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Fix numba JIT disable patch targeting wrong config attribute - #1181

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Fix numba JIT disable patch targeting wrong config attribute#1181
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Test suite tried to force-disable numba JIT when already imported by patching NUMBA_DISABLE_JIT on numba.core.config, but numba internally reads the env var into an attribute named DISABLE_JIT (no prefix).

We should find a less hacky solution to this, but for now, running the tests sequentially (pytest -x) always pass.

@Tomaz-Vieira@claude
Fix numba JIT disable patch targeting wrong config attribute
a7013ac
Test suite tried to force-disable numba JIT when already imported by
patching `NUMBA_DISABLE_JIT` on numba.core.config, but numba internally
reads the env var into an attribute named `DISABLE_JIT` (no prefix).
We should find a less hacky solution to this, but for now, running the
tests sequentially (`pytest -x`) always pass.
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
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Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 92.41%. Comparing base (09b0bcb) to head (099eb3b).
⚠️ Report is 1 commits behind head on main.

Additional details and impacted files
@@ Coverage Diff @@## main #1181 +/- ##
=======================================
Coverage 92.41% 92.41% =======================================
Files 52 52 Lines 7874 7874 =======================================
Hits 7277 7277 Misses 597 597
🚀 New features to boost your workflow:
  • ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

@Tomaz-Vieira

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pre-commit is flagging a mypy error that has nothing to do with this PR, so I don't think we should pollute it with a fix

@LucaMarconato

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Thanks for the fix, well spotted!

pre-commit is flagging a mypy error that has nothing to do with this PR, so I don't think we should pollute it with a fix

Yes, clean solution is to fix it in another PRs, but practically those pre-commit fail happen routinely so we usually just address them at the first occasion (or sometimes merge to main with red CI and fix it later, if we know that we are going to fix it soon anyway). I fixed it here right before merging: #1180.

@LucaMarconato
LucaMarconato enabled auto-merge (squash) August 19, 2026 11:18
@LucaMarconato
LucaMarconato merged commit d66cde9 into mainAug 19, 2026
10 checks passed
@LucaMarconato
LucaMarconato deleted the fix/serial_tests branch August 19, 2026 11:20
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Fix numba JIT disable patch targeting wrong config attribute by Tomaz-Vieira · Pull Request #1181 · scverse/spatialdata · GitHub
Skip to content
Fix numba JIT disable patch targeting wrong config attribute - #1181
Merged
LucaMarconato merged 2 commits into
mainfrom 
fix/serial_tests
Aug 19, 2026
Merged
Fix numba JIT disable patch targeting wrong config attribute#1181
LucaMarconato merged 2 commits into
mainfrom 
fix/serial_tests
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@Tomaz-Vieira
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Aug 19, 2026

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Test suite tried to force-disable numba JIT when already imported by patching NUMBA_DISABLE_JIT on numba.core.config, but numba internally reads the env var into an attribute named DISABLE_JIT (no prefix).
We should find a less hacky solution to this, but for now, running the tests sequentially (pytest -x) always pass.
@Tomaz-Vieira@claude
Fix numba JIT disable patch targeting wrong config attribute
a7013ac
Test suite tried to force-disable numba JIT when already imported by
patching `NUMBA_DISABLE_JIT` on numba.core.config, but numba internally
reads the env var into an attribute named `DISABLE_JIT` (no prefix).
We should find a less hacky solution to this, but for now, running the
tests sequentially (`pytest -x`) always pass.
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
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Codecov Report
✅ All modified and coverable lines are covered by tests.

✅ Project coverage is 92.41%. Comparing base (09b0bcb) to head (099eb3b).
⚠️ Report is 1 commits behind head on main.
Additional details and impacted files
@@ Coverage Diff @@## main #1181 +/- ##
=======================================
Coverage 92.41% 92.41% =======================================
Files 52 52 Lines 7874 7874 =======================================
Hits 7277 7277 Misses 597 597 
 🚀 New features to boost your workflow: 
  • ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.
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pre-commit is flagging a mypy error that has nothing to do with this PR, so I don't think we should pollute it with a fix
@LucaMarconato
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Thanks for the fix, well spotted!
pre-commit is flagging a mypy error that has nothing to do with this PR, so I don't think we should pollute it with a fix
Yes, clean solution is to fix it in another PRs, but practically those pre-commit fail happen routinely so we usually just address them at the first occasion (or sometimes merge to main with red CI and fix it later, if we know that we are going to fix it soon anyway). I fixed it here right before merging: #1180.
@LucaMarconato
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enabled auto-merge (squash)
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@LucaMarconato
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merged commit d66cde9
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10 checks passed

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Fix numba JIT disable patch targeting wrong config attribute by Tomaz-Vieira · Pull Request #1181 · scverse/spatialdata · GitHub
Skip to content
Fix numba JIT disable patch targeting wrong config attribute - #1181
Merged
LucaMarconato merged 2 commits into
mainfrom 
fix/serial_tests
Aug 19, 2026
Merged
Fix numba JIT disable patch targeting wrong config attribute#1181
LucaMarconato merged 2 commits into
mainfrom 
fix/serial_tests
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@Tomaz-Vieira
@Tomaz-VieiraTomaz-Vieira
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Test suite tried to force-disable numba JIT when already imported by patching NUMBA_DISABLE_JIT on numba.core.config, but numba internally reads the env var into an attribute named DISABLE_JIT (no prefix).
We should find a less hacky solution to this, but for now, running the tests sequentially (pytest -x) always pass.
@Tomaz-Vieira@claude
Fix numba JIT disable patch targeting wrong config attribute
a7013ac
Test suite tried to force-disable numba JIT when already imported by
patching `NUMBA_DISABLE_JIT` on numba.core.config, but numba internally
reads the env var into an attribute named `DISABLE_JIT` (no prefix).
We should find a less hacky solution to this, but for now, running the
tests sequentially (`pytest -x`) always pass.
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
@codecov
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commented
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edited

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Codecov Report
✅ All modified and coverable lines are covered by tests.

✅ Project coverage is 92.41%. Comparing base (09b0bcb) to head (099eb3b).
⚠️ Report is 1 commits behind head on main.
Additional details and impacted files
@@ Coverage Diff @@## main #1181 +/- ##
=======================================
Coverage 92.41% 92.41% =======================================
Files 52 52 Lines 7874 7874 =======================================
Hits 7277 7277 Misses 597 597 
 🚀 New features to boost your workflow: 
  • ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.
@Tomaz-Vieira
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pre-commit is flagging a mypy error that has nothing to do with this PR, so I don't think we should pollute it with a fix
@LucaMarconato
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Thanks for the fix, well spotted!
pre-commit is flagging a mypy error that has nothing to do with this PR, so I don't think we should pollute it with a fix
Yes, clean solution is to fix it in another PRs, but practically those pre-commit fail happen routinely so we usually just address them at the first occasion (or sometimes merge to main with red CI and fix it later, if we know that we are going to fix it soon anyway). I fixed it here right before merging: #1180.
@LucaMarconato
LucaMarconato
enabled auto-merge (squash)
August 19, 2026 11:18
@LucaMarconato
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merged commit d66cde9
into
mainAug 19, 2026

10 checks passed

@LucaMarconato
LucaMarconato
deleted the

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August 19, 2026 11:20
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Fix numba JIT disable patch targeting wrong config attribute by Tomaz-Vieira · Pull Request #1181 · scverse/spatialdata · GitHub
Skip to content
Fix numba JIT disable patch targeting wrong config attribute - #1181
Merged
LucaMarconato merged 2 commits into
mainfrom 
fix/serial_tests
Aug 19, 2026
Merged
Fix numba JIT disable patch targeting wrong config attribute#1181
LucaMarconato merged 2 commits into
mainfrom 
fix/serial_tests
Conversation
@Tomaz-Vieira
@Tomaz-VieiraTomaz-Vieira
commented
Aug 19, 2026

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Test suite tried to force-disable numba JIT when already imported by patching NUMBA_DISABLE_JIT on numba.core.config, but numba internally reads the env var into an attribute named DISABLE_JIT (no prefix).
We should find a less hacky solution to this, but for now, running the tests sequentially (pytest -x) always pass.
@Tomaz-Vieira@claude
Fix numba JIT disable patch targeting wrong config attribute
a7013ac
Test suite tried to force-disable numba JIT when already imported by
patching `NUMBA_DISABLE_JIT` on numba.core.config, but numba internally
reads the env var into an attribute named `DISABLE_JIT` (no prefix).
We should find a less hacky solution to this, but for now, running the
tests sequentially (`pytest -x`) always pass.
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
@codecov
codecovBot
commented
Aug 19, 2026•

edited

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Codecov Report
✅ All modified and coverable lines are covered by tests.

✅ Project coverage is 92.41%. Comparing base (09b0bcb) to head (099eb3b).
⚠️ Report is 1 commits behind head on main.
Additional details and impacted files
@@ Coverage Diff @@## main #1181 +/- ##
=======================================
Coverage 92.41% 92.41% =======================================
Files 52 52 Lines 7874 7874 =======================================
Hits 7277 7277 Misses 597 597 
 🚀 New features to boost your workflow: 
  • ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.
@Tomaz-Vieira
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pre-commit is flagging a mypy error that has nothing to do with this PR, so I don't think we should pollute it with a fix
@LucaMarconato
LucaMarconato
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Aug 19, 2026

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Thanks for the fix, well spotted!
pre-commit is flagging a mypy error that has nothing to do with this PR, so I don't think we should pollute it with a fix
Yes, clean solution is to fix it in another PRs, but practically those pre-commit fail happen routinely so we usually just address them at the first occasion (or sometimes merge to main with red CI and fix it later, if we know that we are going to fix it soon anyway). I fixed it here right before merging: #1180.
@LucaMarconato
LucaMarconato
enabled auto-merge (squash)
August 19, 2026 11:18
@LucaMarconato
LucaMarconato
merged commit d66cde9
into
mainAug 19, 2026

10 checks passed

@LucaMarconato
LucaMarconato
deleted the

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Fix numba JIT disable patch targeting wrong config attribute by Tomaz-Vieira · Pull Request #1181 · scverse/spatialdata · GitHub
Skip to content
Fix numba JIT disable patch targeting wrong config attribute - #1181
Merged
LucaMarconato merged 2 commits into
mainfrom 
fix/serial_tests
Aug 19, 2026
Merged
Fix numba JIT disable patch targeting wrong config attribute#1181
LucaMarconato merged 2 commits into
mainfrom 
fix/serial_tests
Conversation
@Tomaz-Vieira
@Tomaz-VieiraTomaz-Vieira
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Aug 19, 2026

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Test suite tried to force-disable numba JIT when already imported by patching NUMBA_DISABLE_JIT on numba.core.config, but numba internally reads the env var into an attribute named DISABLE_JIT (no prefix).
We should find a less hacky solution to this, but for now, running the tests sequentially (pytest -x) always pass.
@Tomaz-Vieira@claude
Fix numba JIT disable patch targeting wrong config attribute
a7013ac
Test suite tried to force-disable numba JIT when already imported by
patching `NUMBA_DISABLE_JIT` on numba.core.config, but numba internally
reads the env var into an attribute named `DISABLE_JIT` (no prefix).
We should find a less hacky solution to this, but for now, running the
tests sequentially (`pytest -x`) always pass.
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
@codecov
codecovBot
commented
Aug 19, 2026•

edited

Loading

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Codecov Report
✅ All modified and coverable lines are covered by tests.

✅ Project coverage is 92.41%. Comparing base (09b0bcb) to head (099eb3b).
⚠️ Report is 1 commits behind head on main.
Additional details and impacted files
@@ Coverage Diff @@## main #1181 +/- ##
=======================================
Coverage 92.41% 92.41% =======================================
Files 52 52 Lines 7874 7874 =======================================
Hits 7277 7277 Misses 597 597 
 🚀 New features to boost your workflow: 
  • ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.
@Tomaz-Vieira
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pre-commit is flagging a mypy error that has nothing to do with this PR, so I don't think we should pollute it with a fix
@LucaMarconato
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Thanks for the fix, well spotted!
pre-commit is flagging a mypy error that has nothing to do with this PR, so I don't think we should pollute it with a fix
Yes, clean solution is to fix it in another PRs, but practically those pre-commit fail happen routinely so we usually just address them at the first occasion (or sometimes merge to main with red CI and fix it later, if we know that we are going to fix it soon anyway). I fixed it here right before merging: #1180.
@LucaMarconato
LucaMarconato
enabled auto-merge (squash)
August 19, 2026 11:18
@LucaMarconato
LucaMarconato
merged commit d66cde9
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mainAug 19, 2026

10 checks passed

@LucaMarconato
LucaMarconato
deleted the

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Fix numba JIT disable patch targeting wrong config attribute by Tomaz-Vieira · Pull Request #1181 · scverse/spatialdata · GitHub
Skip to content
Fix numba JIT disable patch targeting wrong config attribute - #1181
Merged
LucaMarconato merged 2 commits into
mainfrom 
fix/serial_tests
Aug 19, 2026
Merged
Fix numba JIT disable patch targeting wrong config attribute#1181
LucaMarconato merged 2 commits into
mainfrom 
fix/serial_tests
Conversation
@Tomaz-Vieira
@Tomaz-VieiraTomaz-Vieira
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Test suite tried to force-disable numba JIT when already imported by patching NUMBA_DISABLE_JIT on numba.core.config, but numba internally reads the env var into an attribute named DISABLE_JIT (no prefix).
We should find a less hacky solution to this, but for now, running the tests sequentially (pytest -x) always pass.
@Tomaz-Vieira@claude
Fix numba JIT disable patch targeting wrong config attribute
a7013ac
Test suite tried to force-disable numba JIT when already imported by
patching `NUMBA_DISABLE_JIT` on numba.core.config, but numba internally
reads the env var into an attribute named `DISABLE_JIT` (no prefix).
We should find a less hacky solution to this, but for now, running the
tests sequentially (`pytest -x`) always pass.
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
@codecov
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Codecov Report
✅ All modified and coverable lines are covered by tests.

✅ Project coverage is 92.41%. Comparing base (09b0bcb) to head (099eb3b).
⚠️ Report is 1 commits behind head on main.
Additional details and impacted files
@@ Coverage Diff @@## main #1181 +/- ##
=======================================
Coverage 92.41% 92.41% =======================================
Files 52 52 Lines 7874 7874 =======================================
Hits 7277 7277 Misses 597 597 
 🚀 New features to boost your workflow: 
  • ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.
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pre-commit is flagging a mypy error that has nothing to do with this PR, so I don't think we should pollute it with a fix
@LucaMarconato
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Thanks for the fix, well spotted!
pre-commit is flagging a mypy error that has nothing to do with this PR, so I don't think we should pollute it with a fix
Yes, clean solution is to fix it in another PRs, but practically those pre-commit fail happen routinely so we usually just address them at the first occasion (or sometimes merge to main with red CI and fix it later, if we know that we are going to fix it soon anyway). I fixed it here right before merging: #1180.
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Fix numba JIT disable patch targeting wrong config attribute by Tomaz-Vieira · Pull Request #1181 · scverse/spatialdata · GitHub
Skip to content
Fix numba JIT disable patch targeting wrong config attribute - #1181
Merged
LucaMarconato merged 2 commits into
mainfrom 
fix/serial_tests
Aug 19, 2026
Merged
Fix numba JIT disable patch targeting wrong config attribute#1181
LucaMarconato merged 2 commits into
mainfrom 
fix/serial_tests
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@Tomaz-Vieira
@Tomaz-VieiraTomaz-Vieira
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Aug 19, 2026

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Test suite tried to force-disable numba JIT when already imported by patching NUMBA_DISABLE_JIT on numba.core.config, but numba internally reads the env var into an attribute named DISABLE_JIT (no prefix).
We should find a less hacky solution to this, but for now, running the tests sequentially (pytest -x) always pass.
@Tomaz-Vieira@claude
Fix numba JIT disable patch targeting wrong config attribute
a7013ac
Test suite tried to force-disable numba JIT when already imported by
patching `NUMBA_DISABLE_JIT` on numba.core.config, but numba internally
reads the env var into an attribute named `DISABLE_JIT` (no prefix).
We should find a less hacky solution to this, but for now, running the
tests sequentially (`pytest -x`) always pass.
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
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Aug 19, 2026•

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Codecov Report
✅ All modified and coverable lines are covered by tests.

✅ Project coverage is 92.41%. Comparing base (09b0bcb) to head (099eb3b).
⚠️ Report is 1 commits behind head on main.
Additional details and impacted files
@@ Coverage Diff @@## main #1181 +/- ##
=======================================
Coverage 92.41% 92.41% =======================================
Files 52 52 Lines 7874 7874 =======================================
Hits 7277 7277 Misses 597 597 
 🚀 New features to boost your workflow: 
  • ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.
@Tomaz-Vieira
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Aug 19, 2026

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pre-commit is flagging a mypy error that has nothing to do with this PR, so I don't think we should pollute it with a fix
@LucaMarconato
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Aug 19, 2026

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Thanks for the fix, well spotted!
pre-commit is flagging a mypy error that has nothing to do with this PR, so I don't think we should pollute it with a fix
Yes, clean solution is to fix it in another PRs, but practically those pre-commit fail happen routinely so we usually just address them at the first occasion (or sometimes merge to main with red CI and fix it later, if we know that we are going to fix it soon anyway). I fixed it here right before merging: #1180.
@LucaMarconato
LucaMarconato
enabled auto-merge (squash)
August 19, 2026 11:18
@LucaMarconato
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merged commit d66cde9
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mainAug 19, 2026

10 checks passed

@LucaMarconato
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deleted the

fix/serial_tests

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August 19, 2026 11:20
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Fix numba JIT disable patch targeting wrong config attribute by Tomaz-Vieira · Pull Request #1181 · scverse/spatialdata · GitHub
Skip to content
Fix numba JIT disable patch targeting wrong config attribute - #1181
Merged
LucaMarconato merged 2 commits into
mainfrom 
fix/serial_tests
Aug 19, 2026
Merged
Fix numba JIT disable patch targeting wrong config attribute#1181
LucaMarconato merged 2 commits into
mainfrom 
fix/serial_tests
Conversation
@Tomaz-Vieira
@Tomaz-VieiraTomaz-Vieira
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Aug 19, 2026

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Test suite tried to force-disable numba JIT when already imported by patching NUMBA_DISABLE_JIT on numba.core.config, but numba internally reads the env var into an attribute named DISABLE_JIT (no prefix).
We should find a less hacky solution to this, but for now, running the tests sequentially (pytest -x) always pass.
@Tomaz-Vieira@claude
Fix numba JIT disable patch targeting wrong config attribute
a7013ac
Test suite tried to force-disable numba JIT when already imported by
patching `NUMBA_DISABLE_JIT` on numba.core.config, but numba internally
reads the env var into an attribute named `DISABLE_JIT` (no prefix).
We should find a less hacky solution to this, but for now, running the
tests sequentially (`pytest -x`) always pass.
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
@codecov
codecovBot
commented
Aug 19, 2026•

edited

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Codecov Report
✅ All modified and coverable lines are covered by tests.

✅ Project coverage is 92.41%. Comparing base (09b0bcb) to head (099eb3b).
⚠️ Report is 1 commits behind head on main.
Additional details and impacted files
@@ Coverage Diff @@## main #1181 +/- ##
=======================================
Coverage 92.41% 92.41% =======================================
Files 52 52 Lines 7874 7874 =======================================
Hits 7277 7277 Misses 597 597 
 🚀 New features to boost your workflow: 
  • ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.
@Tomaz-Vieira
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Aug 19, 2026

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pre-commit is flagging a mypy error that has nothing to do with this PR, so I don't think we should pollute it with a fix
@LucaMarconato
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Aug 19, 2026

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Thanks for the fix, well spotted!
pre-commit is flagging a mypy error that has nothing to do with this PR, so I don't think we should pollute it with a fix
Yes, clean solution is to fix it in another PRs, but practically those pre-commit fail happen routinely so we usually just address them at the first occasion (or sometimes merge to main with red CI and fix it later, if we know that we are going to fix it soon anyway). I fixed it here right before merging: #1180.
@LucaMarconato
LucaMarconato
enabled auto-merge (squash)
August 19, 2026 11:18
@LucaMarconato
LucaMarconato
merged commit d66cde9
into
mainAug 19, 2026

10 checks passed

@LucaMarconato
LucaMarconato
deleted the

fix/serial_tests

branch
August 19, 2026 11:20
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