Merge pull request #340 from earth-system-radiation/develop

Minor updates - c_bool always, more CI, code formatting and pre-commit.

.cmake-format.py

@@ -1,13 +1,13 @@
-with section("parse"):
+with section("parse"):  # noqa: F821
     additional_commands = {"check_python3_package": {"pargs": 1, "kwargs": {"CODE": 1}}}
 
-with section("format"):
+with section("format"):  # noqa: F821
     dangle_parens = True
     max_lines_hwrap = 0
     keyword_case = "upper"
     autosort = True
 
-with section("lint"):
+with section("lint"):  # noqa: F821
     # The formatter sometimes fails to fit the code into the line limit (C0301) and can
     # disagree with the linter regarding the indentation (C0307):
     disabled_codes = ["C0301", "C0307"]

.git-blame-ignore-revs

@@ -1,2 +1,4 @@
-# Formatted entire CMake code base with cmake-format
-45b43632309cff022326472a8be0fdd5efc8f5c8
+# Formatted entire codebase (#337)
+db7044f9c85b9675b0447d2162001f32b61e0e84
+cc0f75b44d536fd10fa0556474926e58bfbb3f4f
+71520f8bcc8af9611e2a0f70eb3278fcc3064343

.github/workflows/check-api.yml

@@ -33,5 +33,5 @@ jobs:
         $FC --version
         cmake -S . -B build \
          -DCMAKE_BUILD_TYPE=RelWithDebInfo \
-         -DKERNEL_MODE=$RTE_KERNELS
+         -DKERNEL_MODE="$RTE_KERNELS"
         cmake --build build

.github/workflows/containerized-ci.yml

@@ -83,7 +83,7 @@ jobs:
       run: |
           cmake -S . -B build -G "Ninja" \
               -DCMAKE_BUILD_TYPE=${{ matrix.build-type }} \
-              -DRTE_ENABLE_SP=`test 'x${{ matrix.fpmodel }}' = xSP && echo ON || echo OFF` \
+              -DRTE_ENABLE_SP="$(test '${{ matrix.fpmodel }}' = SP && echo ON || echo OFF)" \
               -DKERNEL_MODE=${{ matrix.rte-kernels }} \
               -DBUILD_TESTING=ON
           cmake --build build

.github/workflows/continuous-integration.yml

@@ -24,7 +24,7 @@ jobs:
         gfortran-version: [12, 13, 14]
         gfortran-from: [system, conda]
         fpmodel: [DP, SP]
-        exclude: 
+        exclude:
           - os: ubuntu-24.04
             gfortran-from: conda
           - os: macos-13
@@ -38,7 +38,7 @@ jobs:
             gfortran-version: 14
             gfortran-from: conda
           - os: windows-2022
-        include: 
+        include:
           - os: ubuntu-24.04
             gfortran-version: 13
             gfortran-from: conda
@@ -101,7 +101,7 @@ jobs:
         if: matrix.gfortran-from == 'conda'
         run: |
           conda install -c conda-forge gfortran=${{ matrix.gfortran-version }} -y
-          echo "FC=gfortran" >> $GITHUB_ENV
+          echo "FC=gfortran" >> "$GITHUB_ENV"
       #
       # Install dependencies
       #
@@ -112,15 +112,15 @@ jobs:
       #
       - name: Adjust toolchain
         if: matrix.os == 'windows-2022'
-        run: echo "FC=${FC}.exe" >> $GITHUB_ENV
+        run: echo "FC=${FC}.exe" >> "$GITHUB_ENV"
       #
       # Build libraries, examples, and tests
       #
       - name: Build libraries and tests
         run: |
           cmake -S . -B build -G "Ninja" \
               -DCMAKE_BUILD_TYPE=RelWithDebInfo \
-              -DRTE_ENABLE_SP=`test 'x${{ matrix.fpmodel }}' = xSP && echo ON || echo OFF` \
+              -DRTE_ENABLE_SP="$(test '${{ matrix.fpmodel }}' = SP && echo ON || echo OFF)" \
               -DBUILD_TESTING=ON
           cmake --build build
       #

.github/workflows/gitlab-ci.yml

@@ -103,7 +103,7 @@ jobs:
   #
   lumi-init:
     if: |
-      false && 
+      false &&
       github.repository_owner == 'earth-system-radiation' &&
         ( github.event_name != 'pull_request' ||
           ( github.event.pull_request.head.repo.owner.login == github.repository_owner &&

.github/workflows/module_switcher

@@ -143,4 +143,3 @@ switch_for_module ()
     eval "$sfm_cmd"
   done
 }
-

.github/workflows/style.yml

@@ -9,64 +9,15 @@ on:
       - documentation
   workflow_dispatch:
 
-env:
-  FIND_CMAKE_FILES_CMD: "find '${{ github.workspace }}' -name 'CMakeLists.txt' -o -name '*.cmake' -o -name '*.cmake.in'"
-
 jobs:
-  Format:
-    runs-on: ubuntu-22.04
-    env:
-      DEFAULT: '\033[0m'
-      RED: '\033[0;31m'
-      GREEN: '\033[0;32m'
-      FORMAT_PATCH: '${{ github.workspace }}/format.patch'
-    steps:
-      - name: Check out code
-        uses: actions/checkout@v4
-      - name: Install Python
-        uses: actions/setup-python@v5
-        with:
-          python-version: '>=3.8'
-      - name: Install required tools
-        run: python -m pip install cmake-format
-      - name: Format CMake
-        run: cmake-format -i $(eval "${FIND_CMAKE_FILES_CMD}")
-      - name: Check if patching is required
-        id: patch-required
-        run: |
-          git -C '${{ github.workspace }}' diff --patch-with-raw > "${FORMAT_PATCH}"
-          test -s "${FORMAT_PATCH}" && {
-            printf "${RED}The source code does not meet the format requirements. \
-          Please, apply the patch (see artifacts).${DEFAULT}\n"
-
-            printf "${RED}Note that the result of the formatting might depend \
-          on the versions of the formatting tools. In this project, whatever \
-          formatting this CI job produces if the correct one. If it expects \
-          you to reformat parts of the source code that you did not modify, do \
-          so in a separate commit, which must not be squashed, and list the \
-          commit in the '.git-blame-ignore-revs' file.${DEFAULT}\n"
-
-            exit 1
-          } || {
-            printf "${GREEN}The source code meets the format requirements.${DEFAULT}\n"
-            rm -rf "${FORMAT_PATCH}"
-          }
-      - name: Upload the patch file
-        if: always() && steps.patch-required.outcome == 'failure'
-        uses: actions/upload-artifact@v4
-        with:
-          name: format-patch
-          path: ${{ env.FORMAT_PATCH }}
-  Lint:
+  pre-commit:
     runs-on: ubuntu-22.04
     steps:
       - name: Check out code
         uses: actions/checkout@v4
       - name: Install Python
         uses: actions/setup-python@v5
         with:
-          python-version: '>=3.8'
-      - name: Install required tools
-        run: python -m pip install cmake-format
-      - name: Lint CMake
-        run: cmake-lint $(eval "${FIND_CMAKE_FILES_CMD}")
+          python-version: 3.x
+      - name: Run pre-commit
+        uses: pre-commit/[email protected]

.gitlab/levante.yml

@@ -8,9 +8,10 @@ include:
   - local: '.gitlab/common.yml'
 
 variables:
+  TIME_LIMIT: "05:00"
   SCHEDULER_PARAMETERS: >-
     --account=mh0287
-    --time=05:00
+    --time=${TIME_LIMIT}
     ${EXTRA_SCHEDULER_PARAMETERS}
   EXTRA_SCHEDULER_PARAMETERS:
 
@@ -67,6 +68,9 @@ variables:
     - .nag
     - .common-levante
   variables:
+    # Test executables produced in this configuration are too slow to run within
+    # the default time limit:
+    TIME_LIMIT: "10:00"
     # Compiler flags used for ICON model:
     FFLAGS: -Wc=/sw/spack-levante/gcc-11.2.0-bcn7mb/bin/gcc -f2008 -colour -w=uep -g -gline -O0 -float-store -nan -Wc,-g -Wc,-pipe -Wc,--param,max-vartrack-size=200000000 -Wc,-mno-fma -C=all
 

.gitlab/lumi.yml

@@ -13,13 +13,14 @@ include:
       aud: https://gitlab.com
 
 variables:
+  TIME_LIMIT: "05:00"
   SCHEDULER_PARAMETERS: >-
     --account=project_465000454
     --nodes=1
     --ntasks=1
     --cpus-per-task=4
     --mem-per-cpu=1G
-    --time=05:00
+    --time=${TIME_LIMIT}
     ${EXTRA_SCHEDULER_PARAMETERS}
   EXTRA_SCHEDULER_PARAMETERS:
 

