geone 1.2.14__tar.gz → 1.2.15__tar.gz

geone-1.2.15/MANIFEST.in

@@ -0,0 +1,40 @@
+include src/geone/lib_deesse_core/linux_old_py39/*
+include src/geone/lib_deesse_core/linux_old_py310/*
+include src/geone/lib_deesse_core/linux_old_py311/*
+include src/geone/lib_deesse_core/linux_old_py312/*
+include src/geone/lib_deesse_core/linux_py39/*
+include src/geone/lib_deesse_core/linux_py310/*
+include src/geone/lib_deesse_core/linux_py311/*
+include src/geone/lib_deesse_core/linux_py312/*
+include src/geone/lib_deesse_core/mac_arm64_py39/*
+include src/geone/lib_deesse_core/mac_arm64_py310/*
+include src/geone/lib_deesse_core/mac_arm64_py311/*
+include src/geone/lib_deesse_core/mac_arm64_py312/*
+include src/geone/lib_deesse_core/mac_x86_64_py39/*
+include src/geone/lib_deesse_core/mac_x86_64_py310/*
+include src/geone/lib_deesse_core/mac_x86_64_py311/*
+include src/geone/lib_deesse_core/mac_x86_64_py312/*
+include src/geone/lib_deesse_core/win_py39/*
+include src/geone/lib_deesse_core/win_py310/*
+include src/geone/lib_deesse_core/win_py311/*
+include src/geone/lib_deesse_core/win_py312/*
+include src/geone/lib_geosclassic_core/linux_old_py39/*
+include src/geone/lib_geosclassic_core/linux_old_py310/*
+include src/geone/lib_geosclassic_core/linux_old_py311/*
+include src/geone/lib_geosclassic_core/linux_old_py312/*
+include src/geone/lib_geosclassic_core/linux_py39/*
+include src/geone/lib_geosclassic_core/linux_py310/*
+include src/geone/lib_geosclassic_core/linux_py311/*
+include src/geone/lib_geosclassic_core/linux_py312/*
+include src/geone/lib_geosclassic_core/mac_arm64_py39/*
+include src/geone/lib_geosclassic_core/mac_arm64_py310/*
+include src/geone/lib_geosclassic_core/mac_arm64_py311/*
+include src/geone/lib_geosclassic_core/mac_arm64_py312/*
+include src/geone/lib_geosclassic_core/mac_x86_64_py39/*
+include src/geone/lib_geosclassic_core/mac_x86_64_py310/*
+include src/geone/lib_geosclassic_core/mac_x86_64_py311/*
+include src/geone/lib_geosclassic_core/mac_x86_64_py312/*
+include src/geone/lib_geosclassic_core/win_py39/*
+include src/geone/lib_geosclassic_core/win_py310/*
+include src/geone/lib_geosclassic_core/win_py311/*
+include src/geone/lib_geosclassic_core/win_py312/*

{geone-1.2.14 → geone-1.2.15}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: geone
-Version: 1.2.14
+Version: 1.2.15
 Summary: Geostatistics tools and Multiple Point Statistics
 Author-email: Julien Straubhaar <julien.straubhaar@unine.ch>, Philippe Renard <philippe.renard@unine.ch>
 License: 
@@ -98,16 +98,16 @@ GEONE relies on pre-compiled C libraries (DEESSE and GEOSCLASSIC core)
 
 GEONE is available:
 
-- on [PyPI](https://pypi.org/) (The Python Package Index), for:
-    - linux (x86_64 with GLIBC 2.35) and python 3.9 to 3.12
+- on [PyPI](https://pypi.org/project/geone) (The Python Package Index), for:
+    - linux (x86_64 with GLIBC 2.35 or GLIBC 2.27) and python 3.9 to 3.12
     - mac (x86_64 or arm64) and python 3.9 to 3.12
     - windows and python 3.9 to 3.12
-- on this [Github repository](https://github.com/randlab/geone), for:
+- on the [Github repository](https://github.com/randlab/geone), for:
     - linux (x86_64 with GLIBC 2.35 or GLIBC 2.27) and python 3.7 to 3.12
     - mac (x86_64 or arm64) and python 3.8 to 3.12
     - windows and python 3.7 to 3.12
 
-### Installation from [PyPI](https://pypi.org/)
+### Installation from [PyPI](https://pypi.org/project/geone)
 
 In a terminal type 
 ```
@@ -115,7 +115,7 @@ pip install geone
 ```
 Or, equivalently: `python -m pip install geone`.
 
