update testing notebooks that require expyre

Author: gelzinyte

.github/workflows/pytests.yml

@@ -44,41 +44,41 @@ jobs:
       - name: Install latest ASE from gitlab
         run: pip install git+https://gitlab.com/ase/ase.git
 
-      - name: Install intel-mkl-full for phono3py
-        run: |
-          wget https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS-2019.PUB
-          sudo apt-key add GPG-PUB-KEY-INTEL-SW-PRODUCTS-2019.PUB
-          sudo sh -c 'echo deb https://apt.repos.intel.com/mkl all main > /etc/apt/sources.list.d/intel-mkl.list'
-          sudo apt-get update
-          sudo apt-get install intel-mkl-64bit-2018.2-046
-
-      - name: Install phono3py from source
-        run: |
-            source /opt/intel/compilers_and_libraries_2018.2.199/linux/mkl/bin/mklvars.sh intel64
-
-            git clone https://github.com/phonopy/phonopy
-            cd phonopy
-            python3 setup.py build
-            python3 -m pip install .
-            cd ..
-
-            git clone https://github.com/phonopy/phono3py
-            cd phono3py
-            python3 setup.py build
-            python3 setup.py install
-            cd ..
+      # - name: Install intel-mkl-full for phono3py
+      #   run: |
+      #     wget https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS-2019.PUB
+      #     sudo apt-key add GPG-PUB-KEY-INTEL-SW-PRODUCTS-2019.PUB
+      #     sudo sh -c 'echo deb https://apt.repos.intel.com/mkl all main > /etc/apt/sources.list.d/intel-mkl.list'
+      #     sudo apt-get update
+      #     sudo apt-get install intel-mkl-64bit-2018.2-046
+
+      # - name: Install phono3py from source
+      #   run: |
+      #       source /opt/intel/compilers_and_libraries_2018.2.199/linux/mkl/bin/mklvars.sh intel64
+
+      #       git clone https://github.com/phonopy/phonopy
+      #       cd phonopy
+      #       python3 setup.py build
+      #       python3 -m pip install .
+      #       cd ..
+
+      #       git clone https://github.com/phonopy/phono3py
+      #       cd phono3py
+      #       python3 setup.py build
+      #       python3 setup.py install
+      #       cd ..
 
       - name: Install Quippy from PyPI
         run: pip install quippy-ase
 
-      - name: Julia and ace fit
-        run: |
-          pip install pip install threadpoolctl
-          wget https://julialang-s3.julialang.org/bin/linux/x64/1.8/julia-1.8.1-linux-x86_64.tar.gz
-          tar xzf julia-1.8.1-linux-x86_64.tar.gz
-          # note that this hardwires a particular compatible ACE1pack version
-          echo 'using Pkg; pkg"registry add https://github.com/JuliaRegistries/General"; pkg"registry add https://github.com/JuliaMolSim/MolSim.git"; pkg"add [email protected], ACE1, JuLIP, IPFitting, ASE"' > ace1pack_install.jl
-          ${PWD}/julia-1.8.1/bin/julia ace1pack_install.jl
+      # - name: Julia and ace fit
+      #   run: |
+      #     pip install pip install threadpoolctl
+      #     wget https://julialang-s3.julialang.org/bin/linux/x64/1.8/julia-1.8.1-linux-x86_64.tar.gz
+      #     tar xzf julia-1.8.1-linux-x86_64.tar.gz
+      #     # note that this hardwires a particular compatible ACE1pack version
+      #     echo 'using Pkg; pkg"registry add https://github.com/JuliaRegistries/General"; pkg"registry add https://github.com/JuliaMolSim/MolSim.git"; pkg"add [email protected], ACE1, JuLIP, IPFitting, ASE"' > ace1pack_install.jl
+      #     ${PWD}/julia-1.8.1/bin/julia ace1pack_install.jl
 
       - name: Install wfl (expyre and universalSOAP are dependencies)
         run: pip install .

tests/test_doc_examples.py

@@ -2,7 +2,7 @@
 import shutil
 import json
 import pytest
-import expyre
+from expyre import config 
 
 from .calculators.test_aims import aims_prerequisites
 
@@ -13,26 +13,24 @@ def _get_coding_blocks(nb_file):
         nb = json.load(fo)
     return [''.join(cell['source']) for cell in nb['cells'] if cell['cell_type'] == 'code']
 
-github_slurm_config = pytest.mark.skipif(
-    condition = "github" not in expyre.config.systems, 
-    reason="Missing configuration file for remote execution"
-)
-
 
 @pytest.mark.parametrize(
-    ('nb_file', 'idx_execute'),
+    ('nb_file', 'idx_execute', 'needs_expyre'),
     (
-        pytest.param('examples.buildcell.ipynb', 'all', id='buildcell',
+        pytest.param('examples.buildcell.ipynb', 'all', False, id='buildcell',
             marks=pytest.mark.skipif(not shutil.which("buildcell"), reason="buildcell not in PATH")),
-        pytest.param('examples.dimers.ipynb', 'all', id='dimer structures'),
-        pytest.param('examples.select_fps.ipynb', 'all', id='select fps'),
-        pytest.param('examples.fhiaims_calculator.ipynb', 'all', id='fhiaims_calculator',
+        pytest.param('examples.dimers.ipynb', 'all', False, id='dimer structures'),
+        pytest.param('examples.select_fps.ipynb', 'all', False, id='select fps'),
+        pytest.param('examples.fhiaims_calculator.ipynb', 'all', False, id='fhiaims_calculator',
             marks=aims_prerequisites),
-        pytest.param("examples.daisy_chain_mlip_fitting.ipynb", "all", id="daisy_chain_mlip_fitting",
-            marks=github_slurm_config)
+        pytest.param("examples.daisy_chain_mlip_fitting.ipynb", "all", False, id="daisy_chain_mlip_fitting")
     )
 )
-def test_example(tmp_path, nb_file, idx_execute, monkeypatch):
+def test_example(tmp_path, nb_file, idx_execute, monkeypatch, needs_expyre, expyre_systems):
+    if needs_expyre and "github" not in expyre_systems:
+        print(f'Notebook {nb_file} requires ExPyRe, but system "github" is not in config.json or'
+              f'"EXPYRE_PYTEST_SYSTEMS" environment variable.')
+        return
     print("running test_example", nb_file)
     basepath = os.path.join(f'{os.path.dirname(__file__)}/../docs/source')
     coding_blocks = _get_coding_blocks(f'{basepath}/{nb_file}')