Merge pull request #708 from kordejong/gh707

Add pre-commit hooks for checking markdown formatting and spelling / prose errors
computationalgeography · Aug 14, 2024 · 614b8eb · 614b8eb
2 parents afcee0c + b40141a
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diff --git a/.editorconfig b/.editorconfig
@@ -10,7 +10,7 @@ insert_final_newline = true
 max_line_length = 80
 trim_trailing_whitespace = true
 
-[*.{c,cpp,h,hpp,md,rst,txt}]
+[*.{c,cpp,h,hpp,md,rb,rst,txt,yaml,yml}]
 max_line_length = 110
 
 [*.py]

diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
@@ -1,3 +1,5 @@
 # Contributing
 
-There are various ways to contribute to the development of LUE. Please visit the [Contributing page](https://lue.computationalgeography.org/doc/contribute) in the LUE documentation, which contains information about all of these.
+There are various ways to contribute to the development of LUE. Please visit the [Contributing
+page](https://lue.computationalgeography.org/doc/contribute) in the LUE documentation, which contains
+information about all of these.
diff --git a/.github/ISSUE_TEMPLATE/1_bug_report.yaml b/.github/ISSUE_TEMPLATE/1_bug_report.yaml
@@ -17,7 +17,7 @@ body:
       required: true
 
   - type: textarea
-    id: bug_expexted
+    id: bug_expected
     attributes:
       label: Expected behaviour
       placeholder: A concise description of what you expected to happen.

diff --git a/.mdl_style.rb b/.mdl_style.rb
@@ -0,0 +1,15 @@
+# https://github.com/markdownlint/markdownlint/blob/main/docs/configuration.md
+# https://github.com/markdownlint/markdownlint/blob/main/docs/RULES.md
+all
+exclude_rule 'MD004'
+exclude_rule 'MD005'
+exclude_rule 'MD012'
+exclude_rule 'MD024'
+exclude_rule 'MD030'
+exclude_rule 'MD034'
+exclude_rule 'MD041'
+exclude_rule 'MD046'
+
+# The parameters which can be changed are mentioned in the rules page (Parameters: ...)
+rule 'MD013', :line_length => 110
+rule 'MD007', :indent => 4
diff --git a/.mdlrc b/.mdlrc
@@ -0,0 +1 @@
+style '.mdl_style.rb'
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -18,11 +18,11 @@ repos:
   # - id: check-yaml
   - id: check-added-large-files
 - repo: https://github.com/psf/black
-  rev: 24.4.2
+  rev: 24.8.0
   hooks:
   - id: black
 - repo: https://github.com/pre-commit/mirrors-mypy
-  rev: v1.11.0
+  rev: v1.11.1
   hooks:
   - id: mypy
     # args: [--verbose]
@@ -45,6 +45,22 @@ repos:
         .*\.py|
         .*\.py.in|
       )$
+- repo: https://github.com/markdownlint/markdownlint
+  rev: v0.13.0
+  hooks:
+  - id: markdownlint
+- repo: https://github.com/codespell-project/codespell
+  rev: v2.3.0
+  hooks:
+  - id: codespell
+    additional_dependencies:
+    - tomli
+- repo: https://github.com/crate-ci/typos
+  rev: v1.23.6
+  hooks:
+  - id: typos
+    args: []  # Relevant: don't update files, just report
+# This one last. It is the slowest. --------------------------------------------
 - repo: https://github.com/pocc/pre-commit-hooks
   rev: v1.3.5
   hooks:
@@ -55,6 +71,7 @@ repos:
     exclude: |
       (?x)^(
         source/data_model/cxx/.*|
+        source/data_model/gdal/include/lue/gdal/library.hpp|
         source/data_model/hl/.*|
         source/data_model/python/.*|
         source/data_model/test/.*|

diff --git a/LICENSE.txt b/LICENSE.txt
@@ -18,4 +18,4 @@ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
+SOFTWARE.
diff --git a/README.md b/README.md
@@ -1,4 +1,5 @@
 # LUE
+
 LUE scientific database and environmental modelling framework
 
