Fixed minor PEP 257 style issues using pydocstyle.

Jupyter/README.md

@@ -1,3 +1,3 @@
-Create a mapping file for use in openLCA through Binder:
+# Create a mapping file for use in openLCA through Binder
 
 [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/bl-young/Federal-LCA-Commons-Elementary-Flow-List/Binder?filepath=Jupyter%2Frun_mappings.ipynb)

fedelemflowlist/add_uuid_to_flowmapping.py

@@ -1,3 +1,4 @@
+"""Add docstring."""
 import pandas as pd
 from fedelemflowlist.globals import flowmappingpath,outputpath,list_version_no
 

fedelemflowlist/analysis/flow_list_analysis.py

@@ -1,11 +1,10 @@
-"""
-Functions to perform analysis of a flow list
-"""
+"""Functions to perform analysis of a flow list."""
 import pandas as pd
 
 
 def count_flows_by_class(flowlist):
-    """Counts all and preferred flows by class
+    """
+    Counts all and preferred flows by class.
 
     :param flowlist: A FlowList in standard format
     :return: pandas df with 'Class','No. of Flows','No. of Preferred Flows'

fedelemflowlist/contexts.py

@@ -1,6 +1,8 @@
 """
-Provides a pandas dataframe of all contexts as paths and as a pattern of context classes
-Used by flowlist.py
+Provides a pandas dataframe.
+
+Of all contexts as paths and as a pattern of context classes. Used by
+flowlist.py.
 """
 
 import pandas as pd

fedelemflowlist/flowlist.py

@@ -1,6 +1,7 @@
 """
-Generate the elementary flow master list as a pandas dataframe from input files
-Write it to the output folder
+Generate the elementary flow master list.
+
+As a pandas dataframe from input files. Write it to the output folder.
 """
 
 import pandas as pd
@@ -14,7 +15,8 @@
 altunits_data_types = {'Conversion Factor': flow_list_fields['AltUnitConversionFactor'][0]['dtype']} #AltUnitConversionFactor
 
 def read_in_flowclass_file(flowclass, flowclasstype):
-    """Declare data types for select variables in flow class input files
+    """
+    Declare data types for select variables in flow class input files.
 
     :param flowclass: One of the flow class names
     :param flowclasstype: either 'Flowables','FlowablePrimaryContexts',or 'FlowableAltUnits'
@@ -30,6 +32,7 @@ def read_in_flowclass_file(flowclass, flowclasstype):
     return flowclassfile
 
 def import_secondary_context_membership():
+    """Add docstring."""
     log.info('Read in secondary context membership')
     SecondaryContextMembership = pd.read_csv(inputpath + 'SecondaryContextMembership.csv')
     return SecondaryContextMembership

fedelemflowlist/globals.py

@@ -1,4 +1,4 @@
-"""Set common variables for use in package"""
+"""Set common variables for use in package."""
 import sys
 import os
 import json

fedelemflowlist/jsonld.py

@@ -1,5 +1,4 @@
-"""Writes flow list and mapping files to a JSON-LD zip archive using olca library
-"""
+"""Writes flow list and mapping files to a JSON-LD zip archive using olca library."""
 import datetime
 import logging as log
 import math
@@ -36,9 +35,7 @@ def _isnum(val) -> bool:
 
 
 def _s(val) -> Optional[str]:
-    """Returns the string value of the given value or None if the value is
-       `None`, `NaN`, or `""`.
-    """
+    """Returns the string value of the given value or None if the value is `None`, `NaN`, or `""`."""
     if _isnil(val):
         return None
     return str(val).strip()
@@ -81,7 +78,7 @@ def to_json(self) -> dict:
 
 
 class _MapEntry(object):
-    """ Describes a mapping entry in the Fed.LCA flow list. """
+    """Describes a mapping entry in the Fed.LCA flow list."""
 
     def __init__(self, row):
 
