diff --git a/.github/workflows/development.yaml b/.github/workflows/development.yaml
index 939cbc3e..549f1262 100644
--- a/.github/workflows/development.yaml
+++ b/.github/workflows/development.yaml
@@ -76,8 +76,8 @@ jobs:
needs: build
runs-on: ubuntu-latest
env:
- TWINE_USERNAME: ${{secrets.twine_test_username}}
- TWINE_PASSWORD: ${{secrets.twine_test_password}}
+ TWINE_USERNAME: ${{secrets.twine_username}}
+ TWINE_PASSWORD: ${{secrets.twine_password}}
outputs:
release_upload_url: ${{steps.create_gh_release.outputs.upload_url}}
steps:
@@ -122,7 +122,7 @@ jobs:
docker load < "image-${{env.PKG_NAME}}-${PKG_VERSION}-py3.8-alpine.tar.gz"
docker-compose -f docker-compose-build.yaml run \
-e TWINE_USERNAME=${TWINE_USERNAME} -e TWINE_PASSWORD=${TWINE_PASSWORD} element \
- sh -lc "pip install twine && python -m twine upload --repository testpypi dist/*"
+ sh -lc "pip install twine && python -m twine upload dist/*"
- name: Determine pip artifact paths
run: |
echo "PKG_WHEEL_PATH=$(ls dist/${PKG_NAME}-*.whl)" >> $GITHUB_ENV
diff --git a/CHANGELOG.md b/CHANGELOG.md
index dc2cdacb..04a12c51 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -2,11 +2,19 @@
Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) convention.
-## [0.1.0a3] - 2021-04-26
+
+## [0.1.0b0] - 2021-05-07
+### Added
++ First beta release
+
+
+## [0.1.0a5] - 2021-05-05
### Added
+ Added GitHub Action release process
+ `probe` and `ephys` elements
+ Readers for: `SpikeGLX`, `Open Ephys`, `Kilosort`
+ Probe table supporting: Neuropixels probes 1.0 - 3A, 1.0 - 3B, 2.0 - SS, 2.0 - MS
-[0.1.0a3]: https://github.com/datajoint/element-array-ephys/releases/tag/0.1.0a3
+
+[0.1.0b0]: https://github.com/datajoint/element-array-ephys/compare/0.1.0a5...0.1.0b0
+[0.1.0a5]: https://github.com/datajoint/element-array-ephys/releases/tag/0.1.0a5
diff --git a/README.md b/README.md
index a48741e7..802db8bb 100644
--- a/README.md
+++ b/README.md
@@ -15,7 +15,7 @@ See [Background](Background.md) for the background information and development t
## The Pipeline Architecture
-
+
As the diagram depicts, the array ephys element starts immediately downstream from ***Session***,
and also requires some notion of ***Location*** as a dependency for ***InsertionLocation***.
@@ -27,32 +27,56 @@ and also requires some notion of ***Location*** as a dependency for ***Insertion
+ An electrode here refers to one recordable electrode site on the Neuropixels probe (e.g. for Neuropixels 1.0, there are 960 sites per shank)
+ ***Probe*** - record of an actual physical probe, identifiable by some unique ID (e.g. probe's serial number)
+ ***ElectrodeConfig*** - particular electrode configuration to be used for ephys recording
-+ ***ElectrodeConfig.Electrode*** - corresponding electrodes in ***ProbeType.Electrode*** that are used for recording in this electrode configuration
-(e.g. for Neuropixels 1.0 or 2.0, there can be at most 384 electrodes usable for recording per probe)
++ ***ElectrodeConfig.Electrode*** - corresponding electrodes in ***ProbeType.Electrode*** that are used for recording in this electrode configuration (e.g. for Neuropixels 1.0 or 2.0, there can be at most 384 electrodes usable for recording per probe)
### Extracellular ephys recording
-+ ***ProbeInsertion*** - a surgical insertion of a probe onto the animal.
-Every experimental session consists of one or more ***ProbeInsertion***, with corresponding ***InsertionLocation***
-+ ***EphysRecording*** - each ***ProbeInsertion*** is accompanied by a corresponding ***EphysRecording***,
-specifying the ***ElectrodeConfig*** used for the recording from the ***Probe*** defined in such ***ProbeInsertion***
- + ***get_npx_data_dir*** method - the class ***EphysRecording*** requires user
- to supply a method to retrieve the directory containing the recorded neuropixels data (e.g. `*.ap.meta`, `*.ap.bin`, etc.),
- where the method's input arguments are the primary attributes identifying one ***EphysRecording***
++ ***ProbeInsertion*** - a surgical insertion of a probe in the brain. Every experimental session consists of one or more entries in ***ProbeInsertion*** with a corresponding ***InsertionLocation*** each
++ ***EphysRecording*** - each ***ProbeInsertion*** is accompanied by a corresponding ***EphysRecording***, specifying the ***ElectrodeConfig*** used for the recording from the ***Probe*** defined in such ***ProbeInsertion***
### Clusters and spikes
This ephys element features automatic ingestion for spike sorting results from the ***kilosort*** method.
