Merge branch 'main' into ome-zarr-reading

.github/workflows/mypy.yaml

@@ -15,6 +15,5 @@ jobs:
         uses: actions/checkout@v2
       - name: mypy
         run: |
-          pip install .
-          pip install --upgrade mypy
+          pip install '.[dev]'
           mypy funlib/persistence

.github/workflows/tests.yaml

@@ -6,11 +6,27 @@ on:
 jobs:
   test:
     runs-on: ubuntu-latest
+
+    services:
+      postgres:
+        image: postgres
+        env:
+          POSTGRES_HOST_AUTH_METHOD: trust
+        ports:
+          - 5432:5432
+        options: >-
+          --health-cmd pg_isready
+          --health-interval 10s
+          --health-timeout 5s
+          --health-retries 5
+
     strategy:
       fail-fast: false
       matrix:
         python-version: ["3.9", "3.10"]
-        mongodb-version: ["5.0", "6.0"]
+
+    env:
+       PGUSER: postgres
 
     steps:
       - uses: actions/checkout@v2
@@ -20,11 +36,6 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
 
-      - name: Start MongoDB
-        uses: supercharge/mongodb-github-action@1.8.0
-        with:
-          mongodb-version: ${{ matrix.mongodb-version }}
-
       - name: Install dependencies
         run: pip install ".[dev]"
 

.gitignore

@@ -127,6 +127,6 @@ dmypy.json
 
 # Pyre type checker
 .pyre/
+.vscode/
 
-# VSCode project settings
-.vscode/
+*.sw[pmno]

funlib/persistence/__init__.py

@@ -1,4 +1,4 @@
 from .arrays import Array, open_ds, prepare_ds  # noqa
 
-__version__ = "0.1.0"
+__version__ = "0.2.0"
 __version_info__ = tuple(int(i) for i in __version__.split("."))

funlib/persistence/arrays/datasets.py

@@ -9,8 +9,8 @@
 import logging
 import os
 import shutil
-from typing import Optional
 from pathlib import Path
+from typing import Optional, Union
 
 logger = logging.getLogger(__name__)
 
@@ -214,7 +214,7 @@ def prepare_ds(
     write_roi: Roi = None,
     write_size: Coordinate = None,
     num_channels: Optional[int] = None,
-    compressor: str = "default",
+    compressor: Union[str, dict] = "default",
     delete: bool = False,
     force_exact_write_size: bool = False,
 ) -> Array:

funlib/persistence/graphs/__init__.py

@@ -1,2 +1,2 @@
-from .file_graph_provider import FileGraphProvider  # noqa
-from .mongodb_graph_provider import MongoDbGraphProvider  # noqa
+from .sqlite_graph_database import SQLiteGraphDataBase  # noqa
+from .pgsql_graph_database import PgSQLGraphDatabase  # noqa