@@ -122,8 +119,8 @@ def to_json(self) -> dict:
 
 
 class Writer(object):
-    """Class for writing flows and mappings to json
-    """
+    """Class for writing flows and mappings to json."""
+
     def __init__(self, flow_list: pd.DataFrame,
                  flow_mapping: pd.DataFrame = None):
         self.flow_list = flow_list

fedelemflowlist/uuid_generators.py

@@ -1,6 +1,8 @@
 """
-Methods for UUID generation for flows, contexts
-Uses UUID3 function from UUID package to generate IDs from strings
+Methods for UUID generation.
+
+For flows, contexts, uses UUID3 function from UUID package to generate IDs from
+strings.
 """
 
 import uuid

format specs/Contexts.md

@@ -1,4 +1,4 @@
-## Contexts Input File Format
+# Contexts Input File Format
 
 The context input file is in the form of CSV data with the following fields.
 

format specs/FlowList.md

@@ -1,4 +1,4 @@
-## Flow List format
+# Flow List format
 
 A Flow List is in the form of a pandas data frame with the following fields.
 
@@ -15,7 +15,7 @@ A Flow List is in the form of a pandas data frame with the following fields.
  Context | string | Y | A path-like set of context compartments in the form of directionality/environmental media/environmental compartment... e.g. `emission/air/tropophere`|  
  Flow UUID | string | Y | Unique hexadecimal ID for the flow |
  AltUnit | string | N | Alternate unit for the flow |
- AltUnitConversionFactor | float | N | Conversion factor in the form of alternate units/reference unit | 
+ AltUnitConversionFactor | float | N | Conversion factor in the form of alternate units/reference unit |
 
 \* See the [EPA Report](https://cfpub.epa.gov/si/si_public_search_results.cfm?simpleSearch=0&showCriteria=2&searchAll=elementary+flows&TIMSType=Published+Report&dateBeginPublishedPresented=07%2F31%2F2019)
- for discussion of preferred flows.
+ for discussion of preferred flows.

format specs/FlowMapping.md

@@ -2,21 +2,21 @@
 
 Flow mapping data is in the form of a pandas dataframe with the following fields.
 
-Field |	Type |	Required? | Note |
+Field | Type | Required? | Note |
 ----- | ---- | --------  | ----------- |
 SourceListName | string | Y | Name and version of the source flowlist, e.g. `openLCA1.7` or `TRACI2.1` |
-SourceFlowName	| string | Y | Name of the source flow |
-SourceFlowUUID	| string | N | If no UUID present, UUID generated based on olca algorithm|
+SourceFlowName | string | Y | Name of the source flow |
+SourceFlowUUID | string | N | If no UUID present, UUID generated based on olca algorithm|
 SourceFlowContext | string | Y | Compartments separated by `/`, like `emission/air`|
 SourceUnit | string | Y | A unit abbreviation, like `kg`|
 MatchCondition | string | N |Single character. `=`, `>`,`<`,`~`. Meaning 'equal to','a superset of', 'a subset of', 'a proxy for'. Assumes `=` if not present |
-ConversionFactor | float | N |	Value for multiplying with source flow to equal target flow. Assumes `1` if not present |
+ConversionFactor | float | N | Value for multiplying with source flow to equal target flow. Assumes `1` if not present |
 TargetFlowName | string | Y | Name of the Fed Commons flowable |
-TargetFlowUUID	| string| Y| UUID for Fed Commons flow |
+TargetFlowUUID | string| Y| UUID for Fed Commons flow |
 TargetFlowContext | string | Y | Fed commons context, in form like `emission/air` |
 TargetUnit | string | Y | A unit abbreviation, like `kg`|
-Mapper	| string | N	| Person creating the mapping |
-Verifier |	string | N | Person verifying the mapping |
+Mapper | string | N | Person creating the mapping |
+Verifier | string | N | Person verifying the mapping |
 LastUpdated | datetime | N | Date mapping last updated |
 
 Note that TargetList is not present, because the Fed LCA Commons Elementary Flow List

format specs/FlowableAltUnits.md

@@ -1,4 +1,4 @@
-## Flowable Alternate Units Input File Format
+# Flowable Alternate Units Input File Format
 
 The flowable alternate units input files are in the form of CSV data with the following fields.
 

format specs/FlowablePrimaryContexts.md

@@ -1,4 +1,4 @@
-## Flowable Primary Context Input File Format
+# Flowable Primary Context Input File Format
 
 Flowable primary context input files are the form of CSV data with the following fields.
 

format specs/Flowables.md

@@ -1,4 +1,4 @@
-## Flowables Input File Format
+# Flowables Input File Format
 
 Flowable input files are the form of CSV data with the following fields.
 
