mirror of
https://github.com/fabro-sh/fabro.git
synced 2026-09-06 08:18:58 +00:00
Fabro
parent
1f9a3a6e87
commit
059e63c5eb
5 changed files with 157 additions and 10 deletions
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@ -1,34 +1,62 @@
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{
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"thread.start.current_node": "setup",
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||||
"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<EOF>\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?",
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"command.output": "fatal: destination path '.' already exists and is not an empty directory.\n",
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"internal.fidelity": "compact",
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"thread.setup.current_node": "solve",
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"internal.retry_count.solve": 1,
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"graph.rankdir": "LR",
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"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<EOF>\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",
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"internal.thread_id": "start",
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"failure_class": "deterministic",
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"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<EOF>\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: <n> ## stdout fatal: destination path '.' already exists and is not an empty directory.\n",
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"internal.thread_id": "setup",
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"failure_class": "",
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"command.stderr": "",
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"outcome": "fail",
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"last_response": "All 12 tests pass (8 unit tests + 4 doctests).\n\n## Summary\n\nThe fix is a **one-line change** in `/tmp/astropy_repo/astropy/io/ascii/qdp.py`:\n\n**Line 71 (originally):**\n```python\n_line_type_re = re.com",
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"outcome": "success",
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"internal.retry_count.start": 1,
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"last_stage": "solve",
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"response.solve": "All 12 tests pass (8 unit tests + 4 doctests).\n\n## Summary\n\nThe fix is a **one-line change** in `/tmp/astropy_repo/astropy/io/ascii/qdp.py`:\n\n**Line 71 (originally):**\n```python\n_line_type_re = re.compile(_type_re)\n```\n\n**Changed to:**\n```python\n_line_type_re = re.compile(_type_re, re.IGNORECASE)\n```\n\n**Root cause:** The `_line_type()` function uses a regex to classify QDP file lines. The command regex `r\"READ [TS]ERR(\\s+[0-9]+)+\"` only matched uppercase `READ SERR` / `READ TERR`, but QDP itself is case-insensitive. By adding `re.IGNORECASE` to the `re.compile()` call, the regex now matches commands regardless of case (e.g., `read serr 1 2`, `Read Serr 1 2`, `READ SERR 1 2`).\n\nThe `re.IGNORECASE` flag also makes the `NO` matching case-insensitive, which is correct since QDP is generally case-insensitive. The downstream command parsing in `_get_tables_from_qdp_file` already used `.lower()` on `command[1]`, so no other changes were needed.",
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"internal.retry_count.setup": 1,
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"internal.node_visit_count": 1
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},
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"logs": [],
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"solve": {
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"status": "success",
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"context_updates": {
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"last_stage": "solve",
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"last_response": "All 12 tests pass (8 unit tests + 4 doctests).\n\n## Summary\n\nThe fix is a **one-line change** in `/tmp/astropy_repo/astropy/io/ascii/qdp.py`:\n\n**Line 71 (originally):**\n```python\n_line_type_re = re.com",
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"response.solve": "All 12 tests pass (8 unit tests + 4 doctests).\n\n## Summary\n\nThe fix is a **one-line change** in `/tmp/astropy_repo/astropy/io/ascii/qdp.py`:\n\n**Line 71 (originally):**\n```python\n_line_type_re = re.compile(_type_re)\n```\n\n**Changed to:**\n```python\n_line_type_re = re.compile(_type_re, re.IGNORECASE)\n```\n\n**Root cause:** The `_line_type()` function uses a regex to classify QDP file lines. The command regex `r\"READ [TS]ERR(\\s+[0-9]+)+\"` only matched uppercase `READ SERR` / `READ TERR`, but QDP itself is case-insensitive. By adding `re.IGNORECASE` to the `re.compile()` call, the regex now matches commands regardless of case (e.g., `read serr 1 2`, `Read Serr 1 2`, `READ SERR 1 2`).\n\nThe `re.IGNORECASE` flag also makes the `NO` matching case-insensitive, which is correct since QDP is generally case-insensitive. The downstream command parsing in `_get_tables_from_qdp_file` already used `.lower()` on `command[1]`, so no other changes were needed."
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},
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"notes": "Stage completed: solve",
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"usage": {
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"model": "claude-opus-4-6",
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"cache_read_tokens": 558918,
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"cost": 0.687285
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},
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"files_touched": [
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"/tmp/astropy_repo/astropy/io/ascii/qdp.py"
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],
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"duration_ms": 189492
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},
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"start": {
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"status": "success",
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"duration_ms": 0
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@ -46,11 +74,12 @@
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"duration_ms": 231
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}
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},
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"next_node_id": "solve",
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"next_node_id": "extract_patch",
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"loop_failure_signatures": {
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"setup|deterministic|script failed with exit code: <n> ## stdout fatal: destination path '.' already exists and is not an empty directory.": 1
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},
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}
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88
nodes/solve/prompt.md
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88
nodes/solve/prompt.md
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@ -0,0 +1,88 @@
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Goal: ascii.qdp Table format assumes QDP commands are upper case
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### Description
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ascii.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".
