From 53d24630434ad7c95349c8e28eecba20432296c0 Mon Sep 17 00:00:00 2001
From: Daria Pugacheva <142947564+dapugacheva@users.noreply.github.com>
Date: Mon, 4 Mar 2024 13:06:18 -0800
Subject: [PATCH 01/14] Update readme.md

Update instructions about exiting the software.
---
 readme.md | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/readme.md b/readme.md
index de5a6ea1..3d408ccb 100644
--- a/readme.md
+++ b/readme.md
@@ -127,6 +127,11 @@ As an example of a sensitivity analysis of the urban boundary used for analysis:
 
 ![image](https://github.com/global-healthy-liveable-cities/global-indicators/assets/12984626/c95e1ab4-3d89-49a6-86cb-61718f83dde5)
 
+### Exit the software
+To exit the web application click the exit button in the top right-hand corner or type `exit` in the terminal before closing the web app browser window. At the end of a Jupyter session, in the menu click File > Shut Down. Do not just close your browser tab or terminal window without stopping the web application or Jupyter first.
+
+To run the analysis for your study region visit our website for detailed instructions on how to configure [a new study region](https://global-healthy-liveable-cities.github.io/software/#Details) and what [input data is required](https://global-healthy-liveable-cities.github.io/software/#Data).
+
 ## Citations
 
 The software was developed by the [Global Healthy and Sustainable City Indicators Collaboration](https://www.healthysustainablecities.org/about#team) team, an international partnership of researchers and practitioners, extending methods developed by the [Healthy Liveable Cities Lab](https://cur.org.au/research-programs/healthy-liveable-cities-group/) at RMIT University and incorporating functionality from the [OSMnx](https://github.com/gboeing/osmnx) tool developed by Geoff Boeing.

From ce44e88b36ce9cab9ec060c1ece1d2304f530b79 Mon Sep 17 00:00:00 2001
From: Daria Pugacheva <142947564+dapugacheva@users.noreply.github.com>
Date: Mon, 4 Mar 2024 13:14:19 -0800
Subject: [PATCH 02/14] Update example.ipynb

Update the typo error in the file path of the study region directory in the Sensitivity Analysis description
---
 process/example.ipynb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/process/example.ipynb b/process/example.ipynb
index 62dd5a4c..43086be1 100644
--- a/process/example.ipynb
+++ b/process/example.ipynb
@@ -354,7 +354,7 @@
     "- Analyses could be conducted for different time points using historical data\n",
     "- Finally, data could be modified to represent hypothetical interventions and evaluate their impact on the calculated indicators\n",
     "\n",
-    "To run the following analysis, copy the file `process/configuration/example_ES_Las_Palmas.yml` to a new file named `example_ES_Las_Palmas_test_not_urbanx.yml`.  Open this in a text editor and replace the `ghsl_urban_intersection: true` in the study region boundary to read `ghsl_urban_intersection: false`."
+    "To run the following analysis, copy the file `process/configuration/regions/example_ES_Las_Palmas.yml` to a new file named `example_ES_Las_Palmas_test_not_urbanx.yml`.  Open this in a text editor and replace the `ghsl_urban_intersection: true` in the study region boundary to read `ghsl_urban_intersection: false`."
    ]
   },
   {

From 3b33c1d399b6d71edf90ab8fd4ca0cbb85d11c51 Mon Sep 17 00:00:00 2001
From: Daria Pugacheva <142947564+dapugacheva@users.noreply.github.com>
Date: Mon, 4 Mar 2024 13:28:25 -0800
Subject: [PATCH 03/14] Update _utils.py

Add fill_color parameter to choropleth function
---
 process/subprocesses/_utils.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/process/subprocesses/_utils.py b/process/subprocesses/_utils.py
index 0823c962..a504e80f 100644
--- a/process/subprocesses/_utils.py
+++ b/process/subprocesses/_utils.py
@@ -1575,6 +1575,7 @@ def plot_choropleth_map(
     field: str,
     layer: str = 'indicators_grid_100m',
     layer_id: str = 'grid_id',
+    fill_color: str = '',
     title: str = '',
     attribution: str = '',
 ):
@@ -1590,6 +1591,7 @@ def plot_choropleth_map(
         boundary_centroid=tuple(r.get_centroid()),
         key_on=layer_id,
         fields=[layer_id, field],
+        fill_color=fill_color,
         title=title,
         attribution=attribution,
     )
@@ -1602,6 +1604,7 @@ def choropleth_map(
     key_on: str,
     fields: list,
     boundary_centroid: tuple,
+    fill_color: str,
     title: str,
     attribution: str,
 ):
@@ -1645,7 +1648,7 @@ def choropleth_map(
         key_on=f'feature.properties.{key_on}',
         name='choropleth',
         columns=fields,
-        fill_color='YlGn',
+        fill_color=fill_color,
         fill_opacity=0.7,
         line_opacity=0.1,
         legend_name=title,

