From eab742d5a1f6db8f4f829cfd8f57ade82a1e9561 Mon Sep 17 00:00:00 2001
From: Manuel Weberndorfer <manuel.weberndorfer@id.ethz.ch>
Date: Tue, 8 Feb 2022 15:09:12 +0000
Subject: [PATCH] update versions of python packages
- previous version of black does not support jammy
- perform changes recommended by pylint
---
.gitlab-ci.yml | 4 +-
cpppetsc/tools/generate_xdmf.py | 44 ++++++++---------
docker/Dockerfile | 48 +++++++++----------
.../src/quadrature/generate_quadrature.py | 15 ++----
tests/numeric_diff.py | 8 ++--
tests/run.py | 8 ++--
6 files changed, 59 insertions(+), 68 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 9d09813a..752d73b9 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -93,8 +93,8 @@ check-script:
image: $CI_REGISTRY_IMAGE/dev-real:$CI_COMMIT_REF_SLUG
script:
- find . -name "*.py" -print0 | xargs -0 python3 -m black --check
- - find . -name "*.py" -print0 | xargs -0 python3 -m pylint
- - find . -name "*.py" -print0 | xargs -0 python3 -m mypy --python-version 3.7 --ignore-missing
+ - find . -name "*.py" -print0 | xargs -0 python3 -m pylint --generated-members 'h5py\.File'
+ - find . -name "*.py" -print0 | xargs -0 python3 -m mypy --python-version 3.9 --ignore-missing
- find . -name "*.py" -print0 | xargs -0 python3 -m doctest
.build-library: &build-library
diff --git a/cpppetsc/tools/generate_xdmf.py b/cpppetsc/tools/generate_xdmf.py
index ce72aa6d..44ee807d 100755
--- a/cpppetsc/tools/generate_xdmf.py
+++ b/cpppetsc/tools/generate_xdmf.py
@@ -246,17 +246,17 @@ def add_sliced_hdf_dataitem(
"DataItem",
{"Dimensions": shape_to_xdmf_dimensions((3, item.ndim)), "Format": "XML"},
)
- dimensions.text = "{} {} {}".format(
- shape_to_xdmf_dimensions(
+ dimensions.text = f"""{
+ shape_to_xdmf_dimensions(
tuple(sliced_dimensions.get(i, 0) for i in range(item.ndim))
- ),
- shape_to_xdmf_dimensions(tuple(1 for _ in range(item.ndim))),
- shape_to_xdmf_dimensions(
- tuple(
- 1 if i in sliced_dimensions else item.shape[i] for i in range(item.ndim)
- )
- ),
- )
+ )
+ } {
+ shape_to_xdmf_dimensions(tuple(1 for _ in range(item.ndim)))
+ } {
+ shape_to_xdmf_dimensions(
+ tuple(1 if i in sliced_dimensions else item.shape[i] for i in range(item.ndim))
+ )
+ }"""
add_hdf_dataitem(hyperslab, hdf_file, hdf_path)
return hyperslab
@@ -282,7 +282,7 @@ def add_hdf_dataitem(
"Rank": str(item.ndim),
},
)
- dataitem.text = "{}:{}".format(hdf_file.filename, hdf_path)
+ dataitem.text = f"{hdf_file.filename}:{hdf_path}"
return dataitem
@@ -358,15 +358,13 @@ def add_topology(parent: ET.Element, hdf_file: h5py.File) -> ET.Element:
{"Format": "XML", "Dimensions": str(dataitem_dimension)},
)
dataitem.text = " ".join(
- "{} {}".format(
- " ".join(
- str(type_)
- for type_ in number_of_corners_to_type(
- len(vertices), topological_dimension
- )
- ),
- " ".join(str(vertex) for vertex in vertices),
- )
+ f"""{
+ " ".join(str(type_)
+ for type_ in number_of_corners_to_type(len(vertices), topological_dimension))
+ } {
+ " ".join(str(vertex)
+ for vertex in vertices)
+ }"""
for vertices in read_element_vertices(hdf_file)
)
@@ -411,7 +409,7 @@ def add_field(
- 3 columns: A vector field will be added.
- otherwise: The field is split into scalar fields, and those are added.
"""
- hdf_path = "/fields/{}".format(field_name)
+ hdf_path = "/fields/{field_name}"
item = hdf_file[hdf_path]
shape = item.shape
@@ -456,7 +454,7 @@ def add_field(
parent,
"Attribute",
{
- "Name": "{}[{}]{}".format(field_name, column, postfix),
+ "Name": f"{field_name}[{column}]{postfix}",
"Center": center,
"AttributeType": "Scalar",
},
@@ -519,7 +517,7 @@ def main() -> None:
XDMF to file.
"""
filename = parse_input_filename()
- with open(filename.stem + ".xdmf", "w") as xdmf_file:
+ with open(filename.stem + ".xdmf", "w", encoding="utf-8") as xdmf_file:
xdmf_file.write(hdf_to_xdmf_string(h5py.File(filename, "r")))
diff --git a/docker/Dockerfile b/docker/Dockerfile
index ce80ab90..f513cde5 100644
--- a/docker/Dockerfile
+++ b/docker/Dockerfile
@@ -19,31 +19,31 @@ FROM $BASE_IMAGE
ARG PETSC_SCALAR_TYPE=real
RUN apt-get update && \
- DEBIAN_FRONTEND="noninteractive" \
- TZ="Europe/Zurich" \
- apt-get install -y \
- clang-format \
- cmake \
- g++ \
- git \
- googletest \
- libboost-program-options-dev \
- libeigen3-dev \
- librange-v3-dev \
- ninja-build \
- python3 python3-pip \
- python3-h5py \
- gdb
+ DEBIAN_FRONTEND="noninteractive" \
+ TZ="Europe/Zurich" \
+ apt-get install -y \
+ clang-format \
+ cmake \
+ g++ \
+ git \
+ googletest \
+ libboost-program-options-dev \
+ libeigen3-dev \
+ librange-v3-dev \
+ ninja-build \
+ python3 python3-pip \
+ python3-h5py \
+ gdb
RUN pip3 install \
- mypy==0.790 \
- black==20.8b1 \
- pylint==2.6.0 \
- sympy==1.7.1 \
- gcovr
+ mypy==0.931 \
+ black==22.1.0 \
+ pylint==2.12.2 \
+ sympy==1.7.1 \
+ gcovr==5.0
RUN apt-get update && \
- DEBIAN_FRONTEND="noninteractive" \
- apt-get install -y \
- libpetsc-${PETSC_SCALAR_TYPE}-dev \
- libslepc-${PETSC_SCALAR_TYPE}3.15-dev
+ DEBIAN_FRONTEND="noninteractive" \
+ apt-get install -y \
+ libpetsc-${PETSC_SCALAR_TYPE}-dev \
+ libslepc-${PETSC_SCALAR_TYPE}3.15-dev
diff --git a/elements/src/quadrature/generate_quadrature.py b/elements/src/quadrature/generate_quadrature.py
index 66cbedb1..fa863e0f 100755
--- a/elements/src/quadrature/generate_quadrature.py
+++ b/elements/src/quadrature/generate_quadrature.py
@@ -54,7 +54,7 @@ def compute_gaussian_weights(order: int) -> List[Any]:
return [
2
- / (1 - node ** 2)
+ / (1 - node**2)
/ sympy.diff(
sympy.legendre_poly(order, sympy.Symbol("x"), polys=True), sympy.Symbol("x")
).eval(node)
@@ -133,7 +133,7 @@ def to_initializer_list(values: Any) -> str:
if isinstance(values, (list, tuple)):
result = ", ".join([to_initializer_list(element) for element in values])
return "{{" + result + (", " if result.endswith("}") else "") + "}}"
- return "{:+.16f}".format(float(values))
+ return f"{float(values):+.16f}"
def quadrature_definition(order: int, dimension: int) -> str:
@@ -149,14 +149,9 @@ def quadrature_definition(order: int, dimension: int) -> str:
weights = compute_gaussian_weights_in_dimension(order, dimension)
return (
"AE108_ELEMENTS_QUADRATURE_DEFINE("
- "QuadratureType::Cube, {}, {}, {}, {{{}, {}}}"
- ");".format(
- dimension,
- 2 * order - 1,
- len(nodes),
- to_initializer_list(nodes),
- to_initializer_list(weights),
- )
+ f"QuadratureType::Cube, {dimension}, {2 * order - 1}, {len(nodes)}, "
+ f"{{{to_initializer_list(nodes)}, {to_initializer_list(weights)}}}"
+ ");"
)
diff --git a/tests/numeric_diff.py b/tests/numeric_diff.py
index 4947d12b..1e210876 100755
--- a/tests/numeric_diff.py
+++ b/tests/numeric_diff.py
@@ -83,9 +83,7 @@ def diff_iterables(
math.isclose(values[0], values[1], rel_tol=rel_tol, abs_tol=abs_tol)
or (math.isnan(values[0]) and math.isnan(values[1]))
):
- yield "Line {} differs: '{}' is not '{}'".format(
- index, strings[0].strip(), strings[1].strip()
- )
+ yield f"Line {index} differs: '{strings[0].strip()}' is not '{strings[1].strip()}'"
def main():
@@ -119,8 +117,8 @@ def main():
arguments = parser.parse_args()
- with open(str(arguments.filename_1), "r") as file_1:
- with open(str(arguments.filename_2), "r") as file_2:
+ with open(str(arguments.filename_1), "r", encoding="utf-8") as file_1:
+ with open(str(arguments.filename_2), "r", encoding="utf-8") as file_2:
return sum(
1
for _ in map(
diff --git a/tests/run.py b/tests/run.py
index 693eda6f..7ea16eaa 100755
--- a/tests/run.py
+++ b/tests/run.py
@@ -197,8 +197,8 @@ def diff_files(
ComparisonType.NUMERIC: diff_numeric_string,
}
- with open(value, "r") as value_file:
- with open(reference, "r") as reference_file:
+ with open(value, "r", encoding="utf-8") as value_file:
+ with open(reference, "r", encoding="utf-8") as reference_file:
comparison_to_function.get(comparison, lambda _0, _1, _2: None)(
value_file.read(), reference_file.read(), case
)
@@ -326,7 +326,7 @@ def load_tests(
lambda processes, name=test_name: f"test_{name}_with_{processes}_mpi_processes"
)
- with open(path, "r") as file:
+ with open(path, "r", encoding="utf-8") as file:
test_case_definitions = as_test_case_definitions(
path.parent, json.load(file)
)
@@ -365,7 +365,7 @@ def run_testcase(
mpi_processes=definition.mpi_processes,
)
- with open(directory_path / "stdout.txt", "w") as file:
+ with open(directory_path / "stdout.txt", "w", encoding="utf-8") as file:
file.write(result.stdout)
diff_files(
--
GitLab