Merge pull request #34 from nomad-coe/apply_ruff

- Update Ruff linting
- Add Ruff formatter
- Remove old linters (`pycodestyle` and `pylint`)

.github/workflows/python-actions.yaml

@@ -17,21 +17,25 @@ jobs:
         pip install --upgrade pip
         pip install .[tests]
         pip install types-PyYAML
-    - name: pycodestyle
-      run: |
-        python -m pycodestyle --ignore=E501,E701,E731 *parsers tests
-    - name: pylint
-      run: |
-        python -m pylint *parsers tests
     - name: mypy
       run: |
         python -m mypy --ignore-missing-imports --follow-imports=silent --no-strict-optional *parsers tests
     - name: Test with pytest
       run: |
         python -m pytest -sv tests
 
-  ruff:
+  ruff-linting:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: chartboost/ruff-action@v1
+        with:
+          args: "check ."
+
+  ruff-formatting:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v3
       - uses: chartboost/ruff-action@v1
+        with:
+          args: "format ."

pyproject.toml

@@ -26,9 +26,6 @@ homepage = "https://github.com/nomad-coe/electronic-parsers"
 [project.optional-dependencies]
 tests = [
     'mypy==1.0.1',
-    'pylint==2.13.9',
-    'pylint_plugin_utils==0.5',
-    'pycodestyle==2.8.0',
     'pytest==3.10.0',
     'pytest-timeout==1.4.2',
     'pytest-cov==2.7.1',
@@ -39,11 +36,11 @@ tests = [
     'phonopy==2.11.0',
     'h5py==3.6.0',
     'typing-extensions==4.4.0',
-    'ruff==0.1.4',
+    'ruff==0.1.8',
 ]
 
 [tool.ruff]
-include = ["electronicparsers/*.py", "tests/*.py"]
+include = ["workflowparsers/*.py", "tests/*.py"]
 select = [
     "E", # pycodestyle
     "W", # pycodestyle
@@ -66,6 +63,23 @@ ignore = [
 ]
 fixable = ["ALL"]
 
+# Same as Black.
+line-length = 88
+indent-width = 4
+
+[tool.ruff.format]
+# use single quotes for strings.
+quote-style = "single"
+
+# indent with spaces, rather than tabs.
+indent-style = "space"
+
+# Like Black, respect magic trailing commas.
+skip-magic-trailing-comma = false
+
+# Like Black, automatically detect the appropriate line ending.
+line-ending = "auto"
+
 [tool.setuptools.packages.find]
 include = ["workflowparsers*"]
 

tests/conftest.py

@@ -18,8 +18,9 @@
 #
 import os
 import pytest
+
 # Set up pytest to pass control to the debugger on an exception.
-if os.getenv('_PYTEST_RAISE', "0") != "0":
+if os.getenv('_PYTEST_RAISE', '0') != '0':
 
     @pytest.hookimpl(tryfirst=True)
     def pytest_exception_interact(call):

tests/test_aflowparser.py

@@ -48,15 +48,19 @@ def test_aflowlib(parser):
     sec_calculation = archive.run[0].calculation[0]
     assert sec_calculation.energy.total.value.magnitude == approx(-5.58872856e-18)
     assert sec_calculation.forces.total.value[0][1].magnitude == approx(-2.14691669e-13)
-    assert sec_calculation.thermodynamics[0].enthalpy.magnitude == approx(-5.58872856e-18)
+    assert sec_calculation.thermodynamics[0].enthalpy.magnitude == approx(
+        -5.58872856e-18
+    )
     assert sec_calculation.x_aflow_pressure_residual == approx(2.95)
 
