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Merge pull request #188 from ttngu207/main
Add pytest
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,17 +0,0 @@ | ||
| import os | ||
| import datajoint as dj | ||
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| if "custom" not in dj.config: | ||
| dj.config["custom"] = {} | ||
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| # overwrite dj.config['custom'] values with environment variables if available | ||
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| dj.config["custom"]["database.prefix"] = os.getenv( | ||
| "DATABASE_PREFIX", dj.config["custom"].get("database.prefix", "") | ||
| ) | ||
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| dj.config["custom"]["imaging_root_data_dir"] = os.getenv( | ||
| "IMAGING_ROOT_DATA_DIR", dj.config["custom"].get("imaging_root_data_dir", "") | ||
| ) | ||
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| db_prefix = dj.config["custom"].get("database.prefix", "") | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,3 +1,3 @@ | ||
| """Package metadata.""" | ||
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| __version__ = "0.9.4" | ||
| __version__ = "0.9.5" |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -49,7 +49,7 @@ | |
| } | ||
| ], | ||
| "source": [ | ||
| "from tutorial_pipeline import *" | ||
| "from tests.tutorial_pipeline import *" | ||
| ] | ||
| }, | ||
| { | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,78 +0,0 @@ | ||
| """ | ||
| run all: python -m pytest -sv --cov-report term-missing --cov=element_calcium_imaging --sw -p no:warnings tests/ | ||
| run one: python -m pytest -sv --cov-report term-missing --cov=element_calcium_imaging --sw -p no:warnings --pdb tests/module_name.py -k function_name | ||
| """ | ||
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| import os | ||
| import pathlib | ||
| import sys | ||
| from contextlib import nullcontext | ||
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| import datajoint as dj | ||
| import numpy as np | ||
| import pandas as pd | ||
| import pytest | ||
| from element_interface.utils import find_full_path, find_root_directory | ||
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| # ------------------- SOME CONSTANTS ------------------- | ||
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| _tear_down = False | ||
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| sessions_dirs = [ | ||
| "subject1/session1", | ||
| ] | ||
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| verbose = False | ||
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| logger = dj.logger | ||
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| # ------------------ GENERAL FUCNTION ------------------ | ||
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| class QuietStdOut: | ||
| """If verbose set to false, used to quiet tear_down table.delete prints""" | ||
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| def __enter__(self): | ||
| logger.setLevel("ERROR") | ||
| self._original_stdout = sys.stdout | ||
| sys.stdout = open(os.devnull, "w") | ||
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| def __exit__(self, exc_type, exc_val, exc_tb): | ||
| logger.setLevel("INFO") | ||
| sys.stdout.close() | ||
| sys.stdout = self._original_stdout | ||
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| verbose_context = nullcontext() if verbose else QuietStdOut() | ||
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| # ------------------- FIXTURES ------------------- | ||
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| @pytest.fixture | ||
| def pipeline(): | ||
| with verbose_context: | ||
| print("\n") | ||
| from notebooks import tutorial_pipeline | ||
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| yield { | ||
| "subject": tutorial_pipeline.subject, | ||
| "lab": tutorial_pipeline.lab, | ||
| "imaging": tutorial_pipeline.imaging, | ||
| "scan": tutorial_pipeline.scan, | ||
| "session": tutorial_pipeline.session, | ||
| "Equipment": tutorial_pipeline.Equipment, | ||
| "get_imaging_root_data_dir": tutorial_pipeline.get_imaging_root_data_dir, | ||
| } | ||
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| if _tear_down: | ||
| with verbose_context: | ||
| pipeline.subject.Subject.delete() | ||
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| @pytest.fixture(autouse=True) | ||
| def test_data(pipeline): | ||
| root_dirs = pipeline["get_imaging_root_data_dir"] | ||
| try: | ||
| _ = [find_full_path(root_dirs(), p) for p in sessions_dirs] | ||
| except FileNotFoundError as e: | ||
| print(e) | ||
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