Revise dependencies #822
Revise dependencies #822
Conversation
Across `pyproject.toml` and both `environment.yml`: - Alphabetical sort to allow for easier comparison across toml/yaml files. - Remove dependencies required by other dependencies to reduce build time. - Move `black` to `test` dependencies. Could be `dev` instead? - Move `click` to `test` dependencies. CLI should be its own package. - Add ruff config to `pyproject.toml`. Flake8 replacement to allow removal of `setup.cfg`. - Remove `tqdm`, as it is required by `datajoint` Standard environment: - Add comments for all dependencies specific to position environment to allow for easier comparison across yaml files. - Remove `dask`, as it is required by `ghostipy` - Remove `hdmf`, as it is required by `pynwb` - Remove `pymysql`, as it is required by `datajoint` - Remove `pyyaml`, as it is required by `sortingview` - Remove `pydotplus` from `pip` section, as it is already in `conda` section Position environment: - Rename `_position` or `-position` to `_dlc` or `-dlc` to be more precise. - Remove `ipython`, `numba`, and `tensorflow`, as they are all required by `deeplabcut` - Add items present in standard environment but not in position environment.
|
Have you been able to run any of the notebooks with the current environment (via pip or via conda) |
- `trajectory_analysis_tools` and `replay_trajectory_classification` are superceded by `non_local_detector`. - `dask-cuda` not in use, per @edeno
Unfortunately, it looks like importing |
|
Check out this pull request on See visual diffs & provide feedback on Jupyter Notebooks. Powered by ReviewNB |
|
I've reported the underlying panel issue causing the |
| @@ -21,7 +21,7 @@ class LinearizedPositionV0(SpyglassMixin, dj.Part): # noqa: F811 | |||
| definition = """ | |||
| -> LinearizedPositionOutput | |||
| --- | |||
| -> IntervalLinearizedPosition | |||
There was a problem hiding this comment.
This doesn't change anything from datajoint's perspective right?
There was a problem hiding this comment.
@edeno No, DataJoint looks to the locals() namespace and takes the full_table_name attr of the object, which is not impacted by python-level reassignment
Description
Across
pyproject.tomland bothenvironment.yml:clicktotestdependencies. CLI should be its own package.pyproject.toml. Flake8 replacement to allow removal ofsetup.cfg.tqdm, as it is required bydatajointpanelversion causing import error forghostipyStandard environment:
dask, as it is required byghostipyhdmf, as it is required bypynwbpymysql, as it is required bydatajointpyyaml, as it is required bysortingviewpydotplusfrompipsection, as it is already incondasectionPosition environment:
_positionor-positionto_dlcor-dlcto be more precise.ipython,numba, andtensorflow, as they are all required bydeeplabcutPyPi install check #581 :
pip install .[test]; pytestin a clean conda env runs successfully afterpyproject.tomledits. Is this sufficient to address the issue?Added various fixes to facilitate auto-running the notebooks from a dev environment.
#810 - Add drafted
decompose_namefrom issueChecklist:
CITATION.cff: pending discussionCHANGELOG.md