From 89b5566e0ec5b458eb026fb93320335f110d6e69 Mon Sep 17 00:00:00 2001 From: Fabro Date: Mon, 16 Mar 2026 08:01:32 -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 | 34 +++++++++++++++------- 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, 47 insertions(+), 10 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 0448494da..95a272e80 100644 --- a/checkpoint.json +++ b/checkpoint.json @@ -1,15 +1,17 @@ { - "timestamp": "2026-03-16T12:01:28.623033Z", - "current_node": "solve", + "timestamp": "2026-03-16T12:01:32.644133Z", + "current_node": "extract_patch", "completed_nodes": [ "start", "setup", - "solve" + "solve", + "extract_patch" ], "node_retries": { "solve": 1, "start": 1, - "setup": 1 + "setup": 1, + "extract_patch": 1 }, "context_values": { "internal.run_id": "01KKV85BRMWX7FJZMSSH2HX23D", @@ -20,18 +22,20 @@ "internal.retry_count.solve": 1, "failure_signature": "", "internal.node_visit_count": 1, - "current.preamble": "Goal: ascii.qdp Table format assumes QDP commands are upper case\n### Description\n\nascii.qdp assumes that commands in a QDP file are upper case, for example, for errors they must be \"READ SERR 1 2\" whereas QDP itself is not case sensitive and case use \"read serr 1 2\". \r\n\r\nAs many QDP files are created by hand, the expectation that all commands be all-caps should be removed.\n\n### Expected behavior\n\nThe following qdp file should read into a `Table` with errors, rather than crashing.\r\n```\r\nread serr 1 2 \r\n1 0.5 1 0.5\r\n```\n\n### How to Reproduce\n\nCreate a QDP file:\r\n```\r\n> cat > test.qdp\r\nread serr 1 2 \r\n1 0.5 1 0.5\r\n\r\n\r\n > python\r\nPython 3.10.9 (main, Dec 7 2022, 02:03:23) [Clang 13.0.0 (clang-1300.0.29.30)] on darwin\r\nType \"help\", \"copyright\", \"credits\" or \"license\" for more information.\r\n>>> from astropy.table import Table\r\n>>> Table.read('test.qdp',format='ascii.qdp')\r\nWARNING: table_id not specified. Reading the first available table [astropy.io.ascii.qdp]\r\nTraceback (most recent call last):\r\n...\r\n raise ValueError(f'Unrecognized QDP line: {line}')\r\nValueError: Unrecognized QDP line: read serr 1 2\r\n```\r\n\r\nRunning \"qdp test.qdp\" works just fine.\r\n\n\n### Versions\n\nPython 3.10.9 (main, Dec 7 2022, 02:03:23) [Clang 13.0.0 (clang-1300.0.29.30)]\r\nastropy 5.1\r\nNumpy 1.24.1\r\npyerfa 2.0.0.1\r\nScipy 1.10.0\r\nMatplotlib 3.6.3\r\n\n\n\n\n## Additional Context\n\nWelcome to Astropy 👋 and thank you for your first issue!\n\nA project member will respond to you as soon as possible; in the meantime, please double-check the [guidelines for submitting issues](https://github.com/astropy/astropy/blob/main/CONTRIBUTING.md#reporting-issues) and make sure you've provided the requested details.\n\nGitHub issues in the Astropy repository are used to track bug reports and feature requests; If your issue poses a question about how to use Astropy, please instead raise your question in the [Astropy Discourse user forum](https://community.openastronomy.org/c/astropy/8) and close this issue.\n\nIf you feel that this issue has not been responded to in a timely manner, please send a message directly to the [development mailing list](http://groups.google.com/group/astropy-dev). If the issue is urgent or sensitive in nature (e.g., a security vulnerability) please send an e-mail directly to the private e-mail feedback@astropy.org.\nHuh, so we do have this format... https://docs.astropy.org/en/stable/io/ascii/index.html\r\n\r\n@taldcroft , you know anything about this?\nThis is the format I'm using, which has the issue: https://docs.astropy.org/en/stable/api/astropy.io.ascii.QDP.html\r\n\nThe issue is that the regex that searches for QDP commands is not case insensitive. \r\n\r\nThis attached patch fixes the issue, but I'm sure there's a better way of doing it.\r\n\r\n[qdp.patch](https://github.com/astropy/astropy/files/10667923/qdp.patch)\r\n\n@jak574 - the fix is probably as simple as that. Would you like to put in a bugfix PR?\n\n## Completed stages\n- **setup**: fail\n - Script: `git clone https://github.com/astropy/astropy.git . && git checkout 7269fa3e33e8d02485a647da91a5a2a60a06af61 && 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: ascii.qdp Table format assumes QDP commands are upper case\n### Description\n\nascii.qdp assumes that commands in a QDP file are upper case, for example, for errors they must be \"READ SERR 1 2\" whereas QDP itself is not case sensitive and case use \"read serr 1 2\". \r\n\r\nAs many QDP files are created by hand, the expectation that all commands be all-caps should be removed.