support: having trouble getting started about colrev

[geritwagner]

Thank you for the overview. I have just pushed updates related to the crossref search and language codes. Hopefully, the search is completed successfully with these changes. I assume you did not use the exact query ("microsourcing") because the DOI metadata does not match the keyword.

Can I ask what the original source of the 77 entries is? In cases where the SearchSource is not detected (i.e., low confidence values for all candidates), we could consider selecting the unknown_source per default. I assume that would be less confusing?

Concerning the PicklingError: This is a bug we did not encounter before. Could you check whether it is a bug of source_specific_prep by removing the "colrev.source_specific_prep" entry from settings.json, committing it, and rerunning colrev prep?

[jkitchin]

I did use exactly colrev search -a colrev.crossref:"https://search.crossref.org/?q=+microsourcing&from_ui=yes".

I pulled the new repo. It seems the repo does not work with numpy 1.24.2, and I had to downgrade it to 1.23.5

The last error I got was

from numba.np.ufunc import _internal
SystemError: initialization of _internal failed without raising an exception

it works fine with 1.23.5

The 77 entries came from a bibtex file I have curated for a while from various sources, e.g. from journal TOCs, arxiv, mostly, on the topic of high entropy alloys.

It seems like I am having trouble committing the change to settings.json, it seems stuck on

CoLRev ReviewManager: report.............................................

I can't seem to skip this with --no-verify either...

[jkitchin]

I started a new repo, and now the search command colrev search -a colrev.crossref:"https://search.crossref.org/?q=+microsourcing&from_ui=yes" retrieved only 6 references, and the do seem related to microsourcing.

I am still having trouble committing the change to settings.json, it seems stuck on

CoLRev ReviewManager: report.............................................

I can't seem to skip this with --no-verify either...

update

I managed to bypass the precommit, and got a new pickle related error:

  File "/Users/jkitchin/opt/anaconda3/lib/python3.8/multiprocessing/reduction.py", line 60, in dump
    ForkingPickler(file, protocol).dump(obj)
_pickle.PicklingError: Can't pickle <function ExcludeNonLatinAlphabetsPrep.prepare at 0x7fb372dc3a60>: it's not the same object as colrev.ops.built_in.prep.exclude_non_latin_alphabets.ExcludeNonLatinAlphabetsPrep.prepare

[geritwagner]

I'm glad that the crossref search now works as expected. The numpy issue seems to be a recent bug that should be fixed in the original library. For the 77 entries, the "unknown_source" should be correct, as they don't belong to a single SearchSource.

The PicklingError may be a Mac-specific bug in the multiprocessing-setup. I do not have a Mac at hand to reproduce the issue. It does not occur on my Linux machine/the tests on GitHub actions. The matrix tests for different platforms will hopefully be completed in a few days (see #147). Additional details that could help to resolve the PicklingError would be much appreciated. As a workaround, the loop in colrev/ops/prep.py should not lead to multiprocessing/pickling issues.

[geritwagner]

A quick update: I could not reproduce the PicklingError. One option would be to switch to pathos (dill), which seems to handle pickling more comprehensively than the built-in multiprocessing. In the meantime, colrev prep --cpu 1 should help to avoid any multiprocessing-related issues.

[geritwagner]

The tests on mac are now fully passing. Is the error still raised with the current version/does the colrev prep --cpu 1 solve the issue?

[jkitchin]

I tried updating to Python 3.10. colrev prep did work, without --cpu 1.

but I still have this problem with a current pull on colrev in colrev retrieve:

  File "/Users/jkitchin/anaconda3/lib/python3.10/multiprocessing/reduction.py", line 60, in dump
    ForkingPickler(file, protocol).dump(obj)
_pickle.PicklingError: Can't pickle <function CrossrefSearchSource.__run_parameter_search at 0x7fb7d8aa3640>: attribute lookup CrossrefSearchSource.__run_parameter_search on colrev.ops.built_in.search_sources.crossref failed

I will also note I see a numba error with numpy>1.23.5, and I had to downgrade to 1.23.5 to get it to work.

[geritwagner]

Ok, the Pickling-error may be related to the timeout_decorators (which apparently have limited cross-platform compatibility). I replaced them in the last commit, hoping that it resolves the issue.

[jkitchin]

This seems to have resolved it for me. I think we can close this for now.

[geritwagner]

Great! Thank you for sharing the bug-reports and confirming the issue resolution.