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Merge pull request #176 from kushalbakshi/main
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Update setup dependencies + tutorial setup + fix diagram
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MilagrosMarin authored Dec 21, 2023
2 parents d24f936 + 1ea7c89 commit 0174478
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3 changes: 3 additions & 0 deletions README.md
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Expand Up @@ -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
```
Expand All @@ -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)

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18 changes: 0 additions & 18 deletions element_array_ephys/__init__.py
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@@ -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
4 changes: 2 additions & 2 deletions images/diagram_flowchart.drawio
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@@ -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" />
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2 changes: 1 addition & 1 deletion images/diagram_flowchart.svg
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1,487 changes: 480 additions & 1,007 deletions notebooks/tutorial.ipynb

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21 changes: 19 additions & 2 deletions notebooks/tutorial_pipeline.py
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@@ -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
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10 changes: 5 additions & 5 deletions setup.py
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Expand Up @@ -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"],
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