Fix warnings in docs build

[ivan-aksamentov]

Ths docs build produces a lot of warnings

When running

make docker-docs

here is a relevant part of the output:

checking consistency... /home/user/src/docs/README.md: WARNING: document isn't included in any toctree
/home/user/src/docs/dev/developers-guide-cli.md: WARNING: document isn't included in any toctree
/home/user/src/docs/dev/developers-guide-web.md: WARNING: document isn't included in any toctree
/home/user/src/docs/dev/setup-clion-debugging.md: WARNING: document isn't included in any toctree
done
preparing documents... done
writing output... [100%] user/terminology                                                                                                                                                                                                        
/home/user/src/docs/dev/developers-guide-cli.md:3: WARNING: None:any reference target not found: ../../docs/dev/developers-guide-web
/home/user/src/docs/dev/developers-guide-web.md:5: WARNING: None:any reference target not found: ../../docs/dev/developers-guide-cli
/home/user/src/docs/dev/developers-guide-web.md:15: WARNING: None:any reference target not found: ../../docs/dev/developers-guide-cli
/home/user/src/docs/dev/developers-guide-web.md:54: WARNING: None:any reference target not found: ../../docs/dev/developers-guide-cli
/home/user/src/docs/user/algorithm/01-sequence-alignment.md:5: WARNING: None:any reference target not found: nextclade-cli
/home/user/src/docs/user/algorithm/02-translation.md:5: WARNING: None:any reference target not found: nextclade-web
/home/user/src/docs/user/algorithm/02-translation.md:5: WARNING: None:any reference target not found: nextclade-web
/home/user/src/docs/user/algorithm/02-translation.md:5: WARNING: None:any reference target not found: nextclade-cli
/home/user/src/docs/user/algorithm/02-translation.md:5: WARNING: None:any reference target not found: nextalign-cli
/home/user/src/docs/user/algorithm/02-translation.md:5: WARNING: None:any reference target not found: nextclade-cli
/home/user/src/docs/user/algorithm/03-mutation-calling.md:5: WARNING: None:any reference target not found: nextclade-web
/home/user/src/docs/user/algorithm/03-mutation-calling.md:7: WARNING: None:any reference target not found: nextclade-web
/home/user/src/docs/user/algorithm/03-mutation-calling.md:11: WARNING: None:any reference target not found: nextclade-web
/home/user/src/docs/user/algorithm/03-mutation-calling.md:11: WARNING: None:any reference target not found: nextclade-cli
/home/user/src/docs/user/input-files.md:91: WARNING: Pygments lexer name 'tsv' is not known
/home/user/src/docs/user/input-files.md:123: WARNING: Pygments lexer name 'csv' is not known
/home/user/src/docs/user/nextalign-cli.md:163: WARNING: None:any reference target not found: algorithm
/home/user/src/docs/user/nextclade-cli.md:5: WARNING: None:any reference target not found: algorithm
/home/user/src/docs/user/nextclade-cli.md:179: WARNING: None:any reference target not found: algorithm
/home/user/src/docs/user/nextclade-web.md:156: WARNING: None:any reference target not found: algorithm

Some of these warnings because of the files in docs/dev, which are dev docs and should not be included. But no matter what I add to exclude_patterns it still complains. Current config is:

nextclade/docs/conf.py

Lines 47 to 53 in 15daff8

	# List of patterns, relative to source directory, that match files and
	# directories to ignore when looking for source files.
	# This pattern also affects html_static_path and html_extra_path.
	exclude_patterns = [
	"README.md"
	"dev/**/*"
	]

The renaming warnings might be because of broken links and this seems to be important.

[teezzan]

Hello @ivan-aksamentov,
While I would love to contribute to this awesome project, I have little or no experience dealing with Makefiles. Could you give a little more information that would help solve this issue? A great way to get my feet wet in contribution.

Thanks

[ivan-aksamentov]

Hi @teezzan,

I am not sure what information you need on Makefiles.
Makefile is just a list of rules (named scripts) that you can run conveniently with make command.

Our Makefile is in the root of the project:
/Makefile

GNU make documentation should teach you everything:
https://www.gnu.org/software/make/manual/html_node/Introduction.html

Or perhaps, this tutorial, which is shorter and more practical:
https://www.cs.colby.edu/maxwell/courses/tutorials/maketutor/

---

However, this issue has nothing to do with makefiles. It's about fixing the build process of our documentation website. It just happens that we launch the build with a makefile rule.

The website is here: https://docs.nextstrain.org/projects/nextclade

The source code and instructions for how to build it are in the /docs/ subdirectory of the project. The problem is that the build script gives a lot of warnings, and we want to make them disappear.

Makefile is just for convenience, and you can run the build even without it, if needed.