Merge pull request #87 from USEPA/release_v1.0.3

Release v1.0.3

.github/workflows/python-package.yml

@@ -15,7 +15,7 @@ on:
       - '.gitignore'
   pull_request:
     branches: [master, develop]
-    types: [opened, reopened]   # excludes syncronize to avoid redundant trigger from commits on PRs 
+    types: [opened, reopened, ready_for_review]   # excludes syncronize to avoid redundant trigger from commits on PRs 
     paths-ignore:
       - '**.md'  
       - '**.bib'
@@ -49,22 +49,21 @@ jobs:
         pip install pytest pytest-cov flake8
 
     # install testing
-    - name: Install package and dependencies (non-Windows)
-      if: matrix.os != 'windows-latest'
+    - name: Install package and dependencies
       run: |
         pip install .
         
-    - name: Install package and dependencies (Windows)
-      if: matrix.os == 'windows-latest'
-      run: |
-        pip install .[ImpactWorld]
+    # - name: Install package and dependencies (Windows)
+    #   if: matrix.os == 'windows-latest'
+    #   run: |
+    #     pip install .[ImpactWorld]
 
-    # MS Access install (for Windows) needed for IW+ 
-    - name: Choco install msaccess2010
-      if: matrix.os == 'windows-latest'
-      uses: crazy-max/ghaction-chocolatey@v1
-      with:
-        args: install msaccess2010-redist
+    # # MS Access install (for Windows) needed for IW+
+    # - name: Choco install msaccess2010
+    #   if: matrix.os == 'windows-latest'
+    #   uses: crazy-max/ghaction-chocolatey@v1
+    #   with:
+    #     args: install msaccess2010-redist
 
     # linting & pytest
     - name: Lint with flake8
@@ -76,4 +75,4 @@ jobs:
         
     - name: Test with pytest
       run: |
-        pytest
+        pytest -m "not generate_methods"

.github/workflows/test_methods.yml

@@ -0,0 +1,48 @@
+# This workflow tests the generation of impact methods
+
+name: Generate and store impact methods
+
+on:
+  pull_request:
+    branches: [master, develop]
+    types: [opened, reopened, ready_for_review]   # excludes syncronize to avoid redundant trigger from commits on PRs
+  workflow_dispatch:            # also allow manual trigger, for testing purposes
+
+jobs:
+  generate_methods:
+    runs-on: macos-latest
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python
+      uses: actions/setup-python@v3
+      with:
+        python-version: "3.10"
+
+    - name: Update pip & install testing pkgs
+      run: |
+        python -VV
+        python -m pip install --upgrade pip setuptools wheel
+        pip install pytest pytest-cov flake8
+
+    # install package & dependencies
+    - name: Install package and dependencies
+      run: |
+        pip install .
+
+    - name: Generate and store methods
+      run: |
+        pytest -m generate_methods
+
+    - name: Upload files
+      if: always()
+      uses: actions/upload-artifact@v3.1.1
+      with:
+        # Artifact name
+        name: lciafmt_methods
+        # A file, directory or wildcard patter that describes what to upload
+        path: |
+            # ~/Library/Application Support/lciafmt/*
+            ~/Library/Application Support/lciafmt/diff/*
+        if-no-files-found: warn # 'warn' or 'ignore' are also available, defaults to `warn`
+        # retention-days: 5 # cannot exceed the retention limit set by the repository, organization, or enterprise.

README.md

@@ -16,6 +16,7 @@ The LCIA Formatter v1 was peer-reviewed internally at USEPA and externally throu
 |ReCiPe 2016 Endpoint|National Institute for Public Health and the Environment (The Netherlands)|[LCIA: the ReCiPe Model](https://www.rivm.nl/en/life-cycle-assessment-lca/recipe)|
 |ImpactWorld+ Midpoint*|International Reference Center for Life Cycle of Products, Services and Systems (CIRAIG)|[ImpactWorld+](http://www.impactworldplus.org/en/team.php)|
 |ImpactWorld+ Endpoint*|International Reference Center for Life Cycle of Products, Services and Systems (CIRAIG)|[ImpactWorld+](http://www.impactworldplus.org/en/team.php)|
+|IPCC GWP|Intergovernmental Panel on Climate Change (IPCC)| |
 |FEDEFL Inventory Methods|US Environmental Protection Agency|[FEDEFL Inventory Methods](https://github.com/USEPA/LCIAformatter/wiki/Inventory-Methods)|
 
 \* only works on Windows installations
@@ -24,9 +25,9 @@ The LCIA Formatter v1 was peer-reviewed internally at USEPA and externally throu
 `lciafmt` requires Python 3.7 or greater.
 
