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Fix colab and pybtex issue #2526

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merged 7 commits into from Dec 5, 2022
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Description

This looks like this right now -

image

Now that I think of it, it might be better to not show a warning on importing pybamm (would be too noisy). Rather, we could do -

    def __init__(self):
        # Set of citation keys that have been registered
        self._papers_to_cite = set()

        # Dict mapping citations keys to BibTex entries
        self._all_citations: dict[str, str] = dict()

        if "google.colab" not in sys.modules:
            self.read_citations()
            self._reset()

and then -

def print_citations(filename=None, output_format="text"):
    """See :meth:`Citations.print`"""
    if "google.colab" in sys.modules:
        warnings.warn(
            """pybtex does not work with Google Colab due to a known bug -
            https://bitbucket.org/pybtex-devs/pybtex/issues/148/.
            Please manually cite all the references.""".replace(
                "\n                ", " "
            ),
        )
    else:
        pybamm.citations.print(filename, output_format)

Fixes #2524

Type of change

Please add a line in the relevant section of CHANGELOG.md to document the change (include PR #) - note reverse order of PR #s. If necessary, also add to the list of breaking changes.

  • New feature (non-breaking change which adds functionality)
  • Optimization (back-end change that speeds up the code)
  • Bug fix (non-breaking change which fixes an issue)

Key checklist:

  • No style issues: $ flake8
  • All tests pass: $ python run-tests.py --unit
  • The documentation builds: $ cd docs and then $ make clean; make html

You can run all three at once, using $ python run-tests.py --quick.

Further checks:

  • Code is commented, particularly in hard-to-understand areas
  • Tests added that prove fix is effective or that feature works

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codecov bot commented Dec 5, 2022

Codecov Report

Base: 99.72% // Head: 99.72% // Increases project coverage by +0.00% 🎉

Coverage data is based on head (3377175) compared to base (57fe822).
Patch coverage: 100.00% of modified lines in pull request are covered.

Additional details and impacted files
@@           Coverage Diff            @@
##           develop    #2526   +/-   ##
========================================
  Coverage    99.72%   99.72%           
========================================
  Files          268      268           
  Lines        19311    19315    +4     
========================================
+ Hits         19258    19262    +4     
  Misses          53       53           
Impacted Files Coverage Δ
pybamm/citations.py 100.00% <100.00%> (ø)

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pybamm/citations.py Outdated Show resolved Hide resolved
Co-authored-by: Valentin Sulzer <valentinsulzer@hotmail.com>
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Looks good thanks! Will merge when tests pass

@@ -64,6 +66,12 @@ def test_print_citations(self):
with self.assertRaisesRegex(pybamm.OptionError, "'text' or 'bibtex'"):
pybamm.print_citations("test_citations.txt", "bad format")

# google colab issue - https://github.com/pybamm-team/PyBaMM/issues/2524
sys.modules["google.colab"] = "mock"
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cool test!

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😄

@valentinsulzer valentinsulzer merged commit b072d22 into pybamm-team:develop Dec 5, 2022
@Saransh-cpp Saransh-cpp deleted the fix-colab branch December 6, 2022 05:59
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Google Colab fails to install PyBaMM
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