Lint spacing

README.md

@@ -11,6 +11,7 @@ workflow can be used to analyse environmental risks to infrastructure
 networks using global open data. It is a work in progress.
 
 Goals:
+
 - Automated pipeline for reproducible analysis anywhere in the world
 - Maps per-country and of larger areas
 - Charts/stats of exposure per admin region, per hazard type, scenario, epoch
@@ -20,13 +21,15 @@ Goals:
 - Estimate indirect effects of disruption - people affected, economic activity disrupted
 
 Non-goals:
+
 - Using closed data, which may be appropriate for other projects or use-cases
 - Detailed operational/engineering level simulation
 - Long-term planning
 
 ## Installation
 
 Install `open-gira` by cloning the repository:
+
 ```bash
 git clone https://github.com/nismod/open-gira.git
 ```
@@ -39,11 +42,13 @@ manage these `conda` packages.
 
 Having installed one of the suggested package managers, to create the
 `open-gira` conda environment:
+
 ```bash
 micromamba create -f environment.yml -y
 ```
 
 And to activate the environment:
+
 ```bash
 micromamba activate open-gira
 ```
@@ -52,9 +57,10 @@ micromamba activate open-gira
 
 Some rules use the `wget` utility to download files.
 
-On Linux or MacOS, you may already have the `wget` utility available. If not, 
-it should be possible to install with your usual package manager (e.g. apt, 
+On Linux or MacOS, you may already have the `wget` utility available. If not,
+it should be possible to install with your usual package manager (e.g. apt,
 MacPorts, brew), or else using micromamba:
+
 ```bash
 micromamba install wget
 ```
@@ -80,6 +86,7 @@ Note that all subsequent commands given in the documentation assume that the
 Workflow steps are tested using small sample datasets.
 
 To run the tests:
+
 ```bash
 python -m pytest tests
 ```
@@ -164,5 +171,5 @@ Programme. The views expressed here do not necessarily reflect the UK
 government's official policies.
 
 This research has also been supported by funding from the World Bank
-Group, and the UK Natural Environment Research Council (NERC) through 
+Group, and the UK Natural Environment Research Council (NERC) through
 the UK Centre for Greening Finance and Investment (CGFI).

docs/src/user-guide/usage/network-creation/rail.md

@@ -21,32 +21,34 @@ from user-supplied sources (e.g. rehabilitation costs).
 ## Configuration
 
 To specify a desired network:
+
 - Review and amend the spreadsheets in `bundled_data/transport`, these supply
   information that is used to gap-fill or extend what can be determined from OSM alone.
 - Review and amend `config/config.yaml`:
-    - The `infrastructure_datasets` map should contain a key pointing to an `.osm.pbf`
-      file URL for desired area. There are currently entries for the planet,
-      for (some definition of) continents and several countries. We use
-      the [geofabrik](http://download.geofabrik.de/) service for continent and
-      country-level OSM extracts.
-    - Check the OSM filter file pointed to by `network_filters.rail`.
-      This file specifies which [elements](https://wiki.openstreetmap.org/wiki/Elements)
-      (nodes, ways or relations) to keep (or reject) from the multitude of data
-      in an OSM file. See the filter expressions section
-      [here](https://docs.osmcode.org/osmium/latest/osmium-tags-filter.html)
-      for more information on the syntax of these files.
-    - Check and amend `keep_tags.rail`. This list of strings specifies which
-      `tags` (attributes) to retain on the filtered elements we extract from
-      the `.osm.pbf` file.
-    - Review `slice_count`. This controls the degree of parallelism possible.
-      With it set to 1, there is no spatial slicing (we create the network in
-      a single chunk). To speed network creation for large domains, it can be
-      set to a larger square number. The first square number greater than your
-      number of available CPUs is a good heuristic.
+  - The `infrastructure_datasets` map should contain a key pointing to an `.osm.pbf`
+    file URL for desired area. There are currently entries for the planet,
+    for (some definition of) continents and several countries. We use
+    the [geofabrik](http://download.geofabrik.de/) service for continent and
+    country-level OSM extracts.
+  - Check the OSM filter file pointed to by `network_filters.rail`.
+    This file specifies which [elements](https://wiki.openstreetmap.org/wiki/Elements)
+    (nodes, ways or relations) to keep (or reject) from the multitude of data
+    in an OSM file. See the filter expressions section
+    [here](https://docs.osmcode.org/osmium/latest/osmium-tags-filter.html)
+    for more information on the syntax of these files.
+  - Check and amend `keep_tags.rail`. This list of strings specifies which
+    `tags` (attributes) to retain on the filtered elements we extract from
+    the `.osm.pbf` file.
+  - Review `slice_count`. This controls the degree of parallelism possible.
+    With it set to 1, there is no spatial slicing (we create the network in
+    a single chunk). To speed network creation for large domains, it can be
+    set to a larger square number. The first square number greater than your
+    number of available CPUs is a good heuristic.
 
 ## Creation
 
 And to create the network, by way of example:
+
 ```bash
 snakemake --cores all -- results/egypt-latest_filter-rail/edges.gpq
 ```

docs/src/user-guide/usage/network-creation/road.md

@@ -20,32 +20,34 @@ sources (e.g. rehabilitation costs).
 ## Configuration
 
 To specify a desired network:
+
 - Review and amend the spreadsheets in `bundled_data/transport`, these supply
   information that is used to gap-fill or extend what can be determined from OSM alone.
 - Review and amend `config/config.yaml`:
-    - The `infrastructure_datasets` map should contain a key pointing to an `.osm.pbf`
-      file URL for desired area. There are currently entries for the planet,
-      for (some definition of) continents and several countries. We use
-      the [geofabrik](http://download.geofabrik.de/) service for continent and
-      country-level OSM extracts.
-    - Check the OSM filter file pointed to by `network_filters.road`.
-      This file specifies which [elements](https://wiki.openstreetmap.org/wiki/Elements)
-      (nodes, ways or relations) to keep (or reject) from the multitude of data
-      in an OSM file. See the filter expressions section
-      [here](https://docs.osmcode.org/osmium/latest/osmium-tags-filter.html)
-      for more information on the syntax of these files.
-    - Check and amend `keep_tags.road`. This list of strings specifies which
-      `tags` (attributes) to retain on the filtered elements we extract from
-      the `.osm.pbf` file.
-    - Review `slice_count`. This controls the degree of parallelism possible.
-      With it set to 1, there is no spatial slicing (we create the network in
-      a single chunk). To speed network creation for large domains, it can be
-      set to a larger square number. The first square number greater than your
-      number of available CPUs is a good heuristic.
+  - The `infrastructure_datasets` map should contain a key pointing to an `.osm.pbf`
+    file URL for desired area. There are currently entries for the planet,
+    for (some definition of) continents and several countries. We use
+    the [geofabrik](http://download.geofabrik.de/) service for continent and
+    country-level OSM extracts.
+  - Check the OSM filter file pointed to by `network_filters.road`.
+    This file specifies which [elements](https://wiki.openstreetmap.org/wiki/Elements)
+    (nodes, ways or relations) to keep (or reject) from the multitude of data
+    in an OSM file. See the filter expressions section
+    [here](https://docs.osmcode.org/osmium/latest/osmium-tags-filter.html)
+    for more information on the syntax of these files.
+  - Check and amend `keep_tags.road`. This list of strings specifies which
+    `tags` (attributes) to retain on the filtered elements we extract from
+    the `.osm.pbf` file.
+  - Review `slice_count`. This controls the degree of parallelism possible.
+    With it set to 1, there is no spatial slicing (we create the network in
+    a single chunk). To speed network creation for large domains, it can be
+    set to a larger square number. The first square number greater than your
+    number of available CPUs is a good heuristic.
 
 ## Creation
 
 And to create the network, by way of example:
+
 ```bash
 snakemake --cores all -- results/egypt-latest_filter-road-primary/edges.gpq
 ```

docs/src/user-guide/usage/utilities.md

@@ -5,6 +5,7 @@
 ## Removing intermediate files
 
 You can remove intermediate files by running the `clean` rule.
+
 ```bash
 snakemake --cores 1 -R clean
 ```
@@ -26,6 +27,7 @@ This will write `.gpkg` files beside their source `.geoparquet`.
 
 `matplotlib` plots can be interactive (zoom, pan, etc.), but not as static
 images. Some rules produce pickled plot files. To view these, use:
+
 ```
 python workflow/scripts/unpickle_plot.py <path_to_pickled_plot>
 ```
@@ -34,11 +36,12 @@ python workflow/scripts/unpickle_plot.py <path_to_pickled_plot>
 
 The bash script `archive_results.sh` can be used to back up analysis results.
 Here's an example usage:
+
 ```bash
 ./archive_results.sh results/ /mnt/backup/open-gira
 ```
 
 This will create a timestamped folder in path of the second argument, e.g.
 `/mnt/backup/open-gira/2023-07-24T101756+0100`, containing an archive of results
 (excluding input files downloaded from the internet) and a README describing the
-state of the repository at the time of archive creation.
+state of the repository at the time of archive creation.