fix: validate v3 dtypes when loading/creating v3 metadata - #2209

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jhamman:fix/v3-valid-dtypes
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fix: validate v3 dtypes when loading/creating v3 metadata#2209
jhamman merged 10 commits into
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jhamman:fix/v3-valid-dtypes

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This PR validates data types in v3 metadata. The behavior implemented raises an error if a data type outside of the current v3 spec is discovered in either a zarr.json metadata document or in the Array constructor.

xref: #2200

TODO:

  • Add unit tests and/or doctests in docstrings
  • Add docstrings and API docs for any new/modified user-facing classes and functions
  • New/modified features documented in docs/tutorial.rst
  • Changes documented in docs/release.rst
  • GitHub Actions have all passed
  • Test coverage is 100% (Codecov passes)

@jhammanjhamman mentioned this pull request Sep 18, 2024
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jhamman requested a review from d-v-bSeptember 19, 2024 17:45
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jhamman commented Sep 19, 2024
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Comment threadsrc/zarr/core/array_spec.py Outdated
) -> None:
shape_parsed = parse_shapelike(shape)
dtype_parsed = parse_dtype(dtype)
dtype_parsed = dtype # parsing is likely not needed here

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Suggested change
dtype_parsed=dtype# parsing is likely not needed here
dtype_parsed=dtype

The input type is already np.dtype[Any] so I don't think we need to parse this.

jhamman
jhamman commented Sep 19, 2024
View reviewed changes
Comment threadsrc/zarr/core/metadata/v2.py

def parse_dtype(data: npt.DTypeLike) -> np.dtype[Any]:
# todo: real validation
return np.dtype(data)

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we now parse v2 and v3 dtypes differently.

jhamman
jhamman commented Sep 19, 2024
View reviewed changes
Comment threadsrc/zarr/testing/strategies.py
dtype=npst.scalar_dtypes().filter(lambda x: x.kind != "m"),
dtype=npst.scalar_dtypes().filter(
lambda x: (x.kind not in ["m", "M"]) and (x.byteorder not in [">"])
),

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It is not clear to me how endianness works in v3. As far as I can tell, we are not handling this in a meaningful way today.

cc @dcherian and @d-v-b

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I concur. It's not being handled today

jhamman
jhamman commented Sep 19, 2024
View reviewed changes
Comment threadtests/v3/test_metadata/test_v3.py
async def test_datetime_metadata(fill_value: int, precision: str) -> None:
# @pytest.mark.parametrize("fill_value", [-1, 0, 1, 2932897])
# @pytest.mark.parametrize("precision", ["ns", "D"])
# async def test_datetime_metadata(fill_value: int, precision: str) -> None:

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this test was creating an invalid dtype (datetime). We can leave it in place and bring it back when there is support for this dtype in v3.

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jhamman commented Sep 21, 2024
View reviewed changes
Comment threadtests/v3/test_metadata/test_v3.py
(0, "int16"),
(1e10, "uint64"),
(-999, "float32"),
(1e32, "float64"),

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also add a test for NaN fill values

d-v-b
d-v-b reviewed Sep 23, 2024
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Comment threadsrc/zarr/core/metadata/v3.py
d-v-b
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Comment threadsrc/zarr/core/array_spec.py
d-v-b
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Comment threadsrc/zarr/core/metadata/v2.py
d-v-b
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Comment threadsrc/zarr/core/metadata/v3.py
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Comment threadsrc/zarr/core/metadata/v3.py Outdated
@jhamman@d-v-b
Update src/zarr/core/metadata/v3.py
9736b4b
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
d-v-b
d-v-b reviewed Sep 23, 2024
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Comment threadsrc/zarr/core/metadata/v3.py
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this looks great, thanks!

@jhamman
jhamman merged commit 2d3a36c into zarr-developers:v3Sep 23, 2024
@jhammanjhamman mentioned this pull request Sep 24, 2024
Closed
dcherian added a commit to dcherian/zarr-python that referenced this pull request Sep 24, 2024
@dcherian
Merge branch 'v3' into generalize-stateful-store
ad3df88
* v3:
chore: update pre-commit hooks (zarr-developers#2222)
fix: validate v3 dtypes when loading/creating v3 metadata (zarr-developers#2209)
fix typo in store integration test (zarr-developers#2223)
Basic Zarr-python 2.x compatibility changes (zarr-developers#2098)
Make Group.arrays, groups compatible with v2 (zarr-developers#2213)
Typing fixes to test_indexing (zarr-developers#2193)
Default to RemoteStore for fsspec URIs (zarr-developers#2198)
Make MemoryStore serialiazable (zarr-developers#2204)
[v3] Implement Group methods for empty, full, ones, and zeros (zarr-developers#2210)
implement `store.list_prefix` and `store._set_many` (zarr-developers#2064)
Fixed codec for v2 data with no fill value (zarr-developers#2207)
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, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all 
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}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '

Skip to content
fix: validate v3 dtypes when loading/creating v3 metadata - #2209
Merged
jhamman merged 10 commits into
zarr-developers:v3from 
jhamman:fix/v3-valid-dtypes
Sep 23, 2024
Merged
fix: validate v3 dtypes when loading/creating v3 metadata#2209
jhamman merged 10 commits into
zarr-developers:v3from 
jhamman:fix/v3-valid-dtypes
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@jhamman
@jhammanjhamman
commented
Sep 18, 2024•

edited

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This PR validates data types in v3 metadata. The behavior implemented raises an error if a data type outside of the current v3 spec is discovered in either a zarr.json metadata document or in the Array constructor.
xref: #2200
TODO:
  •  Add unit tests and/or doctests in docstrings
  •  Add docstrings and API docs for any new/modified user-facing classes and functions
  •  New/modified features documented in docs/tutorial.rst
  •  Changes documented in docs/release.rst
  •  GitHub Actions have all passed
  •  Test coverage is 100% (Codecov passes)
@jhammanjhamman
mentioned this pull request
Sep 18, 2024
 Closed

