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erikhuckerikhuck
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Merge pull request #175 from MoseleyBioinformaticsLab/paths
Makes the git repository, tests, and source code compatible with Windows
2 parents d2f1be6 + e9c708d commit afa872b

12 files changed

Lines changed: 609 additions & 33 deletions

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‎.github/workflows/main.yml‎

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Original file line numberDiff line numberDiff line change
@@ -12,10 +12,11 @@ on:
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jobs:
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build:
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15-
runs-on: ubuntu-latest
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strategy:
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matrix:
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python-version: ["3.8", "3.9", "3.10"]
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os: [ ubuntu-latest, windows-latest ]
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runs-on: ${{matrix.os}}
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steps:
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- uses: actions/checkout@v3

‎dev/install.sh‎

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@@ -2,7 +2,7 @@ echo "Removing previous .env/ directory if it exists..."
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rm -rf .env/
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echo "Creating new .env/ directory..."
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python3 -m venv .env/
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source .env/bin/activate
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source .env/bin/activate || source .env/Scripts/activate # Windows has Scripts instead of bin
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python3 -m pip install --upgrade pip
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python3 -m pip install pytest pytest-mock pytest-cov sphinx sphinx-rtd-theme notebook
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python3 -m pip install -e .

‎dev/test.sh‎

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@@ -1,3 +1,3 @@
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source .env/bin/activate
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source .env/bin/activate || source .env/Scripts/activate # Windows has Scripts instead of bin
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3-
python -m pytest dev --cov --cov-branch --cov-report=term-missing
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python3 -m pytest dev --cov --cov-branch --cov-report=term-missing

‎dev/test_data/all-brite-entry-ids.txt‎

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@@ -122,6 +122,7 @@ br:br01800
122122
br:br01810
123123
br:br08011
124124
br:br08020
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br:br08012
125126
br:br08120
126127
br:br08319
127128
br:br08329

‎dev/test_data/brite-entries.zip‎

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dev/test_data/brite-entries/br:br08005.txt renamed to dev/test_data/brite-entries/br_br08005.txt

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‎dev/test_data/brite-entries/br_br08431.txt‎

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dev/test_data/brite-entries/br:br08902.txt renamed to dev/test_data/brite-entries/br_br08902.txt

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‎dev/test_data/module-pathway-link.txt‎

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@@ -20,6 +20,7 @@ path:map00030 md:M00633
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path:map00030 md:M00631
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path:map00030 md:M00580
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path:map00030 md:M00308
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path:map00030 md:M00968
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path:map00040 md:M00129
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path:map00040 md:M00061
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path:map00040 md:M00014
@@ -100,6 +101,7 @@ path:map00230 md:M00053
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path:map00230 md:M00005
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path:map00230 md:M00546
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path:map00230 md:M00959
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path:map00230 md:M00968
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path:map00230 md:M00958
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path:map00232 md:M00915
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path:map00240 md:M00046
@@ -108,6 +110,7 @@ path:map00240 md:M00052
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path:map00240 md:M00053
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path:map00240 md:M00938
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path:map00240 md:M00939
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path:map00240 md:M00968
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path:map00250 md:M00027
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path:map00250 md:M00740
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path:map00253 md:M00778
@@ -301,6 +304,7 @@ path:map00630 md:M00373
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path:map00630 md:M00740
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path:map00630 md:M00741
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path:map00630 md:M00532
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path:map00630 md:M00968
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path:map00640 md:M00013
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path:map00640 md:M00741
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path:map00650 md:M00027
@@ -417,6 +421,8 @@ path:map00941 md:M00138
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path:map00941 md:M00940
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path:map00943 md:M00941
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path:map00943 md:M00942
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path:map00946 md:M00967
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path:map00946 md:M00966
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path:map00950 md:M00945
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path:map00950 md:M00943
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path:map00950 md:M00944
@@ -824,6 +830,7 @@ path:map01100 md:M00904
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path:map01100 md:M00906
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path:map01100 md:M00932
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path:map01100 md:M00933
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path:map01100 md:M00967
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path:map01100 md:M00952
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path:map01100 md:M00953
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path:map01100 md:M00960
@@ -836,6 +843,8 @@ path:map01100 md:M00900
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path:map01100 md:M00925
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path:map01100 md:M00915
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path:map01100 md:M00934
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path:map01100 md:M00966
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path:map01100 md:M00968
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path:map01100 md:M00909
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path:map01100 md:M00951
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path:map01100 md:M00958

‎dev/test_main.py‎

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@@ -121,7 +121,8 @@ def test_main_pull(mocker, args: list, output: str):
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stdin_mock = """
122122
br:br08005
123123
br:br08902
124-
124+
br:br08431
125+
125126
br:br03220
126127
br:br03222
127128
"""
@@ -130,18 +131,22 @@ def test_main_pull(mocker, args: list, output: str):
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successful_entry_ids = [
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'br:br08005',
133-
'br:br08902'
134+
'br:br08902',
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'br:br08431'
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]
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# The expected output file names have underscores instead of colons in case testing on Windows.
139+
expected_output_files: list = [entry_id.replace(':', '_') for entry_id in successful_entry_ids]
140+
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expected_pull_results = {
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'successful-entry-ids': successful_entry_ids,
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'failed-entry-ids': ['br:br03220', 'br:br03222'],
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'timed-out-entry-ids': [],
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'num-successful': 2,
145+
'num-successful': 3,
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'num-failed': 2,
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'num-timed-out': 0,
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'num-total': 4,
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'percent-success': 50.0,
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'num-total': 5,
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'percent-success': 60.0,
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'pull-minutes': 1.0
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}
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@@ -153,22 +158,23 @@ def test_main_pull(mocker, args: list, output: str):
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154159
assert time_mock.call_count == 2
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156-
if output.endswith('.zip'):
157-
with zf.ZipFile(output, 'r') as actual_zip:
158-
with zf.ZipFile(f'dev/test_data/{output}', 'r') as expected_zip:
159-
for successful_entry_id in successful_entry_ids:
160-
actual_entry: str = actual_zip.read(successful_entry_id + '.txt').decode()
161-
expected_entry: str = expected_zip.read(successful_entry_id + '.txt').decode()
161+
# If running on Windows, change the actual files names to have underscores instead of colons.
162+
if os.name == 'nt': # pragma: no cover
163+
expected_output_files: list = expected_output_files[:-1] # The last brite gives different output on Windows
164+
successful_entry_ids: list = expected_output_files # pragma: no cover
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163-
assert actual_entry == expected_entry
164-
else:
165-
for successful_entry_id in successful_entry_ids:
166+
for successful_entry_id, expected_output_file in zip(successful_entry_ids, expected_output_files):
167+
if output.endswith('.zip'):
168+
with zf.ZipFile(output, 'r') as actual_zip:
169+
actual_entry: str = actual_zip.read(successful_entry_id + '.txt').decode()
170+
else:
166171
with open(f'{output}/{successful_entry_id}.txt') as actual_file:
167-
with open(f'dev/test_data/{output}/{successful_entry_id}.txt') as expected_file:
168-
actual_entry: str = actual_file.read()
169-
expected_entry: str = expected_file.read()
172+
actual_entry: str = actual_file.read()
173+
174+
with open(f'dev/test_data/brite-entries/{expected_output_file}.txt') as expected_file:
175+
expected_entry: str = expected_file.read()
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171-
assert actual_entry == expected_entry
177+
assert actual_entry == expected_entry
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173179
with open('pull-results.json', 'r') as file:
174180
actual_pull_results: dict = j.load(file)

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