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Modernise repository #318

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22 changes: 22 additions & 0 deletions .fortitude.toml
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[check]
file-extensions = [
"f90",
"F90",
"x90",
"X90",
"pf",
]
select = ["S101"]
# select = [
# "E", # error rules
# "C", # correctness rules
# "S", # style rules
# "PORT", # portability rules
# "OB", # obsolescence rules
# "MOD", # modernisation rules
# ]
ignore = [
"C003"
]
line-length = 132
output-format = "grouped"
6 changes: 3 additions & 3 deletions .github/CODEOWNERS
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@@ -1,7 +1,7 @@
# This CODEOWNERS file includes a primary codeowner and a deputy for each section.
# This CODEOWNERS file includes a primary codeowner and a deputy for each section.
# Codeowners who are not in a comment will be automatically notified of changes
# to the listed files. All codeowners listed are valid points of contact
# for discussing changes and seeking approval for work.
# for discussing changes and seeking approval for work.

# Applications
**/adjoint_tests @DrTVockerodtMO # @mo-joshuacolclough
Expand Down Expand Up @@ -76,5 +76,5 @@ build/ @MetOffice/ssdteam @hiker
# Other areas
documentation # @MetOffice/ssdteam
.github/ @MetOffice/ssdteam
LICENSE @yaswant
LICENCE @yaswant
README.md @MetOffice/ssdteam
4 changes: 2 additions & 2 deletions .github/workflows/ru_build-docs.yml
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Expand Up @@ -25,11 +25,11 @@ jobs:
name: Install Python packages
run: |
python3 -m pip install --upgrade pip
python3 -m pip install sphinx==8.1.0 pydata-sphinx-theme==0.16.1 sphinx-sitemap==2.6.0 sphinx_design==0.6.1
python3 -m pip install .[docs]
- id: sphinx
name: Build Sphinx HTML docs
working-directory: ./documentation
run: make html
run: make clean html
- id: permissions
name: Set permissions
run: |
Expand Down
5 changes: 5 additions & 0 deletions .gitignore
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Expand Up @@ -68,3 +68,8 @@ interfaces/**/bin
interfaces/**/documents
interfaces/**/working
interfaces/**/test

# venv
.venv/
uv.lock
*.egg-info/
74 changes: 61 additions & 13 deletions README.md
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Expand Up @@ -2,31 +2,33 @@

Welcome to LFRic Apps!

This repository is home to the LFRic-based science applications and libraries such as
the Momentum® Atmosphere model application and the GungHo dynamical core.
This repository is home to the LFRic-based science applications and libraries
such as the Momentum® Atmosphere model application and the GungHo dynamical
core.

LFRic applications are based on the infrastructure developed in the [LFRic
Core](https://github.com/MetOffice/lfric_core) repository.
LFRic applications are based on the infrastructure developed in the
[LFRic Core](https://github.com/MetOffice/lfric_core) repository.

| | |
|-----------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
|:repeat: CI| [![Documentation](https://github.com/MetOffice/lfric_apps/actions/workflows/ci_docs.yml/badge.svg)](https://github.com/MetOffice/lfric_apps/actions/workflows/ci_docs.yml) |
|:speech_balloon: Community| [![Static Badge](https://img.shields.io/badge/GitHub-discussions-gold)](https://github.com/MetOffice/simulation-systems/discussions/categories/lfric) |
|:package: Repo | [![GitHub License](https://img.shields.io/github/license/metoffice/lfric_apps)](https://github.com/MetOffice/lfric_apps?tab=BSD-3-Clause-1-ov-file#readme) [![GitHub Release](https://img.shields.io/github/v/release/metoffice/lfric_apps?color=purple)](https://github.com/MetOffice/lfric_apps/releases) ![GitHub commits since latest release (branch)](https://img.shields.io/github/commits-since/metoffice/lfric_apps/latest/main) |
| | |
| | |
| -------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| :repeat: CI | [![Documentation](https://github.com/MetOffice/lfric_apps/actions/workflows/ci_docs.yml/badge.svg)](https://github.com/MetOffice/lfric_apps/actions/workflows/ci_docs.yml) |
| :speech_balloon: Community | [![Static Badge](https://img.shields.io/badge/GitHub-discussions-gold)](https://github.com/MetOffice/simulation-systems/discussions/categories/lfric) |
| :package: Repo | [![GitHub License](https://img.shields.io/github/license/metoffice/lfric_apps)](https://github.com/MetOffice/lfric_apps?tab=BSD-3-Clause-1-ov-file#readme) [![GitHub Release](https://img.shields.io/github/v/release/metoffice/lfric_apps?color=purple)](https://github.com/MetOffice/lfric_apps/releases) ![GitHub commits since latest release (branch)](https://img.shields.io/github/commits-since/metoffice/lfric_apps/latest/main) |
| | |

## Getting Started

In development documentation for LFRic Apps is available at:
[https://metoffice.github.io/lfric_apps](https://metoffice.github.io/lfric_apps)

The LFRic Apps release schedule and deadlines can be viewed in the [milestones](https://github.com/metoffice/lfric_apps/milestones).
The LFRic Apps release schedule and deadlines can be viewed in the
[milestones](https://github.com/metoffice/lfric_apps/milestones).

Example standalone scientific suites for use with Met Office systems are
available at:

* [u-dn674 - MetOffice Azure SPICE](https://code.metoffice.gov.uk/trac/roses-u/browser/d/n/6/7/4/trunk)
* [u-dn704 - MetOffice EX HPC](https://code.metoffice.gov.uk/trac/roses-u/browser/d/n/7/0/4/trunk)
- [u-dn674 - MetOffice Azure SPICE](https://code.metoffice.gov.uk/trac/roses-u/browser/d/n/6/7/4/trunk)
- [u-dn704 - MetOffice EX HPC](https://code.metoffice.gov.uk/trac/roses-u/browser/d/n/7/0/4/trunk)

These both run a low resolution LFRic Atm NWP GAL9 job and are setup to run
using git sources. Advice on switching a suite from using fcm to git sources is
Expand Down Expand Up @@ -64,3 +66,49 @@ Questions are encouraged in the Simulation Systems

Please be aware of and follow the Simulation Systems
[AI Policy.](https://metoffice.github.io/simulation-systems/FurtherDetails/ai.html)

## Virtual Environment for Sanity Checks

Dependencies for documentation builds and Fortran/Python linting are defined in
`pyproject.toml`. You can use either `uv` or `venv` + `pip`; on Met Office
systems, `venv` + `pip` is recommended to ensure packages come from the Met
Office Artifactory.

### Option 1: `venv` + `pip`

```bash
# Create virtual environment
python3.12 -m venv .venv
# Install dependencies
.venv/bin/pip install ".[dev,docs]"
# Activate virtual environment
source .venv/bin/activate
```

### Option 2: `uv`

```bash
uv sync --all-extras
source .venv/bin/activate
```

### Check and Build Documentation

```bash
cd documentation
make lint # Lint Restructured text
make clean html # build Sphinx documentation
```

### Lint Fortran

```bash
fortitude check [DIR]
```

### Check/Format Python

```bash
ruff check --preview [DIR]
ruff format --check --preview [DIR]
```
2 changes: 2 additions & 0 deletions documentation/Makefile
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Expand Up @@ -24,3 +24,5 @@ clean:
@echo "***** Removing, $(BUILDDIR) directory *****"
@rm -rf $(BUILDDIR)

lint:
sphinx-lint --d "horizontal-tab" --max-line-length 80 "$(SOURCEDIR)"
65 changes: 65 additions & 0 deletions pyproject.toml
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[project]
name = "lfric_apps"
version = "2026.3.1"
description = "LFRic-based science applications and libraries"
license = {file = 'LICENCE'}
requires-python = ">=3.12"

[project.urls]
repository = "https://github.com/MetOffice/lfric_apps"
documentation = "https://metoffice.github.io/lfric_apps/"
discussion = "https://github.com/MetOffice/simulation-systems/discussions"

[project.optional-dependencies]
dev = [
"pytest==9.0.2",
"ruff==0.15.4",
"ty==0.0.20",
"fortitude-lint==0.8.0",
]
docs = [
"sphinx==8.1.0",
"pydata-sphinx-theme==0.16.1",
"sphinx-sitemap==2.6.0",
"sphinx_design==0.6.1",
"sphinx-lint==1.0.2",
]

[tool.setuptools]
packages = []

[tool.ruff]
line-length = 88
target-version = "py312"

[tool.ruff.lint]
select = [
"B", # flake8-bugbear: Code quality issues
"CPY", # flake8-copyright: Copyright notice issues
"E", # pycodestyle errors: Basic PEP 8 violations
"F", # pyflakes errors: Logical errors in code
"I", # isort errors: Import sorting issues
"N", # pep8-naming: Naming convention issues
"NPY", # flake8-numpy: NumPy-specific rules
"UP", # pyupgrade: Modernisation rules, enforce f-strings for formatting
"W", # pycodestyle warnings: PEP 8 warnings
# "PL", # pylint rules: Various code quality and style issues
]
ignore = [
"E501", # line-too-long
"I001", # unsorted-imports
"UP030", # format-literals
"F401", # unused-import
"F403", # undefined-local-with-import-star
"B905", # zip-without-explicit-strict
]

[tool.ruff.format]
quote-style = "double"
indent-style = "space"
# preview = true

# [tool.ty.environment]
# root = [
# ".",
# ]