Add Fortran build stuff and tests

.fprettify.rc

@@ -0,0 +1,2 @@
+indent=4
+whitespace=4

.github/actions/setup/action.yml

@@ -26,4 +26,4 @@ runs:
       shell: bash
       if: ${{ (inputs.run-uv-install == 'true') }}
       run: |
-        uv sync ${{ inputs.uv-dependency-install-flags }}
+        uv sync --no-editable ${{ inputs.uv-dependency-install-flags }}

.github/workflows/bump.yaml

@@ -56,7 +56,7 @@ jobs:
           echo "Bumping to version $NEW_VERSION"
 
           # Build CHANGELOG
-          uv run towncrier build --yes --version v$NEW_VERSION
+          uv run --no-sync towncrier build --yes --version v$NEW_VERSION
 
           # Commit, tag and push
           git commit -a -m "bump: version $BASE_VERSION -> $NEW_VERSION"

.github/workflows/ci.yaml

@@ -23,7 +23,7 @@ jobs:
           uv-dependency-install-flags: "--all-extras --group dev"
       - name: mypy
         run: |
-          MYPYPATH=stubs uv run mypy src
+          MYPYPATH=stubs uv run --no-sync mypy src
 
   docs:
     if: ${{ !github.event.pull_request.draft }}
@@ -41,16 +41,16 @@ jobs:
           uv-dependency-install-flags: "--all-extras --group docs"
       - name: docs
         run: |
-          uv run mkdocs build --strict
+          uv run --no-sync mkdocs build --strict
       - uses: ./.github/actions/setup
         with:
           python-version: "3.11"
           uv-dependency-install-flags: "--all-extras --group docs --group dev"
       - name: docs-with-changelog
         run: |
           # Check CHANGELOG will build too
-          uv run towncrier build --yes
-          uv run mkdocs build --strict
+          uv run --no-sync towncrier build --yes
+          uv run --no-sync mkdocs build --strict
           # Just in case, undo the staged changes
           git restore --staged . && git restore .
 
@@ -65,7 +65,9 @@ jobs:
         with:
           # Exclude local links
           # and the template link in pyproject.toml
-          args: "--exclude 'file://' --exclude '^https://github\\.com/openscm/example-fgen-basic/pull/\\{issue\\}$' ."
+          # Don't check for conda-forge while we haven't released there
+          # Don't check https://www.readthedocs.org/ as it hits rate limits
+          args: "--exclude 'file://' --exclude '^https://github\\.com/openscm/example-fgen-basic/pull/\\{issue\\}$' --exclude '^https://github.com/conda-forge/example-fgen-basic-feedstock$' --exclude '^https://www.readthedocs.org/$' ."
 
   tests:
     strategy:
@@ -97,8 +99,10 @@ jobs:
           uv-dependency-install-flags: "--all-extras --group tests"
       - name: Run tests
         run: |
-          uv run pytest -r a -v src tests --doctest-modules --cov=src --cov-report=term-missing --cov-report=xml
-          uv run coverage report
+
+          COV_DIR=`uv run --no-sync python -c 'from pathlib import  Path; import example_fgen_basic; print(Path(example_fgen_basic.__file__).parent)'`
+          uv run --no-sync pytest -r a -v tests src --doctest-modules --doctest-report ndiff --cov=${COV_DIR} --cov-report=term-missing --cov-report=xml
+          uv run --no-sync coverage report
       - name: Upload coverage reports to Codecov with GitHub Action
         uses: codecov/codecov-action@v4.2.0
         env:
@@ -220,15 +224,13 @@ jobs:
     steps:
       - name: Check out repository
         uses: actions/checkout@v4
-      - name: Setup uv
-        id: setup-uv
-        uses: astral-sh/setup-uv@v4
+      - uses: ./.github/actions/setup
         with:
-          version: "0.8.8"
           python-version: ${{ matrix.python-version }}
+          uv-dependency-install-flags: "--group dev"
       - name: Build package
         run: |
-          uv run python scripts/add-locked-targets-to-pyproject-toml.py
+          uv run --no-sync python scripts/add-locked-targets-to-pyproject-toml.py
           cat pyproject.toml
           uv build
           # Just in case, undo the changes to `pyproject.toml`
@@ -256,5 +258,5 @@ jobs:
         run: |
           TEMP_FILE=$(mktemp)
           uv export --no-dev > $TEMP_FILE
-          uv run liccheck -r $TEMP_FILE -R licence-check.txt
+          uv run --no-sync liccheck -r $TEMP_FILE -R licence-check.txt
           cat licence-check.txt

.github/workflows/deploy.yaml

@@ -36,7 +36,7 @@ jobs:
           python-version: ${{ matrix.python-version }}
       - name: Publish to PyPI
         run: |
-          uv run python scripts/add-locked-targets-to-pyproject-toml.py
+          uv run --no-sync python scripts/add-locked-targets-to-pyproject-toml.py
           uv build
           uv publish
           # Just in case, undo the changes to `pyproject.toml`

.github/workflows/release.yaml

@@ -33,7 +33,7 @@ jobs:
           echo "PROJECT_VERSION=$PROJECT_VERSION" >> $GITHUB_ENV
       - name: Build package for PyPI
         run: |
-          uv run python scripts/add-locked-targets-to-pyproject-toml.py
+          uv run --no-sync python scripts/add-locked-targets-to-pyproject-toml.py
           uv build
           # Just in case, undo the changes to `pyproject.toml`
           git restore --staged . && git restore .
@@ -43,7 +43,7 @@ jobs:
           echo "## Changelog" >> ".github/release_template.md"
           echo "" >> ".github/release_template.md"
           uv add typer
-          uv run python scripts/changelog-to-release-template.py >> ".github/release_template.md"
+          uv run --no-sync python scripts/changelog-to-release-template.py >> ".github/release_template.md"
           echo "" >> ".github/release_template.md"
           echo "## Changes" >> ".github/release_template.md"
           echo "" >> ".github/release_template.md"

.gitignore

@@ -1,16 +1,29 @@
+# Local install dir
+install-example
+
+# Cloned dependencies
+subprojects/test-drive
+
 # Notebooks
 *.ipynb
 
 # Auto-generated docs and helper files
 docs/api/*
 !docs/api/.gitkeep
-
-# pdm stuff
-.pdm-python
+docs/fgen/api/*
+!docs/fgen/api/.gitkeep
+docs/fgen-runtime/api/*
+!docs/fgen-runtime/api/.gitkeep
 
 # Databases
 *.db
 
+# Downloaded wheels
+*.whl
+
+# cmake
+cmake-build-*
+
 # Jupyter cache
 .jupyter_cache
 

.pre-commit-config.yaml

@@ -4,7 +4,12 @@ ci:
   autoupdate_schedule: quarterly
   autoupdate_branch: pre-commit-autoupdate
   # Currently network access isn't supported in the pre-commit CI product.
-  skip: [uv-sync, uv-lock, uv-export]
+  skip: [
+    propagate-pyproject-metadata,
+    uv-sync,
+    uv-lock,
+    uv-export,
+  ]
 
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
@@ -63,3 +68,24 @@ repos:
         args: ["-o", "requirements-only-tests-locked.txt", "--no-hashes", "--no-dev", "--no-emit-project", "--only-group", "tests"]
       # # Not released yet
       # - id: uv-sync
+  - repo: local
+    hooks:
+      - id: propagate-pyproject-metadata
+        name: propagate-pyproject-metadata
+        entry: uv run --no-sync python scripts/propogate-pyproject-metadata.py
+        files: |
+            (?x)^(
+                meson.build|
+                scripts/propogate-pyproject-metadata.py|
+                pyproject.toml
+            )$
+        language: system
+        require_serial: true
+        pass_filenames: false
+      - id: inject-srcs-into-meson-build
+        name: inject-srcs-into-meson-build
+        entry: uv run --no-sync python scripts/inject-srcs-into-meson-build.py
+        files: \.(py|f90|build)$
+        language: system
+        require_serial: true
+        pass_filenames: false

.readthedocs.yaml

@@ -9,11 +9,10 @@ version: 2
 build:
   os: ubuntu-22.04
   tools:
-    python: "3.11"
+    python: "mambaforge-22.9"
   jobs:
     post_install:
-      # RtD seems to be not happy with pdm installs,
-      # hence use pip directly instead.
+      - which python
       - python -m pip install -r requirements-docs-locked.txt
       - python -m pip list
     pre_build:
@@ -22,3 +21,6 @@ build:
 mkdocs:
   configuration: mkdocs.yml
   fail_on_warning: true
+
+conda:
+  environment: environment-docs-conda-base.yml

Makefile

@@ -4,6 +4,10 @@
 # Will likely fail on Windows, but Makefiles are in general not Windows
 # compatible so we're not too worried
 TEMP_FILE := $(shell mktemp)
+# Directory in which to build the Fortran when using a standalone build
+BUILD_DIR := build
+# Coverage directory - needed to trick code cov to look in the right place
+COV_DIR := $(shell uv run --no-sync python -c 'from pathlib import  Path; import example_fgen_basic; print(Path(example_fgen_basic.__file__).parent)')
 
 # A helper script to get short descriptions of each target in the Makefile
 define PRINT_HELP_PYSCRIPT
@@ -24,8 +28,8 @@ help:  ## print short description of each target
 
 .PHONY: checks
 checks:  ## run all the linting checks of the codebase
-	@echo "=== pre-commit ==="; uv run pre-commit run --all-files || echo "--- pre-commit failed ---" >&2; \
-		echo "=== mypy ==="; MYPYPATH=stubs uv run mypy src || echo "--- mypy failed ---" >&2; \
+	@echo "=== pre-commit ==="; uv run --no-sync pre-commit run --all-files || echo "--- pre-commit failed ---" >&2; \
+		echo "=== mypy ==="; MYPYPATH=stubs uv run --no-sync mypy src || echo "--- mypy failed ---" >&2; \
 		echo "======"
 
 .PHONY: ruff-fixes
@@ -37,8 +41,17 @@ ruff-fixes:  ## fix the code using ruff
 	uv run ruff format src tests scripts docs
 
 .PHONY: test
-test:  ## run the tests
-	uv run pytest src tests -r a -v --doctest-modules --doctest-report ndiff --cov=src
+test:  ## run the tests (re-installs the package every time so you might want to run by hand if you're certain that step isn't needed)
+	# Note: passing `src` to pytest causes the `src` directory to be imported
+	# if the package has not already been installed.
+	# This is a problem, as the package is not importable from `src` by itself because the extension module is not available.
+	# As a result, you have to pass `pytest tests src` rather than `pytest src tests`
+	# to ensure that the package is imported from the venv and not `src`.
+	# The issue with this is that code coverage then doesn't work,
+	# because it is looking for lines in `src` to be run,
+	# but they're not because lines in `.venv` are run instead.
+	# We don't have a solution to this yet.
+	uv run --no-editable --reinstall-package example-fgen-basic pytest -r a -v tests src --doctest-modules --doctest-report ndiff --cov=$(COV_DIR)
 
 # Note on code coverage and testing:
 # You must specify cov=src.
@@ -55,15 +68,15 @@ test:  ## run the tests
 
 .PHONY: docs
 docs:  ## build the docs
-	uv run mkdocs build
+	uv run --no-sync mkdocs build
 
 .PHONY: docs-strict
 docs-strict:  ## build the docs strictly (e.g. raise an error on warnings, this most closely mirrors what we do in the CI)
-	uv run mkdocs build --strict
+	uv run --no-sync mkdocs build --strict
 
