WIP copy before refinement and TensorFieldData

.github/workflows/cmake_macos.yml

@@ -69,10 +69,10 @@ jobs:
         python -m pip install -r requirements.txt
 
     - name: Create Build Environment
-      run: cmake -E make_directory ${{runner.workspace}}/build
+      run: cmake -E make_directory ${{github.workspace}}/build
 
     - name: Configure CMake
-      working-directory: ${{runner.workspace}}/build
+      working-directory: ${{github.workspace}}/build
       run: |
         cmake $GITHUB_WORKSPACE -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON \
               -DCMAKE_BUILD_TYPE=RelWithDebInfo \
@@ -81,10 +81,10 @@ jobs:
               -DCMAKE_CXX_FLAGS="-DPHARE_DIAG_DOUBLES=1 "
 
     - name: Build
-      working-directory: ${{runner.workspace}}/build
+      working-directory: ${{github.workspace}}/build
       run: cmake --build . -j 2
 
     - name: Test
-      working-directory: ${{runner.workspace}}/build
+      working-directory: ${{github.workspace}}/build
       run: ctest -j 2 --output-on-failure
 

.github/workflows/cmake_ubuntu.yml

@@ -66,19 +66,19 @@ jobs:
         python -m pip install -r requirements.txt
 
     - name: Create Build Environment
-      run: cmake -E make_directory ${{runner.workspace}}/build
+      run: cmake -E make_directory ${{github.workspace}}/build
 
     - name: Configure CMake
-      working-directory: ${{runner.workspace}}/build
+      working-directory: ${{github.workspace}}/build
       run: |
         set -ex
         export CC=gcc CXX=g++
         [ "${{ matrix.cc }}" = "clang" ] && export CC=clang CXX=clang++
         cmake $GITHUB_WORKSPACE
-        cd ${{runner.workspace}}/PHARE/subprojects/samrai && mkdir build && cd build
+        cd ${{github.workspace}}/subprojects/samrai && mkdir build && cd build
         cmake .. -DENABLE_SAMRAI_TESTS=OFF -DCMAKE_BUILD_TYPE=RelWithDebInfo
         make -j2 && sudo make install && cd ../.. && rm -rf samrai
-        cd ${{runner.workspace}}/build && rm -rf *
+        cd ${{github.workspace}}/build && rm -rf *
         cmake $GITHUB_WORKSPACE -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON --fresh \
               -DCMAKE_BUILD_TYPE=Debug -Dasan=OFF \
               -DCMAKE_C_COMPILER_LAUNCHER=ccache \
@@ -87,9 +87,9 @@ jobs:
               -DCMAKE_CXX_FLAGS="-O3 -DPHARE_DIAG_DOUBLES=1 " -Dphare_configurator=ON
 
     - name: Build
-      working-directory: ${{runner.workspace}}/build
+      working-directory: ${{github.workspace}}/build
       run: cmake --build . -j 1
 
     - name: Test
-      working-directory: ${{runner.workspace}}/build
+      working-directory: ${{github.workspace}}/build
       run: ctest -j 2 --output-on-failure

doc/conventions.md

@@ -0,0 +1,79 @@
+# PHARE Conventions
+
+### Reference document for the code base
+
+
+# Sections
+
+1. C++
+2. Python
+3. CMake
+4. Tests
+5. Etc
+
+<br/>
+
+# 1. C++
+
+## 1.1 General
+
+...
+
+
+<br/>
+
+# 2. Python
+
+## 2.1 General
+
+...
+
+## 2.2 dependencies and imports
+
+Third party depenencies are stated in the file `requirements.txt` in the project root.
+Fewer dependencies is generally better but there should be a cost/benefit assessment for adding new dependencies.
+
+### 2.2.1 Python file import structure.
+
+Generally, we want to avoid importing any dependency at the top of a python script that may rely on binary libraries.
+
+Exceptions to this are things like numpy, which are widely used and tested.
+
+Things to expressly avoid importing at the top of a python script are
+
+- h5py
+- mpi4py
+- scipy.optimize
+
+The first two are noted as they can, and will pull in system libraries such as libmpi.so and libhdf5.so, which may not be the libraries which were used during PHARE build time, this can cause issues at runtime.
+
+scipy.optimize relies on system libraries which may not be available at runtime.
+
+The gist here is to only import these libraries at function scope when you actually need them, so that python files can be imported
+or scanned for tests and not cause issues during these operations, until the functions are used at least.
+
+<br/>
+
+# 3. CMake
+
+## 3.1 General
+
+...
+
+
+<br/>
+
+# 4. Tests
+
+## 4.1 General
+
+...
+
+<br/>
+
+# 5. Etc
+
+## 5.1 General
+
+...
+

pyphare/pyphare/cpp/__init__.py

@@ -3,27 +3,10 @@
 #
 
 
-import json
-
-# continue to use override if set
-_cpp_lib_override = None
-
-
 def cpp_lib(override=None):
     import importlib
 
