Create basic_ci.yml

.github/workflows/basic_ci.yml

@@ -0,0 +1,34 @@
+name: Basic CI
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  basic_tests:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v3
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: 3.11
+    - name: Python info
+      run: |
+        which python
+        python --version
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install -e .[dev]
+    - name: Show pip list
+      run: |
+        pip list
+    - name: Run tests
+      run: |
+        pytest

setup.py

@@ -28,4 +28,9 @@
         "seaborn",
         "standardizeUtils @ git+https://github.com/boecker-lab/standardizeUtils/#egg=standardizeUtils"
     ],
+    extras_require={"dev": ["black",
+                            "pytest",
+                            "pytest-cov",
+                            ],
+    }
 )

tests/test_tokenizer.py

@@ -0,0 +1,41 @@
+import numpy as np
+import matchms
+from massspecgym.transforms import SpecTokenizer
+
+
+def test_spec_tokenizer():
+    spec = matchms.Spectrum(
+        mz=np.array(
+            [
+                45.134823,
+                45.13699,
+                110.096245,
+                130.064972,
+                136.111862,
+                277.16571,
+                289.165924,
+                307.177856,
+                406.223083,
+            ]
+        ),
+        intensities=np.array(
+            [
+                0.01082,
+                0.01064,
+                0.17184,
+                0.1397,
+                0.00874,
+                1.0,
+                0.52842,
+                0.00793,
+                0.43696
+            ]
+        ),
+        metadata={"precursor_mz": 406.22},
+    )
+
+    tokenizer = SpecTokenizer(n_peaks=60)
+    spec_np = tokenizer(spec)
+    assert spec_np.shape == (60, 2)
+    assert (spec_np[:spec.peaks.mz.shape[0], 0] == spec.peaks.mz).all()
+    assert (spec_np[:spec.peaks.intensities.shape[0], 1] == spec.peaks.intensities).all()

tests/test.py → tests/test_utils.py

@@ -51,44 +51,6 @@ def test_pad_spectrum():
         assert False
 
 
-def test_spec_tokenizer():
-    spec = matchms.Spectrum(
-        mz=np.array(
-            [
-                45.134823,
-                45.13699,
-                110.096245,
-                130.064972,
-                136.111862,
-                277.16571,
-                289.165924,
-                307.177856,
-                406.223083,
-            ]
-        ),
-        intensities=np.array(
-            [
-                0.01082,
-                0.01064,
-                0.17184,
-                0.1397,
-                0.00874,
-                1.0,
-                0.52842,
-                0.00793,
-                0.43696
-            ]
-        ),
-        metadata={"precursor_mz": 406.22},
-    )
-
-    tokenizer = SpecTokenizer(n_peaks=60)
-    spec_np = tokenizer(spec)
-    assert spec_np.shape == (60, 2)
-    assert (spec_np[:spec.peaks.mz.shape[0], 0] == spec.peaks.mz).all()
-    assert (spec_np[:spec.peaks.intensities.shape[0], 1] == spec.peaks.intensities).all()
-
-
 def test_morgan_fp():
     mol = Chem.MolFromSmiles("Cn1cnc2c1c(=O)n(C)c(=O)n2C")
     for i in [2048, 4096]: