Literal Enum
# #| hide
# from narr.strs import snake_case
# from narr.axes import NamedAxis, NamedAxes
# from narr.errs import NamedArrayDimsError
# from narr.mixs import NamedArrayDynamicAttrsMixin
# from narr.narr import NamedArray
FeatureTrajectories,
# CellularTrajectories, ExpressionTrajectories,
``` sh
# create conda environment
$ mamba env create -f env.yml
# update conda environment
$ mamba env update -n narr --file env.yml
pip install -e .
# install from pypi
pip install narr
# activate conda environment
$ conda activate narr
# make sure the narr package is installed in development mode
$ pip install -e .
# make changes under nbs/ directory
# ...
# compile to have changes apply to the narr package
$ nbdev_prepare
# publish to pypi
$ nbdev_pypi
# publish to conda
$ nbdev_conda --build_args '-c conda-forge'
$ nbdev_conda --mambabuild --build_args '-c conda-forge -c dsm-72'
Install latest from the GitHub repository:
$ pip install git+https://github.com/dsm-72/narr.git
or from conda
$ conda install -c dsm-72 narr
or from pypi
$ pip install narr
Documentation can be found hosted on GitHub repository pages. Additionally you can find package manager specific guidelines on conda and pypi respectively.
# import numpy as np
# from typing import Callable
# class Trajectories(NamedArray):
# DIMS = NamedAxes([NamedAxis(dim.name, i) for i, dim in enumerate(TrajectoryDim)])
# def to_obsv_x_traj(self, aggr: Callable = np.mean):
# agg_arr = aggr(np.asarray(self.transpose(
# )), axis=2)
# return ObservationTrajectories(agg_arr)
# def to_feat_x_traj(self, aggr: Callable = np.mean):
# agg_arr = aggr(np.asarray(self.transpose(
# TrajectoryDim.feat.name, TrajectoryDim.traj.name, TrajectoryDim.obsv.name,
# )), axis=2)
# return FeatureTrajectories(agg_arr)
# arr = np.random.randint(0, 10, (3, 5, 10))
[0, 3, 8, 7, 2, 9, 9, 9, 1, 7],
[0, 8, 5, 3, 3, 8, 8, 1, 3, 8],
[3, 6, 9, 1, 8, 7, 7, 3, 1, 3],
[0, 0, 2, 9, 1, 6, 6, 8, 1, 7]],
[[5, 9, 5, 7, 3, 2, 1, 0, 9, 5],
[9, 8, 7, 3, 1, 7, 6, 6, 0, 5],
[8, 2, 9, 7, 2, 9, 4, 4, 0, 8],
[2, 8, 2, 2, 0, 6, 6, 8, 6, 9],
[5, 5, 2, 2, 3, 5, 9, 9, 3, 4]],
[[3, 6, 4, 6, 3, 2, 4, 6, 9, 0],
[7, 1, 6, 7, 7, 2, 6, 2, 2, 8],
[2, 3, 6, 2, 5, 5, 2, 6, 2, 0],
[3, 9, 8, 5, 1, 5, 7, 8, 7, 9],
[9, 2, 1, 5, 2, 7, 0, 7, 4, 3]]])
``` python
# Trajectories(arr)
Trajectories([[[9, 7, 1, 4, 8, 2, 3, 3, 3, 1],
[0, 3, 8, 7, 2, 9, 9, 9, 1, 7],
[0, 8, 5, 3, 3, 8, 8, 1, 3, 8],
[3, 6, 9, 1, 8, 7, 7, 3, 1, 3],
[0, 0, 2, 9, 1, 6, 6, 8, 1, 7]],
[[5, 9, 5, 7, 3, 2, 1, 0, 9, 5],
[9, 8, 7, 3, 1, 7, 6, 6, 0, 5],
[8, 2, 9, 7, 2, 9, 4, 4, 0, 8],
[2, 8, 2, 2, 0, 6, 6, 8, 6, 9],
[5, 5, 2, 2, 3, 5, 9, 9, 3, 4]],
[[3, 6, 4, 6, 3, 2, 4, 6, 9, 0],
[7, 1, 6, 7, 7, 2, 6, 2, 2, 8],
[2, 3, 6, 2, 5, 5, 2, 6, 2, 0],
[3, 9, 8, 5, 1, 5, 7, 8, 7, 9],
[9, 2, 1, 5, 2, 7, 0, 7, 4, 3]]])
(3 traj, 5 obsv, 10 feat)
# Trajectories(arr).transpose(1, 0, 2)
Trajectories([[[9, 7, 1, 4, 8, 2, 3, 3, 3, 1],
[5, 9, 5, 7, 3, 2, 1, 0, 9, 5],
[3, 6, 4, 6, 3, 2, 4, 6, 9, 0]],
[[0, 3, 8, 7, 2, 9, 9, 9, 1, 7],
[9, 8, 7, 3, 1, 7, 6, 6, 0, 5],
[7, 1, 6, 7, 7, 2, 6, 2, 2, 8]],
[[0, 8, 5, 3, 3, 8, 8, 1, 3, 8],
[8, 2, 9, 7, 2, 9, 4, 4, 0, 8],
[2, 3, 6, 2, 5, 5, 2, 6, 2, 0]],
[[3, 6, 9, 1, 8, 7, 7, 3, 1, 3],
[2, 8, 2, 2, 0, 6, 6, 8, 6, 9],
[3, 9, 8, 5, 1, 5, 7, 8, 7, 9]],
[[0, 0, 2, 9, 1, 6, 6, 8, 1, 7],
[5, 5, 2, 2, 3, 5, 9, 9, 3, 4],
[9, 2, 1, 5, 2, 7, 0, 7, 4, 3]]])
(5 obsv, 3 traj, 10 feat)
# Trajectories(arr).transpose('obsv', 0, 2)
Trajectories([[[9, 7, 1, 4, 8, 2, 3, 3, 3, 1],
[5, 9, 5, 7, 3, 2, 1, 0, 9, 5],
[3, 6, 4, 6, 3, 2, 4, 6, 9, 0]],
[[0, 3, 8, 7, 2, 9, 9, 9, 1, 7],
[9, 8, 7, 3, 1, 7, 6, 6, 0, 5],
[7, 1, 6, 7, 7, 2, 6, 2, 2, 8]],
[[0, 8, 5, 3, 3, 8, 8, 1, 3, 8],
[8, 2, 9, 7, 2, 9, 4, 4, 0, 8],
[2, 3, 6, 2, 5, 5, 2, 6, 2, 0]],
[[3, 6, 9, 1, 8, 7, 7, 3, 1, 3],
[2, 8, 2, 2, 0, 6, 6, 8, 6, 9],
[3, 9, 8, 5, 1, 5, 7, 8, 7, 9]],
[[0, 0, 2, 9, 1, 6, 6, 8, 1, 7],
[5, 5, 2, 2, 3, 5, 9, 9, 3, 4],
[9, 2, 1, 5, 2, 7, 0, 7, 4, 3]]])
(5 obsv, 3 traj, 10 feat)
# Trajectories(arr).transpose('obsv', 0, 2).to_obsv_x_traj()
NameError: name 'aggr' is not defined