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CHANGELOG

v0.3.7 (2024-11-01)

Fix

  • Fix(spikeglx): robust IMAX value detection from IMEC file (metadata 3.0)

v0.3.6 (2024-10-01)

Chore

  • chore(.github): add new GitHub Action callers for devcontainer, mkdocs, and semantic release (fc8ac1d)

Fix

  • fix(spikeglx): minor bugfix in reading probe model (2d57102)

Unknown

  • Merge pull request #205 from MilagrosMarin/chore/update-gha

chore(.github): add new GitHub Action callers (d091ffc)

  • Merge pull request #202 from ttngu207/main

fix(spikeglx): minor bugfix in reading npx probe model of older versions (780352b)

v0.3.5 (2024-08-19)

Fix

  • fix(spikeglx): minor bugfix (6764f8c)

  • fix: minor bugfix (e8870b9)

  • fix(probe): better handling of different Neuropixels probe types (aaec763)

  • fix(probe_geometry): bugfix in x_coords for probe with staggered electrode positions (54d4fac)

Unknown

  • Merge pull request #199 from ttngu207/main

fix(probe): better handling of different Neuropixels probe types and SpikeGLX meta loader (71d9a42)

  • update: version and changelog (f754392)

  • rearrange: explicitly call probe.create_neuropixels_probe_types() to create entries in ProbeType (46679e6)

  • Merge branch 'dev_separated_create_probe' into nei_nienborg (7f52f59)

  • Merge pull request #198 from BrainCOGS/adding-raw-strings-and-package-minimum

Fix regex patterns and add minimum version for scikit-image (27c56ea)

  • Added minimum version to the setup.py for scikit-image (711dd48)

  • Provided raw annotation for strings with unsupported escape regex sequences (f59b4ab)

  • Merge pull request #185 from datajoint/pytest

Add pytest (9299142)

  • apply black formatting (333f411)

  • update CHANGELOG.md & bump version (a3426eb)

  • tested version of pytest suite (9c033c4)

  • switch ephys to no_curation in tutorial notebook (3ae2cbc)

  • move tutorial_pipeline.py to tests (591a0ed)

  • setup pytest fixture (92026a6)

  • Merge pull request #183 from MilagrosMarin/main

Minor change: remove pypi release from release.yaml (cc36465)

  • update version and changelog (5cfc269)

  • remove PyPi release (dc7863e)

  • Merge pull request #182 from datajoint/staging

fix(probe_geometry): bugfix in x_coords for probe with staggered electrode positions (95d25f2)

  • Merge pull request #181 from ttngu207/main

fix(probe_geometry): bugfix in x_coords for probe with staggered electrode positions (d65b70f)

  • update(version): update CHANGELOG and version (2e79f3d)

v0.3.1 (2024-01-04)

Unknown

  • Merge pull request #178 from MilagrosMarin/main

Update CHANGELOG and version.py (6184b2f)

  • CHANGELOG and version.py updated (bfc0c0a)

  • Merge pull request #176 from kushalbakshi/main

Update setup dependencies + tutorial setup + fix diagram (0174478)

revert: 📝 revert docs dark mode cell text color (d24f936)

  • revert: 📝 revert table style (62172c4)

  • Merge pull request #174 from MilagrosMarin/update_tutorial

Improvements in element-array-ephys tutorial and README (fe4a844)

  • tutorial run with included outputs complete (2a59ea0)

  • Tutorial run with included outputs (40eec3e)

  • Revert deleting SessionDirectory insertion (ad69298)

  • add markdown in setup (abc82ba)

  • ephys tutorial preliminary review to mirror dlc (9e16a23)

  • Merge pull request #173 from kushalbakshi/codespace

Add DevContainers + Codespaces tutorial (140384e)

New spikeglx and probeinterface (3b8efe5)

  • address PR comments

Co-authored-by: Dimitri Yatsenko <[email protected]> (f42f1fc)

  • address PR comments

Co-authored-by: Dimitri Yatsenko <[email protected]> (452ff31)

  • bugfix (4407678)

  • bugfix in geomap to shank conversion (1514613)

  • transform geom map to shank map (9857aef)

  • update spikeglx loader to handle spikeglx ver 20230202 (3994fc7)

  • incorporate probeinterface and probe geometry for all npx probes (224b1c7)

v0.2.11 (2023-06-30)

Unknown

  • Merge pull request #165 from kabilar/patch

Patch issue with nullable attributes (e4dd98a)

  • Temporarily remove Docker image builds (48a1e76)

  • Format with black (d5de596)

  • Update image path (2557877)

  • Update text (8a764e8)

  • Update readme (c530671)

  • Update changelog (d1cf13f)

  • Update GitHub Actions (71bb8e2)

  • Update version and changelog (d4f7fe0)

  • Add default value (01ad1e8)

  • Merge pull request #142 from ttngu207/main

Update kilosort_triggering.py (1d30cb8)

  • update CHANGELOG (5e1f055)

  • Merge branch 'datajoint:main' into main (c5f20b0)

v0.2.10 (2023-05-26)

Unknown

  • Merge pull request #151 from kabilar/main

Fix readability of tables in dark mode (47dea95)

  • Update citation (100913e)

  • Update changelog (0bfca62)

  • Update CSS (15e9ddb)

  • Merge pull request #150 from kabilar/main

Add Kilosort, NWB, and DANDI citations (ad9588f)

Fix notebook output in dark mode (97a57b1)

v0.2.9 (2023-05-11)

Unknown

Fix docs tutorials in dark mode (96d1187)

  • Dark mode notebooks fix (9aab33d)

v0.2.8 (2023-04-28)

Unknown

  • Fix docs tutorials in dark mode (d2367ce)

  • Merge pull request #146 from JaerongA/metrics

Remap metrics.csv column names (6aef807)

v0.2.7 (2023-04-19)

Unknown

  • update changelog and version (6b069e6)

  • add column name mapping for metrics.csv (c97d509)

v0.2.6 (2023-04-18)

Unknown

  • Merge pull request #143 from kabilar/main

Update version and changelog for release (5abecc3)

  • Update ephys_precluster (5993d6e)

  • Update version and changelog (e9b66af)

  • Merge main of datajoint/element-array-ephys (40b5a6d)

  • Merge pull request #144 from JaerongA/main (e487f3a)

  • lowercase all column names in metrics.csv (f35ba0b)

  • Merge pull request #138 from JaerongA/main

Update docs for quality metrics (aabc454)

v0.2.5 (2023-04-13)

Unknown

  • remove schema tag in SkullReference (7192958)

  • add a new tag (b8ef2d9)

  • update schema diagrams to show SkullReference (8ffe6df)

  • Update CHANGELOG.md

Co-authored-by: Kabilar Gunalan <[email protected]> (166c00a)

  • Update docs/src/concepts.md

Co-authored-by: Kabilar Gunalan <[email protected]> (4a304d8)

  • bump version (7ceae8b)

  • add schema diagrams (eb5b0b1)

  • add quality_metrics.ipynb to mkdocs (977b90a)

  • Update docs/src/concepts.md

Co-authored-by: Kabilar Gunalan <[email protected]> (27d5742)

  • Update element_array_ephys/ephys_report.py

Co-authored-by: Kabilar Gunalan <[email protected]> (1e37791)

  • Update requirements.txt

Co-authored-by: Kabilar Gunalan <[email protected]> (46b911b)

  • add nbformat to requirements.txt (2f38cfa)

  • update requirements.txt (eb0d795)

  • update concepts.md (d362792)

  • fix docstring error in qc.py (ea03674)

  • add docstring for qc metric tables (7a89a7f)

  • fix docstring error (9cc4545)

  • Fix typo (e0919ae)

  • Update docs configuration (2dcca99)

  • Fix for PT_ratio to pt_ratio (e4358a5)

  • Update kilosort_triggering.py (8035648)

v0.2.4 (2023-03-10)

Unknown

  • Merge pull request #137 from kabilar/main

Update requirements for plotting widget (2fa46bd)

v0.2.3 (2023-02-14)

Fix

  • fix: 🐛 import from future module

this supports backward compability with typing (4d9ab28)

Unknown

  • Merge pull request #132 from CBroz1/main

Add 0.2.3 release date (e39f9d3)

  • Add 0.2.3 release date (eaeef30)

  • Merge pull request #125 from CBroz1/main

Adjusting pyopenephys requirement for pypi publication (c7f92af)

fix removing outdated files/directory (53f0312)

  • Update kilosort_triggering.py (a34e437)

  • fix removing outdated files/directory (6fb65b3)

  • minor improvement (7c6dc37)

  • Merge pull request #126 from sidhulyalkar/main

Fix multiple hash kilosort output issue (b619bd0)

Cleanup docstrings, add notebook render (d5b9586)

  • Apply suggestions from code review

Co-authored-by: JaerongA <[email protected]> (4796056)

  • Merge pull request #3 from JaerongA/main

fix: 🐛 import from future to support backward compatibility (fd94939)

Co-authored-by: Kabilar Gunalan <[email protected]> (0ec5e3d)

v0.2.2 (2023-01-11)

Unknown

  • Merge pull request #122 from JaerongA/main

Revert import order (eababbc)

  • add back deleted version tags (bd0e76a)

  • merge upstream & resolve conflicts (1feff92)

  • Merge pull request #120 from kushalbakshi/main

Docstring changes for docs API (623a381)

v0.2.1 (2023-01-09)

Chore

  • chore: 🔊 update CHANGELOG (2d43321)

  • chore: ⏪ revert formatting in concepts.md (c16b6bd)

  • chore(deps): 📌 unpin plotly (8504b97)

Documentation

  • docs: 📝 add | update docstrings (4999d64)

  • docs: 📝 name change & add docstring (d9c75c8)

Refactor

  • refactor: ✏️ fix typos (efca82e)

  • refactor(deps): ➖ remove ibllib deps and add acorr func (c613164)

Unknown

  • Merge pull request #116 from JaerongA/ephys_test

modify build_electrodes function (0f518f1)

  • Update element_array_ephys/probe.py

Co-authored-by: Chris Brozdowski <[email protected]> (59c72c4)

  • Update element_array_ephys/probe.py

Co-authored-by: Chris Brozdowski <[email protected]> (c983fa8)

  • Update element_array_ephys/probe.py

Co-authored-by: Chris Brozdowski <[email protected]> (8e53f54)

Add pre-commit & update docstrings & various fixes (61cb23a)

  • pull upstream & resolve merge conflicts (26b6be9)

  • Merge branch 'datajoint:main' into main (c3ad36f)

  • Merge pull request #121 from ttngu207/main

parameterize run_CatGT step from parameters retrieved from ClusteringParamSet table (24df134)

  • Update CHANGELOG.md (f5dff5c)

  • catGT checks and parameterizable (0ade344)

  • improve validate_file logic (63dbd12)

  • update CHANGELOG.md (294d4f5)

  • Update element_array_ephys/version.py

Co-authored-by: Chris Brozdowski <[email protected]> (b343c15)

  • Apply suggestions from code review

Co-authored-by: Kabilar Gunalan <[email protected]> (4651707)

  • Apply suggestions from code review

Co-authored-by: Kabilar Gunalan <[email protected]> (8920b00)

  • Update CHANGELOG.md

Co-authored-by: Kabilar Gunalan <[email protected]> (b29e161)

  • Update CHANGELOG.md

Co-authored-by: Kabilar Gunalan <[email protected]> (2889293)

  • Apply suggestions from code review

Co-authored-by: Kabilar Gunalan <[email protected]> Co-authored-by: Chris Brozdowski <[email protected]> (7e213c5)

  • Update setup.py

Co-authored-by: Chris Brozdowski <[email protected]> (5649b61)

  • ✏️ fix typos (dc85370)

  • pull from upstream (bda30a3)

  • Merge pull request #119 from CBroz1/qc

Add QC dashboard (08d1291)

linter recommended changes, reduce linter exceptions (9a78c15)

  • Apply isort (904ccb9)

  • Apply hooks except isort (5645ebc)

  • See details

  • Apply black
  • Remove trailing whitespace
  • Reduce flake8 exceptions
  • Move imports to top
  • Remove unused imports (e.g., re, pathlib, log_from_json)
  • Add all to init files specifying imports loaded
  • Add noqa: C901 selectively where complexity is high
  • l -> line for _read_meta func in spikeglx.py
  • give version a default value before loading (181677e)

  • fix docstrings (47de1d5)

  • update concepts.md (bc95946)

  • update version.py (6a997e1)

  • pre-commit ignores docs, .github (e52c12e)

  • update changelog.md (8f4ca3f)

  • add to ignored flake8 rules (16de049)

  • import DataJointError (434e16a)

  • update docstring (12098ce)

  • add requirements_dev.txt (d19f97f)

  • add pre-commit-config (278e2f2)

  • Update element_array_ephys/ephys_report.py

Co-authored-by: Chris Brozdowski <[email protected]> (b9fb872)

