docs: use resolvable root-absolute links for internal pages

docs/guides/gha_pure.md

@@ -26,7 +26,7 @@ reasons that a wheel is better than only providing an sdist:
   is going to go
 :::
 
-[on the next page]: guides/gha-wheels
+[on the next page]: /guides/gha_wheels.md
 
 ## Job setup
 

docs/guides/index.md

@@ -35,20 +35,20 @@ your repository with the guidelines, runnable [right in the guide][] via
 WebAssembly! All checks point to a linked badge in the guide.
 :::
 
-[tutorials]:          tutorials/index
-[style]:              guides/style
-[mypy]:               guides/mypy
-[docs]:               guides/docs
-[simple packaging]:   guides/packaging-simple
-[compiled packaging]: guides/packaging-compiled
-[classic packaging]:  guides/packaging-classic
-[coverage]:           guides/coverage
-[gha_basic]:          guides/gha-basic
-[gha_pure]:           guides/gha-pure
-[gha_wheels]:         guides/gha-wheels
-[security]:           guides/security
-[pytest]:             guides/pytest
-[right in the guide]: guides/repo-review
+[tutorials]:          /tutorials/index.md
+[style]:              /guides/style.md
+[mypy]:               /guides/mypy.md
+[docs]:               /guides/docs.md
+[simple packaging]:   /guides/packaging_simple.md
+[compiled packaging]: /guides/packaging_compiled.md
+[classic packaging]:  /guides/packaging_classic.md
+[coverage]:           /guides/coverage.md
+[gha_basic]:          /guides/gha_basic.md
+[gha_pure]:           /guides/gha_pure.md
+[gha_wheels]:         /guides/gha_wheels.md
+[security]:           /guides/security.md
+[pytest]:             /guides/pytest.md
+[right in the guide]: /guides/repo_review.md
 
 [cookiecutter]:             https://cookiecutter.readthedocs.io
 [copier]:                   https://copier.readthedocs.io

docs/guides/mypy.md

@@ -70,7 +70,7 @@ everything. Try to turn on as much as possible, and increase it until you can
 run with full `strict` checking. See the [style page][] for configuration
 suggestions.
 
-[style page]: guides/style
+[style page]: /guides/style.md
 
 For a library to support typing, it has to a) add types using any of the three
 methods, and b) add a `py.typed` empty file to indicate that it's okay to look

docs/guides/packaging_classic.md

@@ -8,7 +8,7 @@ outlined as well.
 There are several popular packaging systems. This guide covers the old
 configuration style for [Setuptools][]. Unless you really need it, you should be
 using the modern style described in [Simple
-Packaging](guides/packaging-simple). The modern style is
+Packaging](/guides/packaging_simple.md). The modern style is
 guided by Python Enhancement Proposals (PEPs), and is more stable than the
 setuptools-specific mechanisms that evolve over the years. This page is kept to
 help users with legacy code (and hopefully upgrade it).

docs/guides/packaging_compiled.md

@@ -40,7 +40,7 @@ The most exciting developments have been new native build backends:
 
 :::{note}
 You should be familiar with [packing a pure Python
-project](guides/packaging-simple) - the metadata
+project](/guides/packaging_simple.md) - the metadata
 configuration is the same.
 :::
 There are also classic setuptools plugins:
@@ -453,4 +453,4 @@ it is free-threaded. 3.13.5 was rushed out to fix it.
 [meson-python]: https://meson-python.readthedocs.io
 [setuptools-rust]: https://setuptools-rust.readthedocs.io/en/latest/
 [maturin]: https://www.maturin.rs
-[gha_wheels]: guides/gha-wheels
+[gha_wheels]: /guides/gha_wheels.md

docs/guides/style.md

@@ -786,7 +786,7 @@ for a specific rule); the standard `# type: ignore` is honored as well.
 :::
 ::::
 
-[mypy page]: guides/mypy
+[mypy page]: /guides/mypy.md
 
 ## Setuptools specific checks
 

docs/index.md

@@ -13,10 +13,10 @@ fellow scientists and research software engineers.
 Jupyter notebooks that are becoming unwieldy? Are changes to some parts of your
 code accidentally breaking other parts of your code? Do you want to present them
 in a more maintainable, reusable, and shareable form? Start at the
-[tutorial](tutorials/index).
+[tutorial](/tutorials/index.md).
 
 **Learn recommended tools and best practices.**
-[Topical guides](guides/index) provide task-based instruction on topics
+[Topical guides](/guides/index.md) provide task-based instruction on topics
 that scientists and research software engineers may encounter as their projects
 evolve and grow. This covers modern packaging ([simple][] or [compiled][]),
 [style checking][], [testing][], [documentation][], [static typing][], [CI][],
@@ -35,12 +35,12 @@ WebAssembly! All checks point to a linked badge in the guide.
 :::
 
 **Learn to write better research code.** A high-level document on
-[principles](principles/index) provides advice based on the
+[principles](/principles/index.md) provides advice based on the
 community's collective experience building code that is easier for researchers
 to use successfully and easier to maintain over time.
 
 **Use our solutions for common tasks.** A growing collection of
-[patterns](patterns/index) provides tested approaches for
+[patterns](/patterns/index.md) provides tested approaches for
 tasks and can be tricky to get exactly right, such as including data files with
 Python packages.
 
