created default package with less dependencies (#13)

.gitignore

@@ -0,0 +1,4 @@
+.venv
+tests/__pycache__/
+src/microjson/__pycache__/
+poetry.lock

pyproject.toml

@@ -27,18 +27,36 @@ where = ["src"]
 
 [tool.poetry.dependencies]
 python = ">=3.9.15,<3.12"
-bfio = {version = "2.3.6", extras = ["all"]}
-scyjava = "^1.9.1"
-typer = "^0.7.0"
-scipy = ">=1.8,<1.9.2"
-filepattern = "^2.0.1"
-fastapi = "^0.103.1"
-llvmlite = "^0.40.1"
-vaex = "^4.17.0"
 pydantic = "^2.3.0"
 scikit-image = "0.20.0"
 geojson-pydantic = "^1.0.2"
 
+
+[tool.poetry.dependencies.bfio]     
+version = "2.3.6"
+extras = ["all"]   
+optional = true
+
+[tool.poetry.dependencies.scipy]     
+version = ">=1.8,<1.9.2"
+optional = true
+
+[tool.poetry.dependencies.filepattern] 
+version = "^2.0.1"
+optional = true
+
+[tool.poetry.dependencies.vaex]      
+version = "^4.17.0"
+optional = true
+
+[tool.poetry.extras]
+all = [
+    "bfio", 
+    "scipy", 
+    "filepattern", 
+    "vaex"
+]
+
 [tool.poetry.dev-dependencies]
 pytest = "^6.2.4"
 nox = "^2022.1.7"

src/microjson/__init__.py

@@ -1,6 +1,4 @@
 from .model import MicroJSON, GeoJSON
-from .utils import gather_example_files
-from .utils import OmeMicrojsonModel
-from .utils import MicrojsonBinaryModel
+
 
 __version__ = "0.1.11"

src/microjson/fileutils.py

@@ -0,0 +1,15 @@
+import os
+
+def gather_example_files(directory) -> list:
+    """
+    Gather all the .json files in a directory and its subdirectories.
+    """
+    files = []
+    # Walk through the directory
+    for dirpath, _, filenames in os.walk(directory):
+        # Filter to just the .json files
+        example_files = [
+            os.path.join(dirpath, f) for f in filenames if f.endswith(".json")
+        ]
+        files.extend(example_files)
+    return files

src/microjson/utils.py

@@ -4,31 +4,43 @@
 import json
 import logging
 import numpy as np
-import vaex
+
 import re
 import shutil
 from concurrent.futures import ThreadPoolExecutor
 from concurrent.futures import as_completed
 from itertools import product
-from scipy import ndimage
+
 import skimage as sk
 from skimage import measure
 from skimage import morphology
-from bfio import BioReader
+
 from sys import platform
 from pathlib import Path
 from typing import Any
 from typing import Union
 import microjson.model as mj
 from multiprocessing import cpu_count
-import filepattern as fp
+
 import warnings
 from microjson import MicroJSON
 from pydantic import ValidationError
 from microjson.model import Feature, Properties
 from typing import Union
 import pydantic
 
+#define conditional imports
+try:
+    from bfio import BioReader
+    import filepattern as fp
+    from scipy import ndimage
+    import vaex
+except ImportError as e:
+    print("""Packages bfio, filepattern, scipy, vaex not installed
+          please install using pip install microjson[all]""")
+    raise e
+
+
 warnings.filterwarnings("ignore")
 
 logger = logging.getLogger(__name__)
@@ -41,21 +53,6 @@
     NUM_THREADS = max(cpu_count() // 2, 2)
 
 
-def gather_example_files(directory) -> list:
-    """
-    Gather all the .json files in a directory and its subdirectories.
-    """
-    files = []
-    # Walk through the directory
-    for dirpath, _, filenames in os.walk(directory):
-        # Filter to just the .json files
-        example_files = [
-            os.path.join(dirpath, f) for f in filenames if f.endswith(".json")
-        ]
-        files.extend(example_files)
-    return files
-
-
 class OmeMicrojsonModel:
     """Generate JSON of segmentations polygon using microjson python package.
 

tests/test_geojson_schema.py

@@ -3,7 +3,7 @@
 import pytest
 from jsonschema import validate
 
-from microjson.utils import gather_example_files
+from microjson.fileutils import gather_example_files
 
 # Load the generated GeoJSON schema
 with open("geojson_schema.json") as f:

tests/test_microjson.py

@@ -2,7 +2,7 @@
 import pytest
 from pydantic import ValidationError
 from microjson.model import MicroJSON, GeoJSON
-from microjson.utils import gather_example_files
+from microjson.fileutils import gather_example_files
 
 
 # Define the directories containing the example JSON files

tests/test_original_schema.py

@@ -2,7 +2,7 @@
 import jsonschema
 import pytest
 from jsonschema import validate
-from microjson.utils import gather_example_files
+from microjson.fileutils import gather_example_files
 
 # Load the original GeoJSON schema
 with open("external/GeoJSON.json") as f:

tests/test_provenance.py

@@ -2,7 +2,7 @@
 import pytest
 from pydantic import ValidationError
 from microjson.model import MicroJSON, GeoJSON
-from microjson.utils import gather_example_files
+from microjson.fileutils import gather_example_files
 
 
 # Define the directories containing the example JSON files

tests/test_tilejson.py

@@ -2,7 +2,7 @@
 import pytest
 from pydantic import ValidationError
 from microjson.tile import TileJSON
-from microjson.utils import gather_example_files
+from microjson.fileutils import gather_example_files
 
 
 # Define the directories containing the example JSON files

tests/test_utils.py

@@ -8,15 +8,35 @@
 from typing import Union
 import numpy as np
 import pytest
-from microjson.utils import OmeMicrojsonModel, MicrojsonBinaryModel
 import skimage as sk
+HAS_BFIO = False
+try:
+    import bfio
+    HAS_BFIO = True
+except ImportError:
+    pass
+
+# Marker registration
+def pytest_configure(config):  # Function to register marker
+    config.addinivalue_line("markers", "requires_extra(name): mark test as needing an extra")
+
 
 def clean_directories() -> None:
     """Remove all temporary directories."""
     for d in Path(".").cwd().iterdir():
         if d.is_dir() and d.name.startswith("tmp"):
             shutil.rmtree(d)
 
+@pytest.fixture(autouse=True)
+def skip_if_extra_not_installed(request):
+    marker = request.node.get_closest_marker("requires_extra")
+    if marker:
+        extra_name = marker.args[0]
+        try:
+            __import__(extra_name)
+        except ImportError:
+            pytest.skip(f"Skipping test because '{extra_name}' extra is not installed.")
+
 
 @pytest.fixture()
 def inp_dir() -> Union[str, Path]:
@@ -58,8 +78,9 @@ def get_params(request: pytest.FixtureRequest) -> pytest.FixtureRequest:
     """To get the parameter of the ome to json."""
     return request.param
 
-
+@pytest.mark.skipif(not HAS_BFIO, reason="Skipping test because 'bfio' extra is not installed.")
 def test_OmeMicrojsonModel(synthetic_images: Path, output_directory: Path, get_params) -> None:
+    from microjson.utils import OmeMicrojsonModel
     """Testing of converting binary images to microjson of objects polygon coordinates."""
 
     inp_dir = synthetic_images
@@ -77,7 +98,9 @@ def test_OmeMicrojsonModel(synthetic_images: Path, output_directory: Path, get_p
 
     clean_directories()
 
+@pytest.mark.skipif(not HAS_BFIO, reason="Skipping test because 'bfio' extra is not installed.")
 def test_MicrojsonBinaryModel(synthetic_images: Path, output_directory: Path, get_params:list[str]) -> None:
+    from microjson.utils import OmeMicrojsonModel, MicrojsonBinaryModel
     """Testing of converting microjson of polygon coordinates of objects back to binary images."""
 
     inp_dir = synthetic_images
@@ -103,7 +126,9 @@ def test_MicrojsonBinaryModel(synthetic_images: Path, output_directory: Path, ge
 def XOR(x, y):
     return x ^ y
 
+@pytest.mark.skipif(not HAS_BFIO, reason="Skipping test because 'bfio' extra is not installed.")
 def test_roundtrip(synthetic_images: Path, output_directory: Path) -> None:
+    from microjson.utils import OmeMicrojsonModel, MicrojsonBinaryModel
     """Testing of reconstructed images from polygon coordinates with original images."""
 
     inp_dir = synthetic_images