Merge pull request #78 from CBroz1/main

Updates for codebook deployment

Author: sidhulyalkar

.github/workflows/u24_workflow_before_release.yaml

@@ -1,4 +1,4 @@
-name: u24_workflow_before_release
+name: u24_workflow_before_release_0.0.1
 on:
   pull_request:
   push:
@@ -16,4 +16,3 @@ jobs:
       jhub_ver: 1.4.2
       py_ver: 3.9
       dist: debian
-      codebook_base_hash: 561b765

.github/workflows/u24_workflow_release_call.yaml

@@ -1,7 +1,7 @@
-name: u24_workflow_release_call
+name: u24_workflow_release_call_0.0.1
 on:
   workflow_run:
-    workflows: ["u24_workflow_tag_to_release"]
+    workflows: ["u24_workflow_tag_to_release_0.0.1"]
     types:
       - completed
 jobs:
@@ -15,7 +15,6 @@ jobs:
       jhub_ver: 1.4.2
       py_ver: 3.9
       dist: debian
-      codebook_base_hash: 561b765
     secrets:
       REGISTRY_USERNAME: ${{secrets.DOCKER_USERNAME}}
       REGISTRY_PASSWORD: ${{secrets.DOCKER_PASSWORD}}

.github/workflows/u24_workflow_tag_to_release.yaml

@@ -1,4 +1,4 @@
-name: u24_workflow_tag_to_release
+name: u24_workflow_tag_to_release_0.0.1
 on:
   push:
     tags:
@@ -13,4 +13,3 @@ jobs:
       jhub_ver: 1.4.2
       py_ver: 3.9
       dist: debian
-      codebook_base_hash: 561b765

CHANGELOG.md

@@ -3,6 +3,11 @@
 Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and
 [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) convention.
 
+## [0.2.2] - 2022-09-18
++ Update - config ephys roots in notebooks for codebook deployment
++ Update - requirements.txt to add element electrode localization
++ Update - add lab.User insert to ingest.py for users with empty element-lab schemas
+
 ## [0.2.1] - 2022-07-22
 + Add - Mention CodeBook data directory in notebooks
 + Add - Mention of config items in notebook 09
@@ -55,4 +60,4 @@ specific forks for tests.
 
 [0.2.1]: https://github.com/datajoint/workflow-array-ephys/compare/0.2.1...0.2.0
 [0.2.0]: https://github.com/datajoint/workflow-array-ephys/compare/0.2.0...0.1.0
-[0.1.0]: https://github.com/datajoint/workflow-array-ephys/releases/tag/0.1.0
+[0.1.0]: https://github.com/datajoint/workflow-array-ephys/releases/tag/0.1.0

notebooks/01-configure.ipynb

@@ -11,30 +11,19 @@
     "\n",
     "## Setup - Working Directory\n",
     "\n",
-    "To run the array ephys workflow, we need to properly set up the DataJoint configuration. The configuration will be saved in a file called `dj_local_conf.json` on each machine and this notebook walks you through the process.\n",
+    "To run the array ephys workflow, we need to properly set up the DataJoint configuration. The configuration can be saved in a local directory as `dj_local_conf.json` or at your root directory as a hidden file. This notebook walks you through the setup process.\n",
     "\n",
-    "**The configuration only needs to be set up once**, if you have gone through the configuration before, directly go to [02-workflow-structure](02-workflow-structure-optional.ipynb).\n",
-    "\n",
-    "As a convention, we set the configuration up in the root directory of the workflow package and always starts importing datajoint and pipeline modules from there."
+    "**The configuration only needs to be set up once**, if you have gone through the configuration before, directly go to [02-workflow-structure](02-workflow-structure-optional.ipynb)."
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 1,
    "id": "dc2dc935",
    "metadata": {},
    "outputs": [],
    "source": [
-    "import os"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# change to the upper level folder\n",
+    "import os\n",
     "if os.path.basename(os.getcwd()) == \"notebooks\": os.chdir(\"..\")\n",
     "import datajoint as dj"
    ]
@@ -119,7 +108,7 @@
     "The root path typically **do not** contain information of subjects or sessions, all data from subjects/sessions should be subdirectories in the root path.\n",
     "\n",
     "- In the example dataset downloaded with [these instructions](00-data-download-optional.ipynb), `/tmp/test_data` will be the root. \n",
-    "- For CodeBook users, the root is `/home/inbox/`\n",
+    "- For CodeBook users, the root is `/home/inbox/0.1.0a4/`\n",
     "\n",
     "```\n",
     "- subject6\n",
@@ -139,7 +128,14 @@
     "# If there is only one root path.\n",
     "dj.config[\"custom\"][\"ephys_root_data_dir\"] = \"/tmp/test_data\"\n",
     "# If there are multiple possible root paths:\n",
-    "dj.config[\"custom\"][\"ephys_root_data_dir\"] = [\"/tmp/test_data\", \"/home/inbox/\"]"
+    "dj.config[\"custom\"][\"ephys_root_data_dir\"] = [\n",
+    "    \"/tmp/test_data/workflow_ephys_data1/\",\n",
+    "    \"/tmp/test_data/workflow_ephys_data2/\",\n",
+    "    \"/tmp/test_data/workflow_localization/\", \n",
+    "    \"/home/inbox/0.1.0a4/workflow_ephys_data1/\",\n",
+    "    \"/home/inbox/0.1.0a4/workflow_ephys_data2/\",\n",
+    "    \"/home/inbox/0.1.0a4/workflow_localization/\"\n",
+    "]"
    ]
   },
   {
@@ -188,46 +184,22 @@
    "source": [
     "## Save configuration\n",
     "\n",
-    "With the proper configurations, we could save this as a file, either as a local json file, or a global file."
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "dcc8b17b",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "dj.config.save_local()"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "9b95596f",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "ls"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "d76904b4",
-   "metadata": {},
-   "source": [
-    "Local configuration file is saved as `dj_local_conf.json` in the root directory of this package `workflow-array-ephys`. Next time if you change your directory to `workflow-array-ephys` before importing datajoint and the pipeline packages, the configurations will get properly loaded.\n",
+    "With the proper configurations, we could save this as a file, either as a local json file, or a global file.\n",
     "\n",
-    "If saved globally, there will be a hidden configuration file saved in your root directory. The configuration will be loaded no matter where the directory is."
+    "Local configuration file is saved as `dj_local_conf.json` in current directory, which is great for project-specific settings.\n",
+    "\n",
+    "For first-time and CodeBook users, we recommend saving globally. This will create a hidden configuration file saved in your root directory, loaded whenever there is no local version to override it."
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
+   "id": "dcc8b17b",
    "metadata": {},
    "outputs": [],
    "source": [
-    "# dj.config.save_global()"
+    "# dj.config.save_local()\n",
+    "dj.config.save_global()"
    ]
   },
   {
@@ -250,7 +222,7 @@
    "formats": "ipynb,py_scripts//py"
   },
   "kernelspec": {
-   "display_name": "Python 3.9.12 ('ele')",
+   "display_name": "Python 3.9.13 ('ele')",
    "language": "python",
    "name": "python3"
   },
@@ -264,11 +236,11 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.12"
+   "version": "3.9.13"
   },
   "vscode": {
    "interpreter": {
-    "hash": "61456c693db5d9aa6731701ec9a9b08ab88a172bee0780139a3679beb166da16"
+    "hash": "d00c4ad21a7027bf1726d6ae3a9a6ef39c8838928eca5a3d5f51f3eb68720410"
    }
   }
  },