  • Update element_array_ephys/ephys_report.py

Co-authored-by: Chris Brozdowski <[email protected]> (61c739f)

  • update docstrings (816a0ed)

  • figures downloaded to temp folder (643637d)

  • Merge pull request #117 from ttngu207/main

remove typing - keep consistency and maintain backward compatibility prior to python 3.9 (678cd95)

  • remove typing - keep consistency and maintain backward compatibility prior to python 3.9 (44a2582)

  • Merge pull request #114 from ttngu207/main

Various fixes and improvements - no new feature (3635a4a)

  • add missing CHANGELOG link (c2c3482)

  • BLACK formatting (cbc3b62)

  • BLACK formatting (6b375f9)

  • Update CHANGELOG.md (72e784b)

  • BLACK formatting (b6ce2f7)

  • Merge branch 'datajoint:main' into main (731c103)

  • Merge pull request #115 from iamamutt/main

Remove ibllib dependency (561df39)

  • Merge pull request #1 from JaerongA/ephys_test

fix module name & add docstrings (dd6e215)

  • Update CHANGELOG.md

Co-authored-by: Chris Brozdowski <[email protected]> (ed5bbb9)

  • update changelog (d07a93f)

  • bugfix - fix "probe_indices" in single probe recording (2676a16)

  • handles single probe recording in "Neuropix-PXI" format (1859085)

  • safeguard in creating/inserting probe types upon probe activation (c2d9f47)

  • bugfix logging median subtraction duration (9ec904f)

  • bugfix in updating median-subtraction duration (8ec0f71)

  • update duration for median_subtraction step (bd2ff1c)

  • update docstring (68fa77c)

  • Apply suggestions from code review

Co-authored-by: Thinh Nguyen <[email protected]> (cd9501c)

  • fix docstring & formatting (9fc7477)

  • fix docstring in probe.py (7958727)

  • feat: (ff3fca0)

  • remove proj() (496c210)

  • revert: 🩹 revert to um (5a7f068)

  • add probe_type in electrode_layouts (633f745)

  • spacing defaults to none (8f6e280)

  • Update element_array_ephys/probe.py

Co-authored-by: Dimitri Yatsenko <[email protected]> (704f6ed)

Update README.md (85a1f0a)

  • Update README.md (7a5f843)

  • Merge branch 'datajoint:main' into main (8dd5f29)

  • Merge pull request #111 from kabilar/main

Fix for cicd and other ux fixes (2e63edc)

  • Move datajoint diagrams (8f006c0)

  • Remove empty spaces to compare with ephys modules (863d9b1)

  • Fix bug (8731def)

  • Fix diagram (566bc64)

  • Update text (48900e8)

  • Merge pull request #110 from CBroz1/docs2

Add diagram text layer (34912bf)

  • Add diagram text layer (638ebc4)

  • Merge pull request #109 from CBroz1/docs2

Docs2 (23bf669)

  • Update diagram (07f0733)

  • Add diagram (38cc7ab)

  • Update logo/styling. Hard wrap (4d22a16)

  • datatype clarification (c353400)

  • fix docstring typo (50d3dd1)

  • Merge pull request #107 from kushalbakshi/main

Updated CHANGELOG (2af7fc5)

v0.2.0 (2022-11-03)

Feature

  • feat: ✨ Merge branch 'plotly' into no_curation_plot (06c1064)

  • feat: ✨ add a report schema and plotting png figures (66743cc)

Fix

  • fix: 🐛 use to_plotly_json() instead of to_json() (69b2796)

Unknown

  • Updated CHANGELOG (bc5afcc)

  • Merge pull request #102 from kushalbakshi/main

Added docs + docstrings (e04841b)

  • Update element_array_ephys/ephys_precluster.py

Co-authored-by: Chris Brozdowski <[email protected]> (a73fcd2)

  • Update element_array_ephys/ephys_no_curation.py

Co-authored-by: Chris Brozdowski <[email protected]> (36b8161)

  • Update element_array_ephys/ephys_chronic.py

Co-authored-by: Chris Brozdowski <[email protected]> (e6e0b21)

  • Update element_array_ephys/ephys_acute.py

Co-authored-by: Chris Brozdowski <[email protected]> (f2d550e)

add to changelog, bump version (89f1d7c)

  • Apply suggestions from code review

Co-authored-by: Kabilar Gunalan <[email protected]> Co-authored-by: Tolga Dincer <[email protected]> (8f3e76e)

  • add to changelog, bump version (02fb576)

  • Merge pull request #103 from JaerongA/no_curation_plot

add ephys_report schema for data visualizations (3e9b675)

  • Update element_array_ephys/plotting/widget.py

Co-authored-by: Thinh Nguyen <[email protected]> (d0c6797)

Co-authored-by: Thinh Nguyen <[email protected]> (e773e94)

  • plot only the shank with the peak electrode (ce9abcc)

  • new method for getting x, y spacing between sites (2eb9540)

  • fix code to calculate site spacing & figure reformatting (b48aaf0)

  • add vscode in .gitignore (48e0744)

  • fixed typo & black formatting (f1d6a87)

  • clean up import & remove wrong documentation (dc9b293)

  • remove zip function (357cda9)

  • remove zip function (290feca)

  • add skip_duplicates=True in probe.Probe.insert (dab5dfe)

  • Apply suggestions from code review

Co-authored-by: Dimitri Yatsenko <[email protected]> (5d50894)

  • Update element_array_ephys/ephys_chronic.py

Co-authored-by: Dimitri Yatsenko <[email protected]> (35d2044)

resolve "activation" and circular dependency (f191214)

Co-authored-by: Chris Brozdowski <[email protected]> (f6b93d7)

  • Update element_array_ephys/ephys_no_curation.py

Co-authored-by: Chris Brozdowski <[email protected]> (486d938)

  • Update element_array_ephys/ephys_chronic.py

Co-authored-by: Chris Brozdowski <[email protected]> (ab1a067)

Co-authored-by: Chris Brozdowski <[email protected]> (2355a46)

Co-authored-by: Chris Brozdowski <[email protected]> (38f2410)

  • Update element_array_ephys/ephys_precluster.py

Co-authored-by: Chris Brozdowski <[email protected]> (ca1441f)

  • Update element_array_ephys/probe.py

Co-authored-by: Chris Brozdowski <[email protected]> (98f8a8c)

  • Updated docstrings after code review (17d9e4a)

  • Changes applied from code review (c75e2d7)

  • Update docs/mkdocs.yaml

Co-authored-by: Chris Brozdowski <[email protected]> (37d6a60)

run_kilosort -> main (db75e4d)

  • Merge pull request #97 from ttngu207/no-curation

pull from main - add QC (03e2d5f)

Ensure Path type for get_spikeglx_meta_filepath (a738ee7)

  • Ensure Path type for get_spikeglx_meta_filepath (0e94252)

  • Merge pull request #91 from ttngu207/no-curation

bugfix for catgt (6757ef7)

  • Update kilosort_triggering.py (71d87ae)

  • Merge pull request #90 from ttngu207/no-curation

enable CatGT (23ca7ca)

  • improve error handling (f60ba3d)

  • bugfix - path search for catgt output (c33d1b0)

  • missing_ok arg only available in python 3.8+ (35da39b)

  • bugfix (fbdbe24)

  • bugfix (aed42ca)

  • enable catgt run (987231b)

  • bugfix in running catgt (5905392)

  • Update kilosort_triggering.py (f9f18d0)

  • Merge pull request #89 from ttngu207/no-curation

implement data compression using mtscomp for openephys and spikeglx for neuropixels data (c153e7f)

  • garbage collect openephys objects (d8aea04)

  • garbage collect openephys objects (97f3d21)

  • implement data compression using mtscomp for openephys and spikeglx neuropixels data (b2bd0ee)

  • Merge pull request #88 from ttngu207/no-curation

overall code cleanup/improvement for more robust and optimal kilosort run (ad8436e)

Changes for codebook deployment (d9c3887)

more robust loading of openephys format (d298b07)

  • more robust loading of openephys format (67039ac)

  • Merge pull request #73 from ttngu207/no-curation

update openephys loader - handling open ephys v0.6.0 (9272ee6)

  • added loading of electrode location for new openephys format (4e367d7)

  • update open ephys loader to handle "STREAM" in latest format (07604e2)

  • Merge pull request #70 from ttngu207/no-curation

bugfix for LFP electrode mapping (747c15f)

Co-authored-by: Dimitri Yatsenko <[email protected]> (720e355)

  • Issue #11 (4a3e0bf)

  • WIP: nwb line length, Readme mention of (e1c9b35)

  • WIP: NWB fix - prevent SQL err by restricting key (b62fd12)

  • WIP: nwb bugfix (49bba8a)

  • Merge pull request #69 from ttngu207/no-curation

Add no-curation version and run kilosort analysis (364f80e)

Co-authored-by: Dimitri Yatsenko <[email protected]> (af864d7)

  • added assertion - safeguard against failed loading of continuous.dat (47babf3)

  • handles new probe naming in latest Open Ephys format (cd5fe70)

  • update openephys loader - handle new open ephys format (11a12ba)

  • Update openephys.py (85c7c8b)

  • configurable paramset_idx for auto ClusteringTask generation (39c8579)

  • bugfix (769de13)

  • Update init.py (e0a9a4f)

  • delete nwb export - rename ephys module -> ephys_acute (c2f8aea)

  • remove unintended prototyping work (83649f5)

  • handle older open ephys format for single probe (bdcfa46)

  • Update requirements.txt (f0b3d4a)

  • Update requirements.txt (7320f9f)

  • Update requirements.txt (cb1a041)

  • rename sess_dir -> session_dir (03cab02)

  • Apply suggestions from code review

Co-authored-by: Dimitri Yatsenko <[email protected]> (f4052cc)

all three ephys files up to date (9dd6b42)

  • applied requested changes (c56cd18)

  • all three ephys files up to date (f2881ca)

  • Merge pull request #3 from ttngu207/nwb-export

bugfix in assigning unit electrode indices (f9a4754)

  • bugfix in assigning unit electrode indices (31bba8c)

  • include probe as part of the electrode_group name for uniqueness (aa47c8a)

  • version bump (8657d58)

  • fix NWB export - null waveforms - back to version 0.1.0b1 (dae36d1)

  • version bump (6107e8e)

  • NWB export fix, specifying which ephys module (8dff08b)

  • handles multi-probe for older OE version (02c4b67)

  • openephys loader - handles signalchain and processor as single element or list (2022e91)

  • for pykilosort's probe, provide both Nchan and NchanTOT (1c39568)

  • handle missing sample_rate from pykilosort params.py (142459d)

  • bugfix in triggering pykilosort (02069c9)

  • clusters extraction - check cluster_group.tsv and cluster_KSLabel.tsv (da10c66)

  • handles extraction of connected channels for NP_PROBE format in OpenEphys (43d6614)

  • bugfix, timedelta as seconds (adffe34)

  • bugfix - extract recording datetime (instead of using experiment datetime) (c213325)

  • bugfix openephys loader (0d16e7e)

  • search recording channels for Open Ephys based on channel names (d105419)

  • bugfix in electrode sites design for Neuropixels UHD probe (f55a6a7)

  • supporting neuropixels UHD in ephys.EphysRecording (db3027b)

  • handles format differences between npx1 vs 3A (e325a30)

  • fix package requirement formatting error (af2b18b)

  • update openephys loader (4250220)

  • minor bugfix in running pykilosort (b6f8f99)

  • using fork of pyopenephys (96931a4)

  • use_C_waves=False for OpenEphys (81d99c8)

  • first prototype for pykilosort (819ff19)

  • triggering kilosort analysis for open-ephys (df599fb)

  • add neuropixels UHD probe type (ddc3b94)

  • specify additional recording-info as part of the params (58b5984)

  • bugfix for running kilosort for Open Ephys data (199a2ba)

  • first prototype for running the ecephys_pipeline with OpenEphys (49ca0be)

  • add nwb export to no-curation ephys (b25f065)

  • Merge pull request #2 from ttngu207/nwb-export

Nwb export (3ebdf23)

  • Update nwb.py (19616ef)

  • handle NWB export with multiple curated clusterings from one session (d07f830)

  • added NWB export (f740aef)

  • minor bugfix (09c1e60)

  • stylistic improvements, addressing code review comments (e8ffe17)

  • Apply suggestions from code review

Co-authored-by: Dimitri Yatsenko <[email protected]> (74e3ead)

  • check ap.bin file validity before triggering kilosort (based on filesize) (beaf765)

  • duration for each module run (19b704b)

  • bugfix logging for kilosort triggering (f34e95d)

  • minor bugfix (55bec01)

  • stage tracking and resumable kilosort run (408532c)

  • minor cleanup (dc7ddd9)

  • improve clusteringtask and waveform ingestion routine (c2ee64f)

  • new version 0.1.0b1 (67341d8)

  • Update kilosort.py (0f0c212)

  • bugfix - no dir created (044c389)

  • add debugging lines (b9f4e92)

  • log the folder creation (ae966aa)

