git clone git@github.com:nixonlab/stellarscope.git stellarscope_dev.git
An environment file is included in this repo.
mamba env create -n stellarscope_dev -f stellarscope_dev.git/environment.yml
conda activate stellarscope_dev
If not using the main branch, check out the correct version
cd stellarscope_dev.git
git pull #just in case anything changed
git checkout main
# here is how you would check out a specific tag:
# git checkout tags/1.3 -b v1.3
Install stellarscope
in interactive mode (-e
) so that changes to the
code are reflected immediately without reinstalling.
# change to repo directory if not already there
# cd stellarscope_dev.git
pip install -e .
Memory profiling and plotting require memory_profiler
and matplotlib
mamba install memory_profiler
mamba install matplotlib
Memory profiling can be run like this:
mprof run stellarscope assign ...<stellarscope args>...
mprof plot
Each subcommand is defined in a top-level module named as
[basecommand]_[subcommand].py
. The module will contain a subclass of
utils.SubcommandOptions
that will
--debug |
Print verbose debug messages |
--devmode |
Run in development mode. Outputs noisy debugging messages and writes intermediate data structures to file. |
--reassign_mode |
Supports multiple comma-separated values for reassignment mode. The first reassignment mode will be written to TE_counts.mtx while the other reassignment modes will be written to TE_counts.{mode}.mtx |