Following is the recommended configuration for a development environment.
cd ~/sibl
/usr/local/bin/python3.9 -m pip install --upgrade pip setuptools wheel
# create a virtual environment
# VS Code docs reference:
# https://code.visualstudio.com/docs/python/environments#_create-a-virtual-environment
/usr/local/bin/python3.9 -m venv .venv # create a virtual environment
# activate the venv with one of the following:
source .venv/bin/activate # for bash shell
source .venv/bin/activate.csh # for c shell
source .venv/bin/activate.fish # for fish shell
.\.venv\Scripts\activate # for powershell
python --version # e.g., Python 3.9.7
pip list
Package Version
---------- -------
pip 21.2.1
setuptools 57.4.0
WARNING: You are using pip version 21.2.3; however, version 22.3.1 is available.
You should consider upgrading via the '~/sibl/.venv/bin/python3.9 -m pip install --upgrade pip' command.
(.venv) ~/sibl>
python -m pip install --upgrade pip
Reference: https://packaging.python.org/en/latest/tutorials/packaging-projects/
packaging_tutorial/
├── LICENSE
├── pyproject.toml
├── README.md
├── src/
│ └── your_package_name_here/
│ ├── __init__.py
│ └── example.py
└── tests/
Create a pyproject.toml, e.g., example .toml reference: https://peps.python.org/pep-0621/#example and general setuptools documentation: https://setuptools.pypa.io/en/latest/index.html
Installing from a local source tree, reference:
# create an editable install (aka development mode)
(.venv) ~/sibl>
python -m pip install -e geo/.[dev] # developer
python -m pip install geo/. # client
# note: `-e .` = `--editable .`
python -m pip install -e geo/src/bind/
python -m pip install -e cli/
Post-install package status:
(.venv) ~/sibl>
pip list
Package Version Editable project location
------------------ ------- -------------------------
anyio 3.6.2
appnope 0.1.3
argon2-cffi 21.3.0
argon2-cffi-bindings 21.2.0
arrow 1.2.3
asttokens 2.2.1
attrs 22.2.0
backcall 0.2.0
beautifulsoup4 4.11.1
black 22.3.0
bleach 6.0.0
cffi 1.15.1
click 8.1.3
comm 0.1.2
contourpy 1.0.7
copyright 0.0.1
coverage 7.1.0
cycler 0.11.0
debugpy 1.6.6
decorator 5.1.1
defusedxml 0.7.1
exceptiongroup 1.1.0
executing 1.2.0
fastjsonschema 2.16.2
flake8 6.0.0
fonttools 4.38.0
fqdn 1.5.1
idna 3.4
imageio 2.25.0
importlib-metadata 6.0.0
iniconfig 2.0.0
ipykernel 6.20.2
ipython 8.8.0
ipython-genutils 0.2.0
isoduration 20.11.0
jedi 0.18.2
Jinja2 3.1.2
jsonpointer 2.3
jsonschema 4.17.3
jupyter_client 8.0.0
jupyter_core 5.1.5
jupyter-events 0.6.3
jupyter_server 2.1.0
jupyter_server_terminals 0.4.4
jupyterlab-pygments 0.2.2
kiwisolver 1.4.4
MarkupSafe 2.1.2
matplotlib 3.6.3
matplotlib-inline 0.1.6
mccabe 0.7.0
mistune 2.0.4
mypy 0.991
mypy-extensions 0.4.3
nbclassic 0.5.0
nbclient 0.7.2
nbconvert 7.2.9
nbformat 5.7.3
nest-asyncio 1.5.6
networkx 3.0
notebook 6.5.2
notebook_shim 0.2.2
numpy 1.24.1
packaging 23.0
pandas 1.5.3
pandocfilters 1.5.0
parso 0.8.3
pathspec 0.11.0
pexpect 4.8.0
pickleshare 0.7.5
Pillow 9.4.0
pip 22.3.1
platformdirs 2.6.2
pluggy 1.0.0
prometheus-client 0.16.0
prompt-toolkit 3.0.36
psutil 5.9.4
ptg 0.0.11 /Users/chovey/sibl/geo
ptyprocess 0.7.0
pure-eval 0.2.2
pybind11 2.10.3
pycodestyle 2.10.0
pycparser 2.21
pyflakes 3.0.1
Pygments 2.14.0
pyparsing 3.0.9
pyrsistent 0.19.3
pytest 7.2.1
pytest-cov 4.0.0
python-dateutil 2.8.2
python-json-logger 2.0.4
pytz 2022.7.1
PyWavelets 1.4.1
PyYAML 6.0
pyzmq 25.0.0
rfc3339-validator 0.1.4
rfc3986-validator 0.1.1
scikit-image 0.19.3
scipy 1.10.0
seaborn 0.12.2
Send2Trash 1.8.0
setuptools 57.4.0
sibl 0.0.10
six 1.16.0
sniffio 1.3.0
soupsieve 2.3.2.post1
stack-data 0.6.2
terminado 0.17.1
tifffile 2023.1.23.1
tinycss2 1.2.1
tomli 2.0.1
tornado 6.2
traitlets 5.8.1
typing_extensions 4.4.0
uri-template 1.2.0
wcwidth 0.2.6
webcolors 1.12
webencodings 0.5.1
websocket-client 1.5.0
xybind 0.0.8 /Users/chovey/sibl/geo/src/bind
xyfigure 0.0.9 /Users/chovey/sibl/cli/src
zipp 3.11.0
Deactivate/Reactivate method: To deactivate any current venv:
deactivate
Deactivate/Reactivate method: To activate the .venv virtual environment:
# activate the venv with one of the following:
source .venv/bin/activate # for bash shell
source .venv/bin/activate.csh # for c shell
source .venv/bin/activate.fish # for fish shell
source .venv/bin/Activate.fish # for powershell
Run from the REPL:
(.venv) python
Python 3.9.7 (v3.9.7:1016ef3790, Aug 30 2021, 16:39:15)
[Clang 6.0 (clang-600.0.57)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> from copyright import command_line as cl
>>> cl.version()
copyright version:
'0.0.1'
>>> quit()
Run from the command line:
(.venv) commands
---------
copyright
---------
This is the command line interface help for Sandia National Laboratories copyright Python module.
Available commands:
commands (this command)
scinfo Describes the installation details.
version Prints the semantic verison of the current installation.
Run the tests with pytest:
(.venv) ~/sibl> pytest -v
(.venv) ~/sibl> pytest geo/ -v # test only the ptg module
And pytest-cov (coverage) with line numbers missing coverage:
(.venv) ~/sibl> pytest --cov=geo --cov-report term-missing
Success! The venv virtual environment .venv has been created,
and the atmesh module is now installed and tested.
# develop code
# uninstall the now-outdated developer installation
pip uninstall ptg
# reinstall the module with the newly developed code
# see original installation instructions above
In the user settings.json, add a reference to the Cubit install location.
Reference: Enable IntelliSense for custom package locations, https://code.visualstudio.com/docs/python/editing#_enable-intellisense-for-custom-package-locations
Before:
"python.autoComplete.extraPaths": [
"~/python_modules"
],
After:
"python.autoComplete.extraPaths": [
"~/python_modules",
"/Applications/Cubit-16.08/Cubit.app/Contents/MacOS"
],
"python.envFile": "${workspaceFolder}/.venv",
Any push to the main branch that contains at least one file with a .py extension will trigger CI. The CI tests against the Black code formatter, against flake8, and assesses code coverage.
The .github/workflows/release.yml automates the build of a release when a git push is specified with a version flag, such as v1.0, v20.15.10 and Git Tag.