Initial CI

.github/dependabot.yml

@@ -0,0 +1,7 @@
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/" # .github/workflows
+    schedule:
+      interval: "monthly"
+    target-branch: "main"

.github/workflows/ci.yml

@@ -0,0 +1,32 @@
+name: CI
+
+on:
+  push:
+  pull_request:
+  workflow_dispatch:
+
+jobs:
+  build:
+    name: Build and test
+    runs-on: ubuntu-22.04
+    strategy:
+      matrix:
+        compiler: [gfortran-10, gfortran-11, gfortran-12]
+        # TODO: Intel
+    defaults:
+      run:
+        shell: bash -l {0}
+    env:
+      BUILD_DIR: build
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Build
+        run: |
+          cmake -B $BUILD_DIR
+          cmake --build $BUILD_DIR
+        env:
+          FC: ${{ matrix.compiler }}
+
+      # TODO: ctest --test-dir $BUILD_DIR

.github/workflows/lint.yml

@@ -0,0 +1,17 @@
+name: Lint
+
+on:
+  push:
+  pull_request:
+  workflow_dispatch:
+
+jobs:
+  lint:
+    name: pre-commit
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+      - uses: pre-commit/[email protected]

.pre-commit-config.yaml

@@ -0,0 +1,23 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: "v4.4.0"
+    hooks:
+      - id: trailing-whitespace
+        args: ['--markdown-linebreak-ext=md,markdown']
+      - id: end-of-file-fixer
+      - id: check-yaml
+
+  - repo: https://github.com/zmoon/findent-pre-commit
+    rev: "65627b8"
+    hooks:
+      # NOTE: doesn't work on Windows currently
+      - id: findent-pypi
+        args: ['-i3']
+
+  - repo: https://github.com/cheshirekow/cmake-format-precommit
+    rev: v0.6.13
+    hooks:
+      - id: cmake-format
+        args: ['--in-place', '--line-width=100']
+      - id: cmake-lint
+        args: ['--line-width=100']

CMakeLists.txt

@@ -0,0 +1,67 @@
+cmake_minimum_required(VERSION 3.5)
+
+project(
+  CATChem
+  VERSION 0.1.0
+  LANGUAGES Fortran)
+
+# If GNU compiler and Debug build type, add extra debug flags
+if(NOT CMAKE_BUILD_TYPE)
+  set(CMAKE_BUILD_TYPE Debug)
+endif()
+message(STATUS "CMAKE_Fortran_COMPILER: ${CMAKE_Fortran_COMPILER}")
+message(STATUS "CMAKE_Fortran_COMPILER_ID: ${CMAKE_Fortran_COMPILER_ID}")
+message(STATUS "CMAKE_BUILD_TYPE: ${CMAKE_BUILD_TYPE}")
+if(CMAKE_Fortran_COMPILER_ID MATCHES "GNU|G95" AND CMAKE_BUILD_TYPE MATCHES "Debug")
+  add_compile_options(
+    -g
+    -Wall
+    -Wextra
+    -Og
+    -pedantic
+    -fcheck=all
+    -ffpe-trap=invalid,zero,overflow
+    -fbacktrace
+    -fmax-errors=1)
+endif()
+
+set(_param_src
+    parameters/catchem_config.F90
+    parameters/catchem_constants.F90
+    parameters/ddep_data_mod.F90
+    parameters/dust_data_mod.F90
+    parameters/opt_data_mod.F90
+    parameters/plume_data_mod.F90
+    parameters/seas_data_mod.F90)
+add_library(CATChem_params STATIC ${_param_src})
+
+set(_scheme_src
+    src/aero_soa_vbs_data_mod.F90
+    src/dep_vertmx_mod.F90
+    src/drydep_gocart_mod.F90
+    src/drydep_wesely_mod.F90
+    src/dust_afwa_mod.F90
+    src/dust_fengsha_mod.F90
+    src/gocart_aerosols_mod.F90
+    src/gocart_chem_mod.F90
+    src/gocart_diag_mod.F90
+    src/gocart_dmsemis_mod.F90
+    src/gocart_dust_default_mod.F90
+    src/gocart_dust_simple_mod.F90
+    src/gocart_seas_default_mod.F90
+    src/gocart_seas_ngac_mod.F90
+    src/gocart_seas_simple_mod.F90
+    src/gocart_settling_mod.F90
+    src/opt_aer_mod.F90
+    src/opt_aer_out_mod.F90
+    src/opt_aer_ra_mod.F90
+    src/opt_averaging_mod.F90
+    src/opt_driver_mod.F90
+    src/opt_gocart_mod.F90
+    src/opt_mod.F90
+    src/plume_rise_mod.F90
+    src/plume_scalar_mod.F90
+    src/plume_zero_mod.F90
+    src/vash_settling_mod.F90)
+add_library(CATChem_schemes STATIC ${_scheme_src})
+target_link_libraries(CATChem_schemes PUBLIC CATChem_params)

