Merge pull request #81 from Remi-Gau/clean_up

[MAINT] add bids example submodule for testing

.gitignore

@@ -1,4 +1,3 @@
-bids-examples
 report.txt
 
 # do not track _version.py for hatch

.gitmodules

@@ -1,3 +1,7 @@
 [submodule "bids/ext/reports/templates"]
 	path = bids/ext/reports/templates
 	url = https://github.com/bids-standard/bids-methods.git
+[submodule "tools/bids-examples"]
+	path = tools/bids-examples
+	url = https://github.com/bids-standard/bids-examples
+	datalad-url = https://github.com/bids-standard/bids-examples

.pre-commit-config.yaml

@@ -26,6 +26,13 @@ repos:
   - id: yamlfmt
     args: [--mapping, '2', --sequence, '2', --offset, '0']
 
+- repo: https://github.com/macisamuele/language-formatters-pre-commit-hooks
+  rev: v2.13.0
+  hooks:
+  - id: pretty-format-toml
+    args: [--autofix, --indent, '4']
+
+
 - repo: https://github.com/asottile/pyupgrade
   rev: v3.15.2
   hooks:

docs/source/conf.py

@@ -79,7 +79,7 @@
 # intersphinx
 # -----------------------------------------------------------------------------
 _python_version_str = f"{sys.version_info.major}.{sys.version_info.minor}"
-_python_doc_base = "https://docs.python.org/" + _python_version_str
+_python_doc_base = f"https://docs.python.org/{_python_version_str}"
 intersphinx_mapping = {
     "python": (_python_doc_base, None),
     "numpy": ("https://numpy.org/doc/stable/", (None, "./_intersphinx/numpy-objects.inv")),

pyproject.toml

@@ -1,88 +1,74 @@
 [build-system]
-requires = ["hatchling", "hatch-vcs"]
 build-backend = "hatchling.build"
-
-[tool.hatch.version]
-source = "vcs"
-
-[tool.hatch.build.targets.wheel]
-packages = ["bids"]
-only-include = ["bids/ext/reports"]
-
-[tool.hatch.build.hooks.vcs]
-version-file = "bids/ext/reports/_version.py"
+requires = ["hatchling", "hatch-vcs"]
 
 [project]
-name = "pybids_reports"
-description = "pybids-reports: report generator for BIDS datasets"
-authors = [{ name = "PyBIDS Developers", email = "[email protected]"}]
-maintainers = [{ name = "PyBIDS Developers", email = "[email protected]" }]
-readme = "README.md"
-license = { file = "LICENSE" }
-requires-python = ">=3.8"
-dependencies = [
-  "chevron",
-  "pybids>=0.15",
-  "nibabel",
-  "num2words",
-  "rich"
-]
+authors = [{name = "PyBIDS Developers", email = "[email protected]"}]
 classifiers = [
-  "Development Status :: 3 - Alpha",
-  "Environment :: Console",
-  "Intended Audience :: Science/Research",
-  "License :: OSI Approved :: MIT License",
-  "Operating System :: OS Independent",
-  "Programming Language :: Python",
-  "Programming Language :: Python :: 3",
-  "Programming Language :: Python :: 3 :: Only",
-  "Topic :: Scientific/Engineering",
+    "Development Status :: 3 - Alpha",
+    "Environment :: Console",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3 :: Only",
+    "Topic :: Scientific/Engineering"
 ]
+dependencies = [
+    "chevron",
+    "pybids>=0.15",
+    "nibabel",
+    "num2words",
+    "rich"
+]
+description = "pybids-reports: report generator for BIDS datasets"
 dynamic = ["version"]
-# version = "0.1.0"
-
-[project.scripts]
-pybids_reports = "bids.ext.reports.cli:cli"
-
-[project.urls]
-Homepage = "http://github.com/bids-standard/pybids-reports"
-Documentation = "https://pybids-reports.readthedocs.io/en/latest/"
-"Bug tracker" = "http://github.com/bids-standard/pybids-reports/issues"
+license = {file = "LICENSE"}
+maintainers = [{name = "PyBIDS Developers", email = "[email protected]"}]
+name = "pybids_reports"
+readme = "README.md"
+requires-python = ">=3.8"
 
 [project.optional-dependencies]
+ci_tests = [
+    "pybids_reports[test]",
+    "pytest-xdist"
+]
+dev = [
+    "pybids_reports[doc]",
+    "pybids_reports[test]"
+]
 doc = [
-  "furo",
-  "myst-parser",
-  "nbsphinx",
-	"numpydoc",
-	"sphinx",
-  "sphinx-argparse",
-  "sphinx-copybutton",
-  "sphinx_gallery",
+    "furo",
+    "myst-parser",
+    "nbsphinx",
+    "numpydoc",
+    "sphinx",
+    "sphinx-argparse",
+    "sphinx-copybutton",
+    "sphinx_gallery"
 ]
-docs=["pybids_reports[doc]"]
+docs = ["pybids_reports[doc]"]
 test = [
     "codecov",
     "flake8-black",
     "flake8-docstrings",
     "flake8-isort",
     "pytest>=3.3",
-    "pytest-cov",
-]
-tests=["pybids_reports[test]"]
-ci_tests = [
-  "pybids_reports[test]",
-  "pytest-xdist"
-]
-dev = [
-  "pybids_reports[doc]",
-  "pybids_reports[test]"
+    "pytest-cov"
 ]
+tests = ["pybids_reports[test]"]
+
+[project.scripts]
+pybids_reports = "bids.ext.reports.cli:cli"
+
+[project.urls]
+"Bug tracker" = "http://github.com/bids-standard/pybids-reports/issues"
+Documentation = "https://pybids-reports.readthedocs.io/en/latest/"
+Homepage = "http://github.com/bids-standard/pybids-reports"
 
 [tool.black]
-line-length = 99
-target-version = ['py38']
-include = '\.pyi?$'
 exclude = '''
 (
   /(
@@ -99,41 +85,61 @@ exclude = '''
   | bids/ext/reports/due.py
 )
 '''
+include = '\.pyi?$'
+line-length = 99
+target-version = ['py38']
 
 [tool.codespell]
-skip = "./.git,bids/ext/reports/tests/data/*"
 ignore-words-list = "te"
+skip = "./.git,bids/ext/reports/tests/data/*"
+
+[tool.coverage.paths]
+source = [
+    "bids/ext/reports",
+    "**/bids/ext/reports"
+]
+
+[tool.coverage.report]
+include_namespace_packages = true
+
+[tool.hatch.build.hooks.vcs]
+version-file = "bids/ext/reports/_version.py"
+
+[tool.hatch.build.targets.wheel]
+only-include = ["bids/ext/reports"]
+packages = ["bids"]
+
+[tool.hatch.version]
+source = "vcs"
+
+[tool.isort]
+combine_as_imports = true
+line_length = 99
+profile = "black"
+skip_gitignore = true
 
 [tool.mypy]
-exclude = ['bids/ext/reports/tests/']
 check_untyped_defs = true
 disallow_any_generics = true
 disallow_incomplete_defs = true
 disallow_untyped_defs = true
+exclude = ['bids/ext/reports/tests/']
 no_implicit_optional = true
 warn_redundant_casts = true
 warn_unused_ignores = true
 
 [[tool.mypy.overrides]]
+ignore_errors = true
 module = [
     'bids.ext.reports.tests.*',
     'bids.ext.reports._version.*',
-    'bids.ext.reports.due.*',
-]
-ignore_errors = true
-
-[tool.coverage.paths]
-source = [
-  "bids/ext/reports",
-  "**/bids/ext/reports",
+    'bids.ext.reports.due.*'
 ]
 
-[tool.coverage.report]
-include_namespace_packages = true
-
-
-[tool.isort]
-combine_as_imports = true
-line_length = 99
-profile = "black"
-skip_gitignore = true
+[tool.pytest.ini_options]
+addopts = "-ra --strict-config --strict-markers --doctest-modules --showlocals -s -vv --durations=0"
+doctest_optionflags = "NORMALIZE_WHITESPACE ELLIPSIS"
+junit_family = "xunit2"
+minversion = "6.0"
+norecursedirs = "bids/ext/reports/templates"
+xfail_strict = true