Merge pull request #103 from JannisHoch/dev

v0.0.6

.travis.yml

@@ -2,6 +2,7 @@
 
 language: python
 python:
+  # - 3.8
   - 3.7
   - 3.6
 

CITATION.cff

@@ -0,0 +1,35 @@
+# YAML 1.2
+---
+cff-version: "1.1.0"
+message: "If you use this software, please cite it using these metadata."
+title: CoPro
+version: "v0.0.6b-joss"
+authors: 
+  -
+    affiliation: "Utrecht University"
+    family-names: Hoch
+    given-names: Jannis
+    orcid: "https://orcid.org/0000-0003-3570-6436"
+  -
+    affiliation: "PBL Netherlands Environmental Assessment Agency"
+    family-names: "de Bruine"
+    given-names: Sophie
+    orcid: "https://orcid.org/0000-0003-3429-349X"
+  -
+    affiliation: "Utrecht University"
+    family-names: Wanders
+    given-names: Niko
+    orcid: "https://orcid.org/0000-0002-7102-5454"
+date-released: 2020-11-17
+doi: "10.5281/zenodo.4264684"
+license: MIT
+repository-code: "https://github.com/JannisHoch/copro"
+keywords: 
+  - conflict
+  - "machine learning"
+  - "climate change"
+  - water
+  - scenarios
+  - projections
+  - "climate security"
+...

README.rst

@@ -7,8 +7,8 @@ CoPro
 
 Welcome to CoPro, a machine-learning tool for conflict risk projections based on climate, environmental, and societal drivers.
 
-.. image:: https://travis-ci.com/JannisHoch/conflict_model.svg?branch=dev
-    :target: https://travis-ci.com/JannisHoch/conflict_model
+.. image:: https://travis-ci.com/JannisHoch/copro.svg?branch=dev
+    :target: https://travis-ci.com/JannisHoch/copro
 
 .. image:: https://img.shields.io/badge/License-MIT-blue.svg
     :target: https://github.com/JannisHoch/copro/blob/dev/LICENSE
@@ -17,7 +17,7 @@ Welcome to CoPro, a machine-learning tool for conflict risk projections based on
     :target: https://copro.readthedocs.io/en/latest/?badge=latest
 
 .. image:: https://img.shields.io/github/v/release/JannisHoch/copro
-    :target: https://github.com/JannisHoch/copro/releases/tag/v0.0.5-pre
+    :target: https://github.com/JannisHoch/copro/releases/tag/v0.0.6
 
 .. image:: https://zenodo.org/badge/254407279.svg
     :target: https://zenodo.org/badge/latestdoi/254407279
@@ -67,12 +67,16 @@ Runner script
 To run the model from command line, a command line script is provided. 
 All data and settings are retrieved from the settings-file which needs to be provided as inline argument.
 
+There are two settings-files, one for evaluating the model for the reference situation, and another one for additionally making projections.
+To make a projection, both files need to be specified with the latter requiring the -proj flag.
+
 .. code-block:: console
 
     $ cd path/to/copro/scripts
     $ python runner.py ../example/example_settings.cfg
+    $ python runner.py ../example/example_settings.cfg -proj ../example/example_settings_proj.cfg
 
-By default, output is stored to the output directory specified in the settings-file. 
+By default, output is stored to the output directory specified in the specific settings-file. 
 
 Documentation
 ---------------

copro/__init__.py

@@ -11,6 +11,6 @@
 from . import models
 from . import plots
 
-__author__ = """Jannis M. Hoch, Niko Wanders, Sophie de Bruin"""
+__author__ = """Jannis M. Hoch, Sophie de Bruin, Niko Wanders"""
 __email__ = 'j.m.hoch@uu.nl'
-__version__ = '0.0.5'
+__version__ = '0.0.6'

copro/conflict.py

@@ -1,7 +1,6 @@
 import geopandas as gpd
 import pandas as pd
 import numpy as np
-import matplotlib.pyplot as plt
 import os, sys
 
 def conflict_in_year_bool(conflict_gdf, extent_gdf, config, sim_year): 
@@ -10,7 +9,7 @@ def conflict_in_year_bool(conflict_gdf, extent_gdf, config, sim_year):
     Args:
         conflict_gdf (geodataframe): geo-dataframe containing georeferenced information of conflict (tested with PRIO/UCDP data)
         extent_gdf (geodataframe): geo-dataframe containing one or more polygons with geometry information for which values are extracted
-        config (config): parsed configuration settings of run
+        config (ConfigParser-object): object containing the parsed configuration-settings of the model.
         sim_year (int): year for which data is extracted
 
     Raises:
@@ -80,11 +79,12 @@ def get_poly_ID(extent_gdf):
 
     return list_ID
 
-def get_poly_geometry(extent_gdf): 
+def get_poly_geometry(extent_gdf, config): 
     """Extracts geometry information for each polygon from geodataframe and saves to list. The geometry column in geodataframe must be named 'geometry'.
 
     Args:
         extent_gdf (geo-dataframe): geo-dataframe containing one or more polygons with geometry information.
+        config (ConfigParser-object): object containing the parsed configuration-settings of the model.
 
     Raises:
         AssertionError: error raised if length of output list does not match length of input geo-dataframe.
@@ -93,7 +93,7 @@ def get_poly_geometry(extent_gdf):
         list: list containing the geometry information extracted from geo-dataframe for each polygon used in the model.
     """    
 
-    print('listing the geometry of all geographical units')
+    if config.getboolean('general', 'verbose'): print('DEBUG: getting the geometry of all geographical units')
 
     # initiatie empty list
     list_geometry = []