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Fix compatibility with new databases #25

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merged 1 commit into from
Oct 29, 2023
Merged

Fix compatibility with new databases #25

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7 changes: 5 additions & 2 deletions q2_micom/_build.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@
import biom
import os
import micom.workflows as mw
from micom.taxonomy import build_from_qiime
from micom.taxonomy import build_from_qiime, rank_prefixes
import pandas as pd
from q2_micom._formats_and_types import (
JSONDirectory,
Expand Down Expand Up @@ -39,7 +39,10 @@ def build_spec(
else:
ranks = [rank]

tax = build_from_qiime(abundance, taxonomy, collapse_on=ranks)
no_rank_prefixes = rank_prefixes(model_files).isna().all()
tax = build_from_qiime(
abundance, taxonomy, collapse_on=ranks, trim_rank_prefix=no_rank_prefixes
)
micom_taxonomy = pd.merge(model_files, tax, on=ranks)
micom_taxonomy = micom_taxonomy[micom_taxonomy.relative > cutoff]
del micom_taxonomy["file"]
Expand Down
28 changes: 14 additions & 14 deletions setup.cfg
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Original file line number Diff line number Diff line change
Expand Up @@ -12,17 +12,17 @@ long_description = file: README.md
long_description_content_type = text/markdown
license = Apache License 2.0
url = https://github.com/micom-dev/q2-micom
classifiers =
classifiers =
Development Status :: 4 - Beta
Intended Audience :: Science/Research
Topic :: Scientific/Engineering :: Bio-Informatics
License :: OSI Approved :: Apache Software License
Programming Language :: Python :: 3
Programming Language :: Python :: 3.6
Programming Language :: Python :: 3.7
Programming Language :: Python :: 3.8
Programming Language :: Python :: 3.9
keywords =
Programming Language :: Python :: 3.10
Programming Language :: Python :: 3.11
keywords =
microbiome
modeling
metabolism
Expand All @@ -32,25 +32,25 @@ keywords =
zip_safe = False
packages = find:
python_requires = >=3.6
install_requires =
install_requires =
cobra>=0.18.1
micom>=0.24.0
micom>=0.33.0
jinja2>=2.10.3
qiime2>=2021.2
rich>=6.0
pandas>=1.0
tests_require =
tests_require =
coverage
pytest
pytest-cov
flake8

[options.package_data]
q2_micom =
q2_micom =
citations.bib

[options.entry_points]
qiime2.plugins =
qiime2.plugins =
q2-micom = q2_micom.plugin_setup:plugin

[bumpversion:file:setup.py]
Expand All @@ -62,7 +62,7 @@ search = __version__ = "{current_version}"
replace = __version__ = "{new_version}"

[tool:pytest]
filterwarnings =
filterwarnings =
ignore::DeprecationWarning
ignore::FutureWarning

Expand All @@ -75,15 +75,15 @@ branch = True
omit = q2_micom/tests/*

[coverage:report]
exclude_lines =
exclude_lines =
pragma: no cover

def __repr__
if self\.debug

raise AssertionError
raise NotImplementedError

if 0:
if __name__ == .__main__.:
ignore_errors = True
Expand Down
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