\n\n### Expected behavior\n\nThe following qdp file should read into a `Table` with errors, rather than crashing.\r\n```\r\nread serr 1 2 \r\n1 0.5 1 0.5\r\n```\n\n### How to Reproduce\n\nCreate a QDP file:\r\n```\r\n> cat > test.qdp\r\nread serr 1 2 \r\n1 0.5 1 0.5\r\n\r\n\r\n > python\r\nPython 3.10.9 (main, Dec 7 2022, 02:03:23) [Clang 13.0.0 (clang-1300.0.29.30)] on darwin\r\nType \"help\", \"copyright\", \"credits\" or \"license\" for more information.\r\n>>> from astropy.table import Table\r\n>>> Table.read('test.qdp',format='ascii.qdp')\r\nWARNING: table_id not specified. Reading the first available table [astropy.io.ascii.qdp]\r\nTraceback (most recent call last):\r\n...\r\n raise ValueError(f'Unrecognized QDP line: {line}')\r\nValueError: Unrecognized QDP line: read serr 1 2\r\n```\r\n\r\nRunning \"qdp test.qdp\" works just fine.\r\n\n\n### Versions\n\nPython 3.10.9 (main, Dec 7 2022, 02:03:23) [Clang 13.0.0 (clang-1300.0.29.30)]\r\nastropy 5.1\r\nNumpy 1.24.1\r\npyerfa 2.0.0.1\r\nScipy 1.10.0\r\nMatplotlib 3.6.3\r\n\n\n\n\n## Additional Context\n\nWelcome to Astropy 👋 and thank you for your first issue!\n\nA project member will respond to you as soon as possible; in the meantime, please double-check the [guidelines for submitting issues](https://github.com/astropy/astropy/blob/main/CONTRIBUTING.md#reporting-issues) and make sure you've provided the requested details.\n\nGitHub issues in the Astropy repository are used to track bug reports and feature requests; If your issue poses a question about how to use Astropy, please instead raise your question in the [Astropy Discourse user forum](https://community.openastronomy.org/c/astropy/8) and close this issue.\n\nIf you feel that this issue has not been responded to in a timely manner, please send a message directly to the [development mailing list](http://groups.google.com/group/astropy-dev). If the issue is urgent or sensitive in nature (e.g., a security vulnerability) please send an e-mail directly to the private e-mail feedback@astropy.org.\nHuh, so we do have this format... https://docs.astropy.org/en/stable/io/ascii/index.html\r\n\r\n@taldcroft , you know anything about this?\nThis is the format I'm using, which has the issue: https://docs.astropy.org/en/stable/api/astropy.io.ascii.QDP.html\r\n\nThe issue is that the regex that searches for QDP commands is not case insensitive. \r\n\r\nThis attached patch fixes the issue, but I'm sure there's a better way of doing it.\r\n\r\n[qdp.patch](https://github.com/astropy/astropy/files/10667923/qdp.patch)\r\n\n@jak574 - the fix is probably as simple as that. Would you like to put in a bugfix PR?\n\n## Completed stages\n- **setup**: fail\n - Script: `git clone https://github.com/astropy/astropy.git . && git checkout 7269fa3e33e8d02485a647da91a5a2a60a06af61 && 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: gpt-5.4, 854.3k tokens in / 6.3k out\n", "last_response": "Implemented the fix in the Astropy checkout at `/home/daytona/workspace/astropy-target`.\n\nChanges:\n- Made QDP `READ SERR` / `READ TERR` command parsing case-insensitive in `astropy/io/ascii/qdp.py`\n- ", "thread.start.current_node": "setup", "thread.setup.current_node": "solve", "graph.rankdir": "LR", - "command.output": "fatal: destination path '.' already exists and is not an empty directory.\n", + "command.output": "diff --git a/astropy-target b/astropy-target\n--- a/astropy-target\n+++ b/astropy-target\n@@ -1 +1 @@\n-Subproject commit 7269fa3e33e8d02485a647da91a5a2a60a06af61\n+Subproject commit 7269fa3e33e8d02485a647da91a5a2a60a06af61-dirty\n", "command.stderr": "", - "current_node": "solve", + "current_node": "extract_patch", "last_stage": "solve", - "internal.thread_id": "setup", + "thread.solve.current_node": "extract_patch", + "internal.thread_id": "solve", "outcome": "success", "response.solve": "Implemented the fix in the Astropy checkout at `/home/daytona/workspace/astropy-target`.\n\nChanges:\n- Made QDP `READ SERR` / `READ TERR` command parsing case-insensitive in `astropy/io/ascii/qdp.py`\n- Added a regression test for lowercase commands in `astropy/io/ascii/tests/test_qdp.py`\n\nValidation:\n- Ran: `python -m pytest astropy/io/ascii/tests/test_qdp.py -q`\n- Result: `9 passed`\n\nPatch summary:\n```diff\n- _command_re = r\"READ [TS]ERR(\\s+[0-9]+)+\"\n+ _command_re = r\"(?i:READ [TS]ERR(\\s+[0-9]+)+)\"\n```", + "internal.retry_count.extract_patch": 1, "graph.goal": "ascii.qdp Table format assumes QDP commands are upper case\n### Description\n\nascii.qdp assumes that commands in a QDP file are upper case, for example, for errors they must be \"READ SERR 1 2\" whereas QDP itself is not case sensitive and case use \"read serr 1 2\". \r\n\r\nAs many QDP files are created by hand, the expectation that all commands be all-caps should be removed.