-### Installation from this [Github repository](https://github.com/randlab/geone)
+### Installation from the [Github repository](https://github.com/randlab/geone)
 
 In a terminal, change directory where to download GEONE, and type
 ```
@@ -178,6 +178,8 @@ In a terminal type
 
 ### Other references 
 - C. Lantuéjoul (2002) Geostatistical Simulation, Models and Algorithms. Springer Verlag, Berlin, 256 p.
+- P. Renard, D. Allard (2013), Connectivity metrics for subsurface flow and transport. Advances in Water Resources 51:168-196, `doi:10.1016/j.advwatres.2011.12.001 <https://doi.org/10.1016/j.advwatres.2011.12.001>`_
+- J. Straubhaar, P. Renard (2024), Exploring substitution random functions composed of stationary multi-Gaussian processes. Stochastic Environmental Research and Risk Assessment, `doi:10.1007/s00477-024-02662-x <https://doi.org/10.1007/s00477-024-02662-x>`_
  -->
 
 ## License

{geone-1.2.14 → geone-1.2.15}/README.md

@@ -21,16 +21,16 @@ GEONE relies on pre-compiled C libraries (DEESSE and GEOSCLASSIC core)
 
 GEONE is available:
 
-- on [PyPI](https://pypi.org/) (The Python Package Index), for:
-    - linux (x86_64 with GLIBC 2.35) and python 3.9 to 3.12
+- on [PyPI](https://pypi.org/project/geone) (The Python Package Index), for:
+    - linux (x86_64 with GLIBC 2.35 or GLIBC 2.27) and python 3.9 to 3.12
     - mac (x86_64 or arm64) and python 3.9 to 3.12
     - windows and python 3.9 to 3.12
-- on this [Github repository](https://github.com/randlab/geone), for:
+- on the [Github repository](https://github.com/randlab/geone), for:
     - linux (x86_64 with GLIBC 2.35 or GLIBC 2.27) and python 3.7 to 3.12
     - mac (x86_64 or arm64) and python 3.8 to 3.12
     - windows and python 3.7 to 3.12
 
-### Installation from [PyPI](https://pypi.org/)
+### Installation from [PyPI](https://pypi.org/project/geone)
 
 In a terminal type 
 ```
@@ -38,7 +38,7 @@ pip install geone
 ```
 Or, equivalently: `python -m pip install geone`.
 
-### Installation from this [Github repository](https://github.com/randlab/geone)
+### Installation from the [Github repository](https://github.com/randlab/geone)
 
 In a terminal, change directory where to download GEONE, and type
 ```
@@ -101,6 +101,8 @@ In a terminal type
 
 ### Other references 
 - C. Lantuéjoul (2002) Geostatistical Simulation, Models and Algorithms. Springer Verlag, Berlin, 256 p.
+- P. Renard, D. Allard (2013), Connectivity metrics for subsurface flow and transport. Advances in Water Resources 51:168-196, `doi:10.1016/j.advwatres.2011.12.001 <https://doi.org/10.1016/j.advwatres.2011.12.001>`_
+- J. Straubhaar, P. Renard (2024), Exploring substitution random functions composed of stationary multi-Gaussian processes. Stochastic Environmental Research and Risk Assessment, `doi:10.1007/s00477-024-02662-x <https://doi.org/10.1007/s00477-024-02662-x>`_
  -->
 
 ## License

{geone-1.2.14 → geone-1.2.15}/geone.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: geone
-Version: 1.2.14
+Version: 1.2.15
 Summary: Geostatistics tools and Multiple Point Statistics
 Author-email: Julien Straubhaar <julien.straubhaar@unine.ch>, Philippe Renard <philippe.renard@unine.ch>
 License: 
@@ -98,16 +98,16 @@ GEONE relies on pre-compiled C libraries (DEESSE and GEOSCLASSIC core)
 
 GEONE is available:
 
-- on [PyPI](https://pypi.org/) (The Python Package Index), for:
-    - linux (x86_64 with GLIBC 2.35) and python 3.9 to 3.12
+- on [PyPI](https://pypi.org/project/geone) (The Python Package Index), for:
+    - linux (x86_64 with GLIBC 2.35 or GLIBC 2.27) and python 3.9 to 3.12
     - mac (x86_64 or arm64) and python 3.9 to 3.12
     - windows and python 3.9 to 3.12
-- on this [Github repository](https://github.com/randlab/geone), for:
+- on the [Github repository](https://github.com/randlab/geone), for:
     - linux (x86_64 with GLIBC 2.35 or GLIBC 2.27) and python 3.7 to 3.12
     - mac (x86_64 or arm64) and python 3.8 to 3.12
     - windows and python 3.7 to 3.12
 
-### Installation from [PyPI](https://pypi.org/)
+### Installation from [PyPI](https://pypi.org/project/geone)
 
 In a terminal type 
 ```
@@ -115,7 +115,7 @@ pip install geone
 ```
 Or, equivalently: `python -m pip install geone`.
 
