Preliminary version of FEM solver.

.gitignore

@@ -1,3 +1,4 @@
+tests/upscale/2d_flow_homo_samples
 # Merge
 *.py.orig
 

.run/pytest in stochastic.run.xml

@@ -3,9 +3,9 @@
     <module name="bgem" />
     <option name="INTERPRETER_OPTIONS" value="" />
     <option name="PARENT_ENVS" value="true" />
-    <option name="SDK_HOME" value="/usr/bin/python3.8" />
+    <option name="SDK_HOME" value="" />
     <option name="WORKING_DIRECTORY" value="" />
-    <option name="IS_MODULE_SDK" value="false" />
+    <option name="IS_MODULE_SDK" value="true" />
     <option name="ADD_CONTENT_ROOTS" value="true" />
     <option name="ADD_SOURCE_ROOTS" value="true" />
     <option name="_new_keywords" value="&quot;&quot;" />

.run/pytest test_bspline_approx.run.xml

@@ -3,9 +3,9 @@
     <module name="bgem" />
     <option name="INTERPRETER_OPTIONS" value="" />
     <option name="PARENT_ENVS" value="true" />
-    <option name="SDK_HOME" value="/usr/bin/python3.8" />
+    <option name="SDK_HOME" value="" />
     <option name="WORKING_DIRECTORY" value="" />
-    <option name="IS_MODULE_SDK" value="false" />
+    <option name="IS_MODULE_SDK" value="true" />
     <option name="ADD_CONTENT_ROOTS" value="true" />
     <option name="ADD_SOURCE_ROOTS" value="true" />
     <option name="_new_keywords" value="&quot;&quot;" />

.run/pytest in gmsh.run.xml → .run/test in gmsh.run.xml

@@ -3,9 +3,9 @@
     <module name="bgem" />
     <option name="INTERPRETER_OPTIONS" value="" />
     <option name="PARENT_ENVS" value="true" />
-    <option name="SDK_HOME" value="/usr/bin/python3.8" />
+    <option name="SDK_HOME" value="" />
     <option name="WORKING_DIRECTORY" value="" />
-    <option name="IS_MODULE_SDK" value="false" />
+    <option name="IS_MODULE_SDK" value="true" />
     <option name="ADD_CONTENT_ROOTS" value="true" />
     <option name="ADD_SOURCE_ROOTS" value="true" />
     <option name="_new_keywords" value="&quot;&quot;" />

.run/test_brep_writer.run.xml

@@ -3,9 +3,9 @@
     <module name="bgem" />
     <option name="INTERPRETER_OPTIONS" value="" />
     <option name="PARENT_ENVS" value="true" />
-    <option name="SDK_HOME" value="/usr/bin/python3.8" />
+    <option name="SDK_HOME" value="" />
     <option name="WORKING_DIRECTORY" value="" />
-    <option name="IS_MODULE_SDK" value="false" />
+    <option name="IS_MODULE_SDK" value="true" />
     <option name="ADD_CONTENT_ROOTS" value="true" />
     <option name="ADD_SOURCE_ROOTS" value="true" />
     <option name="_new_keywords" value="&quot;&quot;" />

.run/tox all.run.xml

@@ -3,7 +3,8 @@
     <module name="bgem" />
     <option name="INTERPRETER_OPTIONS" value="" />
     <option name="PARENT_ENVS" value="true" />
-    <option name="SDK_HOME" value="/usr/bin/python3.8" />
+    <option name="SDK_HOME" value="/usr/bin/python3" />
+    <option name="SDK_NAME" value="Python 3.10 (2)" />
     <option name="WORKING_DIRECTORY" value="" />
     <option name="IS_MODULE_SDK" value="false" />
     <option name="ADD_CONTENT_ROOTS" value="true" />

.run/tox in gmsh.run.xml

@@ -1,9 +1,11 @@
 <component name="ProjectRunConfigurationManager">
   <configuration default="false" name="tox in gmsh" type="Tox" factoryName="Tox">
     <module name="bgem" />
+    <option name="ENV_FILES" value="" />
     <option name="INTERPRETER_OPTIONS" value="" />
     <option name="PARENT_ENVS" value="true" />
-    <option name="SDK_HOME" value="/usr/bin/python3.8" />
+    <option name="SDK_HOME" value="/usr/bin/python3" />
+    <option name="SDK_NAME" value="Python 3.10 (2)" />
     <option name="WORKING_DIRECTORY" value="" />
     <option name="IS_MODULE_SDK" value="false" />
     <option name="ADD_CONTENT_ROOTS" value="true" />

.run/tox in stochastic.run.xml

@@ -3,7 +3,8 @@
     <module name="bgem" />
     <option name="INTERPRETER_OPTIONS" value="" />
     <option name="PARENT_ENVS" value="true" />
-    <option name="SDK_HOME" value="/usr/bin/python3.8" />
+    <option name="SDK_HOME" value="/usr/bin/python3" />
+    <option name="SDK_NAME" value="Python 3.10 (2)" />
     <option name="WORKING_DIRECTORY" value="" />
     <option name="IS_MODULE_SDK" value="false" />
     <option name="ADD_CONTENT_ROOTS" value="true" />

requirements.txt

@@ -1,5 +1,7 @@
 pytest
-numpy
-scipy
-bih
+
+# some test plottings that are not part of auto test suite
+matplotlib
+joblib
 plotly
+pyvista   # fem plot

setup.py

@@ -42,7 +42,8 @@
         # eg: 'keyword1', 'keyword2', 'keyword3',
     ],
 
-    packages=['bgem', 'bgem.polygons', 'bgem.bspline', 'bgem.gmsh', 'bgem.external', 'bgem.geometry', 'bgem.stochastic'], #setuptools.find_packages(where='src'),
+    packages=['bgem', 'bgem.polygons', 'bgem.bspline', 'bgem.gmsh', 'bgem.external', 'bgem.geometry', 'bgem.stochastic',
+              'bgem.core', 'bgem.upscale'], #setuptools.find_packages(where='src'),
     package_dir={'': 'src'},
     #py_modules=[os.path.splitext(os.path.basename(path))[0] for path in glob.glob('src/*.py')],
     # package_data={
@@ -56,7 +57,7 @@
     include_package_data=True,
     zip_safe=False,
     #install_requires=['numpy', 'scipy', 'bih', 'gmsh-sdk<=4.5.1'],
-    install_requires=['numpy>=1.13.4', 'pandas', 'scipy', 'bih', 'gmsh>=4.10.4'],
+    install_requires=['numpy>=1.13.4', 'pandas', 'scipy', 'gmsh>=4.10.4', 'pyyaml-include', 'bih', 'nptyping', 'pyamg', 'attrs'],
     # incompatible changes in SDK in release 4.6.0 to be changed in the new release of bgem
     python_requires='>=3',
     # extras_require={

src/bgem/core/__init__.py

@@ -0,0 +1,7 @@
+from .memoize import EndorseCache, memoize, File
+from .common import substitute_placeholders, sample_from_population, workdir, array_attr
+from .config import dotdict, load_config, apply_variant, dump_config
+from .report import report
+from .flow_call import call_flow, FlowOutput
+
+year = 365.2425 * 24 * 60 * 60

