stoneforge 0.1.6.dev1__tar.gz → 0.2.0b0__tar.gz

stoneforge-0.2.0b0/.gitignore

@@ -0,0 +1,142 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# 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
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# Local tests
+.ml_project
+.pkl
+
+# Overall pickle files
+*.pkl
+
+# ml test
+.mlprj
+catboost_info
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+.vscode/

{stoneforge-0.1.6.dev1/stoneforge.egg-info → stoneforge-0.2.0b0}/PKG-INFO

@@ -1,83 +1,85 @@
-Metadata-Version: 2.1
-Name: stoneforge
-Version: 0.1.6.dev1
-Summary: Geophysics equations, algorithms and methods
-Home-page: https://github.com/giecaruff/stoneforge
-Author: GIECAR - UFF
-License: MIT
-Requires-Python: >=3.10
-Description-Content-Type: text/markdown
-License-File: LICENSE
-Requires-Dist: numpy==1.26.4
-Requires-Dist: pytest==8.1.1
-Requires-Dist: scipy==1.13.0
-Requires-Dist: scikit-learn==1.4.2
-Requires-Dist: xgboost==2.0.3
-Requires-Dist: matplotlib==3.8.4
-Requires-Dist: pandas==2.2.2
-Requires-Dist: catboost==1.2.5
-Requires-Dist: lightgbm==4.3.0
-
-<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 selected data from eleven wildcat wells in the National Petroleum Reserve in Alaska / by F.N. Zihlman and H.L. Oliver.
-Contains data sets from 11 wildcat wells drilled in the National Petroleum Reserve in Alaska (NPRA).
-
-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
-
-Our special thanks to the INDIANA UNIVERSITY for mantaining this dataset
-
-
-Change Log
-==========
-
-0.1.0 (29/01/2022)
-------------------
-- First Release
+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

{stoneforge-0.1.6.dev1 → stoneforge-0.2.0b0}/README.md

@@ -46,10 +46,13 @@ and them verify the installation using the following command in Python:
   
 ## Dataset
 
-The stoneforge dataset comprises selected data from eleven wildcat wells in the National Petroleum Reserve in Alaska / by F.N. Zihlman and H.L. Oliver.
-Contains data sets from 11 wildcat wells drilled in the National Petroleum Reserve in Alaska (NPRA).
+The stoneforge dataset comprises the following data: 
 
-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
+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/)
 
-Our special thanks to the INDIANA UNIVERSITY for mantaining this dataset
+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/pyproject.toml

@@ -0,0 +1,95 @@
+[project]
+name = "stoneforge"
+version = "0.2.0-beta.0"
+authors = [
+    {name = "GIECAR - UFF"},
+    {name = "Wagner M. Lupinacci"},
+    {name = "Fernando Vizeu"},
+    {name = "Fábio Júnior D Fernandes"},
+    {name = "José A. V. Dias"},
+    {name = "Mario M. Ramos"},
+    {name = "Jordan S. Cuno"},
+    {name = "João Vitor A. Estrella"},
+    {name = "Ana Carolina"},
+    {name = "Breno D. Chrispim"},
+]
+description = "Geophysics equations, algorithms and methods"
+readme = "README.md"
+requires-python = ">=3.10"
+dependencies = [
+    "dlisio>=1.0.3",
+    "numpy>=2.2.0",
+    "pytest>=8.3.4",
+    "scipy>=1.14.1",
+    "scikit-learn>=1.6.1",
+    "xgboost>=2.1.4",
+    "matplotlib>=3.10.0",
+    "pandas>=2.2.2",
+    "lightgbm>=4.5.0",
+    "notebook>=6.4.0",
+    "ipympl>=0.8.4"
+]
+classifiers = [
+    "Development Status :: 5 - Production/Stable",
+    "Intended Audience :: Education",
+    "Operating System :: Microsoft :: Windows :: Windows 10",
+    "License :: OSI Approved :: MIT License",
+    "Programming Language :: Python :: 3"
+]
+
+[project.urls]
+homepage = "https://github.com/giecaruff/stoneforge"
+
+[project.license]
+text = "MIT"
+
+
+[tool.hatch.metadata]
+allow-direct-references = true
+
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[dependency-groups]
+dev = [
+    "pytest>=8.3.5",
+    "pytest-cov>=6.1.1",
+    "ruff>=0.11.8",
+    "sphinx>=8.1.3",
+    "sphinx-rtd-theme>=3.0.2",
+]
+
+[tool.hatch.build]
+include = ["stoneforge/**"]  # Include the main package
+exclude = ["tests", "docs"]  # Exclude unnecessary files
+
+[tool.uv]
+package = true
+
+
+[tool.ruff]
+# Set the maximum line length to 79.
+line-length = 79
+indent-width = 4
+
+[tool.ruff.lint]
+extend-select = [
+    "D",   # pydocstyle
+    "NPY", # numPy specific rules npy
+    "PD",  # Pandas-vet
+    "N",   # PEP8
+    "PL",  # Pylint
+]
+
+[tool.ruff.lint.pydocstyle]
+convention = "google"
+
+[tool.pytest.ini_options]
+pythonpath = "stoneforge"
+minversion = "6.0"
+addopts = "-ra -q"
+testpaths = [
+    "tests",
+]
+norecursedirs = [".venv", ".git", "__pycache__"]