@jhamman
jhamman
requested a review
from d-v-bSeptember 19, 2024 17:45
jhamman
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commented
Sep 19, 2024
View reviewed changes
Comment threadsrc/zarr/core/array_spec.py
Outdated

 ) -> None:
 shape_parsed = parse_shapelike(shape)
 dtype_parsed = parse_dtype(dtype)
 dtype_parsed = dtype # parsing is likely not needed here
@jhammanjhammanSep 19, 2024

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Suggested change

dtype_parsed=dtype# parsing is likely not needed here
dtype_parsed=dtype
The input type is already np.dtype[Any] so I don't think we need to parse this.
jhamman
jhamman
commented
Sep 19, 2024
View reviewed changes
Comment threadsrc/zarr/core/metadata/v2.py

def parse_dtype(data: npt.DTypeLike) -> np.dtype[Any]:
 # todo: real validation
 return np.dtype(data)
@jhammanjhammanSep 19, 2024

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we now parse v2 and v3 dtypes differently.
jhamman
jhamman
commented
Sep 19, 2024
View reviewed changes
Comment threadsrc/zarr/testing/strategies.py
 dtype=npst.scalar_dtypes().filter(lambda x: x.kind != "m"),
 dtype=npst.scalar_dtypes().filter(
 lambda x: (x.kind not in ["m", "M"]) and (x.byteorder not in [">"])
 ),
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It is not clear to me how endianness works in v3. As far as I can tell, we are not handling this in a meaningful way today.
cc @dcherian and @d-v-b
@dcheriandcherianSep 19, 2024

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I concur. It's not being handled today
jhamman
jhamman
commented
Sep 19, 2024
View reviewed changes
Comment threadtests/v3/test_metadata/test_v3.py
async def test_datetime_metadata(fill_value: int, precision: str) -> None:
# @pytest.mark.parametrize("fill_value", [-1, 0, 1, 2932897])
# @pytest.mark.parametrize("precision", ["ns", "D"])
# async def test_datetime_metadata(fill_value: int, precision: str) -> None:
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this test was creating an invalid dtype (datetime). We can leave it in place and bring it back when there is support for this dtype in v3.
@jhammanjhamman
mentioned this pull request
Sep 20, 2024
 Closed

6 tasks
jhamman
jhamman
commented
Sep 21, 2024
View reviewed changes
Comment threadtests/v3/test_metadata/test_v3.py
 (0, "int16"),
 (1e10, "uint64"),
 (-999, "float32"),
 (1e32, "float64"),
@jhammanjhammanSep 21, 2024

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also add a test for NaN fill values
d-v-b
d-v-b
reviewed
Sep 23, 2024
View reviewed changes
Comment threadsrc/zarr/core/metadata/v3.py
d-v-b
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reviewed
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View reviewed changes
Comment threadsrc/zarr/core/array_spec.py
d-v-b
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reviewed
Sep 23, 2024
View reviewed changes
Comment threadsrc/zarr/core/metadata/v2.py
d-v-b
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reviewed
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View reviewed changes
Comment threadsrc/zarr/core/metadata/v3.py
d-v-b
d-v-b
reviewed
Sep 23, 2024
View reviewed changes
Comment threadsrc/zarr/core/metadata/v3.py
Outdated

@jhamman@d-v-b
Update src/zarr/core/metadata/v3.py
9736b4b
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
d-v-b
d-v-b
reviewed
Sep 23, 2024
View reviewed changes
Comment threadsrc/zarr/core/metadata/v3.py
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this looks great, thanks!
@jhamman
jhamman
merged commit 2d3a36c
into
zarr-developers:v3Sep 23, 2024
@jhammanjhamman
mentioned this pull request
Sep 24, 2024

Closed

dcherian added a commit
to dcherian/zarr-python
that referenced
this pull request
Sep 24, 2024
@dcherian
Merge branch 'v3' into generalize-stateful-store
ad3df88
* v3:
chore: update pre-commit hooks (zarr-developers#2222)
fix: validate v3 dtypes when loading/creating v3 metadata (zarr-developers#2209)
fix typo in store integration test (zarr-developers#2223)
Basic Zarr-python 2.x compatibility changes (zarr-developers#2098)
Make Group.arrays, groups compatible with v2 (zarr-developers#2213)
Typing fixes to test_indexing (zarr-developers#2193)
Default to RemoteStore for fsspec URIs (zarr-developers#2198)
Make MemoryStore serialiazable (zarr-developers#2204)
[v3] Implement Group methods for empty, full, ones, and zeros (zarr-developers#2210)
implement `store.list_prefix` and `store._set_many` (zarr-developers#2064)
Fixed codec for v2 data with no fill value (zarr-developers#2207)
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Force GitHub README to respect dark mode\n(function() {\n var style = document.createElement('style');\n style.textContent = '\n .markdown-body {\n color-scheme: dark light;\n }\n .markdown-body pre { background: #161b22 !important; }\n .markdown-body code { background: rgba(110, 118, 129, 0.4) !important; }\n .markdown-body table th, .markdown-body table td { border-color: #30363d !important; }\n .markdown-body img { background: #0d1117; }\n .markdown-body blockquote { border-left-color: #8b949e; }\n .markdown-body hr { border-color: #30363d; }\n ';\n document.head.appendChild(style);\n})();", "GitHub Dark Mode README Fix");
}
} catch(__e) { console.warn('[Userscript:GitHub Dark Mode README Fix]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
fix: validate v3 dtypes when loading/creating v3 metadata - #2209
Merged
jhamman merged 10 commits into
zarr-developers:v3from 
jhamman:fix/v3-valid-dtypes
Sep 23, 2024
Merged
fix: validate v3 dtypes when loading/creating v3 metadata#2209
jhamman merged 10 commits into
zarr-developers:v3from 
jhamman:fix/v3-valid-dtypes
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@jhamman
@jhammanjhamman
commented
Sep 18, 2024•

