CIs: formatting

.coveragerc

@@ -3,4 +3,4 @@ omit =
     # omit anything in a .local directory anywhere
     */.local/*
     # omit everything in /usr
-    /usr/*
+    /usr/*

.github/workflows/formatting.yml

@@ -0,0 +1,50 @@
+# This workflow will install Python formatting tool black and check correctness of code format for all python files
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+name: python-package
+
+on:
+  push:
+    branches: [main, develop]
+  pull_request:
+    branches: [main, develop]
+
+jobs:
+  formatting:
+    strategy:
+      matrix:
+        python-version: [3.13]
+        os: [ubuntu-latest, ubuntu-22.04]
+
+    runs-on: ${{matrix.os}}
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+      # - name: Install dependencies
+      #   run: |
+      #     python -m pip install --upgrade pip
+      #     pip install black
+      # - name: black format
+      #   run: |
+      #     black --diff --check .
+      - name: Check files end with newline
+        run: |
+          # Find all files (excluding binary and git files) and check if they end with a newline
+          EXIT_CODE=0
+          while IFS= read -r -d '' file; do
+            # Skip __init__.py files (should not end with newline)
+            if [[ "$file" == *"__init__.py" ]]; then
+              continue
+            fi
+            # Skip binary files
+            if file "$file" | grep -q "text"; then
+              # Check if file ends with a newline
+              if [ -n "$(tail -c 1 "$file")" ]; then
+                echo "ERROR: $file does not end with a newline"
+                EXIT_CODE=1
+              fi
+            fi
+          done < <(find . -type f -not -path '*/\.git/*' -print0)
+          exit $EXIT_CODE

.gitignore

@@ -45,3 +45,6 @@ Sessionx.vim
 tags
 # Persistent undo
 [._]*.un~
+
+# Output files and directories
+build/

examples/BabelStream/.gitignore

@@ -1 +1 @@
-kokkos/babel_stream/babel_stream
+kokkos/babel_stream/babel_stream

examples/ExaMiniMD/.gitignore

@@ -1,2 +1,2 @@
 *.nbi
-*.nbc
+*.nbc

examples/ExaMiniMD/README.md

@@ -2,4 +2,4 @@ This directory contains an implementation of ExaMiniMD written in PyKokkos.
 Original repo: https://github.com/ECP-copa/ExaMiniMD
 SHA: b6db78eeab55ccd95675bbf87b4638bb7a403039
 
-To run: python src/main.py -il input/in.lj --fill
+To run: python src/main.py -il input/in.lj --fill

examples/ExaMiniMD/standalone/.gitignore

@@ -1,2 +1,2 @@
 *.nbi
-*.nbc
+*.nbc

examples/ExaMiniMD/standalone/input.txt

@@ -1,4 +1,4 @@
 V: 0.378024 0.545211 0.640403 || -1.068958 -0.481107 0.561693 || 0.460053 -1.095252 -0.577054 || 0.198839 1.077796 -0.682463 || 1.060739 1.373164 -0.723115 || 0.161829 -1.159987 -1.706320 || 0.039016 0.676862 0.622015 || -0.788906 -0.437339 -0.400488 || -1.359995 0.485555 1.040725 || 0.646287 0.055289 0.411390 || -1.268214 1.074131 0.584679 || 0.008655 -0.592103 0.395507 || -0.264262 -0.487297 -1.688796 || 0.905854 0.130842 0.702301 || -0.700365 -0.408724 -1.521469 || -1.064948 1.048318 0.905022 || 
 Mass: 2.000000 || 0.000000 || 0.000000 || 0.000000 || 0.000000 || 0.000000 || 0.000000 || 0.000000 || 74922952976463886612494639615534525265225649798966677392892387483161181263696273328494175337183569571031983095237201100666603071569423424169407163557637775218342900125680904049529227457647208929519363737595668997040750422300188026968362339945938944.000000 || 0.005000 || 0.002500 || 0.000000 || 0.000000 || 16920071172525382285473125425930026455059225750565119522777865124712019447860338814225844729775420856359922438758568758850413809874236159358595359738524412104577874239900167886037697955889152.000000 || 10589246342251358090997449139234627623056451755240821348127726367574270708878985113278288483606729164319343270646915331883419249485806695294377605875108000780781466778198364969505790109913194980835559245252579557376.000000 || 0.000000 || 
 Type: 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 
-Got: 65.100000
+Got: 65.100000

examples/ExaMiniMD/standalone/src/main.py

@@ -7,4 +7,4 @@ def run() -> None:
     exa_mini_md.run(exa_mini_md.input.nsteps)
 
