transform and models by giovp · Pull Request #52 · scverse/spatialdata

giovp · 2022-11-29T08:40:33Z

This PR implements transforms (#22 and model validation and parsing (#40) for SpatialData.

* add io test * [pre-commit.ci] pre-commit autoupdate (#13) updates: - [github.com/asottile/yesqa: v1.3.0 → v1.4.0](asottile/yesqa@v1.3.0...v1.4.0) - [github.com/PyCQA/flake8: 5.0.1 → 5.0.4](PyCQA/flake8@5.0.1...5.0.4) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

…ldata into feature/transform

see discussion here ome/ome-zarr-py#219

…ldata into feature/transform

for more information, see https://pre-commit.ci

…ldata into feature/transform

for more information, see https://pre-commit.ci

…ldata into feature/transform

for more information, see https://pre-commit.ci

…ldata into feature/transform

giovp · 2022-12-10T15:52:36Z

ok all models test are now there. the table model is a bit flaky but I think fine for now, expecting changes as we play around with datasets. @LucaMarconato IMHO merge whenever you want

LucaMarconato · 2022-12-10T17:00:12Z

Great @giovp, good for me. Please @kevinyamauchi or @ivirshup merge anytime

kevinyamauchi

Thanks for this massive effort @giovp and @LucaMarconato ! This looks like a great start. I propose to optimistically merge this tonight.

I have made a few comments below that I will turn into issues so we can address them as the code base stabilizes.

Thanks again ! 🚀

There are a lot of commented out blocks of code. We should delete them.
Many functions are missing docstrings
The tests look fairly comprehensive, but it is difficult to tell what they are testing. I think we should both break them up into smaller tests and add comments/docstrings to explain what they are testing. Tests are an important form of documentation for contributors - especially contributors who are not part of writing the original code!

kevinyamauchi · 2022-12-11T17:23:06Z

 @property
- def axes_names(self) -> List[str]:
- return [ax.name for ax in self._axes]
+ def axes_names(self) -> Tuple[str, ...]:


I think it makes more sense grammatically to all these axis_names/axis_types

Made an issue #67

kevinyamauchi · 2022-12-11T17:24:36Z

+
+
+@singledispatch
+def get_transform(e: SpatialElement) -> BaseTransformation:


I think we should add a docstring here.

Included this in issue #65

kevinyamauchi · 2022-12-11T17:27:04Z

@@ -0,0 +1,578 @@
+"""This file contains models and schema for SpatialData"""


I think we should split up the models into separate files so it is easier to read/navigate.

Made an issue #66

kevinyamauchi · 2022-12-11T17:36:16Z

+ self.rotation = self._parse_list_into_array(rotation)
+
+ @classmethod
+ def _from_dict(cls, d: Transformation_t) -> Self: # type: ignore[valid-type]


Is this the correct type annotation?

Yes but mypy complains when it see Self. Maybe someone have a look please.

this is indeed weird but I think Self might be valid in newer python versions?

giovp · 2022-12-12T12:45:28Z

LGTM!

giovp · 2022-11-29T08:40:33Z

This PR implements transforms (#22 and model validation and parsing (#40) for SpatialData.

* add io test * [pre-commit.ci] pre-commit autoupdate (#13) updates: - [github.com/asottile/yesqa: v1.3.0 → v1.4.0](asottile/yesqa@v1.3.0...v1.4.0) - [github.com/PyCQA/flake8: 5.0.1 → 5.0.4](PyCQA/flake8@5.0.1...5.0.4) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

…ldata into feature/transform

see discussion here ome/ome-zarr-py#219

…ldata into feature/transform

for more information, see https://pre-commit.ci

…ldata into feature/transform

for more information, see https://pre-commit.ci

…ldata into feature/transform

for more information, see https://pre-commit.ci

…ldata into feature/transform

giovp · 2022-12-10T15:52:36Z

ok all models test are now there. the table model is a bit flaky but I think fine for now, expecting changes as we play around with datasets. @LucaMarconato IMHO merge whenever you want

LucaMarconato · 2022-12-10T17:00:12Z

Great @giovp, good for me. Please @kevinyamauchi or @ivirshup merge anytime

kevinyamauchi

Thanks for this massive effort @giovp and @LucaMarconato ! This looks like a great start. I propose to optimistically merge this tonight.

I have made a few comments below that I will turn into issues so we can address them as the code base stabilizes.

Thanks again ! 🚀

There are a lot of commented out blocks of code. We should delete them.
Many functions are missing docstrings
The tests look fairly comprehensive, but it is difficult to tell what they are testing. I think we should both break them up into smaller tests and add comments/docstrings to explain what they are testing. Tests are an important form of documentation for contributors - especially contributors who are not part of writing the original code!

kevinyamauchi · 2022-12-11T17:23:06Z

 @property
- def axes_names(self) -> List[str]:
- return [ax.name for ax in self._axes]
+ def axes_names(self) -> Tuple[str, ...]:


I think it makes more sense grammatically to all these axis_names/axis_types

Made an issue #67

kevinyamauchi · 2022-12-11T17:24:36Z

+
+
+@singledispatch
+def get_transform(e: SpatialElement) -> BaseTransformation:


I think we should add a docstring here.

Included this in issue #65

kevinyamauchi · 2022-12-11T17:27:04Z

@@ -0,0 +1,578 @@
+"""This file contains models and schema for SpatialData"""


I think we should split up the models into separate files so it is easier to read/navigate.

Made an issue #66

kevinyamauchi · 2022-12-11T17:36:16Z

+ self.rotation = self._parse_list_into_array(rotation)
+
+ @classmethod
+ def _from_dict(cls, d: Transformation_t) -> Self: # type: ignore[valid-type]


Is this the correct type annotation?

Yes but mypy complains when it see Self. Maybe someone have a look please.

this is indeed weird but I think Self might be valid in newer python versions?

giovp · 2022-12-12T12:45:28Z

LGTM!

giovp · 2022-11-29T08:40:33Z

This PR implements transforms (#22 and model validation and parsing (#40) for SpatialData.

