Docs: Sphinx build fails with `FileNotFoundError` in `generate_cookiecutter_cli.py` due to missing output directory

[ojeda-e]

Description

Building Sphinx docs fails because docs/scripts/generate_cookiecutter_cli.py calls shutil.copytree() with a directory that does not exist. The failure happens when conf.py runs generate_cookiecutter_cli() on import.

cookiecutter-mdakit/docs/source/conf.py

Line 23 in 2856a05

from generate_cookiecutter_cli import main as generate_cookiecutter_cli # noqa: E402

Behaviour

The script assumes that the generated project folder is always named example-repository.

cookiecutter-mdakit/docs/scripts/generate_cookiecutter_cli.py

Line 81 in 2856a05

self.repo_name = "example-repository"

In reality, Jinja generates <repo_name> in cookiecutter.json from project_name.

For example, the project name mia_test generates a folder mia_test - not example-repository, and this mismatch is what shutil.copytree() doesn't like.

cookiecutter-mdakit/docs/scripts/generate_cookiecutter_cli.py

Lines 114 to 117 in 2856a05

	source_repo = os.path.join(tmpdir, self.repo_name)
	destination_repo = str(self.example_repo_path.resolve())
	shutil.rmtree(destination_repo, ignore_errors=True)
	shutil.copytree(source_repo, destination_repo)

[orbeckst]

I might have merged PR #158 prematurely. The raw log file for PR #156 shows a failure for the doc workflow after merging in the changes from here as

2026-05-04T23:52:44.4870052Z       File "/home/runner/miniconda3/envs/cookiecutter-mdakit-docs/lib/python3.14/shutil.py", line 652, in copytree
2026-05-04T23:52:44.4870551Z         with os.scandir(src) as itr:
2026-05-04T23:52:44.4870775Z              ~~~~~~~~~~^^^^^
2026-05-04T23:52:44.4871150Z     FileNotFoundError: [Errno 2] No such file or directory: '/tmp/tmpgqh13f2n/my_project_name'

(GitHub seems to be having ongoing issues with displaying outputs from workflow steps (I only see a red "Error:") so the only way I can see details from the action workflows is by looking at the raw logs, which are still available).

[ojeda-e]

@orbeckst, if you don't mind, I addressed this as part of #156 in commit cfdf912

Apparently none of these fields can be empty:

cookiecutter-mdakit/docs/scripts/generate_cookiecutter_cli.py

Lines 87 to 102 in 2856a05

	def generate_cli_output(self) -> str:
	inputs = [
	"My Project Name", # project_name
	self.repo_name, # repo_name
	self.package_name, # package_name
	"A package to do MD analysis", # description
	"my-github-username", # github_username,
	"", # github_host_account
	"My Name", # author_name
	"my_example_email@gmail.com", # author_email
	"", # dependency_source
	"", # include_ReadTheDocs
	"MyAnalysisClass", # template_analysis_class
	""
	""
	]