pyStrata 0.5.0__tar.gz → 0.5.4__tar.gz

pystrata-0.5.4/.gitignore

@@ -0,0 +1,187 @@
+
+# Created by https://www.gitignore.io/api/pycharm,python,linux,windows
+
+# Covers JetBrains IDEs: IntelliJ, RubyMine, PhpStorm, AppCode, PyCharm, CLion, Android Studio and Webstorm
+# Reference: https://intellij-support.jetbrains.com/hc/en-us/articles/206544839
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+.idea/**/dynamic.xml
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+
+# Gradle:
+.idea/**/gradle.xml
+.idea/**/libraries
+
+# CMake
+cmake-build-debug/
+
+# Mongo Explorer plugin:
+.idea/**/mongoSettings.xml
+
+## File-based project format:
+*.iws
+
+## Plugin-specific files:
+
+# IntelliJ
+out/
+
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+.idea_modules/
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+.idea/replstate.xml
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+### Python ###
+# Byte-compiled / optimized / DLL files
+__pycache__/
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+*$py.class
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+# C extensions
+*.so
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+.Python
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+.installed.cfg
+*.egg
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
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+# Unit test / coverage reports
+htmlcov/
+.tox/
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+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*,cover
+.hypothesis/
+.pytest_cache
+
+# Translations
+*.mo
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+# Django stuff:
+*.log
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+
+# Flask stuff:
+instance/
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+docs/_build/
+docs/generated/
+
+# PyBuilder
+target/
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+# IPython Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
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+# dotenv
+.env
+
+# virtualenv
+venv/
+ENV/
+
+# Spyder project settings
+.spyderproject
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+# Rope project settings
+.ropeproject
+
+
+### Linux ###
+*~
+
+# temporary files which can be created if a process still has a handle open of a deleted file
+.fuse_hidden*
+
+# KDE directory preferences
+.directory
+
+# Linux trash folder which might appear on any partition or disk
+.Trash-*
+
+
+### Windows ###
+# Windows image file caches
+Thumbs.db
+ehthumbs.db
+
+# Folder config file
+Desktop.ini
+
+# Recycle Bin used on file shares
+$RECYCLE.BIN/
+
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+scratch.*

pystrata-0.5.4/AUTHORS.md

@@ -0,0 +1,9 @@
+# Authors
+
+## Development Lead
+
+- Albert Kottke \<<albert.kottke@gmail.com>\>
+
+## Contributors
+
+- Maxim Millen

pystrata-0.5.4/CONTRIBUTING.md

@@ -0,0 +1,105 @@
+# Contributing
+
+Contributions are welcome, and they are greatly appreciated! Every
+little bit helps, and credit will always be given.
+
+You can contribute in many ways:
+
+## Types of Contributions
+
+### Report Bugs
+
+Report bugs at <https://github.com/arkottke/pystrata/issues>.
+
+If you are reporting a bug, please include:
+
+-   Your operating system name and version.
+-   Any details about your local setup that might be helpful in
+    troubleshooting.
+-   Detailed steps to reproduce the bug.
+
+### Fix Bugs
+
+Look through the GitHub issues for bugs. Anything tagged with "bug" is
+open to whoever wants to implement it.
+
+### Implement Features
+
+Look through the GitHub issues for features. Anything tagged with
+"feature" is open to whoever wants to implement it.
+
+### Write Documentation
+
+pyStrata could always use more documentation, whether as part of the
+official pyStrata docs, in docstrings, or even on the web in blog posts,
+articles, and such.
+
+### Submit Feedback
+
+The best way to send feedback is to file an issue at
+<https://github.com/arkottke/pystrata/issues>.
+
+If you are proposing a feature:
+
+-   Explain in detail how it would work.
+-   Keep the scope as narrow as possible, to make it easier to
+    implement.
+-   Remember that this is a volunteer-driven project, and that
+    contributions are welcome :)
+
+## Get Started!
+
+Ready to contribute? Here's how to set up pyStrata for
+local development.
+
+1.  Fork the pyStrata repo on [GitHub](https://github.com/arkottke/pystrata)
+
+2.  Clone your fork locally:
+
+        $ git clone git@github.com:your_name_here/pystrata.git
+
+3.  Install your local copy into a virtualenv. Assuming you have
+    virtualenvwrapper installed, this is how you set up your fork for
+    local development:
+
+        $ mkvirtualenv pystrata
+        $ cd pystrata/
+        $ python setup.py develop
+
+4.  Create a branch for local development:
+
+        $ git checkout -b name-of-your-bugfix-or-feature
+
+    Now you can make your changes locally.
+
+5.  When you're done making changes, check that your changes pass
+    flake8 and the tests:
+
+        $ pytest
+
+6.  Commit your changes and push your branch to GitHub:
+
+        $ git add .
+        $ git commit -m "Your detailed description of your changes."
+        $ git push origin name-of-your-bugfix-or-feature
+
+7.  Submit a pull request through the GitHub website.
+
+## Pull Request Guidelines
+
+Before you submit a pull request, check that it meets these guidelines:
+
+1.  The pull request should include tests.
+2.  If the pull request adds functionality, the docs should be updated.
+    Put your new functionality into a function with a docstring, and add
+    the feature to the list in README.md.
+3.  The pull request should work for Python 3.7, 3.8, 3.9, and 3.10
+    and for PyPy. Check
+    <https://travis-ci.org/arkottke/pystrata/pull_requests> and make
+    sure that the tests pass for all supported Python versions.
+
+## Tips
+
+To run a subset of tests:
+
+    $ pytest tests/site_test.py

