.gitignore

@@ -130,3 +130,4 @@ dmypy.json
 notebooks/
 notes/
 
+/viz/*.txt

Dockerfile

@@ -40,7 +40,7 @@ RUN wget -O /usr/local/bin/minio \
 RUN mkdir /app
 
 # Install miniconda
-ARG MINICONDA_VERSION="py38_4.9.2"
+ARG MINICONDA_VERSION="py39_4.10.3"
 RUN wget https://repo.anaconda.com/miniconda/Miniconda3-${MINICONDA_VERSION}-Linux-x86_64.sh \
     && mkdir -p /opt \
     && bash Miniconda3-${MINICONDA_VERSION}-Linux-x86_64.sh -b -p /opt/conda \

environment.yml

@@ -5,25 +5,25 @@ channels:
   - conda-forge
 
 dependencies:
-  - python=3.8
+  - python=3.9
   - pip=21
-  - gdal=3.1
+  - gdal=3.3
   - appdirs=1.4
-  - beautifulsoup4=4.9
-  - click=7
+  - beautifulsoup4=4.10
+  - click=8.0
   - fiona=1.8
-  - gcsfs=0.8
-  - geopandas=0.9
+  - gcsfs=2021.10
+  - geopandas=0.10
   - loguru=0.5
-  - numpy=1.20
-  - pandas=1.2
+  - numpy=1.21
+  - pandas=1.3
   - rasterio=1.2
-  - requests=2.25
-  - s3fs=0.6.0
-  - fsspec=0.9
-  - shapely=1.7
-  - tqdm=4.59
-  - rasterstats=0.14
+  - requests=2.26
+  - s3fs=2021.10
+  - fsspec=2021.10
+  - shapely=1.8
+  - tqdm=4.62
+  - rasterstats=0.16
   - conda-build
   - pytest=6.2
   - pytest-cov

geohealthaccess/cli.py

@@ -219,6 +219,7 @@ def access(
 
     # update moving speeds if a custom file is provided
     if moving_speeds:
+        moving_speeds = moving_speeds.strip()
         with storage.open_(moving_speeds) as f:
             gha.moving_speeds = json.load(f)
 
@@ -227,6 +228,7 @@ def access(
     if areas:
         # areas can be a local, s3 or gcs path
         # and may be provided as a GeoJSON or GPKG
+        areas = areas.strip()
         with TemporaryDirectory(prefix="geohealthaccess_") as tmp_dir:
             areas_tmp = os.path.join(tmp_dir, os.path.basename(areas))
             storage.cp(areas, areas_tmp)
@@ -261,6 +263,8 @@ def access(
 
         for target_ in target:
 
+            target_ = target_.strip()
+
             # load start_points as a geodataframe
             with TemporaryDirectory(prefix="geohealthaccess_") as tmp_dir:
                 target_tmp = os.path.join(tmp_dir, os.path.basename(target_))

geohealthaccess/geohealthaccess.py

@@ -46,10 +46,19 @@ def __init__(
         logs_dir=None,
         log_level="DEBUG",
     ):
-        self.raw_dir = raw_dir
-        self.input_dir = input_dir
-        self.output_dir = output_dir
-        self.logs_dir = logs_dir
+        self.raw_dir = None
+        self.input_dir = None
+        self.output_dir = None
+        self.logs_dir = None
+        if raw_dir:
+            self.raw_dir = raw_dir.strip()
+        if input_dir:
+            self.input_dir = input_dir.strip()
+        if output_dir:
+            self.output_dir = output_dir.strip()
+        if logs_dir:
+            self.logs_dir = logs_dir.strip()
+
         self.log_level = log_level
 
         if len(country) == 3:

pyproject.toml

@@ -16,22 +16,22 @@ keywords = [
 ]
 
 [tool.poetry.dependencies]
-python = ">=3.7"
+python = "^3.9.0"
 appdirs = "^1.4.0"
-beautifulsoup4 = "^4.9.0"
-click = "^7.1.0"
+beautifulsoup4 = "^4.10.0"
+click = "^8.0.0"
 fiona = "^1.8.0"
-gcsfs = "^0.8.0"
-geopandas = "^0.9.0"
+gcsfs = "^2021.10.0"
+geopandas = "^0.10.0"
 loguru = "^0.5.0"
-numpy = "^1.20.0"
-pandas = "^1.2.0"
+numpy = "^1.21.0"
+pandas = "^1.3.0"
 rasterio = "^1.2.0"
-requests = "^2.24.0"
-s3fs = "^0.6.0"
-shapely = "^1.7.0"
-tqdm = "^4.59.0"
-rasterstats = "^0.14.0"
+requests = "^2.26.0"
+s3fs = "^2021.10.0"
+shapely = "^1.8.0"
+tqdm = "^4.62.0"
+rasterstats = "^0.16.0"
 
