WIP patchghostless

.github/workflows/codeql.yml

@@ -16,7 +16,7 @@ jobs:
   analyze:
     name: Analyze
     runs-on: ubuntu-latest
-    container: ghcr.io/pharchive/phare_dep/ubuntu:22.04
+    container: ghcr.io/pharchive/phare_dep/ubuntu:24.04
     permissions:
       actions: read
       contents: read
@@ -35,7 +35,7 @@ jobs:
 
       - name: Configure (cpp)
         if: ${{ matrix.language == 'cpp' }}
-        run: mkdir build; cd build; cmake .. -Dphare_configurator=ON
+        run: . /.venv/bin/activate; mkdir build; cd build; cmake .. -Dphare_configurator=ON
 
       - name: Initialize CodeQL
         uses: github/codeql-action/init@v3
@@ -50,7 +50,7 @@ jobs:
 
       - name: Build cpp
         if: ${{ matrix.language == 'cpp' }}
-        run: cd build; make
+        run: . /.venv/bin/activate; cd build; make
 
       - name: Perform CodeQL Analysis
         uses: github/codeql-action/analyze@v3

pyphare/pyphare/cpp/__init__.py

@@ -22,7 +22,7 @@ def cpp_lib(override=None):
         return importlib.import_module("pybindlibs.cpp")
     try:
         return importlib.import_module("pybindlibs.cpp_dbg")
-    except ImportError:
+    except (ImportError, ModuleNotFoundError):
         return importlib.import_module("pybindlibs.cpp")
 
 

pyphare/pyphare/pharesee/hierarchy/hierarchy_utils.py

@@ -592,6 +592,7 @@ def _compute_scalardiv(patch_datas, **kwargs):
 
 @dataclass
 class EqualityReport:
+    atol: float
     failed: List[Tuple[str, Any, Any]] = field(default_factory=lambda: [])
 
     def __bool__(self):
@@ -602,10 +603,13 @@ def __repr__(self):
             print(msg)
             try:
                 if type(ref) is FieldData:
-                    phut.assert_fp_any_all_close(ref[:], cmp[:], atol=1e-16)
+                    phut.assert_fp_any_all_close(
+                        ref[ref.box], cmp[cmp.box], atol=self.atol
+                    )
             except AssertionError as e:
                 print(e)
-        return self.failed[0][0]
+
+        return self.failed[0][0] if self.failed else "=="
 
     def __call__(self, reason, ref=None, cmp=None):
         self.failed.append((reason, ref, cmp))
@@ -622,7 +626,7 @@ def __reversed__(self):
 
 
 def hierarchy_compare(this, that, atol=1e-16):
-    eqr = EqualityReport()
+    eqr = EqualityReport(atol)
 
     if not isinstance(this, PatchHierarchy) or not isinstance(that, PatchHierarchy):
         return eqr("class type mismatch")

pyphare/pyphare/pharesee/hierarchy/patchdata.py

@@ -82,7 +82,7 @@ def __repr__(self):
 
     def compare(self, that, atol=1e-16):
         return self.field_name == that.field_name and phut.fp_any_all_close(
-            self.dataset[:], that.dataset[:], atol=atol
+            self[self.box], that[that.box], atol=atol
         )
 
     def __eq__(self, that):

pyphare/pyphare/pharesee/particles.py

@@ -205,12 +205,13 @@ def all_assert_sorted(part1, part2):
     )
 
     np.testing.assert_array_equal(part1.iCells[idx1], part2.iCells[idx2])
-    np.testing.assert_allclose(part1.deltas[idx1], part2.deltas[idx2], atol=deltol)
 
     np.testing.assert_allclose(part1.v[idx1, 0], part2.v[idx2, 0], atol=1e-12)
     np.testing.assert_allclose(part1.v[idx1, 1], part2.v[idx2, 1], atol=1e-12)
     np.testing.assert_allclose(part1.v[idx1, 2], part2.v[idx2, 2], atol=1e-12)
 
