💚 Attempt fix (#136)

Co-authored-by: Sunny Sun <[email protected]>
laminlabs · Aug 2, 2024 · 73997f3 · 73997f3
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commit 73997f3
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Showing 25 changed files with 101 additions and 95 deletions.
diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -54,10 +54,7 @@ jobs:
       - name: Cache postgres use
         if: steps.cache-postgres.outputs.cache-hit == 'true'
         run: docker image load --input ~/postgres.tar
-
-      - name: install Python deps
-        run: pip install -U laminci
-
+      - run: pip install "laminci@git+https://x-access-token:${{ secrets.LAMIN_BUILD_DOCS }}@github.com/laminlabs/laminci"
       - name: install postgres graphviz
         run: sudo apt-get -y install graphviz
       - uses: aws-actions/configure-aws-credentials@v1

diff --git a/.github/workflows/doc-changes.yml b/.github/workflows/doc-changes.yml
@@ -0,0 +1,23 @@
+name: doc-changes
+
+on:
+  pull_request_target:
+    branches:
+      - main
+    types:
+      - closed
+
+jobs:
+  latest-changes:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+      - run: pip install "laminci[doc-changes]@git+https://x-access-token:${{ secrets.LAMIN_BUILD_DOCS }}@github.com/laminlabs/laminci"
+      - run: laminci doc-changes
+        env:
+          repo_token: ${{ secrets.GITHUB_TOKEN }}
+          docs_token: ${{ secrets.LAMIN_BUILD_DOCS }}
+          changelog_file: lamin-docs/docs/changelog/soon/usecases.md
diff --git a/.github/workflows/latest-changes.jinja2 b/.github/workflows/latest-changes.jinja2
diff --git a/.github/workflows/latest-changes.yml b/.github/workflows/latest-changes.yml
diff --git a/docs/analysis-flow.ipynb b/docs/analysis-flow.ipynb
@@ -34,7 +34,7 @@
    },
    "outputs": [],
    "source": [
-    "# pip install 'lamindb[jupyter,bionty]'\n",
+    "# !pip install 'lamindb[jupyter,bionty]'\n",
     "!lamin init --storage ./analysis-usecase --schema bionty"
    ]
   },
@@ -363,7 +363,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.1.-1"
+   "version": "3.10.13"
   },
   "nbproject": {
    "id": "eNef4Arw8nNM",

diff --git a/docs/analysis-registries.ipynb b/docs/analysis-registries.ipynb
@@ -661,7 +661,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.1.-1"
+   "version": "3.10.13"
   },
   "nbproject": {
    "id": "hsPU1OENv0LS",

diff --git a/docs/bulkrna.ipynb b/docs/bulkrna.ipynb
@@ -38,7 +38,7 @@
    },
    "outputs": [],
    "source": [
-    "# pip install 'lamindb[jupyter,bionty]'\n",
+    "# !pip install 'lamindb[jupyter,bionty]'\n",
     "!lamin init --storage test-bulkrna --schema bionty"
    ]
   },
@@ -489,7 +489,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.1.-1"
+   "version": "3.10.13"
   },
   "nbproject": {
    "id": "s5V0dNMVwL9i",

diff --git a/docs/cell_marker.ipynb b/docs/cell_marker.ipynb
@@ -355,13 +355,27 @@
     "For any given entity, we can choose from a number of versions:"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "tags": [
+     "hide-output"
+    ]
+   },
+   "outputs": [],
+   "source": [
+    "bt.CellMarker.list_source()"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
-    "bt.Source.filter(entity=\"CellMarker\").df()"
+    "# only lists the sources that are currently used\n",
+    "bt.CellMarker.list_source(currently_used=True).df()"
    ]
   },
   {
@@ -378,7 +392,7 @@
    "outputs": [],
    "source": [
     "source = bt.Source.filter(\n",
-    "    source=\"cellmarker\", version=\"2.0\", organism=\"human\"\n",
+    "    name=\"cellmarker\", version=\"2.0\", organism=\"human\"\n",
     ").one()\n",
     "public = bt.CellMarker.public(source=source)\n",
     "public"

diff --git a/docs/celltypist.ipynb b/docs/celltypist.ipynb
@@ -354,7 +354,7 @@
     "    record = public_records_dict[row[\"ontology_id\"]]\n",
     "    try:\n",
     "        record.add_synonym(row[\"ct_name\"])\n",
-    "    except SystemExit:\n",
+    "    except ValueError:\n",
     "        pass"
    ]
   },

diff --git a/docs/enrichr.ipynb b/docs/enrichr.ipynb
@@ -37,7 +37,7 @@
    },
    "outputs": [],
    "source": [
-    "# pip install 'lamindb[jupyter,bionty]'\n",
+    "# !pip install 'lamindb[jupyter,bionty]'\n",
     "!lamin init --storage ./use-cases-registries --schema bionty"
    ]
   },
@@ -330,7 +330,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.1.-1"
+   "version": "3.10.13"
   },
   "nbproject": {
    "id": "6oxEIEduvo6w",

diff --git a/docs/facs.ipynb b/docs/facs.ipynb
@@ -606,7 +606,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.1.-1"
+   "version": "3.10.13"
   },
   "nbproject": {
    "id": "OWuTtS4SApon",

diff --git a/docs/facs2.ipynb b/docs/facs2.ipynb
@@ -369,7 +369,7 @@
    "outputs": [],
    "source": [
     "collection_v2 = ln.Collection(\n",
-    "    [artifact, collection_v1.artifacts[0]], is_new_version_of=collection_v1, version=\"2\"\n",
+    "    [artifact, collection_v1.ordered_artifacts[0]], is_new_version_of=collection_v1, version=\"2\"\n",
     ")\n",
     "collection_v2.describe()"
    ]

diff --git a/docs/gene.ipynb b/docs/gene.ipynb
@@ -447,13 +447,27 @@
     "For any given entity, we can choose from a number of versions:"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "tags": [
+     "hide-output"
+    ]
+   },
+   "outputs": [],
+   "source": [
+    "bt.Gene.list_source().df()"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
-    "bt.Source.filter(entity=\"Gene\").df()"
+    "# only lists the sources that are currently used\n",
+    "bt.Gene.list_source(currently_used=True).df()"
    ]
   },
   {
@@ -470,7 +484,7 @@
    "outputs": [],
    "source": [
     "source = bt.Source.filter(\n",
-    "    source=\"ensembl\", version=\"release-110\", organism=\"human\"\n",
+    "    name=\"ensembl\", version=\"release-112\", organism=\"human\"\n",
     ").one()\n",
     "public = bt.Gene.public(source=source)\n",
     "public"
@@ -513,7 +527,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.1.-1"
+   "version": "3.10.13"
   }
  },
  "nbformat": 4,

diff --git a/docs/multimodal.ipynb b/docs/multimodal.ipynb
@@ -224,7 +224,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.1.-1"
+   "version": "3.10.13"
   },
   "nbproject": {
    "id": "yMWSFirS6qv2",

diff --git a/docs/project-flow.ipynb b/docs/project-flow.ipynb
@@ -50,30 +50,6 @@
     "```"
    ]
   },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "## Setup"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "Init a test instance:"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "Install the `lamindb` Python package:\n",
-    "```shell\n",
-    "pip install 'lamindb[jupyter,bionty,aws]'\n",
-    "```"
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -84,6 +60,7 @@
    },
    "outputs": [],
    "source": [
+    "# !pip install 'lamindb[jupyter,bionty,aws]'\n",
     "!lamin init --storage ./mydata"
    ]
   },
@@ -423,7 +400,7 @@
    "outputs": [],
    "source": [
     "transform = ln.Transform.search(\"Project flow\").first()\n",
-    "transform.parents.df()"
+    "transform.predecessors.df()"
    ]
   },
   {
@@ -432,7 +409,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "transform.view_parents()"
+    "transform.view_lineage()"
    ]
   },
   {
@@ -663,7 +640,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.1.-1"
+   "version": "3.10.13"
   },
   "nbproject": {
    "id": "1LCd8kco9lZU",

diff --git a/docs/rdf-sparql.ipynb b/docs/rdf-sparql.ipynb
@@ -35,7 +35,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# pip install 'lamindb[aws,bionty]'\n",
+    "# !pip install 'lamindb[aws,bionty]'\n",
     "!lamin load laminlabs/cellxgene"
    ]
   },

diff --git a/docs/scrna.ipynb b/docs/scrna.ipynb
@@ -57,7 +57,7 @@
    },
    "outputs": [],
    "source": [
-    "# pip install 'lamindb[jupyter,aws,bionty]'\n",
+    "# !pip install 'lamindb[jupyter,aws,bionty]' \n",
     "!lamin init --storage ./test-scrna --schema bionty"
    ]
   },
@@ -74,7 +74,6 @@
     "import lamindb as ln\n",
     "import bionty as bt\n",
     "\n",
-    "ln.settings.verbosity = \"hint\"\n",
     "ln.settings.transform.stem_uid = \"Nv48yAceNSh8\"\n",
     "ln.settings.transform.version = \"1\"\n",
     "ln.track()"
@@ -274,7 +273,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "collection.artifacts"
+    "collection.ordered_artifacts"
    ]
   },
   {
@@ -310,7 +309,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.1.-1"
+   "version": "3.10.13"
   },
   "nbproject": {
    "id": "Nv48yAceNSh8",

diff --git a/docs/scrna2.ipynb b/docs/scrna2.ipynb
@@ -34,7 +34,6 @@
     "import lamindb as ln\n",
     "import bionty as bt\n",
     "\n",
-    "ln.settings.verbosity = \"hint\"\n",
     "ln.settings.transform.stem_uid = \"ManDYgmftZ8C\"\n",
     "ln.settings.transform.version = \"1\"\n",
     "ln.track()"
@@ -185,7 +184,7 @@
     "    # search the public ontology and use the ontology id of the top match\n",
     "    ontology_id = bionty.search(name).iloc[0].ontology_id\n",
     "    # create a record by loading the top match from bionty\n",
-    "    record = bt.CellType.from_public(ontology_id=ontology_id)\n",
+    "    record = bt.CellType.from_source(ontology_id=ontology_id)\n",
     "    name_mapper[name] = record.name  # map the original name to standardized name\n",
     "    record.save()\n",
     "    record.add_synonym(name)"
@@ -291,7 +290,7 @@
    "outputs": [],
    "source": [
     "collection_v2 = ln.Collection(\n",
-    "    [artifact, collection_v1.artifacts[0]],\n",
+    "    [artifact, collection_v1.ordered_artifacts.first()],\n",
     "    is_new_version_of=collection_v1,\n",
     ")\n",
     "collection_v2.save()"
@@ -346,7 +345,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.1.-1"
+   "version": "3.10.13"
   },
   "nbproject": {
    "id": "ManDYgmftZ8C",