 [tool.poetry.dev-dependencies]
 pytest = "^6.2.0"

viz/Dockerfile

@@ -3,7 +3,7 @@
 # - AWS_SECRET_ACCESS_KEY
 # - STANDALONE=yes
 
-FROM python:3
+FROM python:3.9.6
 
 RUN apt-get update
 RUN apt-get install -y libgeos-dev libgdal-dev
@@ -17,3 +17,5 @@ COPY assets /code/assets
 
 EXPOSE 8000
 CMD python /code/app.py
+
+WORKDIR /code

viz/assets/density.txt

@@ -0,0 +1,2 @@
+This graphic shows the cumulative proportion of people in a health zone with access to care under increasing travel times. To change the health zone displayed, simply move the mouse to hover over another part of the map. (Note: this view is only available when 'Access estimates by health zone' is selected)
+Such a cross-cutting view of travel times allows a better understanding of the question of access in a given area. Steep increases in the proportion with access might point to acute issues with stockouts of medication or lack of personnel, while a flatter curve may indicate an area that is chronically underserved.

viz/assets/how_to_display.txt

@@ -0,0 +1,4 @@
+When the access estimates by health zone option is selected, it is possible to display the data in three different ways :
+Percent of population with access in each zone : this is a good way to identify health districts with the lowest level of accessibility of health services.
+Percent of population with access with zone population: this is a good way to identify most populous health districts and check the  level of access to care. 
+Number of people without access to care : this is the best way to identify where people don’t have access to care and how many people are affected.

viz/assets/landing.txt

@@ -0,0 +1,5 @@
+This visualization is designed to help understand the accessibility of malaria services in the DRC. It displays the results of a model that esimates the time it takes patients to reach a health facility where they can recieve basic malaria treatment, for each month of the years 2020 and 2021.The model takes different types of information into account:
+Where patients are located, based on 
+Where health facilities are located, and what resources and services are available at each facility based on data from DRC's National Health Information System.
+The physical environment that impacts travel (road networks, land cover, elevation, etc.) based on a mix of openly-available data sources.
+More information on the modeling and the data used as well as the full source code can be found on 

viz/assets/lorem.txt

@@ -0,0 +1,3 @@
+Lorem ipsum dolor sit amet, consectetur adipiscing elit. Cras laoreet ligula vel est fermentum efficitur. Maecenas a elementum orci, rutrum interdum magna. Fusce lobortis lectus id maximus tempor. Quisque nec porttitor ex. Vestibulum sit amet tortor vestibulum, hendrerit ipsum at, fringilla massa. Maecenas vitae est a quam fermentum laoreet ut vitae lectus. Donec ultrices semper elementum.
+Mauris rutrum convallis lacus eget eleifend. Sed fringilla viverra est, nec dignissim nisi. Integer sed iaculis diam. Ut pharetra mauris vitae ligula maximus efficitur. Curabitur congue ante sit amet massa consequat egestas. Nam nec eros non turpis imperdiet blandit. Nam at massa posuere libero semper finibus. Curabitur non vulputate nisi. Praesent non lacinia dolor. Ut elementum, mi non finibus ultricies, ante nibh lobortis tortor, vel mattis elit eros quis leo.
+Maecenas placerat urna non faucibus vehicula. Aenean interdum tortor ut tristique blandit. Ut sit amet metus pulvinar, dictum dui nec, egestas tellus. Proin aliquet, arcu eu sollicitudin dignissim, lorem eros pharetra dolor, nec aliquam sem nulla nec turpis. Quisque cursus enim porta lacus commodo, at lobortis sapien interdum. Nam lobortis neque ac eros pulvinar, nec ornare nisi egestas. Proin a maximus dolor. Aenean sit amet pulvinar felis. Nullam finibus risus in diam ultrices tincidunt. 

viz/assets/style.css

@@ -5,26 +5,6 @@ body {
     overflow: hidden;
 }
 
-.rc-slider-mark-text {
-    transform: rotate(-45deg);
-
-    /* Legacy vendor prefixes that you probably don't need... */
-
-    /* Safari */
-    -webkit-transform: rotate(-45deg);
-
-    /* Firefox */
-    -moz-transform: rotate(-45deg);
-
-    /* IE */
-    -ms-transform: rotate(-45deg);
-
-    /* Opera */
-    -o-transform: rotate(-45deg);
-
-    /* Internet Explorer */
-    filter: progid:DXImageTransform.Microsoft.BasicImage(rotation=2);
-}
 