-    global _cpp_lib_override
-    if override is not None:
-        _cpp_lib_override = override
-    if _cpp_lib_override is not None:
-        return importlib.import_module(_cpp_lib_override)
-
-    if not __debug__:
-        return importlib.import_module("pybindlibs.cpp")
-    try:
-        return importlib.import_module("pybindlibs.cpp_dbg")
-    except ImportError:
-        return importlib.import_module("pybindlibs.cpp")
+    return importlib.import_module("pybindlibs.cpp")
 
 
 def cpp_etc_lib():
@@ -37,6 +20,8 @@ def build_config():
 
 
 def build_config_as_json():
+    import json
+
     return json.dumps(build_config())
 
 

pyphare/pyphare/pharein/diagnostics.py

@@ -307,7 +307,7 @@ def __init__(self, **kwargs):
 
 
 class ParticleDiagnostics(Diagnostics):
-    particle_quantities = ["space_box", "domain", "levelGhost", "patchGhost"]
+    particle_quantities = ["space_box", "domain", "levelGhost"]
     type = "particle"
 
     def __init__(self, **kwargs):

pyphare/pyphare/pharesee/hierarchy/fromh5.py

@@ -15,13 +15,13 @@
 )
 from ...core.gridlayout import GridLayout
 from .hierarchy_utils import field_qties
-import h5py
+
 from pathlib import Path
 from pyphare.core.phare_utilities import listify
 
 
 h5_time_grp_key = "t"
-particle_files_patterns = ("domain", "patchGhost", "levelGhost")
+particle_files_patterns = ("domain", "levelGhost")
 
 
 def get_all_available_quantities_from_h5(filepath, time=0, exclude=["tags"], hier=None):
@@ -129,6 +129,8 @@ def h5_filename_from(diagInfo):
 
 
 def get_times_from_h5(filepath, as_float=True):
+    import h5py  # see doc/conventions.md section 2.1.1
+
     f = h5py.File(filepath, "r")
     if as_float:
         times = np.array(sorted([float(s) for s in list(f[h5_time_grp_key].keys())]))
@@ -216,6 +218,7 @@ def add_time_from_h5(hier, filepath, time, **kwargs):
     # add times to 'hier'
     # we may have a different selection box for that time as for already existing times
     # but we need to keep them, per time
+    import h5py  # see doc/conventions.md section 2.1.1
 
     h5f = h5py.File(filepath, "r")
     selection_box = kwargs.get("selection_box", None)
@@ -239,6 +242,8 @@ def add_data_from_h5(hier, filepath, time):
     if not hier.has_time(time):
         raise ValueError("time does not exist in hierarchy")
 
+    import h5py  # see doc/conventions.md section 2.1.1
+
     h5f = h5py.File(filepath, "r")
 
     # force using the hierarchy selection box at that time if existing
@@ -260,6 +265,8 @@ def new_from_h5(filepath, times, **kwargs):
     # loads all datasets from the filepath h5 file as patchdatas
     # we authorize user to pass only one selection box for all times
     # but in this case they're all the same
+    import h5py  # see doc/conventions.md section 2.1.1
+
     selection_box = kwargs.get("selection_box", [None] * len(times))
     if none_iterable(selection_box) and all_iterables(times):
         selection_box = [selection_box] * len(times)

pyphare/pyphare/pharesee/hierarchy/fromsim.py

@@ -90,7 +90,7 @@ def hierarchy_from_sim(simulator, qty, pop=""):
             # domain... while looping on the patchGhost items, we need to search in
             # the already created patches which one to which add the patchGhost particles
 
-            for ghostParticles in ["patchGhost", "levelGhost"]:
+            for ghostParticles in ["levelGhost"]:
                 if ghostParticles in populationdict:
                     for dwpatch in populationdict[ghostParticles]:
                         v = np.asarray(dwpatch.data.v)

pyphare/pyphare/pharesee/hierarchy/hierarchy_utils.py

@@ -93,24 +93,14 @@ def merge_particles(hierarchy):
                     (pdname, pd) for pdname, pd in pdatas.items() if "domain" in pdname
                 ][0]
 
-                pghost_pdatas = [
-                    (pdname, pd)
-                    for pdname, pd in pdatas.items()
-                    if "patchGhost" in pdname
-                ]
                 lghost_pdatas = [
                     (pdname, pd)
                     for pdname, pd in pdatas.items()
                     if "levelGhost" in pdname
                 ]
 
-                pghost_pdata = pghost_pdatas[0] if pghost_pdatas else None
                 lghost_pdata = lghost_pdatas[0] if lghost_pdatas else None
 
-                if pghost_pdata is not None:
-                    domain_pdata[1].dataset.add(pghost_pdata[1].dataset)
-                    del pdatas[pghost_pdata[0]]
-
                 if lghost_pdata is not None:
                     domain_pdata[1].dataset.add(lghost_pdata[1].dataset)
                     del pdatas[lghost_pdata[0]]

pyphare/pyphare/pharesee/run/run.py

@@ -202,7 +202,7 @@ def GetParticleCount(self, time, **kwargs):
         return c
 
     def GetMass(self, pop_name, **kwargs):
-        list_of_qty = ["density", "flux", "domain", "levelGhost", "patchGhost"]
+        list_of_qty = ["density", "flux", "domain", "levelGhost"]
         list_of_mass = []
 
         import h5py

pyphare/pyphare/pharesee/run/utils.py

@@ -378,7 +378,7 @@ def _compute_pressure(patch_datas, **kwargs):
     Myy = patch_datas["Myy"].dataset[:]
     Myz = patch_datas["Myz"].dataset[:]
     Mzz = patch_datas["Mzz"].dataset[:]
-    massDensity = patch_datas["rho"].dataset[:]
+    massDensity = patch_datas["value"].dataset[:]
     Vix = patch_datas["Vx"].dataset[:]
     Viy = patch_datas["Vy"].dataset[:]
     Viz = patch_datas["Vz"].dataset[:]
@@ -417,10 +417,10 @@ def _compute_pop_pressure(patch_datas, **kwargs):
     Myy = patch_datas[popname + "_Myy"].dataset[:]
     Myz = patch_datas[popname + "_Myz"].dataset[:]
     Mzz = patch_datas[popname + "_Mzz"].dataset[:]
-    Fx = patch_datas[popname + "_Fx"].dataset[:]
-    Fy = patch_datas[popname + "_Fy"].dataset[:]
-    Fz = patch_datas[popname + "_Fz"].dataset[:]
-    N = patch_datas[popname + "_rho"].dataset[:]
+    Fx = patch_datas["x"].dataset[:]
+    Fy = patch_datas["y"].dataset[:]
+    Fz = patch_datas["z"].dataset[:]
+    N = patch_datas["value"].dataset[:]
 
     mass = kwargs["mass"]
 

pyphare/pyphare/simulator/simulator.py

@@ -3,6 +3,7 @@
 #
 
 import os
+import sys
 import datetime
 import atexit
 import time as timem
@@ -91,7 +92,7 @@ def __init__(self, simulation, auto_dump=True, **kwargs):
         self.cpp_sim = None  # BE
         self.cpp_dw = None  # DRAGONS, i.e. use weakrefs if you have to ref these.
         self.post_advance = kwargs.get("post_advance", None)
-
+        self.initialized = False
         self.print_eol = "\n"
         if kwargs.get("print_one_line", True):
             self.print_eol = "\r"
@@ -132,32 +133,28 @@ def setup(self):
             )
             return self
         except Exception:
-            import sys
             import traceback
 
             print('Exception caught in "Simulator.setup()": {}'.format(sys.exc_info()))
             print(traceback.extract_stack())
             raise ValueError("Error in Simulator.setup(), see previous error")
 
     def initialize(self):
-        if self.cpp_sim is not None:
-            raise ValueError(
-                "Simulator already initialized: requires reset to re-initialize"
-            )
         try:
+            if self.initialized:
+                return
             if self.cpp_hier is None:
                 self.setup()
 
             if self.simulation.dry_run:
                 return self
 
             self.cpp_sim.initialize()
+            self.initialized = True
             self._auto_dump()  # first dump might be before first advance
 
             return self
         except Exception:
-            import sys
-
             print(
                 'Exception caught in "Simulator.initialize()": {}'.format(
                     sys.exc_info()[0]
@@ -166,8 +163,6 @@ def initialize(self):
             raise ValueError("Error in Simulator.initialize(), see previous error")
 
     def _throw(self, e):
-        import sys
-
         print_rank0(e)
         sys.exit(1)
 
@@ -264,6 +259,7 @@ def reset(self):
         self.cpp_dw = None
         self.cpp_sim = None
         self.cpp_hier = None
+        self.initialized = False
         if "samrai" in life_cycles:
             type(life_cycles["samrai"]).reset()
         return self
@@ -289,7 +285,7 @@ def interp_order(self):
         return self.cpp_sim.interp_order  # constexpr static value
 
     def _check_init(self):
-        if self.cpp_sim is None:
+        if not self.initialized:
             self.initialize()
 
     def _log_to_file(self):