Default write empty chunks false - #951

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joshmoore wants to merge 18 commits into
zarr-developers:masterfrom
joshmoore:default-write-empty-chunks-false
Closed

Default write empty chunks false#951
joshmoore wants to merge 18 commits into
zarr-developers:masterfrom
joshmoore:default-write-empty-chunks-false

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@joshmoore

@joshmoorejoshmoore commented Jan 26, 2022

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Re-opening #853 from another branch to see if that fixes the github action jobs.

jniand others added 12 commits December 2, 2021 12:48
@jni
Set write_empty_chunks to default to False
6b461a7
@jni
Add release entry for write_empty_chunks default
d09c8d9
@jni
Merge branch 'master' into default-write-empty-chunks-false
a042c8a
@d-v-b
add Empty chunks section to tutorial.rst
5091df0
@joshmoore
Merge branch 'master' into default-write-empty-chunks-false
9d3d83c
@d-v-b
add benchmarky example
21647ab
@d-v-b
Merge branch 'master' ofhttps://github.com/zarr-developers/zarr-python…
b9af4be
… into default-write-empty-chunks-false
@d-v-b
proper formatting of code block
6ad8695
@joshmoore
Fix abstore deprecated strings
422beaa
@joshmoore
Merge branch 'master' into default-write-empty-chunks-false
d27e4ed
@joshmoore
Also catch ValueError in all_equal
1f21139
The call to `np.any(array)` in zarr.util.all_equal triggers the
following ValueError:
```
> return ufunc.reduce(obj, axis, dtype, out, **passkwargs)
E ValueError: invalid literal for int() with base 10: 'baz'
```
Extending the catch block allows test_array_with_categorize_filter
to pass, but it's unclear if this points to a deeper issue.
@joshmoore
Merge branch 'master' into default-write-empty-chunks-false
18971b5
@jakirkham

jakirkham commented Jan 26, 2022•
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Also trying a no change PR ( #952 ) to see if this is a CI issue outside of these changes

@joshmoore

joshmoore commented Jan 26, 2022

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Fewer are hanging but not nothing. 😵‍💫

@jakirkham

jakirkham commented Jan 26, 2022

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It would be good to get a clearer idea on why that is happening. Did we manage to get a log that we could look at? Waited for a while to see if GH Actions would include output, but nothing showed up.

@jni

jni commented Jan 27, 2022

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@joshmoore@jakirkham this is very reminiscent of my own misadventures with test_sync, deadlocks, and CI timeouts. @joshmoore want to try your own advice?

#725 (comment)

Usually slow tests are printed at the end, but if they aren't completing we don't get the list! Can you add pytest -sv to the workflow or add pypi.org/project/pytest-timeout so we can get an idea on what's gone sideways?

This commit adds the timeout:

4e7733c (#725)

@joshmoore

joshmoore commented Jan 27, 2022

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Heh. I think I thought that that was now done everywhere. Pushing a commit with lots of timeouts here now.

@joshmoore
joshmooreforce-pushed the default-write-empty-chunks-false branch from b30abbb to 8b12549CompareJanuary 27, 2022 06:37
@jakirkham

jakirkham commented Jan 27, 2022

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The thing is this hang showed up very recently. It makes me wonder if there is something we changed or a dependency update in the environment that changed, which is causing issues.

For example fasteners was updated recently. To save writing this again, please read this comment ( #952 (comment) ).

@joshmoore

joshmoore commented Jan 27, 2022

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Interesting that not even timeout seems to be working here.

joshmoore added a commit to joshmoore/zarr-python that referenced this pull request Jan 27, 2022
@joshmoore
Pin fasteners to 0.16.3 (seezarr-developers#951)
666b500
@joshmoore
joshmooreforce-pushed the default-write-empty-chunks-false branch from 666b500 to 080a854CompareJanuary 27, 2022 07:35
@joshmoore

joshmoore commented Jan 27, 2022

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0.16.3 seemes safe, @jakirkham. Trying 0.17.1 here now.

@joshmoore

joshmoore commented Jan 27, 2022

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0.17.1 seems to be hanging on 3.9 != 1.21.0 as well.

@joshmoore

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Pushed the commits up to the 0.16.3 pin to #853.

@joshmoorejoshmoore mentioned this pull request Jan 27, 2022
Merged
6 tasks
@jakirkham

jakirkham commented Jan 27, 2022

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The fact that timeout doesn't work makes me wonder if the hang is in C. Is it possible this is NumPy related? Is NumPy 1.22 hanging somewhere? What if we pinned to NumPy 1.20 in the jobs currently skipping 1.21?

@joshmoore
joshmooreforce-pushed the default-write-empty-chunks-false branch from a9fd445 to f222cbeCompareJanuary 27, 2022 13:10
@codecov

codecovBot commented Jan 27, 2022•
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Codecov Report

Merging #951 (a9fd445) into master (e15001b) will decrease coverage by 0.00%.
The diff coverage is n/a.

❗ Current head a9fd445 differs from pull request most recent head 285998e. Consider uploading reports for the commit 285998e to get more accurate results

@@ Coverage Diff @@## master #951 +/- ##
==========================================
- Coverage 99.94% 99.94% -0.01% 
==========================================
Files 32 32 Lines 11225 11134 -91 ==========================================
- Hits 11219 11128 -91 
Misses 6 6
Impacted FilesCoverage Δ
setup.py0.00% <ø> (ø)
zarr/_storage/absstore.py100.00% <ø> (ø)
zarr/core.py100.00% <ø> (ø)
zarr/creation.py100.00% <ø> (ø)
zarr/util.py100.00% <ø> (ø)
zarr/n5.py100.00% <0.00%> (ø)
zarr/storage.py100.00% <0.00%> (ø)
zarr/indexing.py100.00% <0.00%> (ø)
zarr/hierarchy.py100.00% <0.00%> (ø)
... and 11 more

@joshmoore
joshmooreforce-pushed the default-write-empty-chunks-false branch from f222cbe to a062a85CompareJanuary 27, 2022 13:17
@jakirkham

jakirkham commented Jan 28, 2022

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Yeah sorry I think you may be right. Going with 0.16 seems like the right idea. There were deadlock issues in previous 0.17 releases it seems

@joshmoore

joshmoore commented Jan 28, 2022

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Going with 0.16 seems like the right idea.

Yeah, I was feeling pretty good about it until 080a854 timed out again. But perhaps that PR is somehow "tainted".

@jakirkham

jakirkham commented Jan 28, 2022

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Maybe we should run tests with more verbosity? Perhaps that points out which test hangs so we can investigate further

@jakirkham

jakirkham commented Feb 4, 2022

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Power cycling for CI

@jakirkhamjakirkham reopened this Feb 4, 2022
@jakirkham

jakirkham commented Feb 4, 2022•
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Looks like this is going to fail without the NumPy upgrade ( #955 ). Or perhaps the new NumPy conflicts with pinnings we tried here?

@joshmoore

joshmoore commented Feb 4, 2022

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Closing along with #952

Looks like the scare is over.

