From 2e702cf5cbe63993214af5271efd35ac8aac07c6 Mon Sep 17 00:00:00 2001 From: Fabro Date: Mon, 16 Mar 2026 08:00:37 -0400 Subject: [PATCH] checkpoint MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit ⚒️ Generated with [Fabro](https://fabro.sh) --- checkpoint.json | 36 +++++++++++++++------- nodes/extract_patch/script_invocation.json | 5 +++ nodes/extract_patch/script_timing.json | 5 +++ nodes/extract_patch/status.json | 6 ++++ nodes/solve/diff.patch | 7 +++++ 5 files changed, 48 insertions(+), 11 deletions(-) create mode 100644 nodes/extract_patch/script_invocation.json create mode 100644 nodes/extract_patch/script_timing.json create mode 100644 nodes/extract_patch/status.json create mode 100644 nodes/solve/diff.patch diff --git a/checkpoint.json b/checkpoint.json index 9c725bfae..ee5f39a83 100644 --- a/checkpoint.json +++ b/checkpoint.json @@ -1,19 +1,21 @@ { - "timestamp": "2026-03-16T12:00:34.997886Z", - "current_node": "solve", + "timestamp": "2026-03-16T12:00:37.460542Z", + "current_node": "extract_patch", "completed_nodes": [ "start", "setup", - "solve" + "solve", + "extract_patch" ], "node_retries": { - "start": 1, "solve": 1, - "setup": 1 + "setup": 1, + "start": 1, + "extract_patch": 1 }, "context_values": { "graph.rankdir": "LR", - "current_node": "solve", + "current_node": "extract_patch", "internal.node_visit_count": 1, "internal.retry_count.start": 1, "graph.goal": "Modeling's `separability_matrix` does not compute separability correctly for nested CompoundModels\nConsider the following model:\r\n\r\n```python\r\nfrom astropy.modeling import models as m\r\nfrom astropy.modeling.separable import separability_matrix\r\n\r\ncm = m.Linear1D(10) & m.Linear1D(5)\r\n```\r\n\r\nIt's separability matrix as you might expect is a diagonal:\r\n\r\n```python\r\n>>> separability_matrix(cm)\r\narray([[ True, False],\r\n [False, True]])\r\n```\r\n\r\nIf I make the model more complex:\r\n```python\r\n>>> separability_matrix(m.Pix2Sky_TAN() & m.Linear1D(10) & m.Linear1D(5))\r\narray([[ True, True, False, False],\r\n [ True, True, False, False],\r\n [False, False, True, False],\r\n [False, False, False, True]])\r\n```\r\n\r\nThe output matrix is again, as expected, the outputs and inputs to the linear models are separable and independent of each other.\r\n\r\nIf however, I nest these compound models:\r\n```python\r\n>>> separability_matrix(m.Pix2Sky_TAN() & cm)\r\narray([[ True, True, False, False],\r\n [ True, True, False, False],\r\n [False, False, True, True],\r\n [False, False, True, True]])\r\n```\r\nSuddenly the inputs and outputs are no longer separable?\r\n\r\nThis feels like a bug to me, but I might be missing something?\n", @@ -22,17 +24,19 @@ "response.solve": "The fix is applied. Here's a summary:\n\n## Root Cause\n\nIn `astropy/modeling/separable.py`, the `_cstack` function handles the `&` (concatenation) operator for computing separability matrices. When the right operand is already an ndarray (which happens when it's a nested CompoundModel that has already been recursively evaluated by `_separable`), line 245 was:\n\n```python\ncright[-right.shape[0]:, -right.shape[1]:] = 1\n```\n\nThis set the entire bottom-right block to `1`, **discarding** the actual separability information that was computed for the nested compound model. This made all outputs appear to depend on all inputs for that sub-model.\n\n## Fix\n\nChanged line 245 from `= 1` to `= right`:\n\n```python\ncright[-right.shape[0]:, -right.shape[1]:] = right\n```\n\nThis preserves the actual separability matrix computed for the nested compound model, just like the `left` branch already correctly does on line 240 (`= left`).