{stoneforge-0.1.6.dev1 → stoneforge-0.2.0b0}/stoneforge/__init__.py

@@ -6,4 +6,8 @@ from . import preprocessing  # noqa: F401
 from . import rock_physics  # noqa: F401
 
 from . import inversion  # noqa: F401
-from . import wavelets  # noqa: F401
+from . import wavelets  # noqa: F401
+
+__version__ = "0.1.6-beta.2"
+__author__ = "GIECAR - UFF"
+__description__ = "Geophysics equations, algorithms and methods"

stoneforge-0.2.0b0/stoneforge/data_management/__init__.py

@@ -0,0 +1 @@
+from . import las_import

{stoneforge-0.1.6.dev1/stoneforge/preprocessing → stoneforge-0.2.0b0/stoneforge/data_management}/las2.py

@@ -93,12 +93,12 @@ def read(lasfile):
     lasfile : string or file-like object
         The path of the file to read or an existing file-like object to read from.
 
-    Returns
+    Returns:
     -------
     dict
         A dictionary containing the sections of the LAS file.
 
-    Notes
+    Notes:
     -----
     The structure of the returned dictionary is specified below.
     The dictionary keys are the section names: 'version', 'well', 'parameter', 'curve', 'other', 'data'.
@@ -113,12 +113,12 @@ def read(lasfile):
     'description'.
     For information on the structure of a LAS 2.0 line, please also refer to its specification [1]_.
 
-    References
+    References:
     ----------
     .. [1] LAS 2.0 standard - http://www.cwls.org/wp-content/uploads/2017/02/Las2_Update_Feb2017.pdf -
        Retrieved August 14, 2019
 
-    Examples
+    Examples:
     --------
     The examples below contains ficticious data.
     In the first example we see the version information for the file.
@@ -234,8 +234,7 @@ def _section_format_getter(section):
     maxwidths = dict.fromkeys(_line_elements, 0)
     for line in section:
         for key in line:
-            if len(line[key]) > maxwidths[key]:
-                maxwidths[key] = len(line[key])
+            maxwidths[key] = max(maxwidths[key], len(line[key]))
 
     return _default_line_format_format.format(**maxwidths)
 
@@ -275,7 +274,7 @@ def write(lasfile, data, section_titles=None, section_formats=None):
         A dictionary where the key is the section name and value is the format string that will be used to format the
         lines in the respective section. For further information please refer to the Notes section.
 
-    Notes
+    Notes:
     -----
     This function does not guarantee that the output file will follow the LAS 2.0 standard. If mandatory sections or
     lines are missing from the inputs, the file will be written nevertheless. The only required field for the function
@@ -299,16 +298,16 @@ def write(lasfile, data, section_titles=None, section_formats=None):
     logs, "{:>8.4f} {:>8.4f} {:>8.4f}" is the default format.
     Each section format can be individually omitted.
 
-    See Also
+    See Also:
     --------
     read : Reads the contents of a LAS 2.0 file.
 