 #app-main {
     width: 100%;
@@ -33,23 +13,52 @@ body {
     padding: none;
 }
 
-#map-main {
-    margin-left: 1%;
+
+#map-container {
+    margin-left: 0.3%;
     height: 100%;
-    width: 78.5%;
+    width: 79%;
     display: inline-block;
     position: absolute;
 }
 
+/* loading GIF + grey transparency */
+.loader-wrapper {
+    height: inherit;
+}
+
+.loader-wrapper > div {
+    visibility: visible !important;
+    height: inherit;
+}
+
+.loader-wrapper > div > div {
+    background: rgba(0, 0, 0, 0.5);
+}
+
+#map-main {
+    height: 100%;
+    width: 100%;
+}
+
+
+/* controls UI */
 #sidebar {
-    width: 20%;
+    width: 22%;
     border-radius: 5px;
-    margin-top: 0.8%;
-    padding: 6px;
+    margin-top: 0.2%;
+    margin-left: 0.25%;
+    padding: 4px;
     padding-top: none;
     display: inline-block;
 }
 
+#title-container {
+    font-size: 1.2vw !important;
+    color: #2065ab;
+/*     font-weight: bold; */
+}
+
 #ctrls-container {
     background-color: white;
     padding: inherit;
@@ -58,20 +67,112 @@ body {
 
 #ctrls-container > div {
     padding: inherit;
+    font-size: 0.95vw;
 }
 
 div > label {
     display: block;
+    font-size: 0.8vw;
+}
+
+#month {
+    margin-top: 10px;
+    margin-bottom: -25px; 
+}
+
+#slider-output-container {
+    line-height: 34px;
+    border: 1px solid #ccc;
+    border-radius: 4px;
+    padding-left: 10px
+}
+
+.rc-slider-handle {
+  border-color: #007aff;
 }
 
+.rc-slider-handle:hover {
+  border-color: #007aff;
+}
+
+.rc-slider-handle-active:active {
+  border-color: #007aff;
+}
+
+.rc-slider-handle-click-focused:focus {
+    border-color: #007aff;
+}
+
+.rc-slider-handle-click-focused {
+    border-color: #007aff;
+}
+
+
 #density-container {
-    margin-top: 4%;
+    margin-top: 3%;
     padding: inherit;
     border-radius: 5px;
     background-color: white;
 }
 
+#density-title-container {
+    display: flex;
+    padding: 1.5%;
+    font-size: 0.9vw
+}
+
+
+#density-title {
+    width: 90%;
+}
+
 #sources{
     padding: inherit;
     font-size: 10px;
 }
+
+.info-button {
+    color: white;
+    background-color: #a6a6a6;
+    border: 2px solid white;
+    border-radius: 25%;
+    width: 20px;
+    font-size: 14px;
+    font-weight: bold;
+    margin-left: 5px;
+}
+
+.info-button:hover {
+  filter: brightness(110%);
+}
+
+
+/* modal styling */
+
+.modal {
+    position: fixed;
+    z-index: 1002; /* Sit on top, including modebar which has z=1001 */
+    left: 0;
+    top: 0;
+    width: 100%; /* Full width */
+    height: 100%; /* Full height */
+    background-color: rgba(0, 0, 0, 0.6); /* Black w/ opacity */
+
+}
+
+.modal-content {
+    margin: 15%;
+    margin-top: 5%;
+    padding: 30px;
+    background-color: white;
+    text-align: center;
+    border-radius: 4px;
+}
+
+#modal-title, .modal-content > div > h2 {
+    color: #2065ab;
+}
+
+#modal-text {
+    text-align: left;
+}

viz/assets/what_to_display.txt

@@ -0,0 +1,9 @@
+Depending on what you want to understand, you can look at the data in different ways.
+Month: you can select the month for which you want to look at the accessibility of services.
+Travel time: you can choose how fast you think patients should be able to access services.
+Province: you can subset the access estimates to a specific province of the country.
+What to display: to inform your analysis, you can look either at 
+Estimates of accessibility aggregated to the health zone level, such as the percentage of a zone’s population that lives under a given travel time from health services. 
+A high resolution display of the travel times to health facilities. This may help you checking the quality of these estimations, find places with specially low access to health care or analyse the main barriers to access.
+A high resolution  display of where populations live. This may help you see which places should be prioritised to reach the highest number of people.
+To reset the map to its default zoom level, simply double click on the map.