* add io test * [pre-commit.ci] pre-commit autoupdate (#13) updates: - [github.com/asottile/yesqa: v1.3.0 → v1.4.0](asottile/yesqa@v1.3.0...v1.4.0) - [github.com/PyCQA/flake8: 5.0.1 → 5.0.4](PyCQA/flake8@5.0.1...5.0.4) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

…ldata into feature/transform

see discussion here ome/ome-zarr-py#219

…ldata into feature/transform

for more information, see https://pre-commit.ci

…ldata into feature/transform

for more information, see https://pre-commit.ci

…ldata into feature/transform

for more information, see https://pre-commit.ci

…ldata into feature/transform

giovp · 2022-12-10T15:52:36Z

ok all models test are now there. the table model is a bit flaky but I think fine for now, expecting changes as we play around with datasets. @LucaMarconato IMHO merge whenever you want

LucaMarconato · 2022-12-10T17:00:12Z

Great @giovp, good for me. Please @kevinyamauchi or @ivirshup merge anytime

kevinyamauchi

Thanks for this massive effort @giovp and @LucaMarconato ! This looks like a great start. I propose to optimistically merge this tonight.

I have made a few comments below that I will turn into issues so we can address them as the code base stabilizes.

Thanks again ! 🚀

There are a lot of commented out blocks of code. We should delete them.
Many functions are missing docstrings
The tests look fairly comprehensive, but it is difficult to tell what they are testing. I think we should both break them up into smaller tests and add comments/docstrings to explain what they are testing. Tests are an important form of documentation for contributors - especially contributors who are not part of writing the original code!

kevinyamauchi · 2022-12-11T17:23:06Z

 @property
- def axes_names(self) -> List[str]:
- return [ax.name for ax in self._axes]
+ def axes_names(self) -> Tuple[str, ...]:


I think it makes more sense grammatically to all these axis_names/axis_types

Made an issue #67

kevinyamauchi · 2022-12-11T17:24:36Z

+
+
+@singledispatch
+def get_transform(e: SpatialElement) -> BaseTransformation:


I think we should add a docstring here.

Included this in issue #65

kevinyamauchi · 2022-12-11T17:27:04Z

@@ -0,0 +1,578 @@
+"""This file contains models and schema for SpatialData"""


I think we should split up the models into separate files so it is easier to read/navigate.

Made an issue #66

kevinyamauchi · 2022-12-11T17:36:16Z

+ self.rotation = self._parse_list_into_array(rotation)
+
+ @classmethod
+ def _from_dict(cls, d: Transformation_t) -> Self: # type: ignore[valid-type]


Is this the correct type annotation?

Yes but mypy complains when it see Self. Maybe someone have a look please.

this is indeed weird but I think Self might be valid in newer python versions?

giovp · 2022-12-12T12:45:28Z

LGTM!

giovp · 2022-11-29T08:40:33Z

This PR implements transforms (#22 and model validation and parsing (#40) for SpatialData.

* add io test * [pre-commit.ci] pre-commit autoupdate (#13) updates: - [github.com/asottile/yesqa: v1.3.0 → v1.4.0](asottile/yesqa@v1.3.0...v1.4.0) - [github.com/PyCQA/flake8: 5.0.1 → 5.0.4](PyCQA/flake8@5.0.1...5.0.4) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

…ldata into feature/transform

see discussion here ome/ome-zarr-py#219

…ldata into feature/transform

for more information, see https://pre-commit.ci

…ldata into feature/transform

for more information, see https://pre-commit.ci

…ldata into feature/transform

for more information, see https://pre-commit.ci

…ldata into feature/transform

giovp · 2022-12-10T15:52:36Z

ok all models test are now there. the table model is a bit flaky but I think fine for now, expecting changes as we play around with datasets. @LucaMarconato IMHO merge whenever you want

LucaMarconato · 2022-12-10T17:00:12Z

Great @giovp, good for me. Please @kevinyamauchi or @ivirshup merge anytime

kevinyamauchi

Thanks for this massive effort @giovp and @LucaMarconato ! This looks like a great start. I propose to optimistically merge this tonight.

I have made a few comments below that I will turn into issues so we can address them as the code base stabilizes.

Thanks again ! 🚀

There are a lot of commented out blocks of code. We should delete them.
Many functions are missing docstrings
The tests look fairly comprehensive, but it is difficult to tell what they are testing. I think we should both break them up into smaller tests and add comments/docstrings to explain what they are testing. Tests are an important form of documentation for contributors - especially contributors who are not part of writing the original code!

kevinyamauchi · 2022-12-11T17:23:06Z

 @property
- def axes_names(self) -> List[str]:
- return [ax.name for ax in self._axes]
+ def axes_names(self) -> Tuple[str, ...]:


I think it makes more sense grammatically to all these axis_names/axis_types

Made an issue #67

kevinyamauchi · 2022-12-11T17:24:36Z

+
+
+@singledispatch
+def get_transform(e: SpatialElement) -> BaseTransformation:


I think we should add a docstring here.

Included this in issue #65

kevinyamauchi · 2022-12-11T17:27:04Z

@@ -0,0 +1,578 @@
+"""This file contains models and schema for SpatialData"""


I think we should split up the models into separate files so it is easier to read/navigate.

Made an issue #66

kevinyamauchi · 2022-12-11T17:36:16Z

+ self.rotation = self._parse_list_into_array(rotation)
+
+ @classmethod
+ def _from_dict(cls, d: Transformation_t) -> Self: # type: ignore[valid-type]


Is this the correct type annotation?

Yes but mypy complains when it see Self. Maybe someone have a look please.

this is indeed weird but I think Self might be valid in newer python versions?

giovp · 2022-12-12T12:45:28Z

LGTM!

giovp · 2022-11-29T08:40:33Z

This PR implements transforms (#22 and model validation and parsing (#40) for SpatialData.

* add io test * [pre-commit.ci] pre-commit autoupdate (#13) updates: - [github.com/asottile/yesqa: v1.3.0 → v1.4.0](asottile/yesqa@v1.3.0...v1.4.0) - [github.com/PyCQA/flake8: 5.0.1 → 5.0.4](PyCQA/flake8@5.0.1...5.0.4) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

…ldata into feature/transform

see discussion here ome/ome-zarr-py#219

…ldata into feature/transform

for more information, see https://pre-commit.ci

…ldata into feature/transform

for more information, see https://pre-commit.ci

…ldata into feature/transform

for more information, see https://pre-commit.ci

…ldata into feature/transform

giovp · 2022-12-10T15:52:36Z

ok all models test are now there. the table model is a bit flaky but I think fine for now, expecting changes as we play around with datasets. @LucaMarconato IMHO merge whenever you want

LucaMarconato · 2022-12-10T17:00:12Z

Great @giovp, good for me. Please @kevinyamauchi or @ivirshup merge anytime

kevinyamauchi

Thanks for this massive effort @giovp and @LucaMarconato ! This looks like a great start. I propose to optimistically merge this tonight.

I have made a few comments below that I will turn into issues so we can address them as the code base stabilizes.