edited

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This PR validates data types in v3 metadata. The behavior implemented raises an error if a data type outside of the current v3 spec is discovered in either a zarr.json metadata document or in the Array constructor.
xref: #2200
TODO:
  •  Add unit tests and/or doctests in docstrings
  •  Add docstrings and API docs for any new/modified user-facing classes and functions
  •  New/modified features documented in docs/tutorial.rst
  •  Changes documented in docs/release.rst
  •  GitHub Actions have all passed
  •  Test coverage is 100% (Codecov passes)
@jhammanjhamman
mentioned this pull request
Sep 18, 2024
 Closed

@jhamman
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requested a review
from d-v-bSeptember 19, 2024 17:45
jhamman
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commented
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View reviewed changes
Comment threadsrc/zarr/core/array_spec.py
Outdated

 ) -> None:
 shape_parsed = parse_shapelike(shape)
 dtype_parsed = parse_dtype(dtype)
 dtype_parsed = dtype # parsing is likely not needed here
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Suggested change

dtype_parsed=dtype# parsing is likely not needed here
dtype_parsed=dtype
The input type is already np.dtype[Any] so I don't think we need to parse this.
jhamman
jhamman
commented
Sep 19, 2024
View reviewed changes
Comment threadsrc/zarr/core/metadata/v2.py

def parse_dtype(data: npt.DTypeLike) -> np.dtype[Any]:
 # todo: real validation
 return np.dtype(data)
@jhammanjhammanSep 19, 2024

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we now parse v2 and v3 dtypes differently.
jhamman
jhamman
commented
Sep 19, 2024
View reviewed changes
Comment threadsrc/zarr/testing/strategies.py
 dtype=npst.scalar_dtypes().filter(lambda x: x.kind != "m"),
 dtype=npst.scalar_dtypes().filter(
 lambda x: (x.kind not in ["m", "M"]) and (x.byteorder not in [">"])
 ),
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It is not clear to me how endianness works in v3. As far as I can tell, we are not handling this in a meaningful way today.
cc @dcherian and @d-v-b
@dcheriandcherianSep 19, 2024

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I concur. It's not being handled today
jhamman
jhamman
commented
Sep 19, 2024
View reviewed changes
Comment threadtests/v3/test_metadata/test_v3.py
async def test_datetime_metadata(fill_value: int, precision: str) -> None:
# @pytest.mark.parametrize("fill_value", [-1, 0, 1, 2932897])
# @pytest.mark.parametrize("precision", ["ns", "D"])
# async def test_datetime_metadata(fill_value: int, precision: str) -> None:
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this test was creating an invalid dtype (datetime). We can leave it in place and bring it back when there is support for this dtype in v3.
@jhammanjhamman
mentioned this pull request
Sep 20, 2024
 Closed

6 tasks
jhamman
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commented
Sep 21, 2024
View reviewed changes
Comment threadtests/v3/test_metadata/test_v3.py
 (0, "int16"),
 (1e10, "uint64"),
 (-999, "float32"),
 (1e32, "float64"),
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also add a test for NaN fill values
d-v-b
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reviewed
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Comment threadsrc/zarr/core/metadata/v3.py
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Comment threadsrc/zarr/core/array_spec.py
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Comment threadsrc/zarr/core/metadata/v2.py
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Comment threadsrc/zarr/core/metadata/v3.py
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Comment threadsrc/zarr/core/metadata/v3.py
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@jhamman@d-v-b
Update src/zarr/core/metadata/v3.py
9736b4b
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
d-v-b
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Comment threadsrc/zarr/core/metadata/v3.py
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this looks great, thanks!
@jhamman
jhamman
merged commit 2d3a36c
into
zarr-developers:v3Sep 23, 2024
@jhammanjhamman
mentioned this pull request
Sep 24, 2024

Closed

dcherian added a commit
to dcherian/zarr-python
that referenced
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Sep 24, 2024
@dcherian
Merge branch 'v3' into generalize-stateful-store
ad3df88
* v3:
chore: update pre-commit hooks (zarr-developers#2222)
fix: validate v3 dtypes when loading/creating v3 metadata (zarr-developers#2209)
fix typo in store integration test (zarr-developers#2223)
Basic Zarr-python 2.x compatibility changes (zarr-developers#2098)
Make Group.arrays, groups compatible with v2 (zarr-developers#2213)
Typing fixes to test_indexing (zarr-developers#2193)
Default to RemoteStore for fsspec URIs (zarr-developers#2198)
Make MemoryStore serialiazable (zarr-developers#2204)
[v3] Implement Group methods for empty, full, ones, and zeros (zarr-developers#2210)
implement `store.list_prefix` and `store._set_many` (zarr-developers#2064)
Fixed codec for v2 data with no fill value (zarr-developers#2207)
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, '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
fix: validate v3 dtypes when loading/creating v3 metadata - #2209
Merged
jhamman merged 10 commits into
zarr-developers:v3from 
jhamman:fix/v3-valid-dtypes
Sep 23, 2024
Merged
fix: validate v3 dtypes when loading/creating v3 metadata#2209
jhamman merged 10 commits into
zarr-developers:v3from 
jhamman:fix/v3-valid-dtypes
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Sep 18, 2024•

edited

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This PR validates data types in v3 metadata. The behavior implemented raises an error if a data type outside of the current v3 spec is discovered in either a zarr.json metadata document or in the Array constructor.
xref: #2200
TODO:
  •  Add unit tests and/or doctests in docstrings
  •  Add docstrings and API docs for any new/modified user-facing classes and functions
  •  New/modified features documented in docs/tutorial.rst
  •  Changes documented in docs/release.rst
  •  GitHub Actions have all passed
  •  Test coverage is 100% (Codecov passes)
@jhammanjhamman
mentioned this pull request
Sep 18, 2024
 Closed

@jhamman
jhamman
requested a review
from d-v-bSeptember 19, 2024 17:45
jhamman
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commented
Sep 19, 2024
View reviewed changes
Comment threadsrc/zarr/core/array_spec.py
Outdated

 ) -> None:
 shape_parsed = parse_shapelike(shape)
 dtype_parsed = parse_dtype(dtype)
 dtype_parsed = dtype # parsing is likely not needed here
@jhammanjhammanSep 19, 2024

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Suggested change

dtype_parsed=dtype# parsing is likely not needed here
dtype_parsed=dtype
The input type is already np.dtype[Any] so I don't think we need to parse this.
jhamman
jhamman
commented
Sep 19, 2024
View reviewed changes
Comment threadsrc/zarr/core/metadata/v2.py

def parse_dtype(data: npt.DTypeLike) -> np.dtype[Any]:
 # todo: real validation
 return np.dtype(data)
@jhammanjhammanSep 19, 2024

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we now parse v2 and v3 dtypes differently.
jhamman
jhamman
commented
Sep 19, 2024
View reviewed changes
Comment threadsrc/zarr/testing/strategies.py
 dtype=npst.scalar_dtypes().filter(lambda x: x.kind != "m"),
 dtype=npst.scalar_dtypes().filter(
 lambda x: (x.kind not in ["m", "M"]) and (x.byteorder not in [">"])
 ),
@jhammanjhammanSep 19, 2024

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It is not clear to me how endianness works in v3. As far as I can tell, we are not handling this in a meaningful way today.
cc @dcherian and @d-v-b
@dcheriandcherianSep 19, 2024

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I concur. It's not being handled today
jhamman
jhamman
commented
Sep 19, 2024
View reviewed changes
Comment threadtests/v3/test_metadata/test_v3.py
async def test_datetime_metadata(fill_value: int, precision: str) -> None:
# @pytest.mark.parametrize("fill_value", [-1, 0, 1, 2932897])
# @pytest.mark.parametrize("precision", ["ns", "D"])
# async def test_datetime_metadata(fill_value: int, precision: str) -> None:
@jhammanjhammanSep 19, 2024

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this test was creating an invalid dtype (datetime). We can leave it in place and bring it back when there is support for this dtype in v3.
@jhammanjhamman
mentioned this pull request
Sep 20, 2024
 Closed

6 tasks
jhamman
jhamman
commented
Sep 21, 2024
View reviewed changes
Comment threadtests/v3/test_metadata/test_v3.py
 (0, "int16"),
 (1e10, "uint64"),
 (-999, "float32"),
 (1e32, "float64"),
@jhammanjhammanSep 21, 2024

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also add a test for NaN fill values
d-v-b
d-v-b
reviewed
Sep 23, 2024
View reviewed changes
Comment threadsrc/zarr/core/metadata/v3.py
d-v-b
d-v-b
reviewed
Sep 23, 2024
View reviewed changes
Comment threadsrc/zarr/core/array_spec.py
d-v-b
d-v-b
reviewed
Sep 23, 2024
View reviewed changes
Comment threadsrc/zarr/core/metadata/v2.py
d-v-b
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reviewed
Sep 23, 2024
View reviewed changes
Comment threadsrc/zarr/core/metadata/v3.py
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reviewed
Sep 23, 2024
View reviewed changes
Comment threadsrc/zarr/core/metadata/v3.py
Outdated

@jhamman@d-v-b
Update src/zarr/core/metadata/v3.py
9736b4b
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
d-v-b
d-v-b
reviewed
Sep 23, 2024
View reviewed changes
Comment threadsrc/zarr/core/metadata/v3.py
@d-v-b
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Sep 23, 2024

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this looks great, thanks!
@jhamman
jhamman
merged commit 2d3a36c
into
zarr-developers:v3Sep 23, 2024
@jhammanjhamman
mentioned this pull request
Sep 24, 2024

Closed

dcherian added a commit
to dcherian/zarr-python
that referenced
this pull request
Sep 24, 2024
@dcherian
Merge branch 'v3' into generalize-stateful-store
ad3df88
* v3:
chore: update pre-commit hooks (zarr-developers#2222)
fix: validate v3 dtypes when loading/creating v3 metadata (zarr-developers#2209)
fix typo in store integration test (zarr-developers#2223)
Basic Zarr-python 2.x compatibility changes (zarr-developers#2098)
Make Group.arrays, groups compatible with v2 (zarr-developers#2213)
Typing fixes to test_indexing (zarr-developers#2193)
Default to RemoteStore for fsspec URIs (zarr-developers#2198)
Make MemoryStore serialiazable (zarr-developers#2204)
[v3] Implement Group methods for empty, full, ones, and zeros (zarr-developers#2210)
implement `store.list_prefix` and `store._set_many` (zarr-developers#2064)
Fixed codec for v2 data with no fill value (zarr-developers#2207)
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, '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
fix: validate v3 dtypes when loading/creating v3 metadata - #2209
Merged
jhamman merged 10 commits into
zarr-developers:v3from 
jhamman:fix/v3-valid-dtypes
Sep 23, 2024
Merged
fix: validate v3 dtypes when loading/creating v3 metadata#2209
jhamman merged 10 commits into
zarr-developers:v3from 
jhamman:fix/v3-valid-dtypes
Conversation
@jhamman
@jhammanjhamman
commented
Sep 18, 2024•

edited

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This PR validates data types in v3 metadata. The behavior implemented raises an error if a data type outside of the current v3 spec is discovered in either a zarr.json metadata document or in the Array constructor.
xref: #2200
TODO:
  •  Add unit tests and/or doctests in docstrings
  •  Add docstrings and API docs for any new/modified user-facing classes and functions
  •  New/modified features documented in docs/tutorial.rst
  •  Changes documented in docs/release.rst
  •  GitHub Actions have all passed
  •  Test coverage is 100% (Codecov passes)
@jhammanjhamman
mentioned this pull request
Sep 18, 2024
 Closed

