Deleted deprecated code. Made tools have optional deps.

.gitignore

@@ -38,6 +38,7 @@ dist/
 eggs/
 sdist/
 docs/_build
+docs/autoapi/
 cython_debug/
 
 # Hidden files that are definitely unwanted (redundant)

CHANGELOG.md

@@ -4,6 +4,16 @@ Adheres to [Semantic Versioning 2.0](https://semver.org/spec/v2.0.0.html) and
 [Keep a Changelog](https://keepachangelog.com/en/1.0.0/).
 
 
+## [0.2.0] - 2020-09-01
+
+### Removed:
+- `db` subpackage
+- `toml_data` module. Use `NestedDotDict` instead.
+
+### Changed:
+- Made `tools` require the `tools` optional package
+
+
 ## [0.1.0] - 2020-08-06
 
 ### Added:

README.md

@@ -14,7 +14,7 @@
 Adorable little Python functions for you to copy or import.
 
 `pip install pocketutils`. To get the optional packages, use:
-`pip install pocketutils[biochem,db,misc,notebooks,plotting]`
+`pip install pocketutils[tools,biochem,misc,notebooks,plotting]`
 
 Among the more useful are `zip_strict`, `frozenlist`, `SmartEnum`, `is_lambda`, `strip_paired_brackets`,
 `sanitize_path_node`, `TomlData`, `PrettyRecordFactory`, `parallel_with_cursor`, `groupby_parallel`,

pocketutils/__init__.py

@@ -3,21 +3,20 @@
 """
 
 import logging
-from pathlib import Path, PurePath
-from typing import Union
 
-# importlib.metadata is compat with Python 3.8 only
-from importlib_metadata import PackageNotFoundError
-from importlib_metadata import metadata as __load
+# If you need Python < 3.8, change to importlib_metadata and add it as a dependency
+from importlib.metadata import PackageNotFoundError
+from importlib.metadata import metadata as __load
+from pathlib import Path
 
 logger = logging.getLogger(Path(__file__).parent.name)
 
 metadata = None
 try:
     metadata = __load(Path(__file__).absolute().parent.name)
     __status__ = "Development"
-    __copyright__ = "Copyright 2016–2020"
-    __date__ = "2020-08-24"
+    __copyright__ = "Copyright 2020"
+    __date__ = "2020-09-01"
     __uri__ = metadata["home-page"]
     __title__ = metadata["name"]
     __summary__ = metadata["summary"]
@@ -26,21 +25,13 @@
     __author__ = metadata["author"]
     __maintainer__ = metadata["maintainer"]
     __contact__ = metadata["maintainer"]
-except PackageNotFoundError:
+except PackageNotFoundError:  # pragma: no cover
     logger.error(
-        "Could not load package metadata for {}. Is it installed?".format(
-            Path(__file__).absolute().parent.name
-        )
+        f"Could not load package metadata for {Path(__file__).absolute().parent.name}. Is it installed?"
     )
 
-
-def resource(*nodes: Union[PurePath, str]) -> Path:
-    """Gets a path of a resource file under resources/ directory."""
-    return Path(Path(__file__).parent, "resources", *nodes)
-
-
-if __name__ == "__main__":
+if __name__ == "__main__":  # pragma: no cover
     if metadata is not None:
-        print("{} (v{})".format(metadata["name"], metadata["version"]))
+        print(f"{metadata['name']} (v{metadata['version']})")
     else:
         print("Unknown project info")

pocketutils/biochem/tissue_expression.py

@@ -28,7 +28,7 @@ def load(
         filter_fn: Callable[[pd.DataFrame], pd.DataFrame] = pd.DataFrame.dropna,
     ) -> TissueTable:
         """
-        Get a DataFrame of Human Protein Atlas tissue expression data,
+        Gets a DataFrame of Human Protein Atlas tissue expression data,
         indexed by Gene name and with the 'Gene' and 'Reliability' columns dropped.
         The expression level ('Level') is replaced using this map: {'Not detected': 0, 'Low': 1, 'Medium': 2, 'High': 3}.
         Downloads the file from http://www.proteinatlas.org/download/normal_tissue.tsv.zip

pocketutils/biochem/uniprot_go.py

@@ -24,6 +24,7 @@ class FlatGoTerm:
     """
     A Gene Ontology term.
     Not to be confused with GOTerm in goatools: obo_parser.GOTerm
+
     Attributes:
         ID (str); ex: GO:0005737
         kind (str: 'P'==process, 'C'==component, 'F'==function)
@@ -66,7 +67,9 @@ class UniprotGoTerms:
     def fetch_uniprot_data(self, uniprot_ids: Union[str, List[str]]) -> List[Mapping[str, str]]:
         """
         Fetches a list of dicts of UniProt metadata, one per UniProt ID.
-        Raises a ValueError if a UniProt ID wasn't found.
+
+        Raises:
+            ValueError: If a UniProt ID wasn't found.
         """
         if isinstance(uniprot_ids, str):  # not a list type
             uniprot_ids = [uniprot_ids]
@@ -95,7 +98,9 @@ def go_terms_for_uniprot_id_as_df(self, uniprot_id: str) -> pd.DataFrame:
 