\n\nThis is a one-line fix that makes the `right` branch consistent with the `left` branch — both now properly copy the pre-computed separability matrix instead of replacing it with all ones.", "outcome": "success", "last_stage": "solve", + "internal.retry_count.extract_patch": 1, "thread.start.current_node": "setup", "internal.fidelity": "compact", "internal.retry_count.solve": 1, "thread.setup.current_node": "solve", - "internal.thread_id": "setup", + "thread.solve.current_node": "extract_patch", + "internal.thread_id": "solve", "failure_class": "", "internal.run_id": "01KKV857H2RFAYPQBG0N9873NR", - "current.preamble": "Goal: Modeling's `separability_matrix` does not compute separability correctly for nested CompoundModels\nConsider the following model:\r\n\r\n```python\r\nfrom astropy.modeling import models as m\r\nfrom astropy.modeling.separable import separability_matrix\r\n\r\ncm = m.Linear1D(10) & m.Linear1D(5)\r\n```\r\n\r\nIt's separability matrix as you might expect is a diagonal:\r\n\r\n```python\r\n>>> separability_matrix(cm)\r\narray([[ True, False],\r\n [False, True]])\r\n```\r\n\r\nIf I make the model more complex:\r\n```python\r\n>>> separability_matrix(m.Pix2Sky_TAN() & m.Linear1D(10) & m.Linear1D(5))\r\narray([[ True, True, False, False],\r\n [ True, True, False, False],\r\n [False, False, True, False],\r\n [False, False, False, True]])\r\n```\r\n\r\nThe output matrix is again, as expected, the outputs and inputs to the linear models are separable and independent of each other.\r\n\r\nIf however, I nest these compound models:\r\n```python\r\n>>> separability_matrix(m.Pix2Sky_TAN() & cm)\r\narray([[ True, True, False, False],\r\n [ True, True, False, False],\r\n [False, False, True, True],\r\n [False, False, True, True]])\r\n```\r\nSuddenly the inputs and outputs are no longer separable?\r\n\r\nThis feels like a bug to me, but I might be missing something?\n\n\n## Completed stages\n- **setup**: fail\n - Script: `git clone https://github.com/astropy/astropy.git . && git checkout d16bfe05a744909de4b27f5875fe0d4ed41ce607 && sed -i 's/requires = \\[\"setuptools\",/requires = \\[\"setuptools==68.0.0\",/' pyproject.toml && python -m pip install -e .[test] --verbose`\n - Stdout:\n ```\n fatal: destination path '.' already exists and is not an empty directory.\n ```\n - Stderr: (empty)\n\n## Context\n- failure_class: deterministic\n- failure_signature: setup|deterministic|script failed with exit code: ## stdout fatal: destination path '.' already exists and is not an empty directory.\n", + "current.preamble": "Goal: Modeling's `separability_matrix` does not compute separability correctly for nested CompoundModels\nConsider the following model:\r\n\r\n```python\r\nfrom astropy.modeling import models as m\r\nfrom astropy.modeling.separable import separability_matrix\r\n\r\ncm = m.Linear1D(10) & m.Linear1D(5)\r\n```\r\n\r\nIt's separability matrix as you might expect is a diagonal:\r\n\r\n```python\r\n>>> separability_matrix(cm)\r\narray([[ True, False],\r\n [False, True]])\r\n```\r\n\r\nIf I make the model more complex:\r\n```python\r\n>>> separability_matrix(m.Pix2Sky_TAN() & m.Linear1D(10) & m.Linear1D(5))\r\narray([[ True, True, False, False],\r\n [ True, True, False, False],\r\n [False, False, True, False],\r\n [False, False, False, True]])\r\n```\r\n\r\nThe output matrix is again, as expected, the outputs and inputs to the linear models are separable and independent of each other.\r\n\r\nIf however, I nest these compound models:\r\n```python\r\n>>> separability_matrix(m.Pix2Sky_TAN() & cm)\r\narray([[ True, True, False, False],\r\n [ True, True, False, False],\r\n [False, False, True, True],\r\n [False, False, True, True]])\r\n```\r\nSuddenly the inputs and outputs are no longer separable?