lamindb 0.71.0__tar.gz → 0.71.1__tar.gz

{lamindb-0.71.0 → lamindb-0.71.1}/.gitignore

@@ -1,4 +1,5 @@
 # LaminDB
+docsbuild/
 docs/lamin.md
 docs/guide/data-validation.ipynb
 docs/guide/knowledge.ipynb
@@ -58,6 +59,7 @@ test-search2
 test-search3
 test-search4
 test-search5
+
 # General
 .DS_Store
 

{lamindb-0.71.0 → lamindb-0.71.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: lamindb
-Version: 0.71.0
+Version: 0.71.1
 Summary: A data framework for biology.
 Author-email: Lamin Labs <open-source@lamin.ai>
 Requires-Python: >=3.8
@@ -9,10 +9,10 @@ Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
-Requires-Dist: lnschema_core==0.66.0
-Requires-Dist: lamindb_setup==0.71.0
+Requires-Dist: lnschema_core==0.66.3
+Requires-Dist: lamindb_setup==0.71.3
 Requires-Dist: lamin_utils==0.13.2
-Requires-Dist: lamin_cli==0.13.0
+Requires-Dist: lamin_cli==0.13.1
 Requires-Dist: rapidfuzz
 Requires-Dist: pyarrow
 Requires-Dist: typing_extensions!=4.6.0
@@ -37,7 +37,7 @@ Requires-Dist: faker-biology ; extra == "dev"
 Requires-Dist: django-schema-graph ; extra == "erdiagram"
 Requires-Dist: readfcs>=1.1.8 ; extra == "fcs"
 Requires-Dist: lamindb_setup[gcp] ; extra == "gcp"
-Requires-Dist: nbproject==0.10.0 ; extra == "jupyter"
+Requires-Dist: nbproject==0.10.2 ; extra == "jupyter"
 Requires-Dist: nbstripout==0.6.1 ; extra == "jupyter"
 Requires-Dist: nbconvert ; extra == "jupyter"
 Requires-Dist: zarr>=2.16.0 ; extra == "zarr"

{lamindb-0.71.0 → lamindb-0.71.1}/docs/changelog.md

@@ -2,9 +2,9 @@
 
 :::{note}
 
-LaminDB implements "migration-based versioning".
+If using LaminHub, please use the latest version of lamindb.
 
-When upgrading your LaminDB installation to a new `minor` version in `major.minor.patch`, you also migrate your database by calling `lamin migrate deploy`.
+LaminDB implements "migration-based versioning". When upgrading your LaminDB installation to a new `minor` version in `major.minor.patch`, you also migrate your database by calling `lamin migrate deploy`.
 
 :::
 
@@ -14,6 +14,18 @@ When upgrading your LaminDB installation to a new `minor` version in `major.mino
 
 ## 0.71
 
+### 0.71.1 {small}`2024-05-07`
+
+- 🚸  Upload source code of scripts upon `ln.finish()` and no longer upon `ln.track()` [PR](https://github.com/laminlabs/lamindb/pull/1624) [@falexwolf](https://github.com/falexwolf)
+- 🎨 Make `features.add_feature_set` public [PR](https://github.com/laminlabs/lamindb/pull/1626) [@sunnyosun](https://github.com/sunnyosun)
+- 🎨 Use the same `uid` for the same feature set in transfer [PR](https://github.com/laminlabs/lamindb/pull/1621) [@sunnyosun](https://github.com/sunnyosun)
+- 🎨 Upon upload switch to virtual key [PR](https://github.com/laminlabs/lamindb/pull/1622) [@falexwolf](https://github.com/falexwolf)
+- ⚡️ Zarr and cache improvements [PR](https://github.com/laminlabs/lamindb/pull/1620) [@Koncopd](https://github.com/Koncopd)
+- ♻️ Extend valid suffixes to composite suffixes [PR](https://github.com/laminlabs/lamindb/pull/1619) [@falexwolf](https://github.com/falexwolf)
+- 🔥 Remove little-used `artifact.view_tree()` [PR](https://github.com/laminlabs/lamindb/pull/1627) [@falexwolf](https://github.com/falexwolf)
+
+### 0.71.0 {small}`2024-05-01`
+
 - ✨ Manage multiple storage locations with integrity [PR](https://github.com/laminlabs/lamindb/pull/1611) [@falexwolf](https://github.com/falexwolf)
 - 🚚 Add an `instance_uid` field to `Storage` | [374](https://github.com/laminlabs/lnschema-core/pull/374) [falexwolf](https://github.com/falexwolf)
 - 🚸 Proper progress bars for upload and download [PR](https://github.com/laminlabs/lamindb/pull/1610) [@Koncopd](https://github.com/Koncopd)

{lamindb-0.71.0 → lamindb-0.71.1}/docs/faq/keep-artifacts-local.ipynb

@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# Connect with `keep_artifacts_local=True`"
+    "# Keep artifacts local in a cloud instance"
    ]
   },
   {
@@ -19,7 +19,7 @@
    "execution_count": null,
    "metadata": {
     "tags": [
-     "hide-output"
+     "hide-cell"
     ]
    },
    "outputs": [],
@@ -34,7 +34,11 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import lamindb as ln"
+    "import lamindb as ln\n",
+    "\n",
+    "ln.settings.transform.stem_uid = \"l9lFf83aPwRc\"\n",
+    "ln.settings.transform.version = \"1\"\n",
+    "ln.track()"
    ]
   },
   {
@@ -88,6 +92,39 @@
     "ln.Storage.df()"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Update storage description"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "You can add a description to the storage by using the description parameter:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "storage_record = ln.Storage.filter(root=ln.settings.storage_local).one()\n",
+    "storage_record.description = \"Files stored locally in site X on server Y for reason ABC\"\n",
+    "storage_record.save()\n",
+    "ln.Storage.df()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Use local storage"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -105,9 +142,10 @@
    },
    "outputs": [],
    "source": [
-    "filepath = ln.core.datasets.file_fcs()\n",
-    "artifact = ln.Artifact(filepath, description=\"My fcs file\").save()\n",
-    "artifact.path"
+    "original_filepath = ln.core.datasets.file_fcs()\n",
+    "artifact = ln.Artifact(original_filepath, description=\"My fcs file\").save()\n",
+    "local_path = artifact.path\n",
+    "local_path"
    ]
   },
   {
@@ -140,6 +178,7 @@
    },
    "outputs": [],
    "source": [
+    "assert local_path.exists()\n",
     "assert artifact.path.as_posix().startswith(ln.setup.settings.instance.storage_local.root.as_posix())"
    ]
   },
@@ -213,9 +252,18 @@
    },
    "outputs": [],
    "source": [
+    "assert artifact.path.exists()\n",
+    "assert not local_path.exists()\n",
     "assert artifact.path.as_posix().startswith(ln.setup.settings.instance.storage.root.as_posix())"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Direct upload"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -255,7 +303,160 @@
    },
    "outputs": [],
    "source": [
-    "ln.Artifact.df()"
+    "ln.Artifact.df(include=\"storage__root\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "tags": [
+     "hide-cell"
+    ]
+   },
+   "outputs": [],
+   "source": [
+    "assert artifact2.path.exists()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Pre-existing artifacts"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Assume we already have a file in our registered local storage location:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "tags": [
+     "hide-input"
+    ]
+   },
+   "outputs": [],
+   "source": [
+    "file_in_local_storage = ln.core.datasets.file_bam()\n",
+    "file_in_local_storage.rename(\"./my_storage_local/output.bam\")\n",
+    "ln.UPath(\"my_storage_local/\").view_tree()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "If we create an artifact from it, it remains where it is during saving:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "tags": [
+     "hide-output"
+    ]
+   },
+   "outputs": [],
+   "source": [
+    "my_existing_file = ln.Artifact(\"./my_storage_local/output.bam\", description=\"my existing file\").save()\n",
+    "ln.UPath(\"my_storage_local/\").view_tree()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "The storage path of the artifact is constructed using `key` because  `key_is_virtual=False`:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "tags": [
+     "hide-output"
+    ]
+   },
+   "outputs": [],
+   "source": [
+    "my_existing_file"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "However, if we decide to upload the artifact, we'll use the `uid` for constructing the storage path and switch `key_is_virtual=True`:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "tags": [
+     "hide-output"
+    ]
+   },
+   "outputs": [],
+   "source": [
+    "my_existing_file.save(upload=True)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Here is the remote path of the artifact:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "tags": [
+     "hide-output"
+    ]
+   },
+   "outputs": [],
+   "source": [
+    "my_existing_file.path"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "And here are the contents of the storage locations:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "tags": [
+     "hide-output"
+    ]
+   },
+   "outputs": [],
+   "source": [
+    "# the path on S3\n",
+    "ln.setup.settings.storage.root.view_tree()\n",
+    "# the local path\n",
+    "ln.setup.settings.instance.storage_local.root.view_tree()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Delete the test instance"
    ]
   },
   {
@@ -272,7 +473,8 @@
    "outputs": [],
    "source": [
     "artifact.delete(permanent=True)\n",
-    "artifact2.delete(permanent=True)"
+    "artifact2.delete(permanent=True)\n",
+    "my_existing_file.delete(permanent=True)"
    ]
   },
   {

{lamindb-0.71.0 → lamindb-0.71.1}/docs/introduction.ipynb

@@ -66,17 +66,11 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "tags": [
-     "hide-output"
-    ]
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
-    "import lamindb as ln\n",
-    "\n",
-    "# artifacts are stored in a local directory `./lamin-intro`\n",
-    "ln.setup.init(schema=\"bionty\", storage=\"./lamin-intro\")"
+    "# store artifacts in a local directory `./lamin-intro`\n",
+    "!lamin init --storage ./lamin-intro --schema bionty"
    ]
   },
   {
@@ -85,7 +79,7 @@
    "source": [
     "### Track\n",
     "\n",
-    "Run {meth}`~lamindb.track` to track the input and output data of your code."
+    "Run {meth}`~lamindb.track` to track the input and output data of your code ({class}`~lamindb.Transform`)."
    ]
   },
   {
@@ -98,7 +92,9 @@
    },
    "outputs": [],
    "source": [
-    "# tag your notebook or script with auto-generated identifiers\n",
+    "import lamindb as ln\n",
+    "\n",
+    "# auto-generated identifiers for your notebook or script\n",
     "ln.settings.transform.stem_uid = \"FPnfDtJz8qbE\"\n",
     "ln.settings.transform.version = \"1\"\n",
     "\n",