@joshmoore
joshmoore deleted the default-write-empty-chunks-false branch February 4, 2022 10:03
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@joshmoore@jakirkham@jni@d-v-b
, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all 
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})();
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var __re = new RegExp('^' + "github\\.com" + '

Skip to content
Default write empty chunks false - #951
Closed
joshmoore wants to merge 18 commits into
zarr-developers:masterfrom 
joshmoore:default-write-empty-chunks-false
Closed
Default write empty chunks false#951
joshmoore wants to merge 18 commits into
zarr-developers:masterfrom 
joshmoore:default-write-empty-chunks-false
Conversation
@joshmoore
@joshmoorejoshmoore
commented
Jan 26, 2022

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Re-opening #853 from another branch to see if that fixes the github action jobs.
jniand others
added 12 commits
December 2, 2021 12:48
@jni
Set write_empty_chunks to default to False
6b461a7
@jni
Add release entry for write_empty_chunks default
d09c8d9
@jni
Merge branch 'master' into default-write-empty-chunks-false
a042c8a
@d-v-b
add Empty chunks section to tutorial.rst
5091df0
@joshmoore
Merge branch 'master' into default-write-empty-chunks-false
9d3d83c
@d-v-b
add benchmarky example
21647ab
@d-v-b
Merge branch 'master' ofhttps://github.com/zarr-developers/zarr-python…
b9af4be
… into default-write-empty-chunks-false
@d-v-b
proper formatting of code block
6ad8695
@joshmoore
Fix abstore deprecated strings
422beaa
@joshmoore
Merge branch 'master' into default-write-empty-chunks-false
d27e4ed
@joshmoore
Also catch ValueError in all_equal
1f21139
The call to `np.any(array)` in zarr.util.all_equal triggers the
following ValueError:
```
> return ufunc.reduce(obj, axis, dtype, out, **passkwargs)
E ValueError: invalid literal for int() with base 10: 'baz'
```
Extending the catch block allows test_array_with_categorize_filter
to pass, but it's unclear if this points to a deeper issue.
@joshmoore
Merge branch 'master' into default-write-empty-chunks-false
18971b5
@jakirkham
jakirkham
commented
Jan 26, 2022•

edited

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Also trying a no change PR ( #952 ) to see if this is a CI issue outside of these changes
@joshmoore
joshmoore
commented
Jan 26, 2022

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Fewer are hanging but not nothing. 😵‍💫
@jakirkham
jakirkham
commented
Jan 26, 2022

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It would be good to get a clearer idea on why that is happening. Did we manage to get a log that we could look at? Waited for a while to see if GH Actions would include output, but nothing showed up.
@jni
jni
commented
Jan 27, 2022

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@joshmoore@jakirkham this is very reminiscent of my own misadventures with test_sync, deadlocks, and CI timeouts. @joshmoore want to try your own advice?
#725 (comment)
Usually slow tests are printed at the end, but if they aren't completing we don't get the list! Can you add pytest -sv to the workflow or add pypi.org/project/pytest-timeout so we can get an idea on what's gone sideways?
This commit adds the timeout:
4e7733c (#725)
@joshmoore
joshmoore
commented
Jan 27, 2022

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Heh. I think I thought that that was now done everywhere. Pushing a commit with lots of timeouts here now.
@joshmoore
joshmooreforce-pushed
the
default-write-empty-chunks-false
branch
from
b30abbb to
8b12549CompareJanuary 27, 2022 06:37
@jakirkham
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Jan 27, 2022

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The thing is this hang showed up very recently. It makes me wonder if there is something we changed or a dependency update in the environment that changed, which is causing issues.
For example fasteners was updated recently. To save writing this again, please read this comment ( #952 (comment) ).
@joshmoore
joshmoore
commented
Jan 27, 2022

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MemberAuthor
Interesting that not even timeout seems to be working here.
joshmoore added a commit
to joshmoore/zarr-python
that referenced
this pull request
Jan 27, 2022
@joshmoore
Pin fasteners to 0.16.3 (seezarr-developers#951)
666b500
@joshmoore
joshmooreforce-pushed
the
default-write-empty-chunks-false
branch
from
666b500 to
080a854CompareJanuary 27, 2022 07:35
@joshmoore
joshmoore
commented
Jan 27, 2022

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0.16.3 seemes safe, @jakirkham. Trying 0.17.1 here now.
@joshmoore
joshmoore
commented
Jan 27, 2022

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MemberAuthor
0.17.1 seems to be hanging on 3.9 != 1.21.0 as well.
@joshmoore
joshmoore
commented
Jan 27, 2022

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Pushed the commits up to the 0.16.3 pin to #853.
@joshmoorejoshmoore
mentioned this pull request
Jan 27, 2022
 Merged

6 tasks
@jakirkham
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Jan 27, 2022

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The fact that timeout doesn't work makes me wonder if the hang is in C. Is it possible this is NumPy related? Is NumPy 1.22 hanging somewhere? What if we pinned to NumPy 1.20 in the jobs currently skipping 1.21?
@joshmoore
joshmooreforce-pushed
the
default-write-empty-chunks-false
branch
from
a9fd445 to
f222cbeCompareJanuary 27, 2022 13:10
@codecov
codecovBot
commented
Jan 27, 2022•

edited

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Codecov Report
Merging #951 (a9fd445) into master (e15001b) will decrease coverage by 0.00%.

The diff coverage is n/a.
❗ Current head a9fd445 differs from pull request most recent head 285998e. Consider uploading reports for the commit 285998e to get more accurate results
@@ Coverage Diff @@## master #951 +/- ##
==========================================
- Coverage 99.94% 99.94% -0.01% 
==========================================
Files 32 32 Lines 11225 11134 -91 ==========================================
- Hits 11219 11128 -91 
Misses 6 6 
Impacted FilesCoverage Δ
setup.py0.00% <ø> (ø)
zarr/_storage/absstore.py100.00% <ø> (ø)
zarr/core.py100.00% <ø> (ø)
zarr/creation.py100.00% <ø> (ø)
zarr/util.py100.00% <ø> (ø)
zarr/n5.py100.00% <0.00%> (ø)
zarr/storage.py100.00% <0.00%> (ø)
zarr/indexing.py100.00% <0.00%> (ø)
zarr/hierarchy.py100.00% <0.00%> (ø)
... and 11 more
@joshmoore
joshmooreforce-pushed
the
default-write-empty-chunks-false
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from
f222cbe to
a062a85CompareJanuary 27, 2022 13:17
@jakirkham
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Jan 28, 2022

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Yeah sorry I think you may be right. Going with 0.16 seems like the right idea. There were deadlock issues in previous 0.17 releases it seems
@joshmoore
joshmoore
commented
Jan 28, 2022

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MemberAuthor
Going with 0.16 seems like the right idea.
Yeah, I was feeling pretty good about it until 080a854 timed out again. But perhaps that PR is somehow "tainted".
@jakirkham
jakirkham
commented
Jan 28, 2022

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Maybe we should run tests with more verbosity? Perhaps that points out which test hangs so we can investigate further
@jakirkham
jakirkham
commented
Feb 4, 2022

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Power cycling for CI
@jakirkhamjakirkham
reopened this
Feb 4, 2022
@jakirkham
jakirkham
commented
Feb 4, 2022•

edited

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Looks like this is going to fail without the NumPy upgrade ( #955 ). Or perhaps the new NumPy conflicts with pinnings we tried here?
@joshmoore
joshmoore
commented
Feb 4, 2022

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MemberAuthor
Closing along with #952
Looks like the scare is over.
@joshmoore
joshmoore
deleted the

default-write-empty-chunks-false

branch
February 4, 2022 10:03
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@joshmoore@jakirkham@jni@d-v-b

, 'i');
if (__m === '*' || __re.test(location.href)) {
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})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
Default write empty chunks false - #951
Closed
joshmoore wants to merge 18 commits into
zarr-developers:masterfrom 
joshmoore:default-write-empty-chunks-false
Closed
Default write empty chunks false#951
joshmoore wants to merge 18 commits into
zarr-developers:masterfrom 
joshmoore:default-write-empty-chunks-false
Conversation
@joshmoore
@joshmoorejoshmoore
commented
Jan 26, 2022

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Re-opening #853 from another branch to see if that fixes the github action jobs.
jniand others
added 12 commits
December 2, 2021 12:48
@jni
Set write_empty_chunks to default to False
6b461a7
@jni
Add release entry for write_empty_chunks default
d09c8d9
@jni
Merge branch 'master' into default-write-empty-chunks-false
a042c8a
@d-v-b
add Empty chunks section to tutorial.rst
5091df0
@joshmoore
Merge branch 'master' into default-write-empty-chunks-false
9d3d83c
@d-v-b
add benchmarky example
21647ab
@d-v-b
Merge branch 'master' ofhttps://github.com/zarr-developers/zarr-python…
b9af4be
… into default-write-empty-chunks-false
@d-v-b
proper formatting of code block
6ad8695
@joshmoore
Fix abstore deprecated strings
422beaa
@joshmoore
Merge branch 'master' into default-write-empty-chunks-false
d27e4ed
@joshmoore
Also catch ValueError in all_equal
1f21139
The call to `np.any(array)` in zarr.util.all_equal triggers the
following ValueError:
```
> return ufunc.reduce(obj, axis, dtype, out, **passkwargs)
E ValueError: invalid literal for int() with base 10: 'baz'
```
Extending the catch block allows test_array_with_categorize_filter
to pass, but it's unclear if this points to a deeper issue.
@joshmoore
Merge branch 'master' into default-write-empty-chunks-false
18971b5
@jakirkham
jakirkham
commented
Jan 26, 2022•

edited

Loading

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Member
Also trying a no change PR ( #952 ) to see if this is a CI issue outside of these changes
@joshmoore
joshmoore
commented
Jan 26, 2022

Copy link


Copy Markdown

MemberAuthor
Fewer are hanging but not nothing. 😵‍💫
@jakirkham
jakirkham
commented
Jan 26, 2022

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Copy Markdown

Member
It would be good to get a clearer idea on why that is happening. Did we manage to get a log that we could look at? Waited for a while to see if GH Actions would include output, but nothing showed up.
@jni
jni
commented
Jan 27, 2022

Copy link


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Contributor
@joshmoore@jakirkham this is very reminiscent of my own misadventures with test_sync, deadlocks, and CI timeouts. @joshmoore want to try your own advice?
#725 (comment)
Usually slow tests are printed at the end, but if they aren't completing we don't get the list! Can you add pytest -sv to the workflow or add pypi.org/project/pytest-timeout so we can get an idea on what's gone sideways?
This commit adds the timeout:
4e7733c (#725)
@joshmoore
joshmoore
commented
Jan 27, 2022

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MemberAuthor
Heh. I think I thought that that was now done everywhere. Pushing a commit with lots of timeouts here now.
@joshmoore
joshmooreforce-pushed
the
default-write-empty-chunks-false
branch
from
b30abbb to
8b12549CompareJanuary 27, 2022 06:37
@jakirkham
jakirkham
commented
Jan 27, 2022

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The thing is this hang showed up very recently. It makes me wonder if there is something we changed or a dependency update in the environment that changed, which is causing issues.
For example fasteners was updated recently. To save writing this again, please read this comment ( #952 (comment) ).
@joshmoore
joshmoore
commented
Jan 27, 2022

Copy link


Copy Markdown

MemberAuthor
Interesting that not even timeout seems to be working here.
joshmoore added a commit
to joshmoore/zarr-python
that referenced
this pull request
Jan 27, 2022
@joshmoore
Pin fasteners to 0.16.3 (seezarr-developers#951)
666b500
@joshmoore
joshmooreforce-pushed
the
default-write-empty-chunks-false
branch
from
666b500 to
080a854CompareJanuary 27, 2022 07:35
@joshmoore
joshmoore
commented
Jan 27, 2022

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MemberAuthor
0.16.3 seemes safe, @jakirkham. Trying 0.17.1 here now.
@joshmoore
joshmoore
commented
Jan 27, 2022

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MemberAuthor
0.17.1 seems to be hanging on 3.9 != 1.21.0 as well.
@joshmoore
joshmoore
commented
Jan 27, 2022

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MemberAuthor
Pushed the commits up to the 0.16.3 pin to #853.
@joshmoorejoshmoore
mentioned this pull request
Jan 27, 2022
 Merged

6 tasks
@jakirkham
jakirkham
commented
Jan 27, 2022

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The fact that timeout doesn't work makes me wonder if the hang is in C. Is it possible this is NumPy related? Is NumPy 1.22 hanging somewhere? What if we pinned to NumPy 1.20 in the jobs currently skipping 1.21?
@joshmoore
joshmooreforce-pushed
the
default-write-empty-chunks-false
branch
from
a9fd445 to
f222cbeCompareJanuary 27, 2022 13:10
@codecov
codecovBot
commented
Jan 27, 2022•

edited

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Codecov Report
Merging #951 (a9fd445) into master (e15001b) will decrease coverage by 0.00%.

The diff coverage is n/a.
❗ Current head a9fd445 differs from pull request most recent head 285998e. Consider uploading reports for the commit 285998e to get more accurate results
@@ Coverage Diff @@## master #951 +/- ##
==========================================
- Coverage 99.94% 99.94% -0.01% 
==========================================
Files 32 32 Lines 11225 11134 -91 ==========================================
- Hits 11219 11128 -91 
Misses 6 6 
Impacted FilesCoverage Δ
setup.py0.00% <ø> (ø)
zarr/_storage/absstore.py100.00% <ø> (ø)
zarr/core.py100.00% <ø> (ø)
zarr/creation.py100.00% <ø> (ø)
zarr/util.py100.00% <ø> (ø)
zarr/n5.py100.00% <0.00%> (ø)
zarr/storage.py100.00% <0.00%> (ø)
zarr/indexing.py100.00% <0.00%> (ø)
zarr/hierarchy.py100.00% <0.00%> (ø)
... and 11 more
@joshmoore
joshmooreforce-pushed
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@jakirkham
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Yeah sorry I think you may be right. Going with 0.16 seems like the right idea. There were deadlock issues in previous 0.17 releases it seems
@joshmoore
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Going with 0.16 seems like the right idea.
Yeah, I was feeling pretty good about it until 080a854 timed out again. But perhaps that PR is somehow "tainted".
@jakirkham
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Maybe we should run tests with more verbosity? Perhaps that points out which test hangs so we can investigate further
@jakirkham
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Power cycling for CI
@jakirkhamjakirkham
reopened this
Feb 4, 2022
@jakirkham
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Looks like this is going to fail without the NumPy upgrade ( #955 ). Or perhaps the new NumPy conflicts with pinnings we tried here?
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Closing along with #952
Looks like the scare is over.
@joshmoore
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deleted the

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branch
February 4, 2022 10:03
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@joshmoore@jakirkham@jni@d-v-b

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Highlight search terms from Google/DuckDuckGo/Bing referrer\n(function() {\n var ref = document.referrer;\n var terms = [];\n \n if (ref.includes('google.com') || ref.includes('duckduckgo.com') || ref.includes('bing.com')) {\n var url = new URL(ref);\n var q = url.searchParams.get('q') || url.searchParams.get('p');\n if (q) {\n terms = q.split(/\\s+/).filter(function(t) { return t.length > 2; });\n }\n }\n \n if (terms.length === 0) return;\n \n var style = document.createElement('style');\n style.textContent = '.userscript-highlight { background: #fbbf24; color: #1a1a2e; padding: 1px 3px; border-radius: 2px; }';\n document.head.appendChild(style);\n \n function highlight(node) {\n if (node.nodeType === 3) { // text node\n var text = node.textContent;\n var found = false;\n terms.forEach(function(term) {\n var regex = new RegExp('(' + term.replace(/[.*+?^${}()|[\\]\\\\]/g, '\\\\') + ')', 'gi');\n if (regex.test(text)) {\n found = true;\n var frag = document.createDocumentFragment();\n var parts = text.split(regex);\n parts.forEach(function(part, i) {\n if (i % 2 === 0) {\n frag.appendChild(document.createTextNode(part));\n } else {\n var span = document.createElement('span');\n span.className = 'userscript-highlight';\n span.textContent = part;\n frag.appendChild(span);\n }\n });\n node.parentNode.replaceChild(frag, node);\n }\n });\n } else if (node.nodeType === 1 && node.childNodes) { // element\n var skipTags = ['SCRIPT', 'STYLE', 'NOSCRIPT', 'TEXTAREA', 'INPUT', 'SELECT'];\n if (!skipTags.includes(node.tagName)) {\n Array.from(node.childNodes).forEach(highlight);\n }\n }\n }\n \n highlight(document.body);\n \n // Re-highlight on dynamic content\n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1 || node.nodeType === 3) highlight(node);\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Highlight Search Terms");
}
} catch(__e) { console.warn('[Userscript:Highlight Search Terms]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
Default write empty chunks false - #951
Closed
joshmoore wants to merge 18 commits into
zarr-developers:masterfrom 
joshmoore:default-write-empty-chunks-false
Closed
Default write empty chunks false#951
joshmoore wants to merge 18 commits into
zarr-developers:masterfrom 
joshmoore:default-write-empty-chunks-false
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@joshmoore
@joshmoorejoshmoore
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Jan 26, 2022

