Merge branch 'kabi' of CBroz1/workflow-miniscope

kabilar · Apr 30, 2022 · de6438b · de6438b
2 parents f2672f8 + 97d4d53
commit de6438b
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diff --git a/notebooks/00-data-download-optional.ipynb b/notebooks/00-data-download-optional.ipynb
@@ -103,7 +103,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "client.download('workflow-miniscope-test-set', target_directory='/tmp/example_data', revision='v1')"
+    "client.download('workflow-miniscope-test-set', \n",
+    "                target_directory='/tmp/example_data', revision='v1')"
    ]
   },
   {
@@ -142,12 +143,12 @@
  ],
  "metadata": {
   "jupytext": {
-   "formats": "ipynb,scripts//py",
-   "main_language": "python"
+   "formats": "ipynb,scripts//py"
   },
   "kernelspec": {
-   "display_name": "Python 3.7.9 64-bit ('workflow-calcium-imaging': conda)",
-   "name": "python379jvsc74a57bd01a512f474e195e32ad84236879d3bb44800a92b431919ef0b10d543f5012a23c"
+   "display_name": "venv-nwb",
+   "language": "python",
+   "name": "venv-nwb"
   },
   "language_info": {
    "codemirror_mode": {
@@ -159,7 +160,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.9"
+   "version": "3.8.11"
   }
  },
  "nbformat": 4,

diff --git a/notebooks/01-configure.ipynb b/notebooks/01-configure.ipynb
@@ -197,7 +197,8 @@
  ],
  "metadata": {
   "jupytext": {
-   "formats": "ipynb,scripts//py"
+   "formats": "ipynb,scripts//py",
+   "main_language": "python"
   },
   "kernelspec": {
    "display_name": "Python 3.7.9 64-bit ('workflow-calcium-imaging': conda)",

diff --git a/notebooks/02-workflow-structure-optional.ipynb b/notebooks/02-workflow-structure-optional.ipynb
@@ -47,11 +47,14 @@
    ]
   },
   {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "+ Each module contains a schema object that enables interaction with the schema in the database."
-   ]
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "693929a9",
+   "metadata": {
+    "title": "Each module contains a schema object that enables interaction with the schema in the database."
+   },
+   "outputs": [],
+   "source": []
   },
   {
    "cell_type": "code",
@@ -65,11 +68,14 @@
    ]
   },
   {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "+ The table classes in the module corresponds to a table in the schema in the database."
-   ]
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "d0ee126a",
+   "metadata": {
+    "title": "The table classes in the module corresponds to a table in the schema in the database."
+   },
+   "outputs": [],
+   "source": []
   },
   {
    "cell_type": "code",
@@ -90,9 +96,9 @@
     "title": "The first time importing the modules, empty schemas and tables will be created in the database."
    },
    "source": [
-    "+ By importing the modules for the first time, the schemas and tables will be created inside the database.\n",
+    "# + By importing the modules for the first time, the schemas and tables will be created inside the database.\n",
     "\n",
-    "+ Once created, importing modules will not create schemas and tables again, but the existing schemas/tables can be accessed and manipulated by the modules."
+    "# + Once created, importing modules will not create schemas and tables again, but the existing schemas/tables can be accessed and manipulated by the modules."
    ]
   },
   {
@@ -104,7 +110,7 @@
    "source": [
     "## DataJoint tools to explore schemas and tables\n",
     "\n",
-    "+ `dj.list_schemas()`: list all schemas a user has access to in the current database"
+    "# + `dj.list_schemas()`: list all schemas a user has access to in the current database"
    ]
   },
   {
@@ -119,11 +125,14 @@
    ]
   },
   {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "+ `dj.Diagram()`: plot tables and dependencies in a schema. "
-   ]
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "687dbcb3",
+   "metadata": {
+    "title": "`dj.Diagram()`: plot tables and dependencies in a schema."
+   },
+   "outputs": [],
+   "source": []
   },
   {
    "cell_type": "code",
@@ -205,7 +214,7 @@
     "title": "`heading`:"
    },
    "source": [
-    "+ `describe()`: show table definition with foreign key references."
+    "# + `describe()`: show table definition with foreign key references."
    ]
   },
   {
@@ -218,11 +227,14 @@
    ]
   },
   {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "+ `heading`: show attribute definitions regardless of foreign key references"
-   ]
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "08837864",
+   "metadata": {
+    "title": "`heading`: show attribute definitions regardless of foreign key references"
+   },
+   "outputs": [],
+   "source": []
   },
   {
    "cell_type": "code",
@@ -243,7 +255,7 @@
    "source": [
     "# DataJoint Elements installed in `workflow-miniscope`\n",
     "\n",
-    "+ [`lab`](https://github.com/datajoint/element-lab): lab management related information, such as Lab, User, Project, Protocol, Source."
+    "# + [`lab`](https://github.com/datajoint/element-lab): lab management related information, such as Lab, User, Project, Protocol, Source."
    ]
   },
   {
@@ -255,19 +267,15 @@
     "dj.Diagram(lab)"
    ]
   },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "+ [`subject`](https://github.com/datajoint/element-animal): general animal information, such as User, Genetic background."
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "title": "[`subject`](https://github.com/datajoint/element-animal): general animal information, such as User, Genetic background."
+   },
    "outputs": [],
    "source": [
+    "\n",
     "dj.Diagram(subject)"
    ]
   },
@@ -282,19 +290,15 @@
     "subject.Subject.describe();"
    ]
   },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "+ [`session`](https://github.com/datajoint/element-session): General information of experimental sessions."
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "title": "[`session`](https://github.com/datajoint/element-session): General information of experimental sessions."
+   },
    "outputs": [],
    "source": [
+    "\n",
     "dj.Diagram(session)"
    ]
   },
@@ -310,11 +314,14 @@
    ]
   },
   {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "+ [`miniscope`](https://github.com/datajoint/element-miniscope): miniscope raw recording and processed data"
-   ]
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "dc175fed",
+   "metadata": {
+    "title": "[`miniscope`](https://github.com/datajoint/element-miniscope): miniscope raw recording and processed data"
+   },
+   "outputs": [],
+   "source": []
   },
   {
    "cell_type": "code",
@@ -342,7 +349,8 @@
  "metadata": {
   "jupytext": {
    "encoding": "# -*- coding: utf-8 -*-",
-   "formats": "ipynb,scripts//py"
+   "formats": "ipynb,scripts//py",
+   "main_language": "python"
   },
   "kernelspec": {
    "display_name": "Python 3.7.9 64-bit ('workflow-calcium-imaging': conda)",

diff --git a/notebooks/06-drop-optional.ipynb b/notebooks/06-drop-optional.ipynb
@@ -40,7 +40,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "lines_to_next_cell": 0
+   },
    "outputs": [],
    "source": [
     "# miniscope.schema.drop()\n",
@@ -52,18 +54,22 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "lines_to_next_cell": 2
+   },
    "outputs": [],
    "source": []
   }
  ],
  "metadata": {
   "jupytext": {
-   "formats": "ipynb,scripts//py"
+   "formats": "ipynb,scripts//py",
+   "main_language": "python"
   },
   "kernelspec": {
-   "display_name": "Python 3.7.9 64-bit ('workflow-calcium-imaging': conda)",
-   "name": "python379jvsc74a57bd01a512f474e195e32ad84236879d3bb44800a92b431919ef0b10d543f5012a23c"
+   "display_name": "venv-nwb",
+   "language": "python",
+   "name": "venv-nwb"
   },
   "language_info": {
    "codemirror_mode": {
@@ -75,9 +81,9 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.9"
+   "version": "3.8.11"
   }
  },
  "nbformat": 4,
- "nbformat_minor": 2
+ "nbformat_minor": 4
 }