checkpoint

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checkpoint.json

@@ -1,42 +1,42 @@
 {
-  "timestamp": "2026-03-16T12:07:05.934406Z",
-  "current_node": "solve",
+  "timestamp": "2026-03-16T12:07:08.110700Z",
+  "current_node": "extract_patch",
   "completed_nodes": [
     "start",
     "setup",
-    "solve"
+    "solve",
+    "extract_patch"
   ],
   "node_retries": {
+    "extract_patch": 1,
+    "setup": 1,
     "solve": 4,
-    "start": 1,
-    "setup": 1
+    "start": 1
   },
   "context_values": {
     "internal.node_visit_count": 1,
-    "command.output": "fatal: destination path '.' already exists and is not an empty directory.\n",
+    "command.output": "",
     "graph.goal": "Possible bug in io.fits related to D exponents\nI came across the following code in ``fitsrec.py``:\r\n\r\n```python\r\n        # Replace exponent separator in floating point numbers\r\n        if 'D' in format:\r\n            output_field.replace(encode_ascii('E'), encode_ascii('D'))\r\n```\r\n\r\nI think this may be incorrect because as far as I can tell ``replace`` is not an in-place operation for ``chararray`` (it returns a copy). Commenting out this code doesn't cause any tests to fail so I think this code isn't being tested anyway.\n\n\n\n## Additional Context\n\nIt is tested with `astropy/io/fits/tests/test_checksum.py:test_ascii_table_data` but indeed the operation is not inplace and it does not fail. Using 'D' is probably better, but since #5362 (I had vague memory about something like this ^^, see also #5353) anyway 'D' and 'E' are read as double, so I think there is not difference on Astropy side.",
     "thread.setup.current_node": "solve",
     "graph.rankdir": "LR",
     "internal.run_id": "01KKV8D407F7XQCMQDCS4WRYJK",
     "internal.fidelity": "compact",
-    "internal.thread_id": "setup",
-    "failure_class": "transient_infra",
+    "internal.thread_id": "solve",
+    "failure_class": "",
     "internal.retry_count.setup": 1,
     "internal.retry_count.start": 1,
     "thread.start.current_node": "setup",
-    "current.preamble": "Goal: Possible bug in io.fits related to D exponents\nI came across the following code in ``fitsrec.py``:\r\n\r\n```python\r\n        # Replace exponent separator in floating point numbers\r\n        if 'D' in format:\r\n            output_field.replace(encode_ascii('E'), encode_ascii('D'))\r\n```\r\n\r\nI think this may be incorrect because as far as I can tell ``replace`` is not an in-place operation for ``chararray`` (it returns a copy). Commenting out this code doesn't cause any tests to fail so I think this code isn't being tested anyway.\n\n\n\n## Additional Context\n\nIt is tested with `astropy/io/fits/tests/test_checksum.py:test_ascii_table_data` but indeed the operation is not inplace and it does not fail. Using 'D' is probably better, but since #5362 (I had vague memory about something like this ^^, see also #5353) anyway 'D' and 'E' are read as double, so I think there is not difference on Astropy side.\n\n## Completed stages\n- **setup**: fail\n  - Script: `git clone https://github.com/astropy/astropy.git . && git checkout c76af9ed6bb89bfba45b9f5bc1e635188278e2fa && 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: <n> ## stdout fatal: destination path '.' already exists and is not an empty directory.\n",
-    "outcome": "fail",
+    "current.preamble": "Goal: Possible bug in io.fits related to D exponents\nI came across the following code in ``fitsrec.py``:\r\n\r\n```python\r\n        # Replace exponent separator in floating point numbers\r\n        if 'D' in format:\r\n            output_field.replace(encode_ascii('E'), encode_ascii('D'))\r\n```\r\n\r\nI think this may be incorrect because as far as I can tell ``replace`` is not an in-place operation for ``chararray`` (it returns a copy). Commenting out this code doesn't cause any tests to fail so I think this code isn't being tested anyway.\n\n\n\n## Additional Context\n\nIt is tested with `astropy/io/fits/tests/test_checksum.py:test_ascii_table_data` but indeed the operation is not inplace and it does not fail. Using 'D' is probably better, but since #5362 (I had vague memory about something like this ^^, see also #5353) anyway 'D' and 'E' are read as double, so I think there is not difference on Astropy side.\n\n## Completed stages\n- **setup**: fail\n  - Script: `git clone https://github.com/astropy/astropy.git . && git checkout c76af9ed6bb89bfba45b9f5bc1e635188278e2fa && 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**: fail\n\n## Context\n- failure_class: transient_infra\n- failure_signature: solve|transient_infra|api_transient|gemini|rate_limited\n",
+    "outcome": "success",
+    "thread.solve.current_node": "extract_patch",
     "command.stderr": "",
-    "failure_signature": "solve|transient_infra|api_transient|gemini|rate_limited",
-    "current_node": "solve",
+    "internal.retry_count.extract_patch": 1,
+    "failure_signature": "",
+    "current_node": "extract_patch",
     "internal.retry_count.solve": 4
   },
   "logs": [],
   "node_outcomes": {
-    "start": {
-      "status": "success",
-      "duration_ms": 0
-    },
     "solve": {
       "status": "fail",
       "failure": {
@@ -57,15 +57,29 @@
         "failure_class": "deterministic"
       },
       "duration_ms": 19
+    },
+    "start": {
+      "status": "success",
+      "duration_ms": 0
+    },
+    "extract_patch": {
+      "status": "success",
+      "context_updates": {
+        "command.stderr": "",
+        "command.output": ""
+      },
+      "notes": "Script completed: git diff",
+      "duration_ms": 24
     }
   },
-  "next_node_id": "extract_patch",
+  "next_node_id": "exit",
   "loop_failure_signatures": {
     "setup|deterministic|script failed with exit code: <n> ## stdout fatal: destination path '.' already exists and is not an empty directory.": 1
   },
   "node_visits": {
     "start": 1,
+    "solve": 1,
     "setup": 1,
-    "solve": 1
+    "extract_patch": 1
   }
 }

nodes/extract_patch/script_invocation.json

@@ -0,0 +1,5 @@
+{
+  "command": "git diff",
+  "language": "shell",
+  "timeout_ms": null
+}

nodes/extract_patch/script_timing.json

@@ -0,0 +1,5 @@
+{
+  "duration_ms": 22,
+  "exit_code": 0,
+  "timed_out": false
+}

nodes/extract_patch/status.json

@@ -0,0 +1,6 @@
+{
+  "status": "success",
+  "notes": "Script completed: git diff",
+  "failure_reason": null,
+  "timestamp": "2026-03-16T12:07:08.109789+00:00"
+}