From a422a7e60ae79aeeebae3455d093679dc9e85437 Mon Sep 17 00:00:00 2001
From: Daria Pugacheva <142947564+dapugacheva@users.noreply.github.com>
Date: Mon, 4 Mar 2024 13:30:30 -0800
Subject: [PATCH 04/14] Update ghsci.py

Add fill_color parameter to the choropleth map function.
---
 process/subprocesses/ghsci.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/process/subprocesses/ghsci.py b/process/subprocesses/ghsci.py
index 1c2b55c3..5c374fc3 100644
--- a/process/subprocesses/ghsci.py
+++ b/process/subprocesses/ghsci.py
@@ -941,6 +941,7 @@ def choropleth(
         field: str,
         layer: str,
         id: str,
+        fill_color: str,
         title: str,
         save=True,
         attribution: str = 'Global Healthy and Sustainable City Indicators Collaboration',
@@ -961,6 +962,7 @@ def choropleth(
                 layer=layer,
                 layer_id=id,
                 title=title,
+                fill_color=fill_color,
                 attribution=attribution,
             )
             if save:

From 530fd5a19cd891a33b7d90d51a88668f0af924a8 Mon Sep 17 00:00:00 2001
From: Daria Pugacheva <142947564+dapugacheva@users.noreply.github.com>
Date: Mon, 4 Mar 2024 18:31:17 -0800
Subject: [PATCH 05/14] Update example.ipynb

Added fill_color parameter to the choropleth function
---
 process/example.ipynb | 1 +
 1 file changed, 1 insertion(+)

diff --git a/process/example.ipynb b/process/example.ipynb
index 43086be1..fcc57e5a 100644
--- a/process/example.ipynb
+++ b/process/example.ipynb
@@ -1055,6 +1055,7 @@
     "    field='local_walkability',\n",
     "    layer=r.config['grid_summary'],\n",
     "    id='grid_id',\n",
+    "    fill_color='YlGn',
     "    title='Local walkability',\n",
     "    attribution='Global Healthy and Sustainable City Indicators Collaboration'\n",
     ")\n",

From 34791949b2251b1ac77fc8181cee1560e0ca3bb2 Mon Sep 17 00:00:00 2001
From: Daria Pugacheva <142947564+dapugacheva@users.noreply.github.com>
Date: Mon, 4 Mar 2024 18:45:44 -0800
Subject: [PATCH 06/14] Update example.ipynb

---
 process/example.ipynb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/process/example.ipynb b/process/example.ipynb
index fcc57e5a..f635b15e 100644
--- a/process/example.ipynb
+++ b/process/example.ipynb
@@ -1055,7 +1055,7 @@
     "    field='local_walkability',\n",
     "    layer=r.config['grid_summary'],\n",
     "    id='grid_id',\n",
-    "    fill_color='YlGn',
+    "    fill_color='YlGn',\n",
     "    title='Local walkability',\n",
     "    attribution='Global Healthy and Sustainable City Indicators Collaboration'\n",
     ")\n",

From 210dc42f24fab54877512d12487d2dc43d3c4606 Mon Sep 17 00:00:00 2001
From: Daria Pugacheva <142947564+dapugacheva@users.noreply.github.com>
Date: Mon, 4 Mar 2024 18:54:06 -0800
Subject: [PATCH 07/14] Update ghsci.py

Added fill_opacity parameter
---
 process/subprocesses/ghsci.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/process/subprocesses/ghsci.py b/process/subprocesses/ghsci.py
index 5c374fc3..a761c661 100644
--- a/process/subprocesses/ghsci.py
+++ b/process/subprocesses/ghsci.py
@@ -942,6 +942,7 @@ def choropleth(
         layer: str,
         id: str,
         fill_color: str,
+        fill_opacity: float,
         title: str,
         save=True,
         attribution: str = 'Global Healthy and Sustainable City Indicators Collaboration',
@@ -963,6 +964,7 @@ def choropleth(
                 layer_id=id,
                 title=title,
                 fill_color=fill_color,
+                fill_opacity=fill_opacity,
                 attribution=attribution,
             )
             if save:

From 631ed8d687c1c10ff6d0ff1760157537411582ad Mon Sep 17 00:00:00 2001
From: Daria Pugacheva <142947564+dapugacheva@users.noreply.github.com>
Date: Mon, 4 Mar 2024 18:57:17 -0800
Subject: [PATCH 08/14] Update _utils.py

added fill_opacity
---
 process/subprocesses/_utils.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/process/subprocesses/_utils.py b/process/subprocesses/_utils.py
index a504e80f..4ccb31f1 100644
--- a/process/subprocesses/_utils.py
+++ b/process/subprocesses/_utils.py
@@ -1576,6 +1576,7 @@ def plot_choropleth_map(
     layer: str = 'indicators_grid_100m',
     layer_id: str = 'grid_id',
     fill_color: str = '',
+    fill_opacity: float = 0.7,
     title: str = '',
     attribution: str = '',
 ):
@@ -1592,6 +1593,7 @@ def plot_choropleth_map(
         key_on=layer_id,
         fields=[layer_id, field],
         fill_color=fill_color,
+        fill_opacity=fill_opacity,
         title=title,
         attribution=attribution,
     )
@@ -1605,6 +1607,7 @@ def choropleth_map(
     fields: list,
     boundary_centroid: tuple,
     fill_color: str,
+    fill_opacity: float,
     title: str,
     attribution: str,
 ):
@@ -1649,7 +1652,7 @@ def choropleth_map(
         name='choropleth',
         columns=fields,
         fill_color=fill_color,
-        fill_opacity=0.7,
+        fill_opacity=fill_opacity,
         line_opacity=0.1,
         legend_name=title,
     ).add_to(m)

From 214d8e3cf3899a3bd71f20efac1b080f54172299 Mon Sep 17 00:00:00 2001
From: Daria Pugacheva <142947564+dapugacheva@users.noreply.github.com>
Date: Mon, 4 Mar 2024 18:58:30 -0800
Subject: [PATCH 09/14] Update example.ipynb

added fill_color parameter
---
 process/example.ipynb | 1 +
 1 file changed, 1 insertion(+)

diff --git a/process/example.ipynb b/process/example.ipynb
index f635b15e..100b2094 100644
--- a/process/example.ipynb
+++ b/process/example.ipynb
@@ -1056,6 +1056,7 @@
     "    layer=r.config['grid_summary'],\n",
     "    id='grid_id',\n",
     "    fill_color='YlGn',\n",
+    "    fill_opacity=0.7,\n",
     "    title='Local walkability',\n",
     "    attribution='Global Healthy and Sustainable City Indicators Collaboration'\n",
     ")\n",

From 73391676bffa3ced03387bf8d6edbb90c42665a6 Mon Sep 17 00:00:00 2001
From: Daria Pugacheva <142947564+dapugacheva@users.noreply.github.com>
Date: Sat, 16 Mar 2024 16:30:28 -0700
Subject: [PATCH 10/14] Update _utils.py

Add line_opacity function
---
 process/subprocesses/_utils.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/process/subprocesses/_utils.py b/process/subprocesses/_utils.py
index 4ccb31f1..cce1c262 100644
--- a/process/subprocesses/_utils.py
+++ b/process/subprocesses/_utils.py
@@ -1575,8 +1575,9 @@ def plot_choropleth_map(
     field: str,
     layer: str = 'indicators_grid_100m',
     layer_id: str = 'grid_id',
-    fill_color: str = '',
+    fill_color: str = 'YlGn',
     fill_opacity: float = 0.7,
+    line_opacity: float = 0.1,
     title: str = '',
     attribution: str = '',
 ):
@@ -1594,6 +1595,7 @@ def plot_choropleth_map(
         fields=[layer_id, field],
         fill_color=fill_color,
         fill_opacity=fill_opacity,
+        line_opacity=line_opacity,
         title=title,
         attribution=attribution,
     )
@@ -1608,6 +1610,7 @@ def choropleth_map(
     boundary_centroid: tuple,
     fill_color: str,
     fill_opacity: float,
+    line_opacity: float,
     title: str,
     attribution: str,
 ):

From ed91e25e43d10ee5f16acb8df6e5b2373e2680ba Mon Sep 17 00:00:00 2001
From: Daria Pugacheva <142947564+dapugacheva@users.noreply.github.com>
Date: Sat, 16 Mar 2024 16:32:06 -0700
Subject: [PATCH 11/14] Update ghsci.py

added line_opacity
---
 process/subprocesses/ghsci.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/process/subprocesses/ghsci.py b/process/subprocesses/ghsci.py
index a761c661..9b0ea647 100644
--- a/process/subprocesses/ghsci.py
+++ b/process/subprocesses/ghsci.py
@@ -943,6 +943,7 @@ def choropleth(
         id: str,
         fill_color: str,
         fill_opacity: float,
+        line_opacity: float,
         title: str,
         save=True,
         attribution: str = 'Global Healthy and Sustainable City Indicators Collaboration',
@@ -965,6 +966,7 @@ def choropleth(
                 title=title,
                 fill_color=fill_color,
                 fill_opacity=fill_opacity,
+                line_opacity=line_opacity,
                 attribution=attribution,
             )
             if save:

From ac5682d08b643e85107f26090275f24f07cf2b0c Mon Sep 17 00:00:00 2001
From: Daria Pugacheva <142947564+dapugacheva@users.noreply.github.com>
Date: Tue, 19 Mar 2024 14:02:04 -0700
Subject: [PATCH 12/14] Update readme.md

Noted how to stop long running process in the terminal
---
 readme.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/readme.md b/readme.md
index 3d408ccb..487bde50 100644
--- a/readme.md
+++ b/readme.md
@@ -128,7 +128,7 @@ As an example of a sensitivity analysis of the urban boundary used for analysis:
 ![image](https://github.com/global-healthy-liveable-cities/global-indicators/assets/12984626/c95e1ab4-3d89-49a6-86cb-61718f83dde5)
 
 ### Exit the software
-To exit the web application click the exit button in the top right-hand corner or type `exit` in the terminal before closing the web app browser window. At the end of a Jupyter session, in the menu click File > Shut Down. Do not just close your browser tab or terminal window without stopping the web application or Jupyter first.
+To exit the web application click the **exit** button in the top right-hand corner. At the end of a Jupyter session, in the menu click _File > Shut Down_. If you close a browser window with the Jupyter Lab or GHSCI app still running, the underlying server process running these may be interrupted by pressing `Control+C` at the command prompt.
 
 To run the analysis for your study region visit our website for detailed instructions on how to configure [a new study region](https://global-healthy-liveable-cities.github.io/software/#Details) and what [input data is required](https://global-healthy-liveable-cities.github.io/software/#Data).
 

From 5b36f5c28a9b14f67f4cf24ce24e7627bb559345 Mon Sep 17 00:00:00 2001
From: Daria Pugacheva <142947564+dapugacheva@users.noreply.github.com>
Date: Tue, 19 Mar 2024 14:09:58 -0700
Subject: [PATCH 13/14] Update example.ipynb

Added `line_opacity` argument to the choropleth map.
---
 process/example.ipynb | 1 +
 1 file changed, 1 insertion(+)

diff --git a/process/example.ipynb b/process/example.ipynb
index 100b2094..96080357 100644
--- a/process/example.ipynb
+++ b/process/example.ipynb
@@ -1057,6 +1057,7 @@
     "    id='grid_id',\n",
     "    fill_color='YlGn',\n",
     "    fill_opacity=0.7,\n",
+    "    line_opacity=0.1,\n",
     "    title='Local walkability',\n",
     "    attribution='Global Healthy and Sustainable City Indicators Collaboration'\n",
     ")\n",

From 457a3a3363ba0f12d3e4c1a2c3383cb04791a6ed Mon Sep 17 00:00:00 2001
From: Daria Pugacheva <142947564+dapugacheva@users.noreply.github.com>
Date: Tue, 19 Mar 2024 16:02:56 -0700
Subject: [PATCH 14/14] Update example.ipynb

note matplotlib color palete
---
 process/example.ipynb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/process/example.ipynb b/process/example.ipynb
index 96080357..4eb6ee9c 100644
--- a/process/example.ipynb
+++ b/process/example.ipynb
@@ -1078,7 +1078,7 @@
     "\n",
     "![image.png](attachment:01efeb07-053e-48bb-8e5b-736962ab54b9.png)\n",
     "\n",
-    "In the interactive version, you can hover over grid cells to view the value of the specified indicator for that location."
+    "In the interactive version, you can hover over grid cells to view the value of the specified indicator for that location. You can change graphic parameters like fill color, see [how to choose colormaps in matplotlib](https://matplotlib.org/stable/users/explain/colors/colormaps.html#classes-of-colormaps)"
    ]
   },
   {