readthedocs: install graphviz

.github/workflows/ci-tests.yml

@@ -57,7 +57,7 @@ jobs:
       - name: Upgrade setuptools and install tox
         run: |
           pip install -U pip setuptools wheel
-          pip install "tox<4" tox-gh-actions
+          pip install "tox<4" "tox-gh-actions<3"
 
       - name: MyPy cache
         if: ${{ matrix.step == 'mypy' }}
@@ -102,7 +102,7 @@ jobs:
       - name: Upgrade setuptools and install tox
         run: |
           pip install -U pip setuptools wheel
-          pip install tox tox-gh-actions
+          pip install "tox<4" "tox-gh-actions<3"
 
       - if: ${{ matrix.step == 'pydocstyle' && github.event_name == 'pull_request'}}
         name: Create local branch for diff-quality for PRs
@@ -224,7 +224,7 @@ jobs:
       - name: Upgrade setuptools and install tox
         run: |
           pip install -U pip setuptools wheel
-          pip install tox tox-gh-actions
+          pip install "tox<4" "tox-gh-actions<3"
       # # docker for mac install is not currently stable
       # - name: 'SETUP MacOS: load Homebrew cache'
       #   uses: actions/cache@v3

.readthedocs.yml

@@ -16,6 +16,8 @@ build:
   os: ubuntu-22.04
   tools:
     python: "3.11"
+  apt_packages:
+    - graphviz
 
 python:
   install:

Makefile

@@ -25,9 +25,9 @@ MODULE=cwltool
 # `SHELL=bash` doesn't work for some, so don't use BASH-isms like
 # `[[` conditional expressions.
 PYSOURCES=$(wildcard ${MODULE}/**.py tests/*.py) setup.py
-DEVPKGS=diff_cover pylint pep257 pydocstyle tox tox-pyenv \
+DEVPKGS=diff_cover pylint pep257 pydocstyle 'tox<4' tox-pyenv \
 	isort wheel autoflake pyupgrade bandit -rlint-requirements.txt\
-	-rtest-requirements.txt -rmypy-requirements.txt
+	-rtest-requirements.txt -rmypy-requirements.txt -rdocs/requirements.txt
 DEBDEVPKGS=pep8 python-autopep8 pylint python-coverage pydocstyle sloccount \
 	   python-flake8 python-mock shellcheck
 

README.rst

@@ -716,7 +716,7 @@ To run the basic tests after installing `cwltool` execute the following:
 To run various tests in all supported Python environments, we use `tox <https://github.com/common-workflow-language/cwltool/tree/main/tox.ini>`_. To run the test suite in all supported Python environments
 first clone the complete code repository (see the ``git clone`` instructions above) and then run
 the following in the terminal:
-``pip install tox; tox -p``
+``pip install "tox<4"; tox -p``
 
 List of all environment can be seen using:
 ``tox --listenvs``

cwltool/argparser.py

@@ -742,6 +742,8 @@ def get_default_args() -> Dict[str, Any]:
 
 
 class FSAction(argparse.Action):
+    """Base action for our custom actions."""
+
     objclass: Optional[str] = None
 
     def __init__(
@@ -778,6 +780,8 @@ def __call__(
 
 
 class FSAppendAction(argparse.Action):
+    """Appending version of the base action for our custom actions."""
+
     objclass: Optional[str] = None
 
     def __init__(
@@ -832,11 +836,10 @@ class DirectoryAppendAction(FSAppendAction):
 
 
 class AppendAction(argparse.Action):
-    """An argparse action that clears the default values if any value is provided.
+    """An argparse action that clears the default values if any value is provided."""
 
-    Attributes:
-        _called (bool): Initially set to ``False``, changed if any value is appended.
-    """
+    _called: bool
+    """Initially set to ``False``, changed if any value is appended."""
 
     def __init__(
         self,

cwltool/command_line_tool.py

@@ -253,7 +253,6 @@ def revmap_file(
     outside the container. Recognizes files in the pathmapper or remaps
     internal output directories to the external directory.
     """
-
     # builder.outdir is the inner (container/compute node) output directory
     # outdir is the outer (host/storage system) output directory
 

cwltool/context.py

@@ -79,7 +79,7 @@ def log_handler(
 
 
 def set_log_dir(outdir: str, log_dir: str, subdir_name: str) -> str:
-    """Default handler for setting the log directory."""
+    """Set the log directory."""
     if log_dir == "":
         return outdir
     else:

cwltool/process.py

@@ -1203,10 +1203,8 @@ def scandeps(
     urljoin: Callable[[str, str], str] = urllib.parse.urljoin,
     nestdirs: bool = True,
 ) -> MutableSequence[CWLObjectType]:
-
-    """Given a CWL document or input object, search for dependencies
-    (references to external files) of 'doc' and return them as a list
-    of File or Directory objects.
+    """
+    Search for external files references in a CWL document or input object.
 
     Looks for objects with 'class: File' or 'class: Directory' and
     adds them to the list of dependencies.
@@ -1224,7 +1222,6 @@ def scandeps(
       produce the same relative file system locations.
     :returns: A list of File or Directory dependencies
     """
-
     r: MutableSequence[CWLObjectType] = []
     if isinstance(doc, MutableMapping):
         if "id" in doc:

cwltool/singularity.py

@@ -32,15 +32,13 @@
 
 def get_version() -> Tuple[List[int], str]:
     """
-    Parse the output of 'singularity --version' to determine the singularity flavor /
-    distribution (singularity, singularity-ce or apptainer) and the singularity version.
+    Parse the output of 'singularity --version' to determine the flavor and version.
+
     Both pieces of information will be cached.
 
-    Returns
-    -------
-    A tuple containing:
-    - A tuple with major and minor version numbers as integer.
-    - A string with the name of the singularity flavor.
+    :returns: A tuple containing:
+              - A tuple with major and minor version numbers as integer.
+              - A string with the name of the singularity flavor.
     """
     global _SINGULARITY_VERSION  # pylint: disable=global-statement
     global _SINGULARITY_FLAVOR  # pylint: disable=global-statement

docs/index.rst

@@ -9,6 +9,7 @@
    CWLProv
    pythonversions
    processgen
+   autoapi/index
 
 Indices and tables
 ==================