Formats project using ruff

docs/conf.py

@@ -19,7 +19,8 @@
 #
 import os
 import sys
-sys.path.insert(0, os.path.abspath('..'))
+
+sys.path.insert(0, os.path.abspath(".."))
 
 import ssm_client
 
@@ -33,22 +34,22 @@
 
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
-extensions = ['sphinx.ext.autodoc', 'sphinx.ext.viewcode']
+extensions = ["sphinx.ext.autodoc", "sphinx.ext.viewcode"]
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # The suffix(es) of source filenames.
 # You can specify multiple suffix as a list of string:
 #
 # source_suffix = ['.rst', '.md']
-source_suffix = '.rst'
+source_suffix = ".rst"
 
 # The master toctree document.
-master_doc = 'index'
+master_doc = "index"
 
 # General information about the project.
-project = 'ssm-client'
+project = "ssm-client"
 copyright = "2020, Marshall McDonnell"
 author = "Marshall McDonnell"
 
@@ -71,10 +72,10 @@
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This patterns also effect to html_static_path and html_extra_path
-exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
 
 # The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
+pygments_style = "sphinx"
 
 # If true, `todo` and `todoList` produce output, else they produce nothing.
 todo_include_todos = False
@@ -85,7 +86,7 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-#html_theme = 'alabaster'
+# html_theme = 'alabaster'
 html_theme = "sphinx_rtd_theme"
 html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
 
@@ -98,13 +99,13 @@
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+html_static_path = ["_static"]
 
 
 # -- Options for HTMLHelp output ---------------------------------------
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'ssm_clientdoc'
+htmlhelp_basename = "ssm_clientdoc"
 
 
 # -- Options for LaTeX output ------------------------------------------
@@ -113,15 +114,12 @@
     # The paper size ('letterpaper' or 'a4paper').
     #
     # 'papersize': 'letterpaper',
-
     # The font size ('10pt', '11pt' or '12pt').
     #
     # 'pointsize': '10pt',
-
     # Additional stuff for the LaTeX preamble.
     #
     # 'preamble': '',
-
     # Latex figure (float) alignment
     #
     # 'figure_align': 'htbp',
@@ -131,21 +129,21 @@
 # (source start file, target name, title, author, documentclass
 # [howto, manual, or own class]).
 latex_documents = [
-    (master_doc, 'ssm_client.tex',
-     'ssm-client Documentation',
-     'Marshall McDonnell', 'manual'),
+    (
+        master_doc,
+        "ssm_client.tex",
+        "ssm-client Documentation",
+        "Marshall McDonnell",
+        "manual",
+    ),
 ]
 
 
 # -- Options for manual page output ------------------------------------
 
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
-man_pages = [
-    (master_doc, 'ssm_client',
-     'ssm-client Documentation',
-     [author], 1)
-]
+man_pages = [(master_doc, "ssm_client", "ssm-client Documentation", [author], 1)]
 
 
 # -- Options for Texinfo output ----------------------------------------
@@ -154,13 +152,13 @@
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-    (master_doc, 'ssm_client',
-     'ssm-client Documentation',
-     author,
-     'ssm_client',
-     'One line description of project.',
-     'Miscellaneous'),
+    (
+        master_doc,
+        "ssm_client",
+        "ssm-client Documentation",
+        author,
+        "ssm_client",
+        "One line description of project.",
+        "Miscellaneous",
+    ),
 ]
-
-
-

pyproject.toml

@@ -19,6 +19,9 @@ license = {text = "BSD 3-Clause License"}
 notebooks = [
     "jupyter>=1.0.0",
 ]
+":lint" = [
+    "ruff>=0.6.1",
+]
 
 [tool.pdm.dev-dependencies]
 test = [

src/ssm_client/__init__.py

@@ -1,7 +1,7 @@
 """Top-level package for ssm-client."""
 
 __author__ = """Marshall McDonnell"""
-__email__ = '[email protected]'
+__email__ = "[email protected]"
 
 
 from .ssm_rester import SSMRester

src/ssm_client/containers/collection_container.py

@@ -3,8 +3,8 @@
 
 class CollectionContainer:
     def __init__(self, **kwargs):
-        self.__title = kwargs.get('title', None)
-        self.__uri = kwargs.get('uri', None)
+        self.__title = kwargs.get("title", None)
+        self.__uri = kwargs.get("uri", None)
 
     def __eq__(self, other):
         """

src/ssm_client/containers/dataset_container.py

@@ -3,8 +3,8 @@
 
 class DatasetContainer:
     def __init__(self, **kwargs):
-        self.__uuid = kwargs.get('uuid', None)
-        self.__dataset = kwargs.get('dataset', dict())
+        self.__uuid = kwargs.get("uuid", None)
+        self.__dataset = kwargs.get("dataset", dict())
 
     def __eq__(self, other):
         """

src/ssm_client/io/__init__.py

@@ -1,6 +1,3 @@
 from .formats import read, write
 
-__all__ = [
-    'read',
-    'write'
-]
+__all__ = ["read", "write"]

src/ssm_client/io/formats.py

@@ -1,18 +1,18 @@
 from importlib import import_module
 
 
-_MODULE_BASE = 'ssm_client.io.'
+_MODULE_BASE = "ssm_client.io."
 
 
 class UnknownFileTypeError(Exception):
     pass
 
 
 ioformats = {
-    'jcamp': 'jcamp',
-    'rruff': 'rruff',
-    'scidata-jsonld': 'scidata_jsonld',
-    'ssm-json': 'ssm_json',
+    "jcamp": "jcamp",
+    "rruff": "rruff",
+    "scidata-jsonld": "scidata_jsonld",
+    "ssm-json": "ssm_json",
 }
 