\r\n\r\nThis feels like a bug to me, but I might be missing something?\n\n\n## Completed stages\n- **setup**: fail\n - Script: `git clone https://github.com/astropy/astropy.git . && git checkout d16bfe05a744909de4b27f5875fe0d4ed41ce607 && sed -i 's/requires = \\[\"setuptools\",/requires = \\[\"setuptools==68.0.0\",/' pyproject.toml && python -m pip install -e .[test] --verbose`\n - Stdout:\n ```\n fatal: destination path '.' already exists and is not an empty directory.\n ```\n - Stderr: (empty)\n- **solve**: success\n - Model: claude-opus-4-6, 11.4k tokens in / 3.3k out\n - Files: /home/daytona/workspace/astropy_repo/astropy/modeling/separable.py\n", "internal.retry_count.setup": 1, "last_response": "The fix is applied. Here's a summary:\n\n## Root Cause\n\nIn `astropy/modeling/separable.py`, the `_cstack` function handles the `&` (concatenation) operator for computing separability matrices. When the ", - "command.output": "fatal: destination path '.' already exists and is not an empty directory.\n" + "command.output": "diff --git a/astropy_repo b/astropy_repo\n--- a/astropy_repo\n+++ b/astropy_repo\n@@ -1 +1 @@\n-Subproject commit d16bfe05a744909de4b27f5875fe0d4ed41ce607\n+Subproject commit d16bfe05a744909de4b27f5875fe0d4ed41ce607-dirty\n" }, "logs": [], "node_outcomes": { @@ -48,6 +52,15 @@ }, "duration_ms": 212 }, + "extract_patch": { + "status": "success", + "context_updates": { + "command.stderr": "", + "command.output": "diff --git a/astropy_repo b/astropy_repo\n--- a/astropy_repo\n+++ b/astropy_repo\n@@ -1 +1 @@\n-Subproject commit d16bfe05a744909de4b27f5875fe0d4ed41ce607\n+Subproject commit d16bfe05a744909de4b27f5875fe0d4ed41ce607-dirty\n" + }, + "notes": "Script completed: git diff", + "duration_ms": 41 + }, "start": { "status": "success", "duration_ms": 0 @@ -75,13 +88,14 @@ "duration_ms": 144779 } }, - "next_node_id": "extract_patch", + "next_node_id": "exit", "loop_failure_signatures": { "setup|deterministic|script failed with exit code: ## stdout fatal: destination path '.' already exists and is not an empty directory.": 1 }, "node_visits": { "start": 1, "setup": 1, - "solve": 1 + "solve": 1, + "extract_patch": 1 } } \ No newline at end of file diff --git a/nodes/extract_patch/script_invocation.json b/nodes/extract_patch/script_invocation.json new file mode 100644 index 000000000..6d29afc80 --- /dev/null +++ b/nodes/extract_patch/script_invocation.json @@ -0,0 +1,5 @@ +{ + "command": "git diff", + "language": "shell", + "timeout_ms": null +} \ No newline at end of file diff --git a/nodes/extract_patch/script_timing.json b/nodes/extract_patch/script_timing.json new file mode 100644 index 000000000..1627574d2 --- /dev/null +++ b/nodes/extract_patch/script_timing.json @@ -0,0 +1,5 @@ +{ + "duration_ms": 40, + "exit_code": 0, + "timed_out": false +} \ No newline at end of file diff --git a/nodes/extract_patch/status.json b/nodes/extract_patch/status.json new file mode 100644 index 000000000..f1288b577 --- /dev/null +++ b/nodes/extract_patch/status.json @@ -0,0 +1,6 @@ +{ + "status": "success", + "notes": "Script completed: git diff", + "failure_reason": null, + "timestamp": "2026-03-16T12:00:37.460167+00:00" +} \ No newline at end of file diff --git a/nodes/solve/diff.patch b/nodes/solve/diff.patch new file mode 100644 index 000000000..daf6ecf06 --- /dev/null +++ b/nodes/solve/diff.patch @@ -0,0 +1,7 @@ +diff --git a/astropy_repo b/astropy_repo +new file mode 160000 +index 0000000..d16bfe0 +--- /dev/null ++++ b/astropy_repo +@@ -0,0 +1 @@ ++Subproject commit d16bfe05a744909de4b27f5875fe0d4ed41ce607