Do QE tests using user's default config file. Update complete_test.ti…

…n and github CI test to be consistent

.github/workflows/pytests.yml

@@ -182,17 +182,15 @@ jobs:
           ls -l /usr/bin/pw.x
           espresso_command=pw.x
 
-      - name: set up ASE config files (same content but in multiple pytest run directories)
+      - name: set up ASE config files
         run: |
-          export config_file_plain=${HOME}/pytest_plain_config.ini
-          echo "[espresso]" > ${config_file_plain}
-          echo "command = ${espresso_command}" >> ${config_file_plain}
-          echo "pseudo_dir = ${HOME}/pytest_plain" >> ${config_file_plain}
-
-          export config_file_cov=${HOME}/pytest_cov_config.ini
-          echo "[espresso]" > ${config_file_cov}
-          echo "command = ${espresso_command}" >> ${config_file_cov}
-          echo "pseudo_dir = ${HOME}/pytest_cov" >> ${config_file_cov}
+          export config_file=${HOME}/pytest_plain_config.ini
+          echo "[espresso]" > ${config_file}
+          echo "command = ${espresso_command}" >> ${config_file}
+          echo "pseudo_dir = ${HOME}/dummy" >> ${config_file}
+          export ASE_CONFIG_PATH=${config_file}
+          echo ASE_CONFIG_PATH $ASE_CONFIG_PATH
+          cat $ASE_CONFIG_PATH
 
       - name: Lint with flake8
         run: |
@@ -212,7 +210,6 @@ jobs:
           export WFL_NUM_PYTHON_SUBPROCESSES=2
           export OMP_NUM_THREADS=1
           export WFL_JULIA_COMMAND=${PWD}/julia-1.8.1/bin/julia
-          export ASE_CONFIG_PATH=${config_file_plain}
           pytest --runremote --basetemp $HOME/pytest_plain -rxXs
 
       - name: Test with pytest - coverage
@@ -230,7 +227,6 @@ jobs:
           export WFL_NUM_PYTHON_SUBPROCESSES=2
           export OMP_NUM_THREADS=1
           export WFL_JULIA_COMMAND=${PWD}/julia-1.8.1/bin/julia
-          export ASE_CONFIG_PATH=${config_file_cov}
           pytest -v --cov=wfl --cov-report term --cov-report html --cov-config=tests/.coveragerc --cov-report term-missing --cov-report term:skip-covered --runremote --basetemp $HOME/pytest_cov -rxXs
 
       # # DEBUGGING

tests/calculators/test_qe.py

@@ -28,27 +28,24 @@
 from ase.config import cfg as ase_cfg
 from ase.calculators.espresso import EspressoProfile
 
-pytest_command = os.environ.get("PYTEST_WFL_ASE_ESPRESSO_COMMAND")
-if "espresso" in ase_cfg.parser and os.environ.get('OMP_NUM_THREADS') == "1":
-    pytest_command = EspressoProfile.from_config(ase_cfg, "espresso").command
-else:
-    pytest.skip('No command in "espresso" configuration or "OMP_NUM_THREADS" is not set to 1.')
+# do all tests using user's default config file
+# pseudo_dir will be overridden whenever calculator is constructed to ensure that
+# pytest-specific PPs are used
+if not ("espresso" in ase_cfg.parser and os.environ.get('OMP_NUM_THREADS') == "1"):
+    pytest.skip('No "espresso" configuration or "OMP_NUM_THREADS" is not set to 1.')
 
