acumen 0.0.1.dev0__tar.gz → 0.0.2__tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (126) hide show
  1. acumen-0.0.2/.codecov.yaml +17 -0
  2. acumen-0.0.2/.github/ISSUE_TEMPLATE/bug_report.yml +93 -0
  3. acumen-0.0.2/.github/ISSUE_TEMPLATE/config.yml +5 -0
  4. acumen-0.0.2/.github/ISSUE_TEMPLATE/feature_request.yml +11 -0
  5. acumen-0.0.2/.github/workflows/build.yaml +26 -0
  6. acumen-0.0.2/.github/workflows/release.yaml +27 -0
  7. acumen-0.0.2/.github/workflows/test.yaml +113 -0
  8. {acumen-0.0.1.dev0 → acumen-0.0.2}/.gitignore +4 -0
  9. acumen-0.0.2/.pre-commit-config.yaml +38 -0
  10. acumen-0.0.2/.readthedocs.yaml +16 -0
  11. {acumen-0.0.1.dev0 → acumen-0.0.2}/.vscode/settings.json +1 -0
  12. acumen-0.0.2/CHANGELOG.md +74 -0
  13. acumen-0.0.2/PKG-INFO +161 -0
  14. acumen-0.0.2/README.md +111 -0
  15. acumen-0.0.2/docs/_static/css/custom.css +20 -0
  16. {acumen-0.0.1.dev0/src/acumen/assets → acumen-0.0.2/docs/_static/images}/banner.svg +52 -19
  17. acumen-0.0.2/docs/_static/images/logo.png +0 -0
  18. acumen-0.0.2/docs/_static/images/logo.svg +85 -0
  19. acumen-0.0.2/docs/api/bench.md +4 -0
  20. acumen-0.0.2/docs/api/check.md +4 -0
  21. acumen-0.0.2/docs/api/epoch.md +4 -0
  22. acumen-0.0.2/docs/api/fit.md +20 -0
  23. acumen-0.0.2/docs/api/improve.md +4 -0
  24. acumen-0.0.2/docs/api/index.md +87 -0
  25. acumen-0.0.2/docs/api/init.md +4 -0
  26. acumen-0.0.2/docs/api/prepare.md +4 -0
  27. acumen-0.0.2/docs/api/prices.md +4 -0
  28. acumen-0.0.2/docs/api/report.md +4 -0
  29. acumen-0.0.2/docs/api/ship.md +4 -0
  30. acumen-0.0.2/docs/api/tasks.md +4 -0
  31. acumen-0.0.2/docs/api/wiki.md +4 -0
  32. {acumen-0.0.1.dev0 → acumen-0.0.2}/docs/conf.py +10 -0
  33. acumen-0.0.2/docs/extensions/acumen_cli.py +172 -0
  34. acumen-0.0.2/docs/getting_started.md +707 -0
  35. acumen-0.0.2/docs/index.md +19 -0
  36. {acumen-0.0.1.dev0 → acumen-0.0.2}/pyproject.toml +16 -7
  37. {acumen-0.0.1.dev0 → acumen-0.0.2}/src/acumen/__init__.py +128 -22
  38. acumen-0.0.2/src/acumen/agents.py +1224 -0
  39. acumen-0.0.2/src/acumen/bench.py +418 -0
  40. acumen-0.0.2/src/acumen/check.py +673 -0
  41. acumen-0.0.2/src/acumen/cli.py +2660 -0
  42. {acumen-0.0.1.dev0 → acumen-0.0.2}/src/acumen/config.py +72 -12
  43. acumen-0.0.2/src/acumen/data.py +92 -0
  44. {acumen-0.0.1.dev0 → acumen-0.0.2}/src/acumen/env.py +281 -99
  45. acumen-0.0.2/src/acumen/epoch.py +73 -0
  46. {acumen-0.0.1.dev0 → acumen-0.0.2}/src/acumen/grade.py +18 -1
  47. acumen-0.0.2/src/acumen/guard.py +179 -0
  48. acumen-0.0.2/src/acumen/htmldiff.py +144 -0
  49. acumen-0.0.2/src/acumen/improve.py +511 -0
  50. {acumen-0.0.1.dev0 → acumen-0.0.2}/src/acumen/logs.py +146 -35
  51. acumen-0.0.2/src/acumen/markdown.py +158 -0
  52. {acumen-0.0.1.dev0 → acumen-0.0.2}/src/acumen/paths.py +22 -7
  53. acumen-0.0.2/src/acumen/prepare.py +231 -0
  54. acumen-0.0.2/src/acumen/pricefeed.py +325 -0
  55. acumen-0.0.2/src/acumen/prices.py +379 -0
  56. {acumen-0.0.1.dev0 → acumen-0.0.2}/src/acumen/procs.py +3 -4
  57. acumen-0.0.2/src/acumen/prompts.py +1469 -0
  58. {acumen-0.0.1.dev0 → acumen-0.0.2}/src/acumen/report.py +1030 -334
  59. acumen-0.0.2/src/acumen/review.py +456 -0
  60. acumen-0.0.2/src/acumen/runner.py +588 -0
  61. {acumen-0.0.1.dev0 → acumen-0.0.2}/src/acumen/sandbox.py +53 -21
  62. {acumen-0.0.1.dev0 → acumen-0.0.2}/src/acumen/scaffold.py +52 -13
  63. acumen-0.0.2/src/acumen/scriptdiff.py +216 -0
  64. acumen-0.0.2/src/acumen/scrub.py +477 -0
  65. {acumen-0.0.1.dev0 → acumen-0.0.2}/src/acumen/ship.py +106 -53
  66. {acumen-0.0.1.dev0 → acumen-0.0.2}/src/acumen/skills.py +16 -2
  67. {acumen-0.0.1.dev0 → acumen-0.0.2}/src/acumen/taskgen.py +153 -192
