From 41c1b4d99de0fd7a9ff9b92acc08d03e7dddfc78 Mon Sep 17 00:00:00 2001
From: Florian Huber <36473328+florian-huber@users.noreply.github.com>
Date: Fri, 24 May 2024 21:31:09 +0200
Subject: [PATCH 1/4] Create basic_ci.yml

Add first CI
---
 .github/workflows/basic_ci.yml | 29 +++++++++++++++++++++++++++++
 1 file changed, 29 insertions(+)
 create mode 100644 .github/workflows/basic_ci.yml

diff --git a/.github/workflows/basic_ci.yml b/.github/workflows/basic_ci.yml
new file mode 100644
index 0000000..6aeaf98
--- /dev/null
+++ b/.github/workflows/basic_ci.yml
@@ -0,0 +1,29 @@
+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: Install dependencies via pip
+      run: |
+        pip install -e .
+
+    - name: Run tests
+      run: |
+        pytest

From b8d1e29c55a7b84c5ce9cc3969ca69912338e920 Mon Sep 17 00:00:00 2001
From: Florian Huber <36473328+florian-huber@users.noreply.github.com>
Date: Fri, 24 May 2024 21:39:04 +0200
Subject: [PATCH 2/4] add dev dependencies

---
 setup.py | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/setup.py b/setup.py
index c78383b..caa0704 100644
--- a/setup.py
+++ b/setup.py
@@ -28,4 +28,9 @@
         "seaborn",
         "standardizeUtils @ git+https://github.com/boecker-lab/standardizeUtils/#egg=standardizeUtils"
     ],
+    extras_require={"dev": ["black",
+                            "pytest",
+                            "pytest-cov",
+                            ],
+    }
 )

From 22cca16880bb14a0f2de2bf0e4f81d7c89f45609 Mon Sep 17 00:00:00 2001
From: Florian Huber <36473328+florian-huber@users.noreply.github.com>
Date: Fri, 24 May 2024 21:40:59 +0200
Subject: [PATCH 3/4] Update basic_ci.yml

---
 .github/workflows/basic_ci.yml | 15 ++++++++++-----
 1 file changed, 10 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/basic_ci.yml b/.github/workflows/basic_ci.yml
index 6aeaf98..b10ab0d 100644
--- a/.github/workflows/basic_ci.yml
+++ b/.github/workflows/basic_ci.yml
@@ -14,16 +14,21 @@ jobs:
     steps:
     - name: Checkout repository
       uses: actions/checkout@v3
-
     - name: Set up Python
       uses: actions/setup-python@v4
       with:
         python-version: 3.11
-
-    - name: Install dependencies via pip
+    - name: Python info
       run: |
-        pip install -e .
-
+        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

From 85ddb44d28b17e34d792bd80c4814fbff8a9e645 Mon Sep 17 00:00:00 2001
From: Florian Huber <florian.huber@hs-duesseldorf.de>
Date: Fri, 24 May 2024 21:50:27 +0200
Subject: [PATCH 4/4] split test in two files

---
 tests/test_tokenizer.py          | 41 ++++++++++++++++++++++++++++++++
 tests/{test.py => test_utils.py} | 38 -----------------------------
 2 files changed, 41 insertions(+), 38 deletions(-)
 create mode 100644 tests/test_tokenizer.py
 rename tests/{test.py => test_utils.py} (62%)

diff --git a/tests/test_tokenizer.py b/tests/test_tokenizer.py
new file mode 100644
index 0000000..a2443ce
--- /dev/null
+++ b/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()
diff --git a/tests/test.py b/tests/test_utils.py
similarity index 62%
rename from tests/test.py
rename to tests/test_utils.py
index 3284d68..a61b6e1 100644
--- a/tests/test.py
+++ b/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]: