capture and print test_scripts output for debugging CI-testing

gph82 · Jan 3, 2025 · a2f2b10 · a2f2b10
1 parent 23c2f72
commit a2f2b10
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Showing 3 changed files with 22 additions and 2 deletions.
diff --git a/.github/workflows/python-package.macos.yml b/.github/workflows/python-package.macos.yml
@@ -92,7 +92,7 @@ jobs:
       if: ${{ matrix.python-version != '3.7' }}
       run: |
         echo -e '[run]\nomit = *dihedrals.py,*contact_matrix.py' > .coveragerc
-        pytest -n 8 -vs --cov=./ --cov-report=xml --disable-warnings --cov-config=.coveragerc
+        pytest -k Test_ExamplesCLTs -n 8 -vs --cov=./ --cov-report=xml --disable-warnings --cov-config=.coveragerc
     - name: Upload coverage to Codecov
       uses: codecov/codecov-action@v4
       with:

diff --git a/mdciao/examples/examples.py b/mdciao/examples/examples.py
@@ -225,7 +225,7 @@ def run(self, clt,show=True):
         oneline = self._join_args(clt)
         CP = []
         for line in oneline.split("\n\n"):
-            CP.append(_run(line.split()))
+            CP.append(_run(line.split(), capture_output=True))
         if self.test:
             return CP
 

diff --git a/tests/test_scripts.py b/tests/test_scripts.py
@@ -44,6 +44,8 @@ def test_mdc_sites(self):
             CP = self.xCLTs.run("mdc_sites",
                                 # show=True
                                 )
+            print([iCP.stdout.decode().splitlines() for iCP in CP])
+            print([iCP.stderr.decode().splitlines() for iCP in CP])
         assert _np.unique([iCP.returncode for iCP in CP]) == 0
 
     def test_mdc_neighborhood(self):
@@ -52,6 +54,8 @@ def test_mdc_neighborhood(self):
             CP = self.xCLTs.run("mdc_neighborhoods",
                                 # show=True
                                 )
+            print([iCP.stdout.decode().splitlines() for iCP in CP])
+            print([iCP.stderr.decode().splitlines() for iCP in CP])
         assert _np.unique([iCP.returncode for iCP in CP]) == 0
 
     def test_mdc_interface(self):
@@ -60,6 +64,8 @@ def test_mdc_interface(self):
             CP = self.xCLTs.run("mdc_interface",
                                 # show=True
                                 )
+            print([iCP.stdout.decode().splitlines() for iCP in CP])
+            print([iCP.stderr.decode().splitlines() for iCP in CP])
         assert _np.unique([iCP.returncode for iCP in CP]) == 0
 
     def test_mdc_fragments(self):
@@ -68,6 +74,8 @@ def test_mdc_fragments(self):
             CP = self.xCLTs.run("mdc_fragments",
                                 # show=True
                                 )
+            print([iCP.stdout.decode().splitlines() for iCP in CP])
+            print([iCP.stderr.decode().splitlines() for iCP in CP])
         assert _np.unique([iCP.returncode for iCP in CP]) == 0
 
     def test_mdc_BW(self):
@@ -76,6 +84,8 @@ def test_mdc_BW(self):
             CP = self.xCLTs.run("mdc_GPCR_overview",
                                 # show=True
                                 )
+            print([iCP.stdout.decode().splitlines() for iCP in CP])
+            print([iCP.stderr.decode().splitlines() for iCP in CP])
         assert _np.unique([iCP.returncode for iCP in CP]) == 0, CP
 
     def test_mdc_CGN(self):
@@ -84,6 +94,8 @@ def test_mdc_CGN(self):
             CP = self.xCLTs.run("mdc_CGN_overview",
                                 # show=True
                                 )
+            print([iCP.stdout.decode().splitlines() for iCP in CP])
+            print([iCP.stderr.decode().splitlines() for iCP in CP])
         assert _np.unique([iCP.returncode for iCP in CP]) == 0
 
     def test_mdc_pdb(self):
@@ -92,24 +104,32 @@ def test_mdc_pdb(self):
             CP = self.xCLTs.run("mdc_pdb",
                                 # show=True
                                 )
+            print([iCP.stdout.decode().splitlines() for iCP in CP])
+            print([iCP.stderr.decode().splitlines() for iCP in CP])
         assert _np.unique([iCP.returncode for iCP in CP]) == 0
 
     def test_mdc_compare(self):
         with remember_cwd():
             os.chdir(self.tmpdir)
             CP = self.xCLTs.run("mdc_compare")
+            print([iCP.stdout.decode().splitlines() for iCP in CP])
+            print([iCP.stderr.decode().splitlines() for iCP in CP])
             assert _np.unique([iCP.returncode for iCP in CP]) == 0
 
     def test_mdc_residues(self):
         with remember_cwd():
             os.chdir(self.tmpdir)
             CP = self.xCLTs.run("mdc_residues")
+            print([iCP.stdout.decode().splitlines() for iCP in CP])
+            print([iCP.stderr.decode().splitlines() for iCP in CP])
             assert _np.unique([iCP.returncode for iCP in CP]) == 0
 
     def test_mdc_notebooks(self):
         with remember_cwd():
             os.chdir(self.tmpdir)
             CP = self.xCLTs.run("mdc_notebooks")
+            print([iCP.stdout.decode().splitlines() for iCP in CP])
+            print([iCP.stderr.decode().splitlines() for iCP in CP])
             assert _np.unique([iCP.returncode for iCP in CP]) == 0