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As many QDP files are created by hand, the expectation that all commands be all-caps should be removed.
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### Expected behavior
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The following qdp file should read into a `Table` with errors, rather than crashing.
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```
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read serr 1 2
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1 0.5 1 0.5
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```
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### How to Reproduce
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Create a QDP file:
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```
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> cat > test.qdp
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read serr 1 2
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1 0.5 1 0.5
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<EOF>
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> python
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Python 3.10.9 (main, Dec 7 2022, 02:03:23) [Clang 13.0.0 (clang-1300.0.29.30)] on darwin
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Type "help", "copyright", "credits" or "license" for more information.
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>>> from astropy.table import Table
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>>> Table.read('test.qdp',format='ascii.qdp')
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WARNING: table_id not specified. Reading the first available table [astropy.io.ascii.qdp]
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Traceback (most recent call last):
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...
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raise ValueError(f'Unrecognized QDP line: {line}')
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ValueError: Unrecognized QDP line: read serr 1 2
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```
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Running "qdp test.qdp" works just fine.
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### Versions
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Python 3.10.9 (main, Dec 7 2022, 02:03:23) [Clang 13.0.0 (clang-1300.0.29.30)]
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astropy 5.1
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Numpy 1.24.1
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pyerfa 2.0.0.1
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Scipy 1.10.0
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Matplotlib 3.6.3
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## Additional Context
|
||||
|
||||
Welcome to Astropy 👋 and thank you for your first issue!
|
||||
|
||||
A 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.
|
||||
|
||||
GitHub 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.
|
||||
|
||||
If 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.
|
||||
Huh, so we do have this format... https://docs.astropy.org/en/stable/io/ascii/index.html
|
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|
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@taldcroft , you know anything about this?
|
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This is the format I'm using, which has the issue: https://docs.astropy.org/en/stable/api/astropy.io.ascii.QDP.html
|
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|
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The issue is that the regex that searches for QDP commands is not case insensitive.
|
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|
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This attached patch fixes the issue, but I'm sure there's a better way of doing it.
|
||||
|
||||
[qdp.patch](https://github.com/astropy/astropy/files/10667923/qdp.patch)
|
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@jak574 - the fix is probably as simple as that. Would you like to put in a bugfix PR?
|
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## Completed stages
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- **setup**: fail
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- 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`
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- Stdout:
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```
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fatal: destination path '.' already exists and is not an empty directory.
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```
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- Stderr: (empty)
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## Context
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- failure_class: deterministic
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- failure_signature: setup|deterministic|script failed with exit code: <n> ## stdout fatal: destination path '.' already exists and is not an empty directory.
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Fix this GitHub issue in the repository. Make the minimal code change needed.
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5
nodes/solve/provider_used.json
Normal file
5
nodes/solve/provider_used.json
Normal file
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@ -0,0 +1,5 @@
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{
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"mode": "agent",
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"provider": "anthropic",
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"model": "claude-opus-4-6"
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}
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19
nodes/solve/response.md
Normal file
19
nodes/solve/response.md
Normal file
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@ -0,0 +1,19 @@
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All 12 tests pass (8 unit tests + 4 doctests).
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||||
## Summary
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The fix is a **one-line change** in `/tmp/astropy_repo/astropy/io/ascii/qdp.py`:
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**Line 71 (originally):**
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```python
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_line_type_re = re.compile(_type_re)
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```
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**Changed to:**
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```python
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_line_type_re = re.compile(_type_re, re.IGNORECASE)
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```
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**Root cause:** The `_line_type()` function uses a regex to classify QDP file lines. The command regex `r"READ [TS]ERR(\s+[0-9]+)+"` only matched uppercase `READ SERR` / `READ TERR`, but QDP itself is case-insensitive. By adding `re.IGNORECASE` to the `re.compile()` call, the regex now matches commands regardless of case (e.g., `read serr 1 2`, `Read Serr 1 2`, `READ SERR 1 2`).
|
||||
|
||||
The `re.IGNORECASE` flag also makes the `NO` matching case-insensitive, which is correct since QDP is generally case-insensitive. The downstream command parsing in `_get_tables_from_qdp_file` already used `.lower()` on `command[1]`, so no other changes were needed.
|
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6
nodes/solve/status.json
Normal file
6
nodes/solve/status.json
Normal file
|
|
@ -0,0 +1,6 @@
|
|||
{
|
||||
"status": "success",
|
||||
"notes": "Stage completed: solve",
|
||||
"failure_reason": null,
|
||||
"timestamp": "2026-03-16T12:01:19.819709+00:00"
|
||||
}
|
||||
Loading…
Add table
Reference in a new issue