Thanks again ! 🚀

There are a lot of commented out blocks of code. We should delete them.
Many functions are missing docstrings
The tests look fairly comprehensive, but it is difficult to tell what they are testing. I think we should both break them up into smaller tests and add comments/docstrings to explain what they are testing. Tests are an important form of documentation for contributors - especially contributors who are not part of writing the original code!

kevinyamauchi · 2022-12-11T17:23:06Z

 @property
- def axes_names(self) -> List[str]:
- return [ax.name for ax in self._axes]
+ def axes_names(self) -> Tuple[str, ...]:


I think it makes more sense grammatically to all these axis_names/axis_types

Made an issue #67

kevinyamauchi · 2022-12-11T17:24:36Z

+
+
+@singledispatch
+def get_transform(e: SpatialElement) -> BaseTransformation:


I think we should add a docstring here.

Included this in issue #65

kevinyamauchi · 2022-12-11T17:27:04Z

@@ -0,0 +1,578 @@
+"""This file contains models and schema for SpatialData"""


I think we should split up the models into separate files so it is easier to read/navigate.

Made an issue #66

kevinyamauchi · 2022-12-11T17:36:16Z

+ self.rotation = self._parse_list_into_array(rotation)
+
+ @classmethod
+ def _from_dict(cls, d: Transformation_t) -> Self: # type: ignore[valid-type]


Is this the correct type annotation?

Yes but mypy complains when it see Self. Maybe someone have a look please.

this is indeed weird but I think Self might be valid in newer python versions?

giovp · 2022-12-12T12:45:28Z

LGTM!

giovp · 2022-11-29T08:40:33Z

This PR implements transforms (#22 and model validation and parsing (#40) for SpatialData.

* add io test * [pre-commit.ci] pre-commit autoupdate (#13) updates: - [github.com/asottile/yesqa: v1.3.0 → v1.4.0](asottile/yesqa@v1.3.0...v1.4.0) - [github.com/PyCQA/flake8: 5.0.1 → 5.0.4](PyCQA/flake8@5.0.1...5.0.4) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

…ldata into feature/transform

see discussion here ome/ome-zarr-py#219

…ldata into feature/transform

for more information, see https://pre-commit.ci

…ldata into feature/transform

for more information, see https://pre-commit.ci

…ldata into feature/transform

for more information, see https://pre-commit.ci

…ldata into feature/transform

giovp · 2022-12-10T15:52:36Z

ok all models test are now there. the table model is a bit flaky but I think fine for now, expecting changes as we play around with datasets. @LucaMarconato IMHO merge whenever you want

LucaMarconato · 2022-12-10T17:00:12Z

Great @giovp, good for me. Please @kevinyamauchi or @ivirshup merge anytime

kevinyamauchi

Thanks for this massive effort @giovp and @LucaMarconato ! This looks like a great start. I propose to optimistically merge this tonight.

I have made a few comments below that I will turn into issues so we can address them as the code base stabilizes.

Thanks again ! 🚀

There are a lot of commented out blocks of code. We should delete them.
Many functions are missing docstrings
The tests look fairly comprehensive, but it is difficult to tell what they are testing. I think we should both break them up into smaller tests and add comments/docstrings to explain what they are testing. Tests are an important form of documentation for contributors - especially contributors who are not part of writing the original code!

kevinyamauchi · 2022-12-11T17:23:06Z

 @property
- def axes_names(self) -> List[str]:
- return [ax.name for ax in self._axes]
+ def axes_names(self) -> Tuple[str, ...]:


I think it makes more sense grammatically to all these axis_names/axis_types

Made an issue #67

kevinyamauchi · 2022-12-11T17:24:36Z

+
+
+@singledispatch
+def get_transform(e: SpatialElement) -> BaseTransformation:


I think we should add a docstring here.

Included this in issue #65

kevinyamauchi · 2022-12-11T17:27:04Z

@@ -0,0 +1,578 @@
+"""This file contains models and schema for SpatialData"""


I think we should split up the models into separate files so it is easier to read/navigate.

Made an issue #66

kevinyamauchi · 2022-12-11T17:36:16Z

+ self.rotation = self._parse_list_into_array(rotation)
+
+ @classmethod
+ def _from_dict(cls, d: Transformation_t) -> Self: # type: ignore[valid-type]


Is this the correct type annotation?

Yes but mypy complains when it see Self. Maybe someone have a look please.

this is indeed weird but I think Self might be valid in newer python versions?

giovp · 2022-12-12T12:45:28Z

LGTM!

giovp · 2022-11-29T08:40:33Z

This PR implements transforms (#22 and model validation and parsing (#40) for SpatialData.

* add io test * [pre-commit.ci] pre-commit autoupdate (#13) updates: - [github.com/asottile/yesqa: v1.3.0 → v1.4.0](asottile/yesqa@v1.3.0...v1.4.0) - [github.com/PyCQA/flake8: 5.0.1 → 5.0.4](PyCQA/flake8@5.0.1...5.0.4) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

…ldata into feature/transform

see discussion here ome/ome-zarr-py#219

…ldata into feature/transform

for more information, see https://pre-commit.ci

…ldata into feature/transform

for more information, see https://pre-commit.ci

…ldata into feature/transform

for more information, see https://pre-commit.ci

…ldata into feature/transform

giovp · 2022-12-10T15:52:36Z

ok all models test are now there. the table model is a bit flaky but I think fine for now, expecting changes as we play around with datasets. @LucaMarconato IMHO merge whenever you want

LucaMarconato · 2022-12-10T17:00:12Z

Great @giovp, good for me. Please @kevinyamauchi or @ivirshup merge anytime

kevinyamauchi

Thanks for this massive effort @giovp and @LucaMarconato ! This looks like a great start. I propose to optimistically merge this tonight.

I have made a few comments below that I will turn into issues so we can address them as the code base stabilizes.

Thanks again ! 🚀

There are a lot of commented out blocks of code. We should delete them.
Many functions are missing docstrings
The tests look fairly comprehensive, but it is difficult to tell what they are testing. I think we should both break them up into smaller tests and add comments/docstrings to explain what they are testing. Tests are an important form of documentation for contributors - especially contributors who are not part of writing the original code!

kevinyamauchi · 2022-12-11T17:23:06Z

 @property
- def axes_names(self) -> List[str]:
- return [ax.name for ax in self._axes]
+ def axes_names(self) -> Tuple[str, ...]:


I think it makes more sense grammatically to all these axis_names/axis_types

Made an issue #67

kevinyamauchi · 2022-12-11T17:24:36Z

+
+
+@singledispatch
+def get_transform(e: SpatialElement) -> BaseTransformation:


I think we should add a docstring here.