@@ -13,4 +13,4 @@ Flowable input files are the form of CSV data with the following fields.
  Flowable Preferred | int | Y | Indicates whether or not flowable is preferred.* `1` for preferred, `0` for non-preferred |
 
 \* See the [EPA Report](https://cfpub.epa.gov/si/si_public_search_results.cfm?simpleSearch=0&showCriteria=2&searchAll=elementary+flows&TIMSType=Published+Report&dateBeginPublishedPresented=07%2F31%2F2019)
- for discussion of preferred flowables.
+ for discussion of preferred flowables.

format specs/README.md

@@ -1,6 +1,7 @@
-Format specifications for input files, [Flowables](Flowables.md), [FlowablePrimaryContexts](FlowablePrimaryContexts.md),
+# Format specifications for input files
+
+[Flowables](Flowables.md), [FlowablePrimaryContexts](FlowablePrimaryContexts.md),
 [FlowableAltUnits](FlowableAltUnits.md), [Contexts](Contexts.md), and [SecondaryContextMembership](SecondaryContextMembership.md)
  as well as the formats provided and used by `fedelemflowlist`, [FlowList](FlowList.md) and [FlowMapping](FlowMapping.md).
   See the EPA report linked to in the main [README](https://github.com/USEPA/Federal-LCA-Commons-Elementary-Flow-List/)
-   for an explanation of how the input files in these formats are used to create the flow list.   
-
+   for an explanation of how the input files in these formats are used to create the flow list.

format specs/SecondaryContextMembership.md

@@ -1,11 +1,10 @@
-## Secondary Context Membership Input File Format
+# Secondary Context Membership Input File Format
 
 The secondary context membership input file is in the form of CSV data with the following fields.
 Secondary context membership indicates whether or not secondary contexts (see [Contexts](Contexts.md)
 for class definitions) should be associated with flows from this FlowClass with listed primary contexts
  (Directionality and Environmental Media).
 
-
  Field | Type | Required |  Note |
 ----------- |  ---- | ---------| -----  |
  FlowClass | string | Y | The flow class. Same as 'Class' in [FlowList](FlowList.md). |
@@ -22,4 +21,4 @@ for class definitions) should be associated with flows from this FlowClass with
  ContextPreferred* | int | Y | `1` for included and `0` for excluded. See note. |
 
  \* See the [EPA Report]((https://cfpub.epa.gov/si/si_public_search_results.cfm?simpleSearch=0&showCriteria=2&searchAll=elementary+flows&TIMSType=Published+Report&dateBeginPublishedPresented=07%2F31%2F2019))
-  for discussion of preferred secondary contexts.
+  for discussion of preferred secondary contexts.

scripts/add_conversion_to_flowmapping.py

@@ -1,8 +1,9 @@
 """
-Adds conversion factor to mapping files if source unit is an alternate unit
-Requires target unit to be the primary unit
-Existing conversion factor must be set to 1 to avoid replacing manual conversion factors
-Mapping file must already conform to mapping format
+Adds conversion factor to mapping files if source unit is an alternate unit.
+
+Requires target unit to be the primary unit. Existing conversion factor must be
+set to 1 to avoid replacing manual conversion factors. Mapping file must already
+conform to mapping format.
 """
 import pandas as pd
 import fedelemflowlist

scripts/add_uuid_to_flowmapping.py

@@ -1,6 +1,8 @@
 """
-Gets Fed Commons Flow UUID from mapping list and adds it to mapping file(s).
-Mapping file must already conform to mapping format
+Gets Fed Commons Flow UUID.
+
+From mapping list and adds it to mapping file(s). Mapping file must already
+conform to mapping format.
 """
 import pandas as pd
 import fedelemflowlist

scripts/build_recipe_mapping.py

@@ -1,8 +1,9 @@
 """
-Builds the mapping file for ReCiPe using input flowable and context mappings,
-and recipe from the lcia_formatter
+Builds the mapping file for ReCiPe.
+
+Using input flowable and context mappings, and recipe from the lcia_formatter
 Requires lciafmt from lcia_formatter (https://github.com/USEPA/lciaformatter)
-BEWARE this will replace the existing mapping file if it exists in /flowmapping
+BEWARE this will replace the existing mapping file if it exists in /flowmapping.
 """
 