-### Installation from this [Github repository](https://github.com/randlab/geone)
+### Installation from the [Github repository](https://github.com/randlab/geone)
 
 In a terminal, change directory where to download GEONE, and type
 ```
@@ -178,6 +178,8 @@ In a terminal type
 
 ### Other references 
 - C. Lantuéjoul (2002) Geostatistical Simulation, Models and Algorithms. Springer Verlag, Berlin, 256 p.
+- P. Renard, D. Allard (2013), Connectivity metrics for subsurface flow and transport. Advances in Water Resources 51:168-196, `doi:10.1016/j.advwatres.2011.12.001 <https://doi.org/10.1016/j.advwatres.2011.12.001>`_
+- J. Straubhaar, P. Renard (2024), Exploring substitution random functions composed of stationary multi-Gaussian processes. Stochastic Environmental Research and Risk Assessment, `doi:10.1007/s00477-024-02662-x <https://doi.org/10.1007/s00477-024-02662-x>`_
  -->
 
 ## License

{geone-1.2.14 → geone-1.2.15}/geone.egg-info/SOURCES.txt

@@ -1,4 +1,5 @@
 LICENSE
+MANIFEST.in
 README.md
 pyproject.toml
 setup.py
@@ -18,10 +19,24 @@ src/geone/grf.py
 src/geone/img.py
 src/geone/imgplot.py
 src/geone/imgplot3d.py
+src/geone/markovChain.py
 src/geone/multiGaussian.py
 src/geone/pgs.py
 src/geone/randProcess.py
+src/geone/srf.py
 src/geone/tools.py
+src/geone/lib_deesse_core/linux_old_py310/__init__.py
+src/geone/lib_deesse_core/linux_old_py310/_deesse.so
+src/geone/lib_deesse_core/linux_old_py310/deesse.py
+src/geone/lib_deesse_core/linux_old_py311/__init__.py
+src/geone/lib_deesse_core/linux_old_py311/_deesse.so
+src/geone/lib_deesse_core/linux_old_py311/deesse.py
+src/geone/lib_deesse_core/linux_old_py312/__init__.py
+src/geone/lib_deesse_core/linux_old_py312/_deesse.so
+src/geone/lib_deesse_core/linux_old_py312/deesse.py
+src/geone/lib_deesse_core/linux_old_py39/__init__.py
+src/geone/lib_deesse_core/linux_old_py39/_deesse.so
+src/geone/lib_deesse_core/linux_old_py39/deesse.py
 src/geone/lib_deesse_core/linux_py310/__init__.py
 src/geone/lib_deesse_core/linux_py310/_deesse.so
 src/geone/lib_deesse_core/linux_py310/deesse.py
@@ -78,6 +93,18 @@ src/geone/lib_deesse_core/win_py39/_deesse.pyd
 src/geone/lib_deesse_core/win_py39/deesse.py
 src/geone/lib_deesse_core/win_py39/vcruntime140.dll
 src/geone/lib_deesse_core/win_py39/vcruntime140_1.dll
+src/geone/lib_geosclassic_core/linux_old_py310/__init__.py
+src/geone/lib_geosclassic_core/linux_old_py310/_geosclassic.so
+src/geone/lib_geosclassic_core/linux_old_py310/geosclassic.py
+src/geone/lib_geosclassic_core/linux_old_py311/__init__.py
+src/geone/lib_geosclassic_core/linux_old_py311/_geosclassic.so
+src/geone/lib_geosclassic_core/linux_old_py311/geosclassic.py
+src/geone/lib_geosclassic_core/linux_old_py312/__init__.py
+src/geone/lib_geosclassic_core/linux_old_py312/_geosclassic.so
+src/geone/lib_geosclassic_core/linux_old_py312/geosclassic.py
+src/geone/lib_geosclassic_core/linux_old_py39/__init__.py
+src/geone/lib_geosclassic_core/linux_old_py39/_geosclassic.so
+src/geone/lib_geosclassic_core/linux_old_py39/geosclassic.py
 src/geone/lib_geosclassic_core/linux_py310/__init__.py
 src/geone/lib_geosclassic_core/linux_py310/_geosclassic.so
 src/geone/lib_geosclassic_core/linux_py310/geosclassic.py

{geone-1.2.14 → geone-1.2.15}/setup.py

@@ -3,7 +3,7 @@
 # or
 #    pip install . -v
 
-import sys, os, platform, glob
+import sys, os, platform
 import setuptools
 
 COL_CONFIG = '\033[1;36m\033[40m' # bold cyan on black