@jhamman
jhamman
requested a review
from d-v-bSeptember 19, 2024 17:45
jhamman
jhamman
commented
Sep 19, 2024
View reviewed changes
Comment threadsrc/zarr/core/array_spec.py
Outdated

 ) -> None:
 shape_parsed = parse_shapelike(shape)
 dtype_parsed = parse_dtype(dtype)
 dtype_parsed = dtype # parsing is likely not needed here
@jhammanjhammanSep 19, 2024

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Suggested change

dtype_parsed=dtype# parsing is likely not needed here
dtype_parsed=dtype
The input type is already np.dtype[Any] so I don't think we need to parse this.
jhamman
jhamman
commented
Sep 19, 2024
View reviewed changes
Comment threadsrc/zarr/core/metadata/v2.py

def parse_dtype(data: npt.DTypeLike) -> np.dtype[Any]:
 # todo: real validation
 return np.dtype(data)
@jhammanjhammanSep 19, 2024

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we now parse v2 and v3 dtypes differently.
jhamman
jhamman
commented
Sep 19, 2024
View reviewed changes
Comment threadsrc/zarr/testing/strategies.py
 dtype=npst.scalar_dtypes().filter(lambda x: x.kind != "m"),
 dtype=npst.scalar_dtypes().filter(
 lambda x: (x.kind not in ["m", "M"]) and (x.byteorder not in [">"])
 ),
@jhammanjhammanSep 19, 2024

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It is not clear to me how endianness works in v3. As far as I can tell, we are not handling this in a meaningful way today.
cc @dcherian and @d-v-b
@dcheriandcherianSep 19, 2024

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I concur. It's not being handled today
jhamman
jhamman
commented
Sep 19, 2024
View reviewed changes
Comment threadtests/v3/test_metadata/test_v3.py
async def test_datetime_metadata(fill_value: int, precision: str) -> None:
# @pytest.mark.parametrize("fill_value", [-1, 0, 1, 2932897])
# @pytest.mark.parametrize("precision", ["ns", "D"])
# async def test_datetime_metadata(fill_value: int, precision: str) -> None:
@jhammanjhammanSep 19, 2024

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this test was creating an invalid dtype (datetime). We can leave it in place and bring it back when there is support for this dtype in v3.
@jhammanjhamman
mentioned this pull request
Sep 20, 2024
 Closed

6 tasks
jhamman
jhamman
commented
Sep 21, 2024
View reviewed changes
Comment threadtests/v3/test_metadata/test_v3.py
 (0, "int16"),
 (1e10, "uint64"),
 (-999, "float32"),
 (1e32, "float64"),
@jhammanjhammanSep 21, 2024

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also add a test for NaN fill values
d-v-b
d-v-b
reviewed
Sep 23, 2024
View reviewed changes
Comment threadsrc/zarr/core/metadata/v3.py
d-v-b
d-v-b
reviewed
Sep 23, 2024
View reviewed changes
Comment threadsrc/zarr/core/array_spec.py
d-v-b
d-v-b
reviewed
Sep 23, 2024
View reviewed changes
Comment threadsrc/zarr/core/metadata/v2.py
d-v-b
d-v-b
reviewed
Sep 23, 2024
View reviewed changes
Comment threadsrc/zarr/core/metadata/v3.py
d-v-b
d-v-b
reviewed
Sep 23, 2024
View reviewed changes
Comment threadsrc/zarr/core/metadata/v3.py
Outdated

@jhamman@d-v-b
Update src/zarr/core/metadata/v3.py
9736b4b
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
d-v-b
d-v-b
reviewed
Sep 23, 2024
View reviewed changes
Comment threadsrc/zarr/core/metadata/v3.py
@d-v-b
d-v-b
commented
Sep 23, 2024

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this looks great, thanks!
@jhamman
jhamman
merged commit 2d3a36c
into
zarr-developers:v3Sep 23, 2024
@jhammanjhamman
mentioned this pull request
Sep 24, 2024

Closed

dcherian added a commit
to dcherian/zarr-python
that referenced
this pull request
Sep 24, 2024
@dcherian
Merge branch 'v3' into generalize-stateful-store
ad3df88
* v3:
chore: update pre-commit hooks (zarr-developers#2222)
fix: validate v3 dtypes when loading/creating v3 metadata (zarr-developers#2209)
fix typo in store integration test (zarr-developers#2223)
Basic Zarr-python 2.x compatibility changes (zarr-developers#2098)
Make Group.arrays, groups compatible with v2 (zarr-developers#2213)
Typing fixes to test_indexing (zarr-developers#2193)
Default to RemoteStore for fsspec URIs (zarr-developers#2198)
Make MemoryStore serialiazable (zarr-developers#2204)
[v3] Implement Group methods for empty, full, ones, and zeros (zarr-developers#2210)
implement `store.list_prefix` and `store._set_many` (zarr-developers#2064)
Fixed codec for v2 data with no fill value (zarr-developers#2207)
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@jhamman@d-v-b@dcherian

