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 test_field.run.xml

@@ -1,13 +1,16 @@
 <component name="ProjectRunConfigurationManager">
   <configuration default="false" name="pytest test_field" type="tests" factoryName="py.test">
     <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="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="DEBUG_JUST_MY_CODE" value="true" />
+    <option name="RUN_TOOL" value="" />
     <option name="_new_keywords" value="&quot;&quot;" />
     <option name="_new_parameters" value="&quot;-s&quot;" />
     <option name="_new_additionalArguments" value="&quot;&quot;" />

.run/pytest test_gmsh.run.xml

@@ -1,13 +1,16 @@
 <component name="ProjectRunConfigurationManager">
   <configuration default="false" name="pytest test_gmsh" type="tests" factoryName="py.test">
     <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="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="DEBUG_JUST_MY_CODE" value="true" />
+    <option name="RUN_TOOL" value="" />
     <option name="_new_keywords" value="&quot;&quot;" />
     <option name="_new_parameters" value="&quot;&quot;" />
     <option name="_new_additionalArguments" 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" />

AGENTS.md

@@ -0,0 +1,96 @@
+# CODEX context for BGEM library
+
+## Project summary
+
+Bgem library is a intended as an extension or wrapper of GMSH python API.
+It helps to keep tracks of the geometry objects during geometrical operations;
+it introduces `ObjectSet` class keeping the tracks of dimtags and provides wrapper
+functions to GMSH API calls.
+
+Further it provides better interface to GMSH fields, reader/writer for GMSH meshes
+and a HealMesh class that can help fixing degenerated elements in a given mesh.
+
+Submodule called `Stochastic` provides generator for DFN (Discrete Fracture Network)
+based on distributions used in geology.
+
+## Project summary (short)
+
+Robust open source tool for creation of parametric geometries and computational meshes via. Python code. 
+Primary focus are hydrogeological applications with geometries including both random fractures and deterministic natural or anthropogenic features.
+Bgem library is a intended as an extension and/or wrapper of GMSH python API.
+
+## CODEX Ignore Folders
+- Not specified
+
+## CODEX Readonly Folders
+- Not specified
+
+## Project Structure
+- `src/bgem` - source files
+- `tests` - pytest based unit tests of individual source blocks
+- `tutorials` - integrated tests, currently insufficient
+
+## `src/bgem/` Project Source Structure
+
+- `bspline/` - 
+- `geometry/` - 
+- `gmsh/` - main functions providing interface for GMSH API
+- `polygons/` - 
+- `stochastic/` - code for DFN generation
+
+
+## CODEX Guidelines
+- treat keyword 'AGENT:' in comments as a source context dependent message for your further development
+- any comment containing `AGENT:` is an active developer instruction
+- NEVER remove, rewrite, or move an `AGENT:` comment unless you implement that instruction in the same change
+- if you make only a local fix around an `AGENT:` comment, leave the comment untouched
+- if an `AGENT:` instruction looks outdated or wrong, ask before removing it
+- never stage or commit changes yourself
+- Always review your changes before finishing for human review.
+- Do not touch anything outside the repository directory, unless directly asked!
+
+## Status tracking
+- `STATUS.md` is the handoff log for interrupted or multi-turn work. Update it when a session ends with unfinished relevant work, when the user asks for a status review, or when a fresh checkpoint would help the next session continue without re-discovery.
+- Keep newest entry first. Do not rewrite older entries except to fix clearly factual mistakes.
+- Start each entry with one line in this form:
+  `` `YYYY-MM-DD`: `<commit>` @ `<branch>` by `<author>` ``
+- Under each entry keep exactly these sections in order:
+  `## Goal`
+  short statement of the intended task or checkpoint scope
+  `## Changes summary`
+  flat bullets describing committed changes first, then important staged/unstaged/untracked changes if they are relevant to continuing the task
+  `## Verified`
+  flat bullets with commands actually run and the important observed result
+  `## Open items`
+  flat bullets for remaining risks, missing verification, known breakage, or next recommended step
+- Record only repo-relevant facts that help continuation. Skip conversational history, speculation, and incidental noise.
+- When the worktree is dirty, explicitly distinguish committed, staged, unstaged, and untracked changes, but mention only files relevant to the tracked task.
+- Prefer clickable file links for important files mentioned in `STATUS.md`.
+- If verification was partial, say so plainly. Do not imply a full test pass when only compile checks, a single testcase, or CLI smoke checks were run.
+- If a run failed, record the failing command and the actionable failure mode instead of hiding it.
+- Before finishing a task that changed the practical project state, review whether `STATUS.md` still matches the actual branch/worktree state and update it if needed.
+
+## Coding rules
+- Best code, is no code!
+- prefer functional style with poor functions;
+  ideally do not change objects after construction, all methods do calculations
+  only reading the data in the class
+- prefer high level code: numpy, pandas, xarray instead loops and native python structures (lists, dicts)
+- use logging
+- Use logging for debug outputs.
+- use pathlib
+- use attrs for dataclasses
+- use attrs staticmethod/classmethod technique to construct from other data then is stored in the dataclass
+- Be defensive, with strong checks, but only for the user input data.
+  That means error inputs must raise early. Therefore only check for existing keys in input dicts
+  if these will be required down in a long calculation. Otherwise just let KeyError do the job.
+- do not use "guess" default values, only obvious defaults
+- Do not use other config keys in the case of a KeyError, just throw early.
+- Do just basic asserts for consistency for function inputs.
+- Can add more asserts if needed during debugging.
+- NEVER resolve test errors by try blocks
+- NEVER add runtime fallbacks or import shims to compensate for a broken or incomplete environment.
+  If a declared dependency or tool is missing, report the environment problem plainly and fix the environment or tests around it, but do not implement code workarounds.
+- NEVER write "self explanatory" into comments
+- in comments indicate by ?? if you are not certain about intent of particular variable, function, parameter ...
+

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