phinx format

Author: hesspnnl

docs/api.rst

@@ -34,4 +34,3 @@
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
 
 html_theme = "sphinx_rtd_theme"
-html_static_path = ["static"]

docs/conf.py

@@ -7,185 +7,182 @@ The Collection Module is a foundational component that defines common behaviors
 Each subclass is designed to be more user-friendly and specific for certain collections, making them the recommended entry points for using the package. Each function of CollectionSearch can be accessed via each subclass.
 
 NMDC Module
-~~~~~~~~~~
+~~~~~~~~~~~~
 .. autoclass:: nmdc_api_utilities.nmdc_search.NMDCSearch
    :members:
    :undoc-members:
    :show-inheritance:
 
 Collection Module
-~~~~~~~~~~
-
+~~~~~~~~~~~~~~~~~~
 .. autoclass:: nmdc_api_utilities.collection_search.CollectionSearch
    :members:
    :undoc-members:
    :show-inheritance:
 
-
 Latitude Longitude Module
-~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~~~~~~~~~
 .. autoclass:: nmdc_api_utilities.lat_long_filters.LatLongFilters
    :members:
    :undoc-members:
    :show-inheritance:
 
 Functional Search Module
-~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~~~~~~~~
 .. autoclass:: nmdc_api_utilities.functional_search.FunctionalSearch
    :members:
    :undoc-members:
    :show-inheritance:
 
 Collection Helpers
-~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~~
 .. autoclass:: nmdc_api_utilities.collection_helpers.CollectionHelpers
    :members:
    :undoc-members:
    :show-inheritance:
 
 Metadata Module
-~~~~~~~~~~
+~~~~~~~~~~~~~~~~
 .. autoclass:: nmdc_api_utilities.metadata.Metadata
    :members:
    :undoc-members:
    :show-inheritance:
 
 Mint Module
-~~~~~~~~~~
+~~~~~~~~~~~~
 .. autoclass:: nmdc_api_utilities.minter.Minter
    :members:
    :undoc-members:
    :show-inheritance:
 
 BioSample Subclass
-~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~~
 .. autoclass:: nmdc_api_utilities.biosample_search.BiosampleSearch
    :members:
    :undoc-members:
    :show-inheritance:
 
 Calibration Subclass
-~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~~~~
 .. autoclass:: nmdc_api_utilities.calibration_search.CalibrationSearch
    :members:
    :undoc-members:
    :show-inheritance:
 
 Chemical Entity Subclass
-~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~~~~~~~~
 .. autoclass:: nmdc_api_utilities.chemical_entity_search.ChemicalEntitySearch
    :members:
    :undoc-members:
    :show-inheritance:
 
 Collecting Biosamples From Site Subclass
-~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 .. autoclass:: nmdc_api_utilities.collecting_biosamples_from_site_search.CollectingBiosamplesFromSiteSearch
    :members:
    :undoc-members:
    :show-inheritance:
 
 Configuration Subclass
-~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~~~~~~
 .. autoclass:: nmdc_api_utilities.configuration_search.ConfigurationSearch
    :members:
    :undoc-members:
    :show-inheritance:
+
 Data Generation Subclass
-~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~~~~~~~~
 .. autoclass:: nmdc_api_utilities.data_generation_search.DataGenerationSearch
    :members:
    :undoc-members:
    :show-inheritance:
 
 Data Object Subclass
-~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~~~~
 .. autoclass:: nmdc_api_utilities.data_object_search.DataObjectSearch
    :members:
    :undoc-members:
    :show-inheritance:
 
 Field Research From Site Subclass
-~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 .. autoclass:: nmdc_api_utilities.field_research_site_search.FieldResearchSiteSearch
    :members:
    :undoc-members:
    :show-inheritance:
 
 Instrument Subclass
-~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~~~
 .. autoclass:: nmdc_api_utilities.instrument_search.InstrumentSearch
    :members:
    :undoc-members:
    :show-inheritance:
 
 Manifest Subclass
-~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~
 .. autoclass:: nmdc_api_utilities.manifest_search.ManifestSearch
    :members:
    :undoc-members:
    :show-inheritance:
 
 Material Subclass
-~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~
 .. autoclass:: nmdc_api_utilities.material_processing_search.MaterialProcessingSearch
    :members:
    :undoc-members:
    :show-inheritance:
 
 Processed Sample Subclass
-~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~~~~~~~~~
 .. autoclass:: nmdc_api_utilities.processed_sample_search.ProcessedSampleSearch
    :members:
    :undoc-members:
    :show-inheritance:
 
