Add tests

Author: dkurt

.github/workflows/main.yml

@@ -0,0 +1,45 @@
+name: CI
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+
+jobs:
+  run_linux:
+    name: Test on Linux
+    runs-on: ubuntu-18.04
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Install
+      run: |
+        sudo apt-get install -y python3-setuptools
+        python3 -m pip install --upgrade pip
+        python3 -m pip install -r requirements.txt
+        sudo python3 setup.py develop
+
+    - name: Download data and models
+      run: |
+        bonito download --models
+        mkdir reads
+        sudo apt-get install -y megatools
+        megadl 'https://mega.nz/#!dccAET7R!-zq6ECPCzaN5jLjh8ASKRJdcjt-1325pEAtuIcmBGsg' --no-progress
+        unzip reads.zip -d reads
+
+    - name: Test dna_r9.4.1@v2
+      run: |
+        bonito basecaller dna_r9.4.1@v2 --device=cpu reads > ref.fasta
+        bonito basecaller dna_r9.4.1@v2 --use_openvino --device=cpu reads > out.fasta
+        cat ref.fasta
+        cat out.fasta
+        cmp ref.fasta out.fasta
+
+    - name: Test dna_r10.3@v3
+      run: |
+        bonito basecaller dna_r10.3@v3 --device=cpu reads > ref.fasta
+        bonito basecaller dna_r10.3@v3 --use_openvino --device=cpu reads > out.fasta
+        cat ref.fasta
+        cat out.fasta
+        cmp ref.fasta out.fasta

bonito/crf/basecall.py

@@ -60,6 +60,12 @@ def transfer(x):
     """
     Device to host transfer using pinned memory.
     """
+    if not torch.cuda.is_available():
+        return {
+            k: torch.empty(v.shape, pin_memory=False, dtype=v.dtype).copy_(v).numpy()
+            for k, v in x.items()
+        }
+
     torch.cuda.synchronize()
     with torch.cuda.stream(torch.cuda.Stream()):
         return {

bonito/ctc/basecall.py

@@ -37,7 +37,8 @@ def compute_scores(model, batch):
     """
     with torch.no_grad():
         device = next(model.parameters()).device
-        chunks = batch.to(torch.half).to(device)
+        chunks = batch.to(torch.half) if half_supported() else batch
+        chunks = chunks.to(device)
         probs = permute(model(chunks), 'TNC', 'NTC')
     return probs.cpu().to(torch.float32)