     run = archive.run[1]
     assert len(run.system) == len(run.calculation) == 24
     assert run.system[7].atoms.labels[6] == 'O'
-    assert run.system[21].atoms.lattice_vectors[0][1].magnitude == approx(-2.5241880209758e-10)
+    assert run.system[21].atoms.lattice_vectors[0][1].magnitude == approx(
+        -2.5241880209758e-10
+    )
     assert run.calculation[15].energy.total.value.magnitude == approx(-6.9854741e-19)
-    assert run.calculation[9].stress.total.value[2][2].magnitude == approx(-1.594e+08)
+    assert run.calculation[9].stress.total.value[2][2].magnitude == approx(-1.594e08)
     # TODO currently workflow is not a repeating section
     # assert archive.workflow.results.n_deformations == 3
     # assert archive.workflow.results.strain_maximum == pytest.approx(0.01)
@@ -68,7 +72,7 @@ def test_aflowlib(parser):
     run = archive.run[2]
     assert len(run.system) == len(run.calculation) == 28
     assert run.system[3].atoms.positions[3][2].magnitude == approx(5.53515521e-10)
-    assert run.calculation[19].thermodynamics[0].pressure.magnitude == (-1.6886e+09)
+    assert run.calculation[19].thermodynamics[0].pressure.magnitude == (-1.6886e09)
     sec_thermo = archive.workflow2.results
     assert sec_thermo.temperature[12].magnitude == 120
     # assert sec_thermo.thermal_conductivity[18].magnitude == approx(4.924586)
@@ -90,13 +94,19 @@ def test_aflowin(parser):
 
     sec_scc = archive.run[1].calculation[0]
     assert sec_scc.dos_phonon[0].energies[80].magnitude == approx(5.71011064e-22)
-    assert sec_scc.dos_phonon[0].total[0].value[1866].magnitude == approx(2.06688135e+20)
+    assert sec_scc.dos_phonon[0].total[0].value[1866].magnitude == approx(2.06688135e20)
     assert len(sec_scc.band_structure_phonon[0].segment) == 10
-    assert sec_scc.band_structure_phonon[0].segment[3].kpoints[7][1] == approx(1.02984830)
-    assert sec_scc.band_structure_phonon[0].segment[9].energies[0][10][3].magnitude == approx(1.92480691e-21)
+    assert sec_scc.band_structure_phonon[0].segment[3].kpoints[7][1] == approx(
+        1.02984830
+    )
+    assert sec_scc.band_structure_phonon[0].segment[9].energies[0][10][
+        3
+    ].magnitude == approx(1.92480691e-21)
 
     assert archive.workflow2.results.qpoints[9249][0] == approx(-4.7619047619e-02)
-    assert archive.workflow2.results.group_velocity[234][2][0].magnitude == approx(-133.348333)
+    assert archive.workflow2.results.group_velocity[234][2][0].magnitude == approx(
+        -133.348333
+    )
 
     # TODO currently workflow is not a repeating section
     # assert archive.workflow.results.temperature[161].magnitude == approx(1610)

tests/test_asrparser.py

@@ -48,10 +48,14 @@ def test_database():
     cwd = os.getcwd()
     try:
         os.chdir(tests_path)
-        subprocess.Popen(['asr', 'init'], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+        subprocess.Popen(
+            ['asr', 'init'], stdout=subprocess.PIPE, stderr=subprocess.PIPE
+        )
         subprocess.Popen(
             ['asr', 'run', 'asr.c2db.relax -a Si.json -c {"name":"emt"}'],
-            stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+            stdout=subprocess.PIPE,
+            stderr=subprocess.PIPE,
+        )
     except Exception:
         pass
     finally:

tests/test_elasticparser.py

@@ -55,25 +55,27 @@ def test_2nd(parser):
     assert sec_strain[0].value[2][5] == approx(-3.30877062e-16)
     assert sec_strain[3].type == 'cross-validation'
     assert sec_strain[2].eta[1][2] == 0.03
-    assert sec_strain[6].value[2][4] == approx(6.8708895e+12)
+    assert sec_strain[6].value[2][4] == approx(6.8708895e12)
     assert sec_strain[4].polynomial_fit_order == 6
 