  68. acumen-0.0.2/src/acumen/tasks.py +209 -0
  69. acumen-0.0.2/src/acumen/theme.py +51 -0
  70. acumen-0.0.2/src/acumen/training.py +235 -0
  71. acumen-0.0.2/src/acumen/trajectory.py +796 -0
  72. acumen-0.0.2/src/acumen/transcript.py +162 -0
  73. acumen-0.0.2/src/acumen/wiki.py +748 -0
  74. {acumen-0.0.1.dev0 → acumen-0.0.2}/tests/conftest.py +25 -5
  75. acumen-0.0.2/tests/test_cli.py +1849 -0
  76. acumen-0.0.2/tests/test_core.py +5977 -0
  77. acumen-0.0.2/tests/test_data.py +414 -0
  78. acumen-0.0.2/tests/test_scrub.py +296 -0
  79. {acumen-0.0.1.dev0 → acumen-0.0.2}/tests/test_ship_install.py +14 -4
  80. acumen-0.0.1.dev0/.codecov.yaml +0 -17
  81. acumen-0.0.1.dev0/.github/ISSUE_TEMPLATE/bug_report.yml +0 -93
  82. acumen-0.0.1.dev0/.github/ISSUE_TEMPLATE/config.yml +0 -5
  83. acumen-0.0.1.dev0/.github/ISSUE_TEMPLATE/feature_request.yml +0 -11
  84. acumen-0.0.1.dev0/.github/workflows/build.yaml +0 -26
  85. acumen-0.0.1.dev0/.github/workflows/release.yaml +0 -27
  86. acumen-0.0.1.dev0/.github/workflows/test.yaml +0 -107
  87. acumen-0.0.1.dev0/.pre-commit-config.yaml +0 -38
  88. acumen-0.0.1.dev0/.readthedocs.yaml +0 -16
  89. acumen-0.0.1.dev0/CHANGELOG.md +0 -11
  90. acumen-0.0.1.dev0/PKG-INFO +0 -168
  91. acumen-0.0.1.dev0/README.md +0 -121
  92. acumen-0.0.1.dev0/docs/_static/css/custom.css +0 -4
  93. acumen-0.0.1.dev0/docs/_static/images/banner_plate.svg +0 -9
  94. acumen-0.0.1.dev0/docs/api.md +0 -164
  95. acumen-0.0.1.dev0/docs/index.md +0 -12
  96. acumen-0.0.1.dev0/src/acumen/_skills/__init__.py +0 -0
  97. acumen-0.0.1.dev0/src/acumen/_skills/data/SKILL.md +0 -109
  98. acumen-0.0.1.dev0/src/acumen/_skills/data/references/authoring.md +0 -91
  99. acumen-0.0.1.dev0/src/acumen/_skills/data/references/benchmark.md +0 -100
  100. acumen-0.0.1.dev0/src/acumen/_skills/data/references/python-api.md +0 -106
  101. acumen-0.0.1.dev0/src/acumen/_skills/data/references/setup.md +0 -94
  102. acumen-0.0.1.dev0/src/acumen/_skills/data/references/ship.md +0 -53
  103. acumen-0.0.1.dev0/src/acumen/_skills/install.py +0 -185
  104. acumen-0.0.1.dev0/src/acumen/assets/logo.svg +0 -47
  105. acumen-0.0.1.dev0/src/acumen/bench.py +0 -202
  106. acumen-0.0.1.dev0/src/acumen/cli.py +0 -626
  107. acumen-0.0.1.dev0/src/acumen/draft.py +0 -202
  108. acumen-0.0.1.dev0/src/acumen/improve.py +0 -596
  109. acumen-0.0.1.dev0/src/acumen/prompts.py +0 -942
  110. acumen-0.0.1.dev0/src/acumen/runner.py +0 -343
  111. acumen-0.0.1.dev0/src/acumen/tasks.py +0 -144
  112. acumen-0.0.1.dev0/src/acumen/transcript.py +0 -77
  113. acumen-0.0.1.dev0/tests/test_cli.py +0 -207
  114. acumen-0.0.1.dev0/tests/test_core.py +0 -1252
  115. {acumen-0.0.1.dev0 → acumen-0.0.2}/.cruft.json +0 -0
  116. {acumen-0.0.1.dev0 → acumen-0.0.2}/.editorconfig +0 -0
  117. {acumen-0.0.1.dev0 → acumen-0.0.2}/.vscode/extensions.json +0 -0
  118. {acumen-0.0.1.dev0 → acumen-0.0.2}/.vscode/launch.json +0 -0
  119. {acumen-0.0.1.dev0 → acumen-0.0.2}/LICENSE +0 -0
  120. {acumen-0.0.1.dev0 → acumen-0.0.2}/biome.jsonc +0 -0
  121. {acumen-0.0.1.dev0 → acumen-0.0.2}/docs/_static/.gitkeep +0 -0
  122. {acumen-0.0.1.dev0 → acumen-0.0.2}/docs/changelog.md +0 -0
  123. {acumen-0.0.1.dev0 → acumen-0.0.2}/docs/references.bib +0 -0
  124. {acumen-0.0.1.dev0 → acumen-0.0.2}/docs/references.md +0 -0
  125. {acumen-0.0.1.dev0/docs/_static/images → acumen-0.0.2/src/acumen/assets}/banner.svg +0 -0
  126. {acumen-0.0.1.dev0/docs/_static/images → acumen-0.0.2/src/acumen/assets}/logo.svg +0 -0
@@ -0,0 +1,17 @@
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+ # Based on pydata/xarray
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+ codecov:
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+ require_ci_to_pass: no
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+
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+ coverage:
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+ status:
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+ project:
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+ default:
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+ # Require 1% coverage, i.e., always succeed
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+ target: 1
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+ patch: false
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+ changes: false
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+
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+ comment:
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+ layout: diff, flags, files
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+ behavior: once
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+ require_base: no
@@ -0,0 +1,93 @@
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+ name: Bug report
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+ description: Report something that is broken or incorrect
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+ labels: bug
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+ body:
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+ - type: markdown
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+ attributes:
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+ value: |
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+ **Note**: Please read [this guide](https://matthewrocklin.com/blog/work/2018/02/28/minimal-bug-reports)
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+ detailing how to provide the necessary information for us to reproduce your bug. In brief:
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+ * Please provide exact steps how to reproduce the bug in a clean Python environment.
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+ * In case it's not clear what's causing this bug, please provide the data or the data generation procedure.
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+ * Replicate problems on public datasets or share data subsets when full sharing isn't possible.
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+
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+ - type: textarea
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+ id: report
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+ attributes:
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+ label: Report
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+ description: A clear and concise description of what the bug is.
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+ validations:
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+ required: true
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+
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+ - type: textarea
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+ id: versions
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+ attributes:
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+ label: Versions
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+ description: |
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+ Which version of packages.
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+
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+ Please install `session-info2`, run the following command in a notebook,
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+ click the “Copy as Markdown” button, then paste the results into the text box below.
