diff --git a/checkpoint.json b/checkpoint.json index bee1d8a86..9b9ede5a7 100644 --- a/checkpoint.json +++ b/checkpoint.json @@ -1,34 +1,59 @@ { - "timestamp": "2026-03-16T12:02:27.592367Z", - "current_node": "setup", + "timestamp": "2026-03-16T12:05:37.721224Z", + "current_node": "solve", "completed_nodes": [ "start", - "setup" + "setup", + "solve" ], "node_retries": { "setup": 1, + "solve": 1, "start": 1 }, "context_values": { "internal.retry_count.start": 1, - "internal.thread_id": "start", + "internal.thread_id": "setup", "thread.start.current_node": "setup", + "last_response": "Implemented the fix in the cloned Astropy checkout at `/home/daytona/workspace/astropy`.\n\nWhat changed:\n- `astropy/modeling/separable.py`\n - Fixed `_cstack()` so that when the right-hand side is alre", + "last_stage": "solve", "internal.fidelity": "compact", - "failure_class": "deterministic", - "outcome": "fail", + "failure_class": "", + "outcome": "success", "internal.retry_count.setup": 1, "command.output": "fatal: destination path '.' already exists and is not an empty directory.\n", + "thread.setup.current_node": "solve", + "response.solve": "Implemented the fix in the cloned Astropy checkout at `/home/daytona/workspace/astropy`.\n\nWhat changed:\n- `astropy/modeling/separable.py`\n - Fixed `_cstack()` so that when the right-hand side is already a computed separability matrix from a nested `CompoundModel`, it preserves that matrix instead of replacing it with all 1s.\n- `astropy/modeling/tests/test_separable.py`\n - Added a regression test covering `models.Pix2Sky_TAN() & (models.Linear1D(10) & models.Linear1D(5))`.\n\nRoot cause:\n- Nested compound models reach `_cstack()` as ndarray separability matrices.\n- The right-hand ndarray branch incorrectly did:\n - `cright[...] = 1`\n- That flattened all right-side dependencies into “non-separable”.\n- It now correctly does:\n - `cright[...] = right`\n\nValidation:\n- Reproduced the original bug before the change.\n- Ran:\n - `python -m pytest astropy/modeling/tests/test_separable.py -q`\n- Result:\n - `12 passed`\n\nThe original example now returns the expected matrix:\n```python\n[[ True True False False]\n [ True True False False]\n [False False True False]\n [False False False True]]\n```", + "internal.retry_count.solve": 1, "internal.run_id": "01KKV8D5GSGKS4B48NJAMDYHVF", "command.stderr": "", - "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", + "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", "internal.node_visit_count": 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", "graph.rankdir": "LR", - "failure_signature": "setup|deterministic|script failed with exit code: ## stdout fatal: destination path '.' already exists and is not an empty directory.", - "current_node": "setup" + "failure_signature": "", + "current_node": "solve" }, "logs": [], "node_outcomes": { + "solve": { + "status": "success", + "context_updates": { + "last_response": "Implemented the fix in the cloned Astropy checkout at `/home/daytona/workspace/astropy`.\n\nWhat changed:\n- `astropy/modeling/separable.py`\n - Fixed `_cstack()` so that when the right-hand side is alre", + "last_stage": "solve", + "response.solve": "Implemented the fix in the cloned Astropy checkout at `/home/daytona/workspace/astropy`.\n\nWhat changed:\n- `astropy/modeling/separable.py`\n - Fixed `_cstack()` so that when the right-hand side is already a computed separability matrix from a nested `CompoundModel`, it preserves that matrix instead of replacing it with all 1s.\n- `astropy/modeling/tests/test_separable.py`\n - Added a regression test covering `models.Pix2Sky_TAN() & (models.Linear1D(10) & models.Linear1D(5))`.\n\nRoot cause:\n- Nested compound models reach `_cstack()` as ndarray separability matrices.\n- The right-hand ndarray branch incorrectly did:\n - `cright[...] = 1`\n- That flattened all right-side dependencies into “non-separable”.\n- It now correctly does:\n - `cright[...] = right`\n\nValidation:\n- Reproduced the original bug before the change.