 
 @fixture(scope="session")
 def qe_profile_and_pseudo(tmp_path_factory):
     """Quantum Espresso fixture
 
-    - create profile with command from user's profile and pseudo_dir for pytest PPs
     - copies a pseudo-potential for Si
 
     implementation based on:
     https://stackoverflow.com/questions/63417661/pytest-downloading-a-test-file-once-and-using-it-for-multiple-tests
 
     Returns
     -------
-    profile: str
-        EspressoProfile with correct command and pseudo dir for pytest
     pspot_file: str
         Si pseudo potential file name
     """
@@ -66,25 +63,25 @@ def qe_profile_and_pseudo(tmp_path_factory):
     pspot_file = tmp_path_factory.getbasetemp() / "Si.UPF"
     shutil_copy(Path(__file__).parent.parent / "assets" / "QE" / "Si.pz-vbc.UPF", pspot_file)
 
-    return EspressoProfile(command=pytest_command, pseudo_dir=pspot_file.parent), pspot_file.name
+    return pspot_file
 
 
 def test_qe_kpoints(tmp_path, qe_profile_and_pseudo):
 
-    profile, pspot = qe_profile_and_pseudo
+    pspot = qe_profile_and_pseudo
 
     kw = dict(
-        pseudopotentials=dict(Si=pspot),
+        pseudopotentials=dict(Si=pspot.name),
+        pseudo_dir=pspot.parent,
         input_data={"SYSTEM": {"ecutwfc": 40, "input_dft": "LDA",}},
         kpts=(2, 3, 4),
         conv_thr=0.0001,
-        workdir=tmp_path,
-        profile=profile
-    ) 
+        workdir=tmp_path
+    )
 
     # PBC = TTT
     atoms = Atoms("H", cell=[1, 1, 1], pbc=True)
-    properties = ["energy", "stress"] 
+    properties = ["energy", "stress"]
     calc = wfl.calculators.espresso.Espresso(**kw)
     calc.atoms = atoms.copy()
     calc.setup_calc_params(properties)
@@ -168,20 +165,20 @@ def test_qe_kpoints(tmp_path, qe_profile_and_pseudo):
 
 def test_qe_calculation(tmp_path, qe_profile_and_pseudo):
 
-    profile, pspot = qe_profile_and_pseudo
+    pspot = qe_profile_and_pseudo
 
     # atoms
     at = bulk("Si")
     at.positions[0, 0] += 0.01
     at0 = Atoms("Si", cell=[6.0, 6.0, 6.0], positions=[[3.0, 3.0, 3.0]], pbc=False)
 
     kw = dict(
-        pseudopotentials=dict(Si=pspot),
+        pseudopotentials=dict(Si=pspot.name),
+        pseudo_dir=pspot.parent,
         input_data={"SYSTEM": {"ecutwfc": 40, "input_dft": "LDA",}},
         kpts=(2, 2, 2),
         conv_thr=0.0001,
-        workdir=tmp_path,
-        profile=profile
+        workdir=tmp_path
     )
 
     calc = (wfl.calculators.espresso.Espresso, [], kw)
@@ -227,16 +224,16 @@ def test_qe_calculation(tmp_path, qe_profile_and_pseudo):
 
 def test_wfl_Espresso_calc(tmp_path, qe_profile_and_pseudo):
 
-    profile, pspot = qe_profile_and_pseudo
+    pspot = qe_profile_and_pseudo
 
     atoms = Atoms("Si", cell=(2, 2, 2), pbc=[True] * 3)
     kw = dict(
-        pseudopotentials=dict(Si=pspot),
+        pseudopotentials=dict(Si=pspot.name),
+        pseudo_dir=pspot.parent,
         input_data={"SYSTEM": {"ecutwfc": 40, "input_dft": "LDA",}},
         kpts=(2, 2, 2),
-        conv_thr=0.0001,
-        profile=profile
-    ) 
+        conv_thr=0.0001
+    )
 
     calc = wfl.calculators.espresso.Espresso(
         workdir=tmp_path,
@@ -251,49 +248,12 @@ def test_wfl_Espresso_calc(tmp_path, qe_profile_and_pseudo):
 
 def test_wfl_Espresso_calc_via_generic(tmp_path, qe_profile_and_pseudo):
 
