ngio 0.2.0b1__tar.gz → 0.2.0b3__tar.gz

ngio-0.2.0b3/.github/scripts/download_data.sh

@@ -0,0 +1,97 @@
+#!/bin/bash
+# filepath: download_zarr_datasets.sh
+
+# Default download directory
+DOWNLOAD_DIR="data"
+
+# Create download directory if it doesn't exist
+mkdir -p "$DOWNLOAD_DIR"
+
+# Function to check MD5 hash
+check_md5() {
+    local file="$1"
+    local expected="$2"
+    
+    if [[ "$(uname)" == "Darwin" ]]; then
+        # macOS
+        actual=$(md5 -q "$file")
+    else
+        # Linux/Ubuntu
+        actual=$(md5sum "$file" | awk '{print $1}')
+    fi
+
+    echo "Expected: $expected"
+    echo "Actual: $actual"
+    
+    if [[ "$actual" == "$expected" ]]; then
+        return 0  # Success
+    else
+        return 1  # Failure
+    fi
+}
+
+# Function to download a file
+download_file() {
+    local url="$1"
+    local output="$2"
+    
+    echo "Downloading $url to $output..."
+    
+    if command -v curl &> /dev/null; then
+        curl -L -o "$output" "$url"
+    elif command -v wget &> /dev/null; then
+        wget -O "$output" "$url"
+    else
+        echo "Error: Neither curl nor wget is available. Please install one of them."
+        exit 1
+    fi
+}
+
+# Function to process a dataset
+process_dataset() {
+    local filename="$1"
+    local url="$2"
+    local expected_hash="$3"
+    
+    local file_path="$DOWNLOAD_DIR/$filename"
+    
+    echo "Processing $filename..."
+    
+    # Check if file exists and has the correct hash
+    if [[ -f "$file_path" ]] && check_md5 "$file_path" "$expected_hash"; then
+        echo "File exists and has the correct hash."
+    else
+        # File doesn't exist or has incorrect hash
+        if [[ -f "$file_path" ]]; then
+            echo "File exists but has incorrect hash. Redownloading..."
+        else
+            echo "File doesn't exist. Downloading..."
+        fi
+        
+        download_file "$url" "$file_path"
+        
+        # Verify the downloaded file
+        if check_md5 "$file_path" "$expected_hash"; then
+            echo "Download successful and hash verified."
+        else
+            echo "Error: Downloaded file has incorrect hash."
+            return 1
+        fi
+    fi
+    
+    echo "File is ready at $file_path"
+    return 0
+}
+
+# Process the CardioMyocyte dataset
+process_dataset "20200812-CardiomyocyteDifferentiation14-Cycle1.zarr.zip" \
+                "https://zenodo.org/records/13305156/files/20200812-CardiomyocyteDifferentiation14-Cycle1.zarr.zip" \
+                "efc21fe8d4ea3abab76226d8c166452c"
+
+process_dataset "20200812-CardiomyocyteDifferentiation14-Cycle1_mip.zarr.zip" \
+                "https://zenodo.org/records/13305316/files/20200812-CardiomyocyteDifferentiation14-Cycle1_mip.zarr.zip" \
+                "3ed3ea898e0ed42d397da2e1dbe40750"
+# To add more datasets, add more calls to process_dataset like this:
+# process_dataset "filename.zip" "download_url" "expected_md5_hash"
+
+echo "All datasets processed."

ngio-0.2.0b3/.github/workflows/build_docs.yml

@@ -0,0 +1,61 @@
+name: Build Docs
+
+on:
+  push:
+    branches:
+      - 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
+
+  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:
+          python-version: "3.13"
+          cache-dependency-path: "pyproject.toml"
+          cache: "pip"
+
+      - name: Install Dependencies
+        run: |
+          python -m pip install -U pip
+          python -m pip install .[dev]
+          python -m pip install .[docs]
+
+      - name: Configure Git user
+        run: |
+          git config --local user.email "github-actions[bot]@users.noreply.github.com"
+          git config --local user.name "github-actions[bot]"
+        
+      - name: Deploy docs
+        run: |
+          VERSION=$(echo $GITHUB_REF | sed 's/refs\/tags\///' | sed 's/refs\/heads\///')
+          echo "Deploying version $VERSION"
+          # Check if the version is a stable release
+          # Meaning that starts with "v" and contains only numbers and dots
+          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
+            mike deploy --push dev
+            mike set-default --push dev
+            echo "Deployed development version"
+          fi