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Re-opening #853 from another branch to see if that fixes the github action jobs.
jniand others
added 12 commits
December 2, 2021 12:48
@jni
Set write_empty_chunks to default to False
6b461a7
@jni
Add release entry for write_empty_chunks default
d09c8d9
@jni
Merge branch 'master' into default-write-empty-chunks-false
a042c8a
@d-v-b
add Empty chunks section to tutorial.rst
5091df0
@joshmoore
Merge branch 'master' into default-write-empty-chunks-false
9d3d83c
@d-v-b
add benchmarky example
21647ab
@d-v-b
Merge branch 'master' ofhttps://github.com/zarr-developers/zarr-python…
b9af4be
… into default-write-empty-chunks-false
@d-v-b
proper formatting of code block
6ad8695
@joshmoore
Fix abstore deprecated strings
422beaa
@joshmoore
Merge branch 'master' into default-write-empty-chunks-false
d27e4ed
@joshmoore
Also catch ValueError in all_equal
1f21139
The call to `np.any(array)` in zarr.util.all_equal triggers the
following ValueError:
```
> return ufunc.reduce(obj, axis, dtype, out, **passkwargs)
E ValueError: invalid literal for int() with base 10: 'baz'
```
Extending the catch block allows test_array_with_categorize_filter
to pass, but it's unclear if this points to a deeper issue.
@joshmoore
Merge branch 'master' into default-write-empty-chunks-false
18971b5
@jakirkham
jakirkham
commented
Jan 26, 2022•

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Also trying a no change PR ( #952 ) to see if this is a CI issue outside of these changes
@joshmoore
joshmoore
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Jan 26, 2022

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Fewer are hanging but not nothing. 😵‍💫
@jakirkham
jakirkham
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Jan 26, 2022

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It would be good to get a clearer idea on why that is happening. Did we manage to get a log that we could look at? Waited for a while to see if GH Actions would include output, but nothing showed up.
@jni
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@joshmoore@jakirkham this is very reminiscent of my own misadventures with test_sync, deadlocks, and CI timeouts. @joshmoore want to try your own advice?
#725 (comment)
Usually slow tests are printed at the end, but if they aren't completing we don't get the list! Can you add pytest -sv to the workflow or add pypi.org/project/pytest-timeout so we can get an idea on what's gone sideways?
This commit adds the timeout:
4e7733c (#725)
@joshmoore
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Heh. I think I thought that that was now done everywhere. Pushing a commit with lots of timeouts here now.
@joshmoore
joshmooreforce-pushed
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@jakirkham
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The thing is this hang showed up very recently. It makes me wonder if there is something we changed or a dependency update in the environment that changed, which is causing issues.
For example fasteners was updated recently. To save writing this again, please read this comment ( #952 (comment) ).
@joshmoore
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Interesting that not even timeout seems to be working here.
joshmoore added a commit
to joshmoore/zarr-python
that referenced
this pull request
Jan 27, 2022
@joshmoore
Pin fasteners to 0.16.3 (seezarr-developers#951)
666b500
@joshmoore
joshmooreforce-pushed
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from
666b500 to
080a854CompareJanuary 27, 2022 07:35
@joshmoore
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0.16.3 seemes safe, @jakirkham. Trying 0.17.1 here now.
@joshmoore
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Jan 27, 2022

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0.17.1 seems to be hanging on 3.9 != 1.21.0 as well.
@joshmoore
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Pushed the commits up to the 0.16.3 pin to #853.
@joshmoorejoshmoore
mentioned this pull request
Jan 27, 2022
 Merged

6 tasks
@jakirkham
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The fact that timeout doesn't work makes me wonder if the hang is in C. Is it possible this is NumPy related? Is NumPy 1.22 hanging somewhere? What if we pinned to NumPy 1.20 in the jobs currently skipping 1.21?
@joshmoore
joshmooreforce-pushed
the
default-write-empty-chunks-false
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from
a9fd445 to
f222cbeCompareJanuary 27, 2022 13:10
@codecov
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Jan 27, 2022•

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Codecov Report
Merging #951 (a9fd445) into master (e15001b) will decrease coverage by 0.00%.

The diff coverage is n/a.
❗ Current head a9fd445 differs from pull request most recent head 285998e. Consider uploading reports for the commit 285998e to get more accurate results
@@ Coverage Diff @@## master #951 +/- ##
==========================================
- Coverage 99.94% 99.94% -0.01% 
==========================================
Files 32 32 Lines 11225 11134 -91 ==========================================
- Hits 11219 11128 -91 
Misses 6 6 
Impacted FilesCoverage Δ
setup.py0.00% <ø> (ø)
zarr/_storage/absstore.py100.00% <ø> (ø)
zarr/core.py100.00% <ø> (ø)
zarr/creation.py100.00% <ø> (ø)
zarr/util.py100.00% <ø> (ø)
zarr/n5.py100.00% <0.00%> (ø)
zarr/storage.py100.00% <0.00%> (ø)
zarr/indexing.py100.00% <0.00%> (ø)
zarr/hierarchy.py100.00% <0.00%> (ø)
... and 11 more
@joshmoore
joshmooreforce-pushed
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@jakirkham
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Yeah sorry I think you may be right. Going with 0.16 seems like the right idea. There were deadlock issues in previous 0.17 releases it seems
@joshmoore
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Jan 28, 2022

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Going with 0.16 seems like the right idea.
Yeah, I was feeling pretty good about it until 080a854 timed out again. But perhaps that PR is somehow "tainted".
@jakirkham
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Jan 28, 2022

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Maybe we should run tests with more verbosity? Perhaps that points out which test hangs so we can investigate further
@jakirkham
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Feb 4, 2022

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Power cycling for CI
@jakirkhamjakirkham
reopened this
Feb 4, 2022
@jakirkham
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Feb 4, 2022•

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Looks like this is going to fail without the NumPy upgrade ( #955 ). Or perhaps the new NumPy conflicts with pinnings we tried here?
@joshmoore
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Feb 4, 2022

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Closing along with #952
Looks like the scare is over.
@joshmoore
joshmoore
deleted the

default-write-empty-chunks-false

branch
February 4, 2022 10:03
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@joshmoore@jakirkham@jni@d-v-b

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Strip utm_, fbclid, gclid, etc. from all links on page\n(function() {\n var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',\n 'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',\n 'ref', 'ref_src', 'source', 'medium', 'campaign'];\n \n function cleanUrl(url) {\n try {\n var u = new URL(url, window.location.origin);\n var changed = false;\n trackingParams.forEach(function(p) {\n if (u.searchParams.has(p)) {\n u.searchParams.delete(p);\n changed = true;\n }\n });\n return changed ? u.toString() : url;\n } catch (e) {\n return url;\n }\n }\n \n function cleanLinks() {\n document.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n \n cleanLinks();\n \n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1) {\n if (node.tagName === 'A') cleanLinks();\n node.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Remove Tracking Parameters from Links");
}
} catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); }
})();
(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '

Skip to content
Default write empty chunks false - #951
Closed
joshmoore wants to merge 18 commits into
zarr-developers:masterfrom 
joshmoore:default-write-empty-chunks-false
Closed
Default write empty chunks false#951
joshmoore wants to merge 18 commits into
zarr-developers:masterfrom 
joshmoore:default-write-empty-chunks-false
Conversation
@joshmoore
@joshmoorejoshmoore
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Re-opening #853 from another branch to see if that fixes the github action jobs.
jniand others
added 12 commits
December 2, 2021 12:48
@jni
Set write_empty_chunks to default to False
6b461a7
@jni
Add release entry for write_empty_chunks default
d09c8d9
@jni
Merge branch 'master' into default-write-empty-chunks-false
a042c8a
@d-v-b
add Empty chunks section to tutorial.rst
5091df0
@joshmoore
Merge branch 'master' into default-write-empty-chunks-false
9d3d83c
@d-v-b
add benchmarky example
21647ab
@d-v-b
Merge branch 'master' ofhttps://github.com/zarr-developers/zarr-python…
b9af4be
… into default-write-empty-chunks-false
@d-v-b
proper formatting of code block
6ad8695
@joshmoore
Fix abstore deprecated strings
422beaa
@joshmoore
Merge branch 'master' into default-write-empty-chunks-false
d27e4ed
@joshmoore
Also catch ValueError in all_equal
1f21139
The call to `np.any(array)` in zarr.util.all_equal triggers the
following ValueError:
```
> return ufunc.reduce(obj, axis, dtype, out, **passkwargs)
E ValueError: invalid literal for int() with base 10: 'baz'
```
Extending the catch block allows test_array_with_categorize_filter
to pass, but it's unclear if this points to a deeper issue.
@joshmoore
Merge branch 'master' into default-write-empty-chunks-false
18971b5
@jakirkham
jakirkham
commented
Jan 26, 2022•

edited

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Also trying a no change PR ( #952 ) to see if this is a CI issue outside of these changes
@joshmoore
joshmoore
commented
Jan 26, 2022

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MemberAuthor
Fewer are hanging but not nothing. 😵‍💫
@jakirkham
jakirkham
commented
Jan 26, 2022

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Member
It would be good to get a clearer idea on why that is happening. Did we manage to get a log that we could look at? Waited for a while to see if GH Actions would include output, but nothing showed up.
@jni
jni
commented
Jan 27, 2022

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@joshmoore@jakirkham this is very reminiscent of my own misadventures with test_sync, deadlocks, and CI timeouts. @joshmoore want to try your own advice?
#725 (comment)
Usually slow tests are printed at the end, but if they aren't completing we don't get the list! Can you add pytest -sv to the workflow or add pypi.org/project/pytest-timeout so we can get an idea on what's gone sideways?
This commit adds the timeout:
4e7733c (#725)
@joshmoore
joshmoore
commented
Jan 27, 2022

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Heh. I think I thought that that was now done everywhere. Pushing a commit with lots of timeouts here now.
@joshmoore
joshmooreforce-pushed
the
default-write-empty-chunks-false
branch
from
b30abbb to
8b12549CompareJanuary 27, 2022 06:37
@jakirkham
jakirkham
commented
Jan 27, 2022

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The thing is this hang showed up very recently. It makes me wonder if there is something we changed or a dependency update in the environment that changed, which is causing issues.
For example fasteners was updated recently. To save writing this again, please read this comment ( #952 (comment) ).
@joshmoore
joshmoore
commented
Jan 27, 2022

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MemberAuthor
Interesting that not even timeout seems to be working here.
joshmoore added a commit
to joshmoore/zarr-python
that referenced
this pull request
Jan 27, 2022
@joshmoore
Pin fasteners to 0.16.3 (seezarr-developers#951)
666b500
@joshmoore
joshmooreforce-pushed
the
default-write-empty-chunks-false
branch
from
666b500 to
080a854CompareJanuary 27, 2022 07:35
@joshmoore
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Jan 27, 2022

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0.16.3 seemes safe, @jakirkham. Trying 0.17.1 here now.
@joshmoore
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commented
Jan 27, 2022

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0.17.1 seems to be hanging on 3.9 != 1.21.0 as well.
@joshmoore
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commented
Jan 27, 2022

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Pushed the commits up to the 0.16.3 pin to #853.
@joshmoorejoshmoore
mentioned this pull request
Jan 27, 2022
 Merged

6 tasks
@jakirkham
jakirkham
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Jan 27, 2022

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The fact that timeout doesn't work makes me wonder if the hang is in C. Is it possible this is NumPy related? Is NumPy 1.22 hanging somewhere? What if we pinned to NumPy 1.20 in the jobs currently skipping 1.21?
@joshmoore
joshmooreforce-pushed
the
default-write-empty-chunks-false
branch
from
a9fd445 to
f222cbeCompareJanuary 27, 2022 13:10
@codecov
codecovBot
commented
Jan 27, 2022•

edited

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Codecov Report
Merging #951 (a9fd445) into master (e15001b) will decrease coverage by 0.00%.

The diff coverage is n/a.
❗ Current head a9fd445 differs from pull request most recent head 285998e. Consider uploading reports for the commit 285998e to get more accurate results
@@ Coverage Diff @@## master #951 +/- ##
==========================================
- Coverage 99.94% 99.94% -0.01% 
==========================================
Files 32 32 Lines 11225 11134 -91 ==========================================
- Hits 11219 11128 -91 
Misses 6 6 
Impacted FilesCoverage Δ
setup.py0.00% <ø> (ø)
zarr/_storage/absstore.py100.00% <ø> (ø)
zarr/core.py100.00% <ø> (ø)
zarr/creation.py100.00% <ø> (ø)
zarr/util.py100.00% <ø> (ø)
zarr/n5.py100.00% <0.00%> (ø)
zarr/storage.py100.00% <0.00%> (ø)
zarr/indexing.py100.00% <0.00%> (ø)
zarr/hierarchy.py100.00% <0.00%> (ø)
... and 11 more
@joshmoore
joshmooreforce-pushed
the
default-write-empty-chunks-false
branch
from
f222cbe to
a062a85CompareJanuary 27, 2022 13:17
@jakirkham
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Jan 28, 2022

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Yeah sorry I think you may be right. Going with 0.16 seems like the right idea. There were deadlock issues in previous 0.17 releases it seems
@joshmoore
joshmoore
commented
Jan 28, 2022

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MemberAuthor
Going with 0.16 seems like the right idea.
Yeah, I was feeling pretty good about it until 080a854 timed out again. But perhaps that PR is somehow "tainted".
@jakirkham
jakirkham
commented
Jan 28, 2022

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Maybe we should run tests with more verbosity? Perhaps that points out which test hangs so we can investigate further
@jakirkham
jakirkham
commented
Feb 4, 2022

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Power cycling for CI
@jakirkhamjakirkham
reopened this
Feb 4, 2022
@jakirkham
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commented
Feb 4, 2022•

edited

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Looks like this is going to fail without the NumPy upgrade ( #955 ). Or perhaps the new NumPy conflicts with pinnings we tried here?
@joshmoore
joshmoore
commented
Feb 4, 2022

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Closing along with #952
Looks like the scare is over.
@joshmoore
joshmoore
deleted the

default-write-empty-chunks-false

branch
February 4, 2022 10:03
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@joshmoore@jakirkham@jni@d-v-b

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Auto-enable theater mode on YouTube\n(function() {\n function tryTheater() {\n var btn = document.querySelector('button[aria-label=\"Theater mode\"], ytd-player #player button[title=\"Theater mode\"]');\n if (btn && !btn.classList.contains('activated')) {\n btn.click();\n }\n }\n \n // Try immediately\n tryTheater();\n \n // Try after navigation (SPA)\n var lastUrl = location.href;\n setInterval(function() {\n if (location.href !== lastUrl) {\n lastUrl = location.href;\n setTimeout(tryTheater, 500);\n }\n }, 1000);\n \n // Also try on player load\n var observer = new MutationObserver(tryTheater);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "YouTube Theater Mode Default");
}
} catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
Default write empty chunks false - #951
Closed
joshmoore wants to merge 18 commits into
zarr-developers:masterfrom 
joshmoore:default-write-empty-chunks-false
Closed
Default write empty chunks false#951
joshmoore wants to merge 18 commits into
zarr-developers:masterfrom 
joshmoore:default-write-empty-chunks-false
Conversation
@joshmoore
@joshmoorejoshmoore
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Jan 26, 2022

