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Adapt to new alphabase #56

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Adapt to new alphabase #56

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5dc91f9
adapt to new alphabase
mschwoer Nov 26, 2024
22ede7d
get rid of duplicated import
mschwoer Nov 26, 2024
3cd7bfb
Merge branch 'master' into adapt_to_new_alphabase
mschwoer Jan 22, 2025
b47d587
upgrade alphabase version
mschwoer Jan 22, 2025
ae27101
fix tests
mschwoer Jan 22, 2025
514572b
fix tests
mschwoer Jan 22, 2025
4023629
fix tests
mschwoer Jan 22, 2025
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2 changes: 1 addition & 1 deletion requirements/requirements_development.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -6,4 +6,4 @@ sphinx-rtd-theme
bump-my-version
pipdeptree
ipykernel
notebook
notebook
5 changes: 3 additions & 2 deletions requirements/requirements_tests.txt
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Expand Up @@ -4,6 +4,7 @@ matplotlib
wget
seaborn
nbdev>=2.3.9
alphabase>=1.4.0
alphabase>=1.5.0
progressbar
pytest
pytest
nbmake==1.5.3
4 changes: 2 additions & 2 deletions tests/quicktests/run_pipeline_w_different_input_formats.ipynb
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Expand Up @@ -8,7 +8,7 @@
"source": [
"import os\n",
"import directlfq\n",
"import alphabase.test_data_downloader\n",
"import alphabase.tools.data_downloader\n",
"\n",
"# Get the directory of the directlfq package\n",
"directlfq_dir = os.path.dirname(directlfq.__file__)\n",
Expand All @@ -20,7 +20,7 @@
"\n",
"os.makedirs(output_dir, exist_ok=True)\n",
"# Now use the absolute path in the DataShareDownloader call\n",
"alphabase.test_data_downloader.DataShareDownloader(url=\"https://datashare.biochem.mpg.de/s/VJm70w0p2P86tE1\", output_dir=output_dir).download()\n"
"alphabase.tools.data_downloader.DataShareDownloader(url=\"https://datashare.biochem.mpg.de/s/VJm70w0p2P86tE1\", output_dir=output_dir).download()\n"
]
},
{
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2 changes: 1 addition & 1 deletion tests/ratio_tests/compare_diapasef_diann.ipynb
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Expand Up @@ -44,7 +44,7 @@
"metadata": {},
"outputs": [],
"source": [
"import alphabase.test_data_downloader as tdd\n",
"import alphabase.tools.data_downloader as tdd\n",
"\n",
"tdd.DataShareDownloader(url=\"https://datashare.biochem.mpg.de/s/9UoHMjTCJ8TmmlA\", output_dir=\"../../test_data/system_tests/\").download()"
]
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4 changes: 2 additions & 2 deletions tests/ratio_tests/systemtest_ratio_mixed_species1.ipynb
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Expand Up @@ -19,7 +19,7 @@
"source": [
"import os\n",
"import directlfq\n",
"import alphabase.test_data_downloader\n",
"import alphabase.tools.data_downloader\n",
"\n",
"# Get the directory of the directlfq package\n",
"directlfq_dir = os.path.dirname(directlfq.__file__)\n",
Expand All @@ -31,7 +31,7 @@
"\n",
"os.makedirs(output_dir, exist_ok=True)\n",
"# Now use the absolute path in the DataShareDownloader call\n",
"alphabase.test_data_downloader.DataShareDownloader(url=\"https://datashare.biochem.mpg.de/s/zjSHOAzKBaF2Z73\", output_dir=output_dir).download()\n"
"alphabase.tools.data_downloader.DataShareDownloader(url=\"https://datashare.biochem.mpg.de/s/zjSHOAzKBaF2Z73\", output_dir=output_dir).download()\n"
]
},
{
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4 changes: 2 additions & 2 deletions tests/ratio_tests/systemtest_ratio_mixed_species2.ipynb
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Expand Up @@ -19,7 +19,7 @@
"source": [
"import os\n",
"import directlfq\n",
"import alphabase.test_data_downloader\n",
"import alphabase.tools.data_downloader\n",
"\n",
"# Get the directory of the directlfq package\n",
"directlfq_dir = os.path.dirname(directlfq.__file__)\n",
Expand All @@ -31,7 +31,7 @@
"\n",
"os.makedirs(output_dir, exist_ok=True)\n",
"# Now use the absolute path in the DataShareDownloader call\n",
"alphabase.test_data_downloader.DataShareDownloader(url=\"https://datashare.biochem.mpg.de/s/T8sFUGuaQb0d1zP\", output_dir=output_dir).download()\n"
"alphabase.tools.data_downloader.DataShareDownloader(url=\"https://datashare.biochem.mpg.de/s/T8sFUGuaQb0d1zP\", output_dir=output_dir).download()\n"
]
},
{
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6 changes: 2 additions & 4 deletions tests/run_quicktests.sh
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@@ -1,9 +1,7 @@
conda activate directlfq
pip install pytest
pip install nbmake==1.5.3
pip install alphabase>=1.2.1
pip install -r ../requirements/requirements_development.txt
cd quicktests
pytest --nbmake run_pipeline_w_different_input_formats.ipynb
python -m pytest --nbmake run_pipeline_w_different_input_formats.ipynb
directlfq lfq -i ../../test_data/system_tests/quicktests/diann/shortened_input.tsv
cd ..
conda deactivate
4 changes: 2 additions & 2 deletions tests/run_ratio_tests.sh
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Expand Up @@ -4,7 +4,7 @@ cd ratio_tests
pip install pytest
pip install nbmake==1.5.3
echo "Running ratio tests"
pytest --nbmake systemtest_ratio_mixed_species1.ipynb --nbmake-timeout=1800
pytest --nbmake systemtest_ratio_mixed_species2.ipynb --nbmake-timeout=1800
python -m pytest --nbmake systemtest_ratio_mixed_species1.ipynb --nbmake-timeout=1800
python -m pytest --nbmake systemtest_ratio_mixed_species2.ipynb --nbmake-timeout=1800
cd ..
conda deactivate
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