PEP 257 - docstring formatting (#212)

AI-SDC · Jun 3, 2024 · 7f145e7 · 7f145e7
1 parent 9aee52f
commit 7f145e7
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Showing 15 changed files with 231 additions and 233 deletions.
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -37,6 +37,13 @@ repos:
                 .*\.html
             )$
 
+ # Format docstrings
+  - repo: https://github.com/DanielNoord/pydocstringformatter
+    rev: v0.7.3
+    hooks:
+      - id: pydocstringformatter
+        args: ["--style=numpydoc"]
+
   # Ruff, the Python auto-correcting linter/formatter written in Rust
   - repo: https://github.com/astral-sh/ruff-pre-commit
     rev: v0.4.7

diff --git a/acro/acro.py b/acro/acro.py
@@ -47,7 +47,7 @@ class ACRO(Tables, Regression):
     """
 
     def __init__(self, config: str = "default", suppress: bool = False) -> None:
-        """Constructs a new ACRO object and reads parameters from config.
+        """Construct a new ACRO object and reads parameters from config.
 
         Parameters
         ----------
@@ -79,7 +79,7 @@ def __init__(self, config: str = "default", suppress: bool = False) -> None:
         acro_tables.SURVIVAL_THRESHOLD = self.config["survival_safe_threshold"]
 
     def finalise(self, path: str = "outputs", ext="json") -> Records | None:
-        """Creates a results file for checking.
+        """Create a results file for checking.
 
         Parameters
         ----------
@@ -114,7 +114,7 @@ def finalise(self, path: str = "outputs", ext="json") -> Records | None:
         return self.results
 
     def remove_output(self, key: str) -> None:
-        """Removes an output from the results.
+        """Remove an output from the results.
 
         Parameters
         ----------
@@ -124,7 +124,7 @@ def remove_output(self, key: str) -> None:
         self.results.remove(key)
 
     def print_outputs(self) -> str:
-        """Prints the current results dictionary.
+        """Print the current results dictionary.
 
         Returns
         -------
@@ -134,7 +134,7 @@ def print_outputs(self) -> str:
         return self.results.print()
 
     def custom_output(self, filename: str, comment: str = "") -> None:
-        """Adds an unsupported output to the results dictionary.
+        """Add an unsupported output to the results dictionary.
 
         Parameters
         ----------
@@ -158,7 +158,7 @@ def rename_output(self, old: str, new: str) -> None:
         self.results.rename(old, new)
 
     def add_comments(self, output: str, comment: str) -> None:
-        """Adds a comment to an output.
+        """Add a comment to an output.
 
         Parameters
         ----------
@@ -170,7 +170,7 @@ def add_comments(self, output: str, comment: str) -> None:
         self.results.add_comments(output, comment)
 
     def add_exception(self, output: str, reason: str) -> None:
-        """Adds an exception request to an output.
+        """Add an exception request to an output.
 
         Parameters
         ----------
@@ -183,7 +183,7 @@ def add_exception(self, output: str, reason: str) -> None:
 
 
 def add_to_acro(src_path: str, dest_path: str = "sdc_results") -> None:
-    """Adds outputs to an acro object and creates a results file for checking.
+    """Add outputs to an acro object and creates a results file for checking.
 
     Parameters
     ----------

diff --git a/acro/acro_regression.py b/acro/acro_regression.py
@@ -402,7 +402,7 @@ def __check_model_dof(self, name: str, model) -> tuple[str, str, float]:
 
 
 def get_summary_dataframes(results: list[SimpleTable]) -> list[DataFrame]:
-    """Converts a list of SimpleTable objects to a list of DataFrame objects.
+    """Convert a list of SimpleTable objects to a list of DataFrame objects.
 
