fix config file of linkchecker, fix some dead links in docs

Author: SarahAlidoost

.linkspector.yml

@@ -1,3 +1,8 @@
+dirs:
+  - ./docs
+excludedDirs:
+  - ./docs/notebooks
+  - ./docs/overrides
 ignorePatterns:
   - pattern: "^http://localhost"
   - pattern: "^https://doi.org/<replace-with-created-DOI>"
@@ -6,5 +11,4 @@ ignorePatterns:
   - pattern: "^https://test.pypi.org"
   - pattern: "^https://bestpractices.coreinfrastructure.org/projects/<replace-with-created-project-identifier>"
   - pattern: "^https://readthedocs.org/dashboard/import.*"
-
 useGitIgnore: true

docs/bmi.md

@@ -7,7 +7,7 @@ Basic Model Interface. For the model, we generated Matlab Compiler Runtime
 executable file (only available for x86 Linux). This requires installation of
 MCR. The other option is to use the Dockerized version of the executable,
 available on
-[ghcr.io/ecoextreml/stemmus_scope](ghcr.io/ecoextreml/stemmus_scope). For more
+[https://ghcr.io/ecoextreml/stemmus_scope](https://ghcr.io/ecoextreml/stemmus_scope). For more
 information on each method, see the sections below.
 
 ## Installation and setup

docs/downloading_global_data.md

@@ -46,8 +46,9 @@ A simple example for the parsing of the data is in
 
 ## DEM data from Copernicus
 
-A word doc for instructions is available
-[here](https://spacedata.copernicus.eu/documents/20123/121286/Copernicus+DEM+Open+HTTPS+Access.pdf/36c9adad-8488-f463-af43-573e68b7f481?t=1669283200177). A simple example for the parsing of the data is in
+DEM data is provided by Copernicus, see
+[here](https://dataspace.copernicus.eu/explore-data/data-collections/copernicus-contributing-missions/collections-description/COP-DEM).
+A simple example for the parsing of the data is in
 `global_data/data_analysis_notebooks/parse_dem.ipynb`.
 
 ## LAI from Climate Data Store (CDS)
@@ -58,4 +59,4 @@ data is in `global_data/data_analysis_notebooks/parse_LAI.py`.
 
 ## Land cover from Climate Data Store (CDS)
 
-Land cover data is available at [https://cds.climate.copernicus.eu/cdsapp#!/dataset/satellite-land-cover?tab=overview](https://cds.climate.copernicus.eu/cdsapp#!/dataset/satellite-land-cover?tab=overview).
+Land cover data is available at [https://cds.climate.copernicus.eu/datasets/satellite-land-cover](https://cds.climate.copernicus.eu/datasets/satellite-land-cover).

docs/project_setup.md

@@ -7,28 +7,14 @@ text when the development of the software package takes off.
 For a quick reference on software development, we refer to [the software guide
 checklist](https://guide.esciencecenter.nl/#/best_practices/checklist).
 
-## Python versions
-
-This repository is set up with Python versions:
-
-- 3.9
-- 3.10
-- 3.11
-
-Add or remove Python versions based on project requirements. See [the
-guide](https://guide.esciencecenter.nl/#/best_practices/language_guides/python) for more information about Python
-versions.
-
 ## Package management and dependencies
 
-You can use either pip or conda for installing dependencies and package management. This repository does not force you
-to use one or the other, as project requirements differ. For advice on what to use, please check [the relevant section
-of the
+You can use either pip or conda for installing dependencies (see
+`pyproject.toml`) and package management. This repository does not force you to
+use one or the other, as project requirements differ. For advice on what to use,
+please check [the relevant section of the
 guide](https://guide.esciencecenter.nl/#/best_practices/language_guides/python?id=dependencies-and-package-management).
 
-- Runtime dependencies should be added to `setup.cfg` in the `install_requires` list under `[options]`.
-- Development dependencies should be added to `setup.cfg` in one of the lists under `[options.extras_require]`.
-
 ## Packaging/One command install
 
 You can distribute your code using PyPI.
@@ -43,33 +29,18 @@ help you decide which tool to use for packaging.
 - The testing framework used is [PyTest](https://pytest.org)
   - [PyTest introduction](https://pythontest.com/pytest-book/)
   - PyTest is listed as a development dependency
-  - This is configured in `setup.cfg`
+  - This is configured in `pyproject.toml`
 - The project uses GitHub action workflows to automatically run tests on GitHub infrastructure against multiple Python versions
   - Workflows can be found in [`.github/workflows`](../.github/workflows/)
 - [Relevant section in the guide](https://guide.esciencecenter.nl/#/best_practices/language_guides/python?id=testing)
 
 ## Documentation
 
-- Documentation should be put in the [`docs/`](../docs) directory. The contents have been generated using `sphinx-quickstart` (Sphinx version 1.6.5).
-- We recommend writing the documentation using Restructured Text (reST) and Google style docstrings.
-  - [Restructured Text (reST) and Sphinx CheatSheet](https://thomas-cokelaer.info/tutorials/sphinx/rest_syntax.html)
-  - [Google style docstring examples](http://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html).
-- The documentation is set up with the ReadTheDocs Sphinx theme.
-  - Check out its [configuration options](https://sphinx-rtd-theme.readthedocs.io/en/latest/).
-- [AutoAPI](https://sphinx-autoapi.readthedocs.io/) is used to generate documentation for the package Python objects.
-- `.readthedocs.yaml` is the ReadTheDocs configuration file. When ReadTheDocs is building the documentation this package and its development dependencies are installed so the API reference can be rendered.
-- [Relevant section in the guide](https://guide.esciencecenter.nl/#/best_practices/language_guides/python?id=writingdocumentation)
+- Documentation should be put in the `docs/` directory.
 
 ## Coding style conventions and code quality
 
-- [Relevant section in the NLeSC guide](https://guide.esciencecenter.nl/#/best_practices/language_guides/python?id=coding-style-conventions) and [README.dev.md](README.dev.md).
-
-## Continuous code quality
-
-[Sonarcloud](https://sonarcloud.io/) is used to perform quality analysis and code coverage report
-
-- `sonar-project.properties` is the SonarCloud [configuration](https://docs.sonarqube.org/latest/analysis/analysis-parameters/) file
-- `.github/workflows/sonarcloud.yml` is the GitHub action workflow which performs the SonarCloud analysis
+- [Relevant section in the NLeSC guide](https://guide.esciencecenter.nl/#/best_practices/language_guides/python?id=coding-style-conventions).
 
 ## Package version number