-    profile, pspot = qe_profile_and_pseudo
-
-    atoms = Atoms("Si", cell=(2, 2, 2), pbc=[True] * 3)
-    kw = dict(
-        pseudopotentials=dict(Si=pspot),
-        input_data={"SYSTEM": {"ecutwfc": 40, "input_dft": "LDA",}},
-        kpts=(2, 2, 2),
-        conv_thr=0.0001,
-        workdir=tmp_path,
-        profile=profile
-    ) 
-
-    calc = (wfl.calculators.espresso.Espresso, [], kw)
-
-    cfgs = [atoms]*3 + [Atoms("Cu", cell=(2, 2, 2), pbc=[True]*3)]
-    ci = ConfigSet(cfgs)
-    co = OutputSpec()
-    autoparainfo = AutoparaInfo(
-        num_python_subprocesses=0
-    )
-
-    ci = generic.calculate(
-        inputs=ci,
-        outputs=co,
-        calculator=calc,
-        output_prefix='qe_',
-        autopara_info=autoparainfo
-    )
-
-    ats = list(ci)
-    assert not any("qe_calculation_failed" in at.info for at in ats[:-1])
-    assert "qe_calculation_failed" in list(ci)[-1].info
-
-
-def test_wfl_Espresso_no_explicit_profile(tmp_path, qe_profile_and_pseudo, monkeypatch):
-    _, pspot = qe_profile_and_pseudo
-
-    import ase.config
-    ase.config.cfg = ase.config.Config.read()
+    pspot = qe_profile_and_pseudo
 
     atoms = Atoms("Si", cell=(2, 2, 2), pbc=[True] * 3)
     kw = dict(
-        pseudopotentials=dict(Si=pspot),
+        pseudopotentials=dict(Si=pspot.name),
+        pseudo_dir=pspot.parent,
         input_data={"SYSTEM": {"ecutwfc": 40, "input_dft": "LDA",}},
         kpts=(2, 2, 2),
         conv_thr=0.0001,

tests/local_scripts/complete_pytest.tin

@@ -32,7 +32,6 @@ export ASE_VASP_COMMAND_GAMMA=vasp.gamma.serial
 export PYTEST_VASP_POTCAR_DIR=$VASP_PATH/pot/rev_54/PBE
 # QE
 module load dft/pwscf
-espresso_command="env MPIRUN_EXTRA_ARGS='-np 1' pw.x"
 # no ORCA
 
 export OPENBLAS_NUM_THREADS=1
@@ -59,15 +58,7 @@ if [ -d $pytest_dir ]; then
     exit 1
 fi
 
-# set up config file for various (so far just espresso) tests
 mkdir -p $pytest_dir
-export ASE_CONFIG_PATH=$pytest_dir/pytest_wfl_config.ini
-echo "Creating ASE_CONFIG_PATH $ASE_CONFIG_PATH"
-cat << EOF > $ASE_CONFIG_PATH
-[espresso]
-command = $espresso_command
-pseudo_dir = $pytest_dir
-EOF
 
 pytest -v -s --basetemp $pytest_dir ${runremote} --runslow --runperf -rxXs "$@" >> complete_pytest.tin.out 2>&1
 
@@ -76,7 +67,7 @@ l=`egrep '^=.*(passed|failed|skipped|xfailed)' complete_pytest.tin.out`
 echo "summary line $l"
 lp=$( echo $l | sed -E -e 's/ in .*//' -e 's/\s*,\s*/\n/g' )
 
-declare -A expected_n=( ["passed"]="176" ["skipped"]="21" ["warnings"]=823 ["xfailed"]=2 ["xpassed"]=1 )
+declare -A expected_n=( ["passed"]="175" ["skipped"]="21" ["warnings"]=823 ["xfailed"]=2 ["xpassed"]=1 )
 IFS=$'\n'
 for out in $lp; do
     out_n=$(echo $out | sed -e 's/^=* //' -e 's/ .*//' -e 's/,//')