diff --git a/.github/workflows/check-version.yml b/.github/workflows/check-version.yml
index dace69c..7bde778 100644
--- a/.github/workflows/check-version.yml
+++ b/.github/workflows/check-version.yml
@@ -1,7 +1,7 @@
# Check for changes in the upstream template. If changes are found, an issue is created
name: Template check.
on:
- workflow_dispatch:
+ workflow_dispatch:
schedule:
- cron: '0 0 1 * *' # Runs at 00:00 UTC on the 1st day of every month
diff --git a/.github/workflows/pr-ci.yml b/.github/workflows/pr-ci.yml
index 8360155..0e17ea4 100644
--- a/.github/workflows/pr-ci.yml
+++ b/.github/workflows/pr-ci.yml
@@ -33,7 +33,7 @@ jobs:
uses: actions/upload-artifact@v4
with:
name: integration-test-logs-${{ matrix.os }}
- path: tests/integration/resources/geo_boundaries/logs
+ path: tests/integration/resources/module/logs
if-no-files-found: ignore
retention-days: 30
- name: Fail if integration or linting failed
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index de68f35..45bc880 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -12,7 +12,7 @@ repos:
# Repo quality
- id: check-added-large-files
args: [--enforce-all]
- exclude: ^pixi\.lock$
+ exclude: ^(?:pixi\.lock|figures/architecture\.drawio\.png)$
- id: forbid-submodules
- id: check-case-conflict
- id: check-illegal-windows-names
diff --git a/README.md b/README.md
index 832f249..96c2c40 100644
--- a/README.md
+++ b/README.md
@@ -22,15 +22,15 @@ and the `snakemake` [documentation](https://snakemake.readthedocs.io/en/stable/s
Data processing steps:
- 
+ 
1. The configuration file is read to identify the datasets to use as well as the specific countries and regional aggregation (`subtype` in the configuration) to process.
- - Country area data: [GADM](https://gadm.org/), [Overture Maps](https://overturemaps.org/) and [NUTS](https://ec.europa.eu/eurostat/web/gisco/geodata/statistical-units/territorial-units-statistics) divisions are supported.
- - Exclusive Economic Zone (EEZ) data: [Marine regions](https://www.marineregions.org/).
+ - Country landmass data: [eurostat NUTS](https://ec.europa.eu/eurostat/web/gisco/geodata/statistical-units/territorial-units-statistics), [GADM](https://gadm.org/), [geoBoundaries](https://www.geoboundaries.org/), and [Overture Maps](https://overturemaps.org/) are supported.
+ - Exclusive Economic Zone (EEZ) data: [MarineRegions.org](https://www.marineregions.org/).
2. Individual country files are downloaded and harmonised to fit a standardised schema.
- - Contested regions are removed at this stage.
+ - If identified, contested regions are removed at this stage.
- Land is clipped using maritime Exclusive Economic Zones (EEZ).
- Optionally, a Voronoi algorithm is run to separate EEZ areas to fit subnational regions.
3. Each country file is combined and then clipped using its neighbours to minimise overlapping polygons.
@@ -40,7 +40,7 @@ Data processing steps:
> Use the references at the bottom of this page for more details.
> [!CAUTION]
-> To increase the replicability of your workflow, we recommend using NUTS and GADM as sources whenever possible as they are more stable than Overture Maps.
+> To increase the replicability of your workflow, we recommend using NUTS and geoBoundaries as sources whenever possible as they have more stable hosting methods than Overture Maps and GADM.
## Configuration
@@ -86,11 +86,15 @@ snakemake --use-conda --cores 2 # run the workflow!
This module is based on the following research and datasets.
We encourage users to cite both the original source and our workflow.
+- eurostat NUTS (various years). Nomenclature of territorial units for statistics (NUTS).
+ - License: reuse is authorised provided the source is acknowledged.
- GADM 4.1. (2018). Global Administrative Areas (GADM).
- License: GADM data is freely available for academic and non-commercial use. .
-- NUTS (various years). Nomenclature of territorial units for statistics (NUTS).
- - License: reuse is authorised provided the source is acknowledged.
-- Overture Maps Divisions database (most recent version). Overture Maps Foundation.
- - License: ODbL. See and for details.
+- geoBoundaries (most recent version). William & Mary geoLab.
+ - License: varies per dataset type (from CC-BY 4.0 compliant to non-commercial use only).
+ Consult their documentation for details.
+ .
- Marine Regions World EEZ v12 (2023). Flanders Marine Institute (MarineRegions.org).
- License: CC-By. See .
+- Overture Maps Divisions database (most recent version). Overture Maps Foundation.
+ - License: ODbL. See and for details.
diff --git a/config/china_example.yaml b/config/china_example.yaml
index 93caee5..fd19204 100644
--- a/config/china_example.yaml
+++ b/config/china_example.yaml
@@ -1,6 +1,5 @@
# Example of regional disaggregation of a large country
# China has contested borders, which will be removed by the module
-overture_release: "latest"
crs:
projected: "epsg:3857"
geographic: "epsg:4326"
diff --git a/config/config.yaml b/config/config.yaml
index 0d67e1d..31116a0 100644
--- a/config/config.yaml
+++ b/config/config.yaml
@@ -1,5 +1,4 @@
# A minimal example of how to configure this module
-overture_release: "latest"
voronoi_eez:
enabled: True
sample_spacing: 10000 # sample every 10 km
@@ -16,11 +15,13 @@ countries:
subtype: "country"
source: "overture"
NLD:
- subtype: "0"
- source: "gadm"
+ subtype: 0
+ source: "geoboundaries"
+ release_type: "gbOpen"
BEL:
- subtype: "country"
- source: "overture"
+ subtype: 1
+ source: "geoboundaries"
+ release_type: "gbOpen"
CHE:
subtype: "country"
source: "overture"
diff --git a/config/europe_example.yaml b/config/europe_example.yaml
index 10ce4d8..bfa1eb5 100644
--- a/config/europe_example.yaml
+++ b/config/europe_example.yaml
@@ -1,5 +1,4 @@
# A minimal example of how to configure this module
-overture_release: "latest"
voronoi_eez:
enabled: True
sample_spacing: 10000
@@ -7,109 +6,152 @@ crs:
projected: "epsg:3035"
geographic: "epsg:4326"
countries:
+ "ALB":
+ subtype: "1"
+ source: "geoboundaries"
+ release_type: "gbOpen"
"AUT":
subtype: "1"
- source: "gadm"
+ source: "geoboundaries"
+ release_type: "gbOpen"
"BEL":
subtype: "1"
- source: "gadm"
+ source: "geoboundaries"
+ release_type: "gbOpen"
"BGR":
subtype: "1"
- source: "gadm"
- "HRV":
+ source: "geoboundaries"
+ release_type: "gbOpen"
+ "BIH":
subtype: "1"
- source: "gadm"
+ source: "geoboundaries"
+ release_type: "gbOpen"
+ "CHE":
+ subtype: "1"
+ source: "geoboundaries"
+ release_type: "gbOpen"
"CYP":
subtype: "1"
- source: "gadm"
+ source: "geoboundaries"
+ release_type: "gbOpen"
"CZE":
subtype: "1"
- source: "gadm"
+ source: "geoboundaries"
+ release_type: "gbOpen"
+ "DEU":
+ subtype: "1"
+ source: "geoboundaries"
+ release_type: "gbOpen"
"DNK":
- subtype: "2"
+ subtype: "1"
source: "nuts"
- resolution: 03M
+ resolution: 01M
year: 2024
+ "ESP":
+ subtype: "1"
+ source: "geoboundaries"
+ release_type: "gbOpen"
+ extra_eez: 8364
"EST":
subtype: "1"
- source: "gadm"
+ source: "geoboundaries"
+ release_type: "gbOpen"
"FIN":
subtype: "1"
- source: "gadm"
+ source: "geoboundaries"
+ release_type: "gbOpen"
"FRA":
subtype: "1"
- source: "gadm"
- "DEU":
- subtype: "1"
- source: "gadm"
+ source: "geoboundaries"
+ release_type: "gbOpen"
+ "GBR":
+ subtype: "region"
+ source: "overture"
+ "GGY":
+ subtype: "0"
+ source: "geoboundaries"
+ release_type: "gbOpen"
"GRC":
subtype: "1"
- source: "gadm"
+ source: "geoboundaries"
+ release_type: "gbOpen"
+ "HRV":
+ subtype: "1"
+ source: "geoboundaries"
+ release_type: "gbOpen"
"HUN":
subtype: "1"
- source: "gadm"
+ source: "geoboundaries"
+ release_type: "gbOpen"
+ "IMN":
+ subtype: "0"
+ source: "geoboundaries"
+ release_type: "gbOpen"
"IRL":
subtype: "region"
source: "overture"
"ITA":
subtype: "1"
- source: "gadm"
- "LVA":
- subtype: "1"
- source: "gadm"
+ source: "geoboundaries"
+ release_type: "gbOpen"
"LTU":
subtype: "1"
- source: "gadm"
+ source: "geoboundaries"
+ release_type: "gbOpen"
"LUX":
subtype: "1"
- source: "gadm"
+ source: "geoboundaries"
+ release_type: "gbOpen"
+ "LVA":
+ subtype: "1"
+ source: "geoboundaries"
+ release_type: "gbOpen"
+ "MKD":
+ subtype: "1"
+ source: "geoboundaries"
+ release_type: "gbOpen"
+ "MNE":
+ subtype: "1"
+ source: "geoboundaries"
+ release_type: "gbOpen"
"NLD":
subtype: "region"
source: "overture"
+ "NOR":
+ subtype: "1"
+ source: "geoboundaries"
+ release_type: "gbOpen"
"POL":
subtype: "1"
- source: "gadm"
+ source: "geoboundaries"
+ release_type: "gbOpen"
"PRT":
- subtype: "2"
+ subtype: "1"
source: "nuts"
- resolution: 03M
+ resolution: 01M
year: 2024
+ extra_eez: [8361, 8363]
"ROU":
subtype: "1"
- source: "gadm"
+ source: "geoboundaries"
+ release_type: "gbOpen"
+ "SRB":
+ subtype: "1"
+ source: "geoboundaries"
+ release_type: "gbOpen"
"SVK":
subtype: "1"
- source: "gadm"
+ source: "geoboundaries"
+ release_type: "gbOpen"
"SVN":
subtype: "1"
- source: "gadm"
- "ESP":
- subtype: "1"
- source: "gadm"
+ source: "geoboundaries"
+ release_type: "gbOpen"
"SWE":
subtype: "1"
- source: "gadm"
- "GBR":
- subtype: "region"
- source: "overture"
- "ALB":
- subtype: "1"
- source: "gadm"
- "BIH":
- subtype: "1"
- source: "gadm"
- "MKD":
- subtype: "1"
- source: "gadm"
- "MNE":
- subtype: "1"
- source: "gadm"
- "NOR":
- subtype: "1"
- source: "gadm"
- "SRB":
- subtype: "1"
- source: "gadm"
- "CHE":
+ source: "geoboundaries"
+ release_type: "gbOpen"
+ "XKX":
subtype: "1"
- source: "gadm"
+ source: "geoboundaries"
+ release_type: "gbOpen"
diff --git a/config/usa_example.yaml b/config/usa_example.yaml
index 1510184..2d7fe8d 100644
--- a/config/usa_example.yaml
+++ b/config/usa_example.yaml
@@ -1,6 +1,5 @@
# Example of regional disaggregation of a large country
# USA has multiple marine zones, which can be appended as extras
-overture_release: "latest"
voronoi_eez:
enabled: True
sample_spacing: 10000 # sample every 10 km
diff --git a/figures/architecture.drawio.png b/figures/architecture.drawio.png
new file mode 100644
index 0000000..2a8b1fa
Binary files /dev/null and b/figures/architecture.drawio.png differ
diff --git a/figures/rulegraph.png b/figures/rulegraph.png
index 98b1249..52a9524 100644
Binary files a/figures/rulegraph.png and b/figures/rulegraph.png differ
diff --git a/figures/shapes.png b/figures/shapes.png
index 892a5d3..de37835 100644
Binary files a/figures/shapes.png and b/figures/shapes.png differ
diff --git a/pixi.lock b/pixi.lock
index 17edf2a..e34830e 100644
--- a/pixi.lock
+++ b/pixi.lock
@@ -1,108 +1,61 @@
-version: 6
+version: 7
+platforms:
+- name: linux-64
+- name: osx-arm64
+- name: win-64
environments:
default:
channels:
- url: https://conda.anaconda.org/conda-forge/
- url: https://conda.anaconda.org/bioconda/
- options:
- pypi-prerelease-mode: if-necessary-or-explicit
packages:
linux-64:
+ - conda: https://conda.anaconda.org/bioconda/noarch/snakefmt-0.11.2-pyha6daafd_0.conda
+ - conda: https://conda.anaconda.org/bioconda/noarch/snakemake-interface-common-1.22.0-pyhd4c3c12_0.conda
+ - conda: https://conda.anaconda.org/bioconda/noarch/snakemake-interface-executor-plugins-9.3.9-pyhdfd78af_0.tar.bz2
+ - conda: https://conda.anaconda.org/bioconda/noarch/snakemake-interface-logger-plugins-2.0.0-pyhd4c3c12_0.conda
+ - conda: https://conda.anaconda.org/bioconda/noarch/snakemake-interface-report-plugins-1.3.0-pyhd4c3c12_0.conda
+ - conda: https://conda.anaconda.org/bioconda/noarch/snakemake-interface-scheduler-plugins-2.0.2-pyhd4c3c12_0.conda
+ - conda: https://conda.anaconda.org/bioconda/noarch/snakemake-interface-storage-plugins-4.3.2-pyhd4c3c12_0.conda
+ - conda: https://conda.anaconda.org/bioconda/noarch/snakemake-minimal-9.19.0-pyhdfd78af_0.conda
- conda: https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2
- conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2
- - conda: https://conda.anaconda.org/conda-forge/noarch/_python_abi3_support-1.0-hd8ed1ab_2.conda