 LUE is software for storing and manipulating large amounts of information
@@ -27,13 +28,16 @@ the related technology.
     - [Documentation](https://lue.computationalgeography.org/doc)
     - [Publications](https://lue.computationalgeography.org/publication)
 - [R&D team](https://www.computationalgeography.org)
-- [![Chat with us on Matrix](https://img.shields.io/badge/chat-on%20Matrix-%230098D4)](https://matrix.to/#/#lue:matrix.org) (users)
-- [![Chat with us on Matrix](https://img.shields.io/badge/chat-on%20Matrix-%230098D4)](https://matrix.to/#/#lue-dev:matrix.org) (developers)
+- [![Chat with us on Matrix](https://img.shields.io/badge/chat-on%20Matrix-%230098D4)](https://matrix.to/#/#lue:matrix.org)
+  (users)
+- [![Chat with us on Matrix](https://img.shields.io/badge/chat-on%20Matrix-%230098D4)](https://matrix.to/#/#lue-dev:matrix.org)
+  (developers)
 
 [![Latest release](https://zenodo.org/badge/DOI/10.5281/zenodo.5535685.svg)](https://doi.org/10.5281/zenodo.5535685)
 
 
 ## Source code
+
 [![License](https://img.shields.io/github/license/mashape/apistatus.svg)](https://github.com/computationalgeography/lue/)
 [![Codacy Badge](https://app.codacy.com/project/badge/Grade/2c02fc1c5b13424abfc414b82104801d)](https://www.codacy.com/gh/computationalgeography/lue/dashboard?utm_source=github.com&amp;utm_medium=referral&amp;utm_content=computationalgeography/lue&amp;utm_campaign=Badge_Grade)
 [![pre-commit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit)](https://github.com/pre-commit/pre-commit)
@@ -43,18 +47,21 @@ the related technology.
 
 
 ## C/I builds
+
 [![Linux build status](https://github.com/computationalgeography/lue/actions/workflows/linux.yml/badge.svg)](https://github.com/computationalgeography/lue/actions/workflows/linux.yml)
 [![macOS build status](https://github.com/computationalgeography/lue/actions/workflows/macos.yml/badge.svg)](https://github.com/computationalgeography/lue/actions/workflows/macos.yml)
 [![Windows build status](https://github.com/computationalgeography/lue/actions/workflows/windows.yml/badge.svg)](https://github.com/computationalgeography/lue/actions/workflows/windows.yml)
 
 [![Conda packages build status](https://github.com/computationalgeography/lue/actions/workflows/conda.yml/badge.svg)](https://github.com/computationalgeography/lue/actions/workflows/conda.yml)
 
 ## Installation
+
 [![Anaconda-Server Badge](https://anaconda.org/conda-forge/lue/badges/version.svg)](https://anaconda.org/conda-forge/lue)
 [![Anaconda-Server Badge](https://anaconda.org/conda-forge/lue/badges/platforms.svg)](https://anaconda.org/conda-forge/lue)
 [![Anaconda-Server Badge](https://anaconda.org/conda-forge/lue/badges/downloads.svg)](https://anaconda.org/conda-forge/lue)
 
 The easiest way to install LUE is using Conda:
+
 ```bash
 conda install -c conda-forge lue
 ```

diff --git a/conanfile.py b/conanfile.py
@@ -1,6 +1,7 @@
 """
 Conan recipe
 """
+
 import os
 import shutil
 

diff --git a/document/doc/about/project.md b/document/doc/about/project.md
@@ -1,4 +1,5 @@
 (doc-about-project)=
+
 # Project
 
 ```{include} short_description.md

diff --git a/document/doc/about/related.md b/document/doc/about/related.md
@@ -13,11 +13,14 @@
 %    rasdaman / SciDB (distributed storage, computing?)
 %
 %    https://geotrellis.io/
-%    GeoTrellis provides a number of operations to manipulate raster data, including cropping/warping, Map Algebra operations, and rendering operations, as well as vector to raster operations such as Kernel Density and vectorization of raster data.
+%    GeoTrellis provides a number of operations to manipulate raster data, including cropping/warping, Map
+%    Algebra operations, and rendering operations, as well as vector to raster operations such as Kernel
+%    Density and vectorization of raster data.
 %
 %
 %    https://openeo.org/
-%    openEO develops an open API to connect R, Python, JavaScript and other clients to big Earth observation cloud back-ends in a simple and unified way.
+%    openEO develops an open API to connect R, Python, JavaScript and other clients to big Earth observation
+%    cloud back-ends in a simple and unified way.
 %
 %
 %    xarray combined with dask (distributed  computing)
@@ -27,12 +30,13 @@
 %    agents:
 %
 %    https://en.wikipedia.org/wiki/SARL_language
-%    SARL language level are supported by this run-time environment: fully distributed, parallel execution of agent’s behaviors
+%    SARL language level are supported by this run-time environment: fully distributed, parallel execution of
+%    agent’s behaviors
 %
 %    hier vandaan...
 %    https://en.wikipedia.org/wiki/Comparison_of_agent-based_modeling_software
 %
-%    ik denk niet dat netlogo distributed kan, repast misschien wel...
+%    ik denk niet dat netlogo distributed kan, repast misschien well...
 %
 %
 %

diff --git a/document/doc/about/release.md b/document/doc/about/release.md
@@ -1,4 +1,5 @@
 (doc-about-release)=
+
 # Releases
 
 ## 0.3.8 (WIP)

diff --git a/document/doc/contribute/index.md b/document/doc/contribute/index.md
@@ -1,4 +1,5 @@
 (doc-contribute)=
+
 # Contribute
 
 Thank you for investing your time in contributing to this project!

diff --git a/document/doc/contribute/release.md b/document/doc/contribute/release.md
@@ -38,7 +38,7 @@ Information about this can be found on the [lue-feedstock page](https://github.c
 at Github.
 
 The pull request is based on a new branch in a clone of the `lue-feedstock` repository, located in the
-`regro-cf-autotick-bot` Github organisation. To make changes to this branch, the folowing workflow can be
+`regro-cf-autotick-bot` Github organisation. To make changes to this branch, the following workflow can be
 used:
 
 ```bash

diff --git a/document/doc/manual/framework/execute.md b/document/doc/manual/framework/execute.md
@@ -44,6 +44,7 @@ starting LUE Python scripts like this solved the crashes:
 ```bash
 LD_PRELOAD=<prefix>/lib/libtcmalloc_minimal.so.4 python ./my_lue_script.py
 ```
+
 :::
 
 

diff --git a/document/doc/manual/index.md b/document/doc/manual/index.md
@@ -1,2 +1,3 @@
 (doc-manual)=
+
 # Manual
diff --git a/document/doc/manual/install/source.md b/document/doc/manual/install/source.md
@@ -92,8 +92,8 @@ Optional features:
 | ---                                   | ---     | --- |
 | `LUE_QA_WITH_PYTHON_API`              | `FALSE` | Build QA Python API |
 | `LUE_QA_WITH_TESTS`                   | `FALSE` | Build test targets |
-| `LUE_QA_TEST_NR_LOCALITIES_PER_TEST`  | `1`     | Number of localities used when testing the framework |
-| `LUE_QA_TEST_NR_THREADS_PER_LOCALITY` | `1`     | Number of threads per locality used when testing the framework |
+| `LUE_QA_TEST_NR_LOCALITIES_PER_TEST`  | `1`     | Localities used when testing the framework |
+| `LUE_QA_TEST_NR_THREADS_PER_LOCALITY` | `1`     | Threads per locality used when testing the framework |
 | `LUE_QA_TEST_HPX_RUNWRAPPER`          | `none`  | Runwrapper to use (see `hpxrun.py`) |
 | `LUE_QA_TEST_HPX_PARCELPORT`          | `tcp`   | Parcelport to use (see `hpxrun.py`) |
 
@@ -106,7 +106,7 @@ requires that HPX is built with support for networking.
 #### Dependencies
 
