Add pre-commit hooks and fix their issues (#387)

* add pixi.toml file * remove pixi part from pyproject.toml * revert changes to pyproject.ml * add pre-commit hooks and fix all issues * fix import mistake
Deltares · Oct 3, 2024 · f6932b3 · f6932b3
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diff --git a/.github/ISSUE_TEMPLATE/bug_report.yaml b/.github/ISSUE_TEMPLATE/bug_report.yaml
@@ -1,6 +1,6 @@
 ---
 name: Bug Report
-description: Report incorrect behavior 
+description: Report incorrect behavior
 labels: [bug, needs refinement]
 
 body:
@@ -43,7 +43,7 @@ body:
     id: task-list
     attributes:
       description: >
-        Please provide a list of tasks that need to be completed before this issue can be closed. 
+        Please provide a list of tasks that need to be completed before this issue can be closed.
       label: Task list
     validations:
       required: true

diff --git a/.github/ISSUE_TEMPLATE/feature_request.yaml b/.github/ISSUE_TEMPLATE/feature_request.yaml
@@ -25,7 +25,7 @@ body:
     id: task-list
     attributes:
       description: >
-        Please provide a list of tasks that need to be completed before this issue can be closed. 
+        Please provide a list of tasks that need to be completed before this issue can be closed.
       label: Task list
     validations:
       required: true

diff --git a/.github/workflows/publish-to-pypi.yml b/.github/workflows/publish-to-pypi.yml
@@ -1,6 +1,6 @@
 # This is a basic workflow to help you get started with uploading to pypi automatically
 # https://packaging.python.org/tutorials/packaging-projects/
-# 
+#
 # Before running this workflow in your repository, you will need to set up Secrets in your repository settings:
 # - Log in to your (test)PyPI account, go to your account -> your_project -> Publishing
 # - Fill in the required fields
@@ -36,13 +36,13 @@ jobs:
       - uses: actions/checkout@v3
         with:
           fetch-depth: 0
-      
+
       - uses: conda-incubator/setup-miniconda@v2
         name: Setup Miniconda
         with:
           auto-update-conda: true
           python-version: ${{ env.PYTHON_VERSION }}
-    
+
       - name: Install GDAL
         shell: bash -l {0}
         run: conda install -c conda-forge gdal
@@ -51,7 +51,7 @@ jobs:
         shell: bash -l {0}
         run: |
           python -m pip install --upgrade pip
-          python -m pip install . 
+          python -m pip install .
           python -m pip install build
 
       - name: Build package
@@ -80,13 +80,13 @@ jobs:
         run: |
           ls -ltrh
           ls -ltrh dist
-      
+
       - uses: conda-incubator/setup-miniconda@v2
         name: Setup Miniconda
         with:
           auto-update-conda: true
           python-version: ${{ env.PYTHON_VERSION }}
-      
+
       - name: Install GDAL
         shell: bash -l {0}
         run: conda install -c conda-forge gdal
@@ -95,7 +95,7 @@ jobs:
         run: |
           python -m pip install dist/*.whl
           python -c "import ${{ env.PACKAGE_NAME }}; print(${{ env.PACKAGE_NAME }}.__version__)"
-          
+
 
   upload-to-test-pypi:
     environment: release

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -0,0 +1,19 @@
+---
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.6.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
+      - id: check-added-large-files
+      - id: check-ast
+      - id: check-json
+      - id: debug-statements
+      - id: mixed-line-ending
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.6.8
+    hooks:
+      - id: ruff
+        args: [--fix, --exit-non-zero-on-fix]
+      - id: ruff-format
diff --git a/README.rst b/README.rst
@@ -22,7 +22,7 @@ HydroMT-FIAT: HydroMT plugin for Delft-FIAT
 
 HydroMT_ is a python package, developed by Deltares, to build and analyze hydro models.
 It provides a generic model api with attributes to access the model schematization,
-(dynamic) forcing data, results and states. This plugin provides an implementation 
+(dynamic) forcing data, results and states. This plugin provides an implementation
 for the Delft-FIAT_ model.
 
 
@@ -40,7 +40,7 @@ for the Delft-FIAT_ model.
 
