Entry point (#14)

* Add entry point * Update nomad-lab * Fix commit * Move specs to entry point * Add other parser specs * Fix init * Revert * Remove import * Add aliases
nomad-coe · Sep 2, 2024 · defb8c2 · defb8c2
1 parent fd38bde
commit defb8c2
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diff --git a/.github/workflows/python-actions.yaml b/.github/workflows/python-actions.yaml
@@ -14,7 +14,7 @@ jobs:
         pip install --upgrade pip
         pip install '.[tests]' --index-url https://gitlab.mpcdf.mpg.de/api/v4/projects/2187/packages/pypi/simple
         # we need the latest nomad version for testing
-        pip install nomad-lab[infrastructure]@git+https://github.com/nomad-coe/nomad.git@develop
+        #pip install nomad-lab[infrastructure]@git+https://github.com/nomad-coe/nomad.git@develop
         pip install coverage coveralls
     - name: mypy
       run: |

diff --git a/databaseparsers/__init__.py b/databaseparsers/__init__.py
@@ -16,5 +16,55 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 #
+from pydantic import Field
+from typing import Optional
 
-# from .openkim.parser import OpenKIMParser
+from nomad.config.models.plugins import ParserEntryPoint
+
+
+class EntryPoint(ParserEntryPoint):
+    parser_class_name: str = Field(
+        description="""
+        The fully qualified name of the Python class that implements the parser.
+        This class must have a function `def parse(self, mainfile, archive, logger)`.
+    """
+    )
+    code_name: Optional[str]
+    code_homepage: Optional[str]
+    code_category: Optional[str]
+    metadata: Optional[dict] = Field(
+        description="""
+        Metadata passed to the UI. Deprecated. """
+    )
+
+    def load(self):
+        from nomad.parsing import MatchingParserInterface
+
+        return MatchingParserInterface(**self.dict())
+
+
+openkim_parser_entry_point = EntryPoint(
+    name='parsers/openkim',
+    aliases=['parsers/openkim'],
+    description='NOMAD parser for OPENKIM.',
+    python_package='databaseparsers.openkim',
+    mainfile_contents_re=r'openkim|OPENKIM|OpenKIM',
+    mainfile_mime_re='(application/json)|(text/.*)',
+    parser_class_name='databaseparsers.openkim.OpenKIMParser',
+    code_name='OpenKIM',
+    code_homepage='https://openkim.org/',
+    code_category='Database manager',
+    metadata={
+        'codeCategory': 'Database manager',
+        'codeLabel': 'OpenKIM',
+        'codeLabelStyle': 'Capitals: O,K,I,M',
+        'codeName': 'openkim',
+        'codeUrl': 'https://openkim.org/',
+        'parserDirName': 'dependencies/parsers/database/databaseparsers/openkim/',
+        'parserGitUrl': 'https://github.com/nomad-coe/database-parsers.git',
+        'parserSpecific': '',
+        'preamble': '',
+        'status': 'production',
+        'tableOfFiles': '',
+    },
+)
diff --git a/pyproject.toml b/pyproject.toml
@@ -10,8 +10,10 @@ readme = "README.md"
 authors = [{ name = "The NOMAD Authors" }]
 license = { file = "LICENSE" }
 dependencies = [
+    "nomad-lab>=1.3.6.dev1",
     "nomad-schema-plugin-simulation-workflow@git+https://github.com/nomad-coe/nomad-schema-plugin-simulation-workflow.git@develop",
-    "nomad-schema-plugin-run@git+https://github.com/nomad-coe/nomad-schema-plugin-run.git@develop"
+    "nomad-schema-plugin-run@git+https://github.com/nomad-coe/nomad-schema-plugin-run.git@develop",
+    "pydantic>=1.10.8,<2.0.0",
 ]
 
 [project.urls]
@@ -28,40 +30,57 @@ tests = [
     "pytest-cov==2.7.1",
     "astroid==2.11.7",
     "typing-extensions==4.4.0",
-    "ruff==0.1.4",
+    "ruff==0.1.8",
 ]
 
 [tool.ruff]
 include = ["electronicparsers/*.py", "tests/*.py"]
-select = [
+lint.select = [
     "E", # pycodestyle
     "W", # pycodestyle
     "PL", # pylint
 ]
-ignore = [
-    "E501", # Line too long ({width} > {limit} characters)
-    "E701", # Multiple statements on one line (colon)
-    "E731", # Do not assign a lambda expression, use a def
-    "E402",  # Module level import not at top of file
-    "PLR0911", # Too many return statements
-    "PLR0912", # Too many branches
-    "PLR0913", # Too many arguments in function definition
-    "PLR0915", # Too many statements
-    "PLR2004", # Magic value used instead of constant
-    "PLW0603", # Using the global statement
-    "PLW2901", # redefined-loop-name
-    "PLR1714", # consider-using-in
-    "PLR5501", # else-if-used
+lint.ignore = [
+	"E501", # Line too long ({width} > {limit} characters)
+	"E701", # Multiple statements on one line (colon)
+	"E731", # Do not assign a lambda expression, use a def
+	"E402", # Module level import not at top of file
+	"PLR0911", # Too many return statements
+	"PLR0912", # Too many branches
+	"PLR0913", # Too many arguments in function definition
+	"PLR0915", # Too many statements
+	"PLR2004", # Magic value used instead of constant
+	"PLW0603", # Using the global statement
+	"PLW2901", # redefined-loop-name
+	"PLR1714", # consider-using-in
+	"PLR5501", # else-if-used
 ]
-fixable = ["ALL"]
+lint.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 = [
     "databaseparsers*",
 ]
 
-[tool.setuptools.package-data]
-databaseparsers = ["*/metadata.yaml", "*/README.md"]
+[project.entry-points.'nomad.plugin']
+openkimparser = "databaseparsers:openkim_parser_entry_point"
 
 [tool.mypy]
 strict = false

diff --git a/tests/test_openkimparser.py b/tests/test_openkimparser.py
@@ -45,12 +45,18 @@ def test_entry(parser):
     assert sec_system.atoms.positions[1][1].magnitude == approx(1.65893189e-10)
     assert sec_system.atoms.lattice_vectors[2][2].magnitude == approx(3.31786378e-10)
 
-    assert sec_run[0].method[0].force_field.model[0].name == 'LJ_ElliottAkerson_2015_Universal__MO_959249795837_003'
+    assert (
+        sec_run[0].method[0].force_field.model[0].name
+        == 'LJ_ElliottAkerson_2015_Universal__MO_959249795837_003'
+    )
 
     sec_scc = sec_run[8].calculation[0]
     assert sec_scc.energy.total.value.magnitude == approx(4.513135831891813e-19)
 
-    assert sec_run[0].x_openkim_meta['meta.runner.driver.name'] == 'LatticeConstantCubicEnergy'
+    assert (
+        sec_run[0].x_openkim_meta['meta.runner.driver.name']
+        == 'LatticeConstantCubicEnergy'
+    )
 
 
 def test_elastic(parser):
@@ -67,13 +73,19 @@ def test_elastic(parser):
 
 def test_phonon(parser):
     archive = EntryArchive()
-    parser.parse('tests/data/openkim/openkim_archive_phonon-dispersion-relation-cubic-crystal-npt.json', archive, None)
+    parser.parse(
+        'tests/data/openkim/openkim_archive_phonon-dispersion-relation-cubic-crystal-npt.json',
+        archive,
+        None,
+    )
 
     sec_run = archive.run
     assert len(sec_run) == 337
     assert sec_run[0].calculation[0].stress.total.value[0][1].magnitude == approx(0)
     sec_band_structure = sec_run[15].calculation[0].band_structure_phonon[0]
-    assert sec_band_structure.segment[0].energies[0][3][1].magnitude == approx(9.639834657408083e-22)
+    assert sec_band_structure.segment[0].energies[0][3][1].magnitude == approx(
+        9.639834657408083e-22
+    )
     assert np.shape(sec_band_structure.segment[0].kpoints) == (100, 3)
 
     # workflow = archive.workflow
@@ -83,13 +95,19 @@ def test_phonon(parser):
 
 def test_stacking_fault(parser):
     archive = EntryArchive()
-    parser.parse('tests/data/openkim/StackingFaultFccCrystal_0bar_Ac__TE_567672586460_002.json', archive, None)
+    parser.parse(
+        'tests/data/openkim/StackingFaultFccCrystal_0bar_Ac__TE_567672586460_002.json',
+        archive,
+        None,
+    )
 
     sec_run = archive.run
     assert len(sec_run) == 6
     assert sec_run[1].system[0].atoms.labels == ['Ac']
-    assert sec_run[0].system[0].atoms.positions[0][2].magnitude == approx(0.)
-    assert sec_run[2].system[0].atoms.lattice_vectors[2][2].magnitude == approx(5.913618618249901e-10)
+    assert sec_run[0].system[0].atoms.positions[0][2].magnitude == approx(0.0)
+    assert sec_run[2].system[0].atoms.lattice_vectors[2][2].magnitude == approx(
+        5.913618618249901e-10
+    )
 
     # workflow = archive.workflow
     # assert workflow.m_def.name == 'Interface'