pystrata-0.5.4/HISTORY.md

@@ -0,0 +1,92 @@
+# History
+
+## v0.5.4 (2024-03-29)
+
+-   Fix: error in example-08 that didn't reference the modified profiles.
+-   Change: method to create SoilTypes from published curves
+-   Add: Extended example-15 to show how to use published curves in site response models.
+
+## v0.5.3 (2024-03-29)
+
+-   Added published curves
+
+## v0.5.2 (2023-01-18)
+
+-   Fixed: Providing unsmoothed transfer function output
+-   Fixed #18: MenqSoilType
+
+## v0.5.1 (2022-09-22)
+
+-   Fixed: Correlation model from Toro. Previously used rho_0 instead of
+    d_0, and the wrong depth
+-   Renamed: BedrockDepthVariation to HalfSpaceDepthVariation
+-   Fixed: HalfSpaceDepthVariation was removing the last layer
+
+## v0.5.0 (2022-06-14)
+
+-   Renamed to pyStrata
+
+## v0.4.11 (2020-03-31)
+
+-   Added: Depth dependent velocity variation model
+-   Added: Output plotting functionality
+-   Added: Ability to exclude soil type variation from bedrock
+
+## v0.4.10 (2020-03-27)
+
+-   Fixed: Error in SPID variation of G/Gmax
+-   Added: Scaling during read of SMC and AT2 input motions
+
+## v0.4.9 (2020-03-09)
+
+-   Add InitialVelProfile and CompatVelProfile outputs
+
+## v0.4.8 (2019-12-11)
+
+-   Remove Cython and cyko as dependencies
+-   Added a numba based Konno-Ohmachi smoothing
+
+## v0.4.6 (2019-11-12)
+
+-   FIXED #11: Dependencies missing on install.
+
+## v0.4.5 (2019-10-24)
+
+-   FIXED #9: Wrong stress for some Menq components.
+
+## v0.4.4 (2019-05-22)
+
+-   Incremented version because of issue with automated builds.
+
+## v0.4.3 (2019-05-22)
+
+-   FIXED: Bug in MANIFEST.in
+
+## v0.4.2 (2019-05-22)
+
+-   Incremented version because of issue with automated builds.
+
+## v0.4.1 (2019-05-22)
+
+-   Fixed strain profile to use `max_strain`.
+-   Changed README and HISTORY to markdown.
+
+## v0.4.0 (2019-03-11)
+
+-   Added smoothed FourierAmplitudeSpectrum output.
+
+## v0.3.2 (2018-12-02)
+
+-   Fixed building of docs.
+-   Removed stickler.
+-   Version double increment due to pypi naming conflict.
+
+## v0.3.0 (2018-11-30)
+
+-   Converted all damping to decimal.
+-   Added tests for KishidaSoilType.
+-   Added tests against Deepsoil.
+
+## v0.0.1 (2016-04-30)
+
+-   First release on PyPI.

{pyStrata-0.5.0 → pystrata-0.5.4}/MANIFEST.in

@@ -2,3 +2,5 @@ include LICENSE
 include HISTORY.rst
 include README.rst
 include requirements.txt
+
+include src/pystrata/data/*

pystrata-0.5.4/Makefile

@@ -0,0 +1,80 @@
+.PHONY: clean-pyc clean-build docs clean examples
+define BROWSER_PYSCRIPT
+import os, webbrowser, sys
+try:
+	from urllib import pathname2url
+except:
+	from urllib.request import pathname2url
+
+webbrowser.open("file://" + pathname2url(os.path.abspath(sys.argv[1])))
+endef
+export BROWSER_PYSCRIPT
+BROWSER := python -c "$$BROWSER_PYSCRIPT"
+
+help:
+	@echo "clean - remove all build, test, coverage and Python artifacts"
+	@echo "clean-build - remove build artifacts"
+	@echo "clean-pyc - remove Python file artifacts"
+	@echo "clean-test - remove test and coverage artifacts"
+	@echo "test - run tests quickly with the default Python"
+	@echo "examples - run all examples"
+	@echo "coverage - check code coverage quickly with the default Python"
+	@echo "docs - generate Sphinx HTML documentation, including API docs"
+	@echo "release - package and upload a release"
+	@echo "dist - package"
+	@echo "install - install the package to the active Python's site-packages"
+
+clean: clean-build clean-pyc clean-test
+
+clean-build:
+	rm -fr build/
+	rm -fr dist/
+	rm -fr .eggs/
+	find . -name '*.egg-info' -exec rm -fr {} +
+	find . -name '*.egg' -exec rm -f {} +
+
+clean-pyc:
+	find . -name '*.pyc' -exec rm -f {} +
+	find . -name '*.pyo' -exec rm -f {} +
+	find . -name '*~' -exec rm -f {} +
+	find . -name '__pycache__' -exec rm -fr {} +
+
+clean-test:
+	rm -f .coverage
+	rm -fr htmlcov/
+	rm -fr .pytest_cache
+	rm -fr .cache
+
+test:
+	pip install -e .
+	pytest --cov-report html --cov=pystrata tests/
+
+examples:
+	find examples -name 'example*.py' -exec python {} \;
+
+coverage: test
+	coverage report -m
+	coverage html
+	$(BROWSER) htmlcov/index.html
+
+docs:
+	rm -f docs/pystrata.rst
+	rm -f docs/modules.rst
+	$(MAKE) -C docs clean
+	$(MAKE) -C docs html
+	$(BROWSER) docs/_build/html/index.html
+
+servedocs: docs
+	sphinx-autobuild docs docs/_build/html
+
+test-release: clean
+	python -m build
+	python -m twine check dist/*
+	python -m twine upload --repository testpypi dist/*
+
+release: clean
+	python -m build
+	python -m twine upload dist/*
+
+install: clean
+	python setup.py install

pystrata-0.5.4/PKG-INFO

@@ -0,0 +1,112 @@
+Metadata-Version: 2.3
+Name: pyStrata
+Version: 0.5.4
+Summary: Site response analysis with Python.
+Project-URL: Homepage, https://github.com/arkottke/pystrata
+Project-URL: Documentation, https://pystrata.readthedocs.io
+Author-email: Albert Kottke <albert.kottke@gmail.com>
+License-Expression: MIT
+License-File: AUTHORS.md
+License-File: LICENSE
+Requires-Python: >=3.8
+Requires-Dist: matplotlib
+Requires-Dist: numba
+Requires-Dist: numpy
+Requires-Dist: pykooh
+Requires-Dist: pyrvt
+Requires-Dist: scipy
+Requires-Dist: setuptools
+Requires-Dist: tomli
+Description-Content-Type: text/markdown
+
+# pyStrata
+
+Python library for site response analysis.
+
+[![PyPI](https://img.shields.io/pypi/v/pystrata)](https://pypi.org/project/pystrata/)
+[![GitHub Workflow Status](https://img.shields.io/github/actions/workflow/status/arkottke/pystrata/python-app.yml)](https://github.com/arkottke/pystrata/actions/workflows/python-app.yml)
+[![Read the
+Docs](https://img.shields.io/readthedocs/pystrata)](https://pystrata.readthedocs.io/en/latest/)
+[![Codacy coverage](https://img.shields.io/codacy/coverage/6dbbb3a4279744d697b9bfe08af19ded)](https://app.codacy.com/gh/arkottke/pystrata/dashboard)
+![License](https://img.shields.io/badge/license-MIT-blue.svg)
+[![Zenodo](https://zenodo.org/badge/8959678.svg)](https://zenodo.org/badge/latestdoi/8959678)
+[![MyBinder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/arkottke/pystrata/main?filepath=examples)
+
+## Introduction
+
+Site response analyses implemented in Python. This Python packages aims
+to implement many of the features found in
+[Strata](https://github.com/arkottke/strata). These features include:
+- Input motion characterization:
+    - Time series
+    - Random vibration theory
+- Wave propagation or site amplification:
+    - linear
+    - equivalent-linear
+    - equivalent-linear with frequency dependent properties
+    - quarter wavelength
+- Nonlinear curve models:
+    - Predictive models:
+        - Darendeli (2001)
+        - Menq (2004)
+        - Kishida (2012)
+    - Curves:
+        - Vucetic & Dobry (1991)
+        - EPRI (1993)
+        - GEI (1983)
+        - GeoMatrix (1990)
+        - Idriss (1990)
+        - Imperial Valley Soils
+        - Iwasaki
+        - Peninsular Range
+        - Seed & Idriss
+- Site and soil property uncertainty:
+    - Toro (1994) Vs correlation model
+    - G/Gmax and D uncertainty:
+    - Darendeli (2001)
+    - EPRI SPID (2013)
+
+Development of this software is on-going and any contributions are
+encouraged. Previously named `pysra`, but renamed after some sage and
+persistent advice to be better associated with
+[Strata](https://github.com/arkottke/strata).
+
+## Installation
+
+`pystrata` is available via `pip` and can be installed with:
+
+    pip install pystrata
+
+If you are using `conda` and a create a `pystrata` specific
+environmental make sure you install `ipykernels` and `nb_conda_kernels`
+so that the environment is discoverable by `Jupyter` with:
+
+    conda install ipykernel nb_conda_kernels
+
+## Citation
+
+Please cite this software using the following
+[DOI](https://zenodo.org/badge/latestdoi/8959678):
+
+    Albert Kottke & Maxim Millen. (2023). arkottke/pystrata: v0.5.2 (v0.5.2). Zenodo. https://doi.org/10.5281/zenodo.7551992
+
+or with BibTeX:
+
+    @software{albert_kottke_2023_7551992,
+      author       = {Albert Kottke and
+                      Maxim Millen},
+      title        = {arkottke/pystrata: v0.5.2},
+      month        = jan,
+      year         = 2023,
+      publisher    = {Zenodo},
+      version      = {v0.5.2},
+      doi          = {10.5281/zenodo.7551992},
+      url          = {https://doi.org/10.5281/zenodo.7551992}
+    }
+
+## Examples
+
+There are a variety of examples of using `pystrata` within the [examples
+directory](https://github.com/arkottke/pystrata/tree/main/examples). An
+interactive Jupyter interface of these examples is available on
+[![MyBinder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/arkottke/pystrata/main?filepath=examples).