 .. .. code-block:: console
 
-..   pip install hydromt_fiat 
+..   pip install hydromt_fiat
 
 Installation as a User
 ------------
@@ -54,32 +54,32 @@ To create a new environment follow the steps below.
 1. Create a new environment:
 
 .. code-block:: console
-    
+
     conda create -n hydromt_fiat python=3.11.*
 
 2. Activate the environment:
 
 .. code-block:: console
-    
+
     conda activate hydromt_fiat
 
 3. Install conda-forge gdal.
 
 .. code-block:: console
-    
+
     conda install -c conda-forge gdal
 
 4. Install Hydromt-FIAT from Github. After creating the new environment, you need to install all dependencies from the Deltares Github repository. You can use **pip install** to do so:
 
 .. code-block:: console
-    
+
     pip install git+https://github.com/Deltares/hydromt_fiat.git
 
 Existing environment
 If you want to install FIAT into an existing environment, simply activate the desired environment and run:
 
 .. code-block:: console
-    
+
     pip install git+https://github.com/Deltares/hydromt_fiat.git
 
 

diff --git a/binder/environment.yml b/binder/environment.yml
@@ -24,4 +24,3 @@ dependencies:
   - pip:
     - us
     - census
-
diff --git a/binder/postBuild b/binder/postBuild
@@ -1,4 +1,4 @@
 #!/bin/bash
 
 set -ex
-flit install --dep production
+flit install --dep production
diff --git a/docs/_static/fiat_logo.svg b/docs/_static/fiat_logo.svg
diff --git a/docs/api/api_index.rst b/docs/api/api_index.rst
@@ -80,4 +80,4 @@ General methods
 
    fiat.FiatModel.set_geoms
    fiat.FiatModel.read_geoms
-   fiat.FiatModel.write_geoms
+   fiat.FiatModel.write_geoms
diff --git a/docs/data/data_sources.rst b/docs/data/data_sources.rst
@@ -4,7 +4,7 @@
 ======================
 Data Sources
 ======================
-With the HydroMT-FIAT package you can easily access exposure and vulnerability data from different sources. 
+With the HydroMT-FIAT package you can easily access exposure and vulnerability data from different sources.
 The following data sources are currently supported:
 
 
@@ -21,4 +21,4 @@ The following data sources are currently supported:
    national_structure_inventory
    openstreetmap
    jrc
-   hazus
+   hazus
diff --git a/docs/data/hazus.rst b/docs/data/hazus.rst
@@ -4,11 +4,11 @@
 HAZUS flood depth-damage functions
 ===============================================
 
-Users of **HydroMT-FIAT** can directly and easily make use of the depth-damage 
-functions and repair values from `HAZUS 
-<https://www.fema.gov/flood-maps/products-tools/hazus>`_. Hazus is a US-based 
-program and the depth-damage functions are based on US data. The functions and 
-values can be used only together with the `hydromt_fiat_catalog_USA.yml` and 
+Users of **HydroMT-FIAT** can directly and easily make use of the depth-damage
+functions and repair values from `HAZUS
+<https://www.fema.gov/flood-maps/products-tools/hazus>`_. Hazus is a US-based
+program and the depth-damage functions are based on US data. The functions and
+values can be used only together with the `hydromt_fiat_catalog_USA.yml` and
 by providing the following values in the configuration file::
 
     [setup_vulnerability]
@@ -21,6 +21,5 @@ by providing the following values in the configuration file::
     unit = "m"
 
 
-The HAZUS flood depth-damage functions and replacement values are processed into an easy-to-use format 
+The HAZUS flood depth-damage functions and replacement values are processed into an easy-to-use format
 for HydroMT-FIAT and stored in the ``hydromt_fiat/data`` folder.
-
diff --git a/docs/data/jrc.rst b/docs/data/jrc.rst
@@ -4,9 +4,9 @@
 JRC Global flood depth-damage functions
 ===============================================
 
