Add option for auto-yes, list/describe exp version in CLI and fast entry point
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Fixes #102 (closed) : Add
-y/--yes
option when converting for auto-yes -
Fixes #88 (closed) : Move the
import
inside for faster CLI entry point, especially for helper commands -
Fixes #137 (closed) : Pandas warning
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Adds
-l
option for listing experiment versions -
Adds
-E
option for describing a given experiment version (as toml output)Click to expand on help tag
$ time calimag --help Usage: calimag [OPTIONS] [CONFIGFILE] Options: -y, --yes Accept all actions to follow as "y" -l, --list-versions List acceptable "EXPERIMENT_VERSION" in the config file -E, --describe-version [v2021.05:2p_imaging_head_fixed+Simon|v2019.07:2p_imaging_head_fixed+Max|v2021.04:2p_imaging_head_fixed+Max:spontaneous-activity|v2022.05:2p_imaging_head_fixed+Max|v2020.06:2p_imaging_head_fixed+Simon] Describe a given "EXPERIMENT_VERSION" --help Show this message and exit. real 0m0.109s user 0m0.092s sys 0m0.018s
Click to expand on list/describe options
$ time calimag -l Currently these are the acceptable experiment versions: v2021.05:2p_imaging_head_fixed+Simon v2019.07:2p_imaging_head_fixed+Max v2021.04:2p_imaging_head_fixed+Max:spontaneous-activity v2022.05:2p_imaging_head_fixed+Max v2020.06:2p_imaging_head_fixed+Simon For specific experiment version, use `-E`. For example: calimag -E v2021.05:2p_imaging_head_fixed+Simon calimag -E v2019.07:2p_imaging_head_fixed+Max real 0m0.140s user 0m0.105s sys 0m0.035s $ time calimag -E v2019.07:2p_imaging_head_fixed+Max Calimag version 1.5.1.dev54+g1095c4e.d20240130 The teensy config for v2019.07:2p_imaging_head_fixed+Max is [time] unit = "ms" SI_unit = "sec" conversion_factor = 1 [odor] unit = "-" SI_unit = "-" conversion_factor = 1 description = "Odor stimulus ID (raw)." comments = "This may not indicate when the stimulus is ON for each trial. This may not indicate the actual chemical names of the stimulus. Additional information may be needed to infer either." [flow] unit = "cm3/min" SI_unit = "m3/sec" conversion_factor = 5.9999999999999995e-5 description = "Air flow signal from sensor to measure respiration." [wheel] unit = "-" SI_unit = "-" conversion_factor = 1 description = "Raw wheel position from micro-controller." comments = "Any value greater than `WHEEL_MAX_ENCODING=4096` was turned into NaN values. Because this is from Teensy, there is no unit. To get wheel position in `radian` or speed in `meter/second`, additional information may be needed. However, for the former, for simplicity, one may cautiously consider `WHEEL_MAX_ENCODING` as `2 * pi`" [trial] unit = "-" SI_unit = "-" conversion_factor = 1 real 0m0.146s user 0m0.106s sys 0m0.054s
Edited by Tuan Pham