ngio 0.4.5__tar.gz → 0.4.7__tar.gz

{ngio-0.4.5 → ngio-0.4.7}/.github/workflows/build_docs.yml

@@ -3,7 +3,7 @@ name: Build Docs
 on:
   push:
     branches:
-      - dev
+      - hotfix/*
       - main
     tags:
       - "v*"
@@ -18,7 +18,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
         with:
           fetch-depth: 0
       - name: 🐍 Set up Python
@@ -38,7 +38,7 @@ jobs:
         run: |
           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
@@ -47,7 +47,7 @@ jobs:
           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\///')

{ngio-0.4.5 → ngio-0.4.7}/.github/workflows/ci.yml

@@ -4,7 +4,7 @@ on:
   push:
     branches:
       - main
-      - dev
+      - hotfix/*
     tags:
       - "v*"
   pull_request:
@@ -24,7 +24,7 @@ jobs:
     # included in the sdist (unless explicitly excluded)
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
       - run: pipx run check-manifest
 
   test:
@@ -37,7 +37,7 @@ jobs:
         platform: [ubuntu-latest, macos-latest, windows-latest]
 
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
 
       - name: 🐍 Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v6
@@ -51,7 +51,7 @@ 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
@@ -98,7 +98,7 @@ jobs:
       contents: write
 
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
         with:
           fetch-depth: 0
 
@@ -118,4 +118,4 @@ jobs:
       - uses: softprops/action-gh-release@v2
         with:
           generate_release_notes: true
-          files: './dist/*'
+          files: "./dist/*"

{ngio-0.4.5 → ngio-0.4.7}/CHANGELOG.md

@@ -1,5 +1,11 @@
 # Changelog
 
+## [v0.4.6]
+
+### Bug Fixes
+- Fix channel selection from `wavelenght_id`
+- Fix table opening mode to stop wrtiting groups when opening in append mode.
+
 ## [v0.4.5]
 
 ### Bug Fixes

{ngio-0.4.5 → ngio-0.4.7}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ngio
-Version: 0.4.5
+Version: 0.4.7
 Summary: Next Generation file format IO
 Project-URL: homepage, https://github.com/BioVisionCenter/ngio
 Project-URL: repository, https://github.com/BioVisionCenter/ngio

{ngio-0.4.5 → ngio-0.4.7}/src/ngio/common/_masking_roi.py

@@ -168,7 +168,6 @@ def compute_masking_roi(
             z_length = None
         else:
             z_length = max_z - min_z
-
         roi = RoiPixels(
             name=str(label),
             x_length=max_x - min_x,
@@ -178,6 +177,7 @@ def compute_masking_roi(
             x=min_x,
             y=min_y,
             z=min_z,
+            t=min_t,
             label=label,
         )
 

{ngio-0.4.5 → ngio-0.4.7}/src/ngio/images/_image.py

@@ -875,7 +875,7 @@ def _parse_str_or_model(
             )
         elif channel_selection.mode == "wavelength_id":
             return image.get_channel_idx(
-                channel_label=str(channel_selection.identifier)
+                wavelength_id=str(channel_selection.identifier)
             )
         elif channel_selection.mode == "index":
             return int(channel_selection.identifier)

{ngio-0.4.5 → ngio-0.4.7}/src/ngio/images/_label.py

@@ -337,6 +337,6 @@ def derive_label(
 
 def build_masking_roi_table(label: Label) -> MaskingRoiTable:
     """Compute the masking ROI table for a label."""
-    array = label.get_as_dask(axes_order=["t", "z", "y", "x"])
+    array = label.get_as_dask()
     rois = compute_masking_roi(array, label.pixel_size)
     return MaskingRoiTable(rois, reference_label=label.meta.name)

{ngio-0.4.5 → ngio-0.4.7}/src/ngio/tables/_tables_container.py

@@ -359,7 +359,7 @@ ImplementedTables().add_implementation(ConditionTableV1)
 def open_tables_container(
     store: StoreOrGroup,
     cache: bool = False,
-    mode: AccessModeLiteral = "a",
+    mode: AccessModeLiteral = "r+",
     parallel_safe: bool = False,
 ) -> TablesContainer:
     """Open a table handler from a Zarr store."""
@@ -373,7 +373,7 @@ def open_table(
     store: StoreOrGroup,
     backend: TableBackend | None = None,
     cache: bool = False,
-    mode: AccessModeLiteral = "a",
+    mode: AccessModeLiteral = "r+",
     parallel_safe: bool = False,
 ) -> Table:
     """Open a table from a Zarr store."""
@@ -391,7 +391,7 @@ def open_table_as(
     table_cls: type[TableType],
     backend: TableBackend | None = None,
     cache: bool = False,
-    mode: AccessModeLiteral = "a",
+    mode: AccessModeLiteral = "r+",
     parallel_safe: bool = False,
 ) -> TableType:
     """Open a table from a Zarr store as a specific type."""

{ngio-0.4.5 → ngio-0.4.7}/tests/unit/tables/test_table_group.py

@@ -12,7 +12,7 @@ from ngio.utils import NgioValueError
 
 
 def test_table_container(tmp_path: Path):
-    table_group = open_tables_container(tmp_path / "test.zarr")
+    table_group = open_tables_container(tmp_path / "test.zarr", mode="a")
     assert isinstance(table_group, TablesContainer)
     assert table_group.list() == []