Merge branch 'main' into workflow-checker

Author: tetron

.github/workflows/ci-tests.yml

@@ -1,4 +1,4 @@
-name: Continous integration tests
+name: Continuous integration tests
 
 on:
   push:
@@ -32,7 +32,7 @@ jobs:
       TOXENV: ${{ format('py{0}{1}-{2}', matrix.py-ver-major, matrix.py-ver-minor, matrix.step) }}
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
         with:
           fetch-depth: 0
 
@@ -47,7 +47,7 @@ jobs:
         run: sudo usermod -c 'CI Runner' $(whoami)
 
       - name: Set up Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v3
         with:
           python-version: ${{ env.py-semver }}
           cache: pip
@@ -90,12 +90,12 @@ jobs:
       TOXENV: ${{ format('py310-{0}', matrix.step) }}
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
         with:
           fetch-depth: 0
 
       - name: Set up Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v3
         with:
           python-version: ${{ env.py-semver }}
           cache: pip
@@ -123,15 +123,15 @@ jobs:
         container: [docker, singularity, podman]
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - name: Set up Singularity
         uses: eWaterCycle/setup-singularity@v7
         with:
           singularity-version: ${{ env.singularity_version }}
 
       - name: Set up Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v3
         with:
           python-version: 3.9
           cache: pip
@@ -149,15 +149,15 @@ jobs:
     runs-on: ubuntu-20.04
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - name: Set up Singularity
         uses: eWaterCycle/setup-singularity@v7
         with:
           singularity-version: ${{ env.singularity_version }}
 
       - name: Set up Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v3
         with:
           python-version: "3.10"  # quoted, otherwise that turns into the number 3.1
           cache: pip

.github/workflows/codeql-analysis.yml

@@ -23,7 +23,7 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
 
     # Initializes the CodeQL tools for scanning.
     - name: Initialize CodeQL

.github/workflows/quay-publish.yml

@@ -8,7 +8,7 @@ jobs:
   build:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@master
+      - uses: actions/checkout@v3
       - name: Get image tags
         id: image_tags
         run: |

CWLProv.rst

@@ -235,7 +235,7 @@ Note that the `arcp <https://tools.ietf.org/id/draft-soilandreyes-arcp-03.html>`
 Account who launched cwltool
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-If `--enable-user-provenance` was used, the local machine acccount (e.g. Windows or UNIX user name) who started ``cwltool`` is tracked::
+If `--enable-user-provenance` was used, the local machine account (e.g. Windows or UNIX user name) who started ``cwltool`` is tracked::
 
     agent(id:855c6823-bbe7-48a5-be37-b0f07f20c495, [foaf:accountName="stain", prov:type='foaf:OnlineAccount', prov:label="stain"])
 

Makefile

@@ -107,6 +107,10 @@ pydocstyle_report.txt: $(PYSOURCES)
 diff_pydocstyle_report: pydocstyle_report.txt
 	diff-quality --compare-branch=main --violations=pydocstyle --fail-under=100 $^
 
+## codespell   : check for common mispellings
+codespell:
+	codespell -w $(shell git ls-files | grep -v cwltool/schemas | grep -v cwltool/jshint/ | grep -v typeshed)
+
 ## format      : check/fix all code indentation and formatting (runs black)
 format:
 	black --exclude cwltool/schemas setup.py cwltool.py cwltool tests
@@ -190,7 +194,7 @@ pyupgrade: $(PYSOURCES)
 	pyupgrade --exit-zero-even-if-changed --py36-plus $^
 
 release-test: check-python3 FORCE
-	git diff-index --quiet HEAD -- || ( echo You have uncommited changes, please commit them and try again; false )
+	git diff-index --quiet HEAD -- || ( echo You have uncommitted changes, please commit them and try again; false )
 	./release-test.sh
 
 release: release-test

README.rst

@@ -338,7 +338,7 @@ Environment Variables in cwltool
 This reference implementation supports several ways of setting
 environment variables for tools, in addition to the standard
 ``EnvVarRequirement``. The sequence of steps applied to create the
-enviroment is:
+environment is:
 
 0. If the ``--preserve-entire-environment`` flag is present, then begin with the current
    environment, else begin with an empty environment.
@@ -381,7 +381,7 @@ which your tool runs, for example by loading one or more Environment
 Modules. The environment is constructed as above, then the environment
 may modified by the selected tool resolver.  This currently means that
 you cannot override any environment variables set by the selected tool
-resolver. Note that the enviroment given to the configured dependency
+resolver. Note that the environment given to the configured dependency
 resolver has the variable `_CWLTOOL` set to `1` to allow introspection.
 