@@ -75,14 +75,14 @@ with many updates. Improved support for compiled components supported in part
 by NSF grant [OAC-2209877][].
 :::
 
-[simple]:                   guides/packaging-simple
-[compiled]:                 guides/packaging-compiled
-[style checking]:           guides/style
-[testing]:                  guides/pytest
-[documentation]:            guides/docs
-[static typing]:            guides/mypy
-[ci]:                       guides/gha-pure
-[right in the guide]:       guides/repo-review
+[simple]:                   /guides/packaging_simple.md
+[compiled]:                 /guides/packaging_compiled.md
+[style checking]:           /guides/style.md
+[testing]:                  /guides/pytest.md
+[documentation]:            /guides/docs.md
+[static typing]:            /guides/mypy.md
+[ci]:                       /guides/gha_pure.md
+[right in the guide]:       /guides/repo_review.md
 
 [scientific-python/cookie]: https://github.com/scientific-python/cookie
 [repo-review]:              https://repo-review.readthedocs.io

docs/patterns/index.md

@@ -10,9 +10,9 @@ If you would like to use backport packages, see [Backports][].
 
 If you are wondering about public API, see [Exports][].
 
-[including data files]: patterns/data-files
-[backports]: patterns/backports
-[exports]: patterns/exports
+[including data files]: /patterns/data_files.md
+[backports]: /patterns/backports.md
+[exports]: /patterns/exports.md
 
 ```{tableofcontents}
 ```

docs/principles/index.md

@@ -5,8 +5,8 @@ research code. [Process recommendations][] discusses the process of writing
 software, and [Design recommendations][] covers some tips about writing easy to
 read and maintain code.
 
-[Process recommendations]: principles/process
-[Design recommendations]: principles/design
+[Process recommendations]: /principles/process.md
+[Design recommendations]: /principles/design.md
 
 
 ```{tableofcontents}

docs/principles/testing.md

@@ -69,8 +69,8 @@ the test-case to make sure it fails when the code is broken.
 
 A good place to start writing tests is from the perspective of a user of your
 module or library, as described in the [Test
-Tutorial](tutorials/test), and [Testing with pytest
-guide](guides/pytest). These tests follow the "Detroit
+Tutorial](/tutorials/test.md), and [Testing with pytest
+guide](/guides/pytest.md). These tests follow the "Detroit
 School", focusing on behavior, avoiding testing of private attributes,
 minimizing the use of mocks/patches/test-doubles.
 
@@ -393,7 +393,7 @@ run unit tests in your source folder, from your package root, use
 your source repository), use `pytest --pyargs {package name}`.
 
 You can set the default test path in `pyproject.toml`, see: [Configuring
-pytest](guides/pytest#configuring-pytest)
+pytest](/guides/pytest.md#configuring-pytest)
 
 We recommend configuring pytest to run ONLY your fastest, least demanding test
 suite by default.

docs/tutorials/docs.md

@@ -195,7 +195,7 @@ Or you can generate a table that links out to documentation for each object.
 ````
 <!-- rumdl-enable -->
 
-See the [guide](guides/docs) for more information on how to
+See the [guide](/guides/docs.md) for more information on how to
 integrate this into a package, and setup for nox.
 
 [sphinx]: https://www.sphinx-doc.org/
@@ -204,4 +204,4 @@ integrate this into a package, and setup for nox.
 [sphinx-autodoc2]: https://sphinx-autodoc2.readthedocs.io/
 [mkdocs]: https://www.mkdocs.org/
 [mkdocs-material]: https://squidfunk.github.io/mkdocs-material/
-[documentation guide]: guides/docs
+[documentation guide]: /guides/docs.md

docs/tutorials/index.md

@@ -12,9 +12,9 @@ start off on the right foot.
 Keeping in mind that too much software infrastructure can be overwhelming to
 those who haven't yet encountered the need for it, we introduce only the core
 essentials in this opinionated tutorial. From there, we recommend looking
-through the section on [principles](principles/index). As
+through the section on [principles](/principles/index.md). As
 your project grows you may find some good use for the more specific and advanced
-topics covered in the [guides](guides/index).
+topics covered in the [guides](/guides/index.md).
 
 ```{tableofcontents}
 ```

docs/tutorials/module.md

@@ -79,7 +79,7 @@ automatically generate nice-looking HTML documentation later. Notable features:
 - (Optional) There is a section of one or more examples.
 
 We will revisit docstrings in the section on writing
-[documentation](tutorials/docs).
+[documentation](/tutorials/docs.md).
 
 [snell's law]: https://en.wikipedia.org/wiki/Snell%27s_law
 [numpydoc standard]: https://numpydoc.readthedocs.io/en/latest/format.html

docs/tutorials/packaging.md

@@ -125,4 +125,4 @@ In [1]: snell?
 For more about packaging, also see our [packaging guide][].
 
 [version control with git]: https://swcarpentry.github.io/git-novice/
-[packaging guide]: guides/packaging-simple
+[packaging guide]: /guides/packaging_simple.md

docs/tutorials/test.md

@@ -139,4 +139,4 @@ Consult the [pytest documentation][] for more. For more advanced pytest
 suggestions, see our [pytest guide][].
 
 [pytest documentation]: https://docs.pytest.org/en/latest/
-[pytest guide]: guides/pytest
+[pytest guide]: /guides/pytest.md