Included this in issue #65

kevinyamauchi · 2022-12-11T17:27:04Z

@@ -0,0 +1,578 @@
+"""This file contains models and schema for SpatialData"""


I think we should split up the models into separate files so it is easier to read/navigate.

Made an issue #66

kevinyamauchi · 2022-12-11T17:36:16Z

+ self.rotation = self._parse_list_into_array(rotation)
+
+ @classmethod
+ def _from_dict(cls, d: Transformation_t) -> Self: # type: ignore[valid-type]


Is this the correct type annotation?

Yes but mypy complains when it see Self. Maybe someone have a look please.

this is indeed weird but I think Self might be valid in newer python versions?

giovp · 2022-12-12T12:45:28Z

LGTM!

giovp · 2022-11-29T08:40:33Z

This PR implements transforms (#22 and model validation and parsing (#40) for SpatialData.

* add io test * [pre-commit.ci] pre-commit autoupdate (#13) updates: - [github.com/asottile/yesqa: v1.3.0 → v1.4.0](asottile/yesqa@v1.3.0...v1.4.0) - [github.com/PyCQA/flake8: 5.0.1 → 5.0.4](PyCQA/flake8@5.0.1...5.0.4) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

…ldata into feature/transform

see discussion here ome/ome-zarr-py#219

…ldata into feature/transform

for more information, see https://pre-commit.ci

…ldata into feature/transform

for more information, see https://pre-commit.ci

…ldata into feature/transform

for more information, see https://pre-commit.ci

…ldata into feature/transform

giovp · 2022-12-10T15:52:36Z

ok all models test are now there. the table model is a bit flaky but I think fine for now, expecting changes as we play around with datasets. @LucaMarconato IMHO merge whenever you want

LucaMarconato · 2022-12-10T17:00:12Z

Great @giovp, good for me. Please @kevinyamauchi or @ivirshup merge anytime

kevinyamauchi

Thanks for this massive effort @giovp and @LucaMarconato ! This looks like a great start. I propose to optimistically merge this tonight.

I have made a few comments below that I will turn into issues so we can address them as the code base stabilizes.

Thanks again ! 🚀

There are a lot of commented out blocks of code. We should delete them.
Many functions are missing docstrings
The tests look fairly comprehensive, but it is difficult to tell what they are testing. I think we should both break them up into smaller tests and add comments/docstrings to explain what they are testing. Tests are an important form of documentation for contributors - especially contributors who are not part of writing the original code!

kevinyamauchi · 2022-12-11T17:23:06Z

 @property
- def axes_names(self) -> List[str]:
- return [ax.name for ax in self._axes]
+ def axes_names(self) -> Tuple[str, ...]:


I think it makes more sense grammatically to all these axis_names/axis_types

Made an issue #67

kevinyamauchi · 2022-12-11T17:24:36Z

+
+
+@singledispatch
+def get_transform(e: SpatialElement) -> BaseTransformation:


I think we should add a docstring here.

Included this in issue #65

kevinyamauchi · 2022-12-11T17:27:04Z

@@ -0,0 +1,578 @@
+"""This file contains models and schema for SpatialData"""


I think we should split up the models into separate files so it is easier to read/navigate.

Made an issue #66

kevinyamauchi · 2022-12-11T17:36:16Z

+ self.rotation = self._parse_list_into_array(rotation)
+
+ @classmethod
+ def _from_dict(cls, d: Transformation_t) -> Self: # type: ignore[valid-type]


Is this the correct type annotation?

Yes but mypy complains when it see Self. Maybe someone have a look please.

this is indeed weird but I think Self might be valid in newer python versions?

giovp · 2022-12-12T12:45:28Z

LGTM!

giovpand others added 30 commits August 17, 2022 09:05

add io test
cb4ddf6

io for transforms, fixed bugs when testing on the merfish dataset
0981821

merged with main
707f047

bugfix
b7cb647

fixed tests
561d252

Merge branch 'tests/io' into feature/transform
b10419c

workaround against bug with backed dask arrays
140198f

Merge branch 'feature/transform' ofhttps://github.com/scverse/spatia…
5764882
…ldata into feature/transform

woring on a bug with io; fixed repr for points
7ece121

quick code changes for to_zarr bug report
ce23cb7

patched tests after discussion on the to_zarr bug
67c1d7a
see discussion here ome/ome-zarr-py#219

more io tests, fixed related bugs
6221fa2

first io support for polygons
f36ed27

fix precommits
087600d

fix flake8
14c4cd0

wip implementation of the ngff transform
98cd743

Merge branch 'feature/transform' ofhttps://github.com/scverse/spatia…
f8517d7
…ldata into feature/transform

[pre-commit.ci] auto fixes from pre-commit.com hooks
ba85569
for more information, see https://pre-commit.ci

wip transformations, tests pass but io not compatible
3db58b7

Merge branch 'feature/transform' ofhttps://github.com/scverse/spatia…
b694423
…ldata into feature/transform

[pre-commit.ci] auto fixes from pre-commit.com hooks
db61de8
for more information, see https://pre-commit.ci

wip write for new transforms specs
3a83b21

Merge branch 'feature/transform' ofhttps://github.com/scverse/spatia…
569abdd
…ldata into feature/transform

[pre-commit.ci] auto fixes from pre-commit.com hooks
018f290
for more information, see https://pre-commit.ci

fstring in format.py
833bb5c

Merge branch 'feature/transform' ofhttps://github.com/scverse/spatia…
ccfe5e9
…ldata into feature/transform

fix in format.py
8460500

io working for the new transform specs (no coord spaces yet)
f00f7fd

fix in affine
983b638

giovpand others added 4 commits December 8, 2022 23:18

fix models
ea06156

add tqdm
c81008a

fix in test_models
a236e77

fix polygon model
b5e73f3

kevinyamauchi reviewed Dec 10, 2022
View reviewed changes

Comment threadtests/_core/test_transformations.py

giovp added 5 commits December 10, 2022 15:13

test models points
5ed1a21

add test shapes
e6671a2

test table model
f026964

fix table model
fa55f59

try codecov one more time
533fb7a

install codecov
0ef1aa5

LucaMarconato self-requested a review December 10, 2022 17:00

LucaMarconato approved these changes Dec 10, 2022
View reviewed changes

kevinyamauchi approved these changes Dec 11, 2022
View reviewed changes

This was referenced Dec 11, 2022
code cleanup #65
Closed
refactor: split up models into separate files #66
Closed