 To discuss some of these plugins and how to configure them, first consider the
@@ -691,7 +691,7 @@ the following in the terminal:
 
 List of all environment can be seen using:
 ``tox --listenvs``
-and running a specfic test env using:
+and running a specific test env using:
 ``tox -e <env name>``
 and additionally run a specific test using this format:
 ``tox -e py310-unit -- -v tests/test_examples.py::test_scandeps``

cwltool/checker.py

@@ -191,10 +191,9 @@ def static_checker(
     # sink parameters: step_inputs and workflow_outputs
 
     # make a dictionary of source parameters, indexed by the "id" field
-    src_parms = workflow_inputs + step_outputs
-    src_dict = {}  # type: Dict[str, CWLObjectType]
-    for parm in src_parms:
-        src_dict[cast(str, parm["id"])] = parm
+    src_dict: Dict[str, CWLObjectType] = {}
+    for param in workflow_inputs + step_outputs:
+        src_dict[cast(str, param["id"])] = param
 
     step_inputs_val = check_all_types(src_dict, step_inputs, "source", param_to_step)
     workflow_outputs_val = check_all_types(
@@ -343,7 +342,7 @@ def check_all_types(
     """
     Given a list of sinks, check if their types match with the types of their sources.
 
-    sourceField is either "soure" or "outputSource"
+    sourceField is either "source" or "outputSource"
     """
     validation = {"warning": [], "exception": []}  # type: Dict[str, List[SrcSink]]
     for sink in sinks:

cwltool/command_line_tool.py

@@ -598,7 +598,7 @@ def _initialworkdir(self, j: JobBase, builder: Builder) -> None:
                 if isinstance(t, Mapping) and "entry" in t:
                     # Dirent
                     entry_field = cast(str, t["entry"])
-                    # the schema guarentees that 'entry' is a string, so the cast is safe
+                    # the schema guarantees that 'entry' is a string, so the cast is safe
                     entry = builder.do_eval(entry_field, strip_whitespace=False)
                     if entry is None:
                         continue
@@ -634,7 +634,7 @@ def _initialworkdir(self, j: JobBase, builder: Builder) -> None:
                                 )
                             for e in entry:
                                 ec = cast(CWLObjectType, e)
-                                ec["writeable"] = t.get("writable", False)
+                                ec["writable"] = t.get("writable", False)
                             ls.extend(cast(List[CWLObjectType], entry))
                             continue
 

cwltool/docker.py

@@ -78,7 +78,7 @@ def _check_docker_machine_path(path: Optional[str]) -> None:
 
 
 class DockerCommandLineJob(ContainerCommandLineJob):
-    """Runs a CommandLineJob in a sofware container using the Docker engine."""
+    """Runs a CommandLineJob in a software container using the Docker engine."""
 
     def __init__(
         self,

cwltool/env_to_stdout.py

@@ -5,7 +5,7 @@
 
 Ideally we would just use `env -0`, because python (thanks to PEPs 538
 and 540) will set zero to two environment variables to better handle
-Unicode-locale interactions, however BSD familiy implementations of
+Unicode-locale interactions, however BSD family implementations of
 `env` do not all support the `-0` flag so we supply this script that
 produces equivalent output.
 """
@@ -16,15 +16,15 @@
 
 def deserialize_env(data: str) -> Dict[str, str]:
     """Deserialize the output of `env -0` to dictionary."""
-    ans = {}
+    result = {}
     for item in data.strip("\0").split("\0"):
         key, val = item.split("=", 1)
-        ans[key] = val
-    return ans
+        result[key] = val
+    return result
 
 
 def main() -> None:
-    """Print the null-separated enviroment to stdout."""
+    """Print the null-separated environment to stdout."""
     for k, v in os.environ.items():
         print(f"{k}={v}", end="\0")