  • bugfix, convert path to string (94aade7)

  • bugfix (28c4452)

  • updating kilosort_repository depending on which KSVer to be used (38c5be6)

  • include clustering_method into the calculation of param_set_hash (acdab12)

  • make variable naming consistent (a0ea9f7)

  • add kilosort 2.5 as default content (a6cae12)

  • minor bugfix (69c5e51)

  • change default noise_template_use_rf to False (c593baf)

  • missing generate module json (375e437)

  • bugfix (d63561f)

  • handle cases where fileTimeSecs is not available (6788180)

  • bugfix in triggering ecephys_spike_sorting (6bf0eb1)

  • minor tweak/improvements in kilosort triggering (f699ce7)

  • Update kilosort_trigger.py (dd01fd2)

  • flag to create spike sorting output dir (6c646bb)

  • fix missing clustering_method (5cdc994)

  • handles a weird windows/unix path incompatibility (even with pathlib) (ba28637)

  • Merge branch 'no-curation' of https://github.com/ttngu207/element-array-ephys into no-curation (a24bd1a)

  • Apply suggestions from code review

Co-authored-by: Dimitri Yatsenko <[email protected]> (149ef3f)

  • typo fix (9f98195)

  • minor stylistic improvements (a9326ea)

  • remove _required_packages_paths (60105da)

  • triggering Kilosort with ecephys_spike_sorting package (047bfa1)

  • automate ClusteringTask insertion (0d56456)

  • bugfix (a7e7554)

  • Update ephys_no_curation.py (70e93b3)

  • using find_full_path for session dir as well - improve robustness (5420ae0)

  • no-curation, store processed data in user-specified processed_data_dir if provided (4397dd7)

  • helper for ProbeInsertion - auto_generate_entries(session_key) (de84ce0)

  • improve kilosort loading routine - add validate() method (b7c0845)

  • minor bug fix (adfad95)

  • make clustering_output_dir user-input optional, auto infer (590310e)

  • remove Curation (a39a9b1)

  • copied ephys to ephys-no-curation, added recording_duration, make (042cc46)

  • Update README (cdb9182)

  • Populated .md files (d8fca5b)

  • Merge pull request #96 from ttngu207/main

bugfix - remove % in attributes' comments AND add QC to ephys_precluster (4a6bc31)

  • add QC to ephys_precluster (e21302f)

  • bugfix - remove % in attributes' comments (57a1c1d)

  • Merge pull request #87 from ttngu207/main

QC metrics (54c8413)

  • Update CHANGELOG.md

Co-authored-by: Kabilar Gunalan <[email protected]> (7ce35ab)

  • Apply suggestions from code review

Co-authored-by: Dimitri Yatsenko <[email protected]> (100cf84)

Documentation revamp (efedd37)

  • Update with recent styling updates. (c73c7b5)

  • Remove unneeded comment. (0a8a67c)

  • Upgrade documentation to latest design and automation. (a304d31)

  • Create u24_element_release_call.yml (3b98067)

  • Create u24_element_tag_to_release.yml (ddd6a18)

  • Create u24_element_before_release.yml (ac9035d)

  • Merge pull request #84 from A-Baji/documentation

Create documentation template (22c95a8)

v0.1.4 (2022-07-11)

Unknown

  • Merge pull request #83 from kabilar/main

Fix for spike_depths attribute (ee0e179)

v0.1.3 (2022-06-16)

Unknown

  • Merge pull request #79 from kabilar/main

Update precluster_output_dir to nullable (ecd6a4c)

  • Set precluster_output_dir to nullable (90f3ed1)

v0.1.2 (2022-06-09)

Unknown

  • Merge pull request #78 from kabilar/main

Fix for case where pc_features.npy does not exist (a01530c)

  • Fix format (6b6f448)

  • Update element_array_ephys/ephys_chronic.py (558e0b9)

  • Update element_array_ephys/ephys_acute.py (44dbe8c)

  • Update element_array_ephys/readers/kilosort.py

Co-authored-by: Thinh Nguyen <[email protected]> (a392e57)

  • Update element_array_ephys/ephys_precluster.py

Co-authored-by: Thinh Nguyen <[email protected]> (b3922fc)

v0.1.1 (2022-06-01)

Unknown

  • Merge pull request #72 from kabilar/main

Add attributes to describe parameter list (a20ab9b)

Add ephys_precluster module (3eeae51)

Convert to nwb (7a4fba9)

  • Update element_array_ephys/export/nwb/nwb.py

Co-authored-by: Dimitri Yatsenko <[email protected]> (9ee6088)

  • Update element_array_ephys/export/nwb/nwb.py

Co-authored-by: Dimitri Yatsenko <[email protected]> (441cfe2)

  • Merge remote-tracking branch 'origin/convert_to_nwb' into convert_to_nwb (6fc51b0)

  • Update element_array_ephys/export/nwb/nwb.py

Co-authored-by: Kabilar Gunalan <[email protected]> (9f9872c)

  • Update element_array_ephys/export/nwb/nwb.py

Co-authored-by: Kabilar Gunalan <[email protected]> (fb98327)

  • Update element_array_ephys/export/nwb/nwb.py

Co-authored-by: Kabilar Gunalan <[email protected]> (d94453b)

  • remove ephys_no_curation.py (3e07c61)

  • Update element_array_ephys/export/nwb/nwb.py

Co-authored-by: Kabilar Gunalan <[email protected]> (59028cb)

  • Update element_array_ephys/export/nwb/nwb.py

Co-authored-by: Kabilar Gunalan <[email protected]> (068ea3d)

  • trying clustering_query..proj() (c2004ea)

  • rmv units_query (0152c5d)

  • fix insertion record (82c8655)

  • add explanation for index parameter (707adff)

  • Merge remote-tracking branch 'origin/convert_to_nwb' into convert_to_nwb (bc54009)

  • Update element_array_ephys/export/nwb/nwb.py

Co-authored-by: Kabilar Gunalan <[email protected]> (842beec)

  • Update element_array_ephys/export/nwb/nwb.py

Co-authored-by: Kabilar Gunalan <[email protected]> (766f4eb)

  • Update element_array_ephys/export/nwb/nwb.py

Co-authored-by: Kabilar Gunalan <[email protected]> (2526812)

  • Update element_array_ephys/export/nwb/nwb.py

Co-authored-by: Kabilar Gunalan <[email protected]> (15044cf)

  • Update element_array_ephys/export/nwb/nwb.py

Co-authored-by: Kabilar Gunalan <[email protected]> (2e621c0)

