find / -name coverage* 2>&1 | grep -v "Permission denied"
find . -name "intr*"

find / -type f -exec grep -Hn 'text-to-find-here' {} \;
find . -type f -exec grep -Hn 'text-to-find-here' {} \;
find Bio -type f -exec grep -Hn 'BiopythonDeprecationWarning)' {} \;

PATH="$PATH:/usr/local/MGLTools-1.5.6/MGLToolsPckgs/binaries";export PATH

~/PythonProjects/biopython/Tests$ ../../../.local/bin/coverage run test_UniProt_GOA.py

~/PythonProjects/biopython/Tests$ ../../../.local/bin/coverage report -m

git shortlog --summary --numbered --email -- Bio/Phylo/

# When you need to commit ignoring the plugin checks
git commit --no-verify
git commit -m "Some comments" --no-verify
git commit -m "Apply black style to test_NCBITextParser.py, version 19.10b0." --no-verify

sudo service network-manager restart

/usr/local/bin/black --diff ~/PythonProjects/biopython/Bio | grep reformatted
/usr/local/bin/black --diff ~/PythonProjects/biopython/Tests/ | grep 'reformatted\|@@'

# Turn black code style off
# fmt: off

# This comment stops black style adding a blank line here, which causes flake8 D202.

# fmt: on

self.assertRaises(ValueError, p.__add__, p1)

~/PythonProjects/biopython$ python3 -m flake8 --version
python3 -m flake8 PythonProjects/biopython/Tests

pip install Django --upgrade
pip show <module-name>
pip install --force-reinstall MySQL_python==1.2.4

###
### Testing and installing
###

$python3 run_tests.py test_SeqIO.py test_AlignIO.py
$python3 run_tests.py --offline
# Run Doctest within Tests directory
python run_tests.py test_Tutorial.py
python3 run_tests.py doctest

# Maybe worth deleting the previous build directory
# rm -R ~/PythonProjects/biopython/build
# And remove all *.pyc files
# find . -name "*.pyc" -exec rm -rf {} \;
python3 setup.py build
python3 setup.py test
sudo python3 setup.py install

## Install/remove with pip
# Installing Biopython
pip3 install biopython
pip3 install --upgrade biopython
pip3 uninstall biopython

## within Python3, out of the source code, check where Bio defaults to
import sys; print(sys.version)
import platform; print(platform.python_implementation()); print(platform.platform())
import Bio; print(Bio.__version__)

Index of ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/

ISC002 implicitly concatenated string
A502 prefer assertIsNone() instead of comparing to None