{ngio-0.2.0b1 → ngio-0.2.0b3}/.github/workflows/ci.yml

@@ -26,8 +26,24 @@ 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
@@ -44,6 +60,15 @@ jobs:
     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:

{ngio-0.2.0b1 → ngio-0.2.0b3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ngio
-Version: 0.2.0b1
+Version: 0.2.0b3
 Summary: Next Generation file format IO
 Project-URL: homepage, https://github.com/lorenzocerrone/ngio
 Project-URL: repository, https://github.com/lorenzocerrone/ngio
@@ -41,6 +41,7 @@ Requires-Dist: rich; extra == 'dev'
 Requires-Dist: ruff; extra == 'dev'
 Requires-Dist: scikit-image; extra == 'dev'
 Provides-Extra: docs
+Requires-Dist: mike; extra == 'docs'
 Requires-Dist: mkdocs; extra == 'docs'
 Requires-Dist: mkdocs-autorefs; extra == 'docs'
 Requires-Dist: mkdocs-git-committers-plugin-2; extra == 'docs'
@@ -60,7 +61,7 @@ Description-Content-Type: text/markdown
 [![License](https://img.shields.io/pypi/l/ngio.svg?color=green)](https://github.com/lorenzocerrone/ngio/raw/main/LICENSE)
 [![PyPI](https://img.shields.io/pypi/v/ngio.svg?color=green)](https://pypi.org/project/ngio)
 [![Python Version](https://img.shields.io/pypi/pyversions/ngio.svg?color=green)](https://python.org)
-[![CI](https://github.com/lorenzocerrone/ngio/actions/workflows/ci.yml/badge.svg)](https://github.com/lorenzocerrone/ngio/actions/workflows/ci.yml)
+[![CI](https://github.com/fractal-analytics-platform/ngio/actions/workflows/ci.yml/badge.svg)](https://github.com/fractal-analytics-platform/ngio/actions/workflows/ci.yml)
 [![codecov](https://codecov.io/gh/fractal-analytics-platform/ngio/graph/badge.svg?token=FkmF26FZki)](https://codecov.io/gh/fractal-analytics-platform/ngio)
 
 NGIO is a Python library to streamline OME-Zarr image analysis workflows.
@@ -96,3 +97,4 @@ To get started, check out the [Getting Started](https://fractal-analytics-platfo
 | Parallel Iterators | Not started | mid-2025 | Concurrent Iterators for parallel read and write |
 | Full Documentation | Not started | 2025 | Complete Documentation |
 | Release 1.0 (Commitment to API) | Not started | 2025 | API is stable; breaking changes will be avoided |
+

{ngio-0.2.0b1 → ngio-0.2.0b3}/README.md

@@ -3,7 +3,7 @@
 [![License](https://img.shields.io/pypi/l/ngio.svg?color=green)](https://github.com/lorenzocerrone/ngio/raw/main/LICENSE)
 [![PyPI](https://img.shields.io/pypi/v/ngio.svg?color=green)](https://pypi.org/project/ngio)
 [![Python Version](https://img.shields.io/pypi/pyversions/ngio.svg?color=green)](https://python.org)
-[![CI](https://github.com/lorenzocerrone/ngio/actions/workflows/ci.yml/badge.svg)](https://github.com/lorenzocerrone/ngio/actions/workflows/ci.yml)
+[![CI](https://github.com/fractal-analytics-platform/ngio/actions/workflows/ci.yml/badge.svg)](https://github.com/fractal-analytics-platform/ngio/actions/workflows/ci.yml)
 [![codecov](https://codecov.io/gh/fractal-analytics-platform/ngio/graph/badge.svg?token=FkmF26FZki)](https://codecov.io/gh/fractal-analytics-platform/ngio)
 
 NGIO is a Python library to streamline OME-Zarr image analysis workflows.
@@ -39,3 +39,4 @@ To get started, check out the [Getting Started](https://fractal-analytics-platfo
 | Parallel Iterators | Not started | mid-2025 | Concurrent Iterators for parallel read and write |
 | Full Documentation | Not started | 2025 | Complete Documentation |
 | Release 1.0 (Commitment to API) | Not started | 2025 | API is stable; breaking changes will be avoided |
+

{ngio-0.2.0b1 → ngio-0.2.0b3}/docs/notebooks/basic_usage.ipynb

@@ -22,11 +22,17 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "from pathlib import Path\n",
+    "\n",
     "from ngio import open_omezarr_container\n",
     "from ngio.utils import download_ome_zarr_dataset\n",
     "\n",
-    "hcs_path = download_ome_zarr_dataset(\"CardiomyocyteSmallMip\")\n",
+    "# Download the dataset\n",
+    "download_dir = Path(\".\").absolute().parent.parent / \"data\"\n",
+    "hcs_path = download_ome_zarr_dataset(\"CardiomyocyteSmallMip\", download_dir=download_dir)\n",
     "image_path = hcs_path / \"B\" / \"03\" / \"0\"\n",
+    "\n",
+    "# Open the ome-zarr container\n",
     "omezarr_container = open_omezarr_container(image_path)"
    ]
   },

{ngio-0.2.0b1 → ngio-0.2.0b3}/docs/notebooks/image.ipynb

@@ -15,13 +15,19 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "from pathlib import Path\n",
+    "\n",
     "import matplotlib.pyplot as plt\n",
     "\n",
     "from ngio import open_omezarr_container\n",
     "from ngio.utils import download_ome_zarr_dataset\n",
     "\n",
-    "hcs_path = download_ome_zarr_dataset(\"CardiomyocyteSmallMip\")\n",
+    "# Download the dataset\n",
+    "download_dir = Path(\".\").absolute().parent.parent / \"data\"\n",
+    "hcs_path = download_ome_zarr_dataset(\"CardiomyocyteSmallMip\", download_dir=download_dir)\n",
     "image_path = hcs_path / \"B\" / \"03\" / \"0\"\n",
+    "\n",
+    "# Open the ome-zarr container\n",
     "omezarr = open_omezarr_container(image_path)"
    ]
   },

{ngio-0.2.0b1 → ngio-0.2.0b3}/docs/notebooks/processing.ipynb

@@ -33,13 +33,19 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "from pathlib import Path\n",
+    "\n",
     "import matplotlib.pyplot as plt\n",
     "\n",
     "from ngio import open_omezarr_container\n",
     "from ngio.utils import download_ome_zarr_dataset\n",
     "\n",
-    "hcs_path = download_ome_zarr_dataset(\"CardiomyocyteTiny\")\n",
+    "# Download the dataset\n",
+    "download_dir = Path(\".\").absolute().parent.parent / \"data\"\n",
+    "hcs_path = download_ome_zarr_dataset(\"CardiomyocyteTiny\", download_dir=download_dir)\n",
     "image_path = hcs_path / \"B\" / \"03\" / \"0\"\n",
+    "\n",
+    "# Open the ome-zarr container\n",
     "omezarr = open_omezarr_container(image_path)"
    ]
   },

{ngio-0.2.0b1 → ngio-0.2.0b3}/mkdocs.yml

@@ -40,6 +40,8 @@ theme:
     - search.share
 
 extra:
+  version:
+    provider: mike
   social:
     - icon: fontawesome/brands/github
       link: "https://github.com/fractal-analytics-platform/ngio"

{ngio-0.2.0b1 → ngio-0.2.0b3}/pyproject.toml

@@ -76,6 +76,7 @@ docs = [
     "mkdocs-git-revision-date-localized-plugin",
     "mkdocs-git-committers-plugin-2",
     "scikit-image",
+    "mike",
 ]
 
 

{ngio-0.2.0b1 → ngio-0.2.0b3}/src/ngio/common/_array_pipe.py

@@ -179,13 +179,6 @@ def _mask_pipe_common(
         **slice_kwargs,
     )
 
-    if "c" in slice_kwargs.keys():
-        # This makes the strong assumption that the
-        # user is passing the channel axis as "c"
-        # This will fail if the channel axis is queried
-        # with a different on-disk name
-        slice_kwargs.pop("c")
-
     label_patch = get_pipe(
         label_array,
         dimensions=dimensions_label,

{ngio-0.2.0b1 → ngio-0.2.0b3}/src/ngio/images/abstract_image.py

@@ -99,6 +99,36 @@ class AbstractImage(Generic[_image_handler]):
         """Return the dimensions of the image."""
         return self._dimensions
 
+    @property
+    def is_3d(self) -> bool:
+        """Return True if the image is 3D."""
+        return self.dimensions.is_3d
+
+    @property
+    def is_2d(self) -> bool:
+        """Return True if the image is 2D."""
+        return self.dimensions.is_2d
+
+    @property
+    def is_time_series(self) -> bool:
+        """Return True if the image is a time series."""
+        return self.dimensions.is_time_series
+
+    @property
+    def is_2d_time_series(self) -> bool:
+        """Return True if the image is a 2D time series."""
+        return self.dimensions.is_2d_time_series
+
+    @property
+    def is_3d_time_series(self) -> bool:
+        """Return True if the image is a 3D time series."""
+        return self.dimensions.is_3d_time_series
+
+    @property
+    def is_multi_channels(self) -> bool:
+        """Return True if the image is multichannel."""
+        return self.dimensions.is_multi_channels
+
     @property
     def pixel_size(self) -> PixelSize:
         """Return the pixel size of the image."""

{ngio-0.2.0b1 → ngio-0.2.0b3}/src/ngio/images/omezarr_container.py

@@ -125,6 +125,36 @@ class OmeZarrContainer:
         """Return the paths of the levels in the image."""
         return self._images_container.levels_paths
 
+    @property
+    def is_3d(self) -> bool:
+        """Return True if the image is 3D."""
+        return self.get_image().is_3d
+
+    @property
+    def is_2d(self) -> bool:
+        """Return True if the image is 2D."""
+        return self.get_image().is_2d
+
+    @property
+    def is_time_series(self) -> bool:
+        """Return True if the image is a time series."""
+        return self.get_image().is_time_series
+
+    @property
+    def is_2d_time_series(self) -> bool:
+        """Return True if the image is a 2D time series."""
+        return self.get_image().is_2d_time_series
+
+    @property
+    def is_3d_time_series(self) -> bool:
+        """Return True if the image is a 3D time series."""
+        return self.get_image().is_3d_time_series
+
+    @property
+    def is_multi_channels(self) -> bool:
+        """Return True if the image is multichannel."""
+        return self.get_image().is_multi_channels
+
     def initialize_channel_meta(
         self,
         labels: Collection[str] | int | None = None,

{ngio-0.2.0b1 → ngio-0.2.0b3}/src/ngio/ome_zarr_meta/ngio_specs/_ngio_image.py

@@ -342,12 +342,6 @@ class NgioLabelMeta(AbstractNgioImageMeta):
     ) -> None:
         """Initialize the ImageMeta object."""
         super().__init__(version, name, datasets)
-
-        # Make sure that there are no channel axes
-        channel_axis = self.axes_mapper.get_axis("c")
-        if channel_axis is not None:
-            raise NgioValidationError("Label metadata must not have channel axes.")
-
         image_label = (
             ImageLabelSource.default_init(self.version)
             if image_label is None

{ngio-0.2.0b1 → ngio-0.2.0b3}/src/ngio/tables/backends/_anndata_utils.py

@@ -41,6 +41,9 @@ def custom_read_zarr(
     """
     group, _ = open_group_wrapper(store=store, mode="r")
 
+    if not isinstance(group.store, zarr.DirectoryStore):
+        elem_to_read = ["X", "obs", "var"]
+
     if elem_to_read is None:
         elem_to_read = [
             "X",

{ngio-0.2.0b1 → ngio-0.2.0b3}/tests/conftest.py

@@ -6,7 +6,7 @@ import pytest
 
 from ngio.utils import download_ome_zarr_dataset
 
-zenodo_download_dir = Path("tests/data/v04/zenodo_images/")
+zenodo_download_dir = Path(__file__).parent.parent / "data"
 os.makedirs(zenodo_download_dir, exist_ok=True)
 cardiomyocyte_tiny_source_path = download_ome_zarr_dataset(
     "CardiomyocyteTiny", download_dir=zenodo_download_dir

{ngio-0.2.0b1 → ngio-0.2.0b3}/tests/unit/images/test_omezarr_container.py

@@ -79,6 +79,11 @@ def test_create_omezarr_container(tmp_path: Path, array_mode: str):
     assert isinstance(omezarr.__repr__(), str)
     assert omezarr.levels == 3
     assert omezarr.levels_paths == ["0", "1", "2"]
+    assert omezarr.is_3d
+    assert not omezarr.is_time_series
+    assert not omezarr.is_multi_channels
+    assert not omezarr.is_2d_time_series
+    assert not omezarr.is_3d_time_series
 
     image = omezarr.get_image()
 
@@ -152,4 +157,4 @@ def test_remote_omezarr_container():
     # ]
 
     _ = omezarr.get_label("nuclei", path="0")
-    # _ = omezarr.get_table("well_ROI_table")
+    _ = omezarr.get_table("well_ROI_table", check_type="roi_table")

{ngio-0.2.0b1 → ngio-0.2.0b3}/tests/unit/test_ome_zarr_meta/test_unit_ngio_specs.py

@@ -438,7 +438,7 @@ def test_label_meta():
     assert label_meta.get_dataset(pixel_size=datasets[-1].pixel_size).path == "3"
 
 
-def test_fail_label_meta():
+def test_channels_label_meta():
     on_disk_axes = [
         Axis(on_disk_name="t", axis_type=AxisType.time, unit=TimeUnits.s),
         Axis(on_disk_name="c"),
@@ -465,9 +465,4 @@ def test_fail_label_meta():
             s * f for s, f in zip(on_disk_scale, [1, 1, 1, 2, 2], strict=True)
         ]
 
-    with pytest.raises(ValueError):
-        NgioLabelMeta(
-            version="0.4",
-            name="test",
-            datasets=datasets,
-        )
+    _ = NgioLabelMeta(version="0.4", name="test", datasets=datasets)

ngio-0.2.0b1/.github/workflows/build_docs.yml

@@ -1,39 +0,0 @@
-name: Build Docs
-
-on:
-  push:
-    branches:
-      - main
-    tags:
-      - "v*"
-
-jobs:
-  deploy:
-    name: Deploy Docs
-    runs-on: ubuntu-latest
-
-    steps:
-      - uses: actions/checkout@v4
-
-      - name: 🐍 Set up Python
-        uses: actions/setup-python@v5
-        with:
-          python-version: "3.13"
-          cache-dependency-path: "pyproject.toml"
-          cache: "pip"
-
-      - name: Install Dependencies
-        run: |
-          python -m pip install -U pip
-          python -m pip install .[dev]
-          python -m pip install .[docs]
-
-      - name: 📚 Build Docs
-        run: mkdocs build --clean
-
-      # If something goes wrong with --pre tests, we can open an issue in the repo
-      - name: Deploy Docs
-        uses: peaceiris/actions-gh-pages@v4
-        with:
-          personal_token: ${{ secrets.GITHUB_TOKEN }}
-          publish_dir: ./site