+ ***Clustering*** - specify instance(s) of clustering on an ***EphysRecording***, by some ***ClusteringMethod***
- + ***get_ks_data_dir*** method - the class ***Clustering*** requires user
- to supply a method to retrieve the directory containing the kilosort results,
- where the method's input arguments are the primary attributes identifying one ***Clustering***
-+ ***Unit*** - Identified unit(s) from one ***Clustering***, with associated ***ClusterQualityLabel***
- + ***UnitSpikeTimes*** - spike times per unit
- + ***Waveform*** - mean waveform across spikes per unit per recording electrode
++ ***Curation*** - specify instance(s) of curations performed on the output of a given ***Clustering***
++ ***CuratedClustering*** - set of results from a particular round of clustering/curation
+ + ***CuratedClustering.Unit*** - Identified unit(s) from one ***Curation***, and the associated properties (e.g. cluster quality, spike times, spike depths, etc.)
+ + ***WaveformSet*** - A set of spike waveforms for units from a given CuratedClustering
+## Installation
+```
+pip install element-array-ephys
+```
+
+If you already have an older version of ***element-array-ephys*** installed using `pip`, upgrade with
+```
+pip install --upgrade element-array-ephys
+```
## Usage
+### Element activation
+
+To activate the `element-array-ephys`, ones need to provide:
+
+1. Schema names
+ + schema name for the probe module
+ + schema name for the ephys module
+
+2. Upstream tables
+ + Session table
+ + SkullReference table (Reference table for InsertionLocation, specifying the skull reference)
+
+3. Utility functions
+ + get_ephys_root_data_dir()
+ + get_session_directory()
+
+For more detail, check the docstring of the `element-array-ephys`:
+
+ help(probe.activate)
+ help(ephys.activate)
+
+### Example usage
+
See [this project](https://github.com/datajoint/workflow-array-ephys) for an example usage of this Array Electrophysiology Element.
diff --git a/element_array_ephys/version.py b/element_array_ephys/version.py
index ed63f796..5d6e909e 100644
--- a/element_array_ephys/version.py
+++ b/element_array_ephys/version.py
@@ -1,2 +1,2 @@
"""Package metadata."""
-__version__ = '0.1.0a3'
\ No newline at end of file
+__version__ = '0.1.0b0'
\ No newline at end of file
diff --git a/images/attached_array_ephys_element.svg b/images/attached_array_ephys_element.svg
new file mode 100644
index 00000000..1d0764cd
--- /dev/null
+++ b/images/attached_array_ephys_element.svg
@@ -0,0 +1,3 @@
+
+
+
\ No newline at end of file
diff --git a/images/attached_ephys_element.png b/images/attached_ephys_element.png
deleted file mode 100644
index 89c1224b..00000000
Binary files a/images/attached_ephys_element.png and /dev/null differ
diff --git a/images/attached_ephys_element.svg b/images/attached_ephys_element.svg
deleted file mode 100644
index 618daa44..00000000
--- a/images/attached_ephys_element.svg
+++ /dev/null
@@ -1,3 +0,0 @@
-
-
-
\ No newline at end of file
diff --git a/images/attached_ephys_erd.svg b/images/attached_ephys_erd.svg
deleted file mode 100644
index 78789a1e..00000000
--- a/images/attached_ephys_erd.svg
+++ /dev/null
@@ -1,314 +0,0 @@
-
\ No newline at end of file
diff --git a/setup.py b/setup.py
index 88a8feae..eda1c8d6 100644
--- a/setup.py
+++ b/setup.py
@@ -1,7 +1,7 @@
from setuptools import setup, find_packages
from os import path
-pkg_name = [p for p in find_packages() if '.' not in p][0]
+pkg_name = next(p for p in find_packages() if '.' not in p)
here = path.abspath(path.dirname(__file__))
with open(path.join(here, 'README.md'), 'r') as f:
@@ -18,6 +18,7 @@
version=__version__,
description="DataJoint Element for Extracellular Array Electrophysiology",
long_description=long_description,
+ long_description_content_type='text/markdown',
author='DataJoint NEURO',
author_email='info@vathes.com',
license='MIT',