\n- Ran:\n - `python -m pytest astropy/modeling/tests/test_separable.py -q`\n- Result:\n - `12 passed`\n\nThe original example now returns the expected matrix:\n```python\n[[ True True False False]\n [ True True False False]\n [False False True False]\n [False False False True]]\n```" + }, + "notes": "Stage completed: solve", + "usage": { + "model": "gpt-5.4", + "input_tokens": 656033, + "output_tokens": 5940, + "cache_read_tokens": 564224, + "reasoning_tokens": 2467, + "cost": 1.7291825 + }, + "duration_ms": 187578 + }, "start": { "status": "success", "duration_ms": 0 @@ -46,12 +71,13 @@ "duration_ms": 82 } }, - "next_node_id": "solve", + "next_node_id": "extract_patch", "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, + "solve": 1, "setup": 1 } } \ No newline at end of file diff --git a/nodes/solve/prompt.md b/nodes/solve/prompt.md new file mode 100644 index 000000000..111e037eb --- /dev/null +++ b/nodes/solve/prompt.md @@ -0,0 +1,57 @@ +Goal: Modeling's `separability_matrix` does not compute separability correctly for nested CompoundModels +Consider the following model: + +```python +from astropy.modeling import models as m +from astropy.modeling.separable import separability_matrix + +cm = m.Linear1D(10) & m.Linear1D(5) +``` + +It's separability matrix as you might expect is a diagonal: + +```python +>>> separability_matrix(cm) +array([[ True, False], + [False, True]]) +``` + +If I make the model more complex: +```python +>>> separability_matrix(m.Pix2Sky_TAN() & m.Linear1D(10) & m.Linear1D(5)) +array([[ True, True, False, False], + [ True, True, False, False], + [False, False, True, False], + [False, False, False, True]]) +``` + +The output matrix is again, as expected, the outputs and inputs to the linear models are separable and independent of each other. + +If however, I nest these compound models: +```python +>>> separability_matrix(m.Pix2Sky_TAN() & cm) +array([[ True, True, False, False], + [ True, True, False, False], + [False, False, True, True], + [False, False, True, True]]) +``` +Suddenly the inputs and outputs are no longer separable? + +This feels like a bug to me, but I might be missing something? + + +## Completed stages +- **setup**: fail + - 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` + - Stdout: + ``` + fatal: destination path '.' already exists and is not an empty directory. + ``` + - Stderr: (empty) + +## Context +- failure_class: deterministic +- failure_signature: setup|deterministic|script failed with exit code: ## stdout fatal: destination path '.' already exists and is not an empty directory. + + +Fix this GitHub issue in the repository. Make the minimal code change needed. \ No newline at end of file diff --git a/nodes/solve/provider_used.json b/nodes/solve/provider_used.json new file mode 100644 index 000000000..9f9e29e5d --- /dev/null +++ b/nodes/solve/provider_used.json @@ -0,0 +1,5 @@ +{ + "mode": "agent", + "provider": "openai", + "model": "gpt-5.4" +} \ No newline at end of file diff --git a/nodes/solve/response.md b/nodes/solve/response.md new file mode 100644 index 000000000..90b1cdb2c --- /dev/null +++ b/nodes/solve/response.md @@ -0,0 +1,30 @@ +Implemented the fix in the cloned Astropy checkout at `/home/daytona/workspace/astropy`. + +What changed: +- `astropy/modeling/separable.py` + - Fixed `_cstack()` so that when the right-hand side is already a computed separability matrix from a nested `CompoundModel`, it preserves that matrix instead of replacing it with all 1s. +- `astropy/modeling/tests/test_separable.py` + - Added a regression test covering `models.Pix2Sky_TAN() & (models.Linear1D(10) & models.Linear1D(5))`. + +Root cause: +- Nested compound models reach `_cstack()` as ndarray separability matrices. +- The right-hand ndarray branch incorrectly did: + - `cright[...] = 1` +- That flattened all right-side dependencies into “non-separable”. +- It now correctly does: + - `cright[...] = right` + +Validation: +- Reproduced the original bug before the change. +- Ran: + - `python -m pytest astropy/modeling/tests/test_separable.py -q` +- Result: + - `12 passed` + +The original example now returns the expected matrix: +```python +[[ True True False False] + [ True True False False] + [False False True False] + [False False False True]] +``` \ No newline at end of file diff --git a/nodes/solve/status.json b/nodes/solve/status.json new file mode 100644 index 000000000..04cac8589 --- /dev/null +++ b/nodes/solve/status.json @@ -0,0 +1,6 @@ +{ + "status": "success", + "notes": "Stage completed: solve", + "failure_reason": null, + "timestamp": "2026-03-16T12:05:37.719387+00:00" +} \ No newline at end of file