@@ -16,7 +16,6 @@ linux_old_glibc_version = (2, 27) # glibc version for the library in */linux_old
 # Get configuration: platform system, version of python, version of glibc
 try:
     platform_system = platform.system()     # 'Windows' or 'Linux' or 'Darwin' accepted
-
     python_version = sys.version_info[0:2]  # e.g. (3, 10)
 
     try:
@@ -31,8 +30,7 @@ try:
         machine = None
 
 except:
-    print(f'{COL_ERR}ERROR: getting config{COL_RESET}')
-    exit()
+    sys.exit(f'{COL_ERR}ERROR: getting config{COL_RESET}')
 
 print(f'{COL_CONFIG}Your configuration: platform_system={platform_system}, python_version={python_version}, glibc_version={glibc_version}{COL_RESET}')
 
@@ -64,22 +62,7 @@ else:
     prefix = None
 
 # Set suffix
-if python_version == (3, 6):
-    suffix = 'py36'
-elif python_version == (3, 7):
-    suffix = 'py37'
-elif python_version == (3, 8):
-    suffix = 'py38'
-elif python_version == (3, 9):
-    suffix = 'py39'
-elif python_version == (3, 10):
-    suffix = 'py310'
-elif python_version == (3, 11):
-    suffix = 'py311'
-elif python_version == (3, 12):
-    suffix = 'py312'
-else:
-    suffix = None
+suffix = f'py{python_version[0]}{python_version[1]}'
 
 # Set subdir_selected
 if prefix is None or suffix is None:
@@ -87,27 +70,12 @@ if prefix is None or suffix is None:
 else:
     subdir_selected = f'{prefix}_{suffix}'
 
-# Set directories containing the libraries and data files to be kept in source when building package
-supported_py_version = ['39', '310', '311', '312']
-supported_lib = ['linux', 'mac_x86_64', 'mac_arm64', 'win']
-lib_subdir_list = ['_py'.join([li, py]) for li in supported_lib for py in supported_py_version]
-
-if subdir_selected is None or subdir_selected not in lib_subdir_list:
-# if subdir_selected is None or not os.path.isdir(f'src/geone/lib_deesse_core/{subdir_selected}'):
-    print(f'{COL_ERR}ERROR: package geone not available for your configuration [platform_system={platform_system}, python_version={python_version}, glibc_version={glibc_version}]{COL_RESET}')
-    # exit()
-
 # Set directories containing the libraries of the right version
 deesse_core_dir_selected = f'src/geone/lib_deesse_core/{subdir_selected}'
 geosclassic_core_dir_selected = f'src/geone/lib_geosclassic_core/{subdir_selected}'
 
-lib_deesse_target_dir_list = [f'src.geone.lib_deesse_core.{d}' for d in lib_subdir_list]
-lib_deesse_files_list = [glob.glob(f'src/geone/lib_deesse_core/{d}/*') for d in lib_subdir_list]
-
-lib_geosclassic_target_dir_list = [f'src.geone.lib_geosclassic_core.{d}' for d in lib_subdir_list]
-lib_geosclassic_files_list = [glob.glob(f'src/geone/lib_geosclassic_core/{d}/*') for d in lib_subdir_list]
-
-data_files = list(zip(lib_deesse_target_dir_list, lib_deesse_files_list)) + list(zip(lib_geosclassic_target_dir_list, lib_geosclassic_files_list))
+if subdir_selected is None or not os.path.isdir(deesse_core_dir_selected) or not os.path.isdir(geosclassic_core_dir_selected):
+    sys.exit(f'{COL_ERR}ERROR: package geone not available for your configuration [platform_system={platform_system}, python_version={python_version}, glibc_version={glibc_version}]{COL_RESET}')
 
 # Set long_description
 with open("README.md", "r") as file_handle:
@@ -133,8 +101,8 @@ setuptools.setup(
         'geone.deesse_core':['*'],
         'geone.geosclassic_core':['*']
         },
-    include_package_data=True,
-    data_files=data_files, # sources (lib) for all platforms
