Badlands 2.3 PR

badlands/badlands/model.py

@@ -840,6 +840,22 @@ def run_to_time(self, tEnd, verbose=False):
             )
             self.elevation += sub
             self.cumdiff += sub
+
+        # if Underworld coupling is active, force a strata write at the end
+        if self.input.udw==1:
+            purple = "\033[0;35m"
+            endcol = "\033[00m"
+            print(purple + "Stratal layering output to align with Underworld coupling" + endcol)
+            # force a strata write
+            self.write = 1
+            sub = self.strata.buildStrata(
+                self.elevation,
+                self.cumdiff,
+                self.force.sealevel,
+                self.recGrid.boundsPt,
+                self.write,
+                self.outputStep + 1,
+            )
 
         # Create checkpoint files and write HDF5 output
         if (

badlands/meson.build

@@ -0,0 +1,120 @@
+project( 'badlands',
+    'fortran', 'c', 
+    version:'2.3.0',
+    license:'GPLv3',
+    meson_version: '>=1.4.0',
+    default_options : ['warning_level=2', 'python.install_env=auto'])
+
+# make some environment variables
+proj_name = meson.project_name()
+py_mod    = import('python')
+py        = py_mod.find_installation(pure: false)
+py_dep    = py.dependency()
+
+### compile the utils directory
+run_command('make', '-C', 'utils', check : true)
+
+# gather resultant files of the make
+sys_includes  = [
+    'utils/classfv.mod',  
+    'utils/classoro.mod',  
+    'utils/classpd.mod',  
+    'utils/fourrier.mod',  
+    'utils/m_mrgrnk.mod',  
+    'utils/orderpack.mod',
+    'utils/classfv.o',
+    'utils/classoro.o',
+    'utils/classpd.o'
+]
+
+# install sys_includes 
+foreach file : sys_includes
+    configure_file( input: file, output: file.split('/')[1], copy: true)
+endforeach
+
+# gather numpy and fortran include dirs
+incdir_numpy = run_command(py,
+  ['-c', 'import os; os.chdir(".."); import numpy; print(numpy.get_include())'],
+  check : true
+).stdout().strip()
+
+incdir_f2py = run_command(py,
+    ['-c', 'import os; os.chdir(".."); import numpy.f2py; print(numpy.f2py.get_include())'],
+    check : true
+).stdout().strip()
+
+inc_np = include_directories(incdir_numpy, incdir_f2py)
+
+# Dictionary of sources for each extension.
+# Here we index each extension by name.
+# use pre existing pyf files as module headers
+badlands_extensions = {
+    'flowalgo': { 
+        'ext':'utils/flowalgo.f90', 
+        'fsig':'utils/flowalgo.pyf', 
+        'extra_files': 'classfv.o' 
+    },
+    'fvframe':  {
+        'ext': 'utils/fvframe.f90',
+        'fsig': 'utils/fvframe.pyf',
+        'extra_files': 'classfv.o'
+    },
+    'pdalgo':   {
+        'ext': 'utils/pdalgo.f90',
+        'fsig': 'utils/pdalgo.pyf',
+        'extra_files': 'classpd.o'
+    },
+    'ormodel':  {
+        'ext': 'utils/ormodel.f90',
+        'fsig': 'utils/ormodel.pyf',
+        'extra_files': 'classoro.o'
+    },
+    'waveseds': {
+        'ext': 'utils/waveseds.f90',
+        'fsig': 'utils/waveseds.pyf',
+        'extra_files': []
+    },
+    'sfd': {
+        'ext': 'utils/sfd.c',
+        'fsig': 'utils/sfd.pyf',
+        'extra_files': []
+    }
+}
+
+# # Create extension modules
+foreach mod : badlands_extensions.keys()
+    mdict   = badlands_extensions.get(mod)
+    sources = mdict.get('ext')
+    target  = mdict.get('fsig')
+    largs   = mdict.get('extra_files')
+
+    #message('Building extension module: ' + mod)
+    #message(sources)
+    ext_source = custom_target(mod,
+          input : target,  # .f so no F90 wrappers
+          output : [mod+'module.c', mod+'-f2pywrappers.f'],
+          command : [py, '-m', 'numpy.f2py', '@INPUT@']
+
+        # this causes mysterious errors - not sure why
+        #command : [py, '-m', 'numpy.f2py', '@INPUT@', '-m', mod, '--lower']
+    )
+
+    # compile wrapper to shared object and install to python site-packages
+    py.extension_module(mod,
+      [sources, ext_source],
+      incdir_f2py / 'fortranobject.c',
+      link_args: largs, ### DOUBLE CHECK THIS
+      include_directories: inc_np,
+      dependencies : py_dep,
+      subdir: proj_name,
+      install : true
+    )
+
+    message('Extension module: ' + mod + ' to be built and installed')
+endforeach
+
+# Install other data or resources (like LICENSE or README)
+py.install_sources('../LICENSE', subdir: proj_name)
+py.install_sources('./badlands/__init__.py', subdir: proj_name)
+py.install_sources('./badlands/model.py', subdir: proj_name)
+install_subdir('./badlands/', install_dir: py.get_install_dir())

