Refactoring of tests and restructuring of requirements

kalininalab · Sep 29, 2024 · 4e2df12 · 4e2df12
1 parent dcf30f3
commit 4e2df12
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Showing 9 changed files with 22 additions and 12 deletions.
diff --git a/.github/workflows/run_test.yaml b/.github/workflows/run_test.yaml
@@ -1,6 +1,16 @@
 name: Pytest
 
-on: [push]
+on:
+  # Triggers the workflow on push or pull request events but only for the main branch
+  push:
+    branches:
+      - main
+      - dev
+  pull_request:
+    branches:
+      - main
+      - dev
+  workflow_dispatch:  # make is manually start-able
 
 jobs:
   build:

diff --git a/requirements.txt b/requirements.txt
@@ -1,13 +1,13 @@
-torch
-lightning
-torchmetrics
+pandas
 rich
 fair-esm
-wandb
-tokenizers
-transformers
 beartype
+wandb
+torch
+lightning
+torchmetrics
 datasets
+tokenizers
 transformers[torch]
 pytest
 pytest-cov
diff --git a/smtb/tests/__init__.py → tests/__init__.py b/smtb/tests/__init__.py → tests/__init__.py
diff --git a/smtb/tests/fixtures.py → tests/fixtures.py b/smtb/tests/fixtures.py → tests/fixtures.py
diff --git a/smtb/tests/test_data.py → tests/test_data.py b/smtb/tests/test_data.py → tests/test_data.py
@@ -3,7 +3,7 @@
 import pytest
 import torch
 
-from ..data import DownstreamDataModule, DownstreamDataset
+from smtb.data import DownstreamDataModule, DownstreamDataset
 from .fixtures import mock_data_dir
 
 

diff --git a/smtb/tests/test_finetune.py → tests/test_finetune.py b/smtb/tests/test_finetune.py → tests/test_finetune.py
@@ -1,6 +1,6 @@
 import os
 
-from ..train import train
+from smtb.train import train
 from .fixtures import mock_data_dir, sample_config
 
 

diff --git a/smtb/tests/test_model.py → tests/test_model.py b/smtb/tests/test_model.py → tests/test_model.py
@@ -3,7 +3,7 @@
 import pytest
 import torch
 
-from ..model import RegressionModel
+from smtb.model import RegressionModel
 from .fixtures import sample_batch_x, sample_config
 
 

diff --git a/smtb/tests/test_pooling.py → tests/test_pooling.py b/smtb/tests/test_pooling.py → tests/test_pooling.py
@@ -3,7 +3,7 @@
 import pytest
 import torch
 
-from ..model import poolings
+from smtb.model import poolings
 from .fixtures import sample_batch_x, sample_config
 
 

diff --git a/smtb/tests/test_tokenizers.py → tests/test_tokenizers.py b/smtb/tests/test_tokenizers.py → tests/test_tokenizers.py
@@ -4,7 +4,7 @@
 from datasets import Dataset, DatasetDict
 from transformers import PreTrainedTokenizerFast
 
-from ..tokenization import TOKENIZATION_TYPES, train_tokenizer
+from smtb.tokenization import TOKENIZATION_TYPES, train_tokenizer
 
 
 def tokenization_types():