- - conda: https://conda.anaconda.org/conda-forge/noarch/adwaita-icon-theme-49.0-unix_0.conda
- - conda: https://conda.anaconda.org/conda-forge/noarch/amply-0.1.6-pyhd8ed1ab_1.conda
- - conda: https://conda.anaconda.org/conda-forge/noarch/annotated-types-0.7.0-pyhd8ed1ab_1.conda
- - conda: https://conda.anaconda.org/conda-forge/noarch/appdirs-1.4.4-pyhd8ed1ab_1.conda
- - conda: https://conda.anaconda.org/conda-forge/noarch/archspec-0.2.5-pyhd8ed1ab_0.conda
- - conda: https://conda.anaconda.org/conda-forge/noarch/argparse-dataclass-2.0.0-pyhd8ed1ab_1.conda
- - conda: https://conda.anaconda.org/conda-forge/noarch/asttokens-3.0.1-pyhd8ed1ab_0.conda
- conda: https://conda.anaconda.org/conda-forge/linux-64/at-spi2-atk-2.38.0-h0630a04_3.tar.bz2
- conda: https://conda.anaconda.org/conda-forge/linux-64/at-spi2-core-2.40.3-h0630a04_0.tar.bz2
- conda: https://conda.anaconda.org/conda-forge/linux-64/atk-1.0-2.38.0-h04ea711_2.conda
- - conda: https://conda.anaconda.org/conda-forge/noarch/attrs-25.4.0-pyhcf101f3_1.conda
- conda: https://conda.anaconda.org/conda-forge/linux-64/backports.zstd-1.3.0-py312h90b7ffd_0.conda
- conda: https://conda.anaconda.org/conda-forge/linux-64/black-24.10.0-py312h7900ff3_0.conda
- - conda: https://conda.anaconda.org/conda-forge/noarch/boltons-25.0.0-pyhd8ed1ab_0.conda
- conda: https://conda.anaconda.org/conda-forge/linux-64/brotli-python-1.2.0-py312hdb49522_1.conda
- conda: https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_8.conda
- conda: https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.34.6-hb03c661_0.conda
- - conda: https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2026.1.4-hbd8a1cb_0.conda
- conda: https://conda.anaconda.org/conda-forge/linux-64/cairo-1.18.4-he90730b_1.conda
- - conda: https://conda.anaconda.org/conda-forge/noarch/certifi-2026.1.4-pyhd8ed1ab_0.conda
- conda: https://conda.anaconda.org/conda-forge/linux-64/cffi-2.0.0-py312h460c074_1.conda
- - conda: https://conda.anaconda.org/conda-forge/noarch/charset-normalizer-3.4.4-pyhd8ed1ab_0.conda
- - conda: https://conda.anaconda.org/conda-forge/noarch/click-8.3.1-pyh8f84b5b_1.conda
- - conda: https://conda.anaconda.org/conda-forge/noarch/clio-tools-2026.03.30-pyhd8ed1ab_0.conda
- conda: https://conda.anaconda.org/conda-forge/linux-64/coin-or-cbc-2.10.12-h4d16d09_5.conda
- conda: https://conda.anaconda.org/conda-forge/linux-64/coin-or-cgl-0.60.9-hc46dffc_7.conda
- conda: https://conda.anaconda.org/conda-forge/linux-64/coin-or-clp-1.17.10-hc03379b_4.conda
- conda: https://conda.anaconda.org/conda-forge/linux-64/coin-or-osi-0.108.11-hf4fecb4_8.conda
- conda: https://conda.anaconda.org/conda-forge/linux-64/coin-or-utils-2.11.12-hc93afbd_7.conda
- - conda: https://conda.anaconda.org/conda-forge/noarch/colorama-0.4.6-pyhd8ed1ab_1.conda
- - conda: https://conda.anaconda.org/conda-forge/noarch/comm-0.2.3-pyhe01879c_0.conda
- conda: https://conda.anaconda.org/conda-forge/linux-64/conda-25.11.1-py312h7900ff3_0.conda
- - conda: https://conda.anaconda.org/conda-forge/noarch/conda-inject-1.3.2-pyhd8ed1ab_0.conda
- - conda: https://conda.anaconda.org/conda-forge/noarch/conda-libmamba-solver-25.11.0-pyhd8ed1ab_0.conda
- - conda: https://conda.anaconda.org/conda-forge/noarch/conda-package-handling-2.4.0-pyh7900ff3_2.conda
- - conda: https://conda.anaconda.org/conda-forge/noarch/conda-package-streaming-0.12.0-pyhd8ed1ab_0.conda
- - conda: https://conda.anaconda.org/conda-forge/noarch/configargparse-1.7.1-pyhe01879c_0.conda
- - conda: https://conda.anaconda.org/conda-forge/noarch/connection_pool-0.0.3-pyhd3deb0d_0.tar.bz2
- conda: https://conda.anaconda.org/conda-forge/linux-64/cpp-expected-1.3.1-h171cf75_0.conda
- - conda: https://conda.anaconda.org/conda-forge/noarch/cpython-3.12.12-py312hd8ed1ab_1.conda
- conda: https://conda.anaconda.org/conda-forge/linux-64/dbus-1.16.2-h24cb091_1.conda
- conda: https://conda.anaconda.org/conda-forge/linux-64/debugpy-1.8.18-py312h8285ef7_0.conda
- - conda: https://conda.anaconda.org/conda-forge/noarch/decorator-5.2.1-pyhd8ed1ab_0.conda
- - conda: https://conda.anaconda.org/conda-forge/noarch/distro-1.9.0-pyhd8ed1ab_1.conda
- - conda: https://conda.anaconda.org/conda-forge/noarch/docutils-0.22.4-pyhd8ed1ab_0.conda
- - conda: https://conda.anaconda.org/conda-forge/noarch/dpath-2.2.0-pyha770c72_1.conda
- conda: https://conda.anaconda.org/conda-forge/linux-64/epoxy-1.5.10-hb03c661_2.conda
- - conda: https://conda.anaconda.org/conda-forge/noarch/exceptiongroup-1.3.1-pyhd8ed1ab_0.conda
- - conda: https://conda.anaconda.org/conda-forge/noarch/executing-2.2.1-pyhd8ed1ab_0.conda
- conda: https://conda.anaconda.org/conda-forge/linux-64/fmt-12.0.0-h2b0788b_0.conda
- - conda: https://conda.anaconda.org/conda-forge/noarch/font-ttf-dejavu-sans-mono-2.37-hab24e00_0.tar.bz2
- - conda: https://conda.anaconda.org/conda-forge/noarch/font-ttf-inconsolata-3.000-h77eed37_0.tar.bz2
- - conda: https://conda.anaconda.org/conda-forge/noarch/font-ttf-source-code-pro-2.038-h77eed37_0.tar.bz2
- - conda: https://conda.anaconda.org/conda-forge/noarch/font-ttf-ubuntu-0.83-h77eed37_3.conda
- conda: https://conda.anaconda.org/conda-forge/linux-64/fontconfig-2.15.0-h7e30c49_1.conda
- - conda: https://conda.anaconda.org/conda-forge/noarch/fonts-conda-ecosystem-1-0.tar.bz2
- - conda: https://conda.anaconda.org/conda-forge/noarch/fonts-conda-forge-1-hc364b38_1.conda
- conda: https://conda.anaconda.org/conda-forge/linux-64/freetype-2.14.1-ha770c72_0.conda
- conda: https://conda.anaconda.org/conda-forge/linux-64/fribidi-1.0.16-hb03c661_0.conda
- conda: https://conda.anaconda.org/conda-forge/linux-64/frozendict-2.4.7-py312h4c3975b_0.conda
- conda: https://conda.anaconda.org/conda-forge/linux-64/gdk-pixbuf-2.44.4-h2b0a6b4_0.conda
- - conda: https://conda.anaconda.org/conda-forge/noarch/gitdb-4.0.12-pyhd8ed1ab_0.conda
- - conda: https://conda.anaconda.org/conda-forge/noarch/gitpython-3.1.46-pyhd8ed1ab_0.conda
- conda: https://conda.anaconda.org/conda-forge/linux-64/glib-tools-2.86.3-hf516916_0.conda
- conda: https://conda.anaconda.org/conda-forge/linux-64/graphite2-1.3.14-hecca717_2.conda
- conda: https://conda.anaconda.org/conda-forge/linux-64/graphviz-14.1.0-h8b86629_0.conda
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-- conda: https://conda.anaconda.org/conda-forge/linux-64/xorg-libxxf86vm-1.1.6-hb9d3cd8_0.conda
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- license: MIT
- license_family: MIT
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-- conda: https://conda.anaconda.org/conda-forge/linux-64/xorg-xorgproto-2025.1-hb03c661_0.conda
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- license_family: MIT
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-- conda: https://conda.anaconda.org/conda-forge/noarch/xyzservices-2026.3.0-pyhd8ed1ab_0.conda
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- depends:
- - python >=3.9
- license: BSD-3-Clause
- license_family: BSD
- size: 51732
- timestamp: 1774900074457
-- conda: https://conda.anaconda.org/conda-forge/linux-64/yaml-0.2.5-h280c20c_3.conda
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- md5: a77f85f77be52ff59391544bfe73390a
- depends:
- - libgcc >=14
- - __glibc >=2.17,<3.0.a0
- license: MIT
- license_family: MIT
- size: 85189
- timestamp: 1753484064210
-- conda: https://conda.anaconda.org/conda-forge/osx-arm64/yaml-0.2.5-h925e9cb_3.conda
- sha256: b03433b13d89f5567e828ea9f1a7d5c5d697bf374c28a4168d71e9464f5dafac
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- license: MIT
- license_family: MIT
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- timestamp: 1753484079473
- conda: https://conda.anaconda.org/conda-forge/win-64/yaml-0.2.5-h6a83c73_3.conda
sha256: 80ee68c1e7683a35295232ea79bcc87279d31ffeda04a1665efdb43cbd50a309
md5: 433699cba6602098ae8957a323da2664
@@ -13816,28 +14181,6 @@ packages:
license_family: MIT
size: 63944
timestamp: 1753484092156
-- conda: https://conda.anaconda.org/conda-forge/linux-64/yaml-cpp-0.8.0-h3f2d84a_0.conda
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- md5: 92b90f5f7a322e74468bb4909c7354b5
- depends:
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- - libgcc >=13
- - __glibc >=2.17,<3.0.a0
- - libgcc >=13
- license: MIT
- license_family: MIT
- size: 223526
- timestamp: 1745307989800
-- conda: https://conda.anaconda.org/conda-forge/osx-arm64/yaml-cpp-0.8.0-ha1acc90_0.conda
- sha256: 66ba31cfb8014fdd3456f2b3b394df123bbd05d95b75328b7c4131639e299749
- md5: 30475b3d0406587cf90386a283bb3cd0
- depends:
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- - __osx >=11.0
- license: MIT
- license_family: MIT
- size: 136222
- timestamp: 1745308075886
- conda: https://conda.anaconda.org/conda-forge/win-64/yaml-cpp-0.8.0-he0c23c2_0.conda
sha256: 031642d753e0ebd666a76cea399497cc7048ff363edf7d76a630ee0a19e341da
md5: 9bb5064a9fca5ca8e7d7f1ae677354b6
@@ -13852,43 +14195,6 @@ packages:
license_family: MIT
size: 148572
timestamp: 1745308037198
-- conda: https://conda.anaconda.org/conda-forge/noarch/yte-1.9.4-pyhd8ed1ab_0.conda
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- depends:
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- - dpath >=2.1,<3.0
- - python >=3.10
- - pyyaml >=6.0,<7.0
- license: MIT
- license_family: MIT
- size: 16215
- timestamp: 1764250734338
-- conda: https://conda.anaconda.org/conda-forge/linux-64/zeromq-4.3.5-h41580af_10.conda
- sha256: 325d370b28e2b9cc1f765c5b4cdb394c91a5d958fbd15da1a14607a28fee09f6
- md5: 755b096086851e1193f3b10347415d7c
- depends:
- - libgcc >=14
- - __glibc >=2.17,<3.0.a0
- - libstdcxx >=14
- - krb5 >=1.22.2,<1.23.0a0
- - libsodium >=1.0.21,<1.0.22.0a0
- license: MPL-2.0
- license_family: MOZILLA
- size: 311150
- timestamp: 1772476812121
-- conda: https://conda.anaconda.org/conda-forge/osx-arm64/zeromq-4.3.5-h4818236_10.conda
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- md5: e85dcd3bde2b10081cdcaeae15797506
- depends:
- - __osx >=11.0
- - libcxx >=19
- - krb5 >=1.22.2,<1.23.0a0
- - libsodium >=1.0.21,<1.0.22.0a0
- license: MPL-2.0
- license_family: MOZILLA
- size: 245246
- timestamp: 1772476886668
- conda: https://conda.anaconda.org/conda-forge/win-64/zeromq-4.3.5-h507cc87_10.conda
sha256: b8568dfde46edf3455458912ea6ffb760e4456db8230a0cf34ecbc557d3c275f
md5: 1ab0237036bfb14e923d6107473b0021
@@ -13902,36 +14208,6 @@ packages:
license_family: MOZILLA
size: 265665
timestamp: 1772476832995
-- conda: https://conda.anaconda.org/conda-forge/noarch/zipp-3.23.0-pyhcf101f3_1.conda
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- depends:
- - python >=3.10
- - python
- license: MIT
- license_family: MIT
- size: 24194
- timestamp: 1764460141901
-- conda: https://conda.anaconda.org/conda-forge/linux-64/zlib-1.3.2-h25fd6f3_2.conda
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- md5: c2a01a08fc991620a74b32420e97868a
- depends:
- - __glibc >=2.17,<3.0.a0
- - libzlib 1.3.2 h25fd6f3_2
- license: Zlib
- license_family: Other
- size: 95931
- timestamp: 1774072620848
-- conda: https://conda.anaconda.org/conda-forge/osx-arm64/zlib-1.3.2-h8088a28_2.conda
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- md5: f1c0bce276210bed45a04949cfe8dc20
- depends:
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- - libzlib 1.3.2 h8088a28_2
- license: Zlib
- license_family: Other
- size: 81123
- timestamp: 1774072974535
- conda: https://conda.anaconda.org/conda-forge/win-64/zlib-1.3.2-hfd05255_2.conda
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md5: 5187ecf958be3c39110fe691cbd6873e
@@ -13944,27 +14220,6 @@ packages:
license_family: Other
size: 850351
timestamp: 1774072891049
-- conda: https://conda.anaconda.org/conda-forge/linux-64/zlib-ng-2.3.3-hceb46e0_1.conda
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- depends:
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- - libgcc >=14
- - libstdcxx >=14
- license: Zlib