     assert results.elastic_constants_notation_matrix_second_order[1][2] == 'C12'
-    assert results.elastic_constants_matrix_second_order[0][2].magnitude == approx(1.008e+11)
+    assert results.elastic_constants_matrix_second_order[0][2].magnitude == approx(
+        1.008e11
+    )
     assert results.compliance_matrix_second_order[3][3].magnitude == approx(1.75e-12)
-    assert results.bulk_modulus_voigt.magnitude == approx(4.4937e+11)
-    assert results.shear_modulus_voigt.magnitude == approx(5.3074e+11)
-    assert results.bulk_modulus_reuss.magnitude == approx(4.4937e+11)
-    assert results.shear_modulus_reuss.magnitude == approx(5.2574e+11)
-    assert results.bulk_modulus_hill.magnitude == approx(4.4937e+11)
-    assert results.shear_modulus_hill.magnitude == approx(5.2824e+11)
-    assert results.young_modulus_voigt.magnitude == approx(1.14245e+12)
+    assert results.bulk_modulus_voigt.magnitude == approx(4.4937e11)
+    assert results.shear_modulus_voigt.magnitude == approx(5.3074e11)
+    assert results.bulk_modulus_reuss.magnitude == approx(4.4937e11)
+    assert results.shear_modulus_reuss.magnitude == approx(5.2574e11)
+    assert results.bulk_modulus_hill.magnitude == approx(4.4937e11)
+    assert results.shear_modulus_hill.magnitude == approx(5.2824e11)
+    assert results.young_modulus_voigt.magnitude == approx(1.14245e12)
     assert results.poisson_ratio_voigt == 0.08
-    assert results.young_modulus_reuss.magnitude == approx(1.1347e+12)
+    assert results.young_modulus_reuss.magnitude == approx(1.1347e12)
     assert results.poisson_ratio_reuss == 0.08
-    assert results.young_modulus_hill.magnitude == approx(1.13858e+12)
+    assert results.young_modulus_hill.magnitude == approx(1.13858e12)
     assert results.poisson_ratio_hill == 0.08
-    assert results.eigenvalues_elastic[1].magnitude == approx(1.3481e+12)
+    assert results.eigenvalues_elastic[1].magnitude == approx(1.3481e12)
 
     sec_scc = archive.run[0].calculation[0]
     assert len(sec_scc.calculations_path) == 33
@@ -94,9 +96,15 @@ def test_3rd(parser):
     # assert sec_strain[3].value[8][7] == approx(2.06899957e-23)
 
     results = archive.workflow2.results
-    assert results.elastic_constants_matrix_third_order[3][1][3].magnitude == approx(1.274e+10)
-    assert results.elastic_constants_matrix_third_order[5][2][5].magnitude == approx(1.2825e+10)
-    assert results.elastic_constants_matrix_third_order[0][0][1].magnitude == approx(-1.18334e+12)
+    assert results.elastic_constants_matrix_third_order[3][1][3].magnitude == approx(
+        1.274e10
+    )
+    assert results.elastic_constants_matrix_third_order[5][2][5].magnitude == approx(
+        1.2825e10
+    )
+    assert results.elastic_constants_matrix_third_order[0][0][1].magnitude == approx(
+        -1.18334e12
+    )
 
 
 def test_stress(parser):

tests/test_fhivibesparser.py

@@ -43,30 +43,38 @@ def _test_singlepoint(parser):
     assert len(sec_run) == 10
     assert len(sec_run[2].calculation) == 1
 
-    assert sec_run[8].system[0].atoms.positions[3][2].magnitude == approx(5.30098546e-10)
-    assert sec_run[5].system[0].atoms.velocities[1][0].magnitude == approx(-2.18864066e+03)
+    assert sec_run[8].system[0].atoms.positions[3][2].magnitude == approx(
+        5.30098546e-10
+    )
+    assert sec_run[5].system[0].atoms.velocities[1][0].magnitude == approx(
+        -2.18864066e03
+    )
 
     sec_scc = sec_run[9].calculation[0]
     assert len(sec_scc.energy.contributions) == 2
     assert sec_scc.energy.contributions[1].value.magnitude == approx(-1.00925367e-14)
 
     sec_scc = sec_run[3].calculation[0]
-    assert sec_scc.stress.contributions[0].value[1][2].magnitude == approx(-1.42111377e+07)
+    assert sec_scc.stress.contributions[0].value[1][2].magnitude == approx(
+        -1.42111377e07
+    )
 
     sec_scc = sec_run[1].calculation[0]
-    assert sec_scc.stress.total.value[1][1].magnitude == approx(1.49076266e+08)
+    assert sec_scc.stress.total.value[1][1].magnitude == approx(1.49076266e08)
 
     sec_scc = sec_run[6].calculation[0]
     assert sec_scc.forces.total.value[5][2].magnitude == approx(-3.47924808e-10)
 