.pre-commit-config.yaml

@@ -0,0 +1,40 @@
+ci:
+  autofix_prs: false
+  autoupdate_branch: develop
+
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: check-yaml
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+  - repo: https://github.com/rhysd/actionlint
+    rev: v1.7.6
+    hooks:
+      - id: actionlint
+  - repo: https://github.com/cheshirekow/cmake-format-precommit
+    rev: v0.6.13
+    hooks:
+      - id: cmake-format
+      - id: cmake-format
+        name: cmake-format (templates)
+        types: [file]
+        files: \.cmake\.in$
+      - id: cmake-lint
+      - id: cmake-lint
+        name: cmake-lint (templates)
+        types: [file]
+        files: \.cmake\.in$
+  - repo: https://github.com/pycqa/isort
+    rev: 5.13.2
+    hooks:
+      - id: isort
+  - repo: https://github.com/psf/black-pre-commit-mirror
+    rev: 24.10.0
+    hooks:
+      - id: black
+  - repo: https://github.com/csachs/pyproject-flake8
+    rev: v7.0.0
+    hooks:
+      - id: pyproject-flake8

CITATION.cff

@@ -5,10 +5,10 @@ authors:
     given-names: Robert
     orcid: "https://orcid.org/0000-0002-0016-3470"
   - family-names: Iacono
-    given-names: Michael J. 
+    given-names: Michael J.
     orcid: "https://orcid.org/0000-0002-9578-0649"
   - family-names: Alexeev
-    given-names: Dmitry 
+    given-names: Dmitry
     orcid: "https://orcid.org/0000-0002-6425-2181"
   - family-names: Adamidis
     given-names: Panos
@@ -19,12 +19,12 @@ authors:
     given-names: Matthew
     orcid: "https://orcid.org/0000-0003-4764-3348"
   - family-names: Pfister
-    given-names: Erik 
+    given-names: Erik
     orcid: "http://orcid.org/0009-0002-2688-138X"
   - family-names: Polonsky
     given-names: Igor N.
   - family-names: Romero
-    given-names: Nicols A. 
+    given-names: Nicols A.
   - family-names: Kosukhin
     given-names: Sergey S.
   - family-names: Wehe
@@ -35,7 +35,7 @@ license: BSD-3-Clause
 date-released: "2023-11-27"
 version: 1.7
 
-abstract: "RTE+RRTMGP is a set of codes for computing radiative fluxes in planetary atmospheres. 
+abstract: "RTE+RRTMGP is a set of codes for computing radiative fluxes in planetary atmospheres.
   RRTMGP uses a k-distribution to provide an optical description (absorption and possibly Rayleigh optical depth) of the gaseous atmosphere, along with the relevant source functions, on a pre-determined spectral grid given temperatures, pressures, and gas concentration. RTE computes fluxes given spectrally-resolved optical descriptions and source functions. The fluxes are normally summarized or reduced via a user extensible class."
 identifiers:
   - description: "All versions"
@@ -65,4 +65,4 @@ references:
     volume: 11
     number: 10
     pages: 3074-3089
-    year: 2019
+    year: 2019

CMakeLists.txt

@@ -6,6 +6,7 @@ project(
   LANGUAGES Fortran
 )
 
+option(BUILD_SHARED_LIBS "Build shared libraries" OFF)
 option(BUILD_TESTING "Build tests" OFF)
 
 option(RTE_ENABLE_SP "Enable single-precision floating-point model" OFF)
@@ -19,17 +20,24 @@ set_property(CACHE KERNEL_MODE PROPERTY STRINGS ${PREFERRED_KERNEL_MODES})
 
 list(APPEND CMAKE_MODULE_PATH ${PROJECT_SOURCE_DIR}/cmake)
 
+# CMake does not support the NEC compiler and usually mistakes it for GNU:
+if(CMAKE_Fortran_COMPILER_ID STREQUAL GNU)
+  # Check whether the Fortran compiler in use is NEC:
+  include(CheckCompilerIsNEC)
+  check_compiler_is_nec(RTE_RRTMGP_Fortran_is_NEC Fortran)
+endif()
+
 # GNUInstallDirs issues a warning if CMAKE_SIZEOF_VOID_P is not defined, which
-# is the case with NAG. One way to circumvent that is to enable C language for
-# the project:
-if(CMAKE_Fortran_COMPILER_ID STREQUAL NAG)
+# is the case with NAG and NEC. One way to circumvent that is to enable C
+# language for the project:
+if(CMAKE_Fortran_COMPILER_ID STREQUAL NAG OR RTE_RRTMGP_Fortran_is_NEC)
   enable_language(C)
 endif()
 include(GNUInstallDirs)
 
-add_compile_options(
-  $<$<COMPILE_LANG_AND_ID:Fortran,GNU>:-ffree-line-length-none>
-)
+if(CMAKE_Fortran_COMPILER_ID STREQUAL GNU AND NOT RTE_RRTMGP_Fortran_is_NEC)
+  add_compile_options($<$<COMPILE_LANGUAGE:Fortran>:-ffree-line-length-none>)
+endif()
 
 set(CMAKE_Fortran_MODULE_DIRECTORY ${PROJECT_BINARY_DIR}/modules)
 

Contributing.md

@@ -4,16 +4,16 @@ Thanks for considering making a contribution to RTE+RRTMGP.
 
