readthedocs: install graphviz

Author: mr-c

.readthedocs.yml

@@ -12,9 +12,14 @@ sphinx:
 # Optionally build your docs in additional formats such as PDF and ePub
 formats: all
 
-# Optionally set the version of Python and requirements required to build your docs
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"
+  apt_packages:
+    - graphviz
+
 python:
-  version: 3.7
   install:
    - requirements: docs/requirements.txt
    - method: pip

cwl_utils/errors.py

@@ -3,23 +3,23 @@
 
 
 class ArrayMissingItems(BaseException):
-    """From https://github.com/rabix/sbpack/blob/b8404a0859ffcbe1edae6d8f934e51847b003320/sbpack/lib.py"""
+    """From https://github.com/rabix/sbpack/blob/b8404a0859ffcbe1edae6d8f934e51847b003320/sbpack/lib.py ."""
 
 
 class JavascriptException(Exception):
     pass
 
 
 class MissingKeyField(BaseException):
-    """From https://github.com/rabix/sbpack/blob/b8404a0859ffcbe1edae6d8f934e51847b003320/sbpack/lib.py"""
+    """From https://github.com/rabix/sbpack/blob/b8404a0859ffcbe1edae6d8f934e51847b003320/sbpack/lib.py ."""
 
 
 class MissingTypeName(BaseException):
-    """From https://github.com/rabix/sbpack/blob/b8404a0859ffcbe1edae6d8f934e51847b003320/sbpack/lib.py"""
+    """From https://github.com/rabix/sbpack/blob/b8404a0859ffcbe1edae6d8f934e51847b003320/sbpack/lib.py ."""
 
 
 class RecordMissingFields(BaseException):
-    """From https://github.com/rabix/sbpack/blob/b8404a0859ffcbe1edae6d8f934e51847b003320/sbpack/lib.py"""
+    """From https://github.com/rabix/sbpack/blob/b8404a0859ffcbe1edae6d8f934e51847b003320/sbpack/lib.py ."""
 
 
 class SubstitutionError(Exception):

cwl_utils/expression_refactor.py

@@ -110,7 +110,6 @@ def run(args: List[str]) -> int:
 
 def refactor(args: argparse.Namespace) -> int:
     """Primary processing loop."""
-
     return_code = 0
     yaml = YAML(typ="rt")
     yaml.preserve_quotes = True  # type: ignore[assignment]

cwl_utils/image_puller.py

@@ -41,9 +41,7 @@ def _run_command_pull(cmd_pull: List[str]) -> None:
 
 
 class DockerImagePuller(ImagePuller):
-    """
-    Pull docker image with Docker
-    """
+    """Pull docker image with Docker."""
 
     def get_image_name(self) -> str:
         """Get the name of the tarball."""
@@ -73,9 +71,7 @@ def save_docker_image(self) -> None:
 
 
 class SingularityImagePuller(ImagePuller):
-    """
-    Pull docker image with Singularity
-    """
+    """Pull docker image with Singularity."""
 
     CHARS_TO_REPLACE = ["/"]
     NEW_CHAR = "_"

cwl_utils/pack.py

@@ -3,6 +3,8 @@
 #  Copyright (c) 2020 Seven Bridges
 #  See https://github.com/rabix/sbpack/blob/b8404a0859ffcbe1edae6d8f934e51847b003320/LICENSE
 """
+CWL document packing functions.
+
 The link resolution is as follows:
 
 We always have two components: the base and the link

cwl_utils/schemadef.py

@@ -3,7 +3,7 @@
 #  Copyright (c) 2020 Seven Bridges
 #  See https://github.com/rabix/sbpack/blob/b8404a0859ffcbe1edae6d8f934e51847b003320/LICENSE
 """
-Valid forms of user defined types stored in external file
+Valid forms of user defined types stored in external file.
 
 A single dictionary (tests/types/singletype.yml)
 A list of dictionaries (e.g. tests/types/recursive.yml)

cwl_utils/utils.py

@@ -32,7 +32,10 @@
 
 
 def _is_github_symbolic_link(base_url: urllib.parse.ParseResult, contents: str) -> bool:
-    """Look for remote path with contents that is a single line with no new
+    """
+    Test if link is a GitHub style symbolic link.
+
+    Look for remote path with contents that is a single line with no new
     line with an extension.
 
     https://github.com/rabix/sbpack/blob/b8404a0859ffcbe1edae6d8f934e51847b003320/sbpack/lib.py
@@ -82,7 +85,7 @@ def bytes2str_in_dicts(
 def load_linked_file(
     base_url: urllib.parse.ParseResult, link: str, is_import: bool = False
 ) -> Tuple[Any, urllib.parse.ParseResult]:
-    """From https://github.com/rabix/sbpack/blob/b8404a0859ffcbe1edae6d8f934e51847b003320/sbpack/lib.py"""
+    """From https://github.com/rabix/sbpack/blob/b8404a0859ffcbe1edae6d8f934e51847b003320/sbpack/lib.py ."""
     new_url = resolved_path(base_url, link)
 
     if new_url.scheme in ["file://", ""]:
@@ -123,7 +126,7 @@ def load_linked_file(
 def normalize_to_map(
     obj: Union[List[Any], Dict[str, Any]], key_field: str
 ) -> Dict[str, Any]:
-    """From https://github.com/rabix/sbpack/blob/b8404a0859ffcbe1edae6d8f934e51847b003320/sbpack/lib.py"""
+    """From https://github.com/rabix/sbpack/blob/b8404a0859ffcbe1edae6d8f934e51847b003320/sbpack/lib.py ."""
     if isinstance(obj, dict):
         return deepcopy(obj)
     elif isinstance(obj, list):
@@ -144,7 +147,7 @@ def normalize_to_map(
 def normalize_to_list(
     obj: Union[List[Any], Dict[str, Any]], key_field: str, value_field: Optional[str]
 ) -> List[Any]:
-    """From https://github.com/rabix/sbpack/blob/b8404a0859ffcbe1edae6d8f934e51847b003320/sbpack/lib.py"""
+    """From https://github.com/rabix/sbpack/blob/b8404a0859ffcbe1edae6d8f934e51847b003320/sbpack/lib.py ."""
     if isinstance(obj, list):
         return deepcopy(obj)
     elif isinstance(obj, dict):
@@ -165,14 +168,18 @@ def resolved_path(
     base_url: urllib.parse.ParseResult, link: str
 ) -> urllib.parse.ParseResult:
     """
-    Given a base_url ("this document") and a link ("string in this document")
-    return a new url (urllib.parse.ParseResult) that allows us to retrieve the
-    linked document. This function will
+    Derive a resolved path.
+
+    This function will
     1. Resolve the path, which means dot and double dot components are resolved
     2. Use the OS appropriate path resolution for local paths, and network
-       appropriate resolution for network paths
+    appropriate resolution for network paths
 
     From https://github.com/rabix/sbpack/blob/b8404a0859ffcbe1edae6d8f934e51847b003320/sbpack/lib.py
+
+    :param base_url: "this document"
+    :param link: "string in this document"
+    :returns: new URL that allows us to retrieve the linked document
     """
     link_url = urllib.parse.urlparse(link)
     # The link will always Posix

docs/index.rst

@@ -13,6 +13,7 @@ Modules
    :maxdepth: 2
    :caption: Contents:
 
+   autoapi/index
 
 Included Utility Programs
 =========================