, '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
fix: validate v3 dtypes when loading/creating v3 metadata - #2209
Merged
jhamman merged 10 commits into
zarr-developers:v3from 
jhamman:fix/v3-valid-dtypes
Sep 23, 2024
Merged
fix: validate v3 dtypes when loading/creating v3 metadata#2209
jhamman merged 10 commits into
zarr-developers:v3from 
jhamman:fix/v3-valid-dtypes
Conversation
@jhamman
@jhammanjhamman
commented
Sep 18, 2024•

edited

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This PR validates data types in v3 metadata. The behavior implemented raises an error if a data type outside of the current v3 spec is discovered in either a zarr.json metadata document or in the Array constructor.
xref: #2200
TODO:
  •  Add unit tests and/or doctests in docstrings
  •  Add docstrings and API docs for any new/modified user-facing classes and functions
  •  New/modified features documented in docs/tutorial.rst
  •  Changes documented in docs/release.rst
  •  GitHub Actions have all passed
  •  Test coverage is 100% (Codecov passes)
@jhammanjhamman
mentioned this pull request
Sep 18, 2024
 Closed

@jhamman
jhamman
requested a review
from d-v-bSeptember 19, 2024 17:45
jhamman
jhamman
commented
Sep 19, 2024
View reviewed changes
Comment threadsrc/zarr/core/array_spec.py
Outdated

 ) -> None:
 shape_parsed = parse_shapelike(shape)
 dtype_parsed = parse_dtype(dtype)
 dtype_parsed = dtype # parsing is likely not needed here
@jhammanjhammanSep 19, 2024

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Suggested change

dtype_parsed=dtype# parsing is likely not needed here
dtype_parsed=dtype
The input type is already np.dtype[Any] so I don't think we need to parse this.
jhamman
jhamman
commented
Sep 19, 2024
View reviewed changes
Comment threadsrc/zarr/core/metadata/v2.py

def parse_dtype(data: npt.DTypeLike) -> np.dtype[Any]:
 # todo: real validation
 return np.dtype(data)
@jhammanjhammanSep 19, 2024

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we now parse v2 and v3 dtypes differently.
jhamman
jhamman
commented
Sep 19, 2024
View reviewed changes
Comment threadsrc/zarr/testing/strategies.py
 dtype=npst.scalar_dtypes().filter(lambda x: x.kind != "m"),
 dtype=npst.scalar_dtypes().filter(
 lambda x: (x.kind not in ["m", "M"]) and (x.byteorder not in [">"])
 ),
@jhammanjhammanSep 19, 2024

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It is not clear to me how endianness works in v3. As far as I can tell, we are not handling this in a meaningful way today.
cc @dcherian and @d-v-b
@dcheriandcherianSep 19, 2024

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I concur. It's not being handled today
jhamman
jhamman
commented
Sep 19, 2024
View reviewed changes
Comment threadtests/v3/test_metadata/test_v3.py
async def test_datetime_metadata(fill_value: int, precision: str) -> None:
# @pytest.mark.parametrize("fill_value", [-1, 0, 1, 2932897])
# @pytest.mark.parametrize("precision", ["ns", "D"])
# async def test_datetime_metadata(fill_value: int, precision: str) -> None:
@jhammanjhammanSep 19, 2024

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this test was creating an invalid dtype (datetime). We can leave it in place and bring it back when there is support for this dtype in v3.
@jhammanjhamman
mentioned this pull request
Sep 20, 2024
 Closed

6 tasks
jhamman
jhamman
commented
Sep 21, 2024
View reviewed changes
Comment threadtests/v3/test_metadata/test_v3.py
 (0, "int16"),
 (1e10, "uint64"),
 (-999, "float32"),
 (1e32, "float64"),
@jhammanjhammanSep 21, 2024

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also add a test for NaN fill values
d-v-b
d-v-b
reviewed
Sep 23, 2024
View reviewed changes
Comment threadsrc/zarr/core/metadata/v3.py
d-v-b
d-v-b
reviewed
Sep 23, 2024
View reviewed changes
Comment threadsrc/zarr/core/array_spec.py
d-v-b
d-v-b
reviewed
Sep 23, 2024
View reviewed changes
Comment threadsrc/zarr/core/metadata/v2.py
d-v-b
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reviewed
Sep 23, 2024
View reviewed changes
Comment threadsrc/zarr/core/metadata/v3.py
d-v-b
d-v-b
reviewed
Sep 23, 2024
View reviewed changes
Comment threadsrc/zarr/core/metadata/v3.py
Outdated

@jhamman@d-v-b
Update src/zarr/core/metadata/v3.py
9736b4b
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
d-v-b
d-v-b
reviewed
Sep 23, 2024
View reviewed changes
Comment threadsrc/zarr/core/metadata/v3.py
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this looks great, thanks!
@jhamman
jhamman
merged commit 2d3a36c
into
zarr-developers:v3Sep 23, 2024
@jhammanjhamman
mentioned this pull request
Sep 24, 2024

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dcherian added a commit
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@dcherian
Merge branch 'v3' into generalize-stateful-store
ad3df88
* v3:
chore: update pre-commit hooks (zarr-developers#2222)
fix: validate v3 dtypes when loading/creating v3 metadata (zarr-developers#2209)
fix typo in store integration test (zarr-developers#2223)
Basic Zarr-python 2.x compatibility changes (zarr-developers#2098)
Make Group.arrays, groups compatible with v2 (zarr-developers#2213)
Typing fixes to test_indexing (zarr-developers#2193)
Default to RemoteStore for fsspec URIs (zarr-developers#2198)
Make MemoryStore serialiazable (zarr-developers#2204)
[v3] Implement Group methods for empty, full, ones, and zeros (zarr-developers#2210)
implement `store.list_prefix` and `store._set_many` (zarr-developers#2064)
Fixed codec for v2 data with no fill value (zarr-developers#2207)
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, '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");
}
} catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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fix: validate v3 dtypes when loading/creating v3 metadata - #2209
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jhamman merged 10 commits into
zarr-developers:v3from 
jhamman:fix/v3-valid-dtypes
Sep 23, 2024
Merged
fix: validate v3 dtypes when loading/creating v3 metadata#2209
jhamman merged 10 commits into
zarr-developers:v3from 
jhamman:fix/v3-valid-dtypes
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Sep 18, 2024•