-    References
+    References:
     ----------
     .. [1] LAS 2.0 standard - http://www.cwls.org/wp-content/uploads/2017/02/Las2_Update_Feb2017.pdf -
        Retrieved August 14, 2019
 
-    Examples
+    Examples:
     --------
     Minimal example of usage. This would not produce a valid LAS 2.0 file since it is missing many of the mandatory
     sections and lines.

stoneforge-0.2.0b0/stoneforge/data_management/las_import.py

@@ -0,0 +1,19 @@
+import os
+
+def import_folder(self,ext = '.las'):
+
+    # ------------------------------------ #
+    # all paths 
+    files = []
+    # r=root, d=directories, f = files
+    for r, _, f in os.walk(self.data_path):
+        for file in f:
+            if file.endswith(ext):
+                files.append(os.path.join(r, file))
+
+    c_resumo = self.data_path+'\\'
+
+
+    for i in files:
+        n1 = i.replace(c_resumo, '')
+        self.well_names_paths[n1.replace(ext,'')] = i

{stoneforge-0.1.6.dev1 → stoneforge-0.2.0b0}/stoneforge/data_replacement/evaluation.py

@@ -1,5 +1,5 @@
 import numpy as np
-from sklearn.metrics import mean_absolute_error, r2_score
+from sklearn.metrics import r2_score
 #from sklearn.metrics import mean_absolute_percentage_error
 #import pickle mean_absolute_error
 import json

{stoneforge-0.1.6.dev1 → stoneforge-0.2.0b0}/stoneforge/data_replacement/fit.py

@@ -1,22 +1,18 @@
-import numpy as np
 import numpy.typing as npt
 import pickle
 import json
-import warnings
 import os
 
 from sklearn.tree import DecisionTreeRegressor
 from sklearn.svm import SVR
-from sklearn.linear_model import LogisticRegression
 from sklearn.ensemble import RandomForestRegressor
 import lightgbm as lgb
-from catboost.core import CatBoostRegressor
+#from catboost.core import CatBoostRegressor
 from sklearn.model_selection import GridSearchCV
 from sklearn.preprocessing import PolynomialFeatures
 from sklearn.linear_model import LinearRegression
 from xgboost import XGBRegressor
 from sklearn.preprocessing import StandardScaler
-from sklearn.preprocessing import LabelEncoder
 from sklearn.preprocessing import MinMaxScaler
 
 LR_METHODS = [

{stoneforge-0.1.6.dev1 → stoneforge-0.2.0b0}/stoneforge/data_replacement/mldr_project.py

@@ -1,6 +1,4 @@
 import numpy as np
-import matplotlib.pyplot as plt
-import pandas as pd
 import shutil
 import os
 

{stoneforge-0.1.6.dev1 → stoneforge-0.2.0b0}/stoneforge/data_replacement/predict.py

@@ -1,19 +1,10 @@
 import numpy as np
 import numpy.typing as npt
 import pickle
-import warnings
-import json
 import os
 
-from sklearn.linear_model import LinearRegression
-from sklearn.linear_model import LogisticRegression
-from sklearn.svm import SVR
-from sklearn.tree import DecisionTreeRegressor
-from sklearn.ensemble import RandomForestRegressor
 from sklearn.preprocessing import PolynomialFeatures
-from xgboost import XGBRegressor
-import lightgbm as lgb
-from catboost.core import CatBoostRegressor
+#from catboost.core import CatBoostRegressor
 
 "linear_regression_simple",
 "linear_regression_polynomial",

{stoneforge-0.1.6.dev1 → stoneforge-0.2.0b0}/stoneforge/data_replacement/settings.py

@@ -1,8 +1,5 @@
-import numpy as np
-import numpy.typing as npt
 import json
 import pickle
-import warnings
 import os
 
 # TODO: if method is not listed do not execute and gives error to the user
@@ -15,7 +12,7 @@ LR_METHODS = [
     "random_forest_regression",
     'lightgbm_regression',
     'xgboost_regression',
-    'catboost_regression'
+    #'catboost_regression'
 ]
 
 def methods():
@@ -33,7 +30,7 @@ def settings(method: str = "linear_regression_simple", path = ".", verbose = Fal
     if method == "linear_regression_simple" or method  =="linear_regression_polynomial":
         new_settings = {}
         overall_settings = {}
-        if not 'degree' in kwargs:
+        if 'degree' not in kwargs:
             
             #if path:
             #    saves({'degree':1}, os.path.join(path, 'polinomial'))