Run mdformat and generalize noxfile.py

Author: f-PLT

.mdformat.toml

@@ -0,0 +1,2 @@
+number = true
+extensions = ["gfm", "gfm_alerts"]

.pre-commit-config.yaml

@@ -1,4 +1,4 @@
-exclude: ^docs/|/migrations/|Makefile*
+exclude: "^docs/|/migrations/|Makefile*"
 default_stages: [ commit ]
 
 repos:
@@ -56,6 +56,21 @@ repos:
     hooks:
       - id: flynt
 
+  - repo: https://github.com/tcort/markdown-link-check
+    rev: v3.13.7
+    hooks:
+      - id: markdown-link-check
+        args: [ -q ]
+
+  - repo: https://github.com/hukkin/mdformat
+    rev: 0.7.22
+    hooks:
+      - id: mdformat
+        additional_dependencies:
+          - mdformat-gfm
+          - mdformat-gfm-alerts
+
+
 # sets up .pre-commit-ci.yaml to ensure pre-commit dependencies stay up to date
 ci:
   autoupdate_schedule: weekly

CHANGES.md

@@ -1,32 +1,36 @@
 # CHANGES.md
 
 [Unreleased](https://github.com/RolnickLab/geospatial-tools/tree/main) (latest)
--------------------------------------------------------------------------------------
 
-* Refactor the stac.py module to extract logic that belongs more in raster.py
-* Update the makefile
-* Update the project dependencies
-* Add new QA tools : `autoflake`, `autopep8` and `ruff`
+______________________________________________________________________
+
+- Refactor the stac.py module to extract logic that belongs more in raster.py
+- Update the makefile
+- Update the project dependencies
+- Add new QA tools : `autoflake`, `autopep8` and `ruff`
 
 [0.1.3](https://github.com/RolnickLab/geospatial-tools/tree/0.1.3) (2024-09-23)
--------------------------------------------------------------------------------------
+
+______________________________________________________________________
 
 - Convert project to use `nox` instead of `tox` for cluster storage optimization.
 
 [0.1.2](https://github.com/RolnickLab/geospatial-tools/tree/0.1.2) (2024-09-23)
--------------------------------------------------------------------------------------
 
-- Fix `docformatter` with missing extra dependency for use with `pyproject.toml`
+______________________________________________________________________
 
+- Fix `docformatter` with missing extra dependency for use with `pyproject.toml`
 
 [0.1.1](https://github.com/RolnickLab/geospatial-tools/tree/0.1.1) (2024-09-20)
--------------------------------------------------------------------------------------
+
+______________________________________________________________________
 
 - Fix `black` dependency that was not correctly setup in dev dependency group
 
 [0.1.0](https://github.com/RolnickLab/geospatial-tools/tree/0.1.0) (2024-09-20)
--------------------------------------------------------------------------------------
-	
+
+______________________________________________________________________
+
 - Add `resample_tiff_raster.py` script
 - Implement functions for clipping and reprojecting raster images
 - Implement vector functions for grid creation
@@ -35,4 +39,4 @@
 - Implement functions and scripts to search for and process Sentinel 2 products from
   Microsoft's Planetary Computer
 - Add examples of the above in Jupyter notebook formats
-- Add tests and notebook tests
+- Add tests and notebook tests

CONTRIBUTING.md

@@ -17,44 +17,45 @@ To add a new dependency with a specific version:
 poetry add "<dependency_name>==<x.x.x>"
 ```
 
-To add a new dependency to a specific group of dependencies 
+To add a new dependency to a specific group of dependencies
 (for example, the development dependencies):
 
 ```
 poetry add --group dev <dependency_name>
 ```
 
 ## Design patterns
+
 Two main considerations should be made when contributing to this package.
 
 First, a polymorphic approach, using abstract classes and their concrete implementation,
 should be prioritized in order to increase maintainability and extensibility.
 
 Therefore, new additions should try to follow this design pattern and either implement
-new concrete classes or create new abstract classes and their implementations for 
+new concrete classes or create new abstract classes and their implementations for
 completely new behavior or needs.
 
-Avoid multiple levels of inheritance; the approach should be _AbstractClass -> 
-[ConcreteClass1, ConcreteClass2, ...]_ and not 
+Avoid multiple levels of inheritance; the approach should be _AbstractClass ->
+[ConcreteClass1, ConcreteClass2, ...]_ and not
 _AbstractClass -> ChildClass -> GrandChildClass -> ..._
 
-Next, a dependency-injection approach is to be preferred, as well as a composition 
+Next, a dependency-injection approach is to be preferred, as well as a composition
 approach when creating new modules or extending existing ones.
 
 Functional approaches are also acceptable when appropriate, but classes should still
-be used for data management/representation. This can be done with either regular 
+be used for data management/representation. This can be done with either regular
 classes, `dataclasses`, or `pydantic` models.
 
 ## Tests
 
-New contributions should include appropriate tests. Pytest is the preferred library to 
+New contributions should include appropriate tests. Pytest is the preferred library to
 use for testing in this project.
 
 To get started and to learn more about testing in Python:
 
-* [Getting started with testing](https://realpython.com/python-testing/)
-* [Testing in the contest of Machine Learning](https://fullstackdeeplearning.com/course/2022/lecture-3-troubleshooting-and-testing/)
-* [Pytest Documentation](https://docs.pytest.org/en/stable/how-to/index.html)
+- [Getting started with testing](https://realpython.com/python-testing/)
+- [Testing in the contest of Machine Learning](https://fullstackdeeplearning.com/course/2022/lecture-3-troubleshooting-and-testing/)
+- [Pytest Documentation](https://docs.pytest.org/en/stable/how-to/index.html)
 
 ## Docstring and type hinting
 

README.md

@@ -14,18 +14,18 @@ machine there's a good chance this will work.
 
 The following Makefile files should not be modified, but can be consulted:
 
-* [Makefile](Makefile) : Orchestration of the different files
-* [base.make](.make/base.make) : Shared utilities, project agnostic.
+- [Makefile](Makefile) : Orchestration of the different files
+- [base.make](.make/base.make) : Shared utilities, project agnostic.
 
 The following Makefile files are project or user specific:
 
-* [Makefile.variables](Makefile.variables) : Shared project variables.
-* [Makefile.targets](Makefile.targets) : Shared project targets.
-* [Makefile.private](Makefile.private.example) : User specific variables and targets.
-    * This file is ignored by git and should never be committed, as it can also contain
-      secrets.
-    * You can create your own version locally by copying from
-      [Makefile.private.example](Makefile.private.example)
+- [Makefile.variables](Makefile.variables) : Shared project variables.
+- [Makefile.targets](Makefile.targets) : Shared project targets.
+- [Makefile.private](Makefile.private.example) : User specific variables and targets.
+  - This file is ignored by git and should never be committed, as it can also contain
+    secrets.
+  - You can create your own version locally by copying from
+    [Makefile.private.example](Makefile.private.example)
 
 ## Basic Information
 
@@ -49,8 +49,8 @@ streamlining script use as well as fix path issues related to imports.
 
 If on a compute cluster, first load the appropriate python module:
 
-* [How to create a virtual environment for the Mila cluster](docs/environment_creation_mila.md)
-* [How to create an environment for the DRAC cluster](docs/environment_creation_drac.md)
+- [How to create a virtual environment for the Mila cluster](docs/environment_creation_mila.md)
+- [How to create an environment for the DRAC cluster](docs/environment_creation_drac.md)
 
 Installing `pipx` and `poetry`:
 
@@ -97,9 +97,9 @@ on [how to use your poetry virtual environment](https://python-poetry.org/docs/b
 
 You can:
 
-* Use the `poetry run` command to access your executables
-    * ex. `poetry run python your_script.py`, or `poetry run pylint src/`
-* Use the `poetry shell` command to activate and step in your project environment
+- Use the `poetry run` command to access your executables
+  - ex. `poetry run python your_script.py`, or `poetry run pylint src/`
+- Use the `poetry shell` command to activate and step in your project environment
 
 #### Conda
 
@@ -114,7 +114,7 @@ If working on the Mila cluster, first load the appropriate module :
 make conda-create-env
 ```
 
