switch to "src" layout

https://packaging.python.org/en/latest/discussions/src-layout-vs-flat-layout/

Author: mr-c

.readthedocs.yml

@@ -13,7 +13,7 @@ sphinx:
 formats: all
 
 build:
-  os: ubuntu-22.04
+  os: ubuntu-24.04
   tools:
     python: "3.11"
   apt_packages:

Makefile

@@ -26,15 +26,15 @@ EXTRAS="[testing]"
 
 # `SHELL=bash` doesn't work for some, so don't use BASH-isms like
 # `[[` conditional expressions.
-PYSOURCES=$(filter-out $(MODULE)/parser/cwl_v%,$(shell find $(MODULE) -name "*.py")) \
+PYSOURCES=$(filter-out src/$(MODULE)/parser/cwl_v%,$(shell find src/$(MODULE) -name "*.py")) \
 	  create_cwl_from_objects.py load_cwl_by_path.py \
-	  ${MODULE}/parser/cwl_v1_?_utils.py docs/conf.py
+	  src/${MODULE}/parser/cwl_v1_?_utils.py docs/conf.py
 DEVPKGS=build diff_cover pylint pep257 ruff 'tox>=4' \
 	wheel autoflake pyupgrade bandit auto-walrus \
 	-rlint-requirements.txt -rmypy-requirements.txt
 DEBDEVPKGS=pep8 python-autopep8 pylint python-coverage ruff sloccount \
 	   python-flake8 python-mock shellcheck
-VERSION=v$(shell echo $$(tail -n 1 cwl_utils/__meta__.py | awk '{print $$3}'))
+VERSION=v$(shell echo $$(tail -n 1 src/cwl_utils/__meta__.py | awk '{print $$3}'))
 mkfile_dir := $(dir $(abspath $(lastword $(MAKEFILE_LIST))))
 UNAME_S=$(shell uname -s)
 
@@ -80,7 +80,7 @@ docs: FORCE
 
 ## clean                  : clean up all temporary / machine-generated files
 clean: FORCE
-	rm -f ${MODULE}/*.pyc ${MODULE}/tests/*.pyc
+	find src -name '*.pyc' -delete
 	rm -Rf .coverage
 	rm -f diff-cover.html
 
@@ -191,25 +191,25 @@ release: release-test
 flake8: FORCE
 	flake8 $(PYSOURCES)
 
-cwl_utils/parser/cwl_v1_0.py: FORCE
+src/cwl_utils/parser/cwl_v1_0.py: FORCE
 	schema-salad-tool --codegen python \
 		--codegen-parser-info "org.w3id.cwl.v1_0" \
 		https://github.com/common-workflow-language/common-workflow-language/raw/codegen/v1.0/extensions.yml \
 		> $@
 
-cwl_utils/parser/cwl_v1_1.py: FORCE
+src/cwl_utils/parser/cwl_v1_1.py: FORCE
 	schema-salad-tool --codegen python \
 		--codegen-parser-info "org.w3id.cwl.v1_1" \
 		https://github.com/common-workflow-language/cwl-v1.1/raw/codegen/extensions.yml \
 		> $@
 
-cwl_utils/parser/cwl_v1_2.py: FORCE
+src/cwl_utils/parser/cwl_v1_2.py: FORCE
 	schema-salad-tool --codegen python \
 		--codegen-parser-info "org.w3id.cwl.v1_2" \
 		https://github.com/common-workflow-language/cwl-v1.2/raw/codegen/extensions.yml \
 		> $@
 
-regen_parsers: cwl_utils/parser/cwl_v1_*.py
+regen_parsers: src/cwl_utils/parser/cwl_v1_*.py
 
