Merge pull request #143 from asiaszmek/add_github_actions

Add GitHub actions

Author: abukaj

.github/workflows/python-package.yml

@@ -0,0 +1,42 @@
+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+
+name: Python package
+
+on:
+  push:
+    branches: [ "master" ]
+  pull_request:
+    branches: [ "master" ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.8", "3.9", "3.10", "3.11"]
+
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v3
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install flake8 pytest
+        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+
+    - name: Lint with flake8
+      run: |
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    - name: Test with pytest
+      run: |
+        pytest

.travis.yml

@@ -71,7 +71,7 @@ def make_plots(fig_title,
     t_max = np.max(np.abs(true_csd))
     levels = np.linspace(-1*t_max, t_max, 16)
     ind_interest = np.mgrid[0:t_csd_z.shape[2]:np.complex(0,z_steps+2)]
-    ind_interest = np.array(ind_interest, dtype=np.int)[1:-1]
+    ind_interest = np.array(ind_interest, dtype=int)[1:-1]
     for ii, idx in enumerate(ind_interest):
         ax = plt.subplot(gs[ii, 0])
         im = plt.contourf(t_csd_x[:,:,idx], t_csd_y[:,:,idx], true_csd[:,:,idx], 
@@ -131,7 +131,7 @@ def make_plots(fig_title,
     t_max = np.max(np.abs(pre_cv[:,:,:,0]))
     levels_kcsd = np.linspace(-1*t_max, t_max, 16)
     ind_interest = np.mgrid[0:k_csd_z.shape[2]:np.complex(0,z_steps+2)]
-    ind_interest = np.array(ind_interest, dtype=np.int)[1:-1]
+    ind_interest = np.array(ind_interest, dtype=int)[1:-1]
     for ii, idx in enumerate(ind_interest):
         ax = plt.subplot(gs[ii, 2])
         im = plt.contourf(k_csd_x[:,:,idx], k_csd_y[:,:,idx], pre_cv[:,:,idx,0], 
@@ -159,7 +159,7 @@ def make_plots(fig_title,
     t_max = np.max(np.abs(est_csd[:,:,:,0]))
     levels_kcsd = np.linspace(-1*t_max, t_max, 16)
     ind_interest = np.mgrid[0:k_csd_z.shape[2]:np.complex(0,z_steps+2)]
-    ind_interest = np.array(ind_interest, dtype=np.int)[1:-1]
+    ind_interest = np.array(ind_interest, dtype=int)[1:-1]
     for ii, idx in enumerate(ind_interest):
         ax = plt.subplot(gs[ii, 3])
         im = plt.contourf(k_csd_x[:,:,idx], k_csd_y[:,:,idx], est_csd[:,:,idx,0], 

continuous_integration/install.sh

@@ -1,10 +1,12 @@
+from pathlib import Path
 import kCSD2D_reconstruction_from_npx as npx
 import matplotlib.pyplot as plt
 import matplotlib.cm as cm
 import scipy
 import numpy as np
+from numpy.linalg import LinAlgError
 from scipy.signal import filtfilt, butter
-
+import DemoReadSGLXData.readSGLX as readSGLX
 
 def set_axis(ax, x, y, letter=None):
     ax.text(
@@ -198,4 +200,4 @@ def gauss2d(x, y, p):
     make_plot(ax4, k.estm_x, k.estm_y, projection.reshape(true_csd.shape), ele_pos,
                   title='Projection', cmap='bwr')
     plt.tight_layout()
-    plt.savefig('Neuropixels_with_fitted_model.png', dpi=300)
+    plt.savefig('Neuropixels_with_fitted_model.png', dpi=300)

continuous_integration/readme

@@ -93,7 +93,7 @@ def dan_fetch_electrodes(meta):
 def eles_to_rows(eles):
     rows = []
     for ele in eles:
-        rows.append(np.int(np.ceil(ele/2)))
+        rows.append(int(np.ceil(ele/2)))
     return rows
 
 def eles_to_ycoord(eles):

continuous_integration/test_script.sh

@@ -10,7 +10,7 @@
 def eles_to_rows(eles):
     rows = []
     for ele in eles:
-        rows.append(np.int(np.ceil(ele/2)))
+        rows.append(int(np.ceil(ele/2)))
     return rows
 
 def eles_to_ycoord(eles):

figures/kCSD_properties/tutorial_basic_3d.py

@@ -8,7 +8,7 @@
 def eles_to_rows(eles):
     rows = []
     for ele in eles:
-        rows.append(np.int(np.ceil(ele/2)))
+        rows.append(int(np.ceil(ele/2)))
     return rows
 
 def eles_to_ycoord(eles):