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+
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+ ```python
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+ In[1]: import session_info2; session_info2.session_info(dependencies=True)
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+ ```
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+
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+ Alternatively, run this in a console:
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+
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+ ```python
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+ >>> import session_info2; print(session_info2.session_info(dependencies=True)._repr_mimebundle_()["text/markdown"])
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+ ```
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+ render: python
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+ placeholder: |
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+ anndata 0.11.3
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+ ---- ----
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+ charset-normalizer 3.4.1
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+ coverage 7.7.0
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+ psutil 7.0.0
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+ dask 2024.7.1
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+ jaraco.context 5.3.0
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+ numcodecs 0.15.1
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+ jaraco.functools 4.0.1
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+ Jinja2 3.1.6
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+ sphinxcontrib-jsmath 1.0.1
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+ sphinxcontrib-htmlhelp 2.1.0
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+ toolz 1.0.0
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+ session-info2 0.1.2
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+ PyYAML 6.0.2
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+ llvmlite 0.44.0
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+ scipy 1.15.2
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+ pandas 2.2.3
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+ sphinxcontrib-devhelp 2.0.0
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+ h5py 3.13.0
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+ tblib 3.0.0
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+ setuptools-scm 8.2.0
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+ more-itertools 10.3.0
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+ msgpack 1.1.0
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+ sparse 0.15.5
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+ wrapt 1.17.2
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+ jaraco.collections 5.1.0
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+ numba 0.61.0
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+ pyarrow 19.0.1
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+ pytz 2025.1
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+ MarkupSafe 3.0.2
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+ crc32c 2.7.1
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+ sphinxcontrib-qthelp 2.0.0
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+ sphinxcontrib-serializinghtml 2.0.0
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+ zarr 2.18.4
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+ asciitree 0.3.3
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+ six 1.17.0
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+ sphinxcontrib-applehelp 2.0.0
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+ numpy 2.1.3
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+ cloudpickle 3.1.1
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+ sphinxcontrib-bibtex 2.6.3
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+ natsort 8.4.0
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+ jaraco.text 3.12.1
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+ setuptools 76.1.0
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+ Deprecated 1.2.18
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+ packaging 24.2
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+ python-dateutil 2.9.0.post0
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+ ---- ----
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+ Python 3.13.2 | packaged by conda-forge | (main, Feb 17 2025, 14:10:22) [GCC 13.3.0]
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+ OS Linux-6.11.0-109019-tuxedo-x86_64-with-glibc2.39
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+ Updated 2025-03-18 15:47
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+ blank_issues_enabled: false
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+ contact_links:
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+ - name: Scverse Community Forum
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+ url: https://discourse.scverse.org/
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+ about: If you have questions about “How to do X”, please ask them here.
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+ name: Feature request
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+ description: Propose a new feature for acumen
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+ labels: enhancement
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+ body:
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+ - type: textarea
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+ id: description
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+ attributes:
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+ label: Description of feature
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+ description: Please describe your suggestion for a new feature. It might help to describe a problem or use case, plus any alternatives that you have considered.
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+ validations:
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+ required: true
@@ -0,0 +1,26 @@
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+ name: Check Build
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+
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+ on:
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+ push:
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+ branches: [main]
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+ pull_request:
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+ branches: [main]
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+
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+ concurrency:
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+ group: ${{ github.workflow }}-${{ github.ref }}
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+ cancel-in-progress: true
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+
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+ jobs:
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+ package:
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+ runs-on: ubuntu-latest
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+ steps:
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+ - uses: actions/checkout@v6
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+ with:
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+ filter: blob:none
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+ fetch-depth: 0
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+ - name: Install uv
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+ uses: astral-sh/setup-uv@v7
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+ - name: Build package
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+ run: uv build
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+ - name: Check package
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+ run: uvx twine check --strict dist/*.whl
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+ name: Release
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+
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+ on:
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+ release:
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+ types: [published]
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+
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+ # Use "trusted publishing", see https://docs.pypi.org/trusted-publishers/
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+ jobs:
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+ release:
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+ name: Upload release to PyPI
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+ runs-on: ubuntu-latest
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+ environment:
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+ name: pypi
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+ url: https://pypi.org/p/acumen
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+ permissions:
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+ id-token: write # IMPORTANT: this permission is mandatory for trusted publishing
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+ steps:
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+ - uses: actions/checkout@v6
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+ with:
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+ filter: blob:none
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+ fetch-depth: 0
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+ - name: Install uv
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+ uses: astral-sh/setup-uv@v7
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+ - name: Build package
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+ run: uv build
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+ - name: Publish package distributions to PyPI
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+ uses: pypa/gh-action-pypi-publish@release/v1
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+ name: Test
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+
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+ on:
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+ push:
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+ branches: [main]
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+ pull_request:
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+ branches: [main]
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+ schedule:
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+ - cron: "0 5 1,15 * *"
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+
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+ concurrency:
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+ group: ${{ github.workflow }}-${{ github.ref }}
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+ cancel-in-progress: true
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+
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+ jobs:
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+ # Get the test environment from hatch as defined in pyproject.toml.
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+ # This ensures that the pyproject.toml is the single point of truth for test definitions and the same tests are
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+ # run locally and on continuous integration.
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+ # Check [[tool.hatch.envs.hatch-test.matrix]] in pyproject.toml and https://hatch.pypa.io/latest/environment/ for
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+ # more details.
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+ get-environments:
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+ runs-on: ubuntu-slim
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+ outputs:
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+ envs: ${{ steps.get-envs.outputs.envs }}
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+ steps:
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+ - uses: actions/checkout@v6
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+ with:
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+ filter: blob:none
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+ fetch-depth: 0
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+ - name: Install uv
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+ uses: astral-sh/setup-uv@v7
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+ - name: Get test environments
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+ id: get-envs
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+ run: |
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+ ENVS_JSON=$(uvx hatch env show --json | jq -c 'to_entries
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+ | map(
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+ select(.key | startswith("hatch-test"))
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+ | {
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+ name: .key,
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+ label: (if (.key | contains("pre")) then .key + " (PRE-RELEASE DEPENDENCIES)" else .key end),
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+ python: .value.python
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+ }
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+ )')
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+ echo "envs=${ENVS_JSON}" | tee $GITHUB_OUTPUT
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+
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+ # Run tests through hatch. Spawns a separate runner for each environment defined in the hatch matrix obtained above.
