lamindb_setup 0.72.2__tar.gz → 0.73.1__tar.gz

{lamindb_setup-0.72.2 → lamindb_setup-0.73.1}/.github/workflows/build.yml

@@ -12,14 +12,13 @@ jobs:
   # tests only on production hub
   hub-prod:
     runs-on: ubuntu-latest
-    timeout-minutes: 10
+    timeout-minutes: 6
     steps:
       - uses: actions/checkout@v3
       - uses: actions/setup-python@v4
         with:
-          python-version: "3.9" # consciously run one job on Python 3.9
+          python-version: "3.9" # run one job on 3.9
           cache: "pip"
-          cache-dependency-path: ".github/workflows/build.yml"
       - uses: aws-actions/configure-aws-credentials@v2
         with:
           aws-access-key-id: ${{ secrets.AWS_ACCESS_KEY_ID }}
@@ -39,10 +38,12 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        lamin_env:
-          - "staging"
-          - "prod"
-    timeout-minutes: 15
+        include:
+          - lamin_env: "prod"
+            python-version: "3.11"
+          - lamin_env: "staging"
+            python-version: "3.10" # test on 3.10
+    timeout-minutes: 6
     steps:
       - uses: aws-actions/configure-aws-credentials@v2
         with:
@@ -52,7 +53,7 @@ jobs:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v4
         with:
-          python-version: "3.11" # consciously run one job on Python 3.11
+          python-version: ${{ matrix.python-version }}
           cache: "pip"
           cache-dependency-path: ".github/workflows/build.yml"
       - name: checkout laminhub
@@ -92,12 +93,12 @@ jobs:
   # test user access to storage
   storage:
     runs-on: ubuntu-latest
-    timeout-minutes: 10
+    timeout-minutes: 6
     steps:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v4
         with:
-          python-version: "3.10" # consciously run one job on Python 3.10
+          python-version: "3.11" # we need to run everything for coverage on 3.11
           cache: "pip"
           cache-dependency-path: ".github/workflows/build.yml"
       - run: pip install -U laminci
@@ -116,7 +117,7 @@ jobs:
   # test low-level hub functionality
   hub-local:
     runs-on: ubuntu-latest
-    timeout-minutes: 10
+    timeout-minutes: 6
     steps:
       - uses: aws-actions/configure-aws-credentials@v2
         with:
@@ -139,7 +140,7 @@ jobs:
         working-directory: laminhub/rest-hub/supabase
       - uses: actions/setup-python@v4
         with:
-          python-version: "3.11" # consciously run one job on Python 3.11
+          python-version: "3.11" # we need to run everything for coverage on 3.11
           cache: "pip"
           cache-dependency-path: ".github/workflows/build.yml"
       - run: pip install -U laminci
@@ -165,9 +166,8 @@ jobs:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v4
         with:
-          python-version: "3.10"
+          python-version: "3.11"
           cache: "pip"
-          cache-dependency-path: ".github/workflows/build.yml"
       - run: |
           pip install coverage[toml]
           pip install --no-deps .

{lamindb_setup-0.72.2 → lamindb_setup-0.73.1}/.pre-commit-config.yaml

@@ -49,4 +49,4 @@ repos:
     hooks:
       - id: pydocstyle
         args: # google style + __init__, see http://www.pydocstyle.org/en/stable/error_codes.html
-          - --ignore=D100,D101,D102,D103,D104,D106,D107,D203,D204,D213,D215,D400,D401,D403,D404,D406,D407,D408,D409,D412,D413
+          - --ignore=D100,D101,D102,D103,D104,D106,D107,D203,D204,D213,D215,D400,D401,D403,D404,D406,D407,D408,D409,D412,D413,D417

{lamindb_setup-0.72.2 → lamindb_setup-0.73.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: lamindb_setup
-Version: 0.72.2
+Version: 0.73.1
 Summary: Setup & configure LaminDB.
 Author-email: Lamin Labs <laminlabs@gmail.com>
 Description-Content-Type: text/markdown
@@ -11,7 +11,7 @@ Requires-Dist: dj_database_url>=1.3.0,<3.0.0
 Requires-Dist: pydantic[dotenv]<2.0.0
 Requires-Dist: appdirs<2.0.0
 Requires-Dist: requests
-Requires-Dist: universal_pathlib==0.1.4
+Requires-Dist: universal_pathlib==0.2.2
 Requires-Dist: botocore<2.0.0
 Requires-Dist: supabase==2.2.1
 Requires-Dist: urllib3<2 ; extra == "aws"

{lamindb_setup-0.72.2 → lamindb_setup-0.73.1}/docs/changelog.md

@@ -3,6 +3,14 @@
 <!-- prettier-ignore -->
 Name | PR | Developer | Date | Version
 --- | --- | --- | --- | ---
+✨ Add .ome.zarr as composite suffix | [775](https://github.com/laminlabs/lamindb-setup/pull/775) | [sunnyosun](https://github.com/sunnyosun) | 2024-06-05 |
+🏗️ Update instance schema in the hub | [774](https://github.com/laminlabs/lamindb-setup/pull/774) | [fredericenard](https://github.com/fredericenard) | 2024-06-04 |
+⬆️ Migrate to upath 0.2.2 | [723](https://github.com/laminlabs/lamindb-setup/pull/723) | [Koncopd](https://github.com/Koncopd) | 2024-06-02 |
+🐛 Fix trailing slash in upload_from source | [773](https://github.com/laminlabs/lamindb-setup/pull/773) | [Koncopd](https://github.com/Koncopd) | 2024-05-23 | 0.73.0
+🚸 Make `upload_from()`, `download_to()`, and `view_tree()` more user friendly | [772](https://github.com/laminlabs/lamindb-setup/pull/772) | [falexwolf](https://github.com/falexwolf) | 2024-05-23 |
+✨ Resolve s3 bucket region even without access rights | [771](https://github.com/laminlabs/lamindb-setup/pull/771) | [Koncopd](https://github.com/Koncopd) | 2024-05-22 |
+💚 Coverage fix | [770](https://github.com/laminlabs/lamindb-setup/pull/770) | [falexwolf](https://github.com/falexwolf) | 2024-05-22 |
+👷 Fix coverage compute | [769](https://github.com/laminlabs/lamindb-setup/pull/769) | [falexwolf](https://github.com/falexwolf) | 2024-05-22 |
 🐛 Deal with migration errors when keep-artifacts-local is true | [767](https://github.com/laminlabs/lamindb-setup/pull/767) | [falexwolf](https://github.com/falexwolf) | 2024-05-20 | 0.72.2
 ♻️ Do not error if empty dict in `access_aws` | [764](https://github.com/laminlabs/lamindb-setup/pull/764) | [falexwolf](https://github.com/falexwolf) | 2024-05-19 | 0.72.1
 🐛 Keep training slash in aws cache keys | [766](https://github.com/laminlabs/lamindb-setup/pull/766) | [Koncopd](https://github.com/Koncopd) | 2024-05-19 |

{lamindb_setup-0.72.2 → lamindb_setup-0.73.1}/docs/hub-cloud/06-connect-hosted-instance.ipynb

@@ -86,10 +86,11 @@
    "outputs": [],
    "source": [
     "target_dir = root / \"test-dir-upload\"\n",
-    "target_dir.upload_from(test_dir, recursive=True)\n",
+    "target_dir.upload_from(test_dir, create_folder=True) # default\n",
     "\n",
     "assert target_dir.is_dir()\n",
     "assert (target_dir / \"test-dir-upload\").exists()\n",
+    "assert (target_dir / \"test-dir-upload/file1\").exists()\n",
     "\n",
     "target_dir.rmdir()\n",
     "assert not target_dir.exists()"
@@ -101,9 +102,10 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "target_dir.upload_from(test_dir, dir_inplace=True)\n",
+    "target_dir.upload_from(test_dir, create_folder=False)\n",
     "\n",
     "assert target_dir.is_dir()\n",
+    "assert (target_dir / \"file1\").exists()\n",
     "assert not (target_dir / \"test-dir-upload\").exists()"
    ]
   },

{lamindb_setup-0.72.2 → lamindb_setup-0.73.1}/docs/hub-prod/test-cloud-sync.ipynb

@@ -237,7 +237,8 @@
    "source": [
     "time.sleep(1)\n",
     "cloud_file = dir_sync / \"file1\"\n",
-    "cloud_file.touch()  # update cloud timestamp\n",
+    "# update cloud timestamp, exist_ok=False needed due to truncate=not exist_ok in upath\n",
+    "cloud_file.touch(exist_ok=False)  \n",
     "\n",
     "assert cloud_file.modified.timestamp() > local_file_new.stat().st_mtime"
    ]

{lamindb_setup-0.72.2 → lamindb_setup-0.73.1}/lamindb_setup/__init__.py

@@ -34,7 +34,7 @@ Modules & settings:
 
 """
 
-__version__ = "0.72.2"  # denote a release candidate for 0.1.0 with 0.1rc1
+__version__ = "0.73.1"  # denote a release candidate for 0.1.0 with 0.1rc1
 
 import sys
 from os import name as _os_name

{lamindb_setup-0.72.2 → lamindb_setup-0.73.1}/lamindb_setup/_init_instance.py

@@ -16,7 +16,7 @@ from ._silence_loggers import silence_loggers
 from .core import InstanceSettings
 from .core._settings import settings
 from .core._settings_storage import StorageSettings, init_storage
-from .core.upath import convert_pathlike
+from .core.upath import UPath
 
 if TYPE_CHECKING:
     from pydantic import PostgresDsn
@@ -56,6 +56,7 @@ def register_storage_in_instance(ssettings: StorageSettings):
         "region": ssettings.region,
         "instance_uid": instance_uid,
         "created_by_id": current_user_id(),
+        "run": None,
     }
     if ssettings._uid is not None:
         defaults["uid"] = ssettings._uid
@@ -350,7 +351,7 @@ def infer_instance_name(
         return str(db).split("/")[-1]
     if storage == "create-s3":
         raise ValueError("pass name to init if storage = 'create-s3'")
-    storage_path = convert_pathlike(storage)
+    storage_path = UPath(storage)
     if storage_path.name != "":
         name = storage_path.name
     else:

{lamindb_setup-0.72.2 → lamindb_setup-0.73.1}/lamindb_setup/_migrate.py

@@ -68,6 +68,8 @@ class migrate:
     @classmethod
     def deploy(cls) -> None:
         """Deploy a migration."""
+        from ._schema_metadata import update_schema_in_hub
+
         if _check_instance_setup():
             raise RuntimeError("Restart Python session to migrate or use CLI!")
         from lamindb_setup.core._hub_client import call_with_fallback_auth
@@ -104,6 +106,9 @@ class migrate:
         # this populates the hub
         if instance_is_on_hub:
             logger.important(f"updating lamindb version in hub: {lamindb.__version__}")
+            # TODO: integrate update of instance table within update_schema_in_hub & below
+            if settings.instance.dialect != "sqlite":
+                update_schema_in_hub()
             call_with_fallback_auth(
                 update_instance,
                 instance_id=settings.instance._id.hex,