     sec_scc = sec_run[5].calculation[0]
-    assert sec_scc.thermodynamics[0].pressure.magnitude == approx(2.52108927e+07)
+    assert sec_scc.thermodynamics[0].pressure.magnitude == approx(2.52108927e07)
 
     sec_scc = sec_run[2].calculation[0]
-    assert sec_scc.x_fhi_vibes_pressure_kinetic.magnitude == approx(2.08283962e+08)
+    assert sec_scc.x_fhi_vibes_pressure_kinetic.magnitude == approx(2.08283962e08)
 
     sec_scc = sec_run[8].calculation[0]
-    assert sec_scc.x_fhi_vibes_energy_potential_harmonic.magnitude == approx(4.08242214e-20)
+    assert sec_scc.x_fhi_vibes_energy_potential_harmonic.magnitude == approx(
+        4.08242214e-20
+    )
 
 
 def _test_relaxation(parser):
@@ -93,7 +101,9 @@ def _test_relaxation(parser):
     sec_sccs = archive.run[0].calculation
     assert len(sec_sccs) == 3
     assert sec_sccs[2].thermodynamics[0].volume.magnitude == approx(3.97721030e-29)
-    assert sec_sccs[0].energy.contributions[1].value.magnitude == approx(-2.52313962e-15)
+    assert sec_sccs[0].energy.contributions[1].value.magnitude == approx(
+        -2.52313962e-15
+    )
 
 
 def _test_molecular_dynamics(parser):
@@ -103,19 +113,27 @@ def _test_molecular_dynamics(parser):
     assert archive.workflow2.m_def.name == 'MolecularDynamics'
 
     sec_attrs = archive.run[0].method[0].x_fhi_vibes_section_attributes[0]
-    sec_md = sec_attrs.x_fhi_vibes_section_attributes_metadata[0].x_fhi_vibes_section_metadata_MD[0]
+    sec_md = sec_attrs.x_fhi_vibes_section_attributes_metadata[
+        0
+    ].x_fhi_vibes_section_metadata_MD[0]
     assert sec_md.x_fhi_vibes_MD_md_type == 'Langevin'
     assert sec_md.x_fhi_vibes_MD_friction == 0.02
 
     sec_systems = archive.run[0].system
     assert len(sec_systems) == 11
     assert sec_systems[3].atoms.positions[6][1].magnitude == approx(1.39537854e-10)
     assert sec_systems[7].atoms.velocities[1][0].magnitude == approx(-249.97586102)
-    assert sec_systems[2].atoms.lattice_vectors[0][2].magnitude == approx(2.20004000e-21)
+    assert sec_systems[2].atoms.lattice_vectors[0][2].magnitude == approx(
+        2.20004000e-21
+    )
 
     sec_sccs = archive.run[0].calculation
-    assert sec_sccs[4].x_fhi_vibes_heat_flux_0_harmonic[1].magnitude == approx(1.40863863e+13)
-    assert sec_sccs[5].x_fhi_vibes_atom_forces_harmonic[3][0].magnitude == approx(8.40976902e-10)
+    assert sec_sccs[4].x_fhi_vibes_heat_flux_0_harmonic[1].magnitude == approx(
+        1.40863863e13
+    )
+    assert sec_sccs[5].x_fhi_vibes_atom_forces_harmonic[3][0].magnitude == approx(
+        8.40976902e-10
+    )
     assert sec_sccs[6].x_fhi_vibes_momenta[7][2].magnitude == approx(-1.18929315e-24)
 
 
@@ -126,7 +144,9 @@ def _test_phonon(parser):
     assert archive.workflow2.m_def.name == 'Phonon'
 
     sec_attrs = archive.run[0].method[0].x_fhi_vibes_section_attributes[0]
-    sec_phonon = sec_attrs.x_fhi_vibes_section_attributes_metadata[0].x_fhi_vibes_section_metadata_phonopy[0]
+    sec_phonon = sec_attrs.x_fhi_vibes_section_attributes_metadata[
+        0
+    ].x_fhi_vibes_section_metadata_phonopy[0]
     assert sec_phonon.x_fhi_vibes_phonopy_version == '2.6.1'
     sec_atoms = sec_phonon.x_fhi_vibes_section_phonopy_primitive[0]
     assert np.shape(sec_atoms.x_fhi_vibes_atoms_positions) == (2, 3)