switch to "src" layout

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

Author: mr-c

.coveragerc

@@ -1,7 +1,7 @@
 [run]
 branch = True
 source = schema_salad
-omit = schema_salad/tests/*
+omit = src/schema_salad/tests/*
 
 [report]
 exclude_lines =
@@ -11,6 +11,6 @@ exclude_lines =
     if __name__ == .__main__.:
 ignore_errors = True
 omit =
-    schema_salad/tests/*
-    schema_salad/metaschema.py
-    schema_salad/python_codegen_support.py
+    src/schema_salad/tests/*
+    src/schema_salad/metaschema.py
+    src/schema_salad/python_codegen_support.py

.dockerignore

@@ -18,7 +18,7 @@ testenv*/
 *.so
 *.swp
 .github/
-schema_salad/*.so
+src/schema_salad/*.so
 *.Dockerfile
 build-schema_salad-docker.sh
 __pycache__/

.flake8

@@ -6,7 +6,7 @@ extend-ignore = E203,E501,E701,E704
 # when Python 3.10 is the minimum version, re-enable check B905 for zip + strict
 extend-select = B950
 per-file-ignores =
-  schema_salad/metaschema.py:B950
-  schema_salad/tests/*.py:B011
-  schema_salad/tests/test_codegen_errors.py:B950
-  schema_salad/tests/util.py:B950
+  src/schema_salad/metaschema.py:B950
+  src/schema_salad/tests/*.py:B011
+  src/schema_salad/tests/test_codegen_errors.py:B950
+  src/schema_salad/tests/util.py:B950

.readthedocs.yml

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

MANIFEST.in

@@ -1,18 +1,18 @@
 include Makefile LICENSE.txt requirements.txt mypy-requirements.txt test-requirements.txt mypy.ini
-include schema_salad/py.typed
-include schema_salad/avro/*
-recursive-include schema_salad/java *
-recursive-include schema_salad/typescript *
-recursive-include schema_salad/dotnet *
-include schema_salad/tests/*
-include schema_salad/tests/test_schema/*.md
-include schema_salad/tests/test_schema/*.yml
-include schema_salad/tests/test_schema/*.cwl
-recursive-include schema_salad/tests/cpp_tests *.h *.yml
-include schema_salad/tests/foreign/*.cwl
-recursive-include schema_salad/tests/test_real_cwl *
-include schema_salad/metaschema/*
-include schema_salad/tests/docimp/*
+include src/schema_salad/py.typed
+include src/schema_salad/avro/*
+recursive-include src/schema_salad/java *
+recursive-include src/schema_salad/typescript *
+recursive-include src/schema_salad/dotnet *
+include src/schema_salad/tests/*
+include src/schema_salad/tests/test_schema/*.md
+include src/schema_salad/tests/test_schema/*.yml
+include src/schema_salad/tests/test_schema/*.cwl
+recursive-include src/schema_salad/tests/cpp_tests *.h *.yml
+include src/schema_salad/tests/foreign/*.cwl
+recursive-include src/schema_salad/tests/test_real_cwl *
+include src/schema_salad/metaschema/*
+include src/schema_salad/tests/docimp/*
 recursive-include mypy-stubs *.py?
 global-exclude *~
 global-exclude *.pyc

Makefile

@@ -26,7 +26,7 @@ EXTRAS=[pycodegen]
 
 # `SHELL=bash` doesn't work for some, so don't use BASH-isms like
 # `[[` conditional expressions.
-PYSOURCES=$(wildcard ${MODULE}/**.py ${MODULE}/avro/*.py ${MODULE}/tests/*.py) setup.py
+PYSOURCES=$(wildcard src/${MODULE}/**.py src/${MODULE}/avro/*.py src/${MODULE}/tests/*.py) setup.py
 DEVPKGS=-rdev-requirements.txt -rtest-requirements.txt -rmypy-requirements.txt -rlint-requirements.txt
 COVBASE=coverage run --append
 PYTEST_EXTRA ?=
@@ -71,26 +71,27 @@ docs: FORCE
 
 ## clean                  : clean up all temporary / machine-generated files
 clean: FORCE
-	rm -rf ${MODULE}/__pycache__ ${MODULE}/tests/__pycache__ schema_salad/_version.py
-	rm -f *.so ${MODULE}/*.so ${MODULE}/tests/*.so ${MODULE}/avro/*.so
+	find src -type d -name __pycache__ | xargs rm -Rf
+	rm -f src/schema_salad/_version.py
+	find src -type f -name "*.so" -delete
 	python setup.py clean --all || true
 	rm -Rf .coverage
 	rm -f diff-cover.html
 
 # Linting and code style related targets
 ## sort_import            : sorting imports using isort: https://github.com/timothycrosley/isort
-sort_imports: $(filter-out schema_salad/metaschema.py,$(PYSOURCES)) mypy-stubs
+sort_imports: $(filter-out src/schema_salad/metaschema.py,$(PYSOURCES)) mypy-stubs
 	isort $^
 
-remove_unused_imports: $(filter-out schema_salad/metaschema.py,$(PYSOURCES))
+remove_unused_imports: $(filter-out src/schema_salad/metaschema.py,$(PYSOURCES))
 	autoflake --in-place --remove-all-unused-imports $^
 
 pep257: pydocstyle
 ## pydocstyle             : check Python docstring style
-pydocstyle: $(filter-out schema_salad/metaschema.py,$(PYSOURCES))
+pydocstyle: $(filter-out src/schema_salad/metaschema.py,$(PYSOURCES))
 	pydocstyle --add-ignore=D100,D101,D102,D103 $^ || true
 
-pydocstyle_report.txt: $(filter-out schema_salad/metaschema.py,$(PYSOURCES))
+pydocstyle_report.txt: $(filter-out src/schema_salad/metaschema.py,$(PYSOURCES))
 	pydocstyle setup.py $^ > $@ 2>&1 || true
 
 ## diff_pydocstyle_report : check Python docstring style for changed files only
@@ -103,10 +104,10 @@ codespell:
 
 ## format                 : check/fix all code indentation and formatting (runs black)
 format:
-	black --force-exclude metaschema.py --exclude _version.py schema_salad setup.py mypy-stubs
+	black --force-exclude metaschema.py --exclude _version.py src/schema_salad setup.py mypy-stubs
 
 format-check:
-	black --diff --check --force-exclude metaschema.py --exclude _version.py schema_salad setup.py mypy-stubs
+	black --diff --check --force-exclude metaschema.py --exclude _version.py src/schema_salad setup.py mypy-stubs
 
 ## pylint                 : run static code analysis on Python code
 pylint: $(PYSOURCES)
@@ -123,16 +124,16 @@ diff_pylint_report: pylint_report.txt
 .coverage:
 	pytest --cov --cov-config=.coveragerc --cov-report= ${PYTEST_EXTRA}
 	$(COVBASE) -m schema_salad.main \
-		--print-jsonld-context schema_salad/metaschema/metaschema.yml \
+		--print-jsonld-context src/schema_salad/metaschema/metaschema.yml \
 		> /dev/null
 	$(COVBASE) -m schema_salad.main \
-		--print-rdfs schema_salad/metaschema/metaschema.yml \
+		--print-rdfs src/schema_salad/metaschema/metaschema.yml \
 		> /dev/null
 	$(COVBASE) -m schema_salad.main \
-		--print-avro schema_salad/metaschema/metaschema.yml \
+		--print-avro src/schema_salad/metaschema/metaschema.yml \
 		> /dev/null
 	$(COVBASE) -m schema_salad.makedoc --debug \
-		schema_salad/metaschema/metaschema.yml \
+		src/schema_salad/metaschema/metaschema.yml \
 		> /dev/null
 
 coverage.xml: .coverage
@@ -185,12 +186,12 @@ mypyi:
 
 check-metaschema-diff:
 	docker run \
-		-v "$(realpath ${MODULE}/metaschema/):/tmp/:ro" \
+		-v "$(realpath src/${MODULE}/metaschema/):/tmp/:ro" \
 		"quay.io/commonwl/cwltool_module:latest" \
 		schema-salad-doc /tmp/metaschema.yml \
 		> /tmp/metaschema.orig.html
 	schema-salad-doc \
-		"$(realpath ${MODULE}/metaschema/metaschema.yml)" \
+		"$(realpath src/${MODULE}/metaschema/metaschema.yml)" \
 		> /tmp/metaschema.new.html
 	diff -a --color /tmp/metaschema.orig.html /tmp/metaschema.new.html || true
 
@@ -202,9 +203,9 @@ shellcheck: FORCE
 
 ## bandit                 : check for common security issues
 bandit:
-	bandit --recursive --exclude schema_salad/tests/ schema_salad
+	bandit --recursive --exclude src/schema_salad/tests/ src/schema_salad
 
-pyupgrade: $(filter-out schema_salad/metaschema.py,$(PYSOURCES))
+pyupgrade: $(filter-out src/schema_salad/metaschema.py,$(PYSOURCES))
 	pyupgrade --exit-zero-even-if-changed --py310-plus $^
 	auto-walrus $^
 
@@ -225,12 +226,12 @@ release:
 flake8: FORCE
 	flake8 $(PYSOURCES)
 
-schema_salad/metaschema.py: schema_salad/codegen_base.py schema_salad/python_codegen_support.py schema_salad/python_codegen.py schema_salad/metaschema/*.yml
-	schema-salad-tool --codegen python schema_salad/metaschema/metaschema.yml > $@
+src/schema_salad/metaschema.py: src/schema_salad/codegen_base.py src/schema_salad/python_codegen_support.py src/schema_salad/python_codegen.py src/schema_salad/metaschema/*.yml
+	schema-salad-tool --codegen python src/schema_salad/metaschema/metaschema.yml > $@
 
-vpath %.yml schema_salad/tests/cpp_tests
+vpath %.yml src/schema_salad/tests/cpp_tests
 
-schema_salad/tests/cpp_tests/%.h: %.yml
+src/schema_salad/tests/cpp_tests/%.h: %.yml
 	schema-salad-tool --codegen cpp --codegen-target $@ $<
 
 FORCE:

README.rst

@@ -109,7 +109,7 @@ First set of examples is using the `CWL v1.2 schema <https://github.com/common-w
 +-------------+---------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
 | Language    | Repository                                              | Serialization Example                                                                                                                                 | Deserialization Example                                                                                                                                                   |
 +=============+=========================================================+======================================================================================================================================================+============================================================================================================================================================================+
-| Python      | https://github.com/common-workflow-language/cwl-utils/  | `create_cwl_from_objects.py <https://github.com/common-workflow-language/cwl-utils/blob/main/create_cwl_from_objects.py>`_                           | `load_document() <https://github.com/common-workflow-language/cwl-utils/blob/main/cwl_utils/parser/__init__.py#L93>`_                                                      |
+| Python      | https://github.com/common-workflow-language/cwl-utils/  | `create_cwl_from_objects.py <https://github.com/common-workflow-language/cwl-utils/blob/main/create_cwl_from_objects.py>`_                           | `load_document() <https://github.com/common-workflow-language/cwl-utils/blob/main/src/cwl_utils/parser/__init__.py#L93>`_                                                  |
 +-------------+---------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
 | Java        | https://github.com/common-workflow-language/cwljava/    | (Not yet implemented)                                                                                                                                | `PackedWorkflowClassTest.java <https://github.com/common-workflow-language/cwljava/blob/cwl-1.2.0/src/test/java/org/w3id/cwl/cwl1_2/utils/PackedWorkflowClassTest.java>`_  |
 +-------------+---------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
@@ -207,8 +207,8 @@ Here is an example schema to do that::
            type: array
            items: Product
 
-You can check the schema and document in schema_salad/tests/basket_schema.yml
-and schema_salad/tests/basket.yml::
+You can check the schema and document in src/schema_salad/tests/basket_schema.yml
+and src/schema_salad/tests/basket.yml::
 
    $ schema-salad-tool basket_schema.yml basket.yml
    Document `basket.yml` is valid
@@ -257,7 +257,7 @@ provides for robust support of inline documentation.
 
 .. _JSON-LD: http://json-ld.org
 .. _Avro: http://avro.apache.org
-.. _metaschema: https://github.com/common-workflow-language/schema_salad/blob/main/schema_salad/metaschema/metaschema.yml
+.. _metaschema: https://github.com/common-workflow-language/schema_salad/blob/main/src/schema_salad/metaschema/metaschema.yml
 .. _specification: http://www.commonwl.org/v1.2/SchemaSalad.html
 .. _Language: https://github.com/common-workflow-language/cwl-v1.2/blob/v1.2.0/CommandLineTool.yml
 .. _RDF: https://www.w3.org/RDF/

docs/conf.py

@@ -87,7 +87,7 @@
 
 version = _version.version
 
-autoapi_dirs = ["../schema_salad"]
+autoapi_dirs = ["../src/schema_salad"]
 autodoc_typehints = "description"
 autoapi_keep_files = True
 autoapi_ignore = ["*migrations*", "*.pyi"]

lgtm.yml

@@ -6,4 +6,4 @@ extraction:
     index:
       # Specify a list of files and folders to exclude from extraction.
       exclude:
-        - schema_salad/typescript/
+        - src/schema_salad/typescript/

pyproject.toml

@@ -15,7 +15,7 @@ requires = [
 build-backend = "setuptools.build_meta"
 
 [tool.setuptools_scm]
-write_to = "schema_salad/_version.py"
+write_to = "src/schema_salad/_version.py"
 
 [tool.cibuildwheel]
 test-command = "python -m pytest -n auto --junitxml={project}/test-results/junit_$(python -V | awk '{print $2}')_${AUDITWHEEL_PLAT}.xml --pyargs schema_salad"