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This PR validates data types in v3 metadata. The behavior implemented raises an error if a data type outside of the current v3 spec is discovered in either a zarr.json metadata document or in the Array constructor.
xref: #2200
TODO:
  •  Add unit tests and/or doctests in docstrings
  •  Add docstrings and API docs for any new/modified user-facing classes and functions
  •  New/modified features documented in docs/tutorial.rst
  •  Changes documented in docs/release.rst
  •  GitHub Actions have all passed
  •  Test coverage is 100% (Codecov passes)
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Sep 18, 2024
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Comment threadsrc/zarr/core/array_spec.py
Outdated

 ) -> None:
 shape_parsed = parse_shapelike(shape)
 dtype_parsed = parse_dtype(dtype)
 dtype_parsed = dtype # parsing is likely not needed here
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Suggested change

dtype_parsed=dtype# parsing is likely not needed here
dtype_parsed=dtype
The input type is already np.dtype[Any] so I don't think we need to parse this.
jhamman
jhamman
commented
Sep 19, 2024
View reviewed changes
Comment threadsrc/zarr/core/metadata/v2.py

def parse_dtype(data: npt.DTypeLike) -> np.dtype[Any]:
 # todo: real validation
 return np.dtype(data)
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we now parse v2 and v3 dtypes differently.
jhamman
jhamman
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Sep 19, 2024
View reviewed changes
Comment threadsrc/zarr/testing/strategies.py
 dtype=npst.scalar_dtypes().filter(lambda x: x.kind != "m"),
 dtype=npst.scalar_dtypes().filter(
 lambda x: (x.kind not in ["m", "M"]) and (x.byteorder not in [">"])
 ),
@jhammanjhammanSep 19, 2024

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It is not clear to me how endianness works in v3. As far as I can tell, we are not handling this in a meaningful way today.
cc @dcherian and @d-v-b
@dcheriandcherianSep 19, 2024

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I concur. It's not being handled today
jhamman
jhamman
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Sep 19, 2024
View reviewed changes
Comment threadtests/v3/test_metadata/test_v3.py
async def test_datetime_metadata(fill_value: int, precision: str) -> None:
# @pytest.mark.parametrize("fill_value", [-1, 0, 1, 2932897])
# @pytest.mark.parametrize("precision", ["ns", "D"])
# async def test_datetime_metadata(fill_value: int, precision: str) -> None:
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this test was creating an invalid dtype (datetime). We can leave it in place and bring it back when there is support for this dtype in v3.
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Sep 20, 2024
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jhamman
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Sep 21, 2024
View reviewed changes
Comment threadtests/v3/test_metadata/test_v3.py
 (0, "int16"),
 (1e10, "uint64"),
 (-999, "float32"),
 (1e32, "float64"),
@jhammanjhammanSep 21, 2024

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also add a test for NaN fill values
d-v-b
d-v-b
reviewed
Sep 23, 2024
View reviewed changes
Comment threadsrc/zarr/core/metadata/v3.py
d-v-b
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reviewed
Sep 23, 2024
View reviewed changes
Comment threadsrc/zarr/core/array_spec.py
d-v-b
d-v-b
reviewed
Sep 23, 2024
View reviewed changes
Comment threadsrc/zarr/core/metadata/v2.py
d-v-b
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reviewed
Sep 23, 2024
View reviewed changes
Comment threadsrc/zarr/core/metadata/v3.py
d-v-b
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reviewed
Sep 23, 2024
View reviewed changes
Comment threadsrc/zarr/core/metadata/v3.py
Outdated

@jhamman@d-v-b
Update src/zarr/core/metadata/v3.py
9736b4b
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
d-v-b
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reviewed
Sep 23, 2024
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Comment threadsrc/zarr/core/metadata/v3.py
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this looks great, thanks!
@jhamman
jhamman
merged commit 2d3a36c
into
zarr-developers:v3Sep 23, 2024
@jhammanjhamman
mentioned this pull request
Sep 24, 2024

Closed

dcherian added a commit
to dcherian/zarr-python
that referenced
this pull request
Sep 24, 2024
@dcherian
Merge branch 'v3' into generalize-stateful-store
ad3df88
* v3:
chore: update pre-commit hooks (zarr-developers#2222)
fix: validate v3 dtypes when loading/creating v3 metadata (zarr-developers#2209)
fix typo in store integration test (zarr-developers#2223)
Basic Zarr-python 2.x compatibility changes (zarr-developers#2098)
Make Group.arrays, groups compatible with v2 (zarr-developers#2213)
Typing fixes to test_indexing (zarr-developers#2193)
Default to RemoteStore for fsspec URIs (zarr-developers#2198)
Make MemoryStore serialiazable (zarr-developers#2204)
[v3] Implement Group methods for empty, full, ones, and zeros (zarr-developers#2210)
implement `store.list_prefix` and `store._set_many` (zarr-developers#2064)
Fixed codec for v2 data with no fill value (zarr-developers#2207)
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, '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
fix: validate v3 dtypes when loading/creating v3 metadata - #2209
Merged
jhamman merged 10 commits into
zarr-developers:v3from 
jhamman:fix/v3-valid-dtypes
Sep 23, 2024
Merged
fix: validate v3 dtypes when loading/creating v3 metadata#2209
jhamman merged 10 commits into
zarr-developers:v3from 
jhamman:fix/v3-valid-dtypes
Conversation
@jhamman
@jhammanjhamman
commented
Sep 18, 2024•

edited

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This PR validates data types in v3 metadata. The behavior implemented raises an error if a data type outside of the current v3 spec is discovered in either a zarr.json metadata document or in the Array constructor.
xref: #2200
TODO:
  •  Add unit tests and/or doctests in docstrings
  •  Add docstrings and API docs for any new/modified user-facing classes and functions
  •  New/modified features documented in docs/tutorial.rst
  •  Changes documented in docs/release.rst
  •  GitHub Actions have all passed
  •  Test coverage is 100% (Codecov passes)
@jhammanjhamman
mentioned this pull request
Sep 18, 2024
 Closed