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+ test:
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+ needs: get-environments
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+ permissions:
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+ id-token: write # for codecov OIDC
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+ contents: read
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+
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+ strategy:
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+ fail-fast: false
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+ matrix:
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+ os: [ubuntu-latest]
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+ env: ${{ fromJSON(needs.get-environments.outputs.envs) }}
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+
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+ name: ${{ matrix.env.label }}
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+ runs-on: ${{ matrix.os }}
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+ continue-on-error: ${{ contains(matrix.env.name, 'pre') }} # make "all-green" pass even if pre-release job fails
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+
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+ steps:
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+ - uses: actions/checkout@v6
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+ with:
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+ filter: blob:none
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+ fetch-depth: 0
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+ - name: Set up Node.js
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+ uses: actions/setup-node@v6
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+ with:
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+ node-version: 22
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+ - name: Install uv
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+ uses: astral-sh/setup-uv@v7
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+ with:
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+ python-version: ${{ matrix.env.python }}
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+ - name: Install agent CLIs
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+ run: npm install --global @anthropic-ai/claude-code @openai/codex
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+ - name: create hatch environment
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+ run: uvx hatch env create ${{ matrix.env.name }}
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+ - name: list all all installed package versions
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+ run: uvx hatch run ${{ matrix.env.name }}:uv pip list
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+ - name: run tests using hatch
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+ env:
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+ MPLBACKEND: agg
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+ PLATFORM: ${{ matrix.os }}
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+ DISPLAY: :42
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+ run: uvx hatch run ${{ matrix.env.name }}:run-cov -v --color=yes -n auto
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+ - name: generate coverage report
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+ run: |
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+ # See https://coverage.readthedocs.io/page/config.html#run-patch
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+ test -f .coverage || uvx hatch run ${{ matrix.env.name }}:cov-combine
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+ uvx hatch run ${{ matrix.env.name }}:cov-report # report visibly
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+ uvx hatch run ${{ matrix.env.name }}:coverage xml # create report for upload
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+ - name: Upload coverage
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+ uses: codecov/codecov-action@v6
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+ with:
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+ # TODO: set back to true once scverse/acumen is onboarded on Codecov
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+ fail_ci_if_error: false
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+ use_oidc: true
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+
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+ # Check that all tests defined above pass. This makes it easy to set a single "required" test in branch
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+ # protection instead of having to update it frequently. See https://github.com/re-actors/alls-green#why.
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+ check:
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+ name: Tests pass in all hatch environments
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+ if: always()
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+ needs:
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+ - get-environments
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+ - test
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+ runs-on: ubuntu-latest
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+ steps:
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+ - uses: re-actors/alls-green@release/v1
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+ with:
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+ jobs: ${{ toJSON(needs) }}
@@ -11,6 +11,10 @@ __pycache__/
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  # Distribution / packaging
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  /dist/
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+ # uv's resolved dependency set. acumen is a library — consumers resolve their own tree, and
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+ # CI resolves fresh through hatch — so a committed lock would pin nothing that is checked.
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+ /uv.lock
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+
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  # Tests and coverage
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  /data/
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  /node_modules/
@@ -0,0 +1,38 @@
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+ fail_fast: false
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+ default_language_version:
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+ python: python3
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+ default_stages:
5
+ - pre-commit
6
+ - pre-push
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+ minimum_pre_commit_version: 2.16.0
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+ repos:
9
+ - repo: https://github.com/biomejs/pre-commit
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+ rev: v2.6.4
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+ hooks:
12
+ - id: biome-format
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+ exclude: ^\.cruft\.json$ # inconsistent indentation with cruft - file never to be modified manually.
14
+ - repo: https://github.com/tox-dev/pyproject-fmt
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+ rev: v2.30.6
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+ hooks:
17
+ - id: pyproject-fmt
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+ - repo: https://github.com/astral-sh/ruff-pre-commit
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+ rev: v0.17.4
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+ hooks:
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+ - id: ruff-check
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+ types_or: [python, pyi, jupyter]
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+ args: [--fix, --exit-non-zero-on-fix]
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+ - id: ruff-format
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+ types_or: [python, pyi, jupyter]
26
+ - repo: https://github.com/pre-commit/pre-commit-hooks
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+ rev: v6.0.0
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+ hooks:
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+ - id: detect-private-key
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+ - id: check-ast
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+ - id: end-of-file-fixer
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+ - id: mixed-line-ending
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+ args: [--fix=lf]
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+ - id: trailing-whitespace
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+ - id: check-case-conflict
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+ # Check that there are no merge conflicts (could be generated by template sync)
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+ - id: check-merge-conflict
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+ args: [--assume-in-merge]
@@ -0,0 +1,16 @@
1
+ # https://docs.readthedocs.io/page/config-file/v2.html
2
+ version: 2
3
+ build:
4
+ os: ubuntu-24.04
5
+ tools:
6
+ python: "3.14"
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+ nodejs: latest
8
+ jobs:
9
+ create_environment:
10
+ - asdf plugin add uv
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+ - asdf install uv latest
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+ - asdf global uv latest
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+ build:
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+ html:
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+ - uvx hatch run docs:build
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+ - mv docs/_build $READTHEDOCS_OUTPUT
@@ -15,4 +15,5 @@
15
15
  "python.analysis.typeCheckingMode": "basic",
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16
  "python.testing.pytestEnabled": true,
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  "python.testing.pytestArgs": ["-vv", "--color=yes"],
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+ "cursorpyright.analysis.typeCheckingMode": "basic",
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  }
@@ -0,0 +1,74 @@
1
+ # Changelog
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+
3
+ All notable changes to this project will be documented in this file.
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+
5
+ The format is based on [Keep a Changelog][],
6
+ and this project adheres to [Semantic Versioning][].
7
+
8
+ [keep a changelog]: https://keepachangelog.com/
9
+ [semantic versioning]: https://semver.org/
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+
11
+ ## [0.0.2]
12
+
13
+ ### Added
14
+
15
+ - Added `acumen fit --ablation {no-optimize,no-wiki}` to run ablation arms. A report without a `valid` split now uses `test` instead
16
+ - Added `acumen prepare` to build task datasets once into `cache/`, and a `data:` key in `tasks.yaml` that links them into each run
17
+
18
+ ### Changed
19
+
20
+ - Restructured the docs, with a scverse-style README, a Getting started tutorial and one API page per `acumen` subcommand
21
+ - `--agent codex` now installs shipped skills into `~/.agents/skills`, where current Codex looks for them
22
+ - The report now tests success rate and cost separately, with a Benjamini–Hochberg FDR correction per axis
23
+ - Updated the GPT colour ramp in the report so `astra` is the darkest and the other models lighten in even steps
24
+ - Merged the per-command model keys (`draft_model`, `improve_model`, `tasks_model`, `ship_model`, `check_model`) into a single `meta_model` key
25
+ - Transcripts from every provider are now rendered through one shared trajectory model, and each run also writes a `trajectory.json`. `claude-code-log` is no longer a dependency
26
+ - Claude agents now run with the `claude` CLI on `PATH`, falling back to the one bundled in `claude-agent-sdk`
27
+ - `result.json` now records the agent CLI's version as `cli_version`, replacing `sdk_version`
28
+
29
+ ### Fixed
30
+
31
+ - Fixed agent failures reporting a bare "errored: success" instead of the provider's reason
32
+ - Fixed `acumen ship --force` leaving the old installer's tests broken. The ship agent now ports them and runs them before delivering
33
+ - Fixed `acumen ship` failing to push and open the pull request because the agent could not find the operator's git and `gh` credentials
34
+
35
+ ## [0.0.1dev]
36
+
37
+ ### Added
38
+
39
+ - `acumen check` now also reviews each task for inconsistencies between its prompt, answer and reproducer. `--no-review` skips this step
40
+ - Added `acumen check` to verify each task's answer by rerunning its reproducer at `tasks/<id>-<split>.py`
41
+ - `acumen tasks` now keeps one reproducer script per split in `tasks/`
42
+ - Added an optional `needs_script` key to `tasks.yaml` for tasks that need no code
43
+ - Claude and Codex models can now run side by side in benchmarks and drive every meta-agent command
44
+ - `cost_usd` is now computed from each run's token counts, so both providers are priced the same way
45
+ - Added `acumen prices` to show and refresh the rate table, and a `prices:` config key to override it
46