- license_family: Other
- size: 122618
- timestamp: 1770167931827
-- conda: https://conda.anaconda.org/conda-forge/osx-arm64/zlib-ng-2.3.3-hed4e4f5_1.conda
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- depends:
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- - libcxx >=19
- license: Zlib
- license_family: Other
- size: 94375
- timestamp: 1770168363685
- conda: https://conda.anaconda.org/conda-forge/win-64/zlib-ng-2.3.3-h0261ad2_1.conda
sha256: 71332532332d13b5dbe57074ddcf82ae711bdc132affa5a2982a29ffa06dc234
md5: 46a21c0a4e65f1a135251fc7c8663f83
@@ -13976,36 +14231,6 @@ packages:
license_family: Other
size: 124542
timestamp: 1770167984883
-- conda: https://conda.anaconda.org/conda-forge/linux-64/zstandard-0.25.0-py312h5253ce2_1.conda
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- - libgcc >=14
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- - zstd >=1.5.7,<1.6.0a0
- - python_abi 3.12.* *_cp312
- license: BSD-3-Clause
- license_family: BSD
- size: 467133
- timestamp: 1762512686069
-- conda: https://conda.anaconda.org/conda-forge/osx-arm64/zstandard-0.25.0-py313h9734d34_1.conda
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- depends:
- - python
- - cffi >=1.11
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- - __osx >=11.0
- - python 3.13.* *_cp313
- - zstd >=1.5.7,<1.6.0a0
- - python_abi 3.13.* *_cp313
- license: BSD-3-Clause
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- conda: https://conda.anaconda.org/conda-forge/win-64/zstandard-0.25.0-py313h5fd188c_1.conda
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md5: 46f6f9bb324a58a9b081bbc56ade37f2
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license_family: BSD
size: 380854
timestamp: 1762512720226
-- conda: https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.7-hb78ec9c_6.conda
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-- conda: https://conda.anaconda.org/conda-forge/osx-arm64/zstd-1.5.7-hbf9d68e_6.conda
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- conda: https://conda.anaconda.org/conda-forge/win-64/zstd-1.5.7-h534d264_6.conda
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md5: 053b84beec00b71ea8ff7a4f84b55207
diff --git a/pixi.toml b/pixi.toml
index 08725ec..fc18afa 100644
--- a/pixi.toml
+++ b/pixi.toml
@@ -25,8 +25,36 @@ pytz = ">=2026.1.post1"
[tasks]
test-integration = {cmd = "pytest tests/integration_test.py"}
+[tasks.export-conda-spec]
+description = "Export one pixi environment/platform as a conda explicit spec"
+args = ["env", "platform"]
+cmd = "pixi workspace export conda-explicit-spec --environment '{{ env }}' --platform '{{ platform }}' workflow/envs/"
+
+[tasks.rename-conda-spec]
+description = "Rename one pixi conda explicit spec to a Snakemake pin file"
+args = ["env", "platform"]
+cmd = "mv workflow/envs/{{ env }}_{{ platform }}_conda_spec.txt workflow/envs/{{ env }}.{{ platform }}.pin.txt"
+
+[tasks.export-snakemake-pin]
+description = "Export one pixi environment/platform as a Snakemake-compatible conda pin file"
+args = ["env", "platform"]
+depends-on = [
+ { task = "export-conda-spec", args = ["{{ env }}", "{{ platform }}"] },
+ { task = "rename-conda-spec", args = ["{{ env }}", "{{ platform }}"] },
+]
+
+[tasks.export-snakemake-env]
+description = "Export one pixi environment as a Snakemake conda environment"
+args = ["env"]
+depends-on = [
+ { task = "export-snakemake-pin", args = ["{{ env }}", "win-64"] },
+ { task = "export-snakemake-pin", args = ["{{ env }}", "linux-64"] },
+ { task = "export-snakemake-pin", args = ["{{ env }}", "osx-arm64"] },
+]
+cmd = "pixi workspace export conda-environment --environment '{{ env }}' workflow/envs/{{ env }}.yaml"
+
[feature.shape]
-channels = ["conda-forge", "nodefaults"]
+channels = ["conda-forge"]
[feature.shape.dependencies]
boto3 = "1.40.46.*"
@@ -39,6 +67,9 @@ pyarrow = "19.0.1.*"
pycountry = "24.6.1.*"
shapely = "2.1.1.*"
numpy = "2.3.5.*"
+pandas = "3.0.2.*"
+pytz = "2026.2.*"
+requests = "2.33.1.*"
[environments]
shape = { features = ["shape"], no-default-feature = true }
diff --git a/tests/integration/Snakefile b/tests/integration/Snakefile
index 408c8b0..ad71d73 100644
--- a/tests/integration/Snakefile
+++ b/tests/integration/Snakefile
@@ -11,9 +11,9 @@ module module_geo_boundaries:
# Redirect specific module results (outputs)
shapes="results/outputs/shapes.parquet",
# Redirect module intermediate files
- logs="resources/geo_boundaries/logs",
- resources="resources/geo_boundaries/resources",
- results="resources/geo_boundaries/results",
+ logs="resources/module/logs",
+ resources="resources/module/resources",
+ results="resources/module/results",
snakefile:
"../../workflow/Snakefile"
config:
diff --git a/tests/integration/test_config.yaml b/tests/integration/test_config.yaml
index 33cd213..ea3ad94 100644
--- a/tests/integration/test_config.yaml
+++ b/tests/integration/test_config.yaml
@@ -1,12 +1,12 @@
module_geo_boundaries:
- overture_release: "latest"
crs:
projected: "epsg:3857"
geographic: "epsg:4326"
countries:
"MNE":
subtype: "0"
- source: "gadm"
+ source: "geoboundaries"
+ release_type: "gbOpen"
"SVK":
subtype: "country"
source: "overture"
diff --git a/workflow/Snakefile b/workflow/Snakefile
index 2493883..a546796 100644
--- a/workflow/Snakefile
+++ b/workflow/Snakefile
@@ -27,7 +27,8 @@ with open(workflow.source_path("internal/settings.yaml"), "r") as f:
# Add all your includes here.
include: "rules/_utils.smk"
-include: "rules/automatic.smk"
+include: "rules/download.smk"
+include: "rules/harmonise.smk"
include: "rules/build.smk"
diff --git a/workflow/envs/shape.linux-64.pin.txt b/workflow/envs/shape.linux-64.pin.txt
index cf1c159..a434d88 100644
--- a/workflow/envs/shape.linux-64.pin.txt
+++ b/workflow/envs/shape.linux-64.pin.txt
@@ -2,221 +2,218 @@
# platform: linux-64
@EXPLICIT
https://conda.anaconda.org/conda-forge/noarch/tzdata-2025c-hc9c84f9_1.conda#ad659d0a2b3e47e38d829aa8cad2d610
-https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.2.0-he0feb66_16.conda#26c46f90d0e727e95c6c9498a33a09f3
-https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
-https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
-https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.2.0-he0feb66_16.conda#6d0363467e6ed84f11435eb309f2ff06
-https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8
-https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_ha0e22de_103.conda#86bc20552bf46075e3d92b67f089172d
-https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7
+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.2-h25fd6f3_2.conda#d87ff7921124eccd67248aa483c23fec
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.2.0-he0feb66_19.conda#faac990cb7aedc7f3a2224f2c9b0c26c
+https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-20_gnu.conda#a9f577daf3de00bca7c3c76c0ecbd1de
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.2.0-he0feb66_19.conda#57736f29cc2b0ec0b6c2952d3f101b6a
+https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_h366c992_103.conda#cffd3bdd58090148f4cfcd831f4b26ab
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.6-hdb14827_0.conda#fc21868a1a5aacc937e7a18747acb8a5
https://conda.anaconda.org/conda-forge/linux-64/readline-8.3-h853b02a_0.conda#d7d95fc8287ea7bf33e0e7116d2b95ec
-https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2026.1.4-hbd8a1cb_0.conda#bddacf101bb4dd0e51811cb69c7790e2
-https://conda.anaconda.org/conda-forge/linux-64/openssl-3.6.0-h26f9b46_0.conda#9ee58d5c534af06558933af3c845a780
-https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.2.0-h69a702a_16.conda#5a68259fac2da8f2ee6f7bfe49c9eb8b
+https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2026.4.22-hbd8a1cb_0.conda#e18ad67cf881dcadee8b8d9e2f8e5f73
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.6.2-h35e630c_0.conda#da1b85b6a87e141f5140bb9924cecab0
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.2.0-h69a702a_19.conda#331ee9b72b9dff570d56b1302c5ab37d
https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc
-https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.41.3-h5347b49_0.conda#db409b7c1720428638e7c0d509d3e1b5
-https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-15.2.0-h934c35e_16.conda#68f68355000ec3f1d6f26ea13e8f525f
-https://conda.anaconda.org/conda-forge/linux-64/icu-78.1-h33c6efd_0.conda#518e9bbbc3e3486d6a4519192ba690f8
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+https://conda.anaconda.org/conda-forge/linux-64/contourpy-1.3.3-py312h0a2e395_4.conda#43c2bc96af3ae5ed9e8a10ded942aa50
+https://conda.anaconda.org/conda-forge/linux-64/matplotlib-base-3.10.9-py312he3d6523_0.conda#7d499b5b6d150f133800dc3a582771c7
+https://conda.anaconda.org/conda-forge/linux-64/scipy-1.17.1-py312h54fa4ab_0.conda#3e38daeb1fb05a95656ff5af089d2e4c
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@@ -227,40 +224,27 @@ https://conda.anaconda.org/conda-forge/noarch/branca-0.8.2-pyhd8ed1ab_0.conda#1f
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diff --git a/workflow/envs/shape.osx-arm64.pin.txt b/workflow/envs/shape.osx-arm64.pin.txt
index 70b67e7..eff4525 100644
--- a/workflow/envs/shape.osx-arm64.pin.txt
+++ b/workflow/envs/shape.osx-arm64.pin.txt
@@ -2,215 +2,213 @@
# platform: osx-arm64
@EXPLICIT
https://conda.anaconda.org/conda-forge/noarch/tzdata-2025c-hc9c84f9_1.conda#ad659d0a2b3e47e38d829aa8cad2d610
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-https://conda.anaconda.org/conda-forge/osx-arm64/ncurses-6.5-h5e97a16_3.conda#068d497125e4bf8a66bf707254fff5ae
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https://conda.anaconda.org/conda-forge/win-64/python-duckdb-1.2.0-py313h5813708_0.conda#b3c2cbd55b1c0a3dd723d08bbdebba06
https://conda.anaconda.org/conda-forge/noarch/duckdb-1.2.0-h6c4a22f_0.conda#106a9ca2e65f476ff2499ba74c9e1db0
-https://conda.anaconda.org/conda-forge/noarch/jmespath-1.0.1-pyhd8ed1ab_1.conda#972bdca8f30147135f951847b30399ea
+https://conda.anaconda.org/conda-forge/noarch/jmespath-1.1.0-pyhcf101f3_1.conda#cc73a9bd315659dc5307a5270f44786f
https://conda.anaconda.org/conda-forge/noarch/botocore-1.40.76-pyhd8ed1ab_0.conda#4babebd5361bc44503358a519a81a465
https://conda.anaconda.org/conda-forge/noarch/s3transfer-0.14.0-pyhd8ed1ab_0.conda#4e3089ce93822a25408c480dd53561b6
https://conda.anaconda.org/conda-forge/noarch/boto3-1.40.46-pyhd8ed1ab_0.conda#a93057bba32eef7b217733734642bfea
diff --git a/workflow/envs/shape.yaml b/workflow/envs/shape.yaml
index 555e7e8..9857891 100644
--- a/workflow/envs/shape.yaml
+++ b/workflow/envs/shape.yaml
@@ -1,15 +1,18 @@
name: shape
channels:
- - conda-forge
- - nodefaults
+- conda-forge
+- nodefaults
dependencies:
- - boto3 = 1.40.46
- - duckdb = 1.2.0
- - geopandas = 1.0.1
- - ipdb = 0.13.13
- - pandera-geopandas = 0.24
- - pandera-io = 0.24
- - pyarrow = 19.0.1
- - pycountry = 24.6.1
- - shapely = 2.1.1
- - numpy = 2.3.5
+- boto3 1.40.46.*
+- duckdb 1.2.0.*
+- geopandas 1.0.1.*
+- ipdb 0.13.13.*
+- pandera-geopandas 0.24.*
+- pandera-io 0.24.*
+- pyarrow 19.0.1.*
+- pycountry 24.6.1.*
+- shapely 2.1.1.*
+- numpy 2.3.5.*
+- pandas 3.0.2.*
+- pytz 2026.2.*
+- requests 2.33.1.*
diff --git a/workflow/internal/config.schema.yaml b/workflow/internal/config.schema.yaml
index c317e60..07d49f8 100644
--- a/workflow/internal/config.schema.yaml
+++ b/workflow/internal/config.schema.yaml
@@ -1,13 +1,113 @@
$schema: "https://json-schema.org/draft/2020-12/schema"
$defs:
- epsgCode:
+ crsCode:
anyOf:
+ # Compact authority:code, e.g. EPSG:4326, OGC:CRS84, ESRI:102003
- type: string
- pattern: '^(?:[eE][pP][sS][gG]):\d{4,5}$'
+ pattern: "^[A-Za-z][A-Za-z0-9_-]*:[A-Za-z0-9_.-]+$"
+ # Optional legacy shorthand for numeric codes
- type: integer
- minimum: 1000
- maximum: 99999
+ minimum: 1
+
+ countryBase:
+ type: object
+ properties:
+ subtype:
+ description: >
+ "Regional aggregation to download. Varies per dataset."