 if __name__ == "__main__":
-    run()
+    run()

examples/ExaMiniMD/workload/input.txt

@@ -1,4 +1,4 @@
 V: 0.378024 0.545211 0.640403 || -1.068958 -0.481107 0.561693 || 0.460053 -1.095252 -0.577054 || 0.198839 1.077796 -0.682463 || 1.060739 1.373164 -0.723115 || 0.161829 -1.159987 -1.706320 || 0.039016 0.676862 0.622015 || -0.788906 -0.437339 -0.400488 || -1.359995 0.485555 1.040725 || 0.646287 0.055289 0.411390 || -1.268214 1.074131 0.584679 || 0.008655 -0.592103 0.395507 || -0.264262 -0.487297 -1.688796 || 0.905854 0.130842 0.702301 || -0.700365 -0.408724 -1.521469 || -1.064948 1.048318 0.905022 || 
 Mass: 2.000000 || 0.000000 || 0.000000 || 0.000000 || 0.000000 || 0.000000 || 0.000000 || 0.000000 || 74922952976463886612494639615534525265225649798966677392892387483161181263696273328494175337183569571031983095237201100666603071569423424169407163557637775218342900125680904049529227457647208929519363737595668997040750422300188026968362339945938944.000000 || 0.005000 || 0.002500 || 0.000000 || 0.000000 || 16920071172525382285473125425930026455059225750565119522777865124712019447860338814225844729775420856359922438758568758850413809874236159358595359738524412104577874239900167886037697955889152.000000 || 10589246342251358090997449139234627623056451755240821348127726367574270708878985113278288483606729164319343270646915331883419249485806695294377605875108000780781466778198364969505790109913194980835559245252579557376.000000 || 0.000000 || 
 Type: 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 
-Got: 65.100000
+Got: 65.100000

examples/ExaMiniMD/workload/src/main.py

@@ -7,4 +7,4 @@ def run() -> None:
     exa_mini_md.run(exa_mini_md.input.nsteps)
 
 if __name__ == "__main__":
-    run()
+    run()

examples/LogisticRegression/LR.py

@@ -1062,4 +1062,4 @@ def main():
     clf.predict_proba(asarray(X[:2, :]))
     print(clf.score(asarray(X), asarray(y)))
 
-main()
+main()

examples/NaiveBayes/GaussianNB.py

@@ -627,4 +627,4 @@ def main():
     y_pred = gnb.fit(asarray(X_train), asarray(y_train)).predict(asarray(X_test))
     print("Number of mislabeled points out of a total %d points : %d" % (X_test.shape[0], (y_test != y_pred).sum()))
 
-main()
+main()

examples/ParRes/functor/nstream.py

@@ -96,4 +96,4 @@ def run() -> None:
         print("Avg time (ms): %f" % (avgtime/1.e-3))
 
 if __name__ == "__main__":
-    run()
+    run()

examples/ParRes/standalone/nstream.py

@@ -83,4 +83,4 @@ def run() -> None:
         print("Avg time (ms): %f" % (avgtime/1.e-3))
 
 if __name__ == "__main__":
-    run()
+    run()

examples/kokkos/README.md

@@ -1,2 +1,2 @@
 This directory contains examples translated from the main Kokkos repository:
-https://github.com/kokkos/kokkos/tree/develop/example/tutorial
+https://github.com/kokkos/kokkos/tree/develop/example/tutorial

examples/pykokkos/README.md

@@ -1,2 +1,2 @@
 This directory contains examples of how certain features
-are implemented in PyKokkos.
+are implemented in PyKokkos.

examples/pykokkos/team_thread_mdrange.py

@@ -32,4 +32,4 @@ def run():
     print(A)
 
 if __name__ == "__main__":
-    run()
+    run()

pykokkos/core/fusion/access_modes.py

@@ -214,4 +214,4 @@ def get_view_write_indices_and_modes(AST: ast.FunctionDef, view_args: Dict[str,
     visitor.visit(AST)
     access_indices: Dict[Tuple[str, int], Tuple[AccessIndex, AccessMode, str]] = visitor.access_indices
 
-    return access_indices
+    return access_indices

pykokkos/core/fusion/util.py

@@ -76,4 +76,4 @@ def add_parent_refs(classdef: ast.ClassDef) -> ast.ClassDef:
                     grand_child.parent_accessor = field_name
                     grand_child.idx_in_parent = idx
 
-    return classdef
+    return classdef

pykokkos/core/module_setup.py

@@ -224,4 +224,4 @@ def is_compiled(self) -> bool:
         Check if this module is compiled for its execution space
         """
 
