Merge pull request #295 from GSTT-CSC/294-pypi-package-build-is-failing

update numpy and move code coverage badge update to release tests
GSTT-CSC · Jan 3, 2023 · 90f4fa1 · 90f4fa1 · github-actions · Jan 3, 2023
2 parents 01046cb + 78499d9
commit 90f4fa1
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Showing 5 changed files with 22 additions and 16 deletions.
diff --git a/.github/workflows/tests_development.yml b/.github/workflows/tests_development.yml
@@ -58,15 +58,3 @@ jobs:
       with:
         pytest-coverage-path: ./pytest-coverage.txt
         junitxml-path: ./pytest.xml
-
-    - name: Update the coverage Badge
-      if: github.event.pull_request.base.ref == 'main'  # if pull request is merging into main
-      uses: schneegans/[email protected]
-      with:
-        auth: ${{ secrets.PYTEST_COVERAGE_COMMENT }}
-        gistID: ba102d5f3e592fcd50451c2eff8a803d
-        filename: hazen_pytest-coverage-comment.json
-        label: Test coverage
-        message: ${{ steps.coverageComment.outputs.coverage }}
-        color: ${{ steps.coverageComment.outputs.color }}
-        namedLogo: python
diff --git a/.github/workflows/tests_release.yml b/.github/workflows/tests_release.yml
@@ -37,3 +37,20 @@ jobs:
         set -Eeuxo pipefail
         pytest --junitxml=pytest.xml --cov-report=term-missing:skip-covered --cov=hazenlib tests/ | tee pytest-coverage.txt ; echo $?
 
+    - name: Pytest coverage comment
+      id: coverageComment
+      uses: MishaKav/pytest-coverage-comment@main
+      with:
+        pytest-coverage-path: ./pytest-coverage.txt
+        junitxml-path: ./pytest.xml
+
+    - name: Update the coverage Badge
+      uses: schneegans/[email protected]
+      with:
+        auth: ${{ secrets.PYTEST_COVERAGE_COMMENT }}
+        gistID: ba102d5f3e592fcd50451c2eff8a803d
+        filename: hazen_pytest-coverage-comment.json
+        label: Test coverage
+        message: ${{ steps.coverageComment.outputs.coverage }}
+        color: ${{ steps.coverageComment.outputs.color }}
+        namedLogo: python
diff --git a/requirements.txt b/requirements.txt
@@ -1,6 +1,6 @@
 # After making changes for core components please update install_requires in setp.py as well
 pydicom==2.2.2
-numpy==1.21.4
+numpy==1.24.1
 matplotlib==3.5.1
 pytest==7.1.2
 docopt==0.6.2

diff --git a/setup.py b/setup.py
@@ -2,7 +2,7 @@
 from hazenlib import __version__
 
 install_requires = ['pydicom==2.2.2',
-                    'numpy==1.21.4',
+                    'numpy==1.24.1',
                     'matplotlib==3.5.1',
                     'docopt==0.6.2',
                     'opencv-python-headless==4.6.0.66',

diff --git a/tests/test_spatial_resolution.py b/tests/test_spatial_resolution.py
@@ -1,5 +1,6 @@
 import unittest
 import pathlib
+import pytest
 
 import numpy as np
 import pydicom
@@ -414,8 +415,8 @@ def test_mtf(self):
 
     def test_calculate_mtf(self):
         res = self.hazen_spatial_resolution.calculate_mtf(self.hazen_spatial_resolution.data[0])
-        assert res['frequency_encoding_direction'] == self.MTF_FE
-        assert res['phase_encoding_direction'] == self.MTF_PE
+        assert res['frequency_encoding_direction'] == pytest.approx(self.MTF_FE)
+        assert res['phase_encoding_direction'] == pytest.approx(self.MTF_PE)
 
 
 class TestPhilipsResolution(TestSpatialResolution):
File	Stmts	Miss	Cover	Missing
hazenlib
HazenTask.py	26	4	85%	18, 32–34
__init__.py	147	38	74%	138, 142, 152, 157, 194, 201–206, 217, 220–227, 247–249, 267–269, 288–290, 299, 304, 310, 361, 384–386, 394–395, 399
exceptions.py	21	4	81%	17–21
relaxometry.py	317	90	72%	238–256, 631, 690–692, 746, 794–816, 834–849, 1174–1177, 1186–1189, 1201–1214, 1217–1222, 1233–1263
shapes.py	20	9	55%	13, 16, 24–29, 32
snr_map.py	111	5	95%	408, 413–415, 444
tools.py	84	8	90%	43–50, 92, 101, 117
hazenlib/tasks
acr_ghosting.py	116	42	64%	33–53, 91–93, 123–125, 161–194
acr_uniformity.py	89	32	64%	34–54, 121–138
ghosting.py	150	51	66%	18–32, 47, 109–110, 114, 124–125, 151–153, 170–172, 218–256
relaxometry.py	7	2	71%	10–11
slice_position.py	118	22	81%	31, 40–41, 103–104, 130, 210, 217–234
slice_width.py	359	52	86%	34–37, 107, 166–186, 451, 456–457, 463, 468, 530–531, 780–821
snr.py	163	66	60%	62–67, 161–179, 194–203, 221–231, 258–268, 273–283, 314–327, 332–340, 369–382
snr_map.py	7	7	0%	1–11
spatial_resolution.py	247	44	82%	36–39, 62, 147, 206, 332–368
uniformity.py	78	19	76%	42–45, 91–92, 99, 133–147
TOTAL	2076	495	76%