📝 Prettify documentation (#178)

laminlabs · Sep 2, 2022 · e423eab · e423eab
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diff --git a/docs/tutorials/1-rds-setup.ipynb b/docs/tutorials/1-rds-setup.ipynb
@@ -56,28 +56,26 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Two users within an organization are collaborating on this project across several notebooks.\n",
+    "Two users within an organization are collaborating on several projects:\n",
     "\n",
-    "- test-user1: project lead, performs wetlab experiments\n",
-    "- test-user2: data scientist, performs computational analysis"
+    "- `test-user1`: Project lead, performs wetlab experiments.\n",
+    "- `test-user2`: Data scientist, performs computational analysis."
    ]
   },
   {
-   "cell_type": "code",
-   "execution_count": null,
+   "cell_type": "markdown",
    "metadata": {},
-   "outputs": [],
    "source": [
-    "!lndb login test-user1"
+    "The first user logs in to register the projects."
    ]
   },
   {
-   "cell_type": "markdown",
+   "cell_type": "code",
+   "execution_count": null,
    "metadata": {},
+   "outputs": [],
    "source": [
-    "Register a few projects.\n",
-    "\n",
-    "We use [Schmidt22](https://www.science.org/doi/10.1126/science.abj4008) as the project in this R&D team simulation."
+    "!lndb login test-user1"
    ]
   },
   {
@@ -86,10 +84,10 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "_ = ln.db.insert.project(\n",
+    "ln.db.insert.project(\n",
     "    proj_id=\"P001\",\n",
     "    name=\"Optimizing gRNA transfection in primary human T cells\",\n",
-    ")"
+    ");"
    ]
   },
   {
@@ -98,10 +96,10 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "_ = ln.db.insert.project(\n",
+    "ln.db.insert.project(\n",
     "    proj_id=\"P002\",\n",
     "    name=\"T cell enrichment from human PBMCs\",\n",
-    ")"
+    ");"
    ]
   },
   {
@@ -110,13 +108,20 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "_ = ln.db.insert.project(\n",
+    "ln.db.insert.project(\n",
     "    proj_id=\"P003\",\n",
     "    name=(\n",
     "        \"CRISPR activation screens to decode stimulation responses in\"\n",
     "        \" primary human T cells\"\n",
     "    ),\n",
-    ")"
+    ");"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "The 3rd project here is based on [Schmidt _et al._, Science (2022)](https://www.science.org/doi/10.1126/science.abj4008)."
    ]
   }
  ],

diff --git a/docs/tutorials/get-started.ipynb b/docs/tutorials/get-started.ipynb
@@ -39,7 +39,7 @@
    "source": [
     "As a first-time user, sign up your email so that LaminDB can link you to data & analyses.\n",
     "\n",
-    "On the command line, run `lndb signup <email>`. For example: `lndb signup tuser1@foo.com`.[^github]\n",
+    "On the command line, run `lndb signup <email>`.[^github]\n",
     "\n",
     "[^github]: Consider using your GitHub-associated email and handle=username if you have one!"
    ]
@@ -67,7 +67,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "!lndb login test-user1  # test user 1 has handle test-user1"
+    "!lndb login test-user1"
    ]
   },
   {
@@ -85,7 +85,9 @@
    "source": [
     "For this first tutorial, we init a local instance with storage in `mydata/` and a local SQlite database for managing it.\n",
     "\n",
-    "You can also directly pass `s3://my-bucket` to `--storage` or a Postgres URL to `--db`."
+    "You can also directly pass `s3://my-bucket` to `--storage` or a Postgres URL to `--db`.\n",
+    "\n",
+    "We mount 3 default modules for biological entities (`bionty`), a generic wetlab (`wetlab`), and a generic bioinformatics pipline (`bfx`) for this instance."
    ]
   },
   {
@@ -95,7 +97,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "!lndb init --storage mydata --schema bionty,wetlab,bfx  # default bio entity and wetlab schema modules"
+    "!lndb init --storage mydata --schema bionty,wetlab,bfx"
    ]
   },
   {
@@ -104,7 +106,8 @@
    "metadata": {},
    "source": [
     "In this local setup, all instance data is in `mydata/` and all metadata in the SQLite file `mydata/mydata.lndb`.\n",
-    "Settings persist in `~/.lndb/*.env` and can be accessed via [`db.settings`](https://lamin.ai/docs/lndb-setup/lndb_setup.settings)."
+    "\n",
+    "Settings persist in `~/.lndb/instance-mydata.env` (and `~/.lndb/user-....env`) and can be accessed via [`lamindb.settings`](https://lamin.ai/docs/lndb-setup/lndb_setup.settings)."
    ]
   },
   {
@@ -266,7 +269,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.13"
+   "version": "3.9.12"
   },
   "nbproject": {
    "dependency": {

diff --git a/docs/tutorials/introspect.ipynb b/docs/tutorials/introspect.ipynb
@@ -35,7 +35,13 @@
    "id": "964d7a0b",
    "metadata": {},
    "source": [
-    "We currently offer a simple way of introspecting the overall schema:"
+    "You can draw the overall schema that is active in your DB instance using {func}`~lamindb.schema.draw`.\n",
+    "\n",
+    "It is the union of the default and customized schema modules that you mounted to your instance. Here, for example,\n",
+    "\n",
+    "- schema-core: https://lamin.ai/docs/lnschema-core/api\n",
+    "- schema-bionty: https://lamin.ai/docs/lnschema-bionty/api\n",
+    "- schema-wetlab: https://lamin.ai/docs/lnschema-wetlab/api"
    ]
   },
   {
@@ -93,7 +99,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3.9.13 ('py39')",
+   "display_name": "Python 3.9.12 ('base1')",
    "language": "python",
    "name": "python3"
   },
@@ -107,7 +113,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.13"
+   "version": "3.9.12"
   },
   "nbproject": {
    "id": "7j8LCaTr0H1c",
@@ -118,7 +124,7 @@
   },
   "vscode": {
    "interpreter": {
-    "hash": "ae1fefc8646a06dd2e75004cd934adda7c5727b046986a772e3b44b0ffba9754"
+    "hash": "2775e555cdc2d728c54aa22130c79afb1fa4da64f22f2fc6dcc2aa346c4e0672"
    }
   }
  },

diff --git a/lamindb/__init__.py b/lamindb/__init__.py
@@ -11,11 +11,11 @@
 
    db
    schema
+   settings
    datasets
    nb
    dev
 
-To retrieve settings, use `lamindb.settings <https://lamin.ai/docs/lndb-setup/lndb_setup.settings>`__.
 """
 from . import _check_versions
 
@@ -27,3 +27,8 @@
 from . import dev  # noqa
 from . import schema  # noqa
 from ._nb import nb  # noqa
+
+settings.__doc__ = """Settings.
+
+This re-exports `lndb_setup.settings <https://lamin.ai/docs/lndb-setup/lndb_setup.settings>`__.
+"""