Merge pull request #245 from gipert/tests

Unit tests cleanup

.github/workflows/get-dependencies.sh

@@ -1,12 +1,17 @@
 #!/bin/bash
 
-pyver=$(python --version | sed 's|Python \([0-9]*\).\([0-9]*\).[0-9]*|\1\2|')
+[[ -f /etc/os-release ]] && linux_distro=$(awk -F= '/^NAME/{print $2}' /etc/os-release | cut -d ' ' -f1)
 
-if [ "$pyver" -gt "35" ]; then
-    sudo apt-get install -y llvm
-else
-    sudo apt-get install -y llvm-8
-    sudo ln -s /usr/bin/llvm-config-8 /usr/bin/llvm-config
+if [[ "${linux_distro}" == "Ubuntu" || "${linux_distro}" == "Debian" ]]; then
+
+    pyver=$(python --version | sed 's|Python \([0-9]*\).\([0-9]*\).[0-9]*|\1\2|')
+
+    if [ "$pyver" -gt "35" ]; then
+        sudo apt-get install -y llvm
+    else
+        sudo apt-get install -y llvm-8
+        sudo ln -s /usr/bin/llvm-config-8 /usr/bin/llvm-config
+    fi
 fi
 
 python -m pip install --upgrade pip wheel setuptools numpy GitPython pytest

.github/workflows/main.yml

@@ -4,8 +4,6 @@ on:
   push:
     branches:
       - main
-      - master
-      - dev
       - refactor
       - 'releases/**'
   pull_request:
@@ -33,19 +31,24 @@ jobs:
         .github/workflows/get-dependencies.sh
         python -m pip install .
     - name: Run unit tests
-      run: pytest test
+      run: |
+        pytest tests
 
-  test-in-legend-container:
-    name: Test pygama in LEGEND container
-    runs-on: ubuntu-latest
-    container: docker://legendexp/legend-base:latest
+  # test-in-legend-container:
+  #   name: Test pygama in LEGEND container
+  #   runs-on: ubuntu-latest
+  #   container: docker://legendexp/legend-base:${{ matrix.docker-tag }}
+  #   strategy:
+  #     fail-fast: false
+  #     matrix:
+  #       docker-tag: [latest, ubuntu]
 
-    steps:
-    - uses: actions/checkout@v2
-    - name: Install and run unit tests
-      run: |
-        pip install .
-        pytest test
+  #   steps:
+  #   - uses: actions/checkout@v2
+  #   - name: Install and run unit tests
+  #     run: |
+  #       python -m pip install .
+  #       pytest tests
 
   deploy-docs:
     name: Deploy documentation on legend-exp.github.io/pygama

pygama/math/histogram.py

@@ -434,7 +434,7 @@ def plot_hist(hist, bins, var=None, show_stats=False, stats_hloc=0.75, stats_vlo
         dmean = stddev/np.sqrt(N)
 
         mean, dmean = pgu.get_formatted_stats(mean, dmean, 2)
-        stats = '$\mu=%s \pm %s$\n$\sigma=%#.3g$' % (mean, dmean, stddev)
+        stats = r'$\mu=%s \pm %s$\n$\sigma=%#.3g$' % (mean, dmean, stddev)
         stats_fontsize = rcParams['legend.fontsize']
         plt.text(stats_hloc, stats_vloc, stats, transform=plt.gca().transAxes, fontsize = stats_fontsize)
 

pygama/math/peak_fitting.py

@@ -639,8 +639,8 @@ def gauss_tail(x, mu, sigma, tau):
     x = np.asarray(x)
     tmp = ((x-mu)/tau) + ((sigma**2)/(2*tau**2))
     tail_f = np.where(tmp < limit, 
-                      gauss_tail_exact_pdf(x, mu, sigma, tau), 
-                      gauss_tail_approx_pdf(x, mu, sigma, tau))
+                      gauss_tail_exact(x, mu, sigma, tau), 
+                      gauss_tail_approx(x, mu, sigma, tau))
     return tail_f
 
 @nb.njit(**kwd)

pygama/raw/fc/__init__.py

@@ -0,0 +1,3 @@
+"""
+Subpackage documentation
+"""

pygama/raw/orca/__init__.py

@@ -0,0 +1,3 @@
+"""
+Subpackage documentation
+"""

pytest.ini

@@ -0,0 +1,7 @@
+[pytest]
+minversion = 6.0
+addopts = -ra --showlocals --strict-markers --strict-config
+xfail_strict = true
+filterwarnings = error
+log_cli_level = info
+testpaths = tests

tests/functional/test_l200_dataproc.py

@@ -0,0 +1 @@
+

tests/functional/test_teststand_dataproc.py

@@ -0,0 +1 @@
+

tests/integration/test_integration.py

@@ -0,0 +1 @@
+

tests/lgdo/test_lgdo_utils.py

@@ -0,0 +1,38 @@
+import pygama.lgdo.lgdo_utils as lgdo_utils
+import numpy as np
+
+
+def test_get_element_type():
+
+    objs = [
+        ('hi', 'string'),
+        (True, 'bool'),
+        (np.void(0), 'blob'),
+        (int(0), 'real'),
+        (np.uint8(0), 'real'),
+        (float(0), 'real'),
+        (1+1j, 'complex'),
+        (b'hi', 'string'),
+        (np.array(['hi']), 'string'),
+    ]
+
+    for obj, name in objs:
+        get_name = lgdo_utils.get_element_type(obj)
+        assert get_name == name
+
+
+def test_parse_datatype():
+
+    datatypes = [
+        ('real', ('scalar', None, 'real')),
+        ('array<1>{bool}', ('array', (1,), 'bool')),
+        ('fixedsizearray<2>{real}', ('fixedsizearray', (2,), 'real')),
+        ('arrayofequalsizedarrays<3,4>{complex}', ('arrayofequalsizedarrays', (3, 4), 'complex')),
+        ('array<1>{array<1>{blob}}', ('array', (1,), 'array<1>{blob}')),
+        ('struct{field1,field2,fieldn}', ('struct', None, ['field1', 'field2', 'fieldn'])),
+        ('table{col1,col2,coln}', ('table', None, ['col1', 'col2', 'coln'])),
+    ]
+
+    for string, dt_tuple in datatypes:
+        pd_dt_tuple = lgdo_utils.parse_datatype(string)
+        assert pd_dt_tuple == dt_tuple