+    include_package_data=False, # False to prevent files from MANIFEST.in to be included in the wheel (.whl)
+    # data_files=... # do not use! set files to be included in the source distribution (.tar.gz) in MANIFEST.in
     license=open('LICENSE', encoding='utf-8').read()
     # # already defined in pyproject.toml...
     # author="Julien Straubhaar",

{geone-1.2.14 → geone-1.2.15}/src/geone/__init__.py

@@ -12,9 +12,11 @@ from . import img
 from . import imgplot
 from . import imgplot3d
 from . import img
+from . import markovChain
 from . import multiGaussian
 from . import pgs
 from . import randProcess
+from . import srf
 from . import tools
 
 # # import all modules

{geone-1.2.14 → geone-1.2.15}/src/geone/_version.py

@@ -1,6 +1,6 @@
 # Version
 
 # major, minor, micro
-version_info = (1, 2, 14)
+version_info = (1, 2, 15)
 
 __version__ = '.'.join(map(str, version_info))

{geone-1.2.14 → geone-1.2.15}/src/geone/covModel.py

@@ -4071,7 +4071,7 @@ def plot_variogramCloud1D(h, g, decim=1.0, seed=None, grid=True, **kwargs):
         hi = h
         gi = g
 
-    plt.plot(h, g, **kwargs)
+    plt.plot(hi, gi, **kwargs)
     plt.xlabel('h')
     plt.ylabel(r'$1/2(Z(x)-Z(x+h))^2$')
     plt.grid(grid)
@@ -8179,7 +8179,7 @@ def cross_valid_loo(x, v, cov_model, significance=0.05, dmin=None,
     The CRPS at x[i] is defined as
 
     .. math::
-        crps[i] = - \\int_{-\\infty}^{+\\infty}(F[i](y) - \\mathbb{I}(y>v[i]))^2 dy
+        crps[i] = - \\int_{-\\infty}^{+\\infty}(F[i](y) - \\mathbf{1}(y>v[i]))^2 dy
 
     and is equal to
 

{geone-1.2.14 → geone-1.2.15}/src/geone/geosclassicinterface.py

@@ -11588,9 +11588,9 @@ def imgTwoPointStatisticsImage(
 
     References
     ----------
-    - Renard P, Allard D (2013), \
+    - P\. Renard, D\. Allard (2013), \
     Connectivity metrics for subsurface flow and transport. \
-    Adv Water Resour 51:168–196, \
+    Advances in Water Resources 51:168-196, \
     `doi:10.1016/j.advwatres.2011.12.001 <https://doi.org/10.1016/j.advwatres.2011.12.001>`_
     """
     # * correlogram            : g(h) = cor(v(x), v(x+h)) (linear correlation)
@@ -11801,9 +11801,9 @@ def imgConnectivityGammaValue(
 
     References
     ----------
-    - Renard P, Allard D (2013), \
+    - P\. Renard, D\. Allard (2013), \
     Connectivity metrics for subsurface flow and transport. \
-    Adv Water Resour 51:168–196, \
+    Advances in Water Resources 51:168-196, \
     `doi:10.1016/j.advwatres.2011.12.001 <https://doi.org/10.1016/j.advwatres.2011.12.001>`_
     """
     fname = 'imgConnectivityGammaValue'
@@ -11942,9 +11942,9 @@ def imgConnectivityGammaCurves(
 
     References
     ----------
-    - Renard P, Allard D (2013), \
+    - P\. Renard, D\. Allard (2013), \
     Connectivity metrics for subsurface flow and transport. \
-    Adv Water Resour 51:168–196, \
+    Advances in Water Resources 51:168-196, \
     `doi:10.1016/j.advwatres.2011.12.001 <https://doi.org/10.1016/j.advwatres.2011.12.001>`_
     """
     fname = 'imgConnectivityGammaCurves'
@@ -12112,9 +12112,9 @@ def imgConnectivityEulerNumber(
 
     References
     ----------
-    - Renard P, Allard D (2013), \
+    - P\. Renard, D\. Allard (2013), \
     Connectivity metrics for subsurface flow and transport. \
-    Adv Water Resour 51:168–196, \
+    Advances in Water Resources 51:168-196, \
     `doi:10.1016/j.advwatres.2011.12.001 <https://doi.org/10.1016/j.advwatres.2011.12.001>`_
     """
     fname = 'imgConnectivityEulerNumber'