Merge pull request #62 from luigibonati/tutorials_fix

Tutorials_fix
luigibonati · May 29, 2023 · c4f8518 · c4f8518
2 parents afb8ab6 + 959f5ae
commit c4f8518
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diff --git a/.github/workflows/CI.yaml b/.github/workflows/CI.yaml
@@ -59,12 +59,17 @@ jobs:
           pytest -v --cov=mlcolvar --cov-report=xml --color=yes mlcolvar/tests/
           pytest -v --nbmake docs/notebooks/ --ignore=docs/notebooks/tutorials/data/ --cov=mlcolvar --cov-append --cov-report=xml --color=yes 
 
-          cat ./coverage.xml
+      - name: Run notebook tests
+        # conda setup requires this special shell
+        shell: bash -l {0}
+        if: contains( matrix.os, 'ubuntu' )
+        run: |
+          pytest -v --nbmake docs/notebooks/ --ignore=docs/notebooks/tutorials/data/ --cov=mlcolvar --cov-append --cov-report=xml --color=yes 
 
       - name: CodeCov
         uses: codecov/codecov-action@v3
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           file: ./coverage.xml
-          flags: unittests
+          flags: codecov
           name: codecov-${{ matrix.os }}-py${{ matrix.python-version }}
diff --git a/docs/notebooks/paper_experiments/results/multitask/cv_isolines.png b/docs/notebooks/paper_experiments/results/multitask/cv_isolines.png
diff --git a/docs/notebooks/paper_experiments/results/multitask/data/KERNELS b/docs/notebooks/paper_experiments/results/multitask/data/KERNELS
diff --git a/docs/notebooks/paper_experiments/results/multitask/data/sampling.png b/docs/notebooks/paper_experiments/results/multitask/data/sampling.png
diff --git a/docs/notebooks/paper_experiments/results/multitask/data/stats.out b/docs/notebooks/paper_experiments/results/multitask/data/stats.out
diff --git a/docs/notebooks/paper_experiments/results/supervised/cv_isolines.png b/docs/notebooks/paper_experiments/results/supervised/cv_isolines.png
diff --git a/docs/notebooks/paper_experiments/results/supervised/data/KERNELS b/docs/notebooks/paper_experiments/results/supervised/data/KERNELS
diff --git a/docs/notebooks/paper_experiments/results/supervised/data/sampling.png b/docs/notebooks/paper_experiments/results/supervised/data/sampling.png
diff --git a/docs/notebooks/paper_experiments/results/supervised/data/stats.out b/docs/notebooks/paper_experiments/results/supervised/data/stats.out
diff --git a/docs/notebooks/paper_experiments/results/timelagged/deepTICA/data/sampling.png b/docs/notebooks/paper_experiments/results/timelagged/deepTICA/data/sampling.png
diff --git a/docs/notebooks/paper_experiments/results/timelagged/deepTICA/data/stats.out b/docs/notebooks/paper_experiments/results/timelagged/deepTICA/data/stats.out
diff --git a/docs/notebooks/paper_experiments/results/timelagged/opes-y/KERNELS b/docs/notebooks/paper_experiments/results/timelagged/opes-y/KERNELS
diff --git a/docs/notebooks/paper_experiments/results/timelagged/opes-y/histogram.data b/docs/notebooks/paper_experiments/results/timelagged/opes-y/histogram.data
diff --git a/docs/notebooks/paper_experiments/results/timelagged/opes-y/out_potential.data b/docs/notebooks/paper_experiments/results/timelagged/opes-y/out_potential.data
diff --git a/docs/notebooks/paper_experiments/results/timelagged/opes-y/out_potential.dim1.data b/docs/notebooks/paper_experiments/results/timelagged/opes-y/out_potential.dim1.data
diff --git a/docs/notebooks/paper_experiments/results/timelagged/opes-y/out_potential.dim2.data b/docs/notebooks/paper_experiments/results/timelagged/opes-y/out_potential.dim2.data
diff --git a/docs/notebooks/paper_experiments/results/timelagged/opes-y/potential-coeffs.out.data b/docs/notebooks/paper_experiments/results/timelagged/opes-y/potential-coeffs.out.data