updated toml file and relaunched ruff linting

FAIRmat-NFDI · Aug 21, 2024 · 1ee7a38 · 1ee7a38
1 parent 42495bf
commit 1ee7a38
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Showing 19 changed files with 171 additions and 169 deletions.
diff --git a/nomad.yaml b/nomad.yaml
diff --git a/pyproject.toml b/pyproject.toml
@@ -6,34 +6,30 @@ requires = [
 build-backend = "setuptools.build_meta"
 
 [project]
+classifiers = [
+    "Intended Audience :: Developers",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "License :: OSI Approved :: MIT License",
+]
 name = "nomad-material-processing"
 dynamic = ["version"]
 description = "A plugin for NOMAD containing base sections for material processing."
 readme = "README.md"
 authors = [
+    { name = "Sarthak Kapoor", email = '[email protected]' },
     { name = "Hampus Näsström", email = '[email protected]' },
     { name = "Andrea Albino", email = '[email protected]' },
     { name = "Sebastian Brückner", email = '[email protected]' },
 ]
-requires-python = ">=3.9"
-classifiers = [
-    "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3 :: Only",
-    "Programming Language :: Python :: 3.9",
-    "License :: OSI Approved :: Apache Software License",
-]
+license = { file = "LICENSE" }
 dependencies = [
-    "nomad-lab>=1.3.3.dev86",
+    "nomad-lab>=1.3.4",
 ]
-[project.optional-dependencies]
-dev = [
-    "pytest",
-    "ruff",
-    "structlog>=22.3.0",
-]
-
-[project.license]
-file = "LICENSE"
 
 [project.urls]
 "Homepage" = "https://github.com/FAIRmat-NFDI/nomad-material-processing"
@@ -42,38 +38,69 @@ file = "LICENSE"
 [tool.uv]
 index-url = "https://gitlab.mpcdf.mpg.de/api/v4/projects/2187/packages/pypi/simple"
 
+
+[project.optional-dependencies]
+dev = [
+    "pytest",
+    "ruff",
+    "structlog",
+]
+
 [tool.ruff]
 include = ["src/*.py", "tests/*.py"]
-
-exclude = ["dependencies"]
+# Exclude a variety of commonly ignored directories.
+exclude = [
+    ".bzr",
+    ".direnv",
+    ".eggs",
+    ".git",
+    ".git-rewrite",
+    ".hg",
+    ".mypy_cache",
+    ".nox",
+    ".pants.d",
+    ".pytype",
+    ".ruff_cache",
+    ".svn",
+    ".tox",
+    ".venv",
+    "__pypackages__",
+    "_build",
+    "buck-out",
+    "build",
+    "dist",
+    "node_modules",
+    "venv",
+]
 
 # Same as Black.
 line-length = 88
 indent-width = 4
 
 [tool.ruff.lint]
 select = [
-    "E", # pycodestyle
-    "W", # pycodestyle
-    "PL", # pylint
+    # pycodestyle
+    "E",
+    # Pyflakes
+    "F",
+    # pyupgrade
+    "UP",
+    # isort
+    "I",
+    # pylint
+    "PL",
 ]
+
 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
+    "F403", # 'from module import *' used; unable to detect undefined names
 ]
+
 fixable = ["ALL"]
 
+# Allow unused variables when underscore-prefixed.
+dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$"
+
+# this is entirely optional, you can remove this if you wish to
 [tool.ruff.format]
 # use single quotes for strings.
 quote-style = "single"
@@ -87,10 +114,11 @@ skip-magic-trailing-comma = false
 # Like Black, automatically detect the appropriate line ending.
 line-ending = "auto"
 
+[tool.setuptools]
+package-dir = { "" = "src" }
+
 [tool.setuptools.packages.find]
-where = [
-    "src",
-]
+where = ["src"]
 
 [project.entry-points.'nomad.plugin']
 

diff --git a/src/nomad_material_processing/combinatorial.py b/src/nomad_material_processing/combinatorial.py
@@ -1,4 +1,3 @@
-import json
 
 #
 # Copyright The NOMAD Authors.
@@ -20,17 +19,8 @@
 from typing import (
     TYPE_CHECKING,
 )
+
 import plotly.graph_objects as go
-from nomad.datamodel.metainfo.plot import (
-    PlotlyFigure,
-    PlotSection,
-)
-from nomad.metainfo import (
-    Package,
-    Quantity,
-    SubSection,
-    Section,
-)
 from nomad.datamodel.data import (
     ArchiveSection,
     EntryData,
@@ -44,6 +34,16 @@
     CompositeSystem,
     CompositeSystemReference,
 )
+from nomad.datamodel.metainfo.plot import (
+    PlotlyFigure,
+    PlotSection,
+)
+from nomad.metainfo import (
+    Package,
+    Quantity,
+    Section,
+    SubSection,
+)
 
 if TYPE_CHECKING:
     from nomad.datamodel.datamodel import (
@@ -65,8 +65,8 @@ class CombinatorialLibrary(CompositeSystem, EntryData, PlotSection):
 
     def plot(self, archive: 'EntryArchive', logger: 'BoundLogger') -> None:
         from nomad.search import (
-            search,
             MetadataPagination,
+            search,
         )
 
         query = {

diff --git a/src/nomad_material_processing/crystal_growth.py b/src/nomad_material_processing/crystal_growth.py
@@ -18,10 +18,12 @@
 from typing import (
     TYPE_CHECKING,
 )
+
 from nomad.metainfo import (
     Package,
     Section,
 )
+
 from nomad_material_processing.general import (
     SampleDeposition,
 )

diff --git a/src/nomad_material_processing/epitaxy.py b/src/nomad_material_processing/epitaxy.py
@@ -18,10 +18,12 @@
 from typing import (
     TYPE_CHECKING,
 )
+
 from nomad.metainfo import (
     Package,
     Section,
 )
+
 from nomad_material_processing.general import (
     SampleDeposition,
 )

diff --git a/src/nomad_material_processing/general.py b/src/nomad_material_processing/general.py
@@ -8,42 +8,32 @@
         BoundLogger,
     )
 
-from nomad.datamodel.metainfo.annotations import ELNAnnotation, ELNComponentEnum
-
 import numpy as np
-from nomad.datamodel.data import EntryData, ArchiveSection
-
-from nomad.metainfo import (
-    SchemaPackage,
-    Quantity,
-    SubSection,
-    Section,
-    MEnum,
-)
-
+from nomad.config import config
+from nomad.datamodel.data import ArchiveSection, EntryData
+from nomad.datamodel.metainfo.annotations import ELNAnnotation, ELNComponentEnum
 from nomad.datamodel.metainfo.basesections import (
-    ElementalComposition,
     CompositeSystem,
-    SynthesisMethod,
-    ProcessStep,
+    CompositeSystemReference,
+    ElementalComposition,
     Process,
+    ProcessStep,
+    SynthesisMethod,
     SystemComponent,
-    CompositeSystemReference,
-)
-from nomad.datamodel.metainfo.annