Update setup dependencies + tutorial setup + fix diagram

README.md

@@ -28,7 +28,9 @@ environment and notebooks to learn the pipeline.
 ## Getting Started
 
 + Please fork this repository.
+
 + Clone the repository to your computer.
+
 ```bash
      git clone https://github.com/<enter_github_username>/element-array-ephys.git
 ```
@@ -38,6 +40,7 @@ environment and notebooks to learn the pipeline.
      ```bash
      pip install -e .
      ```
+
 + [Interactive tutorial on GitHub
   Codespaces](https://github.com/datajoint/element-array-ephys#interactive-tutorial)
 

element_array_ephys/__init__.py

@@ -1,19 +1 @@
-import os
-import datajoint as dj
-
-if "custom" not in dj.config:
-    dj.config["custom"] = {}
-
-# overwrite dj.config['custom'] values with environment variables if available
-
-dj.config["custom"]["database.prefix"] = os.getenv(
-    "DATABASE_PREFIX", dj.config["custom"].get("database.prefix", "")
-)
-
-dj.config["custom"]["ephys_root_data_dir"] = os.getenv(
-    "EPHYS_ROOT_DATA_DIR", dj.config["custom"].get("ephys_root_data_dir", "")
-)
-
-db_prefix = dj.config["custom"].get("database.prefix", "")
-
 from . import ephys_acute as ephys

images/diagram_flowchart.drawio

@@ -1,6 +1,6 @@
-<mxfile host="app.diagrams.net" modified="2023-10-30T21:18:19.029Z" agent="Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:109.0) Gecko/20100101 Firefox/119.0" etag="5NXZuFNRWHajsz3vhZ10" version="22.0.8" type="github">
+<mxfile host="app.diagrams.net" modified="2023-11-28T18:35:40.905Z" agent="Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:109.0) Gecko/20100101 Firefox/119.0" etag="XDqTBROUJpnBGVnVPucu" version="22.1.4" type="github">
   <diagram id="4ApZs3ESX_rJ877tGElo" name="docs">
-    <mxGraphModel dx="1221" dy="714" grid="1" gridSize="10" guides="1" tooltips="1" connect="1" arrows="1" fold="1" page="1" pageScale="1" pageWidth="1600" pageHeight="1240" math="0" shadow="0">
+    <mxGraphModel dx="1442" dy="1327" grid="1" gridSize="10" guides="1" tooltips="1" connect="1" arrows="1" fold="1" page="1" pageScale="1" pageWidth="1600" pageHeight="1240" math="0" shadow="0">
       <root>
         <mxCell id="0" />
         <mxCell id="1" parent="0" />

notebooks/tutorial_pipeline.py

@@ -1,15 +1,32 @@
+import os
+import pathlib
 import datajoint as dj
 from element_animal import subject
 from element_animal.subject import Subject
-from element_array_ephys import db_prefix, probe, ephys_acute as ephys
+from element_array_ephys import probe, ephys_acute as ephys
 from element_lab import lab
 from element_lab.lab import Lab, Location, Project, Protocol, Source, User
 from element_lab.lab import Device as Equipment
 from element_lab.lab import User as Experimenter
 from element_session import session_with_datetime as session
 from element_session.session_with_datetime import Session
 import element_interface
-import pathlib
+
+
+if "custom" not in dj.config:
+    dj.config["custom"] = {}
+
+# overwrite dj.config['custom'] values with environment variables if available
+
+dj.config["custom"]["database.prefix"] = os.getenv(
+    "DATABASE_PREFIX", dj.config["custom"].get("database.prefix", "")
+)
+
+dj.config["custom"]["ephys_root_data_dir"] = os.getenv(
+    "EPHYS_ROOT_DATA_DIR", dj.config["custom"].get("ephys_root_data_dir", "")
+)
+
+db_prefix = dj.config["custom"].get("database.prefix", "")
 
 
 # Declare functions for retrieving data

setup.py

@@ -41,11 +41,11 @@
     ],
     extras_require={
         "elements": [
-            "element-animal>=0.1.8",
-            "element-event>=0.2.3",
-            "element-interface>=0.4.0",
-            "element-lab>=0.3.0",
-            "element-session>=0.1.5",
+            "element-animal @ git+https://github.com/datajoint/element-animal.git",
+            "element-event @ git+https://github.com/datajoint/element-event.git",
+            "element-interface @ git+https://github.com/datajoint/element-interface.git",
+            "element-lab @ git+https://github.com/datajoint/element-lab.git",
+            "element-session @ git+https://github.com/datajoint/element-session.git",
         ],
         "nwb": ["dandi", "neuroconv[ecephys]", "pynwb"],
         "tests": ["pre-commit", "pytest", "pytest-cov"],