-Users of **HydroMT-FIAT** can directly and easily make use of the `JRC Global flood depth-damage functions and 
-replacement values <https://publications.jrc.ec.europa.eu/repository/handle/JRC105688>`_ [1]. The functions and 
-values can be used only together with the `hydromt_fiat_catalog_global.yml` and 
+Users of **HydroMT-FIAT** can directly and easily make use of the `JRC Global flood depth-damage functions and
+replacement values <https://publications.jrc.ec.europa.eu/repository/handle/JRC105688>`_ [1]. The functions and
+values can be used only together with the `hydromt_fiat_catalog_global.yml` and
 by providing the following values in the configuration file::
 
     [setup_vulnerability]
@@ -19,10 +19,10 @@ by providing the following values in the configuration file::
     unit = "m"
 
 
-The JRC Global flood depth-damage functions and replacement values are processed into an easy-to-use format 
+The JRC Global flood depth-damage functions and replacement values are processed into an easy-to-use format
 for HydroMT-FIAT and stored in the ``hydromt_fiat/data`` folder.
 
 
-[1] Huizinga, J., De Moel, H. and Szewczyk, W., Global flood depth-damage functions: Methodology 
-and the database with guidelines, EUR 28552 EN, Publications Office of the European Union, Luxembourg, 
-2017, ISBN 978-92-79-67781-6, doi:10.2760/16510, JRC105688.
+[1] Huizinga, J., De Moel, H. and Szewczyk, W., Global flood depth-damage functions: Methodology
+and the database with guidelines, EUR 28552 EN, Publications Office of the European Union, Luxembourg,
+2017, ISBN 978-92-79-67781-6, doi:10.2760/16510, JRC105688.
diff --git a/docs/data/national_structure_inventory.rst b/docs/data/national_structure_inventory.rst
@@ -4,16 +4,16 @@
 National Structure Inventory (USA)
 ==================================
 
-For projects in the United States, users of **HydroMT-FIAT** can directly and easily make use 
-of the `National Structure Inventory <https://www.hec.usace.army.mil/confluence/nsi>`_ (NSI). The 
+For projects in the United States, users of **HydroMT-FIAT** can directly and easily make use
+of the `National Structure Inventory <https://www.hec.usace.army.mil/confluence/nsi>`_ (NSI). The
 user can access the data through providing 'NSI' in the configuration file as such::
 
     [setup_exposure_buildings]
     asset_locations = "NSI"
     occupancy_type = "NSI"
     max_potential_damage = "NSI"
 
-The following attributes for Delft-FIAT (left-hand side) will be filled with data from the 
+The following attributes for Delft-FIAT (left-hand side) will be filled with data from the
 corresponding NSI fields (right-hand side)::
 
     "Object ID": "fd_id",
@@ -27,8 +27,8 @@ corresponding NSI fields (right-hand side)::
     "Y Coordinate": "y",
     "Aggregation Label: Census Block": "cbfips"
 
-HydroMT-FIAT obtains the NSI data of the area of interest through the `NSI API 
+HydroMT-FIAT obtains the NSI data of the area of interest through the `NSI API
 <https://www.hec.usace.army.mil/confluence/nsi/technicalreferences/latest/api-reference-guide>`_.
 
-For more information about this data we refer to their online `Technical Documentation 
+For more information about this data we refer to their online `Technical Documentation
 <https://www.hec.usace.army.mil/confluence/nsi/technicalreferences/latest/technical-documentation>`_.
diff --git a/docs/data/openstreetmap.rst b/docs/data/openstreetmap.rst
@@ -4,7 +4,7 @@
 OpenStreetMap Building Footprints and Land Use
 ===============================================
 
-Users of **HydroMT-FIAT** can directly and easily make use of the `OpenStreetMap <https://www.openstreetmap.org/about>`_ 
+Users of **HydroMT-FIAT** can directly and easily make use of the `OpenStreetMap <https://www.openstreetmap.org/about>`_
 (OSM) initiative. The user can access the data through providing 'OSM' in the configuration file as such::
 
     [setup_exposure_buildings]
@@ -14,6 +14,6 @@ Users of **HydroMT-FIAT** can directly and easily make use of the `OpenStreetMap
 HydroMT-FIAT obtains the OSM data of the area of interest through the OSMnx package [1].
 
