3FEDB",
+      "os": "Darwin",
+      "os_version": "25.6.0",
+      "machine": "arm64",
+      "processor": "arm",
+      "cpu_count": 14,
+      "memory_gb": 24.0
+    }
+  },
+  "traction": {
+    "start_time": "2026-10-27T18:17:02.253000",
+    "end_time": "2026-10-27T18:17:44.747000",
+    "environment": "dev",
+    "git_rev": "6a4bdff7eeb375fe9682ea54948f21b0e657103c",
+    "git_dirty": true,
+    "dvc_lock_hash": "sha256:d1d502d7dbc8ec41bf7f4809508c69f63588fdee0648e83e6aaf6e7c33624d78",
+    "calkit_version": "0.49.6.dev9+g6a4bdff7",
+    "calkit_git_rev": "6a4bdff7eeb375fe9682ea54948f21b0e657103c",
+    "system": {
+      "machine_id": "680295DC-2853-59C0-82C9-87907FA3FEDB",
+      "os": "Darwin",
+      "os_version": "25.6.0",
+      "machine": "arm64",
+      "processor": "arm",
+      "cpu_count": 14,
+      "memory_gb": 24.0
+    }
+  }
+}

{calkit_python-0.49.4 → calkit_python-0.50.0}/AGENTS.md

@@ -41,6 +41,14 @@ preceded by a `<!-- prettier-ignore -->` comment. Otherwise Prettier reformats
 the block and strips the 4-space indentation of the admonition body, which
 breaks rendering.
 
+`calkit run` and `calkit status` preprocess the pipeline before asking DVC:
+they check environments and clean notebooks, and compiling a LaTeX stage for
+them maps its document's components into `_calkit/`, since each generates
+dependencies the compiled DVC pipeline reads.
+This runs on every call, so only very fast work belongs there, e.g.,
+skipping unchanged files by size and timestamp rather than reading them.
+Anything slow belongs in a stage.
+
 Agents should never make commits to Git unless asked to.
 
 Tests belong in the test module named after the module the exercised code

{calkit_python-0.49.4 → calkit_python-0.50.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.5
 Name: calkit-python
-Version: 0.49.4
+Version: 0.50.0
 Summary: Reproducibility simplified.
 Project-URL: Homepage, https://calkit.org
 Project-URL: Issues, https://github.com/calkit/calkit/issues
@@ -44,6 +44,7 @@ Requires-Dist: pydantic-settings
 Requires-Dist: pydantic[email]
 Requires-Dist: pygtrie<2.6.0
 Requires-Dist: pyjwt
+Requires-Dist: pypdfium2>=5.13.0
 Requires-Dist: python-dotenv>=1
 Requires-Dist: pywin32; platform_system == 'Windows'
 Requires-Dist: requests

{calkit_python-0.49.4 → calkit_python-0.50.0}/agent-plugin/.claude-plugin/plugin.json

@@ -1,5 +1,5 @@
 {
   "name": "calkit",
   "description": "Agent skills for working with Calkit projects.",
-  "version": "0.2.0"
+  "version": "0.3.0"
 }

calkit_python-0.50.0/agent-plugin/skills/resolve-merge-conflicts/SKILL.md

@@ -0,0 +1,72 @@
+---
+name: resolve-merge-conflicts
+description: Resolve Git merge conflicts in a Calkit project, including
+  dvc.lock, stage run records, and pipeline outputs. Use when the user
+  invokes `/calkit:resolve-merge-conflicts`, asks to merge a branch, or a
+  merge, pull, or rebase stopped with conflicts.
+---
+
+# Resolve merge conflicts
+
+Some conflicted files record what the pipeline ran rather than what anyone
+wrote, so they're resolved per stage by Calkit, not by editing text.
+
+## Division of labor
+
+Done by Calkit, never by hand:
+
+- `dvc.lock` and `.calkit/stage-runs.json`, in the project and any
+  subproject. Don't edit them or take one side whole with
+  `git checkout --ours/--theirs`: that mixes stages, or drops the records of
+  stages that only ran on the other side.
+- Git-tracked pipeline outputs, which are checked out from the side each
+  stage's `dvc.lock` entry came from.
+- `dvc.yaml`, which is generated from `calkit.yaml`. Once `calkit.yaml` is
+  resolved, take either side (`git checkout --ours dvc.yaml`) and run
+  `calkit status`, which rewrites it.
+
+Done by you, with judgment: everything else, e.g., source code,
+`calkit.yaml`, and manuscripts. When the two sides disagree about intent,
+not just text, ask the user.
+
+## Starting a merge
+
+Prefer `calkit merge BRANCH` to `git merge`. It sets up the merge driver,
+resolves what it can, and checks out DVC-tracked outputs afterwards. Most
+stages merge without a conflict: one changed on one side only takes that
+side.
+
+## Stages changed on both sides
+
+Each needs one choice, which decides its `dvc.lock` entry, run record, and
+Git-tracked outputs together:
+
+- `ours` or `theirs`: keep that side's result.
+- `rerun`: keep neither, so `calkit run` reruns it.
+
+You have no terminal for the prompt, so pass choices as options:
+
+```sh
+calkit fix merge-conflicts --theirs fit --rerun figures
+calkit fix merge-conflicts --prefer rerun
+```
+
+Name subproject stages as `calkit check stage-runs` does, e.g.,
+`sub/dvc.yaml:stage`. Run it without options first to list the stages that
+need a choice.
+
+To choose, compare each side's inputs with the merged ones. If the merged
+inputs match one side, keep that side. If they match neither, e.g., both
+sides edited the code, the stage will rerun either way, so choose `rerun`.
+If a stage is expensive to run, or its result is shared with others, ask the
+user. During a rebase, "ours" is the branch being rebased onto, and
+"theirs" is the commit being replayed.
+
+## Finishing
+
+1. Resolve and `git add` the remaining files.
+2. For a merge, run `calkit merge --continue`, with any stage choices still
+   needed. For a rebase or cherry-pick, run `calkit fix merge-conflicts`,
+   then `git rebase --continue` or `git cherry-pick --continue`.
+3. Run `calkit status`, then `calkit run` if stages are stale.
+4. Run `calkit check stage-runs` to confirm every stage matches its run.

{calkit_python-0.49.4 → calkit_python-0.50.0}/browser-ext/src/background/index.ts

@@ -152,6 +152,7 @@ async function handle(message: Request): Promise<unknown> {
           search_for: message.searchFor,
           limit: message.limit ?? 100,
           min_access_level: message.minAccessLevel ?? "write",
+          github_repo: message.githubRepo,
         },
       });
     case "projects.create":
@@ -174,6 +175,10 @@ async function handle(message: Request): Promise<unknown> {
       return request<GithubRepo[]>("/user/github/repos", {
         query: { per_page: message.perPage ?? 100 },
       });
+    case "github.installations":
+      // Where the Calkit GitHub app is installed, without which the hub can't
+      // create or update a project's repo
+      return request<{ total_count: number }>("/user/github-app-installations");
     case "github.pullRequest":
       // Through the hub, which holds a GitHub token, so a private repo
       // resolves where an unauthenticated request would not