badlands/pyproject.toml

@@ -0,0 +1,44 @@
+[build-system]
+requires = ["wheel", "meson>=1.4.0", "meson-python", "numpy"]
+build-backend = "mesonpy"
+
+[project]
+name    = "badlands"
+version = "2.3"
+authors = [ 
+  {name="Tristan Salles", email="[email protected]"},
+]
+description="Basin and Landscape Dynamics (Badlands) is a TIN-based landscape evolution model"
+readme = {file = "../README.md", content-type = "text/markdown"}
+requires-python=">=3.7"
+dependencies = [
+  "triangle",
+  "meshplex@git+https://github.com/kinnala/meshplex",
+  "numpy<2",
+  "six>=1.11.0",
+  "gFlex>=1.1.0",
+  "scikit-image>=0.15",
+  "pandas>=0.24",
+  "scipy>=1.2",
+  "h5py>=2.8.0",
+  "matplotlib>=3.0"
+]
+maintainers = [
+    {name="Julian Giordani", email="[email protected]"},
+    {name="Tristan Salles", email="[email protected]"},
+]
+license = {file = "../LICENSE"}
+classifiers= [
+  "Programming Language :: Python :: 3",
+  "Programming Language :: Python :: 3.7",
+  "Programming Language :: Python :: 3.8",
+  "Programming Language :: Python :: 3.9",
+  "Programming Language :: Python :: 3.10",
+  "Programming Language :: Python :: 3.11",
+  "Programming Language :: Python :: 3.12",
+]
+
+[project.urls]
+Homepage = "https://github.com/badlands-model"
+Documentation = "https://badlands.readthedocs.io/"
+

badlands/requirements.txt

@@ -3,7 +3,6 @@ meshplex@git+https://github.com/kinnala/meshplex
 numpy>=1.15.0
 h5py>=2.8.0
 six>=1.11.0
-setuptools>=38.4.0
 pandas>=0.24
 scipy>=1.2
 scikit-image>=0.15

badlands/setup.py

@@ -1,104 +1,5 @@
-##############################
-# BUILDING PYTHON PACKAGE PYPi
-##############################
-# python3 -m pip install --user --upgrade setuptools wheel
-# python3 setup.py sdist
-# python3 -m pip install --user --upgrade twine
-#  /root/.local/bin/twine check dist/*
-#  /root/.local/bin/twine upload dist/*
-##############################
+# This is a minimal setup.py file for Badlands
+# pyproject.toml outlines the build system and dependencies
 
-from setuptools import setup 
-from numpy.distutils.core import setup, Extension
-
-import glob
-import subprocess
-from os import path
-import io
-
-this_directory = path.abspath(path.dirname(__file__))
-with io.open(path.join(this_directory, "README.md"), encoding="utf-8") as f:
-    long_description = f.read()
-
-sys_includes = []
-subprocess.call(["make", "-C", "utils"])
-sys_includes += glob.glob("utils/*.o")
-sys_includes += glob.glob("utils/*.so")
-sys_includes += glob.glob("utils/*.mod")
-
-# interface for fortran code
-ext1 = Extension(
-    name="badlands.flowalgo",
-    sources=["utils/flowalgo.pyf", "utils/flowalgo.f90"],
-    extra_link_args=["utils/classfv.o"],
-)
-
-ext2 = Extension(
-    name="badlands.fvframe",
-    sources=["utils/fvframe.pyf", "utils/fvframe.f90"],
-    extra_link_args=["utils/classfv.o"],
-)
-
-ext3 = Extension(
-    name="badlands.pdalgo",
-    sources=["utils/pdalgo.pyf", "utils/pdalgo.f90"],
-    extra_link_args=["utils/classpd.o"],
-)
-
-ext4 = Extension(
-    name="badlands.ormodel",
-    sources=["utils/ormodel.pyf", "utils/ormodel.f90"],
-    extra_link_args=["utils/classoro.o"],
-)
-
-ext5 = Extension(
-    name="badlands.waveseds", sources=["utils/waveseds.pyf", "utils/waveseds.f90"]
-)
-
-ext6 = Extension(name="badlands.sfd", sources=["utils/sfd.pyf", "utils/sfd.c"])
-
-if __name__ == "__main__":
-    setup(
-        name="badlands",
-        author="Tristan Salles",
-        author_email="[email protected]",
-        url="https://github.com/badlands-model",
-        version="2.2.4",
-        description="Basin and Landscape Dynamics (Badlands) is a TIN-based landscape evolution model",
-        long_description=long_description,
-        long_description_content_type="text/markdown",
-        ext_modules=[ext1, ext2, ext3, ext4, ext5, ext6],
-        packages=[
-            "badlands",
-            "badlands.flow",
-            "badlands.forcing",
-            "badlands.hillslope",
-            "badlands.simulation",
-            "badlands.surface",
-            "badlands.underland",
-        ],
-        package_data={"badlands": [], "badlands": sys_includes},
-        data_files=[("badlands", sys_includes)],
-        include_package_data=True,
-        install_requires=[
-            "triangle",
-            "meshplex @ git+https://github.com/kinnala/meshplex",
-            "numpy>=1.15.0",
-            "six>=1.11.0",
-            "setuptools>=38.4.0",
-            "gFlex>=1.1.0",
-            "scikit-image>=0.15",
-            "pandas>=0.24",
-            "scipy>=1.2",
-            "h5py>=2.8.0",
-            "matplotlib>=3.0",
-        ],
-        python_requires=">=3.5",
-        classifiers=[
-            "Programming Language :: Python :: 3.5",
-            "Programming Language :: Python :: 3.6",
-            "Programming Language :: Python :: 3.7",
-            "Programming Language :: Python :: 3.8",
-            "Programming Language :: Python :: 3.9",
-        ],
-    )
+from setuptools import setup
+setup()