giovpand others added 6 commits December 12, 2022 13:13

Merge branch 'main' into feature/transform_and_schema
44edabd

update docs
efda324

add register
1bf287d

Merge branch 'fix/docs' into feature/transform_and_schema
d5e7a60

suppress warning
32dd480

fix docs
933ea31

giovp merged commit ef9b92a into mainDec 12, 2022

giovp deleted the feature/transform_and_schema branch December 12, 2022 12:45

kevinyamauchi mentioned this pull request Dec 13, 2022
legacy code to port #48
Closed
3 tasks

giovp mentioned this pull request Dec 15, 2022
write to zarr fails when SpatialImage is created from a xarray.DataArray#59
Closed

kevinyamauchi mentioned this pull request Dec 15, 2022
SpatialData specs proposal #12
Closed

giovpand others added 30 commits August 17, 2022 09:05

add io test
cb4ddf6

io for transforms, fixed bugs when testing on the merfish dataset
0981821

merged with main
707f047

bugfix
b7cb647

fixed tests
561d252

Merge branch 'tests/io' into feature/transform
b10419c

workaround against bug with backed dask arrays
140198f

Merge branch 'feature/transform' ofhttps://github.com/scverse/spatia…
5764882
…ldata into feature/transform

woring on a bug with io; fixed repr for points
7ece121

quick code changes for to_zarr bug report
ce23cb7

patched tests after discussion on the to_zarr bug
67c1d7a
see discussion here ome/ome-zarr-py#219

more io tests, fixed related bugs
6221fa2

first io support for polygons
f36ed27

fix precommits
087600d

fix flake8
14c4cd0

wip implementation of the ngff transform
98cd743

Merge branch 'feature/transform' ofhttps://github.com/scverse/spatia…
f8517d7
…ldata into feature/transform

[pre-commit.ci] auto fixes from pre-commit.com hooks
ba85569
for more information, see https://pre-commit.ci

wip transformations, tests pass but io not compatible
3db58b7

Merge branch 'feature/transform' ofhttps://github.com/scverse/spatia…
b694423
…ldata into feature/transform

[pre-commit.ci] auto fixes from pre-commit.com hooks
db61de8
for more information, see https://pre-commit.ci

wip write for new transforms specs
3a83b21

Merge branch 'feature/transform' ofhttps://github.com/scverse/spatia…
569abdd
…ldata into feature/transform

[pre-commit.ci] auto fixes from pre-commit.com hooks
018f290
for more information, see https://pre-commit.ci

fstring in format.py
833bb5c

Merge branch 'feature/transform' ofhttps://github.com/scverse/spatia…
ccfe5e9
…ldata into feature/transform

fix in format.py
8460500

io working for the new transform specs (no coord spaces yet)
f00f7fd

fix in affine
983b638

giovpand others added 4 commits December 8, 2022 23:18

fix models
ea06156

add tqdm
c81008a

fix in test_models
a236e77

fix polygon model
b5e73f3

kevinyamauchi reviewed Dec 10, 2022
View reviewed changes

Comment threadtests/_core/test_transformations.py

giovp added 5 commits December 10, 2022 15:13

test models points
5ed1a21

add test shapes
e6671a2

test table model
f026964

fix table model
fa55f59

try codecov one more time
533fb7a

install codecov
0ef1aa5

LucaMarconato self-requested a review December 10, 2022 17:00

LucaMarconato approved these changes Dec 10, 2022
View reviewed changes

kevinyamauchi approved these changes Dec 11, 2022
View reviewed changes

This was referenced Dec 11, 2022
code cleanup #65
Closed
refactor: split up models into separate files #66
Closed

giovpand others added 6 commits December 12, 2022 13:13

Merge branch 'main' into feature/transform_and_schema
44edabd

update docs
efda324

add register
1bf287d

Merge branch 'fix/docs' into feature/transform_and_schema
d5e7a60

suppress warning
32dd480

fix docs
933ea31

giovp merged commit ef9b92a into mainDec 12, 2022

giovp deleted the feature/transform_and_schema branch December 12, 2022 12:45

kevinyamauchi mentioned this pull request Dec 13, 2022
legacy code to port #48
Closed
3 tasks

giovp mentioned this pull request Dec 15, 2022
write to zarr fails when SpatialImage is created from a xarray.DataArray#59
Closed

kevinyamauchi mentioned this pull request Dec 15, 2022
SpatialData specs proposal #12
Closed

giovpand others added 30 commits August 17, 2022 09:05

add io test
cb4ddf6

io for transforms, fixed bugs when testing on the merfish dataset
0981821

merged with main
707f047

bugfix
b7cb647

fixed tests
561d252

Merge branch 'tests/io' into feature/transform
b10419c

workaround against bug with backed dask arrays
140198f

Merge branch 'feature/transform' ofhttps://github.com/scverse/spatia…
5764882
…ldata into feature/transform

woring on a bug with io; fixed repr for points
7ece121

quick code changes for to_zarr bug report
ce23cb7

patched tests after discussion on the to_zarr bug
67c1d7a
see discussion here ome/ome-zarr-py#219

more io tests, fixed related bugs
6221fa2

first io support for polygons
f36ed27

fix precommits
087600d

fix flake8
14c4cd0

wip implementation of the ngff transform
98cd743

Merge branch 'feature/transform' ofhttps://github.com/scverse/spatia…
f8517d7
…ldata into feature/transform

[pre-commit.ci] auto fixes from pre-commit.com hooks
ba85569
for more information, see https://pre-commit.ci

wip transformations, tests pass but io not compatible
3db58b7

Merge branch 'feature/transform' ofhttps://github.com/scverse/spatia…
b694423
…ldata into feature/transform

[pre-commit.ci] auto fixes from pre-commit.com hooks
db61de8
for more information, see https://pre-commit.ci

wip write for new transforms specs
3a83b21

Merge branch 'feature/transform' ofhttps://github.com/scverse/spatia…
569abdd
…ldata into feature/transform