 The code in this repository is intended to work with compilers supporting the Fortran 2008 standard. It is also expected to run end-to-end on GPUs when compiled with OpenACC or OpenMP (though OpenMP is still unreliable). Commits are tested automatically against a range of compilers using Github Actions and also resources provided by the [Swiss Supercomputing Center](https://cscs.ch). The testing uses two general codes in `examples/`for which results are compared against existing implemetations,  and custom codes in `tests/` intended to excercise all code options.
 
-##### Did you find a bug? 
+##### Did you find a bug?
 
-Please file an issue on the [Github page](https://github.com/RobertPincus/rte-rrtmgp/issues). Please include a minimal reproducer of the bug it at all possible. 
+Please file an issue on the [Github page](https://github.com/RobertPincus/rte-rrtmgp/issues). Please include a minimal reproducer of the bug it at all possible.
 
 ##### Did you write a patch that fixes a bug?
 
-Please fork this repository, branch from `develop`, make your changes, and open a Github [pull request](https://github.com/RobertPincus/rte-rrtmgp/pulls) against branch `develop`. 
+Please fork this repository, branch from `develop`, make your changes, and open a Github [pull request](https://github.com/RobertPincus/rte-rrtmgp/pulls) against branch `develop`.
 
-##### Did you add functionality? 
+##### Did you add functionality?
 
-Please fork this repository, branch from `develop`, make your changes, and open a Github [pull request](https://github.com/RobertPincus/rte-rrtmgp/pulls) against branch `develop`,  adding a new regression test or comparison against the reference in `tests/verification.py` or `tests/validation-plots.py` as appropriate. Add the test to the `tests` target in `tests/Makefile`.   
+Please fork this repository, branch from `develop`, make your changes, and open a Github [pull request](https://github.com/RobertPincus/rte-rrtmgp/pulls) against branch `develop`,  adding a new regression test or comparison against the reference in `tests/verification.py` or `tests/validation-plots.py` as appropriate. Add the test to the `tests` target in `tests/Makefile`.
 
-RTE+RRTMGP is intended to be a core that users can extend with custom code to suit their own needs. 
+RTE+RRTMGP is intended to be a core that users can extend with custom code to suit their own needs.

README.md

@@ -3,7 +3,7 @@
 [RTE+RRTMGP's GitHub Pages site](https://earth-system-radiation.github.io/rte-rrtmgp/) contains
 a mix of automatically-generated documentation and hand-written descriptions. The documentation is
 incomplete and evolving. Thanks to the folks at [Sourcery Institute](https://www.sourceryinstitute.org)
-for help in setting this up. 
+for help in setting this up.
 
 For the moment the [Wiki](https://github.com/earth-system-radiation/rte-rrtmgp/wiki) may also be useful.
 
@@ -20,22 +20,22 @@ RTE computes fluxes given spectrally-resolved optical descriptions and source fu
 
 A description of building RTE+RRTMGP with an ad hoc homemade system is described in the [documentation](https://earth-system-radiation.github.io/rte-rrtmgp/how-tos/).
 
-See also the `autoconf` branch for a Gnu autotools build system. 
+See also the `autoconf` branch for a Gnu autotools build system.
 
 ## Examples
 
 Two examples are provided in `examples/`, one for clear skies and one including clouds. Directory `tests/` contains regression testing (e.g. to ensure that answers are independent of orientation) and unit testing (to be sure all the code paths are tested). See the README file and codes in each directory for further information.
 
-## Citing the code 
+## Citing the code
 
-Code releases are archived at Zenodo. All releases are available at 
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3403172.svg)](https://doi.org/10.5281/zenodo.3403172). 
+Code releases are archived at Zenodo. All releases are available at
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3403172.svg)](https://doi.org/10.5281/zenodo.3403172).
 The current release is available at: [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.7521518.svg)](https://doi.org/10.5281/zenodo.10211873)
 
 Please cite the code using these DOIs and the information in the `CITATION.cff` file in addition to the reference [paper](https://doi.org/10.1029/2019MS001621)
 
 ## Acknowledgements
 
-The development of RTE+RRTMGP has been funded in the US by the Office of Naval Research, NASA, NOAA, and the Department of Energy. We 
-are grateful for contributions from a range of collaborators at institutions including the Swiss Supercomputing Center, 
-the German Climate Computing Center, and Nvidia. 
+The development of RTE+RRTMGP has been funded in the US by the Office of Naval Research, NASA, NOAA, and the Department of Energy. We
+are grateful for contributions from a range of collaborators at institutions including the Swiss Supercomputing Center,
+the German Climate Computing Center, and Nvidia.