 
-[1] Boeing, G. 2017. "`OSMnx: New Methods for Acquiring, Constructing, Analyzing, and Visualizing Complex 
-Street Networks. <https://geoffboeing.com/publications/osmnx-complex-street-networks/>`_" Computers, Environment 
-and Urban Systems 65, 126-139.
+[1] Boeing, G. 2017. "`OSMnx: New Methods for Acquiring, Constructing, Analyzing, and Visualizing Complex
+Street Networks. <https://geoffboeing.com/publications/osmnx-complex-street-networks/>`_" Computers, Environment
+and Urban Systems 65, 126-139.
diff --git a/docs/index.rst b/docs/index.rst
@@ -2,8 +2,8 @@
 HydroMT-FIAT: Automated and reproducible Delft-FIAT model building
 =====================================================================
 
-With the `HydroMT-FIAT plugin <https://github.com/Deltares/hydromt_fiat>`_, users can easily benefit 
-from the rich set of tools of the `HydroMT package <https://github.com/Deltares/hydromt>`_ to build and update 
+With the `HydroMT-FIAT plugin <https://github.com/Deltares/hydromt_fiat>`_, users can easily benefit
+from the rich set of tools of the `HydroMT package <https://github.com/Deltares/hydromt>`_ to build and update
 `Delft-FIAT <https://github.com/Deltares/Delft-FIAT>`_ models from available global and local data.
 
 This plugin assists the FIAT modeller in:
@@ -12,7 +12,7 @@ This plugin assists the FIAT modeller in:
 - Creating a Social Vulnerability Index (SVI) based on US Census or user-input data.
 - Adjusting and updating components of a Delft-FIAT model and their associated parameters in a consistent way.
 
-The HydroMT-FIAT plugin aims to make the FIAT model building process **fast**, **modular**, and **reproducible** 
+The HydroMT-FIAT plugin aims to make the FIAT model building process **fast**, **modular**, and **reproducible**
 by configuring the model building process from single *yml* file.
 
 For detailed information on HydroMT itself, you can visit the `core documentation <https://deltares.github.io/hydromt/>`_.
@@ -44,18 +44,18 @@ Overview
 Contributing
 ------------
 
-To contribute to HydroMT and the plugin plugin, please follow the 
+To contribute to HydroMT and the plugin plugin, please follow the
 `HydroMT contribution guidelines <https://deltares.github.io/hydromt/latest/contributing.html>`_.
 
 License
 -------
 
 Copyright (c) 2021, Deltares
 
-This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public 
+This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public
 License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
 
-This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty 
+This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty
 of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
 
 You can find the full terms of the GNU General Public License at <https://www.gnu.org/licenses/>.

diff --git a/docs/installation.rst b/docs/installation.rst
@@ -16,32 +16,32 @@ To create a new environment follow the steps below.
 1. Create a new environment:
 
 .. code-block:: console
-    
+
     conda create -n hydromt_fiat python=3.11.*
 
 2. Activate the environment:
 
 .. code-block:: console
-    
+
     conda activate hydromt_fiat
 
 3. Install conda-forge gdal.
 
 .. code-block:: console
-    
+
     conda install -c conda-forge gdal
 
 4. Install Hydromt-FIAT from Github. After creating the new environment, you need to install all dependencies from the Deltares Github repository. You can use **pip install** to do so:
 
 .. code-block:: console
-    
+
     pip install git+https://github.com/Deltares/hydromt_fiat.git
 
 Existing environment
 If you want to install FIAT into an existing environment, simply activate the desired environment and run:
 
 .. code-block:: console
-    
+
     pip install git+https://github.com/Deltares/hydromt_fiat.git
 
 

diff --git a/docs/user_guide/hazard.rst b/docs/user_guide/hazard.rst
@@ -6,4 +6,3 @@ Hazard Module
 =======================
 
 Coming soon..
-
diff --git a/docs/user_guide/social_vulnerability_index.rst b/docs/user_guide/social_vulnerability_index.rst
@@ -6,4 +6,3 @@ Social Vulnerability Index Module
 =================================
 
 Coming soon..
-