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Re-opening #853 from another branch to see if that fixes the github action jobs.
jniand others
added 12 commits
December 2, 2021 12:48
@jni
Set write_empty_chunks to default to False
6b461a7
@jni
Add release entry for write_empty_chunks default
d09c8d9
@jni
Merge branch 'master' into default-write-empty-chunks-false
a042c8a
@d-v-b
add Empty chunks section to tutorial.rst
5091df0
@joshmoore
Merge branch 'master' into default-write-empty-chunks-false
9d3d83c
@d-v-b
add benchmarky example
21647ab
@d-v-b
Merge branch 'master' ofhttps://github.com/zarr-developers/zarr-python…
b9af4be
… into default-write-empty-chunks-false
@d-v-b
proper formatting of code block
6ad8695
@joshmoore
Fix abstore deprecated strings
422beaa
@joshmoore
Merge branch 'master' into default-write-empty-chunks-false
d27e4ed
@joshmoore
Also catch ValueError in all_equal
1f21139
The call to `np.any(array)` in zarr.util.all_equal triggers the
following ValueError:
```
> return ufunc.reduce(obj, axis, dtype, out, **passkwargs)
E ValueError: invalid literal for int() with base 10: 'baz'
```
Extending the catch block allows test_array_with_categorize_filter
to pass, but it's unclear if this points to a deeper issue.
@joshmoore
Merge branch 'master' into default-write-empty-chunks-false
18971b5
@jakirkham
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commented
Jan 26, 2022•

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Also trying a no change PR ( #952 ) to see if this is a CI issue outside of these changes
@joshmoore
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Jan 26, 2022

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Fewer are hanging but not nothing. 😵‍💫
@jakirkham
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It would be good to get a clearer idea on why that is happening. Did we manage to get a log that we could look at? Waited for a while to see if GH Actions would include output, but nothing showed up.
@jni
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@joshmoore@jakirkham this is very reminiscent of my own misadventures with test_sync, deadlocks, and CI timeouts. @joshmoore want to try your own advice?
#725 (comment)
Usually slow tests are printed at the end, but if they aren't completing we don't get the list! Can you add pytest -sv to the workflow or add pypi.org/project/pytest-timeout so we can get an idea on what's gone sideways?
This commit adds the timeout:
4e7733c (#725)
@joshmoore
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Jan 27, 2022

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Heh. I think I thought that that was now done everywhere. Pushing a commit with lots of timeouts here now.
@joshmoore
joshmooreforce-pushed
the
default-write-empty-chunks-false
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from
b30abbb to
8b12549CompareJanuary 27, 2022 06:37
@jakirkham
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Jan 27, 2022

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The thing is this hang showed up very recently. It makes me wonder if there is something we changed or a dependency update in the environment that changed, which is causing issues.
For example fasteners was updated recently. To save writing this again, please read this comment ( #952 (comment) ).
@joshmoore
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Jan 27, 2022

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Interesting that not even timeout seems to be working here.
joshmoore added a commit
to joshmoore/zarr-python
that referenced
this pull request
Jan 27, 2022
@joshmoore
Pin fasteners to 0.16.3 (seezarr-developers#951)
666b500
@joshmoore
joshmooreforce-pushed
the
default-write-empty-chunks-false
branch
from
666b500 to
080a854CompareJanuary 27, 2022 07:35
@joshmoore
joshmoore
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Jan 27, 2022

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0.16.3 seemes safe, @jakirkham. Trying 0.17.1 here now.
@joshmoore
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Jan 27, 2022

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0.17.1 seems to be hanging on 3.9 != 1.21.0 as well.
@joshmoore
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Jan 27, 2022

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Pushed the commits up to the 0.16.3 pin to #853.
@joshmoorejoshmoore
mentioned this pull request
Jan 27, 2022
 Merged

6 tasks
@jakirkham
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Jan 27, 2022

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The fact that timeout doesn't work makes me wonder if the hang is in C. Is it possible this is NumPy related? Is NumPy 1.22 hanging somewhere? What if we pinned to NumPy 1.20 in the jobs currently skipping 1.21?
@joshmoore
joshmooreforce-pushed
the
default-write-empty-chunks-false
branch
from
a9fd445 to
f222cbeCompareJanuary 27, 2022 13:10
@codecov
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Jan 27, 2022•

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Codecov Report
Merging #951 (a9fd445) into master (e15001b) will decrease coverage by 0.00%.

The diff coverage is n/a.
❗ Current head a9fd445 differs from pull request most recent head 285998e. Consider uploading reports for the commit 285998e to get more accurate results
@@ Coverage Diff @@## master #951 +/- ##
==========================================
- Coverage 99.94% 99.94% -0.01% 
==========================================
Files 32 32 Lines 11225 11134 -91 ==========================================
- Hits 11219 11128 -91 
Misses 6 6 
Impacted FilesCoverage Δ
setup.py0.00% <ø> (ø)
zarr/_storage/absstore.py100.00% <ø> (ø)
zarr/core.py100.00% <ø> (ø)
zarr/creation.py100.00% <ø> (ø)
zarr/util.py100.00% <ø> (ø)
zarr/n5.py100.00% <0.00%> (ø)
zarr/storage.py100.00% <0.00%> (ø)
zarr/indexing.py100.00% <0.00%> (ø)
zarr/hierarchy.py100.00% <0.00%> (ø)
... and 11 more
@joshmoore
joshmooreforce-pushed
the
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a062a85CompareJanuary 27, 2022 13:17
@jakirkham
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Yeah sorry I think you may be right. Going with 0.16 seems like the right idea. There were deadlock issues in previous 0.17 releases it seems
@joshmoore
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Going with 0.16 seems like the right idea.
Yeah, I was feeling pretty good about it until 080a854 timed out again. But perhaps that PR is somehow "tainted".
@jakirkham
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Maybe we should run tests with more verbosity? Perhaps that points out which test hangs so we can investigate further
@jakirkham
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Feb 4, 2022

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Power cycling for CI
@jakirkhamjakirkham
reopened this
Feb 4, 2022
@jakirkham
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Feb 4, 2022•

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Looks like this is going to fail without the NumPy upgrade ( #955 ). Or perhaps the new NumPy conflicts with pinnings we tried here?
@joshmoore
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Feb 4, 2022

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Closing along with #952
Looks like the scare is over.
@joshmoore
joshmoore
deleted the

default-write-empty-chunks-false

branch
February 4, 2022 10:03
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@joshmoore@jakirkham@jni@d-v-b

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Remove or un-stick sticky/fixed headers that block content\n(function() {\n function unstick() {\n document.querySelectorAll('header, nav, [role=\"banner\"], .header, .navbar, .sticky, .fixed-top, [style*=\"position: fixed\"], [style*=\"position:sticky\"]').forEach(function(el) {\n if (el.style.position === 'fixed' || el.style.position === 'sticky' || \n getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {\n el.style.position = 'static';\n el.style.top = 'auto';\n el.style.zIndex = 'auto';\n }\n });\n }\n \n unstick();\n \n var observer = new MutationObserver(unstick);\n observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });\n})();", "Kill Sticky Headers");
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})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
Default write empty chunks false - #951
Closed
joshmoore wants to merge 18 commits into
zarr-developers:masterfrom 
joshmoore:default-write-empty-chunks-false
Closed
Default write empty chunks false#951
joshmoore wants to merge 18 commits into
zarr-developers:masterfrom 
joshmoore:default-write-empty-chunks-false
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@joshmoore
@joshmoorejoshmoore
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Jan 26, 2022

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Re-opening #853 from another branch to see if that fixes the github action jobs.
jniand others
added 12 commits
December 2, 2021 12:48
@jni
Set write_empty_chunks to default to False
6b461a7
@jni
Add release entry for write_empty_chunks default
d09c8d9
@jni
Merge branch 'master' into default-write-empty-chunks-false
a042c8a
@d-v-b
add Empty chunks section to tutorial.rst
5091df0
@joshmoore
Merge branch 'master' into default-write-empty-chunks-false
9d3d83c
@d-v-b
add benchmarky example
21647ab
@d-v-b
Merge branch 'master' ofhttps://github.com/zarr-developers/zarr-python…
b9af4be
… into default-write-empty-chunks-false
@d-v-b
proper formatting of code block
6ad8695
@joshmoore
Fix abstore deprecated strings
422beaa
@joshmoore
Merge branch 'master' into default-write-empty-chunks-false
d27e4ed
@joshmoore
Also catch ValueError in all_equal
1f21139
The call to `np.any(array)` in zarr.util.all_equal triggers the
following ValueError:
```
> return ufunc.reduce(obj, axis, dtype, out, **passkwargs)
E ValueError: invalid literal for int() with base 10: 'baz'
```
Extending the catch block allows test_array_with_categorize_filter
to pass, but it's unclear if this points to a deeper issue.
@joshmoore
Merge branch 'master' into default-write-empty-chunks-false
18971b5
@jakirkham
jakirkham
commented
Jan 26, 2022•

edited

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Also trying a no change PR ( #952 ) to see if this is a CI issue outside of these changes
@joshmoore
joshmoore
commented
Jan 26, 2022

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Fewer are hanging but not nothing. 😵‍💫
@jakirkham
jakirkham
commented
Jan 26, 2022

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It would be good to get a clearer idea on why that is happening. Did we manage to get a log that we could look at? Waited for a while to see if GH Actions would include output, but nothing showed up.
@jni
jni
commented
Jan 27, 2022

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@joshmoore@jakirkham this is very reminiscent of my own misadventures with test_sync, deadlocks, and CI timeouts. @joshmoore want to try your own advice?
#725 (comment)
Usually slow tests are printed at the end, but if they aren't completing we don't get the list! Can you add pytest -sv to the workflow or add pypi.org/project/pytest-timeout so we can get an idea on what's gone sideways?
This commit adds the timeout:
4e7733c (#725)
@joshmoore
joshmoore
commented
Jan 27, 2022

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Heh. I think I thought that that was now done everywhere. Pushing a commit with lots of timeouts here now.
@joshmoore
joshmooreforce-pushed
the
default-write-empty-chunks-false
branch
from
b30abbb to
8b12549CompareJanuary 27, 2022 06:37
@jakirkham
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Jan 27, 2022

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The thing is this hang showed up very recently. It makes me wonder if there is something we changed or a dependency update in the environment that changed, which is causing issues.
For example fasteners was updated recently. To save writing this again, please read this comment ( #952 (comment) ).
@joshmoore
joshmoore
commented
Jan 27, 2022

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Interesting that not even timeout seems to be working here.
joshmoore added a commit
to joshmoore/zarr-python
that referenced
this pull request
Jan 27, 2022
@joshmoore
Pin fasteners to 0.16.3 (seezarr-developers#951)
666b500
@joshmoore
joshmooreforce-pushed
the
default-write-empty-chunks-false
branch
from
666b500 to
080a854CompareJanuary 27, 2022 07:35
@joshmoore
joshmoore
commented
Jan 27, 2022

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0.16.3 seemes safe, @jakirkham. Trying 0.17.1 here now.
@joshmoore
joshmoore
commented
Jan 27, 2022

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0.17.1 seems to be hanging on 3.9 != 1.21.0 as well.
@joshmoore
joshmoore
commented
Jan 27, 2022

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MemberAuthor
Pushed the commits up to the 0.16.3 pin to #853.
@joshmoorejoshmoore
mentioned this pull request
Jan 27, 2022
 Merged

6 tasks
@jakirkham
jakirkham
commented
Jan 27, 2022

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The fact that timeout doesn't work makes me wonder if the hang is in C. Is it possible this is NumPy related? Is NumPy 1.22 hanging somewhere? What if we pinned to NumPy 1.20 in the jobs currently skipping 1.21?
@joshmoore
joshmooreforce-pushed
the
default-write-empty-chunks-false
branch
from
a9fd445 to
f222cbeCompareJanuary 27, 2022 13:10
@codecov
codecovBot
commented
Jan 27, 2022•

edited

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Codecov Report
Merging #951 (a9fd445) into master (e15001b) will decrease coverage by 0.00%.

The diff coverage is n/a.
❗ Current head a9fd445 differs from pull request most recent head 285998e. Consider uploading reports for the commit 285998e to get more accurate results
@@ Coverage Diff @@## master #951 +/- ##
==========================================
- Coverage 99.94% 99.94% -0.01% 
==========================================
Files 32 32 Lines 11225 11134 -91 ==========================================
- Hits 11219 11128 -91 
Misses 6 6 
Impacted FilesCoverage Δ
setup.py0.00% <ø> (ø)
zarr/_storage/absstore.py100.00% <ø> (ø)
zarr/core.py100.00% <ø> (ø)
zarr/creation.py100.00% <ø> (ø)
zarr/util.py100.00% <ø> (ø)
zarr/n5.py100.00% <0.00%> (ø)
zarr/storage.py100.00% <0.00%> (ø)
zarr/indexing.py100.00% <0.00%> (ø)
zarr/hierarchy.py100.00% <0.00%> (ø)
... and 11 more
@joshmoore
joshmooreforce-pushed
the
default-write-empty-chunks-false
branch
from
f222cbe to
a062a85CompareJanuary 27, 2022 13:17
@jakirkham
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Jan 28, 2022

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Yeah sorry I think you may be right. Going with 0.16 seems like the right idea. There were deadlock issues in previous 0.17 releases it seems
@joshmoore
joshmoore
commented
Jan 28, 2022

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Going with 0.16 seems like the right idea.
Yeah, I was feeling pretty good about it until 080a854 timed out again. But perhaps that PR is somehow "tainted".
@jakirkham
jakirkham
commented
Jan 28, 2022

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Maybe we should run tests with more verbosity? Perhaps that points out which test hangs so we can investigate further
@jakirkham
jakirkham
commented
Feb 4, 2022

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Power cycling for CI
@jakirkhamjakirkham
reopened this
Feb 4, 2022
@jakirkham
jakirkham
commented
Feb 4, 2022•

edited

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Looks like this is going to fail without the NumPy upgrade ( #955 ). Or perhaps the new NumPy conflicts with pinnings we tried here?
@joshmoore
joshmoore
commented
Feb 4, 2022

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Closing along with #952
Looks like the scare is over.
@joshmoore
joshmoore
deleted the

default-write-empty-chunks-false

branch
February 4, 2022 10:03
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@joshmoore@jakirkham@jni@d-v-b

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Universal Dark Mode - works on any site\n(function() {\n var enabled = true;\n \n function applyDarkMode() {\n if (!enabled) return;\n \n // Create style element if it doesn't exist\n var style = document.getElementById('universal-dark-mode-style');\n if (!style) {\n style = document.createElement('style');\n style.id = 'universal-dark-mode-style';\n document.head.appendChild(style);\n }\n \n // Dark mode CSS - inverts colors but preserves images/video\n style.textContent = '\n /* Invert everything except media */\n html {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #1a1a2e !important;\n }\n \n /* Restore images, videos, iframes, canvas */\n img, video, iframe, canvas, svg, picture, [style*=\"background-image\"] {\n filter: invert(1) hue-rotate(180deg) !important;\n }\n \n /* Preserve specific elements that should not be inverted */\n .no-dark-mode, .no-dark-mode *,\n [data-theme=\"light\"], [data-theme=\"light\"],\n .ace_editor, .ace_editor *,\n .CodeMirror, .CodeMirror *,\n .monaco-editor, .monaco-editor *,\n .markdown-body pre, .markdown-body pre *,\n .highlight, .highlight *,\n pre code, pre code * {\n filter: none !important;\n }\n \n /* Fix common UI elements */\n .modal, .popup, .dropdown-menu, .tooltip, .popover {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #2d2d44 !important;\n border-color: #444 !important;\n }\n \n /* Scrollbars */\n ::-webkit-scrollbar { background: #1a1a2e !important; }\n ::-webkit-scrollbar-thumb { background: #444 !important; }\n ::-webkit-scrollbar-thumb:hover { background: #555 !important; }\n \n /* Selection */\n ::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ';\n }\n \n function removeDarkMode() {\n var style = document.getElementById('universal-dark-mode-style');\n if (style) style.remove();\n }\n \n // Toggle with Alt+Shift+D\n document.addEventListener('keydown', function(e) {\n if (e.altKey && e.shiftKey && e.key === 'D') {\n e.preventDefault();\n enabled = !enabled;\n if (enabled) {\n applyDarkMode();\n console.log('[Universal Dark Mode] Enabled');\n } else {\n removeDarkMode();\n console.log('[Universal Dark Mode] Disabled');\n }\n }\n });\n \n // Apply on load\n applyDarkMode();\n \n // Re-apply on dynamic content\n var observer = new MutationObserver(function(mutations) {\n if (enabled && !document.getElementById('universal-dark-mode-style')) {\n applyDarkMode();\n }\n });\n observer.observe(document.head, { childList: true });\n \n console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');\n})();", "Universal Dark Mode");
}
} catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); }
})();
})();

