Io

.flake8

@@ -38,6 +38,8 @@ ignore =
  E203
  # format string does contain unindexed parameters
  P101
+ RST
+ D
 exclude = .git,__pycache__,build,docs/_build,dist
 per-file-ignores =
  tests/*: D

.github/workflows/build.yaml

@@ -0,0 +1,23 @@
+name: Check Build
+
+on:
+ push:
+ branches: [main]
+ pull_request:
+ branches: [main]
+
+jobs:
+ package:
+ runs-on: ubuntu-latest
+ steps:
+ - uses: actions/checkout@v2
+ - name: Set up Python 3.10
+ uses: actions/setup-python@v2
+ with:
+ python-version: "3.10"
+ - name: Install build dependencies
+ run: python -m pip install --upgrade pip wheel twine build
+ - name: Build package
+ run: python -m build
+ - name: Check package
+ run: twine check --strict dist/*.whl

.github/workflows/test.yaml

@@ -16,7 +16,7 @@ jobs:
  strategy:
  fail-fast: false
  matrix:
- python: ["3.8", "3.10"]
+ python: ["3.9", "3.10"]
  os: [ubuntu-latest]
 
  env:
@@ -60,18 +60,3 @@ jobs:
  CODECOV_NAME: ${{ matrix.python }}-${{ matrix.os }}
  run: |
  codecov --required --flags=unittests
-
- package:
- runs-on: ubuntu-latest
- steps:
- - uses: actions/checkout@v2
- - name: Set up Python 3.10
- uses: actions/setup-python@v2
- with:
- python-version: "3.10"
- - name: Install test dependencies
- run: python -m pip install --upgrade pip wheel twine build
- - name: Build package
- run: python -m build
- - name: Check package
- run: twine check --strict dist/*.whl

.gitignore

@@ -22,3 +22,6 @@ __pycache__/
 # IDEs
 /.idea/
 .vscode
+
+# data
+spatialdata-sandbox

.pre-commit-config.yaml

@@ -10,9 +10,8 @@ repos:
  rev: v0.971
  hooks:
  - id: mypy
- additional_dependencies:
- [numpy==1.22.0, scipy, pandas, types-requests]
- exclude: tests/|docs/
+ additional_dependencies: [numpy==1.22.0, types-requests]
+ exclude: tests/|docs/|temp/|spatialdata/_core/reader.py
  - repo: https://github.com/psf/black
  rev: 22.6.0
  hooks:

README.md

@@ -2,6 +2,7 @@
 
 [![Tests][badge-tests]][link-tests]
 [![Documentation][badge-docs]][link-docs]
+[![pre-commit.ci status](https://results.pre-commit.ci/badge/github/scverse/spatialdata/main.svg)](https://results.pre-commit.ci/latest/github/scverse/spatialdata/main)
 
 [badge-tests]: https://img.shields.io/github/workflow/status/scverse/spatialdata/Test/main
 [link-tests]: https://github.com/scverse/spatialdata.git/actions/workflows/test.yml

pyproject.toml

@@ -22,7 +22,7 @@ version = "0.0.1.dev0"
 requires-python = ">=3.8"
 license = {file = "LICENSE"}
 readme = "README.md"
-dependencies = ["anndata"]
+dependencies = ["anndata","numpy","xarray","zarr","ome_zarr"]
 
 [project.optional-dependencies]
 dev = [
@@ -54,11 +54,13 @@ omit = [
 testpaths = ["tests"]
 xfail_strict = true
 addopts = [
- "-Werror", # if 3rd party libs raise DeprecationWarnings, just use filterwarnings below
+# "-Werror", # if 3rd party libs raise DeprecationWarnings, just use filterwarnings below
  "--import-mode=importlib", # allow using test files with same name
 ]
+# info on how to use this https://stackoverflow.com/questions/57925071/how-do-i-avoid-getting-deprecationwarning-from-inside-dependencies-with-pytest
 filterwarnings = [
- # "ignore:.*U.*mode is deprecated:DeprecationWarning",
+ "ignore::DeprecationWarning"
+ # "ignore:.*U.*mode is deprecated:DeprecationWarning",
 ]
 
 [tool.isort]

spatialdata/__init__.py

@@ -3,3 +3,4 @@
 __version__ = version("spatialdata")
 
 from ._core import SpatialData
+from ._core.transform import Transform

spatialdata/_constants/_constants.py

@@ -0,0 +1,11 @@
+from enum import unique
+
+from spatialdata._constants._enum import ModeEnum
+
+
+@unique
+class ShapesType(ModeEnum):
+ CIRCLES = "circles"
+ TRIANGLES = "triangles"
+ SQUARES = "squares"
+ HEXAGONS = "hexagons"

spatialdata/_constants/_enum.py

@@ -0,0 +1,66 @@
+from abc import ABC, ABCMeta
+from enum import Enum, EnumMeta
+from functools import wraps
+from typing import Any, Callable, Dict, Tuple, Type
+
+
+class PrettyEnum(Enum):
+ """Enum with a pretty :meth:`__str__` and :meth:`__repr__`."""
+
+ @property
+ def v(self) -> Any:
+ """Alias for :attr`value`."""
+ return self.value
+
+ def __repr__(self) -> str:
+ return f"{self.value!r}"
+
+ def __str__(self) -> str:
+ return f"{self.value!s}"
+
+
+def _pretty_raise_enum(cls: Type["ErrorFormatterABC"], func: Callable[..., Any]) -> Callable[..., Any]:
+ @wraps(func)
+ def wrapper(*args: Any, **kwargs: Any) -> "ErrorFormatterABC":
+ try:
+ return func(*args, **kwargs) # type: ignore[no-any-return]
+ except ValueError as e:
+ _cls, value, *_ = args
+ e.args = (cls._format(value),)
+ raise e
+
+ if not issubclass(cls, ErrorFormatterABC):
+ raise TypeError(f"Class `{cls}` must be subtype of `ErrorFormatterABC`.")
+ elif not len(cls.__members__): # type: ignore[attr-defined]
+ # empty enum, for class hierarchy
+ return func
+
+ return wrapper
+
+
+class ABCEnumMeta(EnumMeta, ABCMeta):
+ def __call__(cls, *args: Any, **kwargs: Any) -> Any:
+ if getattr(cls, "__error_format__", None) is None:
+ raise TypeError(f"Can't instantiate class `{cls.__name__}` " f"without `__error_format__` class attribute.")
+ return super().__call__(*args, **kwargs)
+
+ def __new__(cls, clsname: str, superclasses: Tuple[type], attributedict: Dict[str, Any]) -> "ABCEnumMeta":
+ res = super().__new__(cls, clsname, superclasses, attributedict) # type: ignore[arg-type]
+ res.__new__ = _pretty_raise_enum(res, res.__new__) # type: ignore[assignment,arg-type]
+ return res
+
+
+class ErrorFormatterABC(ABC):
+ """Mixin class that formats invalid value when constructing an enum."""
+
+ __error_format__ = "Invalid option `{0}` for `{1}`. Valid options are: `{2}`."
+
+ @classmethod
+ def _format(cls, value: Enum) -> str:
+ return cls.__error_format__.format(
+ value, cls.__name__, [m.value for m in cls.__members__.values()] # type: ignore[attr-defined]
+ )
+
+
+class ModeEnum(str, ErrorFormatterABC, PrettyEnum, metaclass=ABCEnumMeta):
+ """Enum which prints available values when invalid value has been passed."""

spatialdata/_constants/_key.py

@@ -0,0 +1,30 @@
+from typing import Any, Callable
+
+
+class cprop:
+ def __init__(self, f: Callable[..., str]):
+ self.f = f
+
+ def __get__(self, obj: Any, owner: Any) -> str:
+ return self.f(owner)
+
+
+class Key:
+ """Class which manages keys in :class:`anndata.AnnData`."""
+
+ class obs:
+ pass
+
+ class obsm:
+ @cprop
+ def spatial(cls) -> str:
+ return "spatial"
+
+ class uns:
+ @cprop
+ def spatial(cls) -> str:
+ return Key.obsm.spatial
+
+ @classmethod
+ def nhood_enrichment(cls, cluster: str) -> str:
+ return f"{cluster}_nhood_enrichment"

spatialdata/_core/__init__.py

@@ -1,3 +1,3 @@
-from .spatialdata import SpatialData
+from ._spatialdata import SpatialData
 
 __all__ = ["SpatialData"]

.flake8

@@ -38,6 +38,8 @@ ignore =
  E203
  # format string does contain unindexed parameters
  P101
+ RST
+ D
 exclude = .git,__pycache__,build,docs/_build,dist
 per-file-ignores =
  tests/*: D

.github/workflows/build.yaml

@@ -0,0 +1,23 @@
+name: Check Build
+
+on:
+ push:
+ branches: [main]
+ pull_request:
+ branches: [main]
+
+jobs:
+ package:
+ runs-on: ubuntu-latest
+ steps:
+ - uses: actions/checkout@v2
+ - name: Set up Python 3.10
+ uses: actions/setup-python@v2
+ with:
+ python-version: "3.10"
+ - name: Install build dependencies
+ run: python -m pip install --upgrade pip wheel twine build
+ - name: Build package
+ run: python -m build
+ - name: Check package
+ run: twine check --strict dist/*.whl

.github/workflows/test.yaml

@@ -16,7 +16,7 @@ jobs:
  strategy:
  fail-fast: false
  matrix:
- python: ["3.8", "3.10"]
+ python: ["3.9", "3.10"]
  os: [ubuntu-latest]
 
  env:
@@ -60,18 +60,3 @@ jobs:
  CODECOV_NAME: ${{ matrix.python }}-${{ matrix.os }}
  run: |
  codecov --required --flags=unittests
-
- package:
- runs-on: ubuntu-latest
- steps:
- - uses: actions/checkout@v2
- - name: Set up Python 3.10
- uses: actions/setup-python@v2
- with:
- python-version: "3.10"
- - name: Install test dependencies
- run: python -m pip install --upgrade pip wheel twine build
- - name: Build package
- run: python -m build
- - name: Check package
- run: twine check --strict dist/*.whl

.gitignore

@@ -22,3 +22,6 @@ __pycache__/
 # IDEs
 /.idea/
 .vscode
+
+# data
+spatialdata-sandbox

.pre-commit-config.yaml

@@ -10,9 +10,8 @@ repos:
  rev: v0.971
  hooks:
  - id: mypy
- additional_dependencies:
- [numpy==1.22.0, scipy, pandas, types-requests]
- exclude: tests/|docs/
+ additional_dependencies: [numpy==1.22.0, types-requests]
+ exclude: tests/|docs/|temp/|spatialdata/_core/reader.py
  - repo: https://github.com/psf/black
  rev: 22.6.0
  hooks:

README.md

@@ -2,6 +2,7 @@
 
 [![Tests][badge-tests]][link-tests]
 [![Documentation][badge-docs]][link-docs]
+[![pre-commit.ci status](https://results.pre-commit.ci/badge/github/scverse/spatialdata/main.svg)](https://results.pre-commit.ci/latest/github/scverse/spatialdata/main)
 
 [badge-tests]: https://img.shields.io/github/workflow/status/scverse/spatialdata/Test/main
 [link-tests]: https://github.com/scverse/spatialdata.git/actions/workflows/test.yml

pyproject.toml

@@ -22,7 +22,7 @@ version = "0.0.1.dev0"
 requires-python = ">=3.8"
 license = {file = "LICENSE"}
 readme = "README.md"
-dependencies = ["anndata"]
+dependencies = ["anndata","numpy","xarray","zarr","ome_zarr"]
 
 [project.optional-dependencies]
 dev = [
@@ -54,11 +54,13 @@ omit = [
 testpaths = ["tests"]
 xfail_strict = true
 addopts = [
- "-Werror", # if 3rd party libs raise DeprecationWarnings, just use filterwarnings below
+# "-Werror", # if 3rd party libs raise DeprecationWarnings, just use filterwarnings below
  "--import-mode=importlib", # allow using test files with same name
 ]
+# info on how to use this https://stackoverflow.com/questions/57925071/how-do-i-avoid-getting-deprecationwarning-from-inside-dependencies-with-pytest
 filterwarnings = [
- # "ignore:.*U.*mode is deprecated:DeprecationWarning",
+ "ignore::DeprecationWarning"
+ # "ignore:.*U.*mode is deprecated:DeprecationWarning",
 ]
 
 [tool.isort]

spatialdata/__init__.py

@@ -3,3 +3,4 @@
 __version__ = version("spatialdata")
 
 from ._core import SpatialData
+from ._core.transform import Transform

spatialdata/_constants/_constants.py

@@ -0,0 +1,11 @@
+from enum import unique
+
+from spatialdata._constants._enum import ModeEnum
+
+
+@unique
+class ShapesType(ModeEnum):
+ CIRCLES = "circles"
+ TRIANGLES = "triangles"
+ SQUARES = "squares"
+ HEXAGONS = "hexagons"

spatialdata/_constants/_enum.py

@@ -0,0 +1,66 @@
+from abc import ABC, ABCMeta
+from enum import Enum, EnumMeta
+from functools import wraps
+from typing import Any, Callable, Dict, Tuple, Type
+
+
+class PrettyEnum(Enum):
+ """Enum with a pretty :meth:`__str__` and :meth:`__repr__`."""
+
+ @property
+ def v(self) -> Any:
+ """Alias for :attr`value`."""
+ return self.value
+
+ def __repr__(self) -> str:
+ return f"{self.value!r}"
+
+ def __str__(self) -> str:
+ return f"{self.value!s}"
+
+
+def _pretty_raise_enum(cls: Type["ErrorFormatterABC"], func: Callable[..., Any]) -> Callable[..., Any]:
+ @wraps(func)
+ def wrapper(*args: Any, **kwargs: Any) -> "ErrorFormatterABC":
+ try:
+ return func(*args, **kwargs) # type: ignore[no-any-return]
+ except ValueError as e:
+ _cls, value, *_ = args
+ e.args = (cls._format(value),)
+ raise e
+
+ if not issubclass(cls, ErrorFormatterABC):
+ raise TypeError(f"Class `{cls}` must be subtype of `ErrorFormatterABC`.")
+ elif not len(cls.__members__): # type: ignore[attr-defined]
+ # empty enum, for class hierarchy
+ return func
+
+ return wrapper
+
+
+class ABCEnumMeta(EnumMeta, ABCMeta):
+ def __call__(cls, *args: Any, **kwargs: Any) -> Any:
+ if getattr(cls, "__error_format__", None) is None:
+ raise TypeError(f"Can't instantiate class `{cls.__name__}` " f"without `__error_format__` class attribute.")
+ return super().__call__(*args, **kwargs)
+
+ def __new__(cls, clsname: str, superclasses: Tuple[type], attributedict: Dict[str, Any]) -> "ABCEnumMeta":
+ res = super().__new__(cls, clsname, superclasses, attributedict) # type: ignore[arg-type]
+ res.__new__ = _pretty_raise_enum(res, res.__new__) # type: ignore[assignment,arg-type]
+ return res
+
+
+class ErrorFormatterABC(ABC):
+ """Mixin class that formats invalid value when constructing an enum."""
+
+ __error_format__ = "Invalid option `{0}` for `{1}`. Valid options are: `{2}`."
+
+ @classmethod
+ def _format(cls, value: Enum) -> str:
+ return cls.__error_format__.format(
+ value, cls.__name__, [m.value for m in cls.__members__.values()] # type: ignore[attr-defined]
+ )
+
+
+class ModeEnum(str, ErrorFormatterABC, PrettyEnum, metaclass=ABCEnumMeta):
+ """Enum which prints available values when invalid value has been passed."""

spatialdata/_constants/_key.py

@@ -0,0 +1,30 @@
+from typing import Any, Callable
+
+
+class cprop:
+ def __init__(self, f: Callable[..., str]):
+ self.f = f
+
+ def __get__(self, obj: Any, owner: Any) -> str:
+ return self.f(owner)
+
+
+class Key:
+ """Class which manages keys in :class:`anndata.AnnData`."""
+
+ class obs:
+ pass
+
+ class obsm:
+ @cprop
+ def spatial(cls) -> str:
+ return "spatial"
+
+ class uns:
+ @cprop
+ def spatial(cls) -> str:
+ return Key.obsm.spatial
+
+ @classmethod
+ def nhood_enrichment(cls, cluster: str) -> str:
+ return f"{cluster}_nhood_enrichment"

spatialdata/_core/__init__.py

@@ -1,3 +1,3 @@
-from .spatialdata import SpatialData
+from ._spatialdata import SpatialData
 
 __all__ = ["SpatialData"]

.flake8

@@ -38,6 +38,8 @@ ignore =
  E203
  # format string does contain unindexed parameters
  P101
+ RST
+ D
 exclude = .git,__pycache__,build,docs/_build,dist
 per-file-ignores =
  tests/*: D

.github/workflows/build.yaml

@@ -0,0 +1,23 @@
+name: Check Build
+
+on:
+ push:
+ branches: [main]
+ pull_request:
+ branches: [main]
+
+jobs:
+ package:
+ runs-on: ubuntu-latest
+ steps:
+ - uses: actions/checkout@v2
+ - name: Set up Python 3.10
+ uses: actions/setup-python@v2
+ with:
+ python-version: "3.10"
+ - name: Install build dependencies
+ run: python -m pip install --upgrade pip wheel twine build
+ - name: Build package
+ run: python -m build
+ - name: Check package
+ run: twine check --strict dist/*.whl

.github/workflows/test.yaml

@@ -16,7 +16,7 @@ jobs:
  strategy:
  fail-fast: false
  matrix:
- python: ["3.8", "3.10"]
+ python: ["3.9", "3.10"]
  os: [ubuntu-latest]
 
  env:
@@ -60,18 +60,3 @@ jobs:
  CODECOV_NAME: ${{ matrix.python }}-${{ matrix.os }}
  run: |
  codecov --required --flags=unittests
-
- package:
- runs-on: ubuntu-latest
- steps:
- - uses: actions/checkout@v2
- - name: Set up Python 3.10
- uses: actions/setup-python@v2
- with:
- python-version: "3.10"
- - name: Install test dependencies
- run: python -m pip install --upgrade pip wheel twine build
- - name: Build package
- run: python -m build
- - name: Check package
- run: twine check --strict dist/*.whl

.gitignore

@@ -22,3 +22,6 @@ __pycache__/
 # IDEs
 /.idea/
 .vscode
+
+# data
+spatialdata-sandbox

.pre-commit-config.yaml

@@ -10,9 +10,8 @@ repos:
  rev: v0.971
  hooks:
  - id: mypy
- additional_dependencies:
- [numpy==1.22.0, scipy, pandas, types-requests]
- exclude: tests/|docs/
+ additional_dependencies: [numpy==1.22.0, types-requests]
+ exclude: tests/|docs/|temp/|spatialdata/_core/reader.py
  - repo: https://github.com/psf/black
  rev: 22.6.0
  hooks:

README.md

@@ -2,6 +2,7 @@
 
 [![Tests][badge-tests]][link-tests]
 [![Documentation][badge-docs]][link-docs]
+[![pre-commit.ci status](https://results.pre-commit.ci/badge/github/scverse/spatialdata/main.svg)](https://results.pre-commit.ci/latest/github/scverse/spatialdata/main)
 
 [badge-tests]: https://img.shields.io/github/workflow/status/scverse/spatialdata/Test/main
 [link-tests]: https://github.com/scverse/spatialdata.git/actions/workflows/test.yml

pyproject.toml

@@ -22,7 +22,7 @@ version = "0.0.1.dev0"
 requires-python = ">=3.8"
 license = {file = "LICENSE"}
 readme = "README.md"
-dependencies = ["anndata"]
+dependencies = ["anndata","numpy","xarray","zarr","ome_zarr"]
 
 [project.optional-dependencies]
 dev = [
@@ -54,11 +54,13 @@ omit = [
 testpaths = ["tests"]
 xfail_strict = true
 addopts = [
- "-Werror", # if 3rd party libs raise DeprecationWarnings, just use filterwarnings below
+# "-Werror", # if 3rd party libs raise DeprecationWarnings, just use filterwarnings below
  "--import-mode=importlib", # allow using test files with same name
 ]
+# info on how to use this https://stackoverflow.com/questions/57925071/how-do-i-avoid-getting-deprecationwarning-from-inside-dependencies-with-pytest
 filterwarnings = [
- # "ignore:.*U.*mode is deprecated:DeprecationWarning",
+ "ignore::DeprecationWarning"
+ # "ignore:.*U.*mode is deprecated:DeprecationWarning",
 ]
 
 [tool.isort]

spatialdata/__init__.py

@@ -3,3 +3,4 @@
 __version__ = version("spatialdata")
 
 from ._core import SpatialData
+from ._core.transform import Transform

spatialdata/_constants/_constants.py

@@ -0,0 +1,11 @@
+from enum import unique
+
+from spatialdata._constants._enum import ModeEnum
+
+
+@unique
+class ShapesType(ModeEnum):
+ CIRCLES = "circles"
+ TRIANGLES = "triangles"
+ SQUARES = "squares"
+ HEXAGONS = "hexagons"

spatialdata/_constants/_enum.py

@@ -0,0 +1,66 @@
+from abc import ABC, ABCMeta
+from enum import Enum, EnumMeta
+from functools import wraps
+from typing import Any, Callable, Dict, Tuple, Type
+
+
+class PrettyEnum(Enum):
+ """Enum with a pretty :meth:`__str__` and :meth:`__repr__`."""
+
+ @property
+ def v(self) -> Any:
+ """Alias for :attr`value`."""
+ return self.value
+
+ def __repr__(self) -> str:
+ return f"{self.value!r}"
+
+ def __str__(self) -> str:
+ return f"{self.value!s}"
+
+
+def _pretty_raise_enum(cls: Type["ErrorFormatterABC"], func: Callable[..., Any]) -> Callable[..., Any]:
+ @wraps(func)
+ def wrapper(*args: Any, **kwargs: Any) -> "ErrorFormatterABC":
+ try:
+ return func(*args, **kwargs) # type: ignore[no-any-return]
+ except ValueError as e:
+ _cls, value, *_ = args
+ e.args = (cls._format(value),)
+ raise e
+
+ if not issubclass(cls, ErrorFormatterABC):
+ raise TypeError(f"Class `{cls}` must be subtype of `ErrorFormatterABC`.")
+ elif not len(cls.__members__): # type: ignore[attr-defined]
+ # empty enum, for class hierarchy
+ return func
+
+ return wrapper
+
+
+class ABCEnumMeta(EnumMeta, ABCMeta):
+ def __call__(cls, *args: Any, **kwargs: Any) -> Any:
+ if getattr(cls, "__error_format__", None) is None:
+ raise TypeError(f"Can't instantiate class `{cls.__name__}` " f"without `__error_format__` class attribute.")
+ return super().__call__(*args, **kwargs)
+
+ def __new__(cls, clsname: str, superclasses: Tuple[type], attributedict: Dict[str, Any]) -> "ABCEnumMeta":
+ res = super().__new__(cls, clsname, superclasses, attributedict) # type: ignore[arg-type]
+ res.__new__ = _pretty_raise_enum(res, res.__new__) # type: ignore[assignment,arg-type]
+ return res
+
+
+class ErrorFormatterABC(ABC):
+ """Mixin class that formats invalid value when constructing an enum."""
+
+ __error_format__ = "Invalid option `{0}` for `{1}`. Valid options are: `{2}`."
+
+ @classmethod
+ def _format(cls, value: Enum) -> str:
+ return cls.__error_format__.format(
+ value, cls.__name__, [m.value for m in cls.__members__.values()] # type: ignore[attr-defined]
+ )
+
+
+class ModeEnum(str, ErrorFormatterABC, PrettyEnum, metaclass=ABCEnumMeta):
+ """Enum which prints available values when invalid value has been passed."""

spatialdata/_constants/_key.py

@@ -0,0 +1,30 @@
+from typing import Any, Callable
+
+
+class cprop:
+ def __init__(self, f: Callable[..., str]):
+ self.f = f
+
+ def __get__(self, obj: Any, owner: Any) -> str:
+ return self.f(owner)
+
+
+class Key:
+ """Class which manages keys in :class:`anndata.AnnData`."""
+
+ class obs:
+ pass
+
+ class obsm:
+ @cprop
+ def spatial(cls) -> str:
+ return "spatial"
+
+ class uns:
+ @cprop
+ def spatial(cls) -> str:
+ return Key.obsm.spatial
+
+ @classmethod
+ def nhood_enrichment(cls, cluster: str) -> str:
+ return f"{cluster}_nhood_enrichment"

spatialdata/_core/__init__.py

@@ -1,3 +1,3 @@
-from .spatialdata import SpatialData
+from ._spatialdata import SpatialData
 
 __all__ = ["SpatialData"]

.flake8

@@ -38,6 +38,8 @@ ignore =
  E203
  # format string does contain unindexed parameters
  P101
+ RST
+ D
 exclude = .git,__pycache__,build,docs/_build,dist
 per-file-ignores =
  tests/*: D

.github/workflows/build.yaml

@@ -0,0 +1,23 @@
+name: Check Build
+
+on:
+ push:
+ branches: [main]
+ pull_request:
+ branches: [main]
+
+jobs:
+ package:
+ runs-on: ubuntu-latest
+ steps:
+ - uses: actions/checkout@v2
+ - name: Set up Python 3.10
+ uses: actions/setup-python@v2
+ with:
+ python-version: "3.10"
+ - name: Install build dependencies
+ run: python -m pip install --upgrade pip wheel twine build
+ - name: Build package
+ run: python -m build
+ - name: Check package
+ run: twine check --strict dist/*.whl

.github/workflows/test.yaml

@@ -16,7 +16,7 @@ jobs:
  strategy:
  fail-fast: false
  matrix:
- python: ["3.8", "3.10"]
+ python: ["3.9", "3.10"]
  os: [ubuntu-latest]
 
  env:
@@ -60,18 +60,3 @@ jobs:
  CODECOV_NAME: ${{ matrix.python }}-${{ matrix.os }}
  run: |
  codecov --required --flags=unittests
-
- package:
- runs-on: ubuntu-latest
- steps:
- - uses: actions/checkout@v2
- - name: Set up Python 3.10
- uses: actions/setup-python@v2
- with:
- python-version: "3.10"
- - name: Install test dependencies
- run: python -m pip install --upgrade pip wheel twine build
- - name: Build package
- run: python -m build
- - name: Check package
- run: twine check --strict dist/*.whl

.gitignore

@@ -22,3 +22,6 @@ __pycache__/
 # IDEs
 /.idea/
 .vscode
+
+# data
+spatialdata-sandbox

.pre-commit-config.yaml

@@ -10,9 +10,8 @@ repos:
  rev: v0.971
  hooks:
  - id: mypy
- additional_dependencies:
- [numpy==1.22.0, scipy, pandas, types-requests]
- exclude: tests/|docs/
+ additional_dependencies: [numpy==1.22.0, types-requests]
+ exclude: tests/|docs/|temp/|spatialdata/_core/reader.py
  - repo: https://github.com/psf/black
  rev: 22.6.0
  hooks:

README.md

@@ -2,6 +2,7 @@
 
 [![Tests][badge-tests]][link-tests]
 [![Documentation][badge-docs]][link-docs]
+[![pre-commit.ci status](https://results.pre-commit.ci/badge/github/scverse/spatialdata/main.svg)](https://results.pre-commit.ci/latest/github/scverse/spatialdata/main)
 
 [badge-tests]: https://img.shields.io/github/workflow/status/scverse/spatialdata/Test/main
 [link-tests]: https://github.com/scverse/spatialdata.git/actions/workflows/test.yml

pyproject.toml

@@ -22,7 +22,7 @@ version = "0.0.1.dev0"
 requires-python = ">=3.8"
 license = {file = "LICENSE"}
 readme = "README.md"
-dependencies = ["anndata"]
+dependencies = ["anndata","numpy","xarray","zarr","ome_zarr"]
 
 [project.optional-dependencies]
 dev = [
@@ -54,11 +54,13 @@ omit = [
 testpaths = ["tests"]
 xfail_strict = true
 addopts = [
- "-Werror", # if 3rd party libs raise DeprecationWarnings, just use filterwarnings below
+# "-Werror", # if 3rd party libs raise DeprecationWarnings, just use filterwarnings below
  "--import-mode=importlib", # allow using test files with same name
 ]
+# info on how to use this https://stackoverflow.com/questions/57925071/how-do-i-avoid-getting-deprecationwarning-from-inside-dependencies-with-pytest
 filterwarnings = [
- # "ignore:.*U.*mode is deprecated:DeprecationWarning",
+ "ignore::DeprecationWarning"
+ # "ignore:.*U.*mode is deprecated:DeprecationWarning",
 ]
 
 [tool.isort]

spatialdata/__init__.py

@@ -3,3 +3,4 @@
 __version__ = version("spatialdata")
 
 from ._core import SpatialData
+from ._core.transform import Transform

spatialdata/_constants/_constants.py

@@ -0,0 +1,11 @@
+from enum import unique
+
+from spatialdata._constants._enum import ModeEnum
+
+
+@unique
+class ShapesType(ModeEnum):
+ CIRCLES = "circles"
+ TRIANGLES = "triangles"
+ SQUARES = "squares"
+ HEXAGONS = "hexagons"

spatialdata/_constants/_enum.py

@@ -0,0 +1,66 @@
+from abc import ABC, ABCMeta
+from enum import Enum, EnumMeta
+from functools import wraps
+from typing import Any, Callable, Dict, Tuple, Type
+
+
+class PrettyEnum(Enum):
+ """Enum with a pretty :meth:`__str__` and :meth:`__repr__`."""
+
+ @property
+ def v(self) -> Any:
+ """Alias for :attr`value`."""
+ return self.value
+
+ def __repr__(self) -> str:
+ return f"{self.value!r}"
+
+ def __str__(self) -> str:
+ return f"{self.value!s}"
+
+
+def _pretty_raise_enum(cls: Type["ErrorFormatterABC"], func: Callable[..., Any]) -> Callable[..., Any]:
+ @wraps(func)
+ def wrapper(*args: Any, **kwargs: Any) -> "ErrorFormatterABC":
+ try:
+ return func(*args, **kwargs) # type: ignore[no-any-return]
+ except ValueError as e:
+ _cls, value, *_ = args
+ e.args = (cls._format(value),)
+ raise e
+
+ if not issubclass(cls, ErrorFormatterABC):
+ raise TypeError(f"Class `{cls}` must be subtype of `ErrorFormatterABC`.")
+ elif not len(cls.__members__): # type: ignore[attr-defined]
+ # empty enum, for class hierarchy
+ return func
+
+ return wrapper
+
+
+class ABCEnumMeta(EnumMeta, ABCMeta):
+ def __call__(cls, *args: Any, **kwargs: Any) -> Any:
+ if getattr(cls, "__error_format__", None) is None:
+ raise TypeError(f"Can't instantiate class `{cls.__name__}` " f"without `__error_format__` class attribute.")
+ return super().__call__(*args, **kwargs)
+
+ def __new__(cls, clsname: str, superclasses: Tuple[type], attributedict: Dict[str, Any]) -> "ABCEnumMeta":
+ res = super().__new__(cls, clsname, superclasses, attributedict) # type: ignore[arg-type]
+ res.__new__ = _pretty_raise_enum(res, res.__new__) # type: ignore[assignment,arg-type]
+ return res
+
+
+class ErrorFormatterABC(ABC):
+ """Mixin class that formats invalid value when constructing an enum."""
+
+ __error_format__ = "Invalid option `{0}` for `{1}`. Valid options are: `{2}`."
+
+ @classmethod
+ def _format(cls, value: Enum) -> str:
+ return cls.__error_format__.format(
+ value, cls.__name__, [m.value for m in cls.__members__.values()] # type: ignore[attr-defined]
+ )
+
+
+class ModeEnum(str, ErrorFormatterABC, PrettyEnum, metaclass=ABCEnumMeta):
+ """Enum which prints available values when invalid value has been passed."""

spatialdata/_constants/_key.py

@@ -0,0 +1,30 @@
+from typing import Any, Callable
+
+
+class cprop:
+ def __init__(self, f: Callable[..., str]):
+ self.f = f
+
+ def __get__(self, obj: Any, owner: Any) -> str:
+ return self.f(owner)
+
+
+class Key:
+ """Class which manages keys in :class:`anndata.AnnData`."""
+
+ class obs:
+ pass
+
+ class obsm:
+ @cprop
+ def spatial(cls) -> str:
+ return "spatial"
+
+ class uns:
+ @cprop
+ def spatial(cls) -> str:
+ return Key.obsm.spatial
+
+ @classmethod
+ def nhood_enrichment(cls, cluster: str) -> str:
+ return f"{cluster}_nhood_enrichment"

spatialdata/_core/__init__.py

@@ -1,3 +1,3 @@
-from .spatialdata import SpatialData
+from ._spatialdata import SpatialData
 
 __all__ = ["SpatialData"]

.flake8

@@ -38,6 +38,8 @@ ignore =
  E203
  # format string does contain unindexed parameters
  P101
+ RST
+ D
 exclude = .git,__pycache__,build,docs/_build,dist
 per-file-ignores =
  tests/*: D

.github/workflows/build.yaml

@@ -0,0 +1,23 @@
+name: Check Build
+
+on:
+ push:
+ branches: [main]
+ pull_request:
+ branches: [main]
+
+jobs:
+ package:
+ runs-on: ubuntu-latest
+ steps:
+ - uses: actions/checkout@v2
+ - name: Set up Python 3.10
+ uses: actions/setup-python@v2
+ with:
+ python-version: "3.10"
+ - name: Install build dependencies
+ run: python -m pip install --upgrade pip wheel twine build
+ - name: Build package
+ run: python -m build
+ - name: Check package
+ run: twine check --strict dist/*.whl

.github/workflows/test.yaml

@@ -16,7 +16,7 @@ jobs:
  strategy:
  fail-fast: false
  matrix:
- python: ["3.8", "3.10"]
+ python: ["3.9", "3.10"]
  os: [ubuntu-latest]
 
  env:
@@ -60,18 +60,3 @@ jobs:
  CODECOV_NAME: ${{ matrix.python }}-${{ matrix.os }}
  run: |
  codecov --required --flags=unittests
-
- package:
- runs-on: ubuntu-latest
- steps:
- - uses: actions/checkout@v2
- - name: Set up Python 3.10
- uses: actions/setup-python@v2
- with:
- python-version: "3.10"
- - name: Install test dependencies
- run: python -m pip install --upgrade pip wheel twine build
- - name: Build package
- run: python -m build
- - name: Check package
- run: twine check --strict dist/*.whl

.gitignore

@@ -22,3 +22,6 @@ __pycache__/
 # IDEs
 /.idea/
 .vscode
+
+# data
+spatialdata-sandbox

.pre-commit-config.yaml

@@ -10,9 +10,8 @@ repos:
  rev: v0.971
  hooks:
  - id: mypy
- additional_dependencies:
- [numpy==1.22.0, scipy, pandas, types-requests]
- exclude: tests/|docs/
+ additional_dependencies: [numpy==1.22.0, types-requests]
+ exclude: tests/|docs/|temp/|spatialdata/_core/reader.py
  - repo: https://github.com/psf/black
  rev: 22.6.0
  hooks:

README.md

@@ -2,6 +2,7 @@
 
 [![Tests][badge-tests]][link-tests]
 [![Documentation][badge-docs]][link-docs]
+[![pre-commit.ci status](https://results.pre-commit.ci/badge/github/scverse/spatialdata/main.svg)](https://results.pre-commit.ci/latest/github/scverse/spatialdata/main)
 
 [badge-tests]: https://img.shields.io/github/workflow/status/scverse/spatialdata/Test/main
 [link-tests]: https://github.com/scverse/spatialdata.git/actions/workflows/test.yml

pyproject.toml

@@ -22,7 +22,7 @@ version = "0.0.1.dev0"
 requires-python = ">=3.8"
 license = {file = "LICENSE"}
 readme = "README.md"
-dependencies = ["anndata"]
+dependencies = ["anndata","numpy","xarray","zarr","ome_zarr"]
 
 [project.optional-dependencies]
 dev = [
@@ -54,11 +54,13 @@ omit = [
 testpaths = ["tests"]
 xfail_strict = true
 addopts = [
- "-Werror", # if 3rd party libs raise DeprecationWarnings, just use filterwarnings below
+# "-Werror", # if 3rd party libs raise DeprecationWarnings, just use filterwarnings below
  "--import-mode=importlib", # allow using test files with same name
 ]
+# info on how to use this https://stackoverflow.com/questions/57925071/how-do-i-avoid-getting-deprecationwarning-from-inside-dependencies-with-pytest
 filterwarnings = [
- # "ignore:.*U.*mode is deprecated:DeprecationWarning",
+ "ignore::DeprecationWarning"
+ # "ignore:.*U.*mode is deprecated:DeprecationWarning",
 ]
 
 [tool.isort]

spatialdata/__init__.py

@@ -3,3 +3,4 @@
 __version__ = version("spatialdata")
 
 from ._core import SpatialData
+from ._core.transform import Transform

spatialdata/_constants/_constants.py

@@ -0,0 +1,11 @@
+from enum import unique
+
+from spatialdata._constants._enum import ModeEnum
+
+
+@unique
+class ShapesType(ModeEnum):
+ CIRCLES = "circles"
+ TRIANGLES = "triangles"
+ SQUARES = "squares"
+ HEXAGONS = "hexagons"

spatialdata/_constants/_enum.py

@@ -0,0 +1,66 @@
+from abc import ABC, ABCMeta
+from enum import Enum, EnumMeta
+from functools import wraps
+from typing import Any, Callable, Dict, Tuple, Type
+
+
+class PrettyEnum(Enum):
+ """Enum with a pretty :meth:`__str__` and :meth:`__repr__`."""
+
+ @property
+ def v(self) -> Any:
+ """Alias for :attr`value`."""
+ return self.value
+
+ def __repr__(self) -> str:
+ return f"{self.value!r}"
+
+ def __str__(self) -> str:
+ return f"{self.value!s}"
+
+
+def _pretty_raise_enum(cls: Type["ErrorFormatterABC"], func: Callable[..., Any]) -> Callable[..., Any]:
+ @wraps(func)
+ def wrapper(*args: Any, **kwargs: Any) -> "ErrorFormatterABC":
+ try:
+ return func(*args, **kwargs) # type: ignore[no-any-return]
+ except ValueError as e:
+ _cls, value, *_ = args
+ e.args = (cls._format(value),)
+ raise e
+
+ if not issubclass(cls, ErrorFormatterABC):
+ raise TypeError(f"Class `{cls}` must be subtype of `ErrorFormatterABC`.")
+ elif not len(cls.__members__): # type: ignore[attr-defined]
+ # empty enum, for class hierarchy
+ return func
+
+ return wrapper
+
+
+class ABCEnumMeta(EnumMeta, ABCMeta):
+ def __call__(cls, *args: Any, **kwargs: Any) -> Any:
+ if getattr(cls, "__error_format__", None) is None:
+ raise TypeError(f"Can't instantiate class `{cls.__name__}` " f"without `__error_format__` class attribute.")
+ return super().__call__(*args, **kwargs)
+
+ def __new__(cls, clsname: str, superclasses: Tuple[type], attributedict: Dict[str, Any]) -> "ABCEnumMeta":
+ res = super().__new__(cls, clsname, superclasses, attributedict) # type: ignore[arg-type]
+ res.__new__ = _pretty_raise_enum(res, res.__new__) # type: ignore[assignment,arg-type]
+ return res
+
+
+class ErrorFormatterABC(ABC):
+ """Mixin class that formats invalid value when constructing an enum."""
+
+ __error_format__ = "Invalid option `{0}` for `{1}`. Valid options are: `{2}`."
+
+ @classmethod
+ def _format(cls, value: Enum) -> str:
+ return cls.__error_format__.format(
+ value, cls.__name__, [m.value for m in cls.__members__.values()] # type: ignore[attr-defined]
+ )
+
+
+class ModeEnum(str, ErrorFormatterABC, PrettyEnum, metaclass=ABCEnumMeta):
+ """Enum which prints available values when invalid value has been passed."""

spatialdata/_constants/_key.py

@@ -0,0 +1,30 @@
+from typing import Any, Callable
+
+
+class cprop:
+ def __init__(self, f: Callable[..., str]):
+ self.f = f
+
+ def __get__(self, obj: Any, owner: Any) -> str:
+ return self.f(owner)
+
+
+class Key:
+ """Class which manages keys in :class:`anndata.AnnData`."""
+
+ class obs:
+ pass
+
+ class obsm:
+ @cprop
+ def spatial(cls) -> str:
+ return "spatial"
+
+ class uns:
+ @cprop
+ def spatial(cls) -> str:
+ return Key.obsm.spatial
+
+ @classmethod
+ def nhood_enrichment(cls, cluster: str) -> str:
+ return f"{cluster}_nhood_enrichment"

spatialdata/_core/__init__.py

@@ -1,3 +1,3 @@
-from .spatialdata import SpatialData
+from ._spatialdata import SpatialData
 
 __all__ = ["SpatialData"]

.flake8

@@ -38,6 +38,8 @@ ignore =
  E203
  # format string does contain unindexed parameters
  P101
+ RST
+ D
 exclude = .git,__pycache__,build,docs/_build,dist
 per-file-ignores =
  tests/*: D

.github/workflows/build.yaml

@@ -0,0 +1,23 @@
+name: Check Build
+
+on:
+ push:
+ branches: [main]
+ pull_request:
+ branches: [main]
+
+jobs:
+ package:
+ runs-on: ubuntu-latest
+ steps:
+ - uses: actions/checkout@v2
+ - name: Set up Python 3.10
+ uses: actions/setup-python@v2
+ with:
+ python-version: "3.10"
+ - name: Install build dependencies
+ run: python -m pip install --upgrade pip wheel twine build
+ - name: Build package
+ run: python -m build
+ - name: Check package
+ run: twine check --strict dist/*.whl

.github/workflows/test.yaml

@@ -16,7 +16,7 @@ jobs:
  strategy:
  fail-fast: false
  matrix:
- python: ["3.8", "3.10"]
+ python: ["3.9", "3.10"]
  os: [ubuntu-latest]
 
  env:
@@ -60,18 +60,3 @@ jobs:
  CODECOV_NAME: ${{ matrix.python }}-${{ matrix.os }}
  run: |
  codecov --required --flags=unittests
-
- package:
- runs-on: ubuntu-latest
- steps:
- - uses: actions/checkout@v2
- - name: Set up Python 3.10
- uses: actions/setup-python@v2
- with:
- python-version: "3.10"
- - name: Install test dependencies
- run: python -m pip install --upgrade pip wheel twine build
- - name: Build package
- run: python -m build
- - name: Check package
- run: twine check --strict dist/*.whl

.gitignore

@@ -22,3 +22,6 @@ __pycache__/
 # IDEs
 /.idea/
 .vscode
+
+# data
+spatialdata-sandbox

.pre-commit-config.yaml

@@ -10,9 +10,8 @@ repos:
  rev: v0.971
  hooks:
  - id: mypy
- additional_dependencies:
- [numpy==1.22.0, scipy, pandas, types-requests]
- exclude: tests/|docs/
+ additional_dependencies: [numpy==1.22.0, types-requests]
+ exclude: tests/|docs/|temp/|spatialdata/_core/reader.py
  - repo: https://github.com/psf/black
  rev: 22.6.0
  hooks:

README.md

@@ -2,6 +2,7 @@
 
 [![Tests][badge-tests]][link-tests]
 [![Documentation][badge-docs]][link-docs]
+[![pre-commit.ci status](https://results.pre-commit.ci/badge/github/scverse/spatialdata/main.svg)](https://results.pre-commit.ci/latest/github/scverse/spatialdata/main)
 
 [badge-tests]: https://img.shields.io/github/workflow/status/scverse/spatialdata/Test/main
 [link-tests]: https://github.com/scverse/spatialdata.git/actions/workflows/test.yml

pyproject.toml

@@ -22,7 +22,7 @@ version = "0.0.1.dev0"
 requires-python = ">=3.8"
 license = {file = "LICENSE"}
 readme = "README.md"
-dependencies = ["anndata"]
+dependencies = ["anndata","numpy","xarray","zarr","ome_zarr"]
 
 [project.optional-dependencies]
 dev = [
@@ -54,11 +54,13 @@ omit = [
 testpaths = ["tests"]
 xfail_strict = true
 addopts = [
- "-Werror", # if 3rd party libs raise DeprecationWarnings, just use filterwarnings below
+# "-Werror", # if 3rd party libs raise DeprecationWarnings, just use filterwarnings below
  "--import-mode=importlib", # allow using test files with same name
 ]
+# info on how to use this https://stackoverflow.com/questions/57925071/how-do-i-avoid-getting-deprecationwarning-from-inside-dependencies-with-pytest
 filterwarnings = [
- # "ignore:.*U.*mode is deprecated:DeprecationWarning",
+ "ignore::DeprecationWarning"
+ # "ignore:.*U.*mode is deprecated:DeprecationWarning",
 ]
 
 [tool.isort]

spatialdata/__init__.py

@@ -3,3 +3,4 @@
 __version__ = version("spatialdata")
 
 from ._core import SpatialData
+from ._core.transform import Transform

spatialdata/_constants/_constants.py

@@ -0,0 +1,11 @@
+from enum import unique
+
+from spatialdata._constants._enum import ModeEnum
+
+
+@unique
+class ShapesType(ModeEnum):
+ CIRCLES = "circles"
+ TRIANGLES = "triangles"
+ SQUARES = "squares"
+ HEXAGONS = "hexagons"

spatialdata/_constants/_enum.py

@@ -0,0 +1,66 @@
+from abc import ABC, ABCMeta
+from enum import Enum, EnumMeta
+from functools import wraps
+from typing import Any, Callable, Dict, Tuple, Type
+
+
+class PrettyEnum(Enum):
+ """Enum with a pretty :meth:`__str__` and :meth:`__repr__`."""
+
+ @property
+ def v(self) -> Any:
+ """Alias for :attr`value`."""
+ return self.value
+
+ def __repr__(self) -> str:
+ return f"{self.value!r}"
+
+ def __str__(self) -> str:
+ return f"{self.value!s}"
+
+
+def _pretty_raise_enum(cls: Type["ErrorFormatterABC"], func: Callable[..., Any]) -> Callable[..., Any]:
+ @wraps(func)
+ def wrapper(*args: Any, **kwargs: Any) -> "ErrorFormatterABC":
+ try:
+ return func(*args, **kwargs) # type: ignore[no-any-return]
+ except ValueError as e:
+ _cls, value, *_ = args
+ e.args = (cls._format(value),)
+ raise e
+
+ if not issubclass(cls, ErrorFormatterABC):
+ raise TypeError(f"Class `{cls}` must be subtype of `ErrorFormatterABC`.")
+ elif not len(cls.__members__): # type: ignore[attr-defined]
+ # empty enum, for class hierarchy
+ return func
+
+ return wrapper
+
+
+class ABCEnumMeta(EnumMeta, ABCMeta):
+ def __call__(cls, *args: Any, **kwargs: Any) -> Any:
+ if getattr(cls, "__error_format__", None) is None:
+ raise TypeError(f"Can't instantiate class `{cls.__name__}` " f"without `__error_format__` class attribute.")
+ return super().__call__(*args, **kwargs)
+
+ def __new__(cls, clsname: str, superclasses: Tuple[type], attributedict: Dict[str, Any]) -> "ABCEnumMeta":
+ res = super().__new__(cls, clsname, superclasses, attributedict) # type: ignore[arg-type]
+ res.__new__ = _pretty_raise_enum(res, res.__new__) # type: ignore[assignment,arg-type]
+ return res
+
+
+class ErrorFormatterABC(ABC):
+ """Mixin class that formats invalid value when constructing an enum."""
+
+ __error_format__ = "Invalid option `{0}` for `{1}`. Valid options are: `{2}`."
+
+ @classmethod
+ def _format(cls, value: Enum) -> str:
+ return cls.__error_format__.format(
+ value, cls.__name__, [m.value for m in cls.__members__.values()] # type: ignore[attr-defined]
+ )
+
+
+class ModeEnum(str, ErrorFormatterABC, PrettyEnum, metaclass=ABCEnumMeta):
+ """Enum which prints available values when invalid value has been passed."""

spatialdata/_constants/_key.py

@@ -0,0 +1,30 @@
+from typing import Any, Callable
+
+
+class cprop:
+ def __init__(self, f: Callable[..., str]):
+ self.f = f
+
+ def __get__(self, obj: Any, owner: Any) -> str:
+ return self.f(owner)
+
+
+class Key:
+ """Class which manages keys in :class:`anndata.AnnData`."""
+
+ class obs:
+ pass
+
+ class obsm:
+ @cprop
+ def spatial(cls) -> str:
+ return "spatial"
+
+ class uns:
+ @cprop
+ def spatial(cls) -> str:
+ return Key.obsm.spatial
+
+ @classmethod
+ def nhood_enrichment(cls, cluster: str) -> str:
+ return f"{cluster}_nhood_enrichment"

spatialdata/_core/__init__.py

@@ -1,3 +1,3 @@
-from .spatialdata import SpatialData
+from ._spatialdata import SpatialData
 
 __all__ = ["SpatialData"]

.flake8

@@ -38,6 +38,8 @@ ignore =
  E203
  # format string does contain unindexed parameters
  P101
+ RST
+ D
 exclude = .git,__pycache__,build,docs/_build,dist
 per-file-ignores =
  tests/*: D

.github/workflows/build.yaml

@@ -0,0 +1,23 @@
+name: Check Build
+
+on:
+ push:
+ branches: [main]
+ pull_request:
+ branches: [main]
+
+jobs:
+ package:
+ runs-on: ubuntu-latest
+ steps:
+ - uses: actions/checkout@v2
+ - name: Set up Python 3.10
+ uses: actions/setup-python@v2
+ with:
+ python-version: "3.10"
+ - name: Install build dependencies
+ run: python -m pip install --upgrade pip wheel twine build
+ - name: Build package
+ run: python -m build
+ - name: Check package
+ run: twine check --strict dist/*.whl

.github/workflows/test.yaml

@@ -16,7 +16,7 @@ jobs:
  strategy:
  fail-fast: false
  matrix:
- python: ["3.8", "3.10"]
+ python: ["3.9", "3.10"]
  os: [ubuntu-latest]
 
  env:
@@ -60,18 +60,3 @@ jobs:
  CODECOV_NAME: ${{ matrix.python }}-${{ matrix.os }}
  run: |
  codecov --required --flags=unittests
-
- package:
- runs-on: ubuntu-latest
- steps:
- - uses: actions/checkout@v2
- - name: Set up Python 3.10
- uses: actions/setup-python@v2
- with:
- python-version: "3.10"
- - name: Install test dependencies
- run: python -m pip install --upgrade pip wheel twine build
- - name: Build package
- run: python -m build
- - name: Check package
- run: twine check --strict dist/*.whl

.gitignore

@@ -22,3 +22,6 @@ __pycache__/
 # IDEs
 /.idea/
 .vscode
+
+# data
+spatialdata-sandbox

.pre-commit-config.yaml

@@ -10,9 +10,8 @@ repos:
  rev: v0.971
  hooks:
  - id: mypy
- additional_dependencies:
- [numpy==1.22.0, scipy, pandas, types-requests]
- exclude: tests/|docs/
+ additional_dependencies: [numpy==1.22.0, types-requests]
+ exclude: tests/|docs/|temp/|spatialdata/_core/reader.py
  - repo: https://github.com/psf/black
  rev: 22.6.0
  hooks:

README.md

@@ -2,6 +2,7 @@
 
 [![Tests][badge-tests]][link-tests]
 [![Documentation][badge-docs]][link-docs]
+[![pre-commit.ci status](https://results.pre-commit.ci/badge/github/scverse/spatialdata/main.svg)](https://results.pre-commit.ci/latest/github/scverse/spatialdata/main)
 
 [badge-tests]: https://img.shields.io/github/workflow/status/scverse/spatialdata/Test/main
 [link-tests]: https://github.com/scverse/spatialdata.git/actions/workflows/test.yml

pyproject.toml

@@ -22,7 +22,7 @@ version = "0.0.1.dev0"
 requires-python = ">=3.8"
 license = {file = "LICENSE"}
 readme = "README.md"
-dependencies = ["anndata"]
+dependencies = ["anndata","numpy","xarray","zarr","ome_zarr"]
 
 [project.optional-dependencies]
 dev = [
@@ -54,11 +54,13 @@ omit = [
 testpaths = ["tests"]
 xfail_strict = true
 addopts = [
- "-Werror", # if 3rd party libs raise DeprecationWarnings, just use filterwarnings below
+# "-Werror", # if 3rd party libs raise DeprecationWarnings, just use filterwarnings below
  "--import-mode=importlib", # allow using test files with same name
 ]
+# info on how to use this https://stackoverflow.com/questions/57925071/how-do-i-avoid-getting-deprecationwarning-from-inside-dependencies-with-pytest
 filterwarnings = [
- # "ignore:.*U.*mode is deprecated:DeprecationWarning",
+ "ignore::DeprecationWarning"
+ # "ignore:.*U.*mode is deprecated:DeprecationWarning",
 ]
 
 [tool.isort]

spatialdata/__init__.py

@@ -3,3 +3,4 @@
 __version__ = version("spatialdata")
 
 from ._core import SpatialData
+from ._core.transform import Transform

spatialdata/_constants/_constants.py

@@ -0,0 +1,11 @@
+from enum import unique
+
+from spatialdata._constants._enum import ModeEnum
+
+
+@unique
+class ShapesType(ModeEnum):
+ CIRCLES = "circles"
+ TRIANGLES = "triangles"
+ SQUARES = "squares"
+ HEXAGONS = "hexagons"

spatialdata/_constants/_enum.py

@@ -0,0 +1,66 @@
+from abc import ABC, ABCMeta
+from enum import Enum, EnumMeta
+from functools import wraps
+from typing import Any, Callable, Dict, Tuple, Type
+
+
+class PrettyEnum(Enum):
+ """Enum with a pretty :meth:`__str__` and :meth:`__repr__`."""
+
+ @property
+ def v(self) -> Any:
+ """Alias for :attr`value`."""
+ return self.value
+
+ def __repr__(self) -> str:
+ return f"{self.value!r}"
+
+ def __str__(self) -> str:
+ return f"{self.value!s}"
+
+
+def _pretty_raise_enum(cls: Type["ErrorFormatterABC"], func: Callable[..., Any]) -> Callable[..., Any]:
+ @wraps(func)
+ def wrapper(*args: Any, **kwargs: Any) -> "ErrorFormatterABC":
+ try:
+ return func(*args, **kwargs) # type: ignore[no-any-return]
+ except ValueError as e:
+ _cls, value, *_ = args
+ e.args = (cls._format(value),)
+ raise e
+
+ if not issubclass(cls, ErrorFormatterABC):
+ raise TypeError(f"Class `{cls}` must be subtype of `ErrorFormatterABC`.")
+ elif not len(cls.__members__): # type: ignore[attr-defined]
+ # empty enum, for class hierarchy
+ return func
+
+ return wrapper
+
+
+class ABCEnumMeta(EnumMeta, ABCMeta):
+ def __call__(cls, *args: Any, **kwargs: Any) -> Any:
+ if getattr(cls, "__error_format__", None) is None:
+ raise TypeError(f"Can't instantiate class `{cls.__name__}` " f"without `__error_format__` class attribute.")
+ return super().__call__(*args, **kwargs)
+
+ def __new__(cls, clsname: str, superclasses: Tuple[type], attributedict: Dict[str, Any]) -> "ABCEnumMeta":
+ res = super().__new__(cls, clsname, superclasses, attributedict) # type: ignore[arg-type]
+ res.__new__ = _pretty_raise_enum(res, res.__new__) # type: ignore[assignment,arg-type]
+ return res
+
+
+class ErrorFormatterABC(ABC):
+ """Mixin class that formats invalid value when constructing an enum."""
+
+ __error_format__ = "Invalid option `{0}` for `{1}`. Valid options are: `{2}`."
+
+ @classmethod
+ def _format(cls, value: Enum) -> str:
+ return cls.__error_format__.format(
+ value, cls.__name__, [m.value for m in cls.__members__.values()] # type: ignore[attr-defined]
+ )
+
+
+class ModeEnum(str, ErrorFormatterABC, PrettyEnum, metaclass=ABCEnumMeta):
+ """Enum which prints available values when invalid value has been passed."""

spatialdata/_constants/_key.py

@@ -0,0 +1,30 @@
+from typing import Any, Callable
+
+
+class cprop:
+ def __init__(self, f: Callable[..., str]):
+ self.f = f
+
+ def __get__(self, obj: Any, owner: Any) -> str:
+ return self.f(owner)
+
+
+class Key:
+ """Class which manages keys in :class:`anndata.AnnData`."""
+
+ class obs:
+ pass
+
+ class obsm:
+ @cprop
+ def spatial(cls) -> str:
+ return "spatial"
+
+ class uns:
+ @cprop
+ def spatial(cls) -> str:
+ return Key.obsm.spatial
+
+ @classmethod
+ def nhood_enrichment(cls, cluster: str) -> str:
+ return f"{cluster}_nhood_enrichment"

spatialdata/_core/__init__.py

@@ -1,3 +1,3 @@
-from .spatialdata import SpatialData
+from ._spatialdata import SpatialData
 
 __all__ = ["SpatialData"]

.flake8

@@ -38,6 +38,8 @@ ignore =
  E203
  # format string does contain unindexed parameters
  P101
+ RST
+ D
 exclude = .git,__pycache__,build,docs/_build,dist
 per-file-ignores =
  tests/*: D

.github/workflows/build.yaml

@@ -0,0 +1,23 @@
+name: Check Build
+
+on:
+ push:
+ branches: [main]
+ pull_request:
+ branches: [main]
+
+jobs:
+ package:
+ runs-on: ubuntu-latest
+ steps:
+ - uses: actions/checkout@v2
+ - name: Set up Python 3.10
+ uses: actions/setup-python@v2
+ with:
+ python-version: "3.10"
+ - name: Install build dependencies
+ run: python -m pip install --upgrade pip wheel twine build
+ - name: Build package
+ run: python -m build
+ - name: Check package
+ run: twine check --strict dist/*.whl

.github/workflows/test.yaml

@@ -16,7 +16,7 @@ jobs:
  strategy:
  fail-fast: false
  matrix:
- python: ["3.8", "3.10"]
+ python: ["3.9", "3.10"]
  os: [ubuntu-latest]
 
  env:
@@ -60,18 +60,3 @@ jobs:
  CODECOV_NAME: ${{ matrix.python }}-${{ matrix.os }}
  run: |
  codecov --required --flags=unittests
-
- package:
- runs-on: ubuntu-latest
- steps:
- - uses: actions/checkout@v2
- - name: Set up Python 3.10
- uses: actions/setup-python@v2
- with:
- python-version: "3.10"
- - name: Install test dependencies
- run: python -m pip install --upgrade pip wheel twine build
- - name: Build package
- run: python -m build
- - name: Check package
- run: twine check --strict dist/*.whl

.gitignore

@@ -22,3 +22,6 @@ __pycache__/
 # IDEs
 /.idea/
 .vscode
+
+# data
+spatialdata-sandbox

.pre-commit-config.yaml

@@ -10,9 +10,8 @@ repos:
  rev: v0.971
  hooks:
  - id: mypy
- additional_dependencies:
- [numpy==1.22.0, scipy, pandas, types-requests]
- exclude: tests/|docs/
+ additional_dependencies: [numpy==1.22.0, types-requests]
+ exclude: tests/|docs/|temp/|spatialdata/_core/reader.py
  - repo: https://github.com/psf/black
  rev: 22.6.0
  hooks:

README.md

@@ -2,6 +2,7 @@
 
 [![Tests][badge-tests]][link-tests]
 [![Documentation][badge-docs]][link-docs]
+[![pre-commit.ci status](https://results.pre-commit.ci/badge/github/scverse/spatialdata/main.svg)](https://results.pre-commit.ci/latest/github/scverse/spatialdata/main)
 
 [badge-tests]: https://img.shields.io/github/workflow/status/scverse/spatialdata/Test/main
 [link-tests]: https://github.com/scverse/spatialdata.git/actions/workflows/test.yml

pyproject.toml

@@ -22,7 +22,7 @@ version = "0.0.1.dev0"
 requires-python = ">=3.8"
 license = {file = "LICENSE"}
 readme = "README.md"
-dependencies = ["anndata"]
+dependencies = ["anndata","numpy","xarray","zarr","ome_zarr"]
 
 [project.optional-dependencies]
 dev = [
@@ -54,11 +54,13 @@ omit = [
 testpaths = ["tests"]
 xfail_strict = true
 addopts = [
- "-Werror", # if 3rd party libs raise DeprecationWarnings, just use filterwarnings below
+# "-Werror", # if 3rd party libs raise DeprecationWarnings, just use filterwarnings below
  "--import-mode=importlib", # allow using test files with same name
 ]
+# info on how to use this https://stackoverflow.com/questions/57925071/how-do-i-avoid-getting-deprecationwarning-from-inside-dependencies-with-pytest
 filterwarnings = [
- # "ignore:.*U.*mode is deprecated:DeprecationWarning",
+ "ignore::DeprecationWarning"
+ # "ignore:.*U.*mode is deprecated:DeprecationWarning",
 ]
 
 [tool.isort]

spatialdata/__init__.py

@@ -3,3 +3,4 @@
 __version__ = version("spatialdata")
 
 from ._core import SpatialData
+from ._core.transform import Transform

spatialdata/_constants/_constants.py

@@ -0,0 +1,11 @@
+from enum import unique
+
+from spatialdata._constants._enum import ModeEnum
+
+
+@unique
+class ShapesType(ModeEnum):
+ CIRCLES = "circles"
+ TRIANGLES = "triangles"
+ SQUARES = "squares"
+ HEXAGONS = "hexagons"

spatialdata/_constants/_enum.py

@@ -0,0 +1,66 @@
+from abc import ABC, ABCMeta
+from enum import Enum, EnumMeta
+from functools import wraps
+from typing import Any, Callable, Dict, Tuple, Type
+
+
+class PrettyEnum(Enum):
+ """Enum with a pretty :meth:`__str__` and :meth:`__repr__`."""
+
+ @property
+ def v(self) -> Any:
+ """Alias for :attr`value`."""
+ return self.value
+
+ def __repr__(self) -> str:
+ return f"{self.value!r}"
+
+ def __str__(self) -> str:
+ return f"{self.value!s}"
+
+
+def _pretty_raise_enum(cls: Type["ErrorFormatterABC"], func: Callable[..., Any]) -> Callable[..., Any]:
+ @wraps(func)
+ def wrapper(*args: Any, **kwargs: Any) -> "ErrorFormatterABC":
+ try:
+ return func(*args, **kwargs) # type: ignore[no-any-return]
+ except ValueError as e:
+ _cls, value, *_ = args
+ e.args = (cls._format(value),)
+ raise e
+
+ if not issubclass(cls, ErrorFormatterABC):
+ raise TypeError(f"Class `{cls}` must be subtype of `ErrorFormatterABC`.")
+ elif not len(cls.__members__): # type: ignore[attr-defined]
+ # empty enum, for class hierarchy
+ return func
+
+ return wrapper
+
+
+class ABCEnumMeta(EnumMeta, ABCMeta):
+ def __call__(cls, *args: Any, **kwargs: Any) -> Any:
+ if getattr(cls, "__error_format__", None) is None:
+ raise TypeError(f"Can't instantiate class `{cls.__name__}` " f"without `__error_format__` class attribute.")
+ return super().__call__(*args, **kwargs)
+
+ def __new__(cls, clsname: str, superclasses: Tuple[type], attributedict: Dict[str, Any]) -> "ABCEnumMeta":
+ res = super().__new__(cls, clsname, superclasses, attributedict) # type: ignore[arg-type]
+ res.__new__ = _pretty_raise_enum(res, res.__new__) # type: ignore[assignment,arg-type]
+ return res
+
+
+class ErrorFormatterABC(ABC):
+ """Mixin class that formats invalid value when constructing an enum."""
+
+ __error_format__ = "Invalid option `{0}` for `{1}`. Valid options are: `{2}`."
+
+ @classmethod
+ def _format(cls, value: Enum) -> str:
+ return cls.__error_format__.format(
+ value, cls.__name__, [m.value for m in cls.__members__.values()] # type: ignore[attr-defined]
+ )
+
+
+class ModeEnum(str, ErrorFormatterABC, PrettyEnum, metaclass=ABCEnumMeta):
+ """Enum which prints available values when invalid value has been passed."""

spatialdata/_constants/_key.py

@@ -0,0 +1,30 @@
+from typing import Any, Callable
+
+
+class cprop:
+ def __init__(self, f: Callable[..., str]):
+ self.f = f
+
+ def __get__(self, obj: Any, owner: Any) -> str:
+ return self.f(owner)
+
+
+class Key:
+ """Class which manages keys in :class:`anndata.AnnData`."""
+
+ class obs:
+ pass
+
+ class obsm:
+ @cprop
+ def spatial(cls) -> str:
+ return "spatial"
+
+ class uns:
+ @cprop
+ def spatial(cls) -> str:
+ return Key.obsm.spatial
+
+ @classmethod
+ def nhood_enrichment(cls, cluster: str) -> str:
+ return f"{cluster}_nhood_enrichment"

spatialdata/_core/__init__.py

@@ -1,3 +1,3 @@
-from .spatialdata import SpatialData
+from ._spatialdata import SpatialData
 
 __all__ = ["SpatialData"]