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Replace internal pybids calls with installed pybids calls #213

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merged 31 commits into from
Feb 23, 2023

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@tsalo tsalo commented Feb 20, 2023

Closes None, but works toward #199.

Changes proposed in this pull request

  • Replace uses of aslprep.pybids with bids (the installed dependency).

@tsalo tsalo added the maintenance Issues/PRs related to maintenance. Dependency versions, dependencies, etc. label Feb 20, 2023
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Codecov Report

Base: 39.95% // Head: 44.18% // Increases project coverage by +4.22% 🎉

Coverage data is based on head (68bc82e) compared to base (7d4cc20).
Patch coverage: 92.30% of modified lines in pull request are covered.

Additional details and impacted files
@@            Coverage Diff             @@
##             main     #213      +/-   ##
==========================================
+ Coverage   39.95%   44.18%   +4.22%     
==========================================
  Files         192      145      -47     
  Lines       19940    13440    -6500     
==========================================
- Hits         7967     5938    -2029     
+ Misses      11973     7502    -4471     
Impacted Files Coverage Δ
aslprep/cli/parser.py 77.10% <0.00%> (ø)
aslprep/sdcflows/cli/run.py 0.00% <ø> (ø)
aslprep/workflows/base.py 88.46% <ø> (ø)
aslprep/workflows/asl/outputs.py 44.10% <50.00%> (ø)
aslprep/config.py 89.81% <100.00%> (ø)
aslprep/interfaces/bids.py 100.00% <100.00%> (ø)
aslprep/niworkflows/interfaces/bids.py 66.20% <100.00%> (-10.69%) ⬇️
aslprep/niworkflows/reports/core.py 18.29% <100.00%> (ø)
aslprep/niworkflows/reports/tests/test_core.py 27.77% <100.00%> (ø)
aslprep/niworkflows/utils/bids.py 50.50% <100.00%> (ø)
... and 7 more

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@@ -403,8 +403,8 @@ def _compose_view(bg_svgs, fg_svgs, ref=0):
else:
newroots = roots
fig.append(newroots)
fig.root.attrib.pop("width")
fig.root.attrib.pop("height")
fig.root.attrib.pop("width", None)
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does pop not automatically return None?

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It started breaking when I unpinned the svgutils version. I haven't checked what the attrib attribute is, so it might not be a regular dictionary. I copied the fix from the current version of niworkflows.

@tsalo tsalo merged commit 0f68ccc into PennLINC:main Feb 23, 2023
@tsalo tsalo deleted the remove-pybids branch February 23, 2023 16:55
@tsalo tsalo changed the title Replace pybids calls with dependency calls Replace internal pybids calls with installed pybids calls Sep 26, 2023
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3 participants