adding flake8 to precommit, precommit to github workflow (#87)

* adding flake8 to precommit
* adding precommit to github workflow
* updating build instructions
* adding CODE_OF_CONDUCT.md

Author: fschlimb

Diff for: .flake8

@@ -0,0 +1,17 @@
+[flake8]
+filename = *.py
+max_line_length = 80
+max-doc-length = 80
+show-source = True
+extend-ignore = E203
+
+exclude =
+    build
+    .git
+
+
+per-file-ignores =
+    examples/stencil-2d.py: E402
+    scripts/code_gen.py: F821
+    sharpy/__init__.py: F401, E501
+    sharpy/ndarray.py: F401, E501

Diff for: .github/workflows/ci.yml

@@ -118,7 +118,7 @@ jobs:
         run: |
           . $GITHUB_WORKSPACE/third_party/install/miniconda/etc/profile.d/conda.sh
           . $GITHUB_WORKSPACE/third_party/install/miniconda/bin/activate sharpy
-          MLIRROOT=$GITHUB_WORKSPACE/third_party/install/llvm-mlir IMEXROOT=$GITHUB_WORKSPACE/third_party/install/imex python setup.py install
+          MLIRROOT=$GITHUB_WORKSPACE/third_party/install/llvm-mlir IMEXROOT=$GITHUB_WORKSPACE/third_party/install/imex python -m pip install . -v
           # SHARPY_ROOT=`pip show -f sharpy | grep Location | awk '{print $2}'`
           # for some reason we cannot use the idtr from the install, not even a copy works
           libidtr=`ls ${PWD}/build/lib.linux-x86_64-cpython-*/sharpy/libidtr.so`

Diff for: .github/workflows/pre-commit.yml

@@ -0,0 +1,21 @@
+name: pre-commit
+
+on:
+  pull_request:
+  push:
+    branches: [master]
+
+permissions: read-all
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-20.04
+    steps:
+    - uses: actions/[email protected]
+    - uses: actions/setup-python@v5
+      with:
+        python-version: '3.10'
+    - name: Version of clang-format
+      run: |
+        clang-format --version
+    - uses: pre-commit/[email protected]

Diff for: .gitignore

@@ -1,3 +1,6 @@
+src/include/sharpy/p2c_ids.hpp
+.vscode
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]

Diff for: .pre-commit-config.yaml

@@ -17,15 +17,11 @@ repos:
         -   id: fix-byte-order-marker
         -   id: mixed-line-ending
         -   id: trailing-whitespace
--   repo: https://github.com/pocc/pre-commit-hooks
-    rev: v1.3.5
-    hooks:
-    -   id: clang-format
-        args: ["-i"]
 -   repo: https://github.com/psf/black
     rev: 23.12.0
     hooks:
     - id: black
+      args: ["--line-length", "80"]
       language_version: python3
 -   repo: https://github.com/PyCQA/bandit
     rev: '1.7.7'
@@ -37,3 +33,12 @@ repos:
     hooks:
     -   id: isort
         name: isort (python)
+-   repo: https://github.com/pycqa/flake8
+    rev: 5.0.4
+    hooks:
+    -   id: flake8
+-   repo: https://github.com/pocc/pre-commit-hooks
+    rev: v1.3.5
+    hooks:
+    -   id: clang-format
+        args: ["-i"]