[pre-commit.ci] auto fixes from pre-commit.com hooks
018f290
for more information, see https://pre-commit.ci

fstring in format.py
833bb5c

Merge branch 'feature/transform' ofhttps://github.com/scverse/spatia…
ccfe5e9
…ldata into feature/transform

fix in format.py
8460500

io working for the new transform specs (no coord spaces yet)
f00f7fd

fix in affine
983b638

giovpand others added 4 commits December 8, 2022 23:18

fix models
ea06156

add tqdm
c81008a

fix in test_models
a236e77

fix polygon model
b5e73f3

kevinyamauchi reviewed Dec 10, 2022
View reviewed changes

Comment threadtests/_core/test_transformations.py

giovp added 5 commits December 10, 2022 15:13

test models points
5ed1a21

add test shapes
e6671a2

test table model
f026964

fix table model
fa55f59

try codecov one more time
533fb7a

install codecov
0ef1aa5

LucaMarconato self-requested a review December 10, 2022 17:00

LucaMarconato approved these changes Dec 10, 2022
View reviewed changes

kevinyamauchi approved these changes Dec 11, 2022
View reviewed changes

This was referenced Dec 11, 2022
code cleanup #65
Closed
refactor: split up models into separate files #66
Closed

giovpand others added 6 commits December 12, 2022 13:13

Merge branch 'main' into feature/transform_and_schema
44edabd

update docs
efda324

add register
1bf287d

Merge branch 'fix/docs' into feature/transform_and_schema
d5e7a60

suppress warning
32dd480

fix docs
933ea31

giovp merged commit ef9b92a into mainDec 12, 2022

giovp deleted the feature/transform_and_schema branch December 12, 2022 12:45

kevinyamauchi mentioned this pull request Dec 13, 2022
legacy code to port #48
Closed
3 tasks

giovp mentioned this pull request Dec 15, 2022
write to zarr fails when SpatialImage is created from a xarray.DataArray#59
Closed

kevinyamauchi mentioned this pull request Dec 15, 2022
SpatialData specs proposal #12
Closed

giovpand others added 30 commits August 17, 2022 09:05

add io test
cb4ddf6

io for transforms, fixed bugs when testing on the merfish dataset
0981821

merged with main
707f047

bugfix
b7cb647

fixed tests
561d252

Merge branch 'tests/io' into feature/transform
b10419c

workaround against bug with backed dask arrays
140198f

Merge branch 'feature/transform' ofhttps://github.com/scverse/spatia…
5764882
…ldata into feature/transform

woring on a bug with io; fixed repr for points
7ece121

quick code changes for to_zarr bug report
ce23cb7

patched tests after discussion on the to_zarr bug
67c1d7a
see discussion here ome/ome-zarr-py#219

more io tests, fixed related bugs
6221fa2

first io support for polygons
f36ed27

fix precommits
087600d

fix flake8
14c4cd0

wip implementation of the ngff transform
98cd743

Merge branch 'feature/transform' ofhttps://github.com/scverse/spatia…
f8517d7
…ldata into feature/transform

[pre-commit.ci] auto fixes from pre-commit.com hooks
ba85569
for more information, see https://pre-commit.ci

wip transformations, tests pass but io not compatible
3db58b7

Merge branch 'feature/transform' ofhttps://github.com/scverse/spatia…
b694423
…ldata into feature/transform

[pre-commit.ci] auto fixes from pre-commit.com hooks
db61de8
for more information, see https://pre-commit.ci

wip write for new transforms specs
3a83b21

Merge branch 'feature/transform' ofhttps://github.com/scverse/spatia…
569abdd
…ldata into feature/transform

[pre-commit.ci] auto fixes from pre-commit.com hooks
018f290
for more information, see https://pre-commit.ci

fstring in format.py
833bb5c

Merge branch 'feature/transform' ofhttps://github.com/scverse/spatia…
ccfe5e9
…ldata into feature/transform

fix in format.py
8460500

io working for the new transform specs (no coord spaces yet)
f00f7fd

fix in affine
983b638

giovpand others added 4 commits December 8, 2022 23:18

fix models
ea06156

add tqdm
c81008a

fix in test_models
a236e77

fix polygon model
b5e73f3

kevinyamauchi reviewed Dec 10, 2022
View reviewed changes

Comment threadtests/_core/test_transformations.py

giovp added 5 commits December 10, 2022 15:13

test models points
5ed1a21

add test shapes
e6671a2

test table model
f026964

fix table model
fa55f59

try codecov one more time
533fb7a

install codecov
0ef1aa5

LucaMarconato self-requested a review December 10, 2022 17:00

LucaMarconato approved these changes Dec 10, 2022
View reviewed changes

kevinyamauchi approved these changes Dec 11, 2022
View reviewed changes

This was referenced Dec 11, 2022
code cleanup #65
Closed
refactor: split up models into separate files #66
Closed

giovpand others added 6 commits December 12, 2022 13:13

Merge branch 'main' into feature/transform_and_schema
44edabd

update docs
efda324

add register
1bf287d

Merge branch 'fix/docs' into feature/transform_and_schema
d5e7a60

suppress warning
32dd480

fix docs
933ea31

giovp merged commit ef9b92a into mainDec 12, 2022

giovp deleted the feature/transform_and_schema branch December 12, 2022 12:45

kevinyamauchi mentioned this pull request Dec 13, 2022
legacy code to port #48
Closed
3 tasks

giovp mentioned this pull request Dec 15, 2022
write to zarr fails when SpatialImage is created from a xarray.DataArray#59
Closed

kevinyamauchi mentioned this pull request Dec 15, 2022
SpatialData specs proposal #12
Closed

giovpand others added 30 commits August 17, 2022 09:05

add io test
cb4ddf6

io for transforms, fixed bugs when testing on the merfish dataset
0981821

merged with main
707f047

bugfix
b7cb647

fixed tests
561d252

Merge branch 'tests/io' into feature/transform
b10419c

workaround against bug with backed dask arrays
140198f

Merge branch 'feature/transform' ofhttps://github.com/scverse/spatia…
5764882
…ldata into feature/transform

woring on a bug with io; fixed repr for points
7ece121

quick code changes for to_zarr bug report
ce23cb7

patched tests after discussion on the to_zarr bug
67c1d7a
see discussion here ome/ome-zarr-py#219

more io tests, fixed related bugs
6221fa2

first io support for polygons
f36ed27

fix precommits
087600d

fix flake8
14c4cd0

wip implementation of the ngff transform
98cd743

Merge branch 'feature/transform' ofhttps://github.com/scverse/spatia…
f8517d7
…ldata into feature/transform

[pre-commit.ci] auto fixes from pre-commit.com hooks
ba85569
for more information, see https://pre-commit.ci

wip transformations, tests pass but io not compatible
3db58b7

Merge branch 'feature/transform' ofhttps://github.com/scverse/spatia…
b694423
…ldata into feature/transform

[pre-commit.ci] auto fixes from pre-commit.com hooks
db61de8
for more information, see https://pre-commit.ci

wip write for new transforms specs
3a83b21

Merge branch 'feature/transform' ofhttps://github.com/scverse/spatia…
569abdd
…ldata into feature/transform

[pre-commit.ci] auto fixes from pre-commit.com hooks
018f290
for more information, see https://pre-commit.ci

fstring in format.py
833bb5c

Merge branch 'feature/transform' ofhttps://github.com/scverse/spatia…
ccfe5e9
…ldata into feature/transform

fix in format.py
8460500

io working for the new transform specs (no coord spaces yet)
f00f7fd

fix in affine
983b638

giovpand others added 4 commits December 8, 2022 23:18

fix models
ea06156

add tqdm
c81008a

fix in test_models
a236e77

fix polygon model
b5e73f3

kevinyamauchi reviewed Dec 10, 2022
View reviewed changes

Comment threadtests/_core/test_transformations.py

giovp added 5 commits December 10, 2022 15:13

test models points
5ed1a21

add test shapes
e6671a2

test table model
f026964

fix table model
fa55f59

try codecov one more time
533fb7a

install codecov
0ef1aa5

LucaMarconato self-requested a review December 10, 2022 17:00

LucaMarconato approved these changes Dec 10, 2022
View reviewed changes

kevinyamauchi approved these changes Dec 11, 2022
View reviewed changes

This was referenced Dec 11, 2022
code cleanup #65
Closed
refactor: split up models into separate files #66
Closed

giovpand others added 6 commits December 12, 2022 13:13

Merge branch 'main' into feature/transform_and_schema
44edabd

update docs
efda324

add register
1bf287d

Merge branch 'fix/docs' into feature/transform_and_schema
d5e7a60

suppress warning
32dd480

fix docs
933ea31

giovp merged commit ef9b92a into mainDec 12, 2022

giovp deleted the feature/transform_and_schema branch December 12, 2022 12:45

kevinyamauchi mentioned this pull request Dec 13, 2022
legacy code to port #48
Closed
3 tasks

giovp mentioned this pull request Dec 15, 2022
write to zarr fails when SpatialImage is created from a xarray.DataArray#59
Closed

kevinyamauchi mentioned this pull request Dec 15, 2022
SpatialData specs proposal #12
Closed

giovpand others added 30 commits August 17, 2022 09:05

add io test
cb4ddf6

io for transforms, fixed bugs when testing on the merfish dataset
0981821

merged with main
707f047

bugfix
b7cb647

fixed tests
561d252

Merge branch 'tests/io' into feature/transform
b10419c

workaround against bug with backed dask arrays
140198f

Merge branch 'feature/transform' ofhttps://github.com/scverse/spatia…
5764882
…ldata into feature/transform

woring on a bug with io; fixed repr for points
7ece121

quick code changes for to_zarr bug report
ce23cb7

patched tests after discussion on the to_zarr bug
67c1d7a
see discussion here ome/ome-zarr-py#219

more io tests, fixed related bugs
6221fa2

first io support for polygons
f36ed27

fix precommits
087600d

fix flake8
14c4cd0

wip implementation of the ngff transform
98cd743

Merge branch 'feature/transform' ofhttps://github.com/scverse/spatia…
f8517d7
…ldata into feature/transform

[pre-commit.ci] auto fixes from pre-commit.com hooks
ba85569
for more information, see https://pre-commit.ci

wip transformations, tests pass but io not compatible
3db58b7

Merge branch 'feature/transform' ofhttps://github.com/scverse/spatia…
b694423
…ldata into feature/transform

[pre-commit.ci] auto fixes from pre-commit.com hooks
db61de8
for more information, see https://pre-commit.ci

wip write for new transforms specs
3a83b21

Merge branch 'feature/transform' ofhttps://github.com/scverse/spatia…
569abdd
…ldata into feature/transform

[pre-commit.ci] auto fixes from pre-commit.com hooks
018f290
for more information, see https://pre-commit.ci

fstring in format.py
833bb5c

Merge branch 'feature/transform' ofhttps://github.com/scverse/spatia…
ccfe5e9
…ldata into feature/transform

fix in format.py
8460500

io working for the new transform specs (no coord spaces yet)
f00f7fd

fix in affine
983b638

giovpand others added 4 commits December 8, 2022 23:18

fix models
ea06156

add tqdm
c81008a

fix in test_models
a236e77

fix polygon model
b5e73f3

kevinyamauchi reviewed Dec 10, 2022
View reviewed changes

Comment threadtests/_core/test_transformations.py

giovp added 5 commits December 10, 2022 15:13

test models points
5ed1a21

add test shapes
e6671a2

test table model
f026964

fix table model
fa55f59

try codecov one more time
533fb7a

install codecov
0ef1aa5

LucaMarconato self-requested a review December 10, 2022 17:00

LucaMarconato approved these changes Dec 10, 2022
View reviewed changes

kevinyamauchi approved these changes Dec 11, 2022
View reviewed changes

This was referenced Dec 11, 2022
code cleanup #65
Closed
refactor: split up models into separate files #66
Closed

giovpand others added 6 commits December 12, 2022 13:13

Merge branch 'main' into feature/transform_and_schema
44edabd

update docs
efda324

add register
1bf287d

Merge branch 'fix/docs' into feature/transform_and_schema
d5e7a60

suppress warning
32dd480

fix docs
933ea31

giovp merged commit ef9b92a into mainDec 12, 2022

giovp deleted the feature/transform_and_schema branch December 12, 2022 12:45

kevinyamauchi mentioned this pull request Dec 13, 2022
legacy code to port #48
Closed
3 tasks

giovp mentioned this pull request Dec 15, 2022
write to zarr fails when SpatialImage is created from a xarray.DataArray#59
Closed

kevinyamauchi mentioned this pull request Dec 15, 2022
SpatialData specs proposal #12
Closed

giovpand others added 30 commits August 17, 2022 09:05

add io test
cb4ddf6

io for transforms, fixed bugs when testing on the merfish dataset
0981821

merged with main
707f047

bugfix
b7cb647

fixed tests
561d252

Merge branch 'tests/io' into feature/transform
b10419c

workaround against bug with backed dask arrays
140198f

Merge branch 'feature/transform' ofhttps://github.com/scverse/spatia…
5764882
…ldata into feature/transform

woring on a bug with io; fixed repr for points
7ece121

quick code changes for to_zarr bug report
ce23cb7

patched tests after discussion on the to_zarr bug
67c1d7a
see discussion here ome/ome-zarr-py#219

more io tests, fixed related bugs
6221fa2

first io support for polygons
f36ed27

fix precommits
087600d

fix flake8
14c4cd0

wip implementation of the ngff transform
98cd743

Merge branch 'feature/transform' ofhttps://github.com/scverse/spatia…
f8517d7
…ldata into feature/transform