  • Update element_array_ephys/export/nwb/nwb.py

Co-authored-by: Kabilar Gunalan <[email protected]> (a01ee9c)

  • Update element_array_ephys/export/nwb/nwb.py

Co-authored-by: Kabilar Gunalan <[email protected]> (cbefcde)

  • add explanation in docstring of add_ephys_units_to_nwb (3971fe6)

  • Merge remote-tracking branch 'origin/convert_to_nwb' into convert_to_nwb (a7b2abb)

  • Update element_array_ephys/export/nwb/nwb.py (c200699)

  • Update element_array_ephys/export/nwb/nwb.py

Co-authored-by: Kabilar Gunalan <[email protected]> (2ee2bd5)

  • Update element_array_ephys/export/nwb/nwb.py

Co-authored-by: Chris Brozdowski <[email protected]> (9e72773)

  • Merge branch 'main' into convert_to_nwb (b3779e5)

  • fix docstring for get_electrodes_mapping (acdb5f9)

  • Merge remote-tracking branch 'origin/convert_to_nwb' into convert_to_nwb (826335b)

  • Update element_array_ephys/export/nwb/nwb.py

Co-authored-by: Kabilar Gunalan <[email protected]> (49fac08)

  • Update element_array_ephys/export/nwb/nwb.py

Co-authored-by: Kabilar Gunalan <[email protected]> (ba6cbcf)

  • specify releases for dependencies (daccfc4)

  • add docstring for gain_helper (12974ff)

  • Update element_array_ephys/export/nwb/README.md

Co-authored-by: Kabilar Gunalan <[email protected]> (00c3691)

  • Update element_array_ephys/export/nwb/nwb.py

Co-authored-by: Kabilar Gunalan <[email protected]> (abccafa)

  • Update element_array_ephys/export/nwb/README.md

Co-authored-by: Kabilar Gunalan <[email protected]> (24ac2c0)

  • Update element_array_ephys/export/nwb/nwb.py

Co-authored-by: Kabilar Gunalan <[email protected]> (a1fb193)

  • Update element_array_ephys/export/nwb/README.md

Co-authored-by: Kabilar Gunalan <[email protected]> (584c738)

  • Update element_array_ephys/export/nwb/nwb.py

Co-authored-by: Kabilar Gunalan <[email protected]> (c68f2ca)

  • Update element_array_ephys/export/nwb/nwb.py

Co-authored-by: Chris Brozdowski <[email protected]> (3ae6e2d)

  • Update element_array_ephys/ephys_acute.py

Co-authored-by: Chris Brozdowski <[email protected]> (e973743)

  • Update element_array_ephys/export/nwb/nwb.py

Co-authored-by: Kabilar Gunalan <[email protected]> (b373b26)

  • fix imports (cc14671)

  • rmv tests (they are moved to the ephys workflow) (c63c8c4)

  • Merge remote-tracking branch 'cbroz1/ben' into convert_to_nwb

Conflicts:

element_array_ephys/export/nwb/nwb.py (5b942b3)

  • adjust imports in init and nwb.py (782a4a5)

  • Merge pull request #2 from ttngu207/chris-nwb

import the correct ephys module that has been activated (2beb41b)

  • import the correct ephys module that has been activated (b4ffe1d)

  • Merge pull request #1 from ttngu207/chris-nwb

nwb function specification in linking_module (6d7ad7c)

  • nwb function specification in linking_module (bf5e82a)

  • Avoid linking_module issues. See details.

  • add init + schema from git/ttngu207/element_array_ephys@no-curation
  • add ephys_no_curation schema to match the schema ben has been pulling from
    • how should we address this in the element? given not currently default
  • remove unused imports
  • import datajoint and element_interface.utils find_full_path
  • add arguments to main export function:
    • schema names as datajoint config database prefix default
    • ephys_root_data_dir - default to dj.config or none
  • add create_virtual_module statements to avoid activate(schema,linking_module=unknown)
  • declare ephys and probe as global
  • add assert errors for ephys_root_data_dir!=None when needed
  • pass ephys_root_data_dir to relevant functions
  • above permits: from element_array_ephys.export.nwb.nwb import ecephys_session_to_nwb (2595dae)
  • Rebase, squashed. See Details

Add element_data_loader for multiple root dirs Update author Fix import Fix OpenEphys session path Update directory path Add print statement Fix for missing fileTimeSecs Update error message Suggested adds re upstream components Directing to workflow for upstream SkullReference and utility functions (a557b17)

  • rmv subject_id (806684f)

  • import GenericDataChunkIterator from hdmf (a7f4624)

  • add tests for getting lfp data from datajoint (fafdde1)

  • Merge remote-tracking branch 'origin/convert_to_nwb' into convert_to_nwb (63b545d)

  • Update element_array_ephys/export/nwb/nwb.py

Co-authored-by: Kabilar Gunalan <[email protected]> (9374d94)

  • Merge branch 'main' into convert_to_nwb (f8027cc)

  • update import path (6338daf)

  • add tests (4cab8c8)

  • refactor into gains_helper (7953662)

  • correctly set conversion and channel_conversion (7deb00f)

  • ephys.find_full_path (654d567)

  • import os (ba3f86a)

  • standardize slashes (8d3df71)

  • ephys.get_ephys_root_data_dir (e992478)

  • import probe (379ae11)

  • import session_to_nwb (1dccb68)

  • import from workflow pipeline (5de22e0)

  • import from workflow pipeline (1b67629)

  • fix nwbfile_kwargs logic (eb47ee5)

  • fix nwbfile_kwargs logic (96c57f7)

  • add optional session keys to ecephys_session_to_nwb (365b43b)

  • add datetime import (d1f3dab)

  • relative import of ephys (1363214)

  • refactor to include requirements for nwb conversion (013ae7d)

  • add readme for exporting to NWB (19f78b7)

  • add some docstrings (b35ee72)

  • add missing nwbfile arg (a7f846b)

  • Merge remote-tracking branch 'origin/convert_to_nwb' into convert_to_nwb

Conflicts:

element_array_ephys/export/nwb.py (b4d9c0e)

  • Update element_array_ephys/export/nwb.py

Co-authored-by: Dimitri Yatsenko <[email protected]> (e837452)

  • Update element_array_ephys/export/nwb.py

Co-authored-by: Dimitri Yatsenko <[email protected]> (3298341)

  • Update element_array_ephys/export/nwb.py

Co-authored-by: Dimitri Yatsenko <[email protected]> (470b20a)

    • optimize imports

  • black

  • upgrade to latest version of conversion-tools

  • upgrade to latest spikeinterface api

  • (d924d57)