+ anyOf:
+ - type: integer
+ - type: string
+ source:
+ description: |
+ Dataset to use as source.
+ type: string
+ enum: ["overture", "gadm", "nuts", "geoboundaries"]
+ extra_eez:
+ description: >
+ Optional. Additional EEZ zones to append to this country.
+ default: []
+ anyOf:
+ - type: integer
+ - type: array
+ items:
+ type: integer
+ required:
+ - subtype
+ - source
+
+ countryOverture:
+ type: object
+ properties:
+ source:
+ const: "overture"
+
+ countryGadm:
+ type: object
+ properties:
+ source:
+ const: "gadm"
+ subtype:
+ description: "GADM administrative level."
+ anyOf:
+ - type: integer
+ enum: [0, 1, 2, 3, 4]
+ - type: string
+ enum: ["0", "1", "2", "3", "4"]
+
+ countryNuts:
+ type: object
+ properties:
+ source:
+ const: "nuts"
+ subtype:
+ description: "NUTS administrative level."
+ anyOf:
+ - type: integer
+ enum: [0, 1, 2, 3]
+ - type: string
+ enum: ["0", "1", "2", "3"]
+ resolution:
+ description: "Resolution for NUTS source."
+ type: string
+ pattern: "^[0-9]{2}M$"
+ year:
+ description: "Year for NUTS source."
+ type: integer
+ required:
+ - resolution
+ - year
+
+ countryGeoboundaries:
+ type: object
+ properties:
+ source:
+ const: "geoboundaries"
+ subtype:
+ description: "geoBoundaries administrative level."
+ anyOf:
+ - type: integer
+ enum: [0, 1, 2, 3, 4, 5]
+ - type: string
+ enum: ["0", "1", "2", "3", "4", "5"]
+ release_type:
+ description: "geoBoundaries release type (each with different licensing)."
+ type: string
+ enum: ["gbOpen", "gbHumanitarian", "gbAuthoritative"]
+ required:
+ - release_type
+
+ country:
+ type: object
+ allOf:
+ - $ref: "#/$defs/countryBase"
+ - oneOf:
+ - $ref: "#/$defs/countryOverture"
+ - $ref: "#/$defs/countryGadm"
+ - $ref: "#/$defs/countryNuts"
+ - $ref: "#/$defs/countryGeoboundaries"
+ unevaluatedProperties: false
description: "Schema for user-provided configuration files."
type: object
@@ -19,75 +119,34 @@ properties:
projected:
description: "Projected CRS code (for area and length calculation)."
allOf:
- - $ref: '#/$defs/epsgCode'
+ - $ref: "#/$defs/crsCode"
geographic:
description: "Geographic CRS code (for latitude / longitude positioning)."
allOf:
- - $ref: '#/$defs/epsgCode'
+ - $ref: "#/$defs/crsCode"
required:
- projected
- geographic
- additionalProperties: False
+ additionalProperties: false
+
countries:
description: >
Dictionary of countries with each country code as the key.
Country code must be in ISO alpha-3 format (e.g., MEX, CHN, DEU).
type: object
patternProperties:
- "^[A-Z]{3}$": # Keys must be exactly three uppercase letters
- type: object
- properties:
- subtype:
- description: >
- "Regional aggregation to gather (e.g., '0', '1', or '2' for GADM). Names vary per dataset."
- type: string
- source:
- description: |
- Dataset to use as source.
- type: string
- enum: ["overture", "gadm", "nuts"]
- resolution:
- description: "Resolution for NUTS source (required if source is 'nuts')."
- type: string
- pattern: "^[0-9]{2}M$"
- year:
- description: "Year for NUTS source (required if source is 'nuts')."
- type: integer
- extra_eez:
- description: >
- Optional. Additional EEZ zones to append to this country.
- default: []
- anyOf:
- - type: integer
- - type: array
- items:
- type: integer
- required:
- - subtype
- - source
- additionalProperties: false
- allOf:
- - if:
- properties:
- source:
- enum: ["nuts"]
- then:
- required:
- - resolution
- - year
- - else:
- not:
- required:
- - resolution
- - year
+ "^[A-Z]{3}$": # Keys must be exactly three uppercase letters
+ $ref: "#/$defs/country"
minProperties: 1
additionalProperties: false
+
overture_release:
description: |
Overture data release to use. Two options are possible:
- A specific release string in the form of 'yyyy-mm-dd.x'.
- A request for the latest release in the form of 'latest'.
type: string
+ default: "latest"
pattern: "^(?:latest|(?:\\d{4})-(?:0[1-9]|1[0-2])-(?:0[1-9]|[12]\\d|3[01])\\.\\d+)$"
voronoi_eez:
description: >
@@ -103,12 +162,51 @@ properties:
default: false
sample_spacing:
description: >
- Distance between sample points for shorelines.
- Higher for finer splits at the cost of slower processing.
+ Maximum distance between sample points for shorelines.
+ Lower for finer splits at the cost of slower processing.
Matches the unit of the projected CRS.
type: integer
default: 10000
minimum: 1
+ min_samples_per_shoreline:
+ description: >
+ Minimum number of sampled points per touching shoreline component.
+ This helps small islands influence the split even when their coastlines
+ are shorter than `sample_spacing`.
+ type: integer
+ default: 8
+ minimum: 1
+ max_samples_per_maritime:
+ description: >
+ Approximate cap for sampled shoreline points per maritime shape.
+ If exceeded, the algorithm raises the effective sample spacing and
+ skips raw shoreline vertices to keep processing bounded.
+ type: integer
+ default: 50000
+ minimum: 1
+ include_shoreline_vertices:
+ description: >
+ Include existing shoreline vertices as Voronoi generators in addition
+ to adaptive midpoint samples.
+ type: boolean
+ default: true
+ shoreline_search_radius:
+ description: >
+ Distance around maritime polygons used to find the marine-facing
+ country exterior boundary. This handles land and EEZ datasets whose
+ coastlines do not exactly coincide. Matches the unit of the projected
+ CRS.
+ type: integer
+ default: 10000
+ minimum: 0
+ uncovered_area_tolerance:
+ description: >
+ Maximum area loss permitted per EEZ polygon after splitting. An error
+ will be raised if exceeded. Matches the unit of the projected CRS.
+ type: number
+ default: 1
+ minimum: 0
+
required:
- countries
- crs
diff --git a/workflow/internal/settings.yaml b/workflow/internal/settings.yaml
index 44f62ef..2315670 100644
--- a/workflow/internal/settings.yaml
+++ b/workflow/internal/settings.yaml
@@ -1,6 +1,15 @@
# Module settings that users cannot modify.
-nuts:
- epsg: 3035 # will be converted later to the user-requested epsg
voronoi_eez: # defaults for Voronoi EEZ splitting
enabled: false
sample_spacing: 10000
+ min_samples_per_shoreline: 8
+ max_samples_per_maritime: 50000
+ include_shoreline_vertices: true
+ shoreline_search_radius: 10000
+ uncovered_area_tolerance: 1
+timeouts:
+ max_retries: 3
+ connect_seconds: 15
+ read_seconds: 30
+ initial_retry_seconds: 5
+overture_release: "latest"
diff --git a/workflow/report/build_combined_area.rst b/workflow/report/build_combined_area.rst
index 42fa9c4..bcbf5bf 100644
--- a/workflow/report/build_combined_area.rst
+++ b/workflow/report/build_combined_area.rst
@@ -1,2 +1,5 @@
-This module creates a dataset with polygonal data of country boundaries and marine exclusive economic zones (EEZ).
-Several datasources are possible: `GADM `_, `Overture Maps `_ or `NUTS `_.
+Resulting polygonal data of country boundaries and marine exclusive economic zones (EEZ).
+
+Countries: {{ snakemake.params.countries }}
+
+Source datasets: {{ snakemake.params.sources }}
diff --git a/workflow/report/build_country.rst b/workflow/report/build_country.rst
index 6fbf999..c1b0e33 100644
--- a/workflow/report/build_country.rst
+++ b/workflow/report/build_country.rst
@@ -1,3 +1,4 @@
Built combined file for {{ snakemake.wildcards.country }}.
-- Contested EEZ regions are removed.
-- Optionally, EEZ regions are broken down using a Voronoi algorithm.
+
+* If present, contested EEZ regions are removed.
+* Optionally, EEZ regions are broken down using a Voronoi algorithm.
diff --git a/workflow/report/download_harmonised_eez.rst b/workflow/report/download_harmonised_eez.rst
new file mode 100644
index 0000000..2a70269
--- /dev/null
+++ b/workflow/report/download_harmonised_eez.rst
@@ -0,0 +1,3 @@
+Downloaded and harmonised EEZ for {{ snakemake.wildcards.country }}.
+
+Source: Flanders Marine Institute: MarineRegions.org. Available online at `www.marineregions.org `_.
diff --git a/workflow/rules/_utils.smk b/workflow/rules/_utils.smk
index 417517d..e951c1b 100644
--- a/workflow/rules/_utils.smk
+++ b/workflow/rules/_utils.smk
@@ -1,15 +1,18 @@
"""Utility functions for snakemake rule handling."""