README.md

@@ -1,4 +1,3 @@
-# Configurable ATmospheric Chemistry 
+# Configurable ATmospheric Chemistry
 
 This is the repository for the Configurable ATmospheric Chemistry modelling component.
-

docs/_static/style.css

@@ -15,4 +15,4 @@
 
 .wy-nav-top {
   background-color: #ffffff;
-}
+}

docs/develop/developers_guide.rst

@@ -18,11 +18,11 @@ when cloning the repository.
 .. _dev-install-instructions:
 
 How to incorporate updates to CATChem
---------------------------------------------
+-------------------------------------
 
 In order to contribute code to CATChem, you will need to fork the
 repository, make changes on your fork, and submit a pull request with your
-changes. 
+changes.
 
 (a) Fork the GitHub repository to your own GitHub account
     using the "Fork" button near the top right:
@@ -53,11 +53,11 @@ changes.
 (d) Make changes to your fork.
 
 (e) Submit a pull request back to the main CATChem repository with your
-    changes. 
-	
+    changes.
+
 (f) Select two code reviewers (see list under development team section).
 
-(g) Once those two reviewers approve the code, it can be merged into the develop branch. 
+(g) Once those two reviewers approve the code, it can be merged into the develop branch.
 
 .. _clone-notes:
 .. [#clone] Note that in order to do an SSH clone,
@@ -75,3 +75,30 @@ changes.
 
        $ git clone https://github.com/ufs-community/CATChem.git
 
+
+pre-commit setup
+----------------
+
+We use the `pre-commit <https://pre-commit.com/>`__ tool to run automated checks.
+After `installing pre-commit <https://pre-commit.com/#install>`__,
+e.g. with ``pipx`` or ``conda``,
+run ``pre-commit install`` in the repository to set up the hooks.
+
+
+Build and test
+--------------
+
+To build, first configure::
+
+    cmake -B build
+
+then build::
+
+    cmake --build build
+
+To specify a compiler, you can in the configuration step
+use the ``FC`` shell/environment variable
+or the ``CMAKE_Fortran_COMPILER`` CMake variable::
+
+    cmake -B build -DCMAKE_Fortran_COMPILER=/usr/bin/gfortran-12
+    FC=/usr/bin/gfortran-12 cmake -B build

docs/index.rst

@@ -1,28 +1,25 @@
 CATChem
 ==============
 
-**CATChem**  (Configurable ATmospheric Chemistry) is a modelling 
-component that includes all chemical and aerosol processes needed to perform 
-atmospheric chemistry and composition simulations within a model through a 
-flexible, easy to modify, and well-documented infrastructure. CATChem will 
-include the following processes: chemical kinetics, aerosols, photolysis, 
-wet deposition, dry deposition, connections to emissions, and connection to 
-physics schemes. The first use of CATChem will be connecting it to NOAA's 
-Unified Forecasting System (https://ufscommunity.org/) to create UFS-Chem. CATChem and UFS-Chem are 
+**CATChem**  (Configurable ATmospheric Chemistry) is a modelling
+component that includes all chemical and aerosol processes needed to perform
+atmospheric chemistry and composition simulations within a model through a
+flexible, easy to modify, and well-documented infrastructure. CATChem will
+include the following processes: chemical kinetics, aerosols, photolysis,
+wet deposition, dry deposition, connections to emissions, and connection to
+physics schemes. The first use of CATChem will be connecting it to NOAA's
+Unified Forecasting System (https://ufscommunity.org/) to create UFS-Chem. CATChem and UFS-Chem are
 currently under development and more information will be provided soon.
- 
+
 
 .. warning::
-   CATChem is currently under development. The code is public to 
-   encourage collaboration amongst the community. Do not publish results using 
+   CATChem is currently under development. The code is public to
+   encourage collaboration amongst the community. Do not publish results using
    CATChem  without consulting the development team.
 
 .. toctree::
    :maxdepth: 1
    :caption: Contribute
-   
+
    develop/development_team
    develop/developers_guide
-
-
-