+ - Rates are now read from the providers' pricing pages instead of a table shipped with the release
47
+ - `acumen bench` now fails before spending anything when the pricing pages cannot be read
48
+ - `result.json` now records where each run's prices came from and their date
49
+ - The report now flags arms that were priced on different dates
50
+ - Added HTML transcripts for Codex runs
51
+ - `acumen bench` without an arm now benches the baseline and every version in `skills/` in one pass
52
+
53
+ ### Changed
54
+
55
+ - The report's cost vs. success figure now joins each model's versions with arrows instead of using marker shapes
56
+ - The Pareto frontier in the report is now dashed and runs to the right edge of the panel
57
+ - Both backends are now optional, installed with `acumen[claude]`, `acumen[all]` or just the `codex` CLI for Codex
58
+ - `max_turns` and `max_usd` are now enforced for Codex
59
+ - `acumen bench` now supports `--auth {auto,session,api}` and defaults to the provider's subscription
60
+ - Runs that fail because provider usage or credit ran out are now treated as invalid and retried on resume
61
+
62
+ ### Fixed
63
+
64
+ - Fixed baseline runs finding a skill that the target package ships inside itself. The target venv is now cleaned of agent guidance before any agent runs
65
+ - Fixed Claude runs being recorded with the wrong result when a background command kept the session alive
66
+ - Increased the Bash timeout for sandboxed commands to 600 seconds, so long downloads are no longer sent to the background
67
+ - Fixed capped or crashed Codex runs recording a cost of `$0.00`
68
+ - Fixed capped runs being failed even when they had already written a correct answer
69
+ - Fixed sandboxed agents being blocked from hosts that targets need, such as EBI, Zenodo and NCBI
70
+ - Fixed runs whose sandbox could not execute anything being graded as wrong answers instead of infrastructure failures
71
+ - `acumen tasks` now overwrites the untouched `tasks.yaml` placeholder from `acumen init` without `--force`
72
+ - Fixed Codex transcripts being rendered as empty pages
73
+ - Removed "Claude" from the drafting and improving prompts, which are also used by Codex
74
+ - Removed `check_auth` and `auth_available`, which ignored Codex credentials
acumen-0.0.2/PKG-INFO ADDED
@@ -0,0 +1,161 @@
1
+ Metadata-Version: 2.5
2
+ Name: acumen
3
+ Version: 0.0.2
4
+ Summary: Build, Benchmark, and Optimize Agentic Skills for Python Packages.
5
+ Project-URL: Documentation, https://acumen-skills.readthedocs.io/
6
+ Project-URL: Homepage, https://github.com/scverse/acumen
7
+ Project-URL: Source, https://github.com/scverse/acumen
8
+ Author: Pau Badia i Mompel
9
+ Maintainer-email: Pau Badia i Mompel <paubim@stanford.edu>
10
+ License: MIT License
11
+
12
+ Copyright (c) 2026, Pau Badia i Mompel
13
+
14
+ Permission is hereby granted, free of charge, to any person obtaining a copy
15
+ of this software and associated documentation files (the "Software"), to deal
16
+ in the Software without restriction, including without limitation the rights
17
+ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
18
+ copies of the Software, and to permit persons to whom the Software is
19
+ furnished to do so, subject to the following conditions:
20
+
21
+ The above copyright notice and this permission notice shall be included in all
22
+ copies or substantial portions of the Software.
23
+
24
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
25
+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
26
+ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
27
+ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
28
+ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
29
+ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
30
+ SOFTWARE.
31
+ License-File: LICENSE
32
+ Classifier: Programming Language :: Python :: 3 :: Only
33
+ Classifier: Programming Language :: Python :: 3.12
34
+ Classifier: Programming Language :: Python :: 3.13
35
+ Classifier: Programming Language :: Python :: 3.14
36
+ Classifier: Programming Language :: Python :: 3.15
37
+ Requires-Python: >=3.12
38
+ Requires-Dist: matplotlib
39
+ Requires-Dist: numpy
40
+ Requires-Dist: pandas
41
+ Requires-Dist: psutil>=5.9
42
+ Requires-Dist: pyyaml
43
+ Requires-Dist: scipy
44
+ Requires-Dist: session-info2
45
+ Provides-Extra: all
46
+ Requires-Dist: claude-agent-sdk>=0.2.126; extra == 'all'
47
+ Provides-Extra: claude
48
+ Requires-Dist: claude-agent-sdk>=0.2.126; extra == 'claude'
49
+ Description-Content-Type: text/markdown
50
+
51
+ <p align="center">
52
+ <img src="docs/_static/images/banner.svg" alt="acumen" width="360">
53
+ </p>
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+
55
+ <!-- docs-start -->
56
+
57
+ <p align="center"><b>Build, benchmark, and optimize agentic skills for Python packages.</b></p>
58
+
59
+ [![Tests][badge-tests]][tests]
60
+ [![Documentation][badge-docs]][documentation]
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+
62
+ [![Issues][badge-issues]][issue tracker]
63
+ [![Coverage][badge-coverage]][codecoverage]
64
+ [![Stars][badge-stars]](https://github.com/scverse/acumen/stargazers)
65
+
66
+ [![PyPI][badge-pypi]][pypi]
67
+ [![Downloads month][badge-mdown]][down]
68
+ [![Downloads all][badge-adown]][down]
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+
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+ [badge-tests]: https://img.shields.io/github/actions/workflow/status/scverse/acumen/test.yaml?branch=main
71
+ [badge-docs]: https://img.shields.io/readthedocs/acumen-skills
72
+ [badge-issues]: https://img.shields.io/github/issues/scverse/acumen
73
+ [badge-coverage]: https://codecov.io/gh/scverse/acumen/branch/main/graph/badge.svg
74
+ [badge-pypi]: https://img.shields.io/pypi/v/acumen.svg
75
+ [badge-mdown]: https://static.pepy.tech/badge/acumen/month
76
+ [badge-adown]: https://static.pepy.tech/badge/acumen
77
+ [badge-stars]: https://img.shields.io/github/stars/scverse/acumen?style=flat&logo=github&color=yellow
78
+
79
+ `acumen` is a python package to build, benchmark and optimize agentic skills for any Python package.
