mobiedantic 0.1.0__tar.gz → 0.2.0__tar.gz

{mobiedantic-0.1.0 → mobiedantic-0.2.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: mobiedantic
-Version: 0.1.0
+Version: 0.2.0
 Project-URL: Documentation, https://github.com/fmi-faim/mobiedantic#readme
 Project-URL: Issues, https://github.com/fmi-faim/mobiedantic/issues
 Project-URL: Source, https://github.com/fmi-faim/mobiedantic

{mobiedantic-0.1.0 → mobiedantic-0.2.0}/pixi.lock

@@ -583,7 +583,6 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/osx-64/zstandard-0.23.0-py312h331e495_0.conda
       - conda: https://conda.anaconda.org/conda-forge/osx-64/zstd-1.5.6-h915ae27_0.conda
       - pypi: https://files.pythonhosted.org/packages/a0/92/f788d908543faad645c794cc080b221f8c90139b96611ab72911918e29c8/hatch_conda-0.5.2-py3-none-any.whl
-      - pypi: https://files.pythonhosted.org/packages/7a/30/24a74c0ca887d3a75821814d292e1001571d574c4c2b217a858b09ce8b88/uv-0.2.26-py3-none-macosx_10_12_x86_64.whl
       - pypi: .
       win-64:
       - conda: https://conda.anaconda.org/conda-forge/noarch/annotated-types-0.7.0-pyhd8ed1ab_0.conda
@@ -812,7 +811,7 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/win-64/zstandard-0.23.0-py312h7606c53_0.conda
       - conda: https://conda.anaconda.org/conda-forge/win-64/zstd-1.5.6-h0ea2cb4_0.conda
       - pypi: https://files.pythonhosted.org/packages/a0/92/f788d908543faad645c794cc080b221f8c90139b96611ab72911918e29c8/hatch_conda-0.5.2-py3-none-any.whl
-      - pypi: https://files.pythonhosted.org/packages/c3/39/ef4a4737cb78500fc0e3290efea12f484f0d9c666976dd3888f11d4be87c/uv-0.2.25-py3-none-macosx_10_12_x86_64.whl
+      - pypi: https://files.pythonhosted.org/packages/a9/ea/75cd14c055777f21d036466bcf4d7afb49b73f7592d13747d4df1800a22a/uv-0.2.25-py3-none-win_amd64.whl
       - pypi: .
   mobie:
     channels:
@@ -8264,7 +8263,17 @@ packages:
   timestamp: 1716276077462
 - kind: pypi
   name: mobiedantic
-  version: 0.1.dev15+g2b75ef1.d20240719
+  version: 0.1.1.dev1+g7443af1
+  path: .
+  sha256: ee4f165f9d96378272ddb8bf328f59cfd946894ea2ecc99f5db005acf8be3fee
+  requires_dist:
+  - pydantic
+  - hatch-conda<0.6,>=0.5.2 ; extra == 'hatch'
+  requires_python: '>=3.8'
+  editable: true
+- kind: pypi
+  name: mobiedantic
+  version: 0.1.1.dev1+g86b62e8.d20240722
   path: .
   sha256: ee4f165f9d96378272ddb8bf328f59cfd946894ea2ecc99f5db005acf8be3fee
   requires_dist:
@@ -12164,14 +12173,8 @@ packages:
 - kind: pypi
   name: uv
   version: 0.2.25
-  url: https://files.pythonhosted.org/packages/c3/39/ef4a4737cb78500fc0e3290efea12f484f0d9c666976dd3888f11d4be87c/uv-0.2.25-py3-none-macosx_10_12_x86_64.whl
-  sha256: cc1187c0487529c9e0af750a855b540e21f5675c685c0fa400658eb9dc164739
-  requires_python: '>=3.8'
-- kind: pypi
-  name: uv
-  version: 0.2.26
-  url: https://files.pythonhosted.org/packages/7a/30/24a74c0ca887d3a75821814d292e1001571d574c4c2b217a858b09ce8b88/uv-0.2.26-py3-none-macosx_10_12_x86_64.whl
-  sha256: fd3e850921f0d51d093aaeb76d190829eefdc0345439b8f6c06103a0463cc451
+  url: https://files.pythonhosted.org/packages/a9/ea/75cd14c055777f21d036466bcf4d7afb49b73f7592d13747d4df1800a22a/uv-0.2.25-py3-none-win_amd64.whl
+  sha256: 42bb27b5f502087aff68b54a1b8e4b72e93fd6552120eb8cc14a36d204c49ce7
   requires_python: '>=3.8'
 - kind: conda
   name: uv

{mobiedantic-0.1.0 → mobiedantic-0.2.0}/src/mobiedantic/__init__.py

@@ -54,6 +54,26 @@ class Dataset:
         data_format: str = 'ome.zarr',
     ) -> None:
         sources = {}
+        self._update_sources(
+            sources=sources,
+            path_dict=path_dict,
+            channel_index=channel_index,
+            data_format=data_format,
+        )
+        views_dict = {'default': {'uiSelectionGroup': 'view', 'isExclusive': True}}
+        self.model = DatasetSchema(
+            is2D=is2d,
+            sources=sources,
+            views=views_dict,
+        )
+
+    def _update_sources(
+        self,
+        sources: dict[str, Source],
+        path_dict: dict[str, Path],
+        channel_index: int = 0,
+        data_format: str = 'ome.zarr',
+    ):
         for name in path_dict:
             try:
                 source_path = {
@@ -77,11 +97,19 @@ class Dataset:
                 }
             }
             sources[name] = Source(**data)
-        views_dict = {'default': {'uiSelectionGroup': 'view', 'isExclusive': True}}
-        self.model = DatasetSchema(
-            is2D=is2d,
-            sources=sources,
-            views=views_dict,
+
+    def add_sources(
+        self,
+        path_dict: dict[str, Path],
+        *,
+        channel_index: int = 0,
+        data_format: str = 'ome.zarr',
+    ):
+        self._update_sources(
+            sources=self.model.sources,
+            path_dict=path_dict,
+            channel_index=channel_index,
+            data_format=data_format,
         )
 
     def add_merged_grid(
@@ -151,6 +179,15 @@ class Project:
             self.model.defaultDataset = name
         return Dataset(path=dataset_folder)
 
+    def load(self):
+        project_path = self.path / 'project.json'
+        if not project_path.exists():
+            message = f'Project file not found: {project_path}'
+            raise ValueError(message)
+        with open(project_path) as project_file:
+            data = json.loads(project_file.read())
+            self.model = ProjectSchema(**data)
+
     def save(self, *, create_directory: bool = True):
         if self.model is None:
             message = 'Project not initialized.'

mobiedantic-0.2.0/tests/test_api.py

@@ -0,0 +1,145 @@
+from pathlib import Path
+
+import pytest
+
+from mobiedantic import Dataset, Project
+
+
+def test_project(tmp_path):
+    project = Project(tmp_path)
+    project.initialize_model(description='Test project')
+    project.new_dataset('Dataset_1')
+    project.save()
+    assert (tmp_path / 'project.json').exists()
+    assert len(project.model.datasets) == 1
+
+
+def test_dataset(tmp_path):
+    project = Project(tmp_path)
+    project.initialize_model(description='Testing datasets')
+    dataset1: Dataset = project.new_dataset('Dataset_1')
+    sources1 = {
+        'A01': Path('../../non-existent.zarr/A/01/0'),
+        'A02': Path('../../non-existent.zarr/A/02/0'),
+    }
+    dataset1.initialize_with_paths(
+        path_dict=sources1,
+        is2d=True,
+        channel_index=0,
+    )
+    dataset1.add_merged_grid(
+        name='Merged_grid_view',
+        sources=list(sources1),
+    )
+    assert len(dataset1.model.views['default'].sourceDisplays) == 1
+    assert (
+        dataset1.model.views['default'].sourceDisplays[0].imageDisplay.name.root
+        == 'Merged_grid_view'
+    )
+    assert len(dataset1.model.views['default'].sourceTransforms) == 1
+    assert (
+        dataset1.model.views['default']
+        .sourceTransforms[0]
+        .mergedGrid.mergedGridSourceName.root
+        == 'Merged_grid_view'
+    )
+    assert (
+        len(dataset1.model.views['default'].sourceTransforms[0].mergedGrid.sources) == 2
+    )
+    sources2 = {
+        'C01': Path('../../non-existent.zarr/C/01/0'),
+        'C02': Path('../../non-existent.zarr/C/02/0'),
+    }
+    dataset1.add_sources(
+        path_dict=sources2,
+        channel_index=0,
+        data_format='ome.zarr',
+    )
+    dataset1.add_merged_grid(
+        name='Merged_grid_view_2',
+        sources=list(sources2),
+    )
+    assert len(dataset1.model.sources) == 4
+    assert len(dataset1.model.views['default'].sourceDisplays) == 2
+    assert (
+        dataset1.model.views['default'].sourceDisplays[1].imageDisplay.name.root
+        == 'Merged_grid_view_2'
+    )
+    assert len(dataset1.model.views['default'].sourceTransforms) == 2
+    assert (
+        dataset1.model.views['default']
+        .sourceTransforms[1]
+        .mergedGrid.mergedGridSourceName.root
+        == 'Merged_grid_view_2'
+    )
+    assert (
+        len(dataset1.model.views['default'].sourceTransforms[1].mergedGrid.sources) == 2
+    )
+    project.new_dataset('Dataset_2')
+    assert len(project.model.datasets) == 2
+
+
+def test_save_and_load(tmp_path):
+    project = Project(tmp_path)
+    project.initialize_model(description='Testing saving and loading')
+    dataset_name = 'dataset1'
+    dataset = project.new_dataset(dataset_name)
+    sources = {
+        'A01': '/path/to/source',
+    }
+    dataset.initialize_with_paths(
+        path_dict=sources,
+        is2d=True,
+    )
+    dataset.save()
+    project.save()
+
+    project_loaded = Project(tmp_path)
+    project_loaded.load()
+
+    assert project.model == project_loaded.model
+
+    dataset_loaded = Dataset(tmp_path / dataset_name)
+    dataset_loaded.load()
+
+    assert dataset.model == dataset_loaded.model
+
+
+def test_dataset_errors(tmp_path):
+    filename = 'dataset.json'
+    with open(tmp_path / filename, 'w'):
+        pass
+    with pytest.raises(ValueError, match="'path' needs to point to a directory"):
+        Dataset(path=(tmp_path / filename))
+    dataset_dir = tmp_path / 'dataset'
+    dataset = Dataset(path=dataset_dir)
+    with pytest.raises(ValueError, match='Dataset not initialized.'):
+        dataset.save()
+    sources = {
+        'A01': '/path/to/source',
+    }
+    dataset.initialize_with_paths(
+        path_dict=sources,
+        is2d=True,
+    )
+    with pytest.raises(
+        ValueError, match="Dataset folder doesn't exist yet and may not be created."
+    ):
+        dataset.save(create_directory=False)
+    with pytest.raises(ValueError, match='Dataset file not found'):
+        dataset.load()
+
+
+def test_project_errors(tmp_path):
+    project = Project(tmp_path / 'non-existent_subfolder')
+    with pytest.raises(ValueError, match='Project not initialized'):
+        project.save()
+    with pytest.raises(ValueError, match='Project file not found'):
+        project.load()
+    with pytest.raises(ValueError, match='Project not initialized'):
+        project.new_dataset('dataset1')
+    project.initialize_model(description='Test raising errors.')
+    with pytest.raises(
+        ValueError, match="Project folder doesn't exist yet and may not be created."
+    ):
+        project.save(create_directory=False)

mobiedantic-0.1.0/tests/test_api.py

@@ -1,57 +0,0 @@
-from pathlib import Path
-
-from mobiedantic import Project
-
-
-def test_project(tmp_path):
-    project = Project(tmp_path)
-    project.initialize_model(description='Test project')
-    project.new_dataset('Dataset_1')
-    project.save()
-    assert (tmp_path / 'project.json').exists()
-    assert len(project.model.datasets) == 1
-
-
-def test_dataset(tmp_path):
-    project = Project(tmp_path)
-    project.initialize_model(description='Testing datasets')
-    dataset1 = project.new_dataset('Dataset_1')
-    sources1 = {
-        'A01': Path('../../non-existent.zarr/A/01/0'),
-        'A02': Path('../../non-existent.zarr/A/02/0'),
-    }
-    dataset1.initialize_with_paths(
-        path_dict=sources1,
-        is2d=True,
-        channel_index=0,
-    )
-    dataset1.add_merged_grid(
-        name='Merged_grid_view',
-        sources=list(sources1),
-    )
-    assert len(dataset1.model.views['default'].sourceDisplays) == 1
-    assert (
-        dataset1.model.views['default'].sourceDisplays[0].imageDisplay.name.root
-        == 'Merged_grid_view'
-    )
-    assert len(dataset1.model.views['default'].sourceTransforms) == 1
-    assert (
-        dataset1.model.views['default']
-        .sourceTransforms[0]
-        .mergedGrid.mergedGridSourceName.root
-        == 'Merged_grid_view'
-    )
-    assert (
-        len(dataset1.model.views['default'].sourceTransforms[0].mergedGrid.sources) == 2
-    )
-
-    dataset2 = project.new_dataset('Dataset_2')
-    sources2 = {
-        'C01': Path('../../non-existent.zarr/C/01/0'),
-        'C02': Path('../../non-existent.zarr/C/02/0'),
-    }
-    dataset2.initialize_with_paths(
-        path_dict=sources2,
-        is2d=False,
-        channel_index=0,
-    )