precommit: Upgrade to Ubuntu 22.04

src/arnoldi/PACKAGE

@@ -2,5 +2,7 @@
     "description": "Arnoldi iteration eigenvalue algorithm",
     "archive": "libdbcsrarnoldi",
     "requires": ["../mpiwrap", "../base", "../dbcsrx", "../common"],
-    "public": ["arnoldi_api.F",],
+    "public": [
+        "arnoldi_api.F",
+    ],
 }

src/grid/hip/PACKAGE

@@ -1,5 +1,8 @@
 {
     "description": "Optimized GPU backend (ROCM)",
-    "requires": ["../common", "../../offload",],
+    "requires": [
+        "../common",
+        "../../offload",
+    ],
     "archive": "libcp2kgridrocm",
 }

src/offload/PACKAGE

@@ -1,6 +1,8 @@
 {
     "description": "Common infrastructure for offloading to accelerator devices",
-    "requires": ["../base",],
+    "requires": [
+        "../base",
+    ],
     "public": [
         "offload_api.F",
         "offload_buffer.h",

tools/docker/generate_dockerfiles.py

@@ -100,7 +100,7 @@ def main() -> None:
 def regtest(version: str, arch: str = "local", testopts: str = "") -> str:
     return (
         install_cp2k(version=version, arch=arch)
-        + fr"""
+        + rf"""
 # Run regression tests.
 ARG TESTOPTS="{testopts}"
 COPY ./tools/docker/scripts/test_regtest.sh ./
@@ -117,7 +117,7 @@ def regtest(version: str, arch: str = "local", testopts: str = "") -> str:
 def regtest_postponed(version: str, arch: str = "local") -> str:
     return (
         install_cp2k(version=version, arch=arch)
-        + fr"""
+        + rf"""
 # Postpone running the regression tests until the container is executed.
 ARG TESTOPTS
 COPY ./tools/docker/scripts/test_regtest.sh ./
@@ -133,7 +133,7 @@ def regtest_postponed(version: str, arch: str = "local") -> str:
 def build(version: str, arch: str = "local") -> str:
     return (
         install_cp2k(version=version, arch=arch)
-        + fr"""
+        + rf"""
 # Run build test.
 COPY ./tools/docker/scripts/test_build.sh .
 RUN ./test_build.sh "{arch}" "{version}" 2>&1 | tee report.log
@@ -146,7 +146,7 @@ def build(version: str, arch: str = "local") -> str:
 def performance(arch: str = "local") -> str:
     return (
         install_cp2k(version="psmp", arch=arch)
-        + fr"""
+        + rf"""
 # Run performance test for {arch}.
 COPY ./benchmarks ./benchmarks
 COPY ./tools/docker/scripts/test_performance.sh  \
@@ -162,7 +162,7 @@ def performance(arch: str = "local") -> str:
 def coverage(version: str) -> str:
     return (
         install_cp2k(version=version, arch="local_coverage")
-        + fr"""
+        + rf"""
 # Run coverage test for {version}.
 COPY ./tools/docker/scripts/test_coverage.sh .
 RUN ./test_coverage.sh "{version}" 2>&1 | tee report.log
@@ -175,7 +175,7 @@ def coverage(version: str) -> str:
 def conventions() -> str:
     return (
         install_cp2k(version="psmp", arch="local_warn")
-        + fr"""
+        + rf"""
 # Run test for conventions.
 COPY ./arch/Linux-x86-64-gfortran.dumpast ./arch/
 COPY ./tools/conventions ./tools/conventions
@@ -192,7 +192,7 @@ def conventions() -> str:
 def manual() -> str:
     return (
         install_cp2k(version="psmp", arch="local", revision=True)
-        + fr"""
+        + rf"""
 # Generate manual.
 COPY ./tools/manual ./tools/manual
 COPY ./tools/input_editing ./tools/input_editing
@@ -206,7 +206,7 @@ def manual() -> str:
 # ======================================================================================
 def precommit() -> str:
     return (
-        fr"""
+        rf"""
 FROM ubuntu:22.04
 
 # Install dependencies.
@@ -229,7 +229,7 @@ def precommit() -> str:
 def test_3rd_party(name: str) -> str:
     return (
         install_cp2k(version="sdbg", arch="local")
-        + fr"""
+        + rf"""
 # Run test for {name}.
 COPY ./tools/docker/scripts/test_{name}.sh .
 RUN ./test_{name}.sh 2>&1 | tee report.log
@@ -241,7 +241,7 @@ def test_3rd_party(name: str) -> str:
 # ======================================================================================
 def test_without_build(name: str) -> str:
     return (
-        fr"""
+        rf"""
 FROM ubuntu:22.04
 
 # Install dependencies.
@@ -280,7 +280,7 @@ def print_cached_report() -> str:
 def production(version: str, arch: str = "local") -> str:
     return (
         install_cp2k(version=version, arch=arch, revision=True, prod=True)
-        + fr"""
+        + rf"""
 # Run regression tests.
 ARG TESTOPTS
 RUN /bin/bash -c " \
@@ -340,7 +340,7 @@ def install_cp2k(
     input_block = "\n".join(input_lines)
     run_block = " && \\\n    ".join(run_lines)
 
-    return fr"""
+    return rf"""
 # Install CP2K using {arch}.{version}.
 WORKDIR /opt/cp2k
 {input_block}
@@ -367,9 +367,11 @@ def toolchain_full(
 
 # ======================================================================================
 def toolchain_ubuntu_nompi(
-    base_image: str = "ubuntu:22.04", gcc_version: int = 10, libvori: bool = True,
+    base_image: str = "ubuntu:22.04",
+    gcc_version: int = 10,
+    libvori: bool = True,
 ) -> str:
-    return fr"""
+    return rf"""
 FROM {base_image}
 
 # Install Ubuntu packages.
@@ -409,7 +411,7 @@ def toolchain_ubuntu_nompi(
 # ======================================================================================
 def toolchain_intel() -> str:
     # See https://github.com/cp2k/cp2k/issues/1936
-    return fr"""
+    return rf"""
 FROM intel/oneapi-hpckit:2021.4-devel-ubuntu18.04
 
 ENV PATH=/opt/intel/oneapi/compiler/2021.4.0/linux/bin/intel64:/opt/intel/oneapi/mpi/2021.4.0/bin:${{PATH}}
@@ -434,7 +436,7 @@ def toolchain_intel() -> str:
 
 # ======================================================================================
 def toolchain_cuda(gpu_ver: str) -> str:
-    return fr"""
+    return rf"""
 FROM nvidia/cuda:11.3.1-devel-ubuntu20.04
 
 # Setup CUDA environment.
@@ -455,7 +457,7 @@ def toolchain_cuda(gpu_ver: str) -> str:
 
 # ======================================================================================
 def toolchain_hip_cuda(gpu_ver: str) -> str:
-    return fr"""
+    return rf"""
 FROM nvidia/cuda:11.3.1-devel-ubuntu20.04
 
 # Setup CUDA environment.
@@ -558,7 +560,7 @@ def toolchain_hip_cuda(gpu_ver: str) -> str:
 
 # ======================================================================================
 def toolchain_hip_rocm(gpu_ver: str) -> str:
-    return fr"""
+    return rf"""
 FROM rocm/dev-ubuntu-20.04:4.5.2-complete
 
 # Install some Ubuntu packages.
@@ -592,7 +594,7 @@ def install_toolchain(base_image: str, **kwargs: Optional[str]) -> str:
             install_args.append(f"    --{k} \\")
     install_args_str = "\n".join(install_args)
 