 FORCE:
 

docs/conf.py

@@ -81,7 +81,7 @@
 
 version = __version__
 
-autoapi_dirs = ["../cwl_utils"]
+autoapi_dirs = ["../src/cwl_utils"]
 autodoc_typehints = "description"
 autoapi_keep_files = True
 autoapi_ignore = ["*migrations*", "*.pyi", "*tests*"]

load_cwl_by_path.py

@@ -1 +1 @@
-cwl_utils/tests/load_cwl_by_path.py
+src/cwl_utils/tests/load_cwl_by_path.py

pyproject.toml

@@ -71,19 +71,18 @@ cwl-normalizer = "cwl_utils.normalizer:main"
 cwl-inputs-schema-gen = "cwl_utils.inputs_schema_gen:main"
 
 [tool.pytest.ini_options]
-testpaths = ["cwl_utils/tests"]
-addopts = "-rsx -n auto"
+addopts = "-rsx -n auto --pyargs cwl_utils.tests"
 
 [tool.hatch.version]
-path = "cwl_utils/__meta__.py"
+path = "src/cwl_utils/__meta__.py"
 
 [tool.hatch.build.targets.sdist]
 only-include = [
     ".flake8",
     ".coveragerc",
     "create_cwl_from_objects.py",
     "CONTRIBUTING.md",
-    "cwl_utils",
+    "src/cwl_utils",
     "docs",
     "LICENSE",
     "lint-requirements.txt",
@@ -96,11 +95,6 @@ only-include = [
     "tox.ini"
 ]
 
-[tool.hatch.build.targets.wheel]
-only-include = [
-    "cwl_utils",
-]
-
 [tool.hatch.build.targets.wheel.hooks.mypyc]
 enable-by-default = false
 dependencies = [
@@ -112,8 +106,8 @@ dependencies = [
 ]
 require-runtime-dependencies = true
 include = [
-    "/cwl_utils/parser",
-    "/cwl_utils/expression.py"
+    "src/cwl_utils/parser",
+    "src/cwl_utils/expression.py"
 ]
 
 [tool.hatch.envs.test]
@@ -139,4 +133,4 @@ ignore = [
 ]
 
 [tool.bandit]
-exclude_dirs = ["cwl_utils/tests"]
+exclude_dirs = ["src/cwl_utils/tests"]

release-test.sh

@@ -17,7 +17,6 @@ else
     repo=https://github.com/common-workflow-language/cwl-utils.git
     HEAD=$(git rev-parse HEAD)
 fi
-run_tests="bin/py.test --pyargs ${module}"
 pipver=23.1  # minimum required version of pip for Python 3.12
 DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null && pwd )"
 
@@ -34,12 +33,7 @@ then
 	pip install ".${extras}"
 	make test
 	pip uninstall -y ${package} || true; pip uninstall -y ${package} || true; make install
-	mkdir testenv1/not-${module}
-	# if there is a subdir named '${module}' py.test will execute tests
-	# there instead of the installed module's tests
-	pushd testenv1/not-${module}
-	# shellcheck disable=SC2086
-	../${run_tests}; popd
+	make test
 fi
 
 python3 -m venv testenv2
@@ -64,9 +58,8 @@ make test
 cp dist/${module}*tar.gz ../../../testenv3/
 cp dist/${module}*whl ../../../testenv4/
 pip uninstall -y ${package} || true; pip uninstall -y ${package} || true; make install
-popd # ../.. no subdir named ${proj} here, safe for py.testing the installed module
-# shellcheck disable=SC2086
-${run_tests}
+make test
+popd
 popd
 
 # Is the source distribution in testenv2 complete enough to build
@@ -85,10 +78,7 @@ pushd out/${module}*
 make dist
 make test
 pip uninstall -y ${package} || true; pip uninstall -y ${package} || true; make install
-mkdir ../not-${module}
-pushd ../not-${module}
-# shellcheck disable=SC2086
-../../${run_tests}; popd
+make test
 popd
 popd
 
@@ -100,8 +90,5 @@ source bin/activate \
 	&& pip install --force-reinstall -U pip==${pipver} \
         && pip install build wheel
 pip install "$(ls ${module}*.whl)${extras}"
-mkdir not-${module}
-pushd not-${module}
-# shellcheck disable=SC2086
-../${run_tests}; popd
+make test
 popd