Implemented argcomplete for tab-completion #127

spyke7 · 2025-11-08T06:30:21Z

hi maintainers
@orbeckst @lilyminium @hejamu @joaomcteixeira @PicoCentauri
This PR is related to issue #37
I have implemented the argcomplete library for tab-completion, please check this.
I have updated the cli.py file, and tox.ini, README.rst, pyproject.toml, and also test_cli.py
in the test_cli.py I have added a function test_subparser_setup_for_tab_completion - it checks the setup for argcomplete.
Please check this and if any issue please tell me.

@PicoCentauri please check this

📚 Documentation preview 📚: https://mdacli--127.org.readthedocs.build/en/127/

PicoCentauri

Thank you @spyke7!

Looks like a good start. If it just works with one line without further setup even better. I left some firs comments and will try it locally soon.

The docs are the linter are not happy. You can see the errors by clicking on the link in the discussion and also run these locally for better debugging.

The linter should be easily please by running the formatting tox -e format.

For the docs there seemed to be a doubled defined label.

Let me know if you encounter any problems fixing the issues.

README.rst

docs/src/tab-completion.rst

PicoCentauri · 2025-11-10T09:57:25Z

src/mdacli/cli.py

+    argcomplete.autocomplete(ap)
    setup_clients(ap, title=f"{name} Analysis Modules", members=modules)


Shouldn't this be swapped? After we registered all modules?

I think this will still work as it is just a hook
But I will just swap the lines, and then also it will work.
There is no problem in both I guess

PicoCentauri · 2025-11-10T09:58:36Z

tests/test_cli.py

    # Check if it still works if the module name is not the second argument
    subprocess.check_call(["mda", "--debug", args, "-h"])

+def test_subparser_setup_for_tab_completion():


This is a nice test. But I think we should also have a test that the argcompletion is really setup. Maybe check the argcomplete repo how they do it.

spyke7 · 2025-11-10T10:30:34Z

okk
Will be solving the issues soon

spyke7 · 2025-11-10T16:10:29Z

Ya please check now
please check whether the docs are passing or not
if anything I need to change please tell

PicoCentauri · 2025-11-11T09:15:09Z

I did some minor cleanup. But the completion does not work on my machine.

spyke7 · 2025-11-11T11:51:54Z

Wait checking it again @PicoCentauri

spyke7 · 2025-11-11T13:39:21Z

@PicoCentauri
please look at this screenshots and videos
There is one important thing that is to add

# PYTHON_ARGCOMPLETE_OK

write the above inside the environment created
for ex - "path"/mdacli/env/bin/mda

If inside a virtual env -

activate-global-python-argcomplete --user

Here is the video -

https://github.com/user-attachments/assets/3f649c75-38ef-41cd-8378-0511dc37e2c0

pip install -e .
First do the activation
restart terminal
then write python_argcomplete_ok
then do the eval one

PicoCentauri · 2025-11-11T16:18:49Z

Thanks! I will test it again tomorrow!

PicoCentauri

Thanks for the changes. It now also works for me!!!

However, it would be nice if we could avoid having this in the __main__ function. Since this will be used also by downstream projects they now also have to copy this argcomplete logic which will ad some additional boilerplate. Maybe there is a way to avoid having this in the main...

Also, is there a way to do file completion for the -s and -f option only for the files that are supported by MDAnalysis. There are of course fixed choices but want choices only based on the file extension. Not sure if argcomplete can do it.

src/mdacli/cli.py

PicoCentauri · 2025-11-12T15:18:01Z

tests/test_cli.py

Since the tests you added didn't really fail even when before the completion was not working we should maybe think about more robust test cases.

The previous one was checking for setup
Setup was perfect before and after also
PYTHON_ARGCOMPLETE_OK was the main thing
It was not related with test cases, but crucial for bash completion

src/mdacli/cli.py

spyke7 · 2025-11-15T09:49:45Z

Check this for file completion
and also removed the autocomplete from main.py, but everything works fine.
Please check the add_cli_universe function
and also a new function completer I have added. Just review them

PicoCentauri

Very nice. I think we are almost there!

src/mdacli/cli.py

PicoCentauri · 2025-11-17T14:21:28Z

src/mdacli/libcli.py

    )


+def _create_mda_file_completer(format_dict):


I think you don't need the whole dictionary but just the list of keys. Maybe passing a list of file extension makes this function a bit clearer

Suggested change

def _create_mda_file_completer(format_dict):

def _create_extension_completer(extension_list):

We could also make this public as this might be useful in general.

ok please check now, I think previously also, the list was passing?

If you loop through a dictionary what you get are the keys.

PicoCentauri

Very nice. I have two last minor comments and we can merge.

PicoCentauri · 2025-11-18T08:01:34Z

src/mdacli/libcli.py

+        # Determine directory and file prefix
+        if os.path.sep in prefix:
+            prefix_path = Path(prefix)
+            directory = prefix_path.parent if prefix_path.parent != Path() else Path()
+            file_prefix = prefix_path.name
+        else:
+            directory = Path()
+            file_prefix = prefix


This looks to me like a bit complicated LLM code.

I think one can do it without pulling os in and directly converting the prefix to Path object.

hmmm.
Yeah it's looks a bit complicated,, let me do something about it

removed the os
just used the prefix_path only
previously, I thought that using os will be good, but this also works

I mean if you use pathlib you can do everything with it. I usually try either use the newer object style pathlib exclusively or exclusively stick to os.

yeah indeed

docs/requirements.txt

PicoCentauri · 2025-11-18T12:21:27Z

Thanks again @spyke7 for the nice work! 🚀

spyke7 · 2025-11-18T13:13:32Z

Thanks @PicoCentauri for guiding me to make a clean PR. And also I will be working on other issue in MDanalysis.

Implemented argcomplete for tab-completion

cd4d6e9

PicoCentauri requested changes Nov 10, 2025

View reviewed changes

Fixed issues

bf2612a

spyke7 and others added 3 commits November 10, 2025 22:34

Fixed lint

5886961

updated CHANGELOG.rst

1e419fe

some cleanup

63882d3

Updated __main__.py and cli.py

9598696

PicoCentauri requested changes Nov 12, 2025

View reviewed changes

Fixed __main__.py and added file completion for -s and -f

5db75ba

PicoCentauri reviewed Nov 17, 2025

View reviewed changes

Updated libcli.py and also handled the error for args less than 2

bd7e659

PicoCentauri reviewed Nov 18, 2025

View reviewed changes

updated requirements.txt and completer function

87f947f

PicoCentauri approved these changes Nov 18, 2025

View reviewed changes

PicoCentauri merged commit 6333fdf into MDAnalysis:main Nov 18, 2025
11 checks passed

PicoCentauri mentioned this pull request Nov 18, 2025

tab-completion #37

Closed

		argcomplete.autocomplete(ap)
		setup_clients(ap, title=f"{name} Analysis Modules", members=modules)

	def _create_mda_file_completer(format_dict):
	def _create_extension_completer(extension_list):

Implemented argcomplete for tab-completion #127

Implemented argcomplete for tab-completion #127

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spyke7 commented Nov 10, 2025

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spyke7 commented Nov 15, 2025

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PicoCentauri commented Nov 18, 2025

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spyke7 commented Nov 18, 2025

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spyke7 commented Nov 8, 2025 •

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