 
@@ -25,11 +25,11 @@ def _get_ioformat(name):
 
 
 def _readfunc(module, name):
-    return getattr(module, 'read_' + name)
+    return getattr(module, "read_" + name)
 
 
 def _writefunc(module, name):
-    return getattr(module, 'write_' + name)
+    return getattr(module, "write_" + name)
 
 
 def read(filename, ioformat=None, **kwargs) -> dict:

src/ssm_client/io/jcamp.py

@@ -12,7 +12,7 @@ def read_jcamp(filename: str) -> dict:
 
     Args:
         filename (str): Filename to read from for JCAMP-DX files
-    Returns: 
+    Returns:
         scidata_dict (dict): SciData JSON-LD dictionary
     """
     scidata_obj = scidatalib.io.read(filename, ioformat="jcamp")

src/ssm_client/io/scidata_jsonld.py

@@ -11,7 +11,7 @@ def read_scidata_jsonld(filename):
     Return:
         scidata_dict (dict): SciData JSON-LD dictionary
     """
-    with open(filename, 'r') as fileobj:
+    with open(filename, "r") as fileobj:
         scidata_dict = json.load(fileobj)
     return scidata_dict
 
@@ -25,5 +25,5 @@ def write_scidata_jsonld(filename, scidata_dict):
         filename (str): Filename for SciData JSON-LD
         scidata_dict (dict): SciData JSON-LD dictionary to write out
     """
-    with open(filename, 'w') as fileobj:
+    with open(filename, "w") as fileobj:
         json.dump(scidata_dict, fileobj, indent=2)

src/ssm_client/io/ssm_json.py

@@ -1,3 +1,5 @@
+import json
+
 from scidatalib.scidata import SciData
 
 
@@ -10,7 +12,7 @@ def read_ssm_json(filename: str) -> dict:
     Return:
         scidata_dict (dict): SciData JSON-LD dictionary
     """
-    with open(filename, 'r') as fileobj:
+    with open(filename, "r") as fileobj:
         ssm_json_dict = json.load(fileobj)
     scidata_obj = _ssm_json_to_scidata(ssm_json_dict)
     return scidata_obj.output
@@ -64,7 +66,7 @@ def _scidata_to_ssm_json(scidata: SciData) -> dict:
     #   property
     properties = sd.get("property", None)
     if properties:
-        properties = ','.join(properties)
+        properties = ",".join(properties)
         output["scidata"]["property"] = properties
 
     #   methodology
@@ -115,7 +117,6 @@ def _scidata_to_ssm_json(scidata: SciData) -> dict:
     #   dataset
     dataset = sd.get("dataset", None)
     if dataset:
-
         dataseries_list = dataset.get("dataseries", list())
         if dataseries_list:
             output_dataseries_list = list()
@@ -165,10 +166,12 @@ def _scidata_to_ssm_json(scidata: SciData) -> dict:
                             ]
 
                         axis = parameter.get("axis", f"axis-{i}")
-                        output_dataseries_list.append({
-                            f'{axis}': {"parameter": output_parameter},
-                            "hasAxisType": axis
-                        })
+                        output_dataseries_list.append(
+                            {
+                                f"{axis}": {"parameter": output_parameter},
+                                "hasAxisType": axis,
+                            }
+                        )
 
         output_dataseries = output_dataseries_list
         output["scidata"]["dataseries"] = output_dataseries
@@ -188,7 +191,7 @@ def _ssm_json_to_scidata(ssm_json: dict) -> SciData:
     """
     # Construct UID for SciData document from title
     title = ssm_json.get("title", "ssm:dataset")
-    uid = ssm_json.get("uid", f'scidata:jsonld:{title}')
+    uid = ssm_json.get("uid", f"scidata:jsonld:{title}")
 
     # Setup SciData object
     sd = SciData(uid)
@@ -204,7 +207,7 @@ def _ssm_json_to_scidata(ssm_json: dict) -> SciData:
         sd.sources(sources)
 
     properties = ssm_json.get("scidata").get("property", "").split(",")
-    sd.meta['@graph']['scidata']['property'] = properties
+    sd.meta["@graph"]["scidata"]["property"] = properties
 
     description = ssm_json.get("description", "")
     sd.description(description)
@@ -294,4 +297,3 @@ def _ssm_json_to_scidata(ssm_json: dict) -> SciData:
         sd.dataseries(output_dataseries_list)
 
     return sd
-

src/ssm_client/services/collection_service.py

@@ -25,17 +25,17 @@ def _endpoint(self, collection: str = "") -> str:
         Returns:
             endpoint (str): Collection endpoint to use
         """
-        endpoint = f'{self.uri}/{_COLLECTION_ENDPOINT}'
+        endpoint = f"{self.uri}/{_COLLECTION_ENDPOINT}"
         if collection:
-            endpoint += f'/{collection}'
+            endpoint += f"/{collection}"
         return endpoint
 
     @property
     def uri(self):
         """
         URI property for CollectionContainer
         """
-        return f'{self.hostname}'
+        return f"{self.hostname}"
 
     def create(self, title: str) -> CollectionContainer:
         """
@@ -50,7 +50,7 @@ def create(self, title: str) -> CollectionContainer:
         response = requests.post(self._endpoint(), json=json)
         response.raise_for_status()
         return CollectionContainer(**response.json())
-    
+
     def get_collections(self) -> list[CollectionContainer]:
         response = requests.get(self._endpoint())
         response.raise_for_status()