Skip to content

test expected to fail #909

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Closed
wants to merge 1 commit into from
Closed

test expected to fail #909

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
18 changes: 17 additions & 1 deletion tests/test_coordinate_source.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -8,6 +8,7 @@

import mrcfile
import numpy as np
import pytest
from click.testing import CliRunner
from pandas import DataFrame

Expand Down Expand Up @@ -275,7 +276,7 @@ def createTestCtfFiles(self, index):
starfile = StarFile(blocks=blocks)
starfile.write(star_fp)

def createTestRelionCtfFile(self):
def createTestRelionCtfFile(self, reverse_optics_block_rows=False):
"""
Creates example RELION-generated CTF file for a set of micrographs.
"""
Expand All @@ -295,6 +296,11 @@ def createTestRelionCtfFile(self):
["opticsGroup1", 1, 500.0, 700.0, 600.0, 400.0],
["opticsGroup2", 2, 501.0, 701.0, 601.0, 401.0],
]
# Since optics block rows are self-contained,
# reversing their order should have no affect anywhere.
if reverse_optics_block_rows:
optics_block = optics_block[::-1]

blocks["optics"] = DataFrame(optics_block, columns=optics_columns)

micrographs_columns = [
Expand Down Expand Up @@ -539,6 +545,16 @@ def testImportCtfFromRelion(self):
self._testCtfFilters(src)
self._testCtfMetadata(src)

@pytest.mark.xfail(strict=True)
def testImportCtfFromRelionReverseOpticsGroup(self):
self.relion_ctf_file = self.createTestRelionCtfFile(
reverse_optics_block_rows=True
)
src = BoxesCoordinateSource(self.files_box)
src.import_relion_ctf(self.relion_ctf_file)
self._testCtfFilters(src)
self._testCtfMetadata(src)

def testImportCtfFromRelionLegacy(self):
src = BoxesCoordinateSource(self.files_box)
src.import_relion_ctf(self.relion_legacy_ctf_file)
Expand Down