pyvstress 0.0.3

A minimal code to compute vertical stresses in horizontal soil profile.

Rudimentary soil model primarily for vertical stresses under level ground.

Define soil layers, assemble them into soil profile and compute total vertical stresses, pore pressures, and effective vertical stresses at specified locations beneath a level ground. In addition, return requested soil parameters at specified depths. One can use these parameters at specified depths to perform futher analysis. This is a work in progress.

Documentation

pyvstress documentation

References:

• Maxim Millen's eng-tools
• Nico Schlömer and others pygmsh
• Albert Kottke's pysra
• note.nkmk.me

Usage

Sorry for the lack of documentation. I am in the process of learning how to create documentation from python docstrings. I am a slow learner so I do not know when that will be ready. Once that is up, maybe I will include few examples in the documentation. Untill then please refer to the tests and the examples folders.

Requirements

There is a requirements.txt file which was generated using pipreqs. The version number may not be very important. Only Python and Numpy are required for the package:

• python: the latest version, most probably 3.10, but version number may not be too important
• numpy

If you have a .venv virtual environment, pipreqs returns a bunch of packages. In such cases use --ignore .venv.

pipreqs ./ --ignore .venv

Use --force if requirement.txt already exists.

However, these additional packages are required to run the example files and tests with pytest.

• pandas
• matplotlib
• altair
• hancalcs
• pytest

Project folder

pyvstress (Package root directory) ├── build ├── dist ├── docs ├── examples ├── LICENSE.md ├── pyproject.toml ├── pyvstress ├── about.py ├── exceptions.py ├── init.py ├── pycache ├── soil.py └── utility_functions.py ├── pyvstress.egg-info ├── README.md ├── requirements.txt └── tests

Local installation in virtual environment

1. Make a .venv directory in the project folder.
2. Make a virtual environment python -m venv .venv
3. Activate the virtual environment source .venv/bin/activate
4. Install the requirements python -m pip install -r requirements.txt
5. Install the package locally pip install -e .

Above (4) and (5) are run after activating the virtual environment. This will install the package to the virtual environment. Any changes your make to the source code will be reflected in the package.

Build system

Creater a pyproject.toml file. Refer to Setuptools Quickstart Userguide

• Place a pyproject.toml in the root directory of the project. Check the file for this package in the project root directory.

• Install setuptools and build using pip in the virtual environment .venv.

• Run python -m build in the package root directory. This will create .whl and .tar.gz in the /build directory for distribution.

Upload to online repository with twine

• To upload to pypi, twine upload

• To upload to TestPyPi twine upload --repository testpypi dist/*

Installation

I have a version uploaded to pypi pip install pyvstress

If installing packages from TestPyPi then $ pip install --index-url https://test.pypi.org/simple/packagename

Publishing

The documentation is created using the docstrings with Sphinx and published at Read the docs.

1. Install sphinx and sphinx-rtd-theme, in the same environment in which you are building your package. That means you have to be in the virtural environment e.g. source .venv\bin\activate

pip install sphinx
pip install sphinx-rtd-theme

2. Create docs directory in your package directory to hold the documentation files. mkdir docs

3. Run sphinx-quickstart in the docs folder. Provide the information and when asked about creating a separate folder for build type y.

sphinx-quickstart

The docs folder will have

build
source
Makefile
make.bat

Within the source folder there will be two files:

conf.py
index.rst

4. Run the Sphinx API documentation command sphinx-apidoc to generate Sphinx source files.

[user@host docs]$ sphinx-apidoc -o source/ ../pyvstress

5. Edit the conf.py file.

   • a. Change the html_theme to the one of your liking, html_theme = 'sphinx_rtd_theme.
   • b. For autocode generattion from docstrings in the code, specifiy the directory of source code.

   import os
   import sys
   sys.path.insert(0, os.path.abspath('../../pysoil/'))
   

   • c. Also add some extensions

   extensions = ['sphinx.ext.todo', 'sphinx.ext.viewcode', 'sphinx.ext.autodoc']
   

6. Run make htlm, which builds the htlm files in the build/ directory.

7. Log into ReadTheDocs and click on Import Project. Fill out the fields. For the repository URL use https://gitlab.com/geosharma/pyvstress.git. This can be got from CLONE -> Clone with HTPPS URL.

8. Then in Projects -> Admin -> Integration, click on Add Integration and choose GitLab incoming webhook.

9. Then copy the URL starting with readthedocs.org/api/v2/webhook/...../...... and paste it into GitLab Project Settings -> Webhooks References:

• Read the docs
• Sphinx-RTD-Tutorial
• A idiot's guide to Python documentation with Sphinx and ReadTheDocs
• Read the Docs VSC Integration
• Deplyoing a Sphinx project online
• Making Readthedocs for a Python package
• An introduction to Sphinx and Read the Docs for Technical Writers