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Author: Komolehin Israel Timilehin
Last-Update: 2023-12-23 16:35:31
Description: Fix upstream test
--- a/bp/tests/test_insert.py
+++ b/bp/tests/test_insert.py
@@ -1,5 +1,5 @@
import unittest
-import pkg_resources
+import os
from bp import parse_jplace, insert_fully_resolved
import skbio
import pandas as pd
@@ -8,15 +8,14 @@
class InsertTests(unittest.TestCase):
package = 'bp.tests'
def setUp(self):
- self.jplacedata_multiple = \
- open(self.get_data_path('300/placement_mul.jplace')).read()
+ with open(self.get_data_path('300/placement_mul.jplace'), 'r') as file:
+ self.jplacedata_multiple = file.read()
self.final_multiple_fully_resolved = \
skbio.TreeNode.read(self.get_data_path('300/placement.full_resolve.newick'))
def get_data_path(self, filename):
- # adapted from qiime2.plugin.testing.TestPluginBase
- return pkg_resources.resource_filename(self.package,
- 'data/%s' % filename)
+ current_directory = os.getcwd()
+ return current_directory + "/tests/data/" + filename
def test_insert_fully_resolved(self):
exp = self.final_multiple_fully_resolved
--- a/bp/tests/test_io.py
+++ b/bp/tests/test_io.py
@@ -4,7 +4,7 @@
import json
import pandas as pd
import pandas.testing as pdt
-import pkg_resources
+import os
import skbio
import io
import numpy as np
@@ -205,16 +205,15 @@
package = 'bp.tests'
def setUp(self):
- self.jplacedata = open(self.get_data_path('200/placement.jplace'))
- self.jplacedata = self.jplacedata.read()
+ with open(self.get_data_path('200/placement.jplace'), 'r') as file:
+ self.jplacedata = file.read()
no_edge_numbers = re.sub(r"{\d+}", '',
json.loads(self.jplacedata)['tree'])
self.tree = skbio.TreeNode.read([no_edge_numbers])
def get_data_path(self, filename):
- # adapted from qiime2.plugin.testing.TestPluginBase
- return pkg_resources.resource_filename(self.package,
- 'data/%s' % filename)
+ current_directory = os.getcwd()
+ return current_directory + "/tests/data/" + filename
def test_place_jplace_square_braces(self):
self.jplacedata = json.loads(self.jplacedata)
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