pystrata-0.5.4/README.md

@@ -0,0 +1,91 @@
+# pyStrata
+
+Python library for site response analysis.
+
+[![PyPI](https://img.shields.io/pypi/v/pystrata)](https://pypi.org/project/pystrata/)
+[![GitHub Workflow Status](https://img.shields.io/github/actions/workflow/status/arkottke/pystrata/python-app.yml)](https://github.com/arkottke/pystrata/actions/workflows/python-app.yml)
+[![Read the
+Docs](https://img.shields.io/readthedocs/pystrata)](https://pystrata.readthedocs.io/en/latest/)
+[![Codacy coverage](https://img.shields.io/codacy/coverage/6dbbb3a4279744d697b9bfe08af19ded)](https://app.codacy.com/gh/arkottke/pystrata/dashboard)
+![License](https://img.shields.io/badge/license-MIT-blue.svg)
+[![Zenodo](https://zenodo.org/badge/8959678.svg)](https://zenodo.org/badge/latestdoi/8959678)
+[![MyBinder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/arkottke/pystrata/main?filepath=examples)
+
+## Introduction
+
+Site response analyses implemented in Python. This Python packages aims
+to implement many of the features found in
+[Strata](https://github.com/arkottke/strata). These features include:
+- Input motion characterization:
+    - Time series
+    - Random vibration theory
+- Wave propagation or site amplification:
+    - linear
+    - equivalent-linear
+    - equivalent-linear with frequency dependent properties
+    - quarter wavelength
+- Nonlinear curve models:
+    - Predictive models:
+        - Darendeli (2001)
+        - Menq (2004)
+        - Kishida (2012)
+    - Curves:
+        - Vucetic & Dobry (1991)
+        - EPRI (1993)
+        - GEI (1983)
+        - GeoMatrix (1990)
+        - Idriss (1990)
+        - Imperial Valley Soils
+        - Iwasaki
+        - Peninsular Range
+        - Seed & Idriss
+- Site and soil property uncertainty:
+    - Toro (1994) Vs correlation model
+    - G/Gmax and D uncertainty:
+    - Darendeli (2001)
+    - EPRI SPID (2013)
+
+Development of this software is on-going and any contributions are
+encouraged. Previously named `pysra`, but renamed after some sage and
+persistent advice to be better associated with
+[Strata](https://github.com/arkottke/strata).
+
+## Installation
+
+`pystrata` is available via `pip` and can be installed with:
+
+    pip install pystrata
+
+If you are using `conda` and a create a `pystrata` specific
+environmental make sure you install `ipykernels` and `nb_conda_kernels`
+so that the environment is discoverable by `Jupyter` with:
+
+    conda install ipykernel nb_conda_kernels
+
+## Citation
+
+Please cite this software using the following
+[DOI](https://zenodo.org/badge/latestdoi/8959678):
+
+    Albert Kottke & Maxim Millen. (2023). arkottke/pystrata: v0.5.2 (v0.5.2). Zenodo. https://doi.org/10.5281/zenodo.7551992
+
+or with BibTeX:
+
+    @software{albert_kottke_2023_7551992,
+      author       = {Albert Kottke and
+                      Maxim Millen},
+      title        = {arkottke/pystrata: v0.5.2},
+      month        = jan,
+      year         = 2023,
+      publisher    = {Zenodo},
+      version      = {v0.5.2},
+      doi          = {10.5281/zenodo.7551992},
+      url          = {https://doi.org/10.5281/zenodo.7551992}
+    }
+
+## Examples
+
+There are a variety of examples of using `pystrata` within the [examples
+directory](https://github.com/arkottke/pystrata/tree/main/examples). An
+interactive Jupyter interface of these examples is available on
+[![MyBinder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/arkottke/pystrata/main?filepath=examples).

pystrata-0.5.4/examples/README.md

@@ -0,0 +1,22 @@
+# Examples
+
+The examples included here are used to demonstrate the capabilities of `pystrata`.
+The following a brief summaries of the examples:
+
+1. Time series analysis to compute surface response spectrum and site
+amplification functions.
+2. Random vibration theory (RVT) analysis to compute surface response
+spectrum and site amplification functions.
+3. RVT input motion with a variety of site response calculators.
+4. Generate simulated shear-wave velocity profiles.
+5. Generate simulated nonlinear properties.
+6. Time series analysis to compute surface response spectrum and site amplification functions using velocity profiles from geopsy.
+7. RVT calculation using different peak factor calculators.
+8. RVT calculation using a suite of simulated profiles
+9. Quarter-wave length site amplification
+10. Compute ground motion using a suite of peak factors
+11. Extract soil properties from FDM site response calculations
+12. Show the impact of frequency dependent D_min on FDM methods.
+13. Show the impact of the strain limit on the EQL calculation.
+14. Example with multiple input motions and simulated soil profiles.
+15. List of provided nonlinear curves.