  • add documentation (d2b93f2)

    • add lfp from source

  • docstrings

  • json dump insertion into location

  • ignore channel_conversion if all are 1

  • black formatting (8d75a61)

  • add draft convert to nwb (f3dd8d8)

  • Mult rootdirs. If sess_dir, check fullpath. Give OpenEphys fullpath. (720eb00)

  • Add Part table to track order of operations (3d8ec16)

  • Merge branch 'main' of https://github.com/kabilar/element-array-ephys into main (fee5b7c)

  • Merge pull request #1 from kabilar/precluster

Merge to main (1e92b04)

  • Add pre-clustering tables to acute module (c7a155a)

  • Create copy of ephys_acute.py (122d9a2)

  • Merge pull request #64 from kabilar/main

Update README (14517a2)

  • Replace italics with back tick (b3f5b29)

  • Replace italics with back tick (e8350d5)

  • Add ephys schema text (112f325)

  • Add activation text (edc9d5d)

  • Add ephys schema text (ab92d84)

  • Revert "Create copy of ephys_acute.py"

This reverts commit b66109b5e61297a10c1cc8a929115fa5955238e1. (000308f)

  • Add probe schema text (4f8699f)

  • Create copy of ephys_acute.py (c7393fc)

  • Revert "Create copy of ephys_acute.py"

This reverts commit b66109b5e61297a10c1cc8a929115fa5955238e1. (9ddfb4c)

  • Update format (f940a71)

  • Add collapsible sections (338a796)

  • Update format (9b68b03)

  • Add collapsible section (8740b2c)

  • Add citation section (c8ac8e6)

  • Add links to elements.datajoint.org (0bc69c2)

  • Add link to elements.datajoint.org (d11af2f)

  • Move background file to datajoint-elements repo (68c94c1)

  • Create copy of ephys_acute.py (b66109b)

  • Move background file to datajoint-elements repo (f8a3abf)

  • Merge pull request #58 from kabilar/main

Add attributes and rename module (1f7a2a3)

Implement find_full_path within ephys modules (088093d)

Directing to workflow for upstream SkullReference and utility functions (4ca9b32)

chronic and acute probe insertions as different python modules (1fdbcf1)

beta 0 release (7c67f65)

  • beta 0 release (69a5424)

  • Merge pull request #26 from ttngu207/main

bump alpha version for first release on PyPI (7cd92ee)

  • bump alpha version for first release on PyPI (99ab2fa)

  • Merge pull request #25 from ttngu207/main

bump alpha version for first release on pypi (159a2a5)

  • bump alpha version for first release on pypi (ab3cfc9)

  • Merge pull request #24 from ttngu207/main

update README, improve markdown formatting, specify long_description_content_type to markdown, add versioning and GH Action for PyPI release (07f858c)

  • Apply suggestions from code review

Co-authored-by: Dimitri Yatsenko <[email protected]> (98753ed)

added comments to tables (f2ac602)

  • added comments to tables (f05e1fe)

  • Merge pull request #22 from ttngu207/main

bump version - 0.1.0a3 (6fcc31a)

  • Update CHANGELOG.md

Co-authored-by: Raphael Guzman <[email protected]> (8d8683a)

  • bump version - 0.1.0a3 (f500492)

  • Merge pull request #21 from ttngu207/main

GitHub Action for release process (283fad0)

  • minor cleanup (6120883)

  • Apply suggestions from code review

Co-authored-by: Raphael Guzman <[email protected]> (ef3578e)

Co-authored-by: Raphael Guzman <[email protected]> (7cf70d1)

  • for testing - update twine upload to testpypi (ecc0ab2)

  • address review comments, add test-changelog (ef7b6c9)

  • Apply suggestions from code review

Co-authored-by: Raphael Guzman <[email protected]> (17dc100)

  • Update CHANGELOG.md (e04f739)

  • version 0.1.0a3 (f433189)

  • update setup, point back to datajoint github (c7a1940)

  • GH Action bugfix - bump version (f2c9726)

  • bugfix, add SDIST_PKG_NAME (e8632a3)

  • improve package_name parsing (be26e4b)

  • Update development.yaml (ff5f5f9)

  • Update development.yaml (f847aeb)

  • add build to GH action (5052b8e)

  • change package url - for testing GH release only (77f5240)

  • update changelog - bump version to 0.1.0a3 (bae08ad)

  • Update development.yaml (d124407)

  • Update .gitignore (b8eb640)

  • set up release processes for GH Action (a94e726)

  • Merge branch 'main' into GH-action-PyPI-release (b991fbb)

  • add package_version (02f5387)

  • Create CHANGELOG.md (77a7a52)

  • Merge pull request #20 from ttngu207/main

table renames, code cleanup (4cced0e)

  • table renames, code cleanup (236301a)

  • Merge pull request #19 from ttngu207/main

Code cleanup/optimization, variables renaming for clarity (b0fa79f)

  • minor bugfix (9b18415)

  • split find_valid_full_path to find_full_path and find_root_directory (258839b)

  • support .xlsx cluster files (4e824cf)

  • minor wording fix (855f8eb)

  • remove get_clustering_root_data_dir() from docstring (6f01562)

  • allow root_dir to be a list of potential directories - util function find_valid_full_path() for root and path searching (6488fee)

  • code refactor - improve logic for spikeglx_meta file search (e51113b)

  • Update version.py (91a3824)

  • bugfix (669c6e5)

  • improve variables naming in kilosort reader (e761501)

  • improve variables naming (c002646)

  • improve naming, comments (cd28d9b)

  • code-cleanup - variables renaming - addressing PR review's comments (eb7eb2c)

  • Merge pull request #17 from ttngu207/main

specify a separate get_clustering_root_data_dir() - handle cases where raw ephys and clustering results are stored at different root locations (e.g. different mount points) (74a7a56)

Co-authored-by: shenshan <[email protected]> (6f8cd8b)

  • remove Quality Control - will add this as a separate element (33a421b)

  • comment fix (af54831)

  • naming bugfix (75d31a5)

  • rename "OpenEphys" to "Open Ephys" (bc2f528)

  • added QualityControl as a master-table and make ClusterQualityMetrics the part-table now - no need for modified key_source (2c9a787)

  • Waveform table now a master table, with Waveform.Unit as part-table (no need for modified key_source) (31e2320)

  • openephys loader - code cleanup (033240f)

  • creating Neuropixels probe (in ProbeType) as part of probe module activation (655115b)

  • tweaks to LFP and waveform ingestion - do in small batches to mitigate memory issue (dba0a48)

  • minor updates to "jsiegle" PR - code, variable-naming cleanup

Handle cases where the plugin is Neuropix-PXI but NP_PROBE is not present in processor[&#39;EDITOR&#39;] (only PROBE) (dcf8906)

Update Open Ephys data reader (cf39185)

  • Update Open Ephys data reader (a85e835)

  • specify a separate get_clustering_root_data_dir() - handle cases where raw ephys and clustering results are stored a different root locations (e.g. different mount points) (ce90dc6)

  • add version.py (4185ba3)

  • Update .gitignore (f69e491)

  • Merge pull request #13 from ttngu207/main

Mostly code cleanup - formatting (f07d131)

  • more code-cleanup (ea1547f)

  • Update setup.py (15ca803)

  • Update Background.md (0833d10)

  • cleanup (6c490f8)

  • Update README.md (40ce9e6)

  • rename elements-ephys -> element-array-ephys (fa369f0)

  • Update README.md (a573e5c)

  • Update Background.md (cf2f172)

  • Update Background.md (dfff966)

  • added Background section (653b84f)

  • code cleanup - formatting (7ab0c2a)

  • Create CONTRIBUTING.md (1ee37ab)

  • Merge pull request #10 from ttngu207/main

Ephys pipeline with support for multiple curations (983d61a)

  • update diagrams (e98b34f)

  • Update requirements.txt (bab8e1d)

  • bugfix in spikeglx get original channels (f8244c8)

  • Merge branch 'multiple-curations' into main (bfab1dd)

  • bugfix in Unit ingestion (adfd5af)

  • added a CuratedClustering as master table for Unit (7bd751a)

  • Update openephys.py (a889407)

  • minor code cleanup (b0011a1)

  • Curation downstream from Clustering - move Curation insertion in Clustering.make() to a separate utility function (6859e52)

  • Merge branch 'main' into multiple-curations (64bd47d)

  • prototype design for multiple curations (94686f5)

  • Merge pull request #9 from ttngu207/main

keep _timeseries data as memmap int16 type, apply bitvolt conversion at LFP/Waveform extraction step & Bugfix in channel matching for SpikeGLX (70a813b)

  • Update elements_ephys/readers/spikeglx.py

Co-authored-by: Dimitri Yatsenko <[email protected]> (93ea01a)

  • minor formatting, PEP8 (d656108)

  • datajoint version 0.13+ required (39580e1)

  • bugfix - openephys waveform extraction (825407c)

  • bugfix (4afc0f1)

  • try-catch for searching/loading spikeglx files (f3d98b3)

  • keep _timeseries data as memmap int16 type, apply bitvolt conversion only when needed (at LFP or waveform extraction) (f9e5fc2)

  • Update requirements.txt (625c630)

  • Update attached_ephys_element.svg (1411687)

  • added svg diagram (7a0762c)

  • Merge pull request #8 from ttngu207/main

ClusteringTask as manual table - Ingestion support for OpenEphys (f76086c)

  • bugfix: Imax per probe type (56f8fdc)

  • code cleanup - renamed data -> timeseries (6d5ee8b)

  • code cleanup, added docstring & comments to code blocks (e64dafe)

  • Update spikeglx.py (238a511)

  • bugfix in waveform extraction (60e320d)

  • added comment (be82f4e)

  • minor code cleanup (8aa11e2)

  • extract and apply bit-volts conversion for spikeglx loader (b5c11f0)

  • apply channels' gain for the data (8ceeb0b)

  • remove used_in_reference in ElectrodeConfig

this is misleading as it's only relevant for SpikeGLX acquisition for denoting channel visualization (847eeba)

  • bugfix in waveform extraction for OpenEphys (281e37b)

  • bugfix in waveform ingestion (3452ab7)

  • code cleanup (3784238)

  • waveform ingestion for OpenEphys (1d02cf5)

  • extract_spike_waveforms() for OpenEphys (2d6f22c)

  • implement "probe" in OpenEphys as a standalone class (045344d)

  • minor bugfix in channel mapping/fetching (631837d)

  • Update spikeglx.py (af2831c)

  • minor naming bugfix (e9d60d7)

  • rename neuropixels -> spikeglx (07982dc)

  • LFP ingestion for OpenEphys (75149b3)

  • EphysRecording's make() handles OpenEphys (f784f12)

  • Update probe.py (628c7f0)

  • update ephys ingestion routine, refactor electrode config generation (2750aa9)

  • openephys loader, using pyopenephys pkg (5540bbe)

  • Update neuropixels.py (eba6b8c)

  • openephys loader, using open_ephys pkg (a2ba6d6)

  • Update LICENSE (e29180f)

  • Update openephys.py (2545772)

  • ClusteringTask as manual table with user specified paramset_idx and clustering_output_dir (6850702)

  • Merge branch 'main' into OpenEphys-support (7d827a1)

  • infer/store ephys-recording directory, based on session_dir (38927c2)

  • Merge branch 'main' of https://github.com/datajoint/elements-ephys into main (8a16bf2)

  • added AcquisitionSoftware (7de2127)

  • minor bugfix: probe.schema.activate -> probe.activate (e278573)

  • Create open_ephys.py (a28c2da)

  • Merge pull request #7 from ttngu207/main

update docstring for function activate (8893fc8)

  • update wording, required_module -> linking_module (071bf35)

  • update docstring for function activate (f11900f)

  • Merge pull request #6 from ttngu207/main

implement new "activation" mechanism -> using dict, module name or module for requirement (ec58e20)

  • simplify "activate" no explicit requirements check (aa4064c)

  • minor format cleanup (822c5b7)

  • implement new "activation" mechanism -> using dict, module name or module as 'requirement' (c9e7f1e)

  • bugfix in paramset_name -> paramset_idx (852f5a4)

  • Merge pull request #5 from ttngu207/main

minor tweak using schema.database, awaiting schema.is_activated (e9191dd)

  • minor tweak using schema.database, awaiting schema.is_activated (d606233)

  • Merge pull request #4 from dimitri-yatsenko/main

ephys.activate inserts required functions into the module namespace (dadda0d)

code cleanup, bug fix, tested (1cc5119)

  • code cleanup, bug fix, tested (11d2aec)

  • Merge pull request #2 from dimitri-yatsenko/main

Refactor to use schema.activate from DataJoint 0.13 (5834b4a)

  • fix imported class names in the ephys module (b822e63)

  • minor cleanup (5edc3ce)

  • update to comply with datajoint 0.13 deferred schema use (a925450)

  • Merge pull request #1 from ttngu207/main

moved from canonical-ephys (d1decf2)