 Protocol Execution Subclass
-~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 .. autoclass:: nmdc_api_utilities.protocol_execution_search.ProtocolExecutionSearch
    :members:
    :undoc-members:
    :show-inheritance:
 
 Storage Process Subclass
-~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~~~~~~~~
 .. autoclass:: nmdc_api_utilities.storage_process_search.StorageProcessSearch
    :members:
    :undoc-members:
    :show-inheritance:
 
 Study Subclass
-~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~~~~~~~~
 .. autoclass:: nmdc_api_utilities.study_search.StudySearch
    :members:
    :undoc-members:
    :show-inheritance:
 
 Functional Annotation Agg Subclass
-~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 .. autoclass:: nmdc_api_utilities.functional_annotation_agg_search.FunctionalAnnotationAggSearch
    :members:
    :undoc-members:
    :show-inheritance:
 
 Workflow Execution Subclass
-~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 .. autoclass:: nmdc_api_utilities.workflow_execution_search.WorkflowExecutionSearch
    :members:
    :undoc-members:
    :show-inheritance:
 
 Data Processing
-~~~~~~~~~~~~~~~
-
+~~~~~~~~~~~~~~~~
 .. autoclass:: nmdc_api_utilities.data_processing.DataProcessing
    :members:
    :undoc-members:
    :show-inheritance:
 
 Utils
-~~~~~
-
+~~~~~~
 .. autoclass:: nmdc_api_utilities.utils.Utils
    :members:
    :undoc-members:

docs/functions.rst

@@ -126,11 +126,13 @@ def get_record_by_filter(
     ) -> list[dict]:
         """
         Get a record from the NMDC API by its id.
+
         Parameters
         ----------
         filter: str
             The filter to use to query the collection. Must be in MonogDB query format.
                 Resources found here - https://www.mongodb.com/docs/manual/reference/method/db.collection.find/#std-label-method-find-query
+
             Example: {"name":{"my record name"}}
         max_page_size: int
             The number of results to return per page. Default is 25.
@@ -139,12 +141,12 @@ def get_record_by_filter(
             Example: "id,name,description,alternative_identifiers,file_size_bytes,md5_checksum,data_object_type,url,type"
         all_pages: bool
             True to return all pages. False to return the first page. Default is False.
+
         Returns
         -------
         list[dict]
             A list of dictionaries containing the records.
-        Raises
-        ------
+
         """
         results = self.get_records(filter, max_page_size, fields, all_pages)
         return results
@@ -160,6 +162,7 @@ def get_record_by_attribute(
     ):
         """
         Get a record from the NMDC API by its name. Records can be filtered based on their attributes found https://microbiomedata.github.io/nmdc-schema/.
+
         Parameters
         ----------
         attribute_name: str
@@ -173,12 +176,13 @@ def get_record_by_attribute(
         all_pages: bool
             True to return all pages. False to return the first page. Default is False.
         exact_match: bool
-            This var is used to determine if the inputted attribute value is an exact match or a partial match. Default is False, meaning the user does not need to input an exact match.
-            Under the hood this is used to determine if the inputted attribute value should be wrapped in a regex expression.
+            This var is used to determine if the inputted attribute value is an exact match or a partial match. Default is False, meaning the user does not need to input an exact match. Under the hood this is used to determine if the inputted attribute value should be wrapped in a regex expression.
+
         Returns
         -------
         list[dict]
             A list of dictionaries containing the records.
+
         """
 
         if exact_match:

docs/installation.rst

@@ -61,6 +61,7 @@ def split_list(self, input_list: list, chunk_size: int = 100) -> list:
     def rename_columns(self, df: pd.DataFrame, new_col_names: list) -> pd.DataFrame:
         """
         Rename columns in a pandas dataframe.
+
         Parameters
         ----------
         df: pd.DataFrame
@@ -70,10 +71,12 @@ def rename_columns(self, df: pd.DataFrame, new_col_names: list) -> pd.DataFrame:
             Example:
                 If the current column names are - ['old_col1', 'old_col2', 'old_col3']
                 You will need to pass in the new names like - ['new_col1', 'new_col2', 'new_col3']
+
         Returns
         -------
         pd.DataFrame
             A pandas dataframe with renamed columns.
+
         """
         df.columns = new_col_names
         return df
@@ -187,6 +190,7 @@ def extract_field(self, api_results: list, field_name: str) -> list:
         -------
         list
             A list of values for the specified field.
+
         """
         field_list = []
         for item in api_results: