Add reader for ANT Neuro format #12792
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mscheltienne
requested review from
agramfort,
cbrnr,
dengemann and
drammock
as code owners
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One reasonable division would be to have This is similar to we would almost certainly implement something like |
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That's the alternative.. A bit annoying now that I implemented both |
Not too late to yank that release :) And not too bad to copy the code over here, either. But more seriously you could in theory keep the code over there if you wanted. But I think it would make some maintenance stuff harder like if we deprecate something, move some private functions around, change stuff about how |
True, the biggest downside is that a breakage won't be immediately seen, except if some tests are also run in |
not sure what exactly you want to do with it, but does this help? import inspect
from types import FunctionType
from antio.io import read_raw_ant
params = inspect.signature(read_raw_ant).parameters
defaults = tuple(params[key].default for key in params)
func_in_mne_namespace = FunctionType(code=read_raw_ant.__code__, globals=globals(), argdefs=defaults)
func_in_mne_namespace.__doc__ = read_raw_ant.__doc__and now |
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I don't think so, still learning something new in this snippet, but my issue was that I wanted to expose the signature and docstring from a function in an optional dependency, which might be absent from the environment. Anyway, I started moving the code/tests around in |
ah, yeah, I don't think that's possible. the |
i think we've had this discussion previously for bvio oder eeglabio, i don't remember ... but @sappelhoff and @cbrnr were involved |
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This is now ready for review. Do we want to include it in
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I would rather go with 1.9, gives us months to iron out bugs and actually try using it for a bit |
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So we are going to include a binary extension now? I think this needs to be discussed with all devs. |
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No the binary extension lives in the |
larsoner
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larsoner
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Looks good, just a couple of comments!
mne/io/tests/test_read_raw.py
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| @pytest.fixture(scope="module") | ||
| def reader_excluded_from_read_raw() -> set[str]: | ||
| """Set of excluded readers from read_raw.""" | ||
| return { | ||
| "read_raw_bti", | ||
| "read_raw_hitachi", | ||
| "read_raw_neuralynx", | ||
| } | ||
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| def test_all_reader_documented(reader_excluded_from_read_raw: set[str]): | ||
| """Test that all the readers in the documentation are accepted by read_raw.""" | ||
| readers = _get_supported() | ||
| # flatten the dictionaries and retrieve the function names | ||
| functions = [foo.__name__ for value in readers.values() for foo in value.values()] | ||
| # read documentation .rst source file | ||
| doc_file = Path(__file__).parents[3] / "doc" / "api" / "reading_raw_data.rst" | ||
| assert doc_file.exists() | ||
| with open(doc_file) as fid: | ||
| doc = fid.read() | ||
| reader_lines = [ | ||
| line.strip() for line in doc.split("\n") if line.strip().startswith("read_raw_") | ||
| ] | ||
| reader_lines = [ | ||
| elt for elt in reader_lines if elt not in reader_excluded_from_read_raw | ||
| ] | ||
| missing_from_read_raw = set(reader_lines) - set(functions) | ||
| missing_from_doc = set(functions) - set(reader_lines) | ||
| if len(missing_from_doc) != 0 or len(missing_from_read_raw) != 0: | ||
| raise AssertionError( | ||
| "Functions missing from documentation:\n\t" | ||
| f"{'\n\t'.join(missing_from_doc)}\n\n" | ||
| "Functions missing from read_raw:\n\t" | ||
| f"{'\n\t'.join(missing_from_read_raw)}" | ||
| ) | ||
| if sorted(reader_lines) != list(reader_lines): | ||
| raise AssertionError( | ||
| "Functions in documentation are not sorted. Expected order:\n\t" | ||
| f"{'\n\t'.join(sorted(reader_lines))}" | ||
| ) | ||
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| def test_all_reader_documented_in_docstring(): | ||
| """Test that all the readers are documented in read_raw docstring.""" | ||
| readers = _get_supported() | ||
| # flatten the dictionaries and retrieve the function names | ||
| functions = [foo.__name__ for value in readers.values() for foo in value.values()] | ||
| doc = read_raw.__doc__.split("Parameters")[0] | ||
| documented = [elt.strip().split("`")[0] for elt in doc.split("mne.io.")[1:]] | ||
| missing_from_docstring = set(functions) - set(documented) | ||
| if len(missing_from_docstring) != 0: | ||
| raise AssertionError( | ||
| "Functions missing from docstring:\n\t" | ||
| f"{'\n\t'.join(missing_from_docstring)}" | ||
| ) | ||
| if sorted(documented) != documented: | ||
| raise AssertionError("Functions in docstring are not sorted.") |
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@larsoner I added those 2 tests, it did catch a couple of missing readers, 3 of which I excluded because they require a folder or an extension-less file as input.
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Finally green 🎉 |
larsoner
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larsoner
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Just some small optional ideas, feel free to change them or not then we can merge!
| ) | ||
| if sorted(reader_lines) != list(reader_lines): | ||
| raise AssertionError( | ||
| "Functions in documentation are not sorted. Expected order:\n\t" |
Co-authored-by: Eric Larson <larson.eric.d@gmail.com>
5 participants
Closes #3609
Getting the ball rolling now that a first version of
antiois up on PyPI. Open items:I'm not finding a nice way to pull the functionantio.io.read_raw_antand its docstring fromantio, which forces the signature and docstring copy/paste..How to tests without duplicating the tests inantioMaybe it wasn't that smart to defineRawANTandread_raw_antinantio.. the rationale was to move all maintenance of the reader toantio.