import sys
import subprocess
from rich import printReproduce me!
The code base for this repository is available at https://github.com/BiocPy/tutorial.
This book is automatically built to identify issues caused by changes in the dependencies. We use quarto for reproducing the scripts provided in this book.
Pre-requisites
Python
Lets make sure we have all packages we need for this section
sys.version_infosys.version_info(major=3, minor=9, micro=18, releaselevel='final', serial=0)Packages
import math
import biocframe
import biocutils
import genomicranges
import summarizedexperiment
import singlecellexperiment
import multiassayexperiment
import rds2py
import session_info
session_info.show()Click to view session information
----- biocframe 0.5.9 biocutils 0.1.5 genomicranges 0.4.12 multiassayexperiment 0.4.2 rds2py 0.4.2 rich NA session_info 1.0.0 singlecellexperiment 0.4.4 summarizedexperiment 0.4.3 -----
Click to view modules imported as dependencies
PIL 10.2.0 anyio NA arrow 1.3.0 asttokens NA attr 23.2.0 attrs 23.2.0 babel 2.14.0 certifi 2024.02.02 cffi 1.16.0 charset_normalizer 3.3.2 comm 0.2.2 cycler 0.12.1 cython_runtime NA dateutil 2.9.0.post0 debugpy 1.8.1 decorator 5.1.1 defusedxml 0.7.1 exceptiongroup 1.2.0 executing 2.0.1 fastjsonschema NA fqdn NA idna 3.6 importlib_metadata NA importlib_resources NA ipykernel 6.29.3 iranges 0.2.3 isoduration NA jedi 0.19.1 jinja2 3.1.3 json5 0.9.22 jsonpointer 2.4 jsonschema 4.21.1 jsonschema_specifications NA jupyter_events 0.9.1 jupyter_server 2.13.0 jupyterlab_server 2.25.4 kiwisolver 1.4.5 markupsafe 2.1.5 matplotlib 3.8.3 matplotlib_inline 0.1.6 mpl_toolkits NA nbformat 5.10.3 numpy 1.26.4 overrides NA packaging 24.0 pandas 2.2.1 parso 0.8.3 pexpect 4.9.0 platformdirs 4.2.0 prometheus_client NA prompt_toolkit 3.0.43 psutil 5.9.8 ptyprocess 0.7.0 pure_eval 0.2.2 pydev_ipython NA pydevconsole NA pydevd 2.9.5 pydevd_file_utils NA pydevd_plugins NA pydevd_tracing NA pygments 2.17.2 pyparsing 3.1.2 pythonjsonlogger NA pytz 2024.1 referencing NA requests 2.31.0 rfc3339_validator 0.1.4 rfc3986_validator 0.1.1 rpds NA scipy 1.12.0 send2trash NA six 1.16.0 sniffio 1.3.1 stack_data 0.6.3 tornado 6.4 traitlets 5.14.2 typing_extensions NA uri_template NA urllib3 2.2.1 wcwidth 0.2.13 webcolors 1.13 websocket 1.7.0 yaml 6.0.1 zipp NA zmq 25.1.2 zoneinfo NA
----- IPython 8.18.1 jupyter_client 8.6.1 jupyter_core 5.7.2 jupyterlab 4.1.5 notebook 7.1.2 ----- Python 3.9.18 (main, Aug 28 2023, 08:38:32) [GCC 11.4.0] Linux-6.5.0-1016-azure-x86_64-with-glibc2.35 ----- Session information updated at 2024-03-15 22:54