+    np.testing.assert_allclose(part1.deltas[idx1], part2.deltas[idx2], atol=deltol)
+
 
 def any_assert(part1, part2):
     np.testing.assert_equal(part1.size(), part2.size())

pyphare/pyphare/pharesee/run/run.py

@@ -284,9 +284,19 @@ def all_times(self):
             time = np.zeros(len(time_keys))
             for it, t in enumerate(time_keys):
                 time[it] = float(t)
-            ts[quantities_per_file[basename]] = time
+            if basename in quantities_per_file:
+                ts[quantities_per_file[basename]] = time
             ff.close()
         return ts
 
+    def all_pops(self):
+        pops = set()
+        for file in self.available_diags:
+            basename = os.path.basename(file).split(".")[0]
+            if basename.startswith("ions_pop_"):
+                if any([basename.endswith(k) for k in ["density", "flux", "domain"]]):
+                    pops.add(basename[9:].split("_")[0])
+        return list(pops)
+
     def times(self, qty):
         return self.all_times()[qty]

res/cmake/def.cmake

@@ -205,12 +205,12 @@ if (test AND ${PHARE_EXEC_LEVEL_MIN} GREATER 0) # 0 = no tests
     endfunction(add_phare_test)
 
     function(add_python3_test name file directory)
-      add_test(NAME py3_${name} COMMAND mpirun -n ${PHARE_MPI_PROCS} ${PHARE_MPIRUN_POSTFIX} python3 -u ${file} WORKING_DIRECTORY ${directory})
+      add_test(NAME py3_${name} COMMAND mpirun -n ${PHARE_MPI_PROCS} ${PHARE_MPIRUN_POSTFIX} ${Python_EXECUTABLE} -u ${file} WORKING_DIRECTORY ${directory})
       set_exe_paths_(py3_${name})
     endfunction(add_python3_test)
 
     function(add_mpi_python3_test N name file directory)
-      add_test(NAME py3_${name}_mpi_n_${N} COMMAND mpirun -n ${N} ${PHARE_MPIRUN_POSTFIX} python3 ${file} WORKING_DIRECTORY ${directory})
+      add_test(NAME py3_${name}_mpi_n_${N} COMMAND mpirun -n ${N} ${PHARE_MPIRUN_POSTFIX} ${Python_EXECUTABLE} ${file} WORKING_DIRECTORY ${directory})
       set_exe_paths_(py3_${name}_mpi_n_${N})
     endfunction(add_mpi_python3_test)
 
@@ -273,7 +273,7 @@ if (test AND ${PHARE_EXEC_LEVEL_MIN} GREATER 0) # 0 = no tests
       else()
         add_test(
             NAME py3_${target}_mpi_n_${N}
-            COMMAND mpirun -n ${N} ${PHARE_MPIRUN_POSTFIX} python3 -u ${file} ${CLI_ARGS}
+            COMMAND mpirun -n ${N} ${PHARE_MPIRUN_POSTFIX} ${Python_EXECUTABLE} -u ${file} ${CLI_ARGS}
             WORKING_DIRECTORY ${directory})
         set_exe_paths_(py3_${target}_mpi_n_${N})
       endif()

res/cmake/test.cmake

@@ -34,14 +34,9 @@ if (test AND ${PHARE_EXEC_LEVEL_MIN} GREATER 0) # 0 = no tests
   add_subdirectory(tests/initializer)
 
 
+  add_subdirectory(tests/amr/data/field)
   add_subdirectory(tests/amr/data/particles)
-  add_subdirectory(tests/amr/data/field/coarsening)
-  add_subdirectory(tests/amr/data/field/copy_pack)
-  add_subdirectory(tests/amr/data/field/geometry)
-  add_subdirectory(tests/amr/data/field/overlap)
-  add_subdirectory(tests/amr/data/field/refine)
-  add_subdirectory(tests/amr/data/field/variable)
-  add_subdirectory(tests/amr/data/field/time_interpolate)
+
   add_subdirectory(tests/amr/resources_manager)
   add_subdirectory(tests/amr/messengers)
   add_subdirectory(tests/amr/models)