src/bgem/core/common.py

@@ -0,0 +1,169 @@
+import os.path
+from typing import *
+import shutil
+import attrs
+import numpy.typing as npt
+
+from pathlib import Path
+import numpy as np
+import logging
+
+from .memoize import File
+
+class workdir:
+    """
+    Context manager for creation and usage of a workspace dir.
+
+    name: the workspace directory
+    inputs: list of files and directories to copy into the workspaceand
+        TODO: fine a sort of robust ad portable reference
+    clean: if true the workspace would be deleted at the end of the context manager.
+    TODO: clean_before / clean_after
+    TODO: File constructor taking current workdir environment, openning virtually copied files.
+    TODO: Workdir would not perform change of working dir, but provides system interface for: subprocess, file openning
+          only perform CD just before executing a subprocess also interacts with concept of an executable.
+    portable reference and with lazy evaluation. Optional true copy possible.
+    """
+    CopyArgs = Union[str, Tuple[str, str]]
+    def __init__(self, name:str="sandbox", inputs:List[CopyArgs] = None, clean=False):
+
+        if inputs is None:
+            inputs = []
+        self._inputs = inputs
+        self.work_dir = os.path.abspath(name)
+        Path(self.work_dir).mkdir(parents=True, exist_ok=True)
+        self._clean = clean
+        self._orig_dir = os.getcwd()
+
+    def copy(self, src, dest=None):
+        """
+        :param src: Realtive or absolute path.
+        :param dest: Relative path with respect to work dir.
+                    Default is the same as the relative source path,
+                    for abs path it is the just the last name in the path.
+        """
+        if isinstance(src, File):
+            src = src.path
+        if isinstance(dest, File):
+            dest = dest.path
+        #if dest == ".":
+        #    if os.path.isabs(src):
+        #        dest = os.path.basename(src)
+        #    else:
+        #        dest = src
+        if dest is None:
+            dest = ""
+        dest = os.path.join(self.work_dir, dest, os.path.basename(src))
+        dest_dir, _ = os.path.split(dest)
+        if not os.path.isdir(dest_dir):
+            #print(f"MAKE DIR: {dest_dir}")
+            Path(dest_dir).mkdir(parents=True, exist_ok=True)
+        abs_src = os.path.abspath(src)
+
+        # ensure that we always update the target
+        if os.path.isdir(dest):
+            shutil.rmtree(dest)
+        elif os.path.isfile(dest):
+            os.remove(dest)
+
+        # TODO: perform copy, link or redirectio to src during extraction of the File object from dictionary
+        # assumes custom tag for file, file_link, file_copy etc.
+        if os.path.isdir(src):
+            #print(f"COPY DIR: {abs_src} TO DESTINATION: {dest}")
+            shutil.copytree(abs_src, dest, dirs_exist_ok=True)
+        else:
+            try:
+                shutil.copy2(abs_src, dest)
+            except FileNotFoundError:
+                FileNotFoundError(f"COPY FILE: {abs_src} TO DESTINATION: {dest}")
+
+    def __enter__(self):
+        for item in self._inputs:
+            #print(f"treat workspace item: {item}")
+            if isinstance(item, Tuple):
+                self.copy(*item)
+            else:
+                self.copy(item)
+        os.chdir(self.work_dir)
+
+        return self.work_dir
+
+    def __exit__(self, type, value, traceback):
+        os.chdir(self._orig_dir)
+        if self._clean:
+            shutil.rmtree(self.work_dir)
+
+
+def substitute_placeholders(file_in: str, file_out: str, params: Dict[str, Any]):
+    """
+    In the template `file_in` substitute the placeholders in format '<name>'
+    according to the dict `params`. Write the result to `file_out`.
+    TODO: set Files into params, in order to compute hash from them.
+    TODO: raise for missing value in dictionary
+    """
+    used_params = []
+    files = []
+    with open(file_in, 'r') as src:
+        text = src.read()
+    for name, value in params.items():
+        if isinstance(value, File):
+            files.append(value)
+            value = value.path
+        placeholder = '<%s>' % name
+        n_repl = text.count(placeholder)
+        if n_repl > 0:
+            used_params.append(name)
+            text = text.replace(placeholder, str(value))
+    with open(file_out, 'w') as dst:
+        dst.write(text)
+
+    return File(file_out, files), used_params
+
+
+# Directory for all flow123d main input templates.
+# These are considered part of the software.
+
+# TODO: running with stdout/ stderr capture, test for errors, log but only pass to the main in the case of
+# true error
+
+def array_attr(shape, dtype=np.double, default=[]):
+    """
+    Numpy array attribut definition for the attrs library.
+    - shape and dtype specification and auto conversion
+    - defalut empty array
+    """
+    # Unfortunately broadcast_to does not support -1 in the target_shape
+    # assume shape in form (-1, ...).
+    assert shape[0] == -1
+
+    def converter(x):
+        rev_shape = reversed( (len(x), *shape[1:]) )
+        return np.broadcast_to(np.array(x).T, rev_shape).T
+
+    return attrs.field(
+        type=npt.NDArray[dtype],
+        converter=converter,
+        default=default)
+
+
+def sample_from_population(n_samples:int, frequency:Union[np.array, int]):
+    if type(frequency) is int:
+        frequency = np.full(len(frequency), 1, dtype=int)
+    else:
+        frequency = np.array(frequency, dtype=int)
+
+    cumul_freq = np.cumsum(frequency)
+    total_samples = np.sum(frequency)
+    samples = np.random.randint(0, total_samples, size=n_samples + 1)
+    samples[-1] = total_samples # stopper
+    sample_seq = np.sort(samples)
+    # put samples into bins given by cumul_freq
+    bin_samples = np.empty_like(samples)
+    i_sample = 0
+    for ifreq, c_freq in enumerate(cumul_freq):
+
+        while sample_seq[i_sample] < c_freq:
+            bin_samples[i_sample] = ifreq
+            i_sample += 1
+
+    return bin_samples[:-1]