-def get_country_filename(country: str):
+def get_country_file(country: str):
"""Build unique file names to avoid overwriting source files."""
source = config["countries"][country]["source"]
subtype = config["countries"][country]["subtype"]
- filename = f"{source}_{country}_{subtype}"
+ filename = f"{source}/harmonise/{country}_{subtype}"
if source == "nuts":
resolution = config["countries"][country]["resolution"]
year = config["countries"][country]["year"]
-
filename += f"_{year}_{resolution}"
+ elif source == "geoboundaries":
+ release = config["countries"][country]["release_type"]
+ filename += f"_{release}"
+
return filename
diff --git a/workflow/rules/automatic.smk b/workflow/rules/automatic.smk
deleted file mode 100644
index eebf8ac..0000000
--- a/workflow/rules/automatic.smk
+++ /dev/null
@@ -1,96 +0,0 @@
-"""Rules to used to download resource files.
-
-Small transformations might be performed to make the data easier to work with.
-"""
-
-
-rule download_country_overture:
- output:
- path="/automatic/land/overture_{country}_{subtype}.parquet",
- log:
- "/{country}/download_country_overture_{subtype}.log",
- conda:
- "../envs/shape.yaml"
- params:
- version=config["overture_release"],
- message:
- "Download '{wildcards.country}_{wildcards.subtype}' dataset from Overture Maps."
- script:
- "../scripts/download_country_overture.py"
-
-
-rule download_country_gadm:
- output:
- path=temp("/automatic/land/raw_gadm_{country}_{subtype}.parquet"),
- log:
- "/{country}/download_country_gadm_{subtype}.log",
- conda:
- "../envs/shape.yaml"
- message:
- "Download '{wildcards.country}_{wildcards.subtype}' dataset from GADM."
- script:
- "../scripts/download_country_gadm.py"
-
-
-rule standardise_country_gadm:
- input:
- raw=rules.download_country_gadm.output.path,
- output:
- standardised="/automatic/land/gadm_{country}_{subtype}.parquet",
- log:
- "/{country}/standardise_country_gadm_{subtype}.log",
- conda:
- "../envs/shape.yaml"
- params:
- country_id=lambda wc: str(wc.country),
- subtype=lambda wc: str(wc.subtype),
- message:
- "Standardise '{wildcards.country}_{wildcards.subtype}' GADM dataset."
- script:
- "../scripts/standardise_country_gadm.py"
-
-
-rule download_nuts:
- output:
- path="/automatic/nuts/nuts_{subtype}_{resolution}_{year}.parquet",
- log:
- "/download_nuts_{subtype}_{resolution}_{year}.log",
- conda:
- "../envs/shape.yaml"
- params:
- epsg=internal["nuts"]["epsg"],
- message:
- "Download '{wildcards.subtype}_{wildcards.resolution}_{wildcards.year}' from NUTS."
- script:
- "../scripts/download_nuts.py"
-
-
-rule standardise_country_nuts:
- input:
- raw=rules.download_nuts.output.path,
- output:
- path="/automatic/land/nuts_{country}_{subtype}_{year}_{resolution}.parquet",
- log:
- "/{country}/standardise_country_nuts_{subtype}_{year}_{resolution}.log",
- conda:
- "../envs/shape.yaml"
- message:
- "Standardise '{wildcards.country}' NUTS dataset for '{wildcards.subtype}_{wildcards.resolution}_{wildcards.year}'."
- script:
- "../scripts/standardise_country_nuts.py"
-
-
-rule download_marine_eez_area:
- output:
- path="/automatic/eez/{country}.parquet",
- plot="/automatic/eez/{country}.png",
- log:
- "/{country}/download_marine_eez_area.log",
- conda:
- "../envs/shape.yaml"
- params:
- extra_eez=lambda wc: config["countries"][wc.country].get("extra_eez", []),
- message:
- "Download and standardise '{wildcards.country}' EEZ dataset."
- script:
- "../scripts/download_marine_eez_area.py"
diff --git a/workflow/rules/build.smk b/workflow/rules/build.smk
index c2b7c55..3fb64f8 100644
--- a/workflow/rules/build.smk
+++ b/workflow/rules/build.smk
@@ -3,7 +3,7 @@
rule build_country:
input:
- land=lambda wc: f"/automatic/land/{get_country_filename(wc.country)}.parquet",
+ land=lambda wc: f"/automatic/{get_country_file(wc.country)}.parquet",
maritime="/automatic/eez/{country}.parquet",
output:
country="/automatic/country/{country}.parquet",
@@ -11,7 +11,7 @@ rule build_country:
"/automatic/country/{country}.png",
caption="../report/build_country.rst",
category="Module Geo-Boundaries",
- subcategory="Combined countries",
+ subcategory="Country area",
),
log:
"/{country}/build_country.log",
@@ -46,6 +46,8 @@ rule build_combined_area:
"../envs/shape.yaml"
params:
crs=config["crs"],
+ countries=sorted([i for i in config["countries"]]),
+ sources=sorted(set([i["source"] for i in config["countries"].values()])),
message:
"Combine land and marine polygons."
script:
diff --git a/workflow/rules/download.smk b/workflow/rules/download.smk
new file mode 100644
index 0000000..171616b
--- /dev/null
+++ b/workflow/rules/download.smk
@@ -0,0 +1,49 @@
+"""Rules to used to download resource files."""
+
+
+rule download_geoboundaries:
+ output:
+ path="/automatic/geoboundaries/download/{country}_{subtype}_{release_type}.parquet",
+ log:
+ "/geoboundaries/download/{country}_{subtype}_{release_type}.log",
+ localrule: True
+ conda:
+ "../envs/shape.yaml"
+ params:
+ timeouts=internal["timeouts"],
+ message:
+ "Downloading '{wildcards.country}_{wildcards.subtype}_{wildcards.release_type}' dataset from geoBoundaries."
+ script:
+ "../scripts/download_geoboundaries.py"
+
+
+rule download_gadm:
+ output:
+ path="/automatic/gadm/download/{country}_{subtype}.parquet",
+ log:
+ "/gadm/download/{country}_{subtype}.log",
+ localrule: True
+ conda:
+ "../envs/shape.yaml"
+ params:
+ timeouts=internal["timeouts"],
+ message:
+ "Download '{wildcards.country}_{wildcards.subtype}' dataset from GADM."
+ script:
+ "../scripts/download_gadm.py"
+
+
+rule download_nuts:
+ output:
+ path="/automatic/nuts/download/{subtype}_{resolution}_{year}.parquet",
+ log:
+ "/nuts/download/{subtype}_{resolution}_{year}.log",
+ localrule: True
+ conda:
+ "../envs/shape.yaml"
+ params:
+ timeouts=internal["timeouts"],
+ message:
+ "Download '{wildcards.subtype}_{wildcards.resolution}_{wildcards.year}' from NUTS."
+ script:
+ "../scripts/download_nuts.py"
diff --git a/workflow/rules/harmonise.smk b/workflow/rules/harmonise.smk
new file mode 100644
index 0000000..2723a1a
--- /dev/null
+++ b/workflow/rules/harmonise.smk
@@ -0,0 +1,88 @@
+"""Rules to used to harmonise country files."""
+
+
+rule harmonise_geoboundaries:
+ input:
+ raw=rules.download_geoboundaries.output.path,
+ output:
+ path="/automatic/geoboundaries/harmonise/{country}_{subtype}_{release_type}.parquet",
+ log:
+ "/geoboundaries/harmonise/{country}_{subtype}_{release_type}.log",
+ conda:
+ "../envs/shape.yaml"
+ message:
+ "Harmonising '{wildcards.country}_{wildcards.subtype}_{wildcards.release_type}' dataset from geoBoundaries."
+ script:
+ "../scripts/harmonise_geoboundaries.py"
+
+
+rule download_harmonised_overture:
+ output:
+ path="/automatic/overture/harmonise/{country}_{subtype}.parquet",
+ log:
+ "/overture/download_and_harmonise/{country}_{subtype}.log",
+ localrule: True
+ conda:
+ "../envs/shape.yaml"
+ params:
+ version=config.get("overture_release", internal["overture_release"]),
+ message:
+ "Downloading harmonised '{wildcards.country}_{wildcards.subtype}' dataset from Overture Maps."
+ script:
+ "../scripts/download_harmonised_overture.py"
+
+
+rule harmonise_gadm:
+ input:
+ raw=rules.download_gadm.output.path,
+ output:
+ standardised="/automatic/gadm/harmonise/{country}_{subtype}.parquet",
+ log:
+ "/gadm/harmonise/{country}_{subtype}.log",
+ conda:
+ "../envs/shape.yaml"
+ params:
+ country_id=lambda wc: str(wc.country),
+ subtype=lambda wc: str(wc.subtype),
+ message:
+ "Harmonising '{wildcards.country}_{wildcards.subtype}' GADM dataset."
+ script:
+ "../scripts/harmonise_gadm.py"
+
+
+rule harmonise_nuts:
+ input:
+ raw=rules.download_nuts.output.path,
+ output:
+ path="/automatic/nuts/harmonise/{country}_{subtype}_{year}_{resolution}.parquet",
+ log:
+ "/nuts/harmonise/{country}_{subtype}_{year}_{resolution}.log",
+ conda:
+ "../envs/shape.yaml"
+ message:
+ "Harmonising '{wildcards.country}' NUTS dataset for '{wildcards.subtype}_{wildcards.resolution}_{wildcards.year}'."
+ script:
+ "../scripts/harmonise_nuts.py"
+
+
+rule download_harmonised_eez:
+ output:
+ path="/automatic/eez/{country}.parquet",
+ plot=report(
+ "/automatic/eez/{country}.png",
+ caption="../report/download_harmonised_eez.rst",
+ category="Module Geo-Boundaries",
+ subcategory="EEZ area",
+ ),
+ log:
+ "/eez/download_harmonised/{country}.log",
+ localrule: True
+ conda:
+ "../envs/shape.yaml"
+ params:
+ extra_eez=lambda wc: config["countries"][wc.country].get("extra_eez", []),
+ timeouts=internal["timeouts"],
+ message:
+ "Download and harmonise '{wildcards.country}' EEZ dataset."
+ script:
+ "../scripts/download_harmonised_eez.py"
diff --git a/workflow/scripts/_schemas.py b/workflow/scripts/_schemas.py
index 38b69b6..af705f5 100644
--- a/workflow/scripts/_schemas.py
+++ b/workflow/scripts/_schemas.py
@@ -3,6 +3,8 @@
from pandera.typing.pandas import Series
from shapely.validation import make_valid
+SUPPORTED_DATASETS = ["gadm", "overture", "marineregions", "nuts", "geoboundaries"]
+
class ShapesSchema(pa.DataFrameModel):
"""Schema for geographic shapes."""
@@ -19,7 +21,7 @@ class Config:
"Identifier of the shape's context."
geometry: GeoSeries
"Shape (multi)polygon."
- parent: Series[str] = pa.Field(isin=["gadm", "overture", "marineregions", "nuts"])
+ parent: Series[str] = pa.Field(isin=SUPPORTED_DATASETS)
"Parent dataset."
parent_subtype: Series[str]
"Region disaggregation level in the parent dataset."
diff --git a/workflow/scripts/_utils.py b/workflow/scripts/_utils.py
index 6868249..266d441 100644
--- a/workflow/scripts/_utils.py
+++ b/workflow/scripts/_utils.py
@@ -1,11 +1,37 @@
"""Reusable utility functions."""
+import time
+from dataclasses import dataclass
+from pathlib import Path
+
import geopandas as gpd
+import requests
from matplotlib import pyplot as plt
from matplotlib.axes import Axes
from matplotlib.figure import Figure
from pyproj import CRS
+RETRY_STATUS_CODES = {408, 429, 500, 502, 503, 504}
+RETRY_EXCEPTIONS = (
+ requests.exceptions.ConnectionError,
+ requests.exceptions.Timeout,
+ requests.exceptions.ChunkedEncodingError,
+)
+
+
+@dataclass
+class DownloadTimeouts:
+ """Generic class for handling timeouts across data sources."""
+
+ max_retries: int
+ connect_seconds: int
+ read_seconds: int
+ initial_retry_seconds: int
+
+ @property
+ def request_timeout(self) -> tuple[int, int]:
+ return (self.connect_seconds, self.read_seconds)
+
def check_crs_config(crs: dict[str, int | str]) -> dict[str, CRS]:
"""Check the crs configuration settings."""
@@ -20,8 +46,46 @@ def check_crs_config(crs: dict[str, int | str]) -> dict[str, CRS]:
def plot_shapes(shapes: gpd.GeoDataFrame, crs: str | int | CRS) -> tuple[Figure, Axes]:
"""Generate a nice figure of dataframes that fit the module's schema."""
gdf = shapes.copy().to_crs(crs)
+ colors = {"land": "olive", "maritime": "tab:blue"}
fig, ax = plt.subplots(layout="constrained")
- gdf.boundary.plot(ax=ax, color="black", lw=0.5)
- ax = gdf.plot(ax=ax, column="shape_class", legend=False)
+ ax = gdf.plot(
+ ax=ax,
+ column="shape_class",
+ color=gdf["shape_class"].map(colors),
+ legend=False,
+ zorder=-1,
+ )
+ gdf.boundary.plot(ax=ax, color="black", lw=0.5, zorder=1)
ax.set(xticks=[], yticks=[], xlabel="", ylabel="")
return fig, ax
+
+
+def retry_wait_seconds(
+ retry_number: int, initial_wait: float, *, max_wait: float = 60
+) -> None:
+ """Return exponential backoff wait time for a retry number starting at 0."""
