ngio 0.3.1__tar.gz → 0.3.3__tar.gz

ngio-0.3.3/.github/pull_request_template.md

@@ -0,0 +1,3 @@
+
+## Checklist before merging
+- [ ] I added an appropriate entry to `CHANGELOG.md`

{ngio-0.3.1 → ngio-0.3.3}/.github/workflows/build_docs.yml

@@ -4,28 +4,23 @@ on:
   push:
     branches:
       - dev
+      - main
     tags:
       - "v*"
 
-jobs:
-  download-test-ome-zarr:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-      - name: Check and Download Artifacts
-        run: |
-          bash .github/scripts/download_data.sh
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
 
+jobs:
   deploy:
     name: Deploy Docs
-    needs: download-test-ome-zarr
     runs-on: ubuntu-latest
 
     steps:
       - uses: actions/checkout@v4
         with:
           fetch-depth: 0
-
       - name: 🐍 Set up Python
         uses: actions/setup-python@v5
         with:
@@ -44,6 +39,15 @@ jobs:
           git config --local user.email "github-actions[bot]@users.noreply.github.com"
           git config --local user.name "github-actions[bot]"
         
+      - name: Restore shared data cache
+        id: cache-data
+        uses: actions/cache@v4
+        with:
+          path: data/
+          key: "${{ runner.os }}-data-${{ hashFiles('tests/conftest.py') }}"
+          restore-keys: |
+            "${{ runner.os }}-data-"
+            
       - name: Deploy docs
         run: |
           VERSION=$(echo $GITHUB_REF | sed 's/refs\/tags\///' | sed 's/refs\/heads\///')
@@ -53,9 +57,10 @@ jobs:
           if [[ $GITHUB_REF == refs/tags/* ]] && [[ $VERSION =~ ^v[0-9.]+$ ]]; then
             mike deploy --push --update-aliases $VERSION stable
             mike set-default --push stable
-            echo "Deployed stable version"
-          else
+            echo "Deployed stable version $VERSION (stable)"
+
+          elif [[ $GITHUB_REF == refs/heads/dev ]]; then
             mike deploy --push dev
             mike set-default --push dev
-            echo "Deployed development version"
+            echo "Deployed development version (dev)"
           fi

{ngio-0.3.1 → ngio-0.3.3}/.github/workflows/ci.yml

@@ -27,49 +27,18 @@ jobs:
       - uses: actions/checkout@v4
       - run: pipx run check-manifest
 
-  
-  download-test-ome-zarr:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-      - name: Check and Download Artifacts
-        run: |
-          bash .github/scripts/download_data.sh
-      - name: Upload Artifacts
-        uses: actions/upload-artifact@v4
-        with:
-          name: data
-          path: data
-
-
   test:
     name: ${{ matrix.platform }} (${{ matrix.python-version }})
-    needs: download-test-ome-zarr
     runs-on: ${{ matrix.platform }}
     strategy:
       fail-fast: false
       matrix:
         python-version: ["3.11", "3.12", "3.13"]
         platform: [ubuntu-latest, macos-latest, windows-latest]
-        # platform: [ubuntu-latest, macos-latest]
-        exclude:
-          - python-version: "3.11"
-            platform: windows-latest
-          - python-version: "3.12"
-            platform: windows-latest
 
     steps:
       - uses: actions/checkout@v4
 
-      - uses: actions/download-artifact@v4
-        with:
-          name: data
-          path: data
-
-      - name: Check Artifacts
-        run: |
-          ls -l data
-
       - name: 🐍 Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v5
         with:
@@ -82,6 +51,15 @@ jobs:
           python -m pip install -U pip
           # if running a cron job, we add the --pre flag to test against pre-releases
           python -m pip install .[test] ${{ github.event_name == 'schedule' && '--pre' || ''  }}
+      
+      - name: Restore shared data cache
+        id: cache-data
+        uses: actions/cache@v4
+        with:
+          path: data/
+          key: "${{ runner.os }}-data-${{ hashFiles('tests/conftest.py') }}"
+          restore-keys: |
+            "${{ runner.os }}-data-"
 
       - name: 🧪 Run Tests
         run: pytest
@@ -101,7 +79,6 @@ jobs:
           update_existing: true
 
       - name: Coverage
-        if: ${{ matrix.python-version == '3.10' }} && ${{ matrix.platform == 'ubuntu-latest' }}
         uses: codecov/codecov-action@v5
         with:
           token: ${{ secrets.CODECOV_TOKEN }}

ngio-0.3.3/CHANGELOG.md

@@ -0,0 +1,18 @@
+# Changelog
+
+## [v0.3.3]
+
+### Chores
+
+- improve dataset download process and streamline the CI workflows
+
+## [v0.3.2]
+
+### API Changes
+
+- change table backend default to `anndata_v1` for backward compatibility. This will be chaanged again when ngio `v0.2.x` is no longer supported.
+
+### Bug Fixes
+
+- fix [#13](https://github.com/fractal-analytics-platform/fractal-converters-tools/issues/13) (converters tools)
+- fix [#88](https://github.com/fractal-analytics-platform/ngio/issues/88)

{ngio-0.3.1 → ngio-0.3.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ngio
-Version: 0.3.1
+Version: 0.3.3
 Summary: Next Generation file format IO
 Project-URL: homepage, https://github.com/fractal-analytics-platform/ngio
 Project-URL: repository, https://github.com/fractal-analytics-platform/ngio

{ngio-0.3.1 → ngio-0.3.3}/docs/getting_started/0_quickstart.md

@@ -57,7 +57,7 @@ from ngio.utils import download_ome_zarr_dataset
 
 # Download a sample dataset
 download_dir = Path("./data")
-download_dir = Path(".").absolute().parent.parent / "data" # markdown-exec: hide
+download_dir = Path(".").absolute() / "data" # markdown-exec: hide
 hcs_path = download_ome_zarr_dataset("CardiomyocyteSmallMip", download_dir=download_dir)
 image_path = hcs_path / "B" / "03" / "0"
 ```

{ngio-0.3.1 → ngio-0.3.3}/docs/getting_started/1_ome_zarr_containers.md

@@ -9,7 +9,7 @@ from ngio.utils import download_ome_zarr_dataset
 
 # Download a sample dataset
 download_dir = Path("./data")
-download_dir = Path(".").absolute().parent.parent / "data" # markdown-exec: hide
+download_dir = Path(".").absolute() / "data" # markdown-exec: hide
 hcs_path = download_ome_zarr_dataset("CardiomyocyteSmallMip", download_dir=download_dir)
 image_path = hcs_path / "B" / "03" / "0"
 

{ngio-0.3.1 → ngio-0.3.3}/docs/getting_started/4_masked_images.md

@@ -10,7 +10,7 @@ from ngio import open_ome_zarr_container
 from ngio.utils import download_ome_zarr_dataset
 
 # Download a sample dataset
-download_dir = Path(".").absolute().parent.parent / "data" 
+download_dir = Path(".").absolute() / "data" 
 hcs_path = download_ome_zarr_dataset("CardiomyocyteSmallMip", download_dir=download_dir)
 image_path = hcs_path / "B" / "03" / "0"
 

{ngio-0.3.1 → ngio-0.3.3}/docs/getting_started/5_hcs.md

@@ -10,7 +10,7 @@ Let's open an `OmeZarrPlate` object.
 >>> from pathlib import Path # markdown-exec: hide
 >>> from ngio.utils import download_ome_zarr_dataset
 >>> from ngio import open_ome_zarr_plate
->>> download_dir = Path(".").absolute().parent.parent / "data" # markdown-exec: hide
+>>> download_dir = Path(".").absolute() / "data" # markdown-exec: hide
 >>> hcs_path = download_ome_zarr_dataset("CardiomyocyteSmallMip", download_dir=download_dir)
 >>> ome_zarr_plate = open_ome_zarr_plate(hcs_path)
 >>> ome_zarr_plate
@@ -111,6 +111,7 @@ The `OmeZarrPlate` object provides a method to get the image objects in a well.
 Ngio provides a utility function to create a plate.
 
 The first step is to create a list of `ImageInWellPath` objects. Each `ImageInWellPath` object contains the path to the image and the corresponding well.
+
 ```python exec="true" source="console" session="hcs_plate"
 from ngio import ImageInWellPath
 list_of_images = [ImageInWellPath(path="0", row="A", column=0),
@@ -124,6 +125,7 @@ list_of_images = [ImageInWellPath(path="0", row="A", column=0),
     The order in which the images are added is not important. The `rows` and `columns` attributes of the plate will be sorted in alphabetical/numerical order.
 
 Then, you can create the plate using the `create_empty_plate` function.
+
 ```pycon exec="true" source="console" session="hcs_plate"
 >>> from ngio import create_empty_plate
 >>> plate = create_empty_plate(store="new_plate.zarr", name="test_plate", images=list_of_images, overwrite=True)
@@ -131,7 +133,7 @@ Then, you can create the plate using the `create_empty_plate` function.
 >>> print(plate) # markdown-exec: hide
 ```
 
-This has created a new empty plate with the metadata correctly set. But no images have been added yet. 
+This has created a new empty plate with the metadata correctly set. But no images have been added yet.
 
 ### Modifying the plate
 

{ngio-0.3.1 → ngio-0.3.3}/docs/table_specs/table_types/roi_table.md

@@ -33,7 +33,7 @@ Moreover the ROI table must include the following columns:
 
 Additionally, each ROI can include the following optional columns:
 
-- `x_micrometer_original` and `y_micrometer_original` which are the original coordinates of the ROI in micrometers. These are typically used when the data is saved in different coordinates during conversion, e.g. to avoid overwriting data from overlapping ROIs.
+- `x_micrometer_original`, `y_micrometer_original` and `z_micrometer_original` which are the original coordinates of the ROI in micrometers. These are typically used when the data is saved in different coordinates during conversion, e.g. to avoid overwriting data from overlapping ROIs.
 - `translation_x`, `translation_y` and `translation_z`, which are used during registration of multiplexing acquisitions.
 
 The user can also add additional columns to the ROI table, but these columns will not be exposed in the ROI table API.

{ngio-0.3.1 → ngio-0.3.3}/src/ngio/common/_roi.py

@@ -57,6 +57,7 @@ class Roi(BaseModel):
             x_length=_to_raster(self.x_length, pixel_size.x, dim_x),
             y_length=_to_raster(self.y_length, pixel_size.y, dim_y),
             z_length=_to_raster(self.z_length, pixel_size.z, dim_z),
+            **self.model_extra,
         )
 
     def zoom(self, zoom_factor: float = 1) -> "Roi":
@@ -94,6 +95,7 @@ class RoiPixels(BaseModel):
             y_length=_to_world(self.y_length, pixel_size.y),
             z_length=_to_world(self.z_length, pixel_size.z),
             unit=pixel_size.space_unit,
+            **self.model_extra,
         )
 
     def to_slices(self) -> dict[str, slice]:

{ngio-0.3.1 → ngio-0.3.3}/src/ngio/hcs/_plate.py

@@ -27,6 +27,7 @@ from ngio.ome_zarr_meta import (
 )
 from ngio.tables import (
     ConditionTable,
+    DefaultTableBackend,
     FeatureTable,
     GenericRoiTable,
     MaskingRoiTable,
@@ -199,7 +200,7 @@ class OmeZarrWell:
         )
 
 
-def _buil_extras(paths: Collection[str]) -> list[dict[str, str]]:
+def _build_extras(paths: Collection[str]) -> list[dict[str, str]]:
     """Build the extras for the images.
 
     Args:
@@ -944,7 +945,7 @@ class OmeZarrPlate:
         self,
         name: str,
         table: Table,
-        backend: TableBackend = "anndata",
+        backend: TableBackend = DefaultTableBackend,
         overwrite: bool = False,
     ) -> None:
         """Add a table to the image."""
@@ -1020,7 +1021,7 @@ class OmeZarrPlate:
                 if 'lazy', the table will be loaded as a lazy frame.
         """
         images = self.get_images(acquisition=acquisition)
-        extras = _buil_extras(images.keys())
+        extras = _build_extras(images.keys())
         return concatenate_image_tables(
             images=images.values(),
             extras=extras,
@@ -1054,7 +1055,7 @@ class OmeZarrPlate:
                 if 'lazy', the table will be loaded as a lazy frame.
         """
         images = self.get_images(acquisition=acquisition)
-        extras = _buil_extras(images.keys())
+        extras = _build_extras(images.keys())
         return concatenate_image_tables_as(
             images=images.values(),
             extras=extras,
@@ -1087,7 +1088,7 @@ class OmeZarrPlate:
                 if 'lazy', the table will be loaded as a lazy frame.
         """
         images = await self.get_images_async(acquisition=acquisition)
-        extras = _buil_extras(images.keys())
+        extras = _build_extras(images.keys())
         return await concatenate_image_tables_async(
             images=images.values(),
             extras=extras,
@@ -1121,7 +1122,7 @@ class OmeZarrPlate:
                 if 'lazy', the table will be loaded as a lazy frame.
         """
         images = await self.get_images_async(acquisition=acquisition)
-        extras = _buil_extras(images.keys())
+        extras = _build_extras(images.keys())
         return await concatenate_image_tables_as_async(
             images=images.values(),
             extras=extras,

{ngio-0.3.1 → ngio-0.3.3}/src/ngio/images/_ome_zarr_container.py

@@ -23,6 +23,7 @@ from ngio.ome_zarr_meta.ngio_specs import (
 )
 from ngio.tables import (
     ConditionTable,
+    DefaultTableBackend,
     FeatureTable,
     GenericRoiTable,
     MaskingRoiTable,
@@ -501,7 +502,7 @@ class OmeZarrContainer:
         self,
         name: str,
         table: Table,
-        backend: TableBackend = "anndata",
+        backend: TableBackend = DefaultTableBackend,
         overwrite: bool = False,
     ) -> None:
         """Add a table to the image."""
@@ -831,7 +832,7 @@ def create_ome_zarr_from_array(
         axes_names=axes_names,
         name=name,
         chunks=chunks,
-        dtype=array.dtype,
+        dtype=str(array.dtype),
         overwrite=overwrite,
         version=version,
     )

{ngio-0.3.1 → ngio-0.3.3}/src/ngio/tables/__init__.py

@@ -15,6 +15,7 @@ from ngio.tables._tables_container import (
     open_tables_container,
 )
 from ngio.tables.backends import (
+    DefaultTableBackend,
     ImplementedTableBackends,
     TableBackend,
     TableBackendProtocol,
@@ -23,6 +24,7 @@ from ngio.tables.v1._generic_table import GenericTable
 
 __all__ = [
     "ConditionTable",
+    "DefaultTableBackend",
     "FeatureTable",
     "GenericRoiTable",
     "GenericTable",

{ngio-0.3.1 → ngio-0.3.3}/src/ngio/tables/_abstract_table.py

@@ -10,6 +10,7 @@ from anndata import AnnData
 
 from ngio.tables.backends import (
     BackendMeta,
+    DefaultTableBackend,
     ImplementedTableBackends,
     TableBackend,
     TableBackendProtocol,
@@ -203,7 +204,7 @@ class AbstractBaseTable(ABC):
     def set_backend(
         self,
         handler: ZarrGroupHandler | None = None,
-        backend: TableBackend = "anndata",
+        backend: TableBackend = DefaultTableBackend,
     ) -> None:
         """Set the backend of the table."""
         if handler is None:

{ngio-0.3.1 → ngio-0.3.3}/src/ngio/tables/_tables_container.py

@@ -8,6 +8,7 @@ import polars as pl
 
 from ngio.tables.backends import (
     BackendMeta,
+    DefaultTableBackend,
     TableBackend,
     TabularData,
 )
@@ -90,13 +91,13 @@ class Table(Protocol):
     def set_backend(
         self,
         handler: ZarrGroupHandler | None = None,
-        backend: TableBackend = "anndata",
+        backend: TableBackend = DefaultTableBackend,
     ) -> None:
         """Set the backend store and path for the table.
 
         Either a handler or a backend must be provided.
 
-        If the hanlder in none it will be inferred from the backend.
+        If the handler in none it will be inferred from the backend.
         If the backend is none, it will be inferred from the group attrs
         """
         ...
@@ -314,7 +315,7 @@ class TablesContainer:
         self,
         name: str,
         table: Table,
-        backend: TableBackend = "anndata",
+        backend: TableBackend = DefaultTableBackend,
         overwrite: bool = False,
     ) -> None:
         """Add a table to the group."""
@@ -406,7 +407,7 @@ def open_table_as(
 def write_table(
     store: StoreOrGroup,
     table: Table,
-    backend: TableBackend = "anndata",
+    backend: TableBackend = DefaultTableBackend,
     cache: bool = False,
     mode: AccessModeLiteral = "a",
     parallel_safe: bool = False,

{ngio-0.3.1 → ngio-0.3.3}/src/ngio/tables/backends/__init__.py

@@ -6,6 +6,7 @@ from ngio.tables.backends._csv import CsvTableBackend
 from ngio.tables.backends._json import JsonTableBackend
 from ngio.tables.backends._parquet import ParquetTableBackend
 from ngio.tables.backends._table_backends import (
+    DefaultTableBackend,
     ImplementedTableBackends,
     TableBackend,
     TableBackendProtocol,
@@ -32,6 +33,7 @@ __all__ = [
     "AnnDataBackend",
     "BackendMeta",
     "CsvTableBackend",
+    "DefaultTableBackend",
     "ImplementedTableBackends",
     "JsonTableBackend",
     "ParquetTableBackend",

{ngio-0.3.1 → ngio-0.3.3}/src/ngio/tables/backends/_abstract_backend.py

@@ -19,7 +19,7 @@ from ngio.utils import NgioValueError, ZarrGroupHandler
 class BackendMeta(BaseModel):
     """Metadata for the backend."""
 
-    backend: str = "anndata"
+    backend: str = "anndata_v1"
     index_key: str | None = None
     index_type: Literal["int", "str"] | None = None
 

{ngio-0.3.1 → ngio-0.3.3}/src/ngio/tables/backends/_table_backends.py

@@ -223,3 +223,4 @@ ImplementedTableBackends().add_backend(
 )
 
 TableBackend = Literal["anndata", "json", "csv", "parquet"] | str | TableBackendProtocol
+DefaultTableBackend = "anndata_v1"

{ngio-0.3.1 → ngio-0.3.3}/src/ngio/tables/v1/_condition_table.py

@@ -23,7 +23,7 @@ class ConditionTableV1(AbstractBaseTable):
     The condition table is a generic table that does not
     have a specific definition.
 
-    It is used to store informations about the particular conditions
+    It is used to store information about the particular conditions
     used to generate the data.
     - How much drug was used in the experiment
     - What treatment was used

{ngio-0.3.1 → ngio-0.3.3}/src/ngio/tables/v1/_roi_table.py

@@ -47,11 +47,20 @@ REQUIRED_COLUMNS = [
 ORIGIN_COLUMNS = [
     "x_micrometer_original",
     "y_micrometer_original",
+    "z_micrometer_original",
 ]
 
 TRANSLATION_COLUMNS = ["translation_x", "translation_y", "translation_z"]
 
-PLATE_COLUMNS = ["plate_name", "row", "column", "path", "acquisition"]
+PLATE_COLUMNS = [
+    "plate_name",
+    "row",
+    "column",
+    "path_in_well",
+    "path_in_plate",
+    "acquisition_id",
+    "acquisition_name",
+]
 
 INDEX_COLUMNS = [
     "FieldIndex",
@@ -390,7 +399,8 @@ class MaskingRoiTableV1(GenericRoiTableV1):
             meta = MaskingRoiTableV1Meta()
 
         if reference_label is not None:
-            meta.region = RegionMeta(path=reference_label)
+            path = f"../labels/{reference_label}"
+            meta.region = RegionMeta(path=path)
 
         if meta.index_key is None:
             meta.index_key = "label"

{ngio-0.3.1 → ngio-0.3.3}/src/ngio/utils/__init__.py

@@ -3,7 +3,11 @@
 import os
 
 from ngio.common._common_types import ArrayLike
-from ngio.utils._datasets import download_ome_zarr_dataset, list_ome_zarr_datasets
+from ngio.utils._datasets import (
+    download_ome_zarr_dataset,
+    list_ome_zarr_datasets,
+    print_datasets_infos,
+)
 from ngio.utils._errors import (
     NgioFileExistsError,
     NgioFileNotFoundError,
@@ -34,13 +38,13 @@ __all__ = [
     "NgioValueError",
     "StoreOrGroup",
     "ZarrGroupHandler",
-    # Datasets
+    # Other
     "download_ome_zarr_dataset",
-    # Fractal
     "fractal_fsspec_store",
     "list_ome_zarr_datasets",
     # Logger
     "ngio_logger",
     "open_group_wrapper",
+    "print_datasets_infos",
     "set_logger_level",
 ]