     Parameters
     ----------

diff --git a/acro/acro_stata_parser.py b/acro/acro_stata_parser.py
@@ -1,5 +1,6 @@
 """
-File with commands to manage the stata-acro interface
+File with commands to manage the stata-acro interface.
+
 Jim Smith 2023 @[email protected]
 MIT licenses apply.
 """
@@ -14,10 +15,7 @@
 
 
 def apply_stata_ifstmt(raw: str, all_data: pd.DataFrame) -> pd.DataFrame:
-    """
-    Parses an if statement from stata format
-    then uses it to subset a dataframe by contents.
-    """
+    """Parse an if statement from stata format then use it to subset a dataframe by contents."""
     if len(raw) == 0:
         return all_data
 
@@ -36,8 +34,9 @@ def apply_stata_ifstmt(raw: str, all_data: pd.DataFrame) -> pd.DataFrame:
 
 def parse_location_token(token: str, last: int) -> int:
     """
-    Parses index position tokens from stata syntax
-    stata allows f and F for first item  and l/L for last.
+    Parse index position tokens from stata syntax.
+
+    Stata allows f and F for first item  and l/L for last.
     """
     lookup: dict = {"f": 0, "F": 0, "l": last, "L": last}
     if token in ["f", "F", "l", "L"]:
@@ -54,10 +53,7 @@ def parse_location_token(token: str, last: int) -> int:
 
 
 def apply_stata_expstmt(raw: str, all_data: pd.DataFrame) -> pd.DataFrame:
-    """
-    Parses an in exp statement from stata and uses it
-    to subset a dataframe by set of row indices.
-    """
+    """Parse an in exp statement from stata and use it to subset a dataframe by row indices."""
     last = len(all_data) - 1
     if "/" not in raw:
         pos = parse_location_token(raw, last)
@@ -86,11 +82,9 @@ def apply_stata_expstmt(raw: str, all_data: pd.DataFrame) -> pd.DataFrame:
 
 
 def find_brace_word(word: str, raw: str):
-    """
-    Given a word followed by a (
-    finds and returns as a list of strings
-    the rest of the contents up to the closing ).
-    first returned value is True/False depending on parsing ok.
+    """Return contents as a list of strings between '(' following a word and the closing ')'.
+
+    First returned value is True/False depending on parsing ok.
     """
     result = []
     idx = raw.find(word)
@@ -113,7 +107,7 @@ def find_brace_word(word: str, raw: str):
 
 
 def extract_aggfun_values_from_options(details, contents_found, content, varnames):
-    """Extracts the aggfunc and the values from the content."""
+    """Extract the aggfunc and the values from the content."""
     # contents can be variable names or aggregation functions
     details["aggfuncs"], details["values"] = list([]), list([])
     if contents_found and len(content) > 0:
@@ -132,7 +126,8 @@ def extract_aggfun_values_from_options(details, contents_found, content, varname
 def parse_table_details(
     varlist: list, varnames: list, options: str, stata_version: str
 ) -> dict:
-    """Function to parse stata-16 style table calls
+    """Parse stata-16 style table calls.
+
     Note this is not for latest version of stata, syntax here:
     https://www.stata.com/manuals16/rtable.pdf
     >> table rowvar [colvar [supercolvar] [if] [in] [weight] [, options].
@@ -202,8 +197,9 @@ def parse_and_run(  # pylint: disable=too-many-arguments,too-many-locals
     stata_version: str,
 ) -> pd.DataFrame:
     """
+    Run the appropriate command on a pre-existing ACRO object stata_acro.
+
     Takes a dataframe and the parsed stata command line.
-    Runs the appropriate command on a pre-existing ACRO object stata_acro
     Returns the result as a formatted string.
     """
     # sanity checking
@@ -248,7 +244,7 @@ def parse_and_run(  # pylint: disable=too-many-arguments,too-many-locals
 
 
 def run_session_command(command: str, varlist: list) -> str:
-    """Runs session commands that are data-independent."""
+    """Run session commands that are data-independent."""
     outcome = ""
 
     if command == "init":
@@ -285,8 +281,9 @@ def run_session_command(command: str, varlist: list) -> str:
 
 
 def run_output_command(command: str, varlist: list) -> str:
-    """Runs outcome-level commands
-    first element of varlist is output affected
+    """Run outcome-level commands.
+
+    First element of varlist is output affected
     rest (if relevant) is string passed to command.
     """
     outcome = ""
@@ -324,9 +321,7 @@ def run_output_command(command: str, varlist: list) -> str:
 
 
 def extract_var_within_parentheses(input_string):
-    """Given a string, this function extracts the words within the first parentheses
-    from a string.
-    """
+    """Extract the words within the first parentheses from a string."""
     string = ""
     string_match = re.match(r"\((.*?)\)", input_string)
     if string_match:
@@ -336,7 +331,7 @@ def extract_var_within_parentheses(input_string):
 
 
 def extract_var_before_parentheses(input_string):
-    """Given a string, this function extracts the words before the first parentheses."""
+    """Extract the words before the first parentheses."""
     string = ""
     string_match = re.match(r"^(.*?)\(", input_string)
     if string_match:
@@ -346,7 +341,8 @@ def extract_var_before_parentheses(input_string):
 
 
 def extract_table_var(input_string):
-    """Given a string, this function extracts the words within the parentheses.
+    """Extract the words within the parentheses.
+
     If there are no parentheses the string is returned.
     """
     string = ""
@@ -359,9 +355,9 @@ def extract_table_var(input_string):
 
 
 def extract_colstring_tablestring(input_string):
-    """Given a string, this function extracts the column and the tables
-    variables as a string. It goes through different options eg. whether
-    the column string is between paranthese or not.
+    """Extract the column and the tables variables as a string.
+
+    It goes through different options eg. whether the column string is between paranthese or not.
     """
     colstring = ""
     tablestring = ""
@@ -382,9 +378,9 @@ def extract_colstring_tablestring(input_string):
 
 
 def extract_strings(input_string):
-    """Given a string, this function extracts the index, column and the tables
-    variables as a string. It goes through different options eg. whether
-    the index string is between paranthese or not.
+    """Extract the index, column and the tables variables as a string.
+
+    It goes through different options eg. whether the index string is between paranthese or not.
     """
     rowstring = ""
     colstring = ""
@@ -412,11 +408,11 @@ def extract_strings(input_string):
 
 
 def creates_datasets(data, details):
-    """This function returns the full dataset if the tables parameter is empty.
+    """Return the full dataset if the tables parameter is empty.
+
     Otherwise, it divides the dataset to small dataset each one is the dataset when
     the tables parameter is equal to one of it is unique values.
     """
-
     set_of_data = {"Total": data}
     msg = ""
     # if tables var parameter was assigned, each table will
@@ -449,10 +445,7 @@ def run_table_command(  # pylint: disable=too-many-arguments,too-many-locals
     options: str,
     stata_version: str,
 ) -> str:
-    """
-    Converts a stata table command into an acro.crosstab
-    then returns a prettified versaion of the cross_tab dataframe.
-    """
+    """Convert a stata table command into an acro.crosstab and return a prettified dataframe."""
     weights_empty = len(weights) == 0
     if not weights_empty:  # pragma
         return f"weights not currently implemented for _{weights}_\n"
@@ -534,7 +527,7 @@ def run_table_command(  # pylint: disable=too-many-arguments,too-many-locals
 
 
 def run_regression(command: str, data: pd.DataFrame, varlist: list) -> str:
-    """Interprets and runs appropriate regression command."""
+    """Interpret and run appropriate regression command."""
     # get components of formula
     depvar = varlist[0]
     indep_vars = varlist[1:]
@@ -562,7 +555,7 @@ def run_regression(command: str, data: pd.DataFrame, varlist: list) -> str:
 
 
 def get_regr_results(results: sm_iolib_summary.Summary, title: str) -> str:
-    """Translates statsmodels.io.summary object into prettified table."""
+    """Translate statsmodels.io.summary object into prettified table."""
     res_str = title + "\n"
     for table in acro_regression.get_summary_dataframes(results.summary().tables):
         res_str += prettify_table_string(table, separator=",") + "\n"