+ timeout = min(initial_wait * 2 ** (retry_number), max_wait)
+ time.sleep(timeout)
+
+
+def download_file(url: str, path: Path, timeouts: DownloadTimeouts) -> None:
+ """Download URL content to path, retrying transient failures."""
+ max_retries = timeouts.max_retries
+ for attempt in range(max_retries + 1):
+ try:
+ with requests.get(url, timeout=timeouts.request_timeout) as response:
+ if response.status_code in RETRY_STATUS_CODES and attempt < max_retries:
+ retry_wait_seconds(attempt, timeouts.initial_retry_seconds)
+ continue
+
+ response.raise_for_status()
+ path.write_bytes(response.content)
+ return
+ except RETRY_EXCEPTIONS as exc:
+ if attempt == max_retries:
+ raise RuntimeError(f"Failed download for {url!r}.") from exc
+ retry_wait_seconds(attempt, timeouts.initial_retry_seconds)
+
+ raise RuntimeError(
+ f"Maximum retries {max_retries} reached without a valid response"
+ )
diff --git a/workflow/scripts/build_combined_area.py b/workflow/scripts/build_combined_area.py
index c3b8d51..ce63718 100644
--- a/workflow/scripts/build_combined_area.py
+++ b/workflow/scripts/build_combined_area.py
@@ -80,7 +80,6 @@ def main() -> None:
combined.to_parquet(snakemake.output.combined)
fig, _ = _utils.plot_shapes(combined, crs["projected"])
- fig.suptitle("Combined shapes")
fig.savefig(snakemake.output.plot, dpi=200, bbox_inches="tight")
diff --git a/workflow/scripts/build_country.py b/workflow/scripts/build_country.py
index 1198197..47e6e7e 100644
--- a/workflow/scripts/build_country.py
+++ b/workflow/scripts/build_country.py
@@ -3,6 +3,7 @@
import math
import sys
from collections.abc import Iterator
+from dataclasses import dataclass
from typing import TYPE_CHECKING, Any
import _schemas
@@ -10,7 +11,7 @@
import geopandas as gpd
import pandas as pd
from pyproj import CRS
-from shapely import voronoi_polygons
+from shapely import make_valid, voronoi_polygons
from shapely.geometry import (
GeometryCollection,
LineString,
@@ -19,6 +20,7 @@
Point,
)
from shapely.geometry.base import BaseGeometry
+from shapely.ops import linemerge, unary_union
if TYPE_CHECKING:
snakemake: Any
@@ -26,25 +28,172 @@
ROUND_DECIMALS: int = 3
+@dataclass(frozen=True)
+class VoronoiConfig:
+ """Voronoi settings from the configuration."""
+
+ enabled: bool
+ sample_spacing: int
+ min_samples_per_shoreline: int
+ max_samples_per_maritime: int
+ include_shoreline_vertices: bool
+ shoreline_search_radius: int
+ uncovered_area_tolerance: float
+
+
+@dataclass(frozen=True)
+class ShorelineLine:
+ """A shoreline line and the land shape that generated it."""
+
+ assigned_shape_id: str
+ geometry: LineString
+
+
def _iter_lines(geom: BaseGeometry) -> Iterator[LineString]:
+ """Yield line components from a possibly nested geometry."""
if geom.is_empty:
return
if isinstance(geom, LineString):
yield geom
- return
- if isinstance(geom, MultiLineString):
+ elif isinstance(geom, MultiLineString):
yield from geom.geoms
- return
- if isinstance(geom, GeometryCollection):
+ elif isinstance(geom, GeometryCollection):
for part in geom.geoms:
yield from _iter_lines(part)
-def _sample_line_midpoints(line: LineString, spacing: float) -> list[Point]:
- if line.length == 0:
+def _merge_lines(lines: list[LineString]) -> list[LineString]:
+ """Merge connected line fragments into longer line components."""
+ result: list[LineString] = []
+ if lines:
+ merged = unary_union(lines)
+ if isinstance(merged, LineString):
+ result = [merged]
+ else:
+ result = list(_iter_lines(linemerge(merged)))
+ return result
+
+
+def _sample_line_midpoints(
+ line: LineString, spacing: float, min_samples: int = 1
+) -> list[Point]:
+ """Sample evenly spaced midpoint locations along a line."""
+ length = line.length
+ points: list[Point] = []
+ if length != 0:
+ n = max(1, min_samples, math.ceil(length / spacing))
+ points = [line.interpolate((i + 0.5) * length / n) for i in range(n)]
+ return points
+
+
+def _sample_line_vertices(line: LineString) -> list[Point]:
+ """Sample existing line vertices without adding ambiguous open-line endpoints."""
+ coords = list(line.coords)
+ if len(coords) < 2:
return []
- n = max(1, math.ceil(line.length / spacing))
- return [line.interpolate((i + 0.5) * line.length / n) for i in range(n)]
+ if line.is_ring:
+ coords = coords[:-1]
+ else:
+ coords = coords[1:-1]
+ return [Point(coord) for coord in coords]
+
+
+def _collect_shoreline_lines(
+ maritime_row, land: gpd.GeoDataFrame, *, shoreline_search_radius: float
+) -> list[ShorelineLine]:
+ """Find marine-facing exterior shoreline lines for a maritime shape."""
+ country_boundary = land.geometry.union_all().boundary
+ coastal_band = maritime_row.geometry.buffer(max(0, shoreline_search_radius))
+ candidate_land = land.iloc[land.sindex.query(coastal_band, predicate="intersects")]
+
+ shoreline_lines: list[ShorelineLine] = []
+ for land_row in candidate_land.itertuples(index=False):
+ shoreline = land_row.geometry.boundary.intersection(country_boundary)
+ shoreline = shoreline.intersection(coastal_band)
+ shoreline_lines.extend(
+ ShorelineLine(land_row.shape_id, line)
+ for line in _merge_lines(list(_iter_lines(shoreline)))
+ )
+ return shoreline_lines
+
+
+def _deduplicate_seed_records(
+ seeds: list[dict[str, object]],
+) -> list[dict[str, object]]:
+ """Keep one seed per coordinate and drop coordinates assigned to multiple shapes."""
+ grouped: dict[tuple[float, float], list[dict[str, object]]] = {}
+ for seed in seeds:
+ point = seed["geometry"]
+ if not isinstance(point, Point):
+ raise TypeError("Expected shoreline seed geometry to be a Point.")
+ key = (round(point.x, ROUND_DECIMALS), round(point.y, ROUND_DECIMALS))
+ grouped.setdefault(key, []).append(seed)
+
+ deduplicated = []
+ for matches in grouped.values():
+ assigned_ids = {match["assigned_shape_id"] for match in matches}
+ if len(assigned_ids) == 1:
+ deduplicated.append(matches[0])
+ return deduplicated
+
+
+def _sample_lines(
+ shoreline_lines: list[ShorelineLine],
+ spacing: float,
+ min_samples: int,
+ include_vertices: bool,
+) -> list[dict[str, object]]:
+ """Convert shoreline lines into assigned Voronoi seed records."""
+ sampled_seeds: list[dict[str, object]] = []
+ for shoreline_line in shoreline_lines:
+ points = _sample_line_midpoints(shoreline_line.geometry, spacing, min_samples)
+ if include_vertices:
+ points.extend(_sample_line_vertices(shoreline_line.geometry))
+
+ sampled_seeds.extend(
+ {"assigned_shape_id": shoreline_line.assigned_shape_id, "geometry": p}
+ for p in points
+ )
+ return _deduplicate_seed_records(sampled_seeds)
+
+
+def _make_shoreline_seed_records(
+ shoreline_lines: list[ShorelineLine],
+ *,
+ sample_spacing: float,
+ min_samples_per_shoreline: int,
+ max_samples_per_maritime: int,
+ include_shoreline_vertices: bool,
+) -> list[dict[str, object]]:
+ """Create bounded shoreline seed records for one maritime split."""
+ min_samples_per_shoreline = max(1, min_samples_per_shoreline)
+ max_samples_per_maritime = max(1, max_samples_per_maritime)
+
+ seeds = _sample_lines(
+ shoreline_lines,
+ sample_spacing,
+ min_samples_per_shoreline,
+ include_shoreline_vertices,
+ )
+ if len(seeds) > max_samples_per_maritime:
+ total_length = sum(line.geometry.length for line in shoreline_lines)
+ adaptive_spacing = max(
+ sample_spacing, total_length / max(1, max_samples_per_maritime)
+ )
+ adaptive_min_samples = max(
+ 1,
+ min(
+ min_samples_per_shoreline,
+ max_samples_per_maritime // max(1, len(shoreline_lines)),
+ ),
+ )
+ seeds = _sample_lines(
+ shoreline_lines,
+ adaptive_spacing,
+ adaptive_min_samples,
+ include_vertices=False,
+ )
+ return seeds
def _split_one_maritime(
@@ -52,55 +201,53 @@ def _split_one_maritime(
land: gpd.GeoDataFrame,
*,
crs: int | str,
- sample_spacing: float,
- coverage_area_tolerance: float,
-) -> gpd.GeoDataFrame:
+ voronoi_config: VoronoiConfig,
+) -> tuple[gpd.GeoDataFrame, gpd.GeoDataFrame]:
+ """Split a single maritime shape to fit the coastline."""
if land.empty:
raise ValueError(
f"No land shapes found for country_id={maritime_row.country_id!r}."
)
- # Sample through the shoreline
- boundary = maritime_row.geometry.boundary
- candidate_land = land.iloc[land.sindex.query(boundary, predicate="intersects")]
-
- seeds: list[dict[str, object]] = []
- for land_row in candidate_land.itertuples(index=False):
- shoreline = land_row.geometry.boundary.intersection(boundary)
-
- for line in _iter_lines(shoreline):
- for point in _sample_line_midpoints(line, sample_spacing):
- seeds.append(
- {"assigned_shape_id": land_row.shape_id, "geometry": point}
- )
+ sample_spacing = voronoi_config.sample_spacing
+ shoreline_lines = _collect_shoreline_lines(
+ maritime_row,
+ land,
+ shoreline_search_radius=voronoi_config.shoreline_search_radius,
+ )
+ seeds = _make_shoreline_seed_records(
+ shoreline_lines,
+ sample_spacing=sample_spacing,
+ min_samples_per_shoreline=voronoi_config.min_samples_per_shoreline,
+ max_samples_per_maritime=voronoi_config.max_samples_per_maritime,
+ include_shoreline_vertices=voronoi_config.include_shoreline_vertices,
+ )
if not seeds:
raise ValueError(
f"No touching shoreline regions found for maritime shape {maritime_row.shape_id!r}."
)
seed_gdf = gpd.GeoDataFrame(seeds, geometry="geometry", crs=crs)
- # Drop seeds too close to each other
- xy = seed_gdf.geometry.map(
- lambda p: (round(p.x, ROUND_DECIMALS), round(p.y, ROUND_DECIMALS))
- )
- seed_gdf = seed_gdf.loc[~xy.duplicated()].reset_index(drop=True)
-
base_row = maritime_row._asdict()
assigned_ids = seed_gdf["assigned_shape_id"].unique()
if len(assigned_ids) == 1:
# Nothing to do
pieces = gpd.GeoDataFrame([base_row.copy()], geometry="geometry", crs=crs)
+ cells = gpd.GeoDataFrame(geometry=[], crs=crs)
else:
# Run Voronoi
+ maritime_geometry = make_valid(maritime_row.geometry)
cells = gpd.GeoDataFrame(
geometry=list(
voronoi_polygons(
MultiPoint(list(seed_gdf.geometry)),
- extend_to=maritime_row.geometry.envelope.buffer(sample_spacing * 2),
+ extend_to=maritime_geometry.envelope.buffer(sample_spacing * 2),
).geoms
),
crs=crs,
)
+ cells["geometry"] = cells.geometry.map(make_valid)
+
# Identify where each voronoi cell belongs
cells = gpd.sjoin(
cells,
@@ -114,17 +261,15 @@ def _split_one_maritime(
)
# Keep only cells on the maritime area and test for completeness
- cells["geometry"] = cells.geometry.intersection(maritime_row.geometry)
+ cells["geometry"] = cells.geometry.intersection(maritime_geometry)
cells = cells.loc[~cells.geometry.is_empty & (cells.geometry.area > 0)]
pieces = (
cells[["assigned_shape_id", "geometry"]]
.dissolve(by="assigned_shape_id", as_index=False)
.rename(columns={"assigned_shape_id": "_assigned_shape_id"})
)
- uncovered_area = maritime_row.geometry.difference(
- pieces.geometry.union_all()
- ).area
- if uncovered_area > coverage_area_tolerance:
+ uncovered_area = maritime_geometry.difference(pieces.geometry.union_all()).area
+ if uncovered_area > voronoi_config.uncovered_area_tolerance:
raise RuntimeError(
f"Voronoi split did not fully cover maritime shape {maritime_row.shape_id!r}. "
f"Uncovered area: {uncovered_area}"
@@ -141,40 +286,49 @@ def _split_one_maritime(
piece_rows.append(piece)
pieces = gpd.GeoDataFrame(piece_rows, geometry="geometry", crs=crs)
- return pieces
+ return pieces, cells
def split_maritime_by_shoreline_voronoi(
- shapes: gpd.GeoDataFrame,
- *,
- crs: dict[str, CRS],
- sample_spacing: float = 10_000.0,
- coverage_area_tolerance: float = 1.0,
-) -> gpd.GeoDataFrame:
+ shapes: gpd.GeoDataFrame, *, crs: dict[str, CRS], voronoi_config: VoronoiConfig
+) -> tuple[gpd.GeoDataFrame, gpd.GeoDataFrame]:
"""Split EEZ zones to fit shoreline land regions."""