 class GoTermsAtLevel:
     """
-    Example: go_term_ancestors_for_uniprot_id_as_df('P42681', 2)
+    Gene ontology terms organized by level.
+    Example:
+        >>> go_term_ancestors_for_uniprot_id_as_df('P42681', 2)
     """
 
     def __init__(self) -> None:
@@ -127,8 +132,9 @@ def get_ancestors_of_go_term(self, term_id: str, level: int) -> Iterable[GOTerm]
         From a GO term in the form 'GO:0007344', returns a set of ancestor GOTerm objects at the specified level.
         The traversal is restricted to is-a relationships.
         Note that the level is the minimum number of steps to the root.
-            Arguments:
-                level: starting at 0 (root)
+
+        Args:
+            level: starting at 0 (root)
         """
 
         def traverse_up(term, buildup_set, level):
@@ -149,9 +155,10 @@ def go_term_ancestors_for_uniprot_id(
         Gets the GO terms associated with a UniProt ID and returns a set of their ancestors at the specified level.
         The traversal is restricted to is-a relationships.
         Note that the level is the minimum number of steps to the root.
-            Arguments:
-                level: starting at 0 (root)
-                kinds_allowed: a set containing any combination of 'P', 'F', or 'C'
+
+        Args:
+            level: starting at 0 (root)
+            kinds_allowed: a set containing any combination of 'P', 'F', or 'C'
         """
         if kinds_allowed is None:
             kinds_allowed = ["P", "F", "C"]

pocketutils/core/__init__.py

@@ -112,15 +112,18 @@ def _new_type(
     ) -> Type[LazyWrapped]:
         """
         Creates a new mutable wrapped type.
-        For ex:
-        ```
-        LazyRemoteTime = LazyWrap.new_type('RemoteTime', lambda: urllib...)
-        dt = LazyRemoteTime()  # nothing happens
-        print(dt.get())  # has a value
-        ```
-        :param dtype: The name of the data type, such as 'datetime' if generator=datetime.now
-        :param generator: This is called to (lazily) initialize an instance of the LazyWrapped
-        :return: A new class subclassing LazyWrapped
+
+        Example:
+            >>> LazyRemoteTime = LazyWrap.new_type('RemoteTime', lambda: ...)
+            >>> dt = LazyRemoteTime()  # nothing happens
+            >>> dt.get()  # has a value
+
+        Args:
+            dtype: The name of the data type, such as 'datetime' if generator=datetime.now
+            generator: This is called to (lazily) initialize an instance of the LazyWrapped
+
+        Returns:
+            A new class subclassing LazyWrapped
         """
 
         class X(superclass):
@@ -144,7 +147,7 @@ class SmartEnum(enum.Enum):
     def of(cls, v):
         """
         Returns the member of this enum class from a string with the member's name,
-        case-insentive and stripping whitespace.
+        case-insensitive and stripping whitespace.
         Will return ``v`` if ``v`` is already an instance of this class.
         """
         if isinstance(v, cls):

pocketutils/core/dot_dict.py

@@ -14,7 +14,7 @@ class NestedDotDict:
     A thin wrapper around a nested dict to make getting values easier.
     Keys must not contain dots (.), which are reserved for splitting of values.
     This class is especially useful for TOML but also works well for JSON and Python dicts.
-    Also see ``toml_data``. This has some advantages.
+    Also see ``toml_data``. ``NestedDotDict`` has some advantages over it.
     """
 
     @classmethod

pocketutils/core/exceptions.py

@@ -29,8 +29,10 @@ def args(**names):
         """
         Decorator.
         Add a __init__ that calls the superclass and takes any argument in names.
-        The __init__ will set: (self.name =value if name is passed else None) for all name in names.
-        :param names: A map from str to Type
+        The __init__ will set: (self.name=value if name is passed else None) for all name in names.
+
+        Args:
+            names: A map from str to Type
         """
         assert not any([s == "info" or s.startswith("__") and s.endswith("__") for s in names])
 

pocketutils/core/internal.py

@@ -70,9 +70,11 @@ def expanded(cls, item, depth=1):
 def nicesize(nbytes: int, space: str = "") -> str:
     """
     Uses IEC 1998 units, such as KiB (1024).
-    :param nbytes: Number of bytes
-    :param space: Separator between digits and units
-    :return: Formatted string
+        nbytes: Number of bytes
+        space: Separator between digits and units
+
+        Returns:
+            Formatted string
     """
     data = {
         "PiB": 1024 ** 5,

pocketutils/core/iterators.py

@@ -68,9 +68,11 @@ def __next__(self) -> T:
 class TieredIterator(SeqIterator):
     """
     A SizedIterator that iterates over every tuples of combination from multiple sequences.
-    Ex:
-    it = TieredIterator([[1, 2, 3], [5, 6]])
-    list(it)  # [(1,5), (1,6), (2,5), (2,6), (3,5), (3,6)]
+
+    Example:
+        >>> it = TieredIterator([[1, 2, 3], [5, 6]])
+        >>> list(it)
+        [(1,5), (1,6), (2,5), (2,6), (3,5), (3,6)]
     """
 
     # noinspection PyMissingConstructor