-2. Activate `conda` environment (substitute with your <CONDA_TOOL> if something else
+2. Activate `conda` environment (substitute with your \<CONDA_TOOL> if something else
    than `conda`:
 
 ```
@@ -154,8 +154,8 @@ This also installs and configures the `pre-commit` hook. See ...
 This project assumes environment management will be done with `conda`, a classic
 python virtual environment, or directly through `poetry`.
 
-* [Poetry](https://python-poetry.org/docs/basic-usage/)
-* [Conda](https://conda.io/projects/conda/en/latest/user-guide/getting-started.html)
+- [Poetry](https://python-poetry.org/docs/basic-usage/)
+- [Conda](https://conda.io/projects/conda/en/latest/user-guide/getting-started.html)
 
 While it is possible to manage the environment with, for example, pyenv or virtualenv,
 those specific use cases are not supported by the Makefile and require users to set up
@@ -176,10 +176,10 @@ information.
 
 Your project will need a virtual environment for your dependencies.
 
-* [How to create a virtual environment for the Mila cluster](docs/environment_creation_mila.md)
-* [How to create an environment for the DRAC cluster](docs/environment_creation_drac.md)
-* [How to create a Conda environment](docs/conda_environment_creation.md)
-* [Migrating to DRAC from another environment](docs/migrating_to_drac.md)
+- [How to create a virtual environment for the Mila cluster](docs/environment_creation_mila.md)
+- [How to create an environment for the DRAC cluster](docs/environment_creation_drac.md)
+- [How to create a Conda environment](docs/conda_environment_creation.md)
+- [Migrating to DRAC from another environment](docs/migrating_to_drac.md)
 
 There are different ways of managing your python version in these environments. On the
 clusters, you have access to different python modules, and through `conda` you have access

data/README.md

@@ -4,10 +4,10 @@
 
 ### International
 
-* [NASA's EarthData](https://www.earthdata.nasa.gov/)
-* [USGS Earth Explorer](https://earthexplorer.usgs.gov/)
-* [Copernicus Open Access Hub](https://scihub.copernicus.eu/)
-* [Climate Data Store](https://cds.climate.copernicus.eu/cdsapp#!/home)
+- [NASA's EarthData](https://www.earthdata.nasa.gov/)
+- [USGS Earth Explorer](https://earthexplorer.usgs.gov/)
+- [Copernicus Open Access Hub](https://scihub.copernicus.eu/)
+- [Climate Data Store](https://cds.climate.copernicus.eu/cdsapp#!/home)
 
 ## Satellite data
 
@@ -25,9 +25,9 @@ The tiling grid can be found here in KML format : [](https://sentiwiki.copernicu
 
 ### Canada
 
-* [GEO.ca](https://geo.ca/) : Canada's geographic information portal
-* [Données Québec](https://www.donneesquebec.ca/) : Quebec's open data portal
+- [GEO.ca](https://geo.ca/) : Canada's geographic information portal
+- [Données Québec](https://www.donneesquebec.ca/) : Quebec's open data portal
 
 ### USA
 
-* [Cartographic Boundaries, Census Office](https://www.census.gov/geographies/mapping-files/time-series/geo/carto-boundary-file.html)
+- [Cartographic Boundaries, Census Office](https://www.census.gov/geographies/mapping-files/time-series/geo/carto-boundary-file.html)

notebooks/README.md

@@ -1,3 +1,3 @@
 # Notebooks
 
-Place to store all the project's notebooks
+Place to store all the project's notebooks