+ cells = gpd.GeoDataFrame(geometry=[], crs=shapes.crs)
+ if not voronoi_config.enabled:
+ return shapes, cells
+
shapes = shapes.copy().to_crs(crs["projected"])
land = shapes.loc[shapes["shape_class"].eq("land")]
maritime = shapes.loc[shapes["shape_class"].eq("maritime")]
if maritime.empty:
- return ValueError("Requested voronoi without maritime shapes.")
+ raise ValueError("Requested voronoi without maritime shapes.")
- split_maritime = [
+ split_results = [
_split_one_maritime(
maritime_row,
land.loc[land["country_id"].eq(maritime_row.country_id)],
- sample_spacing=sample_spacing,
- coverage_area_tolerance=coverage_area_tolerance,
+ voronoi_config=voronoi_config,
crs=shapes.crs,
)
for maritime_row in maritime.itertuples(index=False)
]
+ split_maritime = [pieces for pieces, _ in split_results]
result = pd.concat([land, *split_maritime], ignore_index=True)
+
+ cell_frames = [i for _, i in split_results if not i.empty]
+ if cell_frames:
+ cells = gpd.GeoDataFrame(
+ pd.concat(cell_frames, ignore_index=True),
+ geometry="geometry",
+ crs=shapes.crs,
+ )
+
result = result.to_crs(crs["geographic"])
result.geometry = result.geometry.buffer(0)
- return result
+ return result, cells
def combine_shapes(
@@ -194,6 +348,12 @@ def combine_shapes(
return combined
+def plot_voronoi_cells(ax: _utils.Axes, cells: gpd.GeoDataFrame, crs: CRS) -> None:
+ """Show voronoi tessellation."""
+ projected_cells = cells.copy().to_crs(crs)
+ projected_cells.boundary.plot(ax=ax, lw=0.2, color="lightgrey", zorder=0)
+
+
def main() -> None:
"""Main snakemake process."""
crs = _utils.check_crs_config(snakemake.params.crs)
@@ -211,16 +371,19 @@ def main() -> None:
shapes = combine_shapes(land, maritime, crs["geographic"])
shapes = _schemas.ShapesSchema.validate(shapes)
- voronoi = snakemake.params.voronoi
- if not maritime.empty and voronoi["enabled"]:
- shapes = split_maritime_by_shoreline_voronoi(
- shapes, crs=crs, sample_spacing=voronoi["sample_spacing"]
+ voronoi_config = VoronoiConfig(**snakemake.params.voronoi)
+ cells = None
+ if not maritime.empty and voronoi_config.enabled:
+ shapes, cells = split_maritime_by_shoreline_voronoi(
+ shapes, crs=crs, voronoi_config=voronoi_config
)
shapes = _schemas.ShapesSchema.validate(shapes)
+
shapes.to_parquet(snakemake.output.country)
+ fig, ax = _utils.plot_shapes(shapes, crs["projected"])
+ if cells is not None and not cells.empty:
+ plot_voronoi_cells(ax, cells, crs["projected"])
- fig, _ = _utils.plot_shapes(shapes, crs["projected"])
- fig.suptitle(f"{country} shapes")
fig.savefig(snakemake.output.plot, dpi=200, bbox_inches="tight")
diff --git a/workflow/scripts/download_country_gadm.py b/workflow/scripts/download_country_gadm.py
deleted file mode 100644
index 3eb7a36..0000000
--- a/workflow/scripts/download_country_gadm.py
+++ /dev/null
@@ -1,56 +0,0 @@
-"""Download data from the GADM database.
-
-Built for version 4.1 of the dataset.
-
-https://gadm.org/index.html
-"""
-
-import sys
-from typing import TYPE_CHECKING, Any
-
-import geopandas as gpd
-import requests
-
-if TYPE_CHECKING:
- snakemake: Any
-
-
-GADM_URL = (
- "https://geodata.ucdavis.edu/gadm/gadm4.1/json/gadm41_{country}_{subtype}.json{zip}"
-)
-GADM_CRS = "EPSG:4326"
-
-
-def download_country_gadm(country: str, subtype: str) -> gpd.GeoDataFrame:
- """Download country and save it to parquet."""
- session = requests.Session()
- gdf: gpd.GeoDataFrame | None = None
-
- for zip_ext in (".zip", ""):
- uri = GADM_URL.format(country=country, subtype=subtype, zip=zip_ext)
- try:
- r = session.get(uri, stream=True, timeout=30)
- r.raise_for_status()
- # URL is valid, read and format
- gdf = gpd.read_file(uri).to_crs(GADM_CRS)
- break
- except Exception:
- continue
-
- if gdf is None:
- raise RuntimeError(f"Could not fetch GADM request for {country!r}:{subtype!r}.")
-
- return gdf
-
-
-def main():
- """Main snakemake process."""
- country = download_country_gadm(
- snakemake.wildcards.country, snakemake.wildcards.subtype
- )
- country.to_parquet(snakemake.output.path)
-
-
-if __name__ == "__main__":
- sys.stderr = open(snakemake.log[0], "w")
- main()
diff --git a/workflow/scripts/download_gadm.py b/workflow/scripts/download_gadm.py
new file mode 100644
index 0000000..e437a64
--- /dev/null
+++ b/workflow/scripts/download_gadm.py
@@ -0,0 +1,61 @@
+"""Download data from the GADM database.
+
+Built for version 4.1 of the dataset.
+https://gadm.org/index.html
+"""
+
+import sys
+import tempfile
+from pathlib import Path
+from typing import TYPE_CHECKING, Any
+
+import geopandas as gpd
+from _utils import DownloadTimeouts, download_file
+
+if TYPE_CHECKING:
+ snakemake: Any
+
+
+GADM_URL = (
+ "https://geodata.ucdavis.edu/gadm/gadm4.1/json/gadm41_{country}_{subtype}.json{zip}"
+)
+GADM_CRS = "EPSG:4326"
+
+
+def download_country_gadm(
+ country: str, subtype: str, timeouts: DownloadTimeouts
+) -> gpd.GeoDataFrame:
+ """Attempts to download country GADM data in .json or zipped json."""
+ last_error: Exception | None = None
+
+ for zip_ext in (".zip", ""):
+ url = GADM_URL.format(country=country, subtype=subtype, zip=zip_ext)
+ try:
+ with tempfile.TemporaryDirectory() as tmp_dir:
+ tmp_path = Path(tmp_dir) / f"download.json{zip_ext}"
+
+ download_file(url, tmp_path, timeouts)
+ gdf = gpd.read_file(tmp_path)
+ if gdf.empty:
+ raise RuntimeError(f"Downloaded empty GADM file from {url!r}.")
+ return gdf.to_crs(GADM_CRS)
+
+ except Exception as exc:
+ last_error = exc
+ raise RuntimeError(
+ f"Could not fetch GADM request for {country!r}:{subtype!r}."
+ ) from last_error
+
+
+def main():
+ """Main snakemake process."""
+ timeouts = DownloadTimeouts(**snakemake.params.timeouts)
+ country = download_country_gadm(
+ snakemake.wildcards.country, snakemake.wildcards.subtype, timeouts
+ )
+ country.to_parquet(snakemake.output.path)
+
+
+if __name__ == "__main__":
+ sys.stderr = open(snakemake.log[0], "w")
+ main()
diff --git a/workflow/scripts/download_geoboundaries.py b/workflow/scripts/download_geoboundaries.py
new file mode 100644
index 0000000..526c80e
--- /dev/null
+++ b/workflow/scripts/download_geoboundaries.py
@@ -0,0 +1,73 @@
+"""Download data from the geoBoundaries API.
+
+https://www.geoboundaries.org/api.html
+"""
+
+import json
+import sys
+import tempfile
+from pathlib import Path
+from typing import TYPE_CHECKING, Any
+
+import geopandas as gpd
+from _utils import DownloadTimeouts, download_file
+
+if TYPE_CHECKING:
+ snakemake: Any
+
+
+GEOBOUNDARIES_API_URL = (
+ "https://www.geoboundaries.org/api/current/{release_type}/{country}/ADM{subtype}/"
+)
+GEOBOUNDARIES_CRS = "EPSG:4326"
+
+
+def download_country_geoboundaries(
+ country: str, subtype: str, release_type: str, timeouts: DownloadTimeouts
+) -> gpd.GeoDataFrame:
+ """Download country data from geoBoundaries.
+
+ Uses the current geoBoundaries API endpoint.
+ The concrete dataset version returned in the metadata JSON response.
+ """
+ api_url = GEOBOUNDARIES_API_URL.format(
+ release_type=release_type, country=country, subtype=subtype
+ )
+
+ with tempfile.TemporaryDirectory() as tmp_dir:
+ tmp_path = Path(tmp_dir)
+
+ metadata_path = tmp_path / "metadata.json"
+ download_file(api_url, metadata_path, timeouts)
+
+ metadata = json.loads(metadata_path.read_text())
+ geojson_url = metadata["gjDownloadURL"]
+
+ geojson_path = tmp_path / "download.geojson"
+ download_file(geojson_url, geojson_path, timeouts)
+
+ gdf = gpd.read_file(geojson_path)
+ if gdf.empty:
+ raise RuntimeError(
+ f"Downloaded empty geoBoundaries file from {geojson_url!r}."
+ )
+
+ return gdf.to_crs(GEOBOUNDARIES_CRS)
+
+
+def main():
+ """Main snakemake process."""
+ timeouts = DownloadTimeouts(**snakemake.params.timeouts)
+
+ country = download_country_geoboundaries(
+ snakemake.wildcards.country,
+ snakemake.wildcards.subtype,
+ snakemake.wildcards.release_type,
+ timeouts,
+ )
+ country.to_parquet(snakemake.output.path)
+
+
+if __name__ == "__main__":
+ sys.stderr = open(snakemake.log[0], "w")
+ main()
diff --git a/workflow/scripts/download_marine_eez_area.py b/workflow/scripts/download_harmonised_eez.py
similarity index 58%
rename from workflow/scripts/download_marine_eez_area.py
rename to workflow/scripts/download_harmonised_eez.py
index 1924eaf..3a52578 100644
--- a/workflow/scripts/download_marine_eez_area.py
+++ b/workflow/scripts/download_harmonised_eez.py
@@ -1,12 +1,17 @@
"""Download data from the Marineregions database.
https://www.marineregions.org/
+Constructs EEZ datasets per country
+- In cases where no EEZ is available for a country an empty dataframe will be saved.
+- Optionally, additional EEZs may be downloaded if specified in `extra_eez`.
+ - These should result in an error if the code is invalid.
"""
import sys
from typing import TYPE_CHECKING, Any
import _schemas
+import _utils
import geopandas as gpd
import pandas as pd
import requests
@@ -17,6 +22,7 @@
WFS_BASE = "https://geo.vliz.be/geoserver/MarineRegions/wfs"
WFS_VERSION = "2.0.0"
+CRS_MARINE_REGIONS = "EPSG:4326"
def _raise_for_geoserver_exception(response: requests.Response) -> None:
@@ -37,8 +43,43 @@ def _raise_for_geoserver_exception(response: requests.Response) -> None:
)
+def _get_wfs_response(
+ params: dict[str, str], timeouts: _utils.DownloadTimeouts
+) -> requests.Response:
+ """Call the MarineRegions WFS API, retrying transient request failures."""
+ max_retries = timeouts.max_retries
+ for attempt in range(max_retries + 1):
+ try:
+ response = requests.get(
+ WFS_BASE, params=params, timeout=timeouts.request_timeout
+ )
+
+ if response.status_code in _utils.RETRY_STATUS_CODES:
+ if attempt < max_retries:
+ _utils.retry_wait_seconds(attempt, timeouts.initial_retry_seconds)
+ continue
+ _raise_for_geoserver_exception(response)
+ response.raise_for_status()
+
+ if response.status_code >= 400:
+ _raise_for_geoserver_exception(response)
+ response.raise_for_status()
+
+ _raise_for_geoserver_exception(response)
+ return response
+
+ except _utils.RETRY_EXCEPTIONS as exc:
+ if attempt == max_retries:
+ raise RuntimeError(
+ f"Failed MarineRegions WFS request after {max_retries} retries."