80
+ An agentic skill is a short set of plain-text instructions that helps a coding agent use a package correctly.
81
+ Given a package and a few tasks, `acumen` trains a skill in the same way one would train a model.
82
+ In every epoch, coding agents attempt the training tasks, and `acumen` learns from the errors they make to rewrite the skill.
83
+ Each new version is scored on held-out validation tasks, training stops once validation no longer improves, and the best version is evaluated one last time on an untouched test set.
84
+ With the final skill, coding agents are more successful at solving tasks that require using the Python package than they are without the skill.
85
+
86
+ [//]: # "numfocus-fiscal-sponsor-attribution"
87
+
88
+ `acumen` is part of the scverse® project ([website](https://scverse.org), [governance](https://scverse.org/about/roles)) and is fiscally sponsored by [NumFOCUS](https://numfocus.org/).
89
+ If you like scverse® and want to support our mission, please consider making a tax-deductible [donation](https://numfocus.org/donate-to-scverse) to help the project pay for developer time, professional services, travel, workshops, and a variety of other needs.
90
+
91
+ <div align="center">
92
+ <a href="https://numfocus.org/project/scverse">
93
+ <img
94
+ src="https://raw.githubusercontent.com/numfocus/templates/master/images/numfocus-logo.png"
95
+ width="200"
96
+ >
97
+ </a>
98
+ </div>
99
+
100
+ ## Getting started
101
+
102
+ Please refer to the [documentation][],
103
+ in particular, the [Getting started][getting started] tutorial and the [API documentation][].
104
+
105
+ ## Installation
106
+
107
+ You need to have Python 3.12 or newer installed on your system.
108
+ If you don't have Python installed, we recommend installing [uv][].
109
+
110
+ `acumen` runs its agents with Claude, Codex, or both, and you only need to install the backend you use.
111
+ There are several alternative options to install `acumen`:
112
+
113
+ 1. Install the latest stable release from [PyPI][pypi] to run Claude models (requires an Anthropic API key or a `claude` login):
114
+
115
+ ```bash
116
+ pip install acumen[claude]
117
+ ```
118
+
119
+ 2. Install the latest stable release from [PyPI][pypi] to run Codex models (requires the `codex` CLI on your `PATH` and a Codex login or API key):
120
+
121
+ ```bash
122
+ pip install acumen
123
+ ```
124
+
125
+ 3. Install the latest stable release from [PyPI][pypi] to run both:
126
+
127
+ ```bash
128
+ pip install acumen[all]
129
+ ```
130
+
131
+ 4. Install the latest development version:
132
+
133
+ ```bash
134
+ pip install "acumen[all] @ git+https://github.com/scverse/acumen.git@main"
135
+ ```
136
+
137
+ ## Release notes
138
+
139
+ See the [changelog][].
140
+
141
+ ## Contact
142
+
143
+ For questions and help requests, you can reach out in the [scverse discourse][].
144
+ If you found a bug, please use the [issue tracker][].
145
+
146
+ ## Citation
147
+
148
+ > t.b.a
149
+
150
+ [uv]: https://github.com/astral-sh/uv
151
+ [scverse discourse]: https://discourse.scverse.org/
152
+ [scverse]: https://scverse.org/
153
+ [issue tracker]: https://github.com/scverse/acumen/issues
154
+ [tests]: https://github.com/scverse/acumen/actions/workflows/test.yaml
155
+ [documentation]: https://acumen-skills.readthedocs.io/
156
+ [getting started]: https://acumen-skills.readthedocs.io/page/getting_started.html
157
+ [changelog]: https://acumen-skills.readthedocs.io/page/changelog.html
158
+ [api documentation]: https://acumen-skills.readthedocs.io/page/api/index.html
159
+ [pypi]: https://pypi.org/project/acumen
160
+ [down]: https://pepy.tech/project/acumen
161
+ [codecoverage]: https://codecov.io/gh/scverse/acumen