@jhamman
jhamman
requested a review
from d-v-bSeptember 19, 2024 17:45
jhamman
jhamman
commented
Sep 19, 2024
View reviewed changes
Comment threadsrc/zarr/core/array_spec.py
Outdated

 ) -> None:
 shape_parsed = parse_shapelike(shape)
 dtype_parsed = parse_dtype(dtype)
 dtype_parsed = dtype # parsing is likely not needed here
@jhammanjhammanSep 19, 2024

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Suggested change

dtype_parsed=dtype# parsing is likely not needed here
dtype_parsed=dtype
The input type is already np.dtype[Any] so I don't think we need to parse this.
jhamman
jhamman
commented
Sep 19, 2024
View reviewed changes
Comment threadsrc/zarr/core/metadata/v2.py

def parse_dtype(data: npt.DTypeLike) -> np.dtype[Any]:
 # todo: real validation
 return np.dtype(data)
@jhammanjhammanSep 19, 2024

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we now parse v2 and v3 dtypes differently.
jhamman
jhamman
commented
Sep 19, 2024
View reviewed changes
Comment threadsrc/zarr/testing/strategies.py
 dtype=npst.scalar_dtypes().filter(lambda x: x.kind != "m"),
 dtype=npst.scalar_dtypes().filter(
 lambda x: (x.kind not in ["m", "M"]) and (x.byteorder not in [">"])
 ),
@jhammanjhammanSep 19, 2024

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It is not clear to me how endianness works in v3. As far as I can tell, we are not handling this in a meaningful way today.
cc @dcherian and @d-v-b
@dcheriandcherianSep 19, 2024

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I concur. It's not being handled today
jhamman
jhamman
commented
Sep 19, 2024
View reviewed changes
Comment threadtests/v3/test_metadata/test_v3.py
async def test_datetime_metadata(fill_value: int, precision: str) -> None:
# @pytest.mark.parametrize("fill_value", [-1, 0, 1, 2932897])
# @pytest.mark.parametrize("precision", ["ns", "D"])
# async def test_datetime_metadata(fill_value: int, precision: str) -> None:
@jhammanjhammanSep 19, 2024

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this test was creating an invalid dtype (datetime). We can leave it in place and bring it back when there is support for this dtype in v3.
@jhammanjhamman
mentioned this pull request
Sep 20, 2024
 Closed

6 tasks
jhamman
jhamman
commented
Sep 21, 2024
View reviewed changes
Comment threadtests/v3/test_metadata/test_v3.py
 (0, "int16"),
 (1e10, "uint64"),
 (-999, "float32"),
 (1e32, "float64"),
@jhammanjhammanSep 21, 2024

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also add a test for NaN fill values
d-v-b
d-v-b
reviewed
Sep 23, 2024
View reviewed changes
Comment threadsrc/zarr/core/metadata/v3.py
d-v-b
d-v-b
reviewed
Sep 23, 2024
View reviewed changes
Comment threadsrc/zarr/core/array_spec.py
d-v-b
d-v-b
reviewed
Sep 23, 2024
View reviewed changes
Comment threadsrc/zarr/core/metadata/v2.py
d-v-b
d-v-b
reviewed
Sep 23, 2024
View reviewed changes
Comment threadsrc/zarr/core/metadata/v3.py
d-v-b
d-v-b
reviewed
Sep 23, 2024
View reviewed changes
Comment threadsrc/zarr/core/metadata/v3.py
Outdated

@jhamman@d-v-b
Update src/zarr/core/metadata/v3.py
9736b4b
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
d-v-b
d-v-b
reviewed
Sep 23, 2024
View reviewed changes
Comment threadsrc/zarr/core/metadata/v3.py
@d-v-b
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Sep 23, 2024

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this looks great, thanks!
@jhamman
jhamman
merged commit 2d3a36c
into
zarr-developers:v3Sep 23, 2024
@jhammanjhamman
mentioned this pull request
Sep 24, 2024

Closed

dcherian added a commit
to dcherian/zarr-python
that referenced
this pull request
Sep 24, 2024
@dcherian
Merge branch 'v3' into generalize-stateful-store
ad3df88
* v3:
chore: update pre-commit hooks (zarr-developers#2222)
fix: validate v3 dtypes when loading/creating v3 metadata (zarr-developers#2209)
fix typo in store integration test (zarr-developers#2223)
Basic Zarr-python 2.x compatibility changes (zarr-developers#2098)
Make Group.arrays, groups compatible with v2 (zarr-developers#2213)
Typing fixes to test_indexing (zarr-developers#2193)
Default to RemoteStore for fsspec URIs (zarr-developers#2198)
Make MemoryStore serialiazable (zarr-developers#2204)
[v3] Implement Group methods for empty, full, ones, and zeros (zarr-developers#2210)
implement `store.list_prefix` and `store._set_many` (zarr-developers#2064)
Fixed codec for v2 data with no fill value (zarr-developers#2207)
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