 Install a release directly from github using pip. From a command line interface, run:
-> pip install git+https://github.com/USEPA/LCIAformatter.git@v1.0.1#egg=lciafmt
+> pip install git+https://github.com/USEPA/LCIAformatter.git@v1.0.3#egg=lciafmt
 
-where you can replace 'v1.0.1' with the version you wish to use under [Releases](https://github.com/USEPA/LCIAformatter/releases).
+where you can replace 'v1.0.3' with the version you wish to use under [Releases](https://github.com/USEPA/LCIAformatter/releases).
 
 Alternatively, to install from the most current point on the repository:
 ```

lciafmt/__init__.py

@@ -17,9 +17,11 @@
 import lciafmt.jsonld as jsonld
 import lciafmt.traci as traci
 import lciafmt.recipe as recipe
+import lciafmt.ipcc as ipcc
 import lciafmt.fedefl_inventory as fedefl_inventory
 import lciafmt.util as util
 import lciafmt.endpoint as ep
+import lciafmt.custom as custom
 
 
 from enum import Enum
@@ -32,6 +34,7 @@ class Method(Enum):
     RECIPE_2016 = "ReCiPe 2016"
     FEDEFL_INV = "FEDEFL Inventory"
     ImpactWorld = "ImpactWorld"
+    IPCC = "IPCC"
 
     def get_metadata(cls):
         """Return the stored metadata."""
@@ -101,7 +104,10 @@ def get_method(method_id, add_factors_for_missing_contexts=True,
     :param url: str, alternate url for method, defaults to url in method config
     :return: DataFrame of method in standard format
     """
-    method_id = util.check_as_class(method_id)
+    if not method_id:
+        return custom.get_custom_method(file=file)
+    else:
+        method_id = util.check_as_class(method_id)
     if method_id == Method.TRACI:
         return traci.get(add_factors_for_missing_contexts, file=file, url=None)
     if method_id == Method.RECIPE_2016:
@@ -110,6 +116,8 @@ def get_method(method_id, add_factors_for_missing_contexts=True,
     if method_id == Method.ImpactWorld:
         import lciafmt.iw as impactworld
         return impactworld.get(file=file, url=url)
+    if method_id == Method.IPCC:
+        return ipcc.get()
     if method_id == Method.FEDEFL_INV:
         return fedefl_inventory.get(subset)
 
@@ -172,9 +180,9 @@ def get_mapped_method(method_id, indicators=None, methods=None) -> pd.DataFrame:
             mapped_method = map_flows(method, system=mapping_system,
                                       case_insensitive=case_insensitive)
             mapped_method = util.collapse_indicators(mapped_method)
-            util.store_method(mapped_method, method_id)
         else:
             mapped_method = method
+        util.store_method(mapped_method, method_id)
     if indicators is not None:
         mapped_method = mapped_method[mapped_method['Indicator'].isin(indicators)]
         if len(mapped_method) == 0:
@@ -216,3 +224,28 @@ def supported_indicators(method_id) -> list:
         return list(indicators)
     else:
         return None
+
+
+def apply_lcia_method(df, method_id) -> pd.DataFrame:
+    """Applies characterization factors to a dataframe.
+
+    :param df: dataframe containing 'FlowAmount' and 'FlowUUID' columns
+    :param method_id: class Method or str, based on id field of
+        supported_methods
+    :return: DataFrame with impact method applied as 'Impact' column
+    """
+    if 'FlowUUID' not in df.columns or 'FlowAmount' not in df.columns:
+        raise TypeError ('DataFrame must containt "FlowUUID" and '
+                         '"FlowAmount" columns')
+    impact_method = (
+        get_mapped_method(method_id)
+        .drop(columns=['Flowable', 'Context', 'Location', 'Location UUID',
+                       'CAS No', 'Method UUID','Indicator UUID','Unit'])
+        .rename(columns={'Flow UUID':'FlowUUID'}))
+
+    impacts = df.merge(impact_method, how = 'inner',
+                       on = ['FlowUUID'])
+    impacts['Impact'] = (impacts['FlowAmount'] *
+                         impacts['Characterization Factor'])
+
+    return impacts

lciafmt/custom.py

@@ -0,0 +1,25 @@
+# custom.py (lciafmt)
+# !/usr/bin/env python3
+# coding=utf-8
+"""
+Functions to create custom manual methods
+"""
+
+import pandas as pd
+
+from lciafmt.df import lciafmt_cols
+
+def get_custom_method(file: str=None, input_df=None):
+    """Converts a dataframe or a csv filepath to a dataframe suitable for
+    lciafmt. If `file` is passed, input_df is ignored.
+    """
+    if file:
+        input_df = pd.read_csv(file)
+    if (pd.Series(['Characterization Factor', 'Flowable', 'Context'])
+            .isin(input_df.columns).all()):
+        df = input_df.reindex(columns=lciafmt_cols)
+        df = df.fillna('')
+        return df
+    else:
+        raise Exception
+