-        return CppSetup.is_compiled(self.get_output_dir(self.main, self.metadata, self.space, self.types_signature, self.restrict_signature))
+        return CppSetup.is_compiled(self.get_output_dir(self.main, self.metadata, self.space, self.types_signature, self.restrict_signature))

pykokkos/core/parsers/parser.py

@@ -459,4 +459,4 @@ def is_workunit(node: ast.stmt, pk_import: str) -> bool:
                 if (attribute.value.id == pk_import and Decorator.is_work_unit(attribute.attr)):
                     return True
 
-        return False
+        return False

pykokkos/core/template_Makefile

@@ -41,4 +41,4 @@ run: $(TARGET)
 
 clean:
 	rm *.o
-	rm $(TARGET)
+	rm $(TARGET)

pykokkos/core/translators/members.py

@@ -290,4 +290,4 @@ def get_random_pool(self, classdef: ast.ClassDef, source: Tuple[List[str], int],
             declref = n
             decltype = t
 
-        return declref, decltype
+        return declref, decltype

pykokkos/core/translators/symbols_pass.py

@@ -181,4 +181,4 @@ def get_error_messages(self, nodes: Dict[ast.AST, ErrorStatus]) -> List[str]:
             message: str = f"File \"{self.path}\", line {node.lineno}:\n {error.value} symbol {symbol} used"
             messages.append(message)
 
-        return messages
+        return messages

pykokkos/core/type_inference/args_type_inference.py

@@ -495,4 +495,4 @@ def restore_original_args(workunit_str: str, tree: ast.AST) -> ast.AST:
         # first call, store the original params
         ORIGINAL_PARAMS[workunit_str] = pickle.dumps(tree.args.args)
 
-    return tree
+    return tree

pykokkos/interface/atomic/atomic_fetch_op.py

@@ -110,4 +110,4 @@ def atomic_compare_exchange(
         indices: List[int],
         comparison_value: int,
         new_value: int) -> int:
-    pass
+    pass

pykokkos/interface/execution_policy.py

@@ -199,4 +199,4 @@ def __init__(self, team_member: TeamMember, count: int):
 
 class TeamThreadMDRange(ExecutionPolicy):
     def __init__(self, *args) -> None:
-        pass
+        pass

pykokkos/interface/execution_space.py

@@ -56,4 +56,4 @@ def __init__(self, space: ExecutionSpace, stream = None):
 
             self.instance = instance_constructor(stream.ptr, False)
         else:
-            self.instance = instance_constructor()
+            self.instance = instance_constructor()

pykokkos/interface/layout.py

@@ -23,4 +23,4 @@ def get_default_layout(space: MemorySpace) -> Layout:
     if space is MemorySpace.HostSpace:
         return Layout.LayoutRight
     else:
-        return Layout.LayoutLeft
+        return Layout.LayoutLeft

pykokkos/interface/mathematical_special_functions.py

@@ -3,4 +3,4 @@ def cyl_bessel_j0(input: float) -> float:
     pass
 
 def cyl_bessel_j1(input: float) -> float:
-    pass
+    pass

pykokkos/interface/parallel_dispatch.py

@@ -254,4 +254,4 @@ def execute(space: ExecutionSpace, workload: object) -> None:
 
 
 def flush():
-    runtime_singleton.runtime.flush_trace()
+    runtime_singleton.runtime.flush_trace()

pykokkos/interface/random.py

@@ -19,4 +19,4 @@ def rand(dtype: type):
     :param dtype: the data type of the number to be generated
     """
 
-    pass
+    pass

pykokkos/lib/manipulate.py

@@ -78,4 +78,4 @@ def expand_dims(view, axis=0):
             out = pk.View([view.shape[0], 1, view.shape[1]], pk.double)
             pk.parallel_for(view.shape[0], expand_dims_1_impl_2d_double, view=view, out=out)
 
-    return out
+    return out

tests.sh

@@ -4,4 +4,4 @@ readonly RC_FILE="${_DIR}"/.coveragerc
 
 coverage run --rcfile="${RC_FILE}" -m unittest discover -s "${TESTS_DIR}"
 coverage report
-coverage xml -o cov.xml
+coverage xml -o cov.xml

tests/loop_fusion_kernels.py

@@ -178,4 +178,4 @@ def main():
 
 
 if __name__ == "__main__":
-    main()
+    main()

tests/test_parallelfor.py

@@ -41,4 +41,4 @@
 #             self.assertEqual(result, expected_result)
 
 # if __name__ == '__main__':
-#     unittest.main()
+#     unittest.main()