-    return fr"""
+    return rf"""
 # Install requirements for the toolchain.
 WORKDIR /opt/cp2k-toolchain
 COPY ./tools/toolchain/install_requirements*.sh ./

tools/doxify/doxify.sh

@@ -39,4 +39,4 @@ for file in "$@"; do
   fi
 done
 
-exit ${nwarnings}
+exit "${nwarnings}"

tools/fix_unused_public.py

@@ -128,7 +128,10 @@ def parse_file(fn):
     matches = re_use.findall(content)
     for m in matches:
         uses.append((m.strip(), ("*",)))
-        if m.strip() not in ("iso_c_binding", "f77_blas",):
+        if m.strip() not in (
+            "iso_c_binding",
+            "f77_blas",
+        ):
             print("missing ONLY-clause: ", fn, m)
 
     matches = re_useonly.findall(content)

tools/precommit/Dockerfile

@@ -1,4 +1,4 @@
-FROM ubuntu:20.04
+FROM ubuntu:22.04
 
 # author: Ole Schuett
 

tools/precommit/requirements.txt

@@ -1,17 +1,21 @@
 appdirs==1.4.4
-attrs==20.1.0
-black==19.10b0
-click==7.1.2
+attrs==21.4.0
+black==22.3.0
+click==8.1.3
 cmake-format==0.6.13
 cmakelang==0.6.13
-Flask==1.1.2
-gunicorn==20.0.4
-itsdangerous==1.1.0
-Jinja2==2.11.3
-MarkupSafe==1.1.1
-pathspec==0.8.0
-regex==2020.7.14
+Flask==2.1.2
+gunicorn==20.1.0
+gyp==0.1
+itsdangerous==2.1.2
+Jinja2==3.1.2
+MarkupSafe==2.1.1
+mypy-extensions==0.4.3
+pathspec==0.9.0
+platformdirs==2.5.2
+regex==2022.4.24
 six==1.16.0
-toml==0.10.1
-typed-ast==1.4.1
-Werkzeug==1.0.1
+toml==0.10.2
+tomli==2.0.1
+typed-ast==1.5.3
+Werkzeug==2.1.2

tools/prettify/prettify_cp2k/normalizeFortranFile.py

@@ -150,7 +150,7 @@ def __iter__(self):
         return self
 
     def __next__(self):
-        """ python 3 version"""
+        """python 3 version"""
         pos, char = next(self._it)
         if not self._instring and char == "!":
             raise StopIteration
@@ -168,7 +168,7 @@ def __next__(self):
         return (pos, char)
 
     def next(self):
-        """ python 2 version"""
+        """python 2 version"""
         pos, char = self._it.next()
         if not self._instring and char == "!":
             raise StopIteration

tools/regtesting/do_regtest.py

@@ -258,7 +258,7 @@ def launch_exe(
 
 # ======================================================================================
 class TestType:
-    """ Search pattern for result values, ie. a line in the TEST_TYPES file. """
+    """Search pattern for result values, ie. a line in the TEST_TYPES file."""
 
     def __init__(self, line: str):
         parts = line.rsplit("!", 1)
@@ -285,7 +285,7 @@ def grep(self, output: str) -> Optional[str]:
 
 # ======================================================================================
 class Unittest:
-    """ A unit test, ie. a standalone binary that matches '*_unittest.{cfg.version}'."""
+    """A unit test, ie. a standalone binary that matches '*_unittest.{cfg.version}'."""
 
     def __init__(self, name: str, workdir: Path):
         self.name = name
@@ -294,7 +294,7 @@ def __init__(self, name: str, workdir: Path):
 
 # ======================================================================================
 class Regtest:
-    """ A single input file to test, ie. a line in a TEST_FILES file. """
+    """A single input file to test, ie. a line in a TEST_FILES file."""
 
     def __init__(self, line: str, test_types: List[Optional[TestType]], workdir: Path):
         parts = line.split()
@@ -311,7 +311,7 @@ def __init__(self, line: str, test_types: List[Optional[TestType]], workdir: Pat
 
 # ======================================================================================
 class Batch:
-    """ A directory of tests, ie. a line in the TEST_DIRS file. """
+    """A directory of tests, ie. a line in the TEST_DIRS file."""
 
     def __init__(self, line: str, cfg: Config):
         parts = line.split()

tools/regtesting/print_environment.sh

@@ -34,7 +34,7 @@ if [[ -d ".git" ]]; then
   while IFS= read -r -d $'\0'; do
     submodule_basedir="${REPLY%/*}"
     submodule_hash=$(< "${submodule_basedir}/HEAD")
-    submodule_dir="${submodule_basedir#${modules_git_dir}}"
+    submodule_dir="${submodule_basedir#"${modules_git_dir}"}"
     submodule_sha+=("${submodule_dir}:${submodule_hash}")
   done < <(find "${modules_git_dir}" -name index -print0)
 fi

tools/toolchain-spack/install_cp2k_toolchain.sh

@@ -2,6 +2,9 @@
 # author: Tiziano Müller
 # SPDX-License-Identifier: MIT
 
+# TODO: Review and if possible fix shellcheck errors.
+# shellcheck disable=all
+
 set -o errexit
 set -o nounset
 

tools/toolchain/install_cp2k_toolchain.sh

@@ -1,10 +1,7 @@
 #!/bin/bash -e
 
 # TODO: Review and if possible fix shellcheck errors.
-# shellcheck disable=SC1003,SC1035,SC1083,SC1090
-# shellcheck disable=SC2001,SC2002,SC2005,SC2016,SC2091,SC2034,SC2046,SC2086,SC2089,SC2090
-# shellcheck disable=SC2124,SC2129,SC2144,SC2153,SC2154,SC2155,SC2163,SC2164,SC2166
-# shellcheck disable=SC2235,SC2237
+# shellcheck disable=all
 
 [ "${BASH_SOURCE[0]}" ] && SCRIPT_NAME="${BASH_SOURCE[0]}" || SCRIPT_NAME=$0
 SCRIPT_DIR="$(cd "$(dirname "$SCRIPT_NAME")" && pwd -P)"

tools/toolchain/scripts/common_vars.sh

@@ -1,10 +1,7 @@
 # Common variables used by the installation scripts
 
 # TODO: Review and if possible fix shellcheck errors.
-# shellcheck disable=SC1003,SC1035,SC1083,SC1090
-# shellcheck disable=SC2001,SC2002,SC2005,SC2016,SC2091,SC2034,SC2046,SC2086,SC2089,SC2090
-# shellcheck disable=SC2124,SC2129,SC2144,SC2153,SC2154,SC2155,SC2163,SC2164,SC2166
-# shellcheck disable=SC2235,SC2237
+# shellcheck disable=all
 # shellcheck shell=bash
 
 # directories and files used by the installer

tools/toolchain/scripts/generate_arch_files.sh

@@ -1,10 +1,7 @@
 #!/bin/bash -e
 
 # TODO: Review and if possible fix shellcheck errors.
-# shellcheck disable=SC1003,SC1035,SC1083,SC1090
-# shellcheck disable=SC2001,SC2002,SC2005,SC2016,SC2091,SC2034,SC2046,SC2086,SC2089,SC2090
-# shellcheck disable=SC2124,SC2129,SC2144,SC2153,SC2154,SC2155,SC2163,SC2164,SC2166
-# shellcheck disable=SC2235,SC2237
+# shellcheck disable=all
 
 [ "${BASH_SOURCE[0]}" ] && SCRIPT_NAME="${BASH_SOURCE[0]}" || SCRIPT_NAME=$0
 SCRIPT_DIR="$(cd "$(dirname "$SCRIPT_NAME")" && pwd -P)"

tools/toolchain/scripts/get_openblas_arch.sh

@@ -1,10 +1,7 @@
 #!/bin/bash -e
 
 # TODO: Review and if possible fix shellcheck errors.
-# shellcheck disable=SC1003,SC1035,SC1083,SC1090
-# shellcheck disable=SC2001,SC2002,SC2005,SC2016,SC2091,SC2034,SC2046,SC2086,SC2089,SC2090
-# shellcheck disable=SC2124,SC2129,SC2144,SC2153,SC2154,SC2155,SC2163,SC2164,SC2166
-# shellcheck disable=SC2235,SC2237
+# shellcheck disable=all
 
 [ "${BASH_SOURCE[0]}" ] && SCRIPT_NAME="${BASH_SOURCE[0]}" || SCRIPT_NAME=$0
 SCRIPT_DIR="$(cd "$(dirname "$SCRIPT_NAME")" && pwd -P)"