[pre-commit.ci] auto fixes from pre-commit.com hooks
ba85569
for more information, see https://pre-commit.ci

wip transformations, tests pass but io not compatible
3db58b7

Merge branch 'feature/transform' ofhttps://github.com/scverse/spatia…
b694423
…ldata into feature/transform

[pre-commit.ci] auto fixes from pre-commit.com hooks
db61de8
for more information, see https://pre-commit.ci

wip write for new transforms specs
3a83b21

Merge branch 'feature/transform' ofhttps://github.com/scverse/spatia…
569abdd
…ldata into feature/transform

[pre-commit.ci] auto fixes from pre-commit.com hooks
018f290
for more information, see https://pre-commit.ci

fstring in format.py
833bb5c

Merge branch 'feature/transform' ofhttps://github.com/scverse/spatia…
ccfe5e9
…ldata into feature/transform

fix in format.py
8460500

io working for the new transform specs (no coord spaces yet)
f00f7fd

fix in affine
983b638

giovpand others added 4 commits December 8, 2022 23:18

fix models
ea06156

add tqdm
c81008a

fix in test_models
a236e77

fix polygon model
b5e73f3

kevinyamauchi reviewed Dec 10, 2022
View reviewed changes

Comment threadtests/_core/test_transformations.py

giovp added 5 commits December 10, 2022 15:13

test models points
5ed1a21

add test shapes
e6671a2

test table model
f026964

fix table model
fa55f59

try codecov one more time
533fb7a

install codecov
0ef1aa5

LucaMarconato self-requested a review December 10, 2022 17:00

LucaMarconato approved these changes Dec 10, 2022
View reviewed changes

kevinyamauchi approved these changes Dec 11, 2022
View reviewed changes

This was referenced Dec 11, 2022
code cleanup #65
Closed
refactor: split up models into separate files #66
Closed

giovpand others added 6 commits December 12, 2022 13:13

Merge branch 'main' into feature/transform_and_schema
44edabd

update docs
efda324

add register
1bf287d

Merge branch 'fix/docs' into feature/transform_and_schema
d5e7a60

suppress warning
32dd480

fix docs
933ea31

giovp merged commit ef9b92a into mainDec 12, 2022

giovp deleted the feature/transform_and_schema branch December 12, 2022 12:45

kevinyamauchi mentioned this pull request Dec 13, 2022
legacy code to port #48
Closed
3 tasks

giovp mentioned this pull request Dec 15, 2022
write to zarr fails when SpatialImage is created from a xarray.DataArray#59
Closed

kevinyamauchi mentioned this pull request Dec 15, 2022
SpatialData specs proposal #12
Closed

giovpand others added 30 commits August 17, 2022 09:05

add io test
cb4ddf6

io for transforms, fixed bugs when testing on the merfish dataset
0981821

merged with main
707f047

bugfix
b7cb647

fixed tests
561d252

Merge branch 'tests/io' into feature/transform
b10419c

workaround against bug with backed dask arrays
140198f

Merge branch 'feature/transform' ofhttps://github.com/scverse/spatia…
5764882
…ldata into feature/transform

woring on a bug with io; fixed repr for points
7ece121

quick code changes for to_zarr bug report
ce23cb7

patched tests after discussion on the to_zarr bug
67c1d7a
see discussion here ome/ome-zarr-py#219

more io tests, fixed related bugs
6221fa2

first io support for polygons
f36ed27

fix precommits
087600d

fix flake8
14c4cd0

wip implementation of the ngff transform
98cd743

Merge branch 'feature/transform' ofhttps://github.com/scverse/spatia…
f8517d7
…ldata into feature/transform

[pre-commit.ci] auto fixes from pre-commit.com hooks
ba85569
for more information, see https://pre-commit.ci

wip transformations, tests pass but io not compatible
3db58b7

Merge branch 'feature/transform' ofhttps://github.com/scverse/spatia…
b694423
…ldata into feature/transform

[pre-commit.ci] auto fixes from pre-commit.com hooks
db61de8
for more information, see https://pre-commit.ci

wip write for new transforms specs
3a83b21

Merge branch 'feature/transform' ofhttps://github.com/scverse/spatia…
569abdd
…ldata into feature/transform

[pre-commit.ci] auto fixes from pre-commit.com hooks
018f290
for more information, see https://pre-commit.ci

fstring in format.py
833bb5c

Merge branch 'feature/transform' ofhttps://github.com/scverse/spatia…
ccfe5e9
…ldata into feature/transform

fix in format.py
8460500

io working for the new transform specs (no coord spaces yet)
f00f7fd

fix in affine
983b638

giovpand others added 4 commits December 8, 2022 23:18

fix models
ea06156

add tqdm
c81008a

fix in test_models
a236e77

fix polygon model
b5e73f3

kevinyamauchi reviewed Dec 10, 2022
View reviewed changes

Comment threadtests/_core/test_transformations.py

giovp added 5 commits December 10, 2022 15:13

test models points
5ed1a21

add test shapes
e6671a2

test table model
f026964

fix table model
fa55f59

try codecov one more time
533fb7a

install codecov
0ef1aa5

LucaMarconato self-requested a review December 10, 2022 17:00

LucaMarconato approved these changes Dec 10, 2022
View reviewed changes

kevinyamauchi approved these changes Dec 11, 2022
View reviewed changes

This was referenced Dec 11, 2022
code cleanup #65
Closed
refactor: split up models into separate files #66
Closed

giovpand others added 6 commits December 12, 2022 13:13

Merge branch 'main' into feature/transform_and_schema
44edabd

update docs
efda324

add register
1bf287d

Merge branch 'fix/docs' into feature/transform_and_schema
d5e7a60

suppress warning
32dd480

fix docs
933ea31

giovp merged commit ef9b92a into mainDec 12, 2022

giovp deleted the feature/transform_and_schema branch December 12, 2022 12:45

kevinyamauchi mentioned this pull request Dec 13, 2022
legacy code to port #48
Closed
3 tasks

giovp mentioned this pull request Dec 15, 2022
write to zarr fails when SpatialImage is created from a xarray.DataArray#59
Closed

kevinyamauchi mentioned this pull request Dec 15, 2022
SpatialData specs proposal #12
Closed



		@singledispatch
		def get_transform(e: SpatialElement) -> BaseTransformation:

		@@ -0,0 +1,578 @@
		"""This file contains models and schema for SpatialData"""

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