stoneforge 0.2.0b0__tar.gz → 0.2.0b2__tar.gz

stoneforge-0.2.0b2/CHANGELOG.txt

@@ -0,0 +1,6 @@
+Change Log
+==========
+
+0.1.0 (29/01/2022)
+------------------
+- First Release

stoneforge-0.2.0b2/MANIFEST.in

@@ -0,0 +1 @@
+global-include *.txt *.py

{stoneforge-0.2.0b0 → stoneforge-0.2.0b2}/PKG-INFO

@@ -1,85 +1,84 @@
-Metadata-Version: 2.4
-Name: stoneforge
-Version: 0.2.0b0
-Summary: Geophysics equations, algorithms and methods
-Project-URL: homepage, https://github.com/giecaruff/stoneforge
-Author: GIECAR - UFF, Wagner M. Lupinacci, Fernando Vizeu, Fábio Júnior D Fernandes, José A. V. Dias, Mario M. Ramos, Jordan S. Cuno, João Vitor A. Estrella, Ana Carolina, Breno D. Chrispim
-License: MIT
-License-File: LICENSE
-Classifier: Development Status :: 5 - Production/Stable
-Classifier: Intended Audience :: Education
-Classifier: License :: OSI Approved :: MIT License
-Classifier: Operating System :: Microsoft :: Windows :: Windows 10
-Classifier: Programming Language :: Python :: 3
-Requires-Python: >=3.10
-Requires-Dist: dlisio>=1.0.3
-Requires-Dist: ipympl>=0.8.4
-Requires-Dist: lightgbm>=4.5.0
-Requires-Dist: matplotlib>=3.10.0
-Requires-Dist: notebook>=6.4.0
-Requires-Dist: numpy>=2.2.0
-Requires-Dist: pandas>=2.2.2
-Requires-Dist: pytest>=8.3.4
-Requires-Dist: scikit-learn>=1.6.1
-Requires-Dist: scipy>=1.14.1
-Requires-Dist: xgboost>=2.1.4
-Description-Content-Type: text/markdown
-
-<p align="center">
-<img src="https://raw.githubusercontent.com/giecaruff/logos/main/APPY/stoneforge.png" width="400"/>
-
-<h2 align="center">Algorithms, methods and equations for geophysics in Python</h2>
-
-<p align="center">
-Part of the <strong>Appy</strong> project
-</p>
-
-
-
-<p align="center">
-<a href="https://giecaruff.github.io/sites/"><strong>Documentation</strong> (latest)</a> |
-<a href="http://gcr.sites.uff.br/"><strong>Institutional</strong> (GIECAR website)</a> 
-</p>
-
-
-<p align="center">
-<a href="https://github.com/giecaruff/stoneforge/actions"><img src="https://github.com/giecaruff/stoneforge/actions/workflows/CI.yml/badge.svg" alt="Latest version on PyPI"/></a>
-<a href="https://badge.fury.io/py/stoneforge"><img src="https://badge.fury.io/py/stoneforge.svg" alt="PyPI version" height="20"></a>
-</p>
-  
-<!-- 
-[![https://github.com/giecaruff/stoneforge/actions](https://github.com/giecaruff/stoneforge/actions/workflows/CI.yml/badge.svg)](https://github.com/giecaruff/stoneforge/actions)
--->
-
-  
-## About
-
-The Stoneforge library is linked to the GIECAR laboratory at the Universidade Federal Fluminense (UFF) related to the Geology and Geophysics Departmnet <a href="http://geologiaegeofisica.sites.uff.br/"> (GGO)</a>, and its purpose is to teach and develop routines in Python to solve geological and geophysical problems.
-
-
-## Installation and first steps
-
-To install stoneforge use the following syntax in your command interpreter environment:
-
-```
-$pip install stoneforge
-```
-
-and them verify the installation using the following command in Python:
-
-```
->>> import stoneforge
-```
-  
-## Dataset
-
-The stoneforge dataset comprises the following data: 
-
-Four .las data from wildcat wells in the National Petroleum Reserve in Alaska. Those where drilled in the National Petroleum Reserve in Alaska (NPRA). </br>
-[USGS Well Index](https://pubs.usgs.gov/of/1999/ofr-99-0015/Wells/WellIdx.htm)
-
-Two .dlis data from the Mississippi Fan (Gulf of Mexico) from the DSDP (Deep Sea Drilling Project); DSDP Leg 96 - Hole 616; Processed and Original data. </br>
-[DSDP Leg 96 - Hole 616](https://mlp.ldeo.columbia.edu/data/dsdp/leg96/616/)
-
-Zihlman, F. N creator ; Oliver, H. L ; Geological Survey (U.S.)
-Reston, Va. : Denver, Colo : U.S. Dept. of the Interior, U.S. Geological Survey1999
+Metadata-Version: 2.4
+Name: stoneforge
+Version: 0.2.0b2
+Summary: Geophysics equations, algorithms and methods
+Author: GIECAR - UFF, Wagner M. Lupinacci, Fernando Vizeu, Fábio Júnior D Fernandes, José A. V. Dias, Mario M. Ramos, Jordan S. Cuno, João Vitor A. Estrella, Ana Carolina, Breno D. Chrispim
+License-Expression: MIT
+Project-URL: homepage, https://github.com/giecaruff/stoneforge
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Intended Audience :: Education
+Classifier: Operating System :: Microsoft :: Windows :: Windows 10
+Classifier: Programming Language :: Python :: 3
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: dlisio>=1.0.3
+Requires-Dist: numpy>=2.2.0
+Requires-Dist: pytest>=8.3.4
+Requires-Dist: scipy>=1.14.1
+Requires-Dist: scikit-learn>=1.6.1
+Requires-Dist: matplotlib>=3.10.0
+Requires-Dist: pandas>=2.2.2
+Requires-Dist: lightgbm>=4.5.0
+Requires-Dist: ipympl>=0.8.4
+Requires-Dist: ipykernel>=6.30.0
+Dynamic: license-file
+
+<p align="center">
+<img src="https://raw.githubusercontent.com/giecaruff/logos/main/APPY/stoneforge.png" width="400"/>
+
+<h2 align="center">Algorithms, methods and equations for geophysics in Python</h2>
+
+<p align="center">
+Part of the <strong>Appy</strong> project
+</p>
+
+
+
+<p align="center">
+<a href="https://giecaruff.github.io/stoneforge/"><strong>Documentation</strong> (latest)</a> |
+<a href="http://gcr.sites.uff.br/"><strong>Institutional</strong> (GIECAR website)</a> 
+</p>
+
+
+<p align="center">
+<a href="https://github.com/giecaruff/stoneforge/actions"><img src="https://github.com/giecaruff/stoneforge/actions/workflows/CI.yml/badge.svg" alt="Latest version on PyPI"/></a>
+<a href="https://badge.fury.io/py/stoneforge"><img src="https://badge.fury.io/py/stoneforge.svg" alt="PyPI version" height="20"></a>
+</p>
+  
+<!-- 
+[![https://github.com/giecaruff/stoneforge/actions](https://github.com/giecaruff/stoneforge/actions/workflows/CI.yml/badge.svg)](https://github.com/giecaruff/stoneforge/actions)
+-->
+
+  
+## About
+
+The Stoneforge library is linked to the GIECAR laboratory at the Universidade Federal Fluminense (UFF) related to the Geology and Geophysics Departmnet <a href="http://geologiaegeofisica.sites.uff.br/"> (GGO)</a>, and its purpose is to teach and develop routines in Python to solve geological and geophysical problems.
+
+
+## Installation and first steps
+
+To install stoneforge use the following syntax in your command interpreter environment:
+
+```
+$pip install stoneforge
+```
+
+and them verify the installation using the following command in Python:
+
+```
+>>> import stoneforge
+```
+  
+## Dataset
+
+The stoneforge dataset comprises the following data: 
+
+Four .las data from wildcat wells in the National Petroleum Reserve in Alaska. Those where drilled in the National Petroleum Reserve in Alaska (NPRA). </br>
+[USGS Well Index](https://pubs.usgs.gov/of/1999/ofr-99-0015/Wells/WellIdx.htm)
+
+Two .dlis data from the Mississippi Fan (Gulf of Mexico) from the DSDP (Deep Sea Drilling Project); DSDP Leg 96 - Hole 616; Processed and Original data. </br>
+[DSDP Leg 96 - Hole 616](https://mlp.ldeo.columbia.edu/data/dsdp/leg96/616/)
+
+Zihlman, F. N creator ; Oliver, H. L ; Geological Survey (U.S.)
+Reston, Va. : Denver, Colo : U.S. Dept. of the Interior, U.S. Geological Survey1999

{stoneforge-0.2.0b0 → stoneforge-0.2.0b2}/README.md

@@ -10,7 +10,7 @@ Part of the <strong>Appy</strong> project
 
 
 <p align="center">
-<a href="https://giecaruff.github.io/sites/"><strong>Documentation</strong> (latest)</a> |
+<a href="https://giecaruff.github.io/stoneforge/"><strong>Documentation</strong> (latest)</a> |
 <a href="http://gcr.sites.uff.br/"><strong>Institutional</strong> (GIECAR website)</a> 
 </p>
 
@@ -55,4 +55,4 @@ Two .dlis data from the Mississippi Fan (Gulf of Mexico) from the DSDP (Deep Sea
 [DSDP Leg 96 - Hole 616](https://mlp.ldeo.columbia.edu/data/dsdp/leg96/616/)
 
 Zihlman, F. N creator ; Oliver, H. L ; Geological Survey (U.S.)
-Reston, Va. : Denver, Colo : U.S. Dept. of the Interior, U.S. Geological Survey1999
+Reston, Va. : Denver, Colo : U.S. Dept. of the Interior, U.S. Geological Survey1999

stoneforge-0.2.0b2/docs/_build/html/_sources/index.rst.txt

@@ -0,0 +1,43 @@
+.. Stoneforge documentation master file, created by
+   sphinx-quickstart on Mon May 27 13:42:11 2024.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to Stoneforge's documentation!
+======================================
+
+**Version**: 1.4
+
+**Stoneforge** is a Python library for geophysics equations, algorithms and methods that also,
+are used in the software Appy. It is linked to the GIECAR laboratory at the Universidade Federal
+Fluminense (UFF) related to the Geology and Geophysics Departament (GGO), and its purpose is to teach
+and develop routines in Python to solve geological and geophysical problems. Main APPy references are :footcite:t:`estrella2022sbgf,estrella2022seg`.
+
+.. note::
+   This project is under active development as of May 2024.
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   usage/installation
+   usage/quickstart
+
+   modules/petrophysics
+   modules/rockphysics
+   modules/pseudowells
+   modules/machinelearning/index
+   modules/preprocessing
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
+
+References
+----------------
+
+.. footbibliography::

stoneforge-0.2.0b2/docs/_build/html/_sources/modules/machinelearning/classification.rst.txt

@@ -0,0 +1,39 @@
+=========================
+Classification
+=========================
+
+This section contains documentation for the Classification module (Machine learning).
+
+.. automodule:: stoneforge.machine_learning.classification
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+Settings (Classification)
+--------------------------------
+
+.. automodule:: stoneforge.machine_learning.classification.settings
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+Fit (Classification)
+--------------------------------
+
+.. automodule:: stoneforge.machine_learning.classification.fit
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+Predict (Classification)
+--------------------------------
+
+.. automodule:: stoneforge.machine_learning.classification.predict
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+References
+--------------------------------
+
+.. footbibliography::

stoneforge-0.2.0b2/docs/_build/html/_sources/modules/machinelearning/index.rst.txt

@@ -0,0 +1,10 @@
+Machine Learning
+================
+
+This section contains machine learning methods used in Stoneforge.
+
+.. toctree::
+   :maxdepth: 1
+
+   classification
+   regression

stoneforge-0.2.0b2/docs/_build/html/_sources/modules/machinelearning/regression.rst.txt

@@ -0,0 +1,39 @@
+=========================
+Regression
+=========================
+
+This section contains documentation for the Regression module in (machine learning).
+
+.. automodule:: stoneforge.machine_learning.regression
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+Settings (Regression)
+--------------------------------
+
+.. automodule:: stoneforge.machine_learning.regression.settings
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+Fit (Regression)
+--------------------------------
+
+.. automodule:: stoneforge.machine_learning.regression.fit
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+Predict (Regression)
+--------------------------------
+
+.. automodule:: stoneforge.machine_learning.regression.predict
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+References
+--------------------------------
+
+.. footbibliography::

stoneforge-0.2.0b2/docs/_build/html/_sources/modules/petrophysics.rst.txt

@@ -0,0 +1,39 @@
+=========================
+Petrophysics
+=========================
+
+This section contains documentation for the Petrophysics module. We indicate the reference (Pt-Br) of :footcite:t:`freire2020youtube` for the methods used in this module.
+
+.. automodule:: stoneforge.petrophysics
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+Porosity
+---------------
+
+.. automodule:: stoneforge.petrophysics.porosity
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+Shale Volume
+----------------
+
+.. automodule:: stoneforge.petrophysics.shale_volume
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+Water Saturation
+----------------
+
+.. automodule:: stoneforge.petrophysics.water_saturation
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+References
+----------------
+
+.. footbibliography::

stoneforge-0.2.0b2/docs/_build/html/_sources/modules/preprocessing.rst.txt

@@ -0,0 +1,28 @@
+=========================
+Preprocessing
+=========================
+
+This section contains documentation for the Preprocessing module.
+NOTE: Those methods will be modified in the future to be more flexible and
+to allow for more complex workflows.
+
+.. automodule:: stoneforge.preprocessing
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+Data Management
+-------------------------
+
+.. automodule:: stoneforge.preprocessing.data_management
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+Data Processing
+-------------------------
+
+.. automodule:: stoneforge.preprocessing.data_processing
+    :members:
+    :undoc-members:
+    :show-inheritance:

stoneforge-0.2.0b2/docs/_build/html/_sources/modules/pseudowells.rst.txt

@@ -0,0 +1,23 @@
+=========================
+Pseudo Wells
+=========================
+
+This section contains documentation for the Pseudo Wells module.
+
+.. automodule:: stoneforge.pseudo_wells
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+Monte Carlo Simulations
+-------------------------
+
+.. automodule:: stoneforge.pseudo_wells.monte_carlo_simulations
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+References
+----------------
+
+.. footbibliography::

stoneforge-0.2.0b2/docs/_build/html/_sources/modules/rockphysics.rst.txt

@@ -0,0 +1,47 @@
+=========================
+Rock Physics
+=========================
+
+This section contains documentation for the Rock Physics module. We indicate the reference (Pt-Br) of :footcite:t:`wagner2020rock_physics` for the methods used in this module.
+
+.. automodule:: stoneforge.rock_physics
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+Elastic Constants
+---------------------
+
+.. automodule:: stoneforge.rock_physics.elastic_constants
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+Fluid Substitution
+---------------------
+
+.. automodule:: stoneforge.rock_physics.fluid_substitution
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+Gem
+----------------
+
+.. automodule:: stoneforge.rock_physics.gem
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+Rock Physics Bounds
+---------------------
+
+.. automodule:: stoneforge.rock_physics.rock_physics_bounds
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+References
+----------------
+
+.. footbibliography::

stoneforge-0.2.0b2/docs/_build/html/_sources/usage/installation.rst.txt

@@ -0,0 +1,40 @@
+=========================
+Installing Stoneforge
+=========================
+
+This guide will walk you through the installation of the the Stoneforge library.
+
+Prerequisites
+=============
+
+Before you begin, ensure you have met the following requirements:
+
+* You have installed Python 3.8 or later (with pip).
+* You have a Windows/Linux/Mac machine.
+
+Installation
+============
+
+To install Stoneforge, follow these steps:
+
+Windows, Linux and macOS
+------------------------
+
+1. Open your terminal.
+
+2. Install the Stoneforge package with pip:
+
+.. code-block:: bash
+
+   pip install stoneforge
+
+Verify Installation
+===================
+
+To verify that Stoneforge has been installed correctly, type the following command in your terminal:
+
+.. code-block:: bash
+
+   pip show stoneforge
+
+If no error message is displayed, the installation was successful!

stoneforge-0.2.0b2/docs/_build/html/_sources/usage/quickstart.rst.txt

@@ -0,0 +1,28 @@
+=========================
+Quickstart
+=========================
+
+.. code-block:: bash
+
+   pip install stoneforge
+
+   (...)
+
+.. code-block:: python
+
+   from stoneforge.preprocessing import las_import
+   from stoneforge.petrophysics import shale_volume, porosity, water_saturation
+
+   # Import a LAS file
+   # This will return a DataFrame with the data and a dictionary with the units
+   data,units = las_import("..//stoneforge//datasets/DP1.las")
+
+   # Remove non sampling rows
+   data_c = data[~data.isin([-999.0]).any(axis=1)]
+
+   # Calculate shale volume
+   GR = np.array(data_c["GR"])
+   GR_min = np.percentile(GR, 10)
+   GR_max = np.percentile(GR, 90)
+
+   VSH = shale_volume.vshale_larionov(GR, GR_min, GR_max, "larionov")

stoneforge-0.2.0b2/docs/conf.py

@@ -0,0 +1,47 @@
+# -*- coding: utf-8 -*-
+"""conf.py — Configuração do Sphinx para a documentação do projeto."""
+
+import os
+import sys
+
+# para localizar os pacotes no diretório pai
+sys.path.insert(0, os.path.abspath("../stoneforge"))
+
+# -- Project information -----------------------------------------------------
+
+project = "Stoneforge"
+author = "APPy Team"
+copyright = "2024 GIECAR Laboratory, Universidade Federal Fluminense (UFF)"
+
+# -- General configuration ---------------------------------------------------
+
+# Note: The variable 'project_copyright' is used to avoid conflict with the built-in 'copyright'.
+
+extensions = [
+    "sphinx.ext.napoleon",
+    "sphinxcontrib.bibtex",
+    "sphinx.ext.autodoc",
+    "sphinx_autodoc_typehints",
+    "sphinx.ext.viewcode",
+]
+
+# -- HTML output -------------------------------------------------------------
+
+html_theme = "sphinx_rtd_theme"
+
+# -- Customização de HTML ----------------------------------------------------
+
+html_theme_options = {
+    "navigation_depth": 4,
+    "collapse_navigation": False,
+    "sticky_navigation": True,
+}
+
+# -- Napoleon settings (para docstrings estilo Google/Numpy) -----------------
+
+napoleon_numpy_docstring = True
+
+# -- Autodoc settings --------------------------------------------------------
+
+bibtex_bibfiles = ['refs.bib']
+bibtex_default_style = 'plain'  # or 'unsrt', 'alpha', etc.