synchronize setup.py & requirements.txt

Makefile

@@ -111,9 +111,14 @@ pydocstyle_report.txt: $(PYSOURCES)
 diff_pydocstyle_report: pydocstyle_report.txt
 	diff-quality --compare-branch=main --violations=pydocstyle --fail-under=100 $^
 
-## codespell              : check for common misspellings
-codespell:
-	codespell -w $(shell git ls-files | grep -v cwltool/schemas | grep -v cwltool/jshint/ | grep -v mypy-stubs)
+## codespell-check        : check for common misspellings
+codespell-check:
+	@codespell $(shell git ls-files | grep -v cwltool/schemas | grep -v cwltool/jshint/ | grep -v mypy-stubs) \
+		|| (echo Probable typo foun. Run \"make codespell-fix\" to accept suggested fixes, or add the word to the ignore list in setup.cfg ; exit 1)
+
+## codespell-fix          : fix common misspellings
+codespell-fix:
+	@codespell -w $(shell git ls-files | grep -v cwltool/schemas | grep -v cwltool/jshint/ | grep -v mypy-stubs)
 
 ## format                 : check/fix all code indentation and formatting (runs black)
 format:

cwltool/workflow.py

@@ -42,7 +42,7 @@
 
 
 def default_make_tool(toolpath_object: CommentedMap, loadingContext: LoadingContext) -> Process:
-    """Instatiate the given CWL Process."""
+    """Instantiate the given CWL Process."""
     if not isinstance(toolpath_object, MutableMapping):
         raise WorkflowException("Not a dict: '%s'" % toolpath_object)
     if "class" in toolpath_object:

requirements.txt

@@ -1,12 +1,11 @@
 requests>=2.6.1
-ruamel.yaml>=0.16.0,<0.17.27;python_version>='3.10'
+ruamel.yaml>=0.16.0,<0.17.28;python_version>='3.10'
 ruamel.yaml>=0.15,<0.17.28
 rdflib>=4.2.2,<6.4
 rdflib>= 4.2.2, < 6.0.0;python_version<='3.6'
 shellescape>=3.4.1,<3.9
 schema-salad>=8.4,<9
 prov==1.5.1
-bagit==1.8.1
 mypy-extensions
 psutil>=5.6.6
 typing-extensions

setup.cfg

@@ -9,4 +9,4 @@ use_parentheses = True
 line_length = 88
 
 [codespell]
-ignore-words-list=ORE,ore,RO,ro
+ignore-words-list=ORE,ore,RO,ro,recuse

setup.py

@@ -113,20 +113,22 @@
         "requests >= 2.6.1",  # >= 2.6.1 to workaround
         # https://github.com/ionrock/cachecontrol/issues/137
         "ruamel.yaml >= 0.15, < 0.17.28",
+        "ruamel.yaml >= 0.16.0, <0.17.28;python_version>='3.10'",
         "rdflib >= 4.2.2, < 6.4.0",
         "rdflib >= 4.2.2, < 6.0.0;python_version<='3.6'",
         "shellescape >= 3.4.1, < 3.9",
         "schema-salad >= 8.4, < 9",
+        "prov == 1.5.1",
         "mypy-extensions",
         "psutil >= 5.6.6",
-        "prov == 1.5.1",
-        "bagit >= 1.6.4",
         "typing-extensions",
+        "importlib_resources>=1.4",
+        "importlib_metadata;python_version<'3.8'",
         "coloredlogs",
         "pydot >= 1.4.1",
+        "argcomplete",
         "pyparsing != 3.0.2",  # breaks --print-dot (pydot) https://github.com/pyparsing/pyparsing/issues/319
         "pyparsing < 3 ;python_version<='3.6'",  # breaks --print-dot (pydot)
-        "argcomplete",
         "cwl-utils >= 0.22",
     ],
     extras_require={
@@ -136,6 +138,7 @@
     setup_requires=PYTEST_RUNNER,
     test_suite="tests",
     tests_require=[
+        "bagit >= 1.6.4, < 1.9",
         "pytest >= 6.2, < 7.4",
         "mock >= 2.0.0",
         "pytest-mock >= 1.10.0",

test-requirements.txt

@@ -1,3 +1,4 @@
+bagit >= 1.6.4, <1.9
 pytest >= 6.2, < 7.4
 pytest-xdist
 pytest-httpserver

tox.ini

@@ -67,7 +67,7 @@ commands_pre =
 commands =
   py3{6,7,8,9,10,11}-unit: make coverage-report coverage.xml PYTEST_EXTRA={posargs}
   py3{6,7,8,9,10,11}-bandit: bandit -r cwltool
-  py3{6,7,8,9,10,11}-lint: make flake8 format-check codespell
+  py3{6,7,8,9,10,11}-lint: make flake8 format-check codespell-check
   py3{7,8,9,10,11}-mypy: make mypy mypyc PYTEST_EXTRA={posargs}
   py37-mypy: make mypy_3.6
   py311-shellcheck: make shellcheck