 - Nlohmann JSON
-- `LUE_QA_WITH_TESTS`: Boost filesytem, sytem, unit-test framework libraries
+- `LUE_QA_WITH_TESTS`: Boost filesystem, system, unit-test framework libraries
 - `LUE_QA_WITH_PYTHON_API`: pybind11, Python
 
 
@@ -115,8 +115,8 @@ requires that HPX is built with support for networking.
 There are at least three options for installing prerequisite libraries and tools:
 
 1. Install using platform specific package manager
-2. Install using Conan, either before building LUE or by the LUE build scripts
-3. Build by the LUE build scripts
+1. Install using Conan, either before building LUE or by the LUE build scripts
+1. Build by the LUE build scripts
 
 The next variables determine what happens in each case by default.
 

diff --git a/document/doc/pcraster/status.md b/document/doc/pcraster/status.md
@@ -502,6 +502,7 @@ these differences as much as possible.
 *   - ycoordinate
     - 🗑
     - Not sure why this is useful...
+
 :::
 
 %    In LUE, not in PCRaster:

diff --git a/document/doc/quick_start/index.md b/document/doc/quick_start/index.md
@@ -1,5 +1,5 @@
 # Quick start
 
-Here, you will find just enough information to get started with using LUE. It is targetted at model
+Here, you will find just enough information to get started with using LUE. It is targeted at model
 developers. We will be implementing [Conway's Game of
 Life](https://en.wikipedia.org/wiki/Conway's_Game_of_Life) and execute it in parallel, using a single process.
diff --git a/document/doc/quick_start/python.md b/document/doc/quick_start/python.md
@@ -1,6 +1,7 @@
 # Game of Life in Python
 
 ## Install
+
 ```bash
 conda install -c conda-forge lue
 ```

diff --git a/document/doc/reference/python/framework/trigonometry.rst b/document/doc/reference/python/framework/trigonometry.rst
@@ -17,7 +17,7 @@ Trigonometry
 
    Compute the principal value of the arc cosine
 
-   :parm cosine: Datastructure containing cosines
+   :param cosine: Datastructure containing cosines
    :return: New instance of the same datastructure as passed in
 
    This function is overloaded for arrays containing float32 and float64 elements.
@@ -27,7 +27,7 @@ Trigonometry
 
    Compute the principal value of the arc sine
 
-   :parm sine: Datastructure containing sines
+   :param sine: Datastructure containing sines
    :return: New instance of the same datastructure as passed in
 
    This function is overloaded for arrays containing float32 and float64 elements.
@@ -37,7 +37,7 @@ Trigonometry
 
    Compute the principal value of the arc tangent
 
-   :parm tangent: Datastructure containing tangents
+   :param tangent: Datastructure containing tangents
    :return: New instance of the same datastructure as passed in
 
    This function is overloaded for arrays containing float32 and float64 elements.
@@ -47,8 +47,8 @@ Trigonometry
 
    Compute the arc tangent of y/x
 
-   :parm y: Datastructure containing distances in y-direction
-   :parm x: Datastructure containing distances in x-direction
+   :param y: Datastructure containing distances in y-direction
+   :param x: Datastructure containing distances in x-direction
    :return: New instance of the same datastructure as passed in
 
    This function is overloaded for arrays containing float32 and float64 elements.
@@ -60,7 +60,7 @@ Trigonometry
 
    Compute the cosine
 
-   :parm angle: Datastructure containing angles in radians
+   :param angle: Datastructure containing angles in radians
    :return: New instance of the same datastructure as passed in
 
    This function is overloaded for arrays containing float32 and float64 elements.
@@ -70,7 +70,7 @@ Trigonometry
 
    Compute the sine
 
-   :parm angle: Datastructure containing angles in radians
+   :param angle: Datastructure containing angles in radians
    :return: New instance of the same datastructure as passed in
 
    This function is overloaded for arrays containing float32 and float64 elements.
@@ -80,7 +80,7 @@ Trigonometry
 
    Compute the tangent
 
-   :parm angle: Datastructure containing angles in radians
+   :param angle: Datastructure containing angles in radians
    :return: New instance of the same datastructure as passed in
 
    This function is overloaded for arrays containing float32 and float64 elements.
diff --git a/document/luepy/case_study/elevation.py b/document/luepy/case_study/elevation.py
@@ -36,7 +36,7 @@
 ### time_boxes = time_domain.reserve(nr_time_boxes)
 ### # A box is defined by a begin and end time point (two coordinates per box)
 ### # Here, we configure time boxes with a duration of 10 days. The time
-### # inbetween the boxes is time were we don't have information.
+### # in between the boxes is time were we don't have information.
 ### time_boxes[:] = np.array([  # Dummy data...
 ###         [10,  20],
 ###         [30,  40],
@@ -67,7 +67,7 @@
 ### nr_cells = nr_cells.reshape(nr_areas, 2)
 ### space_discretization.values.reserve(nr_areas)[:] = nr_cells
 ###
-### # Re-use nr_cells array with shapes of spatial fields, but add information
+### # Reuse nr_cells array with shapes of spatial fields, but add information
 ### # about the number of time steps. The resulting values will be
 ### # [nr_time_steps, nr_rows, nr_cols], where nr_rows, nr_cols is different
 ### # for each raster.

diff --git a/document/luepy/discretization.rst b/document/luepy/discretization.rst
@@ -1,6 +1,10 @@
 Discretization
 ==============
-LUE property values can be discretized. This is one way to store the continuous variation of some property value through the time and/or space domain. For example, to store the continuous variation of topographic elevation in an area, to folowing approach can be used (assuming elevation does not change over the time considered):
+
+LUE property values can be discretized. This is one way to store the continuous variation of some property
+value through the time and/or space domain. For example, to store the continuous variation of topographic
+elevation in an area, to following approach can be used (assuming elevation does not change over the time
+considered):
 
 - property set
     - time domain: omnipresent
@@ -18,7 +22,8 @@ LUE property values can be discretized. This is one way to store the continuous
 
 The result of this layout is a representation in the LUE data model of zero or more rasters. In general, the information required to understand the way a property value is discretized is stored itself in a property. This discretization property is a property like any other property, but it is linked to a property whose values are discretized using a special keyword (`lue_space_discretization` in the above example). This means that the domain of a discretization property can be different from the property being discretized.
 
-In the folowing sections the approach is described of storing continuous varying property values according to different kinds of discretization.
+In the following sections the approach is described of storing continuous varying property values according to
+different kinds of discretization.
 
 
 Variation through time

diff --git a/document/luepy/installation.rst b/document/luepy/installation.rst
@@ -14,7 +14,7 @@ The LUE package can be installed with `conda`::
 
         $ pip install --upgrade lue
 
-    During the installation a C++ compiler will be used to compile some source files. The LUE C++ sources depend on the folowing packages to be installed:
+    During the installation a C++ compiler will be used to compile some source files. The LUE C++ sources depend on the following packages to be installed:
 
     - `boost`_ C++ libraries (headers)
     - `hdf5`_ C library (library and headers)

diff --git a/document/luepy/naming.rst b/document/luepy/naming.rst
@@ -5,7 +5,7 @@ The LUE datamodel requires you to provide names for various things. Here, we pro
 
 Style
 -----
-See `PEP 8 -- Style Guide for Python Code`_, especially the `section about naming conventions`_ for information about styling Python code in general. Given the information in PEP 8, we adopted the folowing naming rule for naming things in de LUE datamodel: "use lowercase with words separated by underscores as necessary to improve readability".
+See `PEP 8 -- Style Guide for Python Code`_, especially the `section about naming conventions`_ for information about styling Python code in general. Given the information in PEP 8, we adopted the following naming rule for naming things in de LUE datamodel: "use lowercase with words separated by underscores as necessary to improve readability".
 
 
 .. _PEP 8 -- Style Guide for Python Code: https://www.python.org/dev/peps/pep-0008/
-Original file line number
+Diff line change
@@ Expand Up / @@ -44,6 +44,7 @@ starting LUE Python scripts like this solved the crashes: @@
     ```bash
     LD_PRELOAD=<prefix>/lib/libtcmalloc_minimal.so.4 python ./my_lue_script.py
     ```
     :::
@@ Expand Down @@