Skip to content
Default write empty chunks false - #951
Closed
joshmoore wants to merge 18 commits into
zarr-developers:masterfrom 
joshmoore:default-write-empty-chunks-false
Closed
Default write empty chunks false#951
joshmoore wants to merge 18 commits into
zarr-developers:masterfrom 
joshmoore:default-write-empty-chunks-false
Conversation
@joshmoore
@joshmoorejoshmoore
commented
Jan 26, 2022

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Re-opening #853 from another branch to see if that fixes the github action jobs.
jniand others
added 12 commits
December 2, 2021 12:48
@jni
Set write_empty_chunks to default to False
6b461a7
@jni
Add release entry for write_empty_chunks default
d09c8d9
@jni
Merge branch 'master' into default-write-empty-chunks-false
a042c8a
@d-v-b
add Empty chunks section to tutorial.rst
5091df0
@joshmoore
Merge branch 'master' into default-write-empty-chunks-false
9d3d83c
@d-v-b
add benchmarky example
21647ab
@d-v-b
Merge branch 'master' ofhttps://github.com/zarr-developers/zarr-python…
b9af4be
… into default-write-empty-chunks-false
@d-v-b
proper formatting of code block
6ad8695
@joshmoore
Fix abstore deprecated strings
422beaa
@joshmoore
Merge branch 'master' into default-write-empty-chunks-false
d27e4ed
@joshmoore
Also catch ValueError in all_equal
1f21139
The call to `np.any(array)` in zarr.util.all_equal triggers the
following ValueError:
```
> return ufunc.reduce(obj, axis, dtype, out, **passkwargs)
E ValueError: invalid literal for int() with base 10: 'baz'
```
Extending the catch block allows test_array_with_categorize_filter
to pass, but it's unclear if this points to a deeper issue.
@joshmoore
Merge branch 'master' into default-write-empty-chunks-false
18971b5
@jakirkham
jakirkham
commented
Jan 26, 2022•

edited

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Also trying a no change PR ( #952 ) to see if this is a CI issue outside of these changes
@joshmoore
joshmoore
commented
Jan 26, 2022

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MemberAuthor
Fewer are hanging but not nothing. 😵‍💫
@jakirkham
jakirkham
commented
Jan 26, 2022

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Member
It would be good to get a clearer idea on why that is happening. Did we manage to get a log that we could look at? Waited for a while to see if GH Actions would include output, but nothing showed up.
@jni
jni
commented
Jan 27, 2022

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Contributor
@joshmoore@jakirkham this is very reminiscent of my own misadventures with test_sync, deadlocks, and CI timeouts. @joshmoore want to try your own advice?
#725 (comment)
Usually slow tests are printed at the end, but if they aren't completing we don't get the list! Can you add pytest -sv to the workflow or add pypi.org/project/pytest-timeout so we can get an idea on what's gone sideways?
This commit adds the timeout:
4e7733c (#725)
@joshmoore
joshmoore
commented
Jan 27, 2022

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MemberAuthor
Heh. I think I thought that that was now done everywhere. Pushing a commit with lots of timeouts here now.
@joshmoore
joshmooreforce-pushed
the
default-write-empty-chunks-false
branch
from
b30abbb to
8b12549CompareJanuary 27, 2022 06:37
@jakirkham
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commented
Jan 27, 2022

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The thing is this hang showed up very recently. It makes me wonder if there is something we changed or a dependency update in the environment that changed, which is causing issues.
For example fasteners was updated recently. To save writing this again, please read this comment ( #952 (comment) ).
@joshmoore
joshmoore
commented
Jan 27, 2022

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MemberAuthor
Interesting that not even timeout seems to be working here.
joshmoore added a commit
to joshmoore/zarr-python
that referenced
this pull request
Jan 27, 2022
@joshmoore
Pin fasteners to 0.16.3 (seezarr-developers#951)
666b500
@joshmoore
joshmooreforce-pushed
the
default-write-empty-chunks-false
branch
from
666b500 to
080a854CompareJanuary 27, 2022 07:35
@joshmoore
joshmoore
commented
Jan 27, 2022

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0.16.3 seemes safe, @jakirkham. Trying 0.17.1 here now.
@joshmoore
joshmoore
commented
Jan 27, 2022

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MemberAuthor
0.17.1 seems to be hanging on 3.9 != 1.21.0 as well.
@joshmoore
joshmoore
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Jan 27, 2022

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Pushed the commits up to the 0.16.3 pin to #853.
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Jan 27, 2022
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@jakirkham
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Jan 27, 2022

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The fact that timeout doesn't work makes me wonder if the hang is in C. Is it possible this is NumPy related? Is NumPy 1.22 hanging somewhere? What if we pinned to NumPy 1.20 in the jobs currently skipping 1.21?
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Jan 27, 2022•

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Codecov Report
Merging #951 (a9fd445) into master (e15001b) will decrease coverage by 0.00%.

The diff coverage is n/a.
❗ Current head a9fd445 differs from pull request most recent head 285998e. Consider uploading reports for the commit 285998e to get more accurate results
@@ Coverage Diff @@## master #951 +/- ##
==========================================
- Coverage 99.94% 99.94% -0.01% 
==========================================
Files 32 32 Lines 11225 11134 -91 ==========================================
- Hits 11219 11128 -91 
Misses 6 6 
Impacted FilesCoverage Δ
setup.py0.00% <ø> (ø)
zarr/_storage/absstore.py100.00% <ø> (ø)
zarr/core.py100.00% <ø> (ø)
zarr/creation.py100.00% <ø> (ø)
zarr/util.py100.00% <ø> (ø)
zarr/n5.py100.00% <0.00%> (ø)
zarr/storage.py100.00% <0.00%> (ø)
zarr/indexing.py100.00% <0.00%> (ø)
zarr/hierarchy.py100.00% <0.00%> (ø)
... and 11 more
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@jakirkham
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Jan 28, 2022

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Yeah sorry I think you may be right. Going with 0.16 seems like the right idea. There were deadlock issues in previous 0.17 releases it seems
@joshmoore
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Jan 28, 2022

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Going with 0.16 seems like the right idea.
Yeah, I was feeling pretty good about it until 080a854 timed out again. But perhaps that PR is somehow "tainted".
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Jan 28, 2022

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Maybe we should run tests with more verbosity? Perhaps that points out which test hangs so we can investigate further
@jakirkham
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Feb 4, 2022

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Power cycling for CI
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Feb 4, 2022
@jakirkham
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Feb 4, 2022•

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Looks like this is going to fail without the NumPy upgrade ( #955 ). Or perhaps the new NumPy conflicts with pinnings we tried here?
@joshmoore
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Feb 4, 2022

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Closing along with #952
Looks like the scare is over.
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February 4, 2022 10:03
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4 participants

@joshmoore@jakirkham@jni@d-v-b