+ ) from exc
+ _utils.retry_wait_seconds(attempt, timeouts.initial_retry_seconds)
+
+ raise RuntimeError(f"Failed MarineRegions WFS request after {max_retries} retries.")
+
+
def get_eez_by_cql(
- cql_filter: str, *, srs_name: str = "EPSG:4326", timeout: int = 180
+ cql_filter: str, timeouts: _utils.DownloadTimeouts
) -> gpd.GeoDataFrame | None:
"""Fetch EEZ polygons using a raw WFS CQL filter."""
params = {
@@ -48,51 +89,27 @@ def get_eez_by_cql(
"typeNames": "eez",
"outputFormat": "application/json",
"cql_filter": cql_filter,
- "srsName": srs_name,
+ "srsName": CRS_MARINE_REGIONS,
}
-
- response = requests.get(WFS_BASE, params=params, timeout=timeout)
-
- if response.status_code >= 400:
- # Attempt to explain the failure, otherwise just raise status.
- _raise_for_geoserver_exception(response)
- response.raise_for_status()
- # Attempt to explain 200 failures too.
- _raise_for_geoserver_exception(response)
+ response = _get_wfs_response(params, timeouts)
data = response.json()
if "features" not in data:
raise RuntimeError(
- f"Unexpected JSON payload (no 'features'). First keys: {list(data)[:20]}"
+ f"Unexpected JSON payload from MarineRegions. First keys: {list(data)[:20]}"
)
result = None
if data["features"]:
# Let geopandas build the frame, CRS will match request
- result = gpd.GeoDataFrame.from_features(data["features"], crs=srs_name)
+ result = gpd.GeoDataFrame.from_features(
+ data["features"], crs=CRS_MARINE_REGIONS
+ )
if result.empty:
result = None
return result
-def get_country_eez_by_iso3(
- iso3: str,
- *,
- id_col: str = "iso_ter1",
- srs_name: str = "EPSG:4326",
- timeout: int = 180,
-) -> gpd.GeoDataFrame | None:
- """Fetch EEZ polygons by ISO3 code using WFS + CQL."""
- return get_eez_by_cql(f"{id_col}='{iso3}'", srs_name=srs_name, timeout=timeout)
-
-
-def get_country_eez_by_mrgid(
- mrgid: int, *, srs_name: str = "EPSG:4326", timeout: int = 180
-) -> gpd.GeoDataFrame | None:
- """Fetch EEZ polygons by Marine Regions ID."""
- return get_eez_by_cql(f"mrgid={mrgid}", srs_name=srs_name, timeout=timeout)
-
-
def transform_to_schema(
gdf: gpd.GeoDataFrame | None, country_id: str
) -> gpd.GeoDataFrame:
@@ -138,7 +155,16 @@ def plot(gdf: gpd.GeoDataFrame, country: str):
"""Simple plot of the shape."""
fig, ax = plt.subplots(layout="constrained")
if gdf.empty:
- ax.set_title(f"{country!r} has no EEZ")
+ ax.text(
+ 0.5,
+ 0.5,
+ f"{country!r} has no EEZ",
+ ha="center",
+ va="center",
+ transform=ax.transAxes,
+ fontsize=24,
+ )
+ ax.set_axis_off()
else:
gdf.plot(
"contested",
@@ -150,37 +176,48 @@ def plot(gdf: gpd.GeoDataFrame, country: str):
"loc": "upper left",
},
)
- ax.set_title(f"{country!r}: EEZ")
return fig, ax
-def main() -> None:
- """Main snakemake process."""
- iso3 = snakemake.wildcards.country
- extra_eez = snakemake.params.extra_eez
- if not isinstance(extra_eez, list):
- extra_eez = [extra_eez]
+def download_eezs(
+ country: str, extra_eez: list[str], timeouts: _utils.DownloadTimeouts
+) -> gpd.GeoDataFrame:
+ """Download EEZ data as requested.
- eez_gdfs = []
+ If no EEZ exists for a country, the dataframe will be empty.
+ """
+ eez_gdfs: list[gpd.GeoDataFrame] = []
- iso3_eez = get_country_eez_by_iso3(iso3)
+ iso3_eez = get_eez_by_cql(f"iso_ter1='{country}'", timeouts)
if iso3_eez is not None:
eez_gdfs.append(iso3_eez)
for mrgid in extra_eez:
- extra_gdf = get_country_eez_by_mrgid(int(mrgid))
+ extra_gdf = get_eez_by_cql(f"mrgid={int(mrgid)}", timeouts)
if extra_gdf is None:
raise RuntimeError(f"Configured extra_eez {mrgid!r} returned no features")
eez_gdfs.append(extra_gdf)
combined_gdf = None
if eez_gdfs:
- combined_gdf = pd.concat([i for i in eez_gdfs if i is not None])
+ combined_gdf = pd.concat(eez_gdfs, ignore_index=True)
+
+ return transform_to_schema(combined_gdf, country)
+
+
+def main() -> None:
+ """Main snakemake process."""
+ country = snakemake.wildcards.country
+ extra_eez = snakemake.params.extra_eez
+
+ timeouts = _utils.DownloadTimeouts(**snakemake.params.timeouts)
+ if not isinstance(extra_eez, list):
+ extra_eez = [extra_eez]
- gdf = transform_to_schema(combined_gdf, iso3)
+ gdf = download_eezs(country, extra_eez, timeouts)
gdf.to_parquet(snakemake.output.path)
- fig, _ = plot(gdf, iso3)
+ fig, _ = plot(gdf, country)
fig.savefig(snakemake.output.plot, bbox_inches="tight", dpi=200)
diff --git a/workflow/scripts/download_country_overture.py b/workflow/scripts/download_harmonised_overture.py
similarity index 85%
rename from workflow/scripts/download_country_overture.py
rename to workflow/scripts/download_harmonised_overture.py
index 0ca070c..02db71c 100644
--- a/workflow/scripts/download_country_overture.py
+++ b/workflow/scripts/download_harmonised_overture.py
@@ -7,13 +7,15 @@
import boto3
import duckdb
+import geopandas as gpd
import pycountry
+from _schemas import ShapesSchema
from botocore import UNSIGNED
from botocore.config import Config
if TYPE_CHECKING:
snakemake: Any
-sys.stderr = open(snakemake.log[0], "w")
+
S3_REGION = "us-west-2"
S3_BUCKET = f"overturemaps-{S3_REGION}"
@@ -133,10 +135,35 @@ class AS shape_class,
)
-if __name__ == "__main__":
+def validate_country_overture(
+ path: str, country: str, subtype: str, version: str
+) -> None:
+ """Run quick checks against our schema."""
+ gdf = gpd.read_parquet(path)
+ if gdf.empty:
+ raise ValueError(
+ f"Invalid request for '{country}-{subtype}-{version}'. "
+ "Please evaluate your request at https://overturemaps.org/."
+ )
+ ShapesSchema.validate(gdf)
+
+
+def main() -> None:
+ """Main snakemake process."""
download_country_overture(
country=snakemake.wildcards.country,
subtype=snakemake.wildcards.subtype,
version=snakemake.params.version,
path=snakemake.output.path,
)
+ validate_country_overture(
+ country=snakemake.wildcards.country,
+ subtype=snakemake.wildcards.subtype,
+ version=snakemake.params.version,
+ path=snakemake.output.path,
+ )
+
+
+if __name__ == "__main__":
+ sys.stderr = open(snakemake.log[0], "w")
+ main()
diff --git a/workflow/scripts/download_nuts.py b/workflow/scripts/download_nuts.py
index 938bd52..c6ebedd 100644
--- a/workflow/scripts/download_nuts.py
+++ b/workflow/scripts/download_nuts.py
@@ -1,30 +1,46 @@
"""NUTS download functionality."""
import sys
+import tempfile
+from pathlib import Path
from typing import TYPE_CHECKING, Any
import geopandas as gpd
+from _utils import DownloadTimeouts, download_file
if TYPE_CHECKING:
snakemake: Any
-sys.stderr = open(snakemake.log[0], "w")
-URL = "https://gisco-services.ec.europa.eu/distribution/v2/nuts/gpkg/NUTS_RG_{resolution}_{year}_{epsg}_LEVL_{level}.gpkg"
+URL = "https://gisco-services.ec.europa.eu/distribution/v2/nuts/gpkg/NUTS_RG_{resolution}_{year}_{crs}_LEVL_{level}.gpkg"
+NUTS_CRS = 3035
-def download_nuts_version(year: int, resolution: str, level: str, epsg: str, path: str):
+
+def download_nuts_version(
+ year: int, resolution: str, level: str, timeouts: DownloadTimeouts
+) -> gpd.GeoDataFrame:
"""Download an aggregated NUTS datafile for the requested configuration."""
- gdf = gpd.read_file(
- URL.format(year=year, resolution=resolution, epsg=epsg, level=level)
- )
- assert gdf.crs.equals(epsg)
- gdf.to_parquet(path)
+ url = URL.format(year=year, resolution=resolution, crs=NUTS_CRS, level=level)
+ with tempfile.TemporaryDirectory() as temp_dir:
+ tmp_path = Path(temp_dir) / "download.gpkg"
+ download_file(url, tmp_path, timeouts)
+ gdf = gpd.read_file(tmp_path)
+ if not gdf.crs.equals(NUTS_CRS):
+ raise ValueError(f"NUTS in unexpected CRS: got {gdf.crs}, expected {NUTS_CRS}.")
+ return gdf
-if __name__ == "__main__":
- download_nuts_version(
+
+def main():
+ """Main snakemake process."""
+ gdf = download_nuts_version(
year=snakemake.wildcards.year,
resolution=snakemake.wildcards.resolution,
level=snakemake.wildcards.subtype,
- epsg=snakemake.params.epsg,
- path=snakemake.output.path,
+ timeouts=DownloadTimeouts(**snakemake.params.timeouts),
)
+ gdf.to_parquet(snakemake.output.path)
+
+
+if __name__ == "__main__":
+ sys.stderr = open(snakemake.log[0], "w")
+ main()
diff --git a/workflow/scripts/standardise_country_gadm.py b/workflow/scripts/harmonise_gadm.py
similarity index 100%
rename from workflow/scripts/standardise_country_gadm.py
rename to workflow/scripts/harmonise_gadm.py
diff --git a/workflow/scripts/harmonise_geoboundaries.py b/workflow/scripts/harmonise_geoboundaries.py
new file mode 100644
index 0000000..3a88b80
--- /dev/null
+++ b/workflow/scripts/harmonise_geoboundaries.py
@@ -0,0 +1,55 @@
+"""Harmonise a geoBoundaries country dataset into a cross-compatible shape.
+
+NOTE: there is not enough metadata to filter contested regions in this dataset!
+"""
+
+import sys
+from typing import TYPE_CHECKING, Any
+
+import _schemas
+import geopandas as gpd
+
+if TYPE_CHECKING:
+ snakemake: Any
+
+
+def harmonise_geoboundaries(
+ input_path: str, country_id: str, release_type: str
+) -> gpd.GeoDataFrame:
+ """Harmonise a geoBoundaries dataset including metadata."""
+ gdf = gpd.read_parquet(input_path)
+
+ shape_type = gdf["shapeType"].astype("string")
+ shape_id = gdf["shapeID"].astype("string")
+
+ harmonised = gpd.GeoDataFrame(
+ {
+ "shape_id": f"{release_type}_{country_id}_" + shape_type + "_" + shape_id,
+ "country_id": country_id,
+ "shape_class": "land",
+ "geometry": gdf["geometry"],
+ "parent": "geoboundaries",
+ "parent_subtype": f"{release_type}_" + shape_type,
+ "parent_id": shape_id,
+ "parent_name": gdf["shapeName"],
+ },
+ geometry="geometry",
+ crs=gdf.crs,
+ ).reset_index(drop=True)
+
+ return _schemas.ShapesSchema.validate(harmonised)
+
+
+def main():
+ """Main snakemake process."""
+ gdf = harmonise_geoboundaries(
+ input_path=snakemake.input.raw,
+ country_id=snakemake.wildcards.country,
+ release_type=snakemake.wildcards.release_type,
+ )
+ gdf.to_parquet(snakemake.output.path)
+
+
+if __name__ == "__main__":
+ sys.stderr = open(snakemake.log[0], "w")
+ main()
diff --git a/workflow/scripts/standardise_country_nuts.py b/workflow/scripts/harmonise_nuts.py
similarity index 100%
rename from workflow/scripts/standardise_country_nuts.py
rename to workflow/scripts/harmonise_nuts.py