 .PHONY: docs-serve
 docs-serve:  ## serve the docs locally
-	uv run mkdocs serve
+	uv run --no-sync mkdocs serve
 
 .PHONY: changelog-draft
 changelog-draft:  ## compile a draft of the next changelog
@@ -79,5 +92,30 @@ licence-check:  ## Check that licences of the dependencies are suitable
 
 .PHONY: virtual-environment
 virtual-environment:  ## update virtual environment, create a new one if it doesn't already exist
-	uv sync --all-extras --group all-dev
-	uv run pre-commit install
+	uv sync --no-editable --all-extras --group all-dev
+	uv run --no-sync pre-commit install
+
+.PHONY: format-fortran
+format-fortran:  ## format the Fortran files
+	uv run fprettify -r src -c .fprettify.rc
+
+$(BUILD_DIR):  # setup the standlone Fortran build directory
+	uv run meson setup $(BUILD_DIR)
+
+.PHONY: build-fortran
+build-fortran: | $(BUILD_DIR)  ## build/compile the Fortran (including the extension module)
+	uv run meson compile -C build -v
+
+.PHONY: test-fortran
+test-fortran: build-fortran  ## run the Fortran tests
+	uv run meson test -C build -v
+
+.PHONY: install-fortran
+install-fortran: build-fortran  ## install the Fortran (including the extension module)
+	uv run meson install -C build -v
+	# # Can also do this to see where things go without making a mess
+	# uv run meson install -C build --destdir ../install-example
+
+.PHONY: clean
+clean:  ## clean all build artefacts
+	rm -rf $(BUILD_DIR)

changelog/2.feature.md

@@ -0,0 +1 @@
+Add basic functionality that wraps Fortran

config/install-mod.py

@@ -0,0 +1,50 @@
+#!/usr/bin/env python3
+"""
+Originally copied from: https://github.com/toml-f/toml-f/blob/main/config/install-mod.py
+
+Using the MIT License, copyright notice below
+(from https://github.com/toml-f/toml-f/blob/main/LICENSE-MIT)
+
+Copyright (c) 2019-2021 Sebastian Ehlert
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+"""
+
+from os import environ, listdir, makedirs
+from os.path import exists, isdir, join
+from shutil import copy
+from sys import argv
+
+build_dir = environ["MESON_BUILD_ROOT"]
+
+if "MESON_INSTALL_DESTDIR_PREFIX" in environ:
+    install_dir = environ["MESON_INSTALL_DESTDIR_PREFIX"]
+
+else:
+    install_dir = environ["MESON_INSTALL_PREFIX"]
+
+include_dir = argv[1] if len(argv) > 1 else "include"
+module_dir = join(install_dir, include_dir)
+
+modules = []
+for d in listdir(build_dir):
+    bd = join(build_dir, d)
+    if isdir(bd):
+        for f in listdir(bd):
+            if f.endswith(".mod"):
+                modules.append(join(bd, f))
+
+if not exists(module_dir):
+    makedirs(module_dir)
+
+for mod in modules:
+    print("Installing (from custom python script)", mod, "to", module_dir)
+    copy(mod, module_dir)

config/meson.build

@@ -0,0 +1,25 @@
+os = host_machine.system()
+
+if os == 'windows'
+  add_project_link_arguments(
+    '-Wl,--allow-multiple-definition',
+    language: 'fortran',
+  )
+endif
+
+fc = meson.get_compiler('fortran')
+fc_id = fc.get_id()
+
+if fc_id == 'gcc'
+  # from previous setup: "-g -O0 -Wall -fimplicit-none -fcheck=all,no-recursion
+  # -fbacktrace -Wno-unused-dummy-argument -Wno-unused-function"
+  add_project_arguments(
+    '-fbacktrace',
+    '-fcheck=all,no-recursion',
+    '-ffree-line-length-none',
+    '-fimplicit-none',
+    '-Wno-unused-dummy-argument',
+    '-Wno-unused-function',
+    language: 'fortran',
+  )
+endif