\n\n### Expected behavior\n\nThe following qdp file should read into a `Table` with errors, rather than crashing.\r\n```\r\nread serr 1 2 \r\n1 0.5 1 0.5\r\n```\n\n### How to Reproduce\n\nCreate a QDP file:\r\n```\r\n> cat > test.qdp\r\nread serr 1 2 \r\n1 0.5 1 0.5\r\n\r\n\r\n > python\r\nPython 3.10.9 (main, Dec 7 2022, 02:03:23) [Clang 13.0.0 (clang-1300.0.29.30)] on darwin\r\nType \"help\", \"copyright\", \"credits\" or \"license\" for more information.\r\n>>> from astropy.table import Table\r\n>>> Table.read('test.qdp',format='ascii.qdp')\r\nWARNING: table_id not specified. Reading the first available table [astropy.io.ascii.qdp]\r\nTraceback (most recent call last):\r\n...\r\n raise ValueError(f'Unrecognized QDP line: {line}')\r\nValueError: Unrecognized QDP line: read serr 1 2\r\n```\r\n\r\nRunning \"qdp test.qdp\" works just fine.\r\n\n\n### Versions\n\nPython 3.10.9 (main, Dec 7 2022, 02:03:23) [Clang 13.0.0 (clang-1300.0.29.30)]\r\nastropy 5.1\r\nNumpy 1.24.1\r\npyerfa 2.0.0.1\r\nScipy 1.10.0\r\nMatplotlib 3.6.3\r\n\n\n\n\n## Additional Context\n\nWelcome to Astropy 👋 and thank you for your first issue!\n\nA project member will respond to you as soon as possible; in the meantime, please double-check the [guidelines for submitting issues](https://github.com/astropy/astropy/blob/main/CONTRIBUTING.md#reporting-issues) and make sure you've provided the requested details.\n\nGitHub issues in the Astropy repository are used to track bug reports and feature requests; If your issue poses a question about how to use Astropy, please instead raise your question in the [Astropy Discourse user forum](https://community.openastronomy.org/c/astropy/8) and close this issue.\n\nIf you feel that this issue has not been responded to in a timely manner, please send a message directly to the [development mailing list](http://groups.google.com/group/astropy-dev). If the issue is urgent or sensitive in nature (e.g., a security vulnerability) please send an e-mail directly to the private e-mail feedback@astropy.org.\nHuh, so we do have this format... https://docs.astropy.org/en/stable/io/ascii/index.html\r\n\r\n@taldcroft , you know anything about this?\nThis is the format I'm using, which has the issue: https://docs.astropy.org/en/stable/api/astropy.io.ascii.QDP.html\r\n\nThe issue is that the regex that searches for QDP commands is not case insensitive. \r\n\r\nThis attached patch fixes the issue, but I'm sure there's a better way of doing it.\r\n\r\n[qdp.patch](https://github.com/astropy/astropy/files/10667923/qdp.patch)\r\n\n@jak574 - the fix is probably as simple as that. Would you like to put in a bugfix PR?" }, "logs": [], @@ -52,6 +56,15 @@ }, "duration_ms": 225 }, + "extract_patch": { + "status": "success", + "context_updates": { + "command.stderr": "", + "command.output": "diff --git a/astropy-target b/astropy-target\n--- a/astropy-target\n+++ b/astropy-target\n@@ -1 +1 @@\n-Subproject commit 7269fa3e33e8d02485a647da91a5a2a60a06af61\n+Subproject commit 7269fa3e33e8d02485a647da91a5a2a60a06af61-dirty\n" + }, + "notes": "Script completed: git diff", + "duration_ms": 246 + }, "solve": { "status": "success", "context_updates": { @@ -71,13 +84,14 @@ "duration_ms": 191412 } }, - "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": { "solve": 1, + "start": 1, "setup": 1, - "start": 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..8d0413138 --- /dev/null +++ b/nodes/extract_patch/script_timing.json @@ -0,0 +1,5 @@ +{ + "duration_ms": 244, + "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..fc815370c --- /dev/null +++ b/nodes/extract_patch/status.json @@ -0,0 +1,6 @@ +{ + "status": "success", + "notes": "Script completed: git diff", + "failure_reason": null, + "timestamp": "2026-03-16T12:01:32.642965+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..6a5b4eb3c --- /dev/null +++ b/nodes/solve/diff.patch @@ -0,0 +1,7 @@ +diff --git a/astropy-target b/astropy-target +new file mode 160000 +index 0000000..7269fa3 +--- /dev/null ++++ b/astropy-target +@@ -0,0 +1 @@ ++Subproject commit 7269fa3e33e8d02485a647da91a5a2a60a06af61