 import pandas as pd

scripts/build_traci2.1_mapping.py

@@ -1,8 +1,9 @@
 """
-Builds the mapping file for TRACI2.1 using input flowable and context mappings,
-and TRACI2.1 from the lcia_formatter
+Builds the mapping file for TRACI2.1.
+
+Using input flowable and context mappings, and TRACI2.1 from the lcia_formatter
 Requires lciafmt from lcia_formatter (https://github.com/USEPA/lciaformatter)
-BEWARE this will replace the existing mapping file if it exists in /flowmapping
+BEWARE this will replace the existing mapping file if it exists in /flowmapping.
 """
 
 import pandas as pd

scripts/compare_old_flowlist.py

@@ -1,5 +1,6 @@
 """
 Use an archived flowlist parquet file to load in and compare with the current list.
+
 Write csvs of the new flows and expired flows in csv format, write new flows to JSON-LD
 Currently compares only by UUID.
 """

scripts/determine_unused_flowables_formapping.py

@@ -1,6 +1,8 @@
 """
-Determines FEDEFL flowables not used in a mapping and exports those flowables to csv
-output: csv with columns 'Class','Flowable','CAS No','Formula','Synonyms'
+Determines FEDEFL flowables not used in a mapping and exports.
+
+Those flowables to csv output: csv with columns 'Class','Flowable','CAS No',
+'Formula','Synonyms'.
 """
 
 import fedelemflowlist

scripts/extract_flow_data_from_Excel.py

@@ -1,8 +1,9 @@
 """
-Flow data were originally developed in Excel. This script extracts those data
-and writes them to csv files.
-WARNING: This will replace the existing input files
-The flow class files should match the class names in the flowlistspecs
+Flow data were originally developed in Excel.
+
+This script extracts those data and writes them to csv files. WARNING: This will
+replace the existing input files The flow class files should match the class
+names in the flowlistspecs.
 """
 
 import pandas as pd

scripts/extract_mapping_data_from_Excel.py

@@ -1,7 +1,9 @@
 """
-For mapping data were originally developed in Excel where flowables. This was developed specifically
-for the USLCI mapping. This script extracts those data and writes them to csv files.
-WARNING: This will replace the existing input files
+For mapping data were originally developed in Excel where flowables.
+
+This was developed specifically for the USLCI mapping. This script extracts
+those data and writes them to csv files. WARNING: This will replace the existing
+input files.
 """
 
 import pandas as pd

scripts/get_all_mappings.py

@@ -1,6 +1,8 @@
 """
-Combines all mapping files to help maintain consistency in future future mappings
-output: xlsx in the mapping format
+Combines all mapping files.
+
+To help maintain consistency in future future mappings
+output: xlsx in the mapping format.
 """
 
 import fedelemflowlist

scripts/summarize_flowlist.py

@@ -1,6 +1,4 @@
-"""
-Uses fedelemflowlist analysis functions to perform and export basic analysis
-"""
+"""Uses fedelemflowlist analysis functions to perform and export basic analysis."""
 import fedelemflowlist
 from fedelemflowlist.analysis.flow_list_analysis import count_flows_by_class,\
     count_flowables_by_class, list_contexts

scripts/write_all_flows.py

@@ -1,6 +1,4 @@
-"""
-Writes preferred flows to a JSON-LD archive in the output folder
-"""
+"""Writes preferred flows to a JSON-LD archive in the output folder."""
 import fedelemflowlist
 from fedelemflowlist.globals import outputpath,flow_list_specs
 

scripts/write_flows_and_mappings.py

@@ -1,6 +1,4 @@
-"""
-Exports flows and flowmappings for a selecting mapping file
-"""
+"""Exports flows and flowmappings for a selecting mapping file."""
 import fedelemflowlist
 import pandas as pd
 from fedelemflowlist.globals import outputpath

scripts/write_preferred_flows.py

@@ -1,6 +1,4 @@
-"""
-Writes preferred flows to a JSON-LD archive in the output folder
-"""
+"""Writes preferred flows to a JSON-LD archive in the output folder."""
 import fedelemflowlist
 from fedelemflowlist.globals import outputpath, flow_list_specs