transform and models (#52)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Isaac Virshup <[email protected]> Co-authored-by: Macbook Marconato <[email protected]> Co-authored-by: Luca Marconato <[email protected]> Co-authored-by: Kevin Yamauchi <[email protected]>
scverse · Dec 12, 2022 · ef9b92a · ef9b92a
1 parent 365982a
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diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml
@@ -44,6 +44,7 @@ jobs:
             - name: Install test dependencies
               run: |
                   python -m pip install --upgrade pip wheel
+                  pip install pytest-cov
                   pip install codecov
             - name: Install dependencies
               run: |

diff --git a/.gitignore b/.gitignore
@@ -26,3 +26,9 @@ __pycache__/
 # data
 spatialdata-sandbox
 *.zarr/
+
+# temp files
+temp/
+
+# rst generated from myst
+docs/generated
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -11,7 +11,7 @@ repos:
       hooks:
           - id: black
     - repo: https://github.com/pre-commit/mirrors-prettier
-      rev: v2.7.1
+      rev: v3.0.0-alpha.4
       hooks:
           - id: prettier
     - repo: https://github.com/asottile/blacken-docs
@@ -23,7 +23,7 @@ repos:
       hooks:
           - id: isort
     - repo: https://github.com/pre-commit/mirrors-mypy
-      rev: v0.982
+      rev: v0.991
       hooks:
           - id: mypy
             additional_dependencies: [numpy==1.22.0, types-requests]
@@ -40,7 +40,7 @@ repos:
                 - flake8-bugbear
                 - flake8-blind-except
     - repo: https://github.com/pre-commit/pre-commit-hooks
-      rev: v4.3.0
+      rev: v4.4.0
       hooks:
           - id: detect-private-key
           - id: check-ast
@@ -49,8 +49,9 @@ repos:
             args: [--fix=lf]
           - id: trailing-whitespace
           - id: check-case-conflict
+          - id: check-docstring-first
     - repo: https://github.com/PyCQA/autoflake
-      rev: v1.7.1
+      rev: v2.0.0
       hooks:
           - id: autoflake
             args:
@@ -59,7 +60,7 @@ repos:
                 - --remove-unused-variable
                 - --ignore-init-module-imports
     - repo: https://github.com/PyCQA/flake8
-      rev: 5.0.4
+      rev: 6.0.0
       hooks:
           - id: flake8
             additional_dependencies:
@@ -70,7 +71,20 @@ repos:
                 - flake8-bugbear
                 - flake8-blind-except
     - repo: https://github.com/asottile/pyupgrade
-      rev: v3.0.0
+      rev: v3.2.2
       hooks:
           - id: pyupgrade
             args: [--py3-plus, --py38-plus, --keep-runtime-typing]
+    - repo: https://github.com/pre-commit/pygrep-hooks
+      rev: v1.9.0
+      hooks:
+          - id: python-no-eval
+          - id: python-use-type-annotations
+          - id: python-check-blanket-noqa
+          - id: rst-backticks
+          - id: rst-directive-colons
+          - id: rst-inline-touching-normal
+    - repo: https://github.com/PyCQA/doc8
+      rev: v1.0.0
+      hooks:
+          - id: doc8
diff --git a/README.md b/README.md
@@ -13,7 +13,7 @@
 [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
 
-Up-to-date design doc [here](docs/design_doc.md#Abstract)
+Up-to-date design doc [here](https://github.com/scverse/spatialdata/blob/main/docs/design_doc.md)
 
 ## Getting started
 

diff --git a/docs/_templates/autosummary/class.rst b/docs/_templates/autosummary/class.rst
@@ -38,6 +38,7 @@ Attributes
 ~~~~~~~~~~~
 
 {% for item in attributes %}
+
 {{ item }}
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
@@ -54,6 +55,7 @@ Methods
 
 {% for item in methods %}
 {%- if item != '__init__' %}
+
 {{ item }}
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 

diff --git a/docs/api.md b/docs/api.md
@@ -1 +1,63 @@
 # API
+
+```{eval-rst}
+.. module:: spatialdata
+```
+
+## SpatialData
+
+The `SpatialData` class.
+
+```{eval-rst}
+.. autosummary::
+    :toctree: generated
+
+    SpatialData
+```
+
+## Models
+
+The elements (building-blocks) that consitute `SpatialData`.
+
+### Regions
+
+#### Raster
+
+```{eval-rst}
+.. autosummary::
+    :toctree: generated
+
+    Image2DModel
+    Image3DModel
+    Labels2DModel
+    Labels2DModel
+```
+
+#### Polygons
+
+#### Shapes
+
+```{eval-rst}
+.. autosummary::
+    :toctree: generated
+
+    ShapesModel
+```
+
+### Points
+
+```{eval-rst}
+.. autosummary::
+    :toctree: generated
+
+    PointsModel
+```
+
+### Table
+
+```{eval-rst}
+.. autosummary::
+    :toctree: generated
+
+    TableModel
+```
diff --git a/docs/conf.py b/docs/conf.py
@@ -89,13 +89,26 @@
 intersphinx_mapping = {
     "anndata": ("https://anndata.readthedocs.io/en/stable/", None),
     "numpy": ("https://numpy.org/doc/stable/", None),
+    "geopandas": ("https://geopandas.org/en/stable/", None),
+    "xarray": ("https://docs.xarray.dev/en/stable/", None),
 }
 
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path.
-exclude_patterns = ["_build", "Thumbs.db", ".DS_Store", "**.ipynb_checkpoints"]
+exclude_patterns = [
+    "_build",
+    "Thumbs.db",
+    "**.ipynb_checkpoints",
+    "generated/spatialdata.PolygonsModel.rst",
+]
+# Ignore warnings.
+nitpicky = False  # TODO: solve upstream.
+# nitpick_ignore = [
+#     ("py:class", "spatial_image.SpatialImage"),
+#     ("py:class", "multiscale_spatial_image.multiscale_spatial_image.MultiscaleSpatialImage"),
+# ]
 
 
 # -- Options for HTML output -------------------------------------------------

diff --git a/docs/design_doc.md b/docs/design_doc.md
@@ -280,6 +280,20 @@ Transforms map Elements between coordinate systems. Each `Transform` object must
 
 Here is a short list of examples of the elements used to represent some spatial omics datasets. Real world will be available as notebooks [in this repository](https://github.com/scverse/spatialdata-notebooks), furthermore, some draft [implementations are available here](https://github.com/giovp/spatialdata-sandbox).
 
+API
+
+```python
+import spatialdata as sd
+from spatialdata import SpatialData
+
+sdata = SpatialData(...)
+points = sd.transform(sdata.points["image1"], tgt="tgt_space")
+sdata = sd.transform(sdata, tgt="tgt_space")
+```
+
+The transfromation object should not have a method to apply itself to an element.
+`SpatialData` can have a `transform` method, that can be applied to either a `SpatialData` object or an element.
+
 #### Layout of a SpatialData object
 
 The layout of some common datasets.

diff --git a/pyproject.toml b/pyproject.toml
@@ -22,15 +22,31 @@ version = "0.0.1.dev0"
 requires-python = ">=3.8"
 license = {file = "LICENSE"}
 readme = "README.md"
-dependencies = ["anndata","numpy","xarray","zarr","ome_zarr", "pyarrow"]
+dependencies = [
+    "anndata",
+    "numpy",
+    "xarray",
+    "zarr",
+    "ome_zarr",
+    "spatial_image",
+    "multiscale_spatial_image",
+    "xarray-schema",
+    "pygeos",
+    "geopandas",
+    "shapely==2.0rc2",
+    "pyarrow",
+    "rich",
+    "tqdm",
+    "typing_extensions>=4.0.0",
+]
 
 [project.optional-dependencies]
 dev = [
     # dev version generation
     "bump2version",
 ]
 doc = [
-    "sphinx>=4",
+    "sphinx>=4.5",
     "sphinx-book-theme>=0.3.3",
     "myst-nb",
     "sphinxcontrib-bibtex>=1.0.0",
@@ -91,3 +107,6 @@ exclude = '''
 
 [tool.jupytext]
 formats = "ipynb,md"
+
+[tool.doc8]
+ignore-path = "/docs/_templates/autosummary/*.rst"
diff --git a/spatialdata/__init__.py b/spatialdata/__init__.py
@@ -2,5 +2,53 @@
 
 __version__ = version("spatialdata")
 
-from spatialdata._core.spatialdata import SpatialData
-from spatialdata._core.transform import Transform
+__all__ = [
+    "SpatialData",
+    "Identity",
+    # "MapIndex",
+    "MapAxis",
+    "Translation",
+    "Scale",
+    "Affine",
+    "Rotation",
+    "Sequence",
+    # "Displacements",
+    # "Coordinates",
+    # "VectorField",
+    # "InverseOf",
+    # "Bijection",
+    # "ByDimension",
+    "Image3DModel",
+    "Image2DModel",
+    "Labels2DModel",
+    "Labels3DModel",
+    "PointsModel",
+    "PolygonsModel",
+    "ShapesModel",
+    "TableModel",
+    "SpatialElement",
+    "get_transform",
+    "set_transform",
+]
+
+from spatialdata._core._spatialdata import SpatialData
+from spatialdata._core.core_utils import SpatialElement, get_transform, set_transform
+from spatialdata._core.models import (
+    Image2DModel,
+    Image3DModel,
+    Labels2DModel,
+    Labels3DModel,
+    PointsModel,
+    PolygonsModel,
+    ShapesModel,
+    TableModel,
+)
+from spatialdata._core.transformations import (  # Bijection,; ByDimension,; Coordinates,; Displacements,; InverseOf,; MapIndex,; VectorField,
+    Affine,
+    Identity,
+    MapAxis,
+    Rotation,
+    Scale,
+    Sequence,
+    Translation,
+)
diff --git a/spatialdata/_constants/_constants.py b/spatialdata/_constants/_constants.py
@@ -0,0 +1,15 @@
+from enum import unique
+
+from spatialdata._constants._enum import ModeEnum
+
+
+@unique
+class RasterType(ModeEnum):
+    IMAGE = "Image"
+    LABEL = "Label"
+
+
+@unique
+class ShapeType(ModeEnum):
+    CIRCLE = "Circle"
+    SQUARE = "Square"
diff --git a/spatialdata/_core/__init__.py b/spatialdata/_core/__init__.py
@@ -1 +1 @@
-from spatialdata._core.spatialdata import SpatialData
+from spatialdata._core._spatialdata import SpatialData
Original file line number	Diff line number	Diff line change
		@@ -1 +1 @@
		from spatialdata._core.spatialdata import SpatialData
		from spatialdata._core._spatialdata import SpatialData