Diff for: CODE_OF_CONDUCT.md

@@ -0,0 +1,76 @@
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+In the interest of fostering an open and welcoming environment, we as
+contributors and maintainers pledge to making participation in our project and
+our community a harassment-free experience for everyone, regardless of age, body
+size, disability, ethnicity, sex characteristics, gender identity and expression,
+level of experience, education, socio-economic status, nationality, personal
+appearance, race, religion, or sexual identity and orientation.
+
+## Our Standards
+
+Examples of behavior that contributes to creating a positive environment
+include:
+
+* Using welcoming and inclusive language
+* Being respectful of differing viewpoints and experiences
+* Gracefully accepting constructive criticism
+* Focusing on what is best for the community
+* Showing empathy towards other community members
+
+Examples of unacceptable behavior by participants include:
+
+* The use of sexualized language or imagery and unwelcome sexual attention or
+ advances
+* Trolling, insulting/derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or electronic
+ address, without explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+ professional setting
+
+## Our Responsibilities
+
+Project maintainers are responsible for clarifying the standards of acceptable
+behavior and are expected to take appropriate and fair corrective action in
+response to any instances of unacceptable behavior.
+
+Project maintainers have the right and responsibility to remove, edit, or
+reject comments, commits, code, wiki edits, issues, and other contributions
+that are not aligned to this Code of Conduct, or to ban temporarily or
+permanently any contributor for other behaviors that they deem inappropriate,
+threatening, offensive, or harmful.
+
+## Scope
+
+This Code of Conduct applies both within project spaces and in public spaces
+when an individual is representing the project or its community. Examples of
+representing a project or community include using an official project e-mail
+address, posting via an official social media account, or acting as an appointed
+representative at an online or offline event. Representation of a project may be
+further defined and clarified by project maintainers.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported by contacting the project team at [email protected]. All
+complaints will be reviewed and investigated and will result in a response that
+is deemed necessary and appropriate to the circumstances. The project team is
+obligated to maintain confidentiality with regard to the reporter of an incident.
+Further details of specific enforcement policies may be posted separately.
+
+Project maintainers who do not follow or enforce the Code of Conduct in good
+faith may face temporary or permanent repercussions as determined by other
+members of the project's leadership.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4,
+available at https://www.contributor-covenant.org/version/1/4/code-of-conduct.html
+
+[homepage]: https://www.contributor-covenant.org
+
+For answers to common questions about this code of conduct, see
+https://www.contributor-covenant.org/faq

Diff for: README.md

@@ -23,7 +23,7 @@ export IMEXROOT=<your-IMEX-install-dir>
 ## Building sharpy
 
 ```bash
-python setup.py develop
+python -m pip install .
 ```
 
 If your compiler does not default to a recent (e.g. g++ >= 9) version, try something like `CC=gcc-9 CXX=g++-9 python setup.py develop`

Diff for: Security.md renamed to SECURITY.md

@@ -161,7 +161,9 @@ def run(nopt, backend, iterations, datatype):
 
         fini = sync = lambda x=None: None
         if comm is not None:
-            assert comm.Get_size() == 1, "Numpy backend only supports serial execution."
+            assert (
+                comm.Get_size() == 1
+            ), "Numpy backend only supports serial execution."
     else:
         raise ValueError(f'Unknown backend: "{backend}"')
 

Diff for: examples/black_scholes.py

@@ -99,19 +99,31 @@ def info(s):
 
     # coordinate arrays
     x_t_2d = fromfunction(
-        lambda i, j: xmin + i * dx + dx / 2, (nx, ny), dtype=dtype, device=device
+        lambda i, j: xmin + i * dx + dx / 2,
+        (nx, ny),
+        dtype=dtype,
+        device=device,
     )
     y_t_2d = fromfunction(
-        lambda i, j: ymin + j * dy + dy / 2, (nx, ny), dtype=dtype, device=device
+        lambda i, j: ymin + j * dy + dy / 2,
+        (nx, ny),
+        dtype=dtype,
+        device=device,
     )
     x_u_2d = fromfunction(
         lambda i, j: xmin + i * dx, (nx + 1, ny), dtype=dtype, device=device
     )
     y_u_2d = fromfunction(
-        lambda i, j: ymin + j * dy + dy / 2, (nx + 1, ny), dtype=dtype, device=device
+        lambda i, j: ymin + j * dy + dy / 2,
+        (nx + 1, ny),
+        dtype=dtype,
+        device=device,
     )
     x_v_2d = fromfunction(
-        lambda i, j: xmin + i * dx + dx / 2, (nx, ny + 1), dtype=dtype, device=device
+        lambda i, j: xmin + i * dx + dx / 2,
+        (nx, ny + 1),
+        dtype=dtype,
+        device=device,
     )
     y_v_2d = fromfunction(
         lambda i, j: ymin + j * dy, (nx, ny + 1), dtype=dtype, device=device
@@ -189,7 +201,9 @@ def bathymetry(x_t_2d, y_t_2d, lx, ly):
         return bath * np.full(T_shape, 1.0, dtype, device=device)
 
     # inital elevation
-    u0, v0, e0 = exact_solution(0, x_t_2d, y_t_2d, x_u_2d, y_u_2d, x_v_2d, y_v_2d)
+    u0, v0, e0 = exact_solution(
+        0, x_t_2d, y_t_2d, x_u_2d, y_u_2d, x_v_2d, y_v_2d
+    )
     e[:, :] = e0
     u[:, :] = u0
     v[:, :] = v0
@@ -229,10 +243,14 @@ def rhs(u, v, e):
         hu[1:-1, :] = 0.5 * (H[:-1, :] + H[1:, :]) * u[1:-1, :]
         hv[:, 1:-1] = 0.5 * (H[:, :-1] + H[:, 1:]) * v[:, 1:-1]
 
-        dedt = -1.0 * ((hu[1:, :] - hu[:-1, :]) / dx + (hv[:, 1:] - hv[:, :-1]) / dy)
+        dedt = -1.0 * (
+            (hu[1:, :] - hu[:-1, :]) / dx + (hv[:, 1:] - hv[:, :-1]) / dy
+        )
 
         # total depth at F points
-        H_at_f[1:-1, 1:-1] = 0.25 * (H[1:, 1:] + H[:-1, 1:] + H[1:, :-1] + H[:-1, :-1])
+        H_at_f[1:-1, 1:-1] = 0.25 * (
+            H[1:, 1:] + H[:-1, 1:] + H[1:, :-1] + H[:-1, :-1]
+        )
         H_at_f[0, 1:-1] = 0.5 * (H[0, 1:] + H[0, :-1])
         H_at_f[-1, 1:-1] = 0.5 * (H[-1, 1:] + H[-1, :-1])
         H_at_f[1:-1, 0] = 0.5 * (H[1:, 0] + H[:-1, 0])
@@ -312,6 +330,7 @@ def step(u, v, e, u1, v1, e1, u2, v2, e2):
     initial_v = None
     initial_e = None
     tic = time_mod.perf_counter()
+    block_tic = 0
     for i in range(nt + 1):
         sync()
         t = i * dt
@@ -356,9 +375,12 @@ def step(u, v, e, u1, v1, e1, u2, v2, e2):
             info(
                 f"{i_export:2d} {i:4d} {t:.3f} elev={elev_max:7.5f} "
                 f"u={u_max:7.5f} q={q_max:8.5f} dV={diff_v: 6.3e} "
-                f"PE={total_pe:7.2e} KE={total_ke:7.2e} dE={diff_e: 6.3e}" + tcpu_str
+                f"PE={total_pe:7.2e} KE={total_ke:7.2e} dE={diff_e: 6.3e}"
+                + tcpu_str
             )
-            if not benchmark_mode and (elev_max > 1e3 or not math.isfinite(elev_max)):
+            if not benchmark_mode and (
+                elev_max > 1e3 or not math.isfinite(elev_max)
+            ):
                 raise ValueError(f"Invalid elevation value: {elev_max}")
             i_export += 1
             next_t_export = i_export * t_export
@@ -372,7 +394,9 @@ def step(u, v, e, u1, v1, e1, u2, v2, e2):
     duration = time_mod.perf_counter() - tic
     info(f"Duration: {duration:.2f} s")
 
-    e_exact = exact_solution(t, x_t_2d, y_t_2d, x_u_2d, y_u_2d, x_v_2d, y_v_2d)[2]
+    e_exact = exact_solution(t, x_t_2d, y_t_2d, x_u_2d, y_u_2d, x_v_2d, y_v_2d)[
+        2
+    ]
     err2 = (e_exact - e) * (e_exact - e) * dx * dy / lx / ly
     err_L2 = math.sqrt(float(np.sum(err2, all_axes)))
     info(f"L2 error: {err_L2:7.15e}")

Diff for: examples/shallow_water.py

@@ -57,7 +57,8 @@
 import sys
 
 print(
-    "Python version = ", str(sys.version_info.major) + "." + str(sys.version_info.minor)
+    "Python version = ",
+    str(sys.version_info.major) + "." + str(sys.version_info.minor),
 )
 if sys.version_info >= (33, 3):
     from time import process_time as timer
@@ -81,7 +82,8 @@ def main():
     if len(sys.argv) < 3:
         print("argument count = ", len(sys.argv))
         sys.exit(
-            "Usage: ./stencil <# iterations> <array dimension> [<star/stencil> <radius>]"
+            "Usage: ./stencil <# iterations> <array dimension>"
+            " [<star/stencil> <radius>]"
         )
 
     iterations = int(sys.argv[1])
@@ -182,7 +184,9 @@ def main():
                 b = n - r
                 for s in range(-r, r + 1):
                     for t in range(-r, r + 1):
-                        B[r:b, r:b] += W[r + t, r + s] * A[r + t : b + t, r + s : b + s]
+                        B[r:b, r:b] += (
+                            W[r + t, r + s] * A[r + t : b + t, r + s : b + s]
+                        )
         A[:, :] = A + 1.0
 
     np.sync()
@@ -205,10 +209,17 @@ def main():
     if abs(norm - reference_norm) < epsilon:
         print("Solution validates")
     else:
-        print("ERROR: L1 norm = ", norm, " Reference L1 norm = ", reference_norm)
+        print(
+            "ERROR: L1 norm = ", norm, " Reference L1 norm = ", reference_norm
+        )
     flops = (2 * stencil_size + 1) * active_points
     avgtime = stencil_time / iterations
-    print("Rate (MFlops/s): ", 1.0e-6 * flops / avgtime, " Avg time (s): ", avgtime)
+    print(
+        "Rate (MFlops/s): ",
+        1.0e-6 * flops / avgtime,
+        " Avg time (s): ",
+        avgtime,
+    )
 
 
 if __name__ == "__main__":

Diff for: examples/stencil-2d.py

@@ -99,10 +99,16 @@ def info(s):
 
     # coordinate arrays
     x_t_2d = fromfunction(
-        lambda i, j: xmin + i * dx + dx / 2, (nx, ny), dtype=dtype, device=device
+        lambda i, j: xmin + i * dx + dx / 2,
+        (nx, ny),
+        dtype=dtype,
+        device=device,
     )
     y_t_2d = fromfunction(
-        lambda i, j: ymin + j * dy + dy / 2, (nx, ny), dtype=dtype, device=device
+        lambda i, j: ymin + j * dy + dy / 2,
+        (nx, ny),
+        dtype=dtype,
+        device=device,
     )
 
     T_shape = (nx, ny)
@@ -207,6 +213,7 @@ def step(u, v, e, u1, v1, e1, u2, v2, e2):
     next_t_export = 0
     initial_v = None
     tic = time_mod.perf_counter()
+    block_tic = 0
     for i in range(nt + 1):
         sync()
         t = i * dt
@@ -233,7 +240,9 @@ def step(u, v, e, u1, v1, e1, u2, v2, e2):
                 f"{i_export:2d} {i:4d} {t:.3f} elev={elev_max:7.5f} "
                 f"u={u_max:7.5f} dV={diff_v: 6.3e} " + tcpu_str
             )
-            if not benchmark_mode and (elev_max > 1e3 or not math.isfinite(elev_max)):
+            if not benchmark_mode and (
+                elev_max > 1e3 or not math.isfinite(elev_max)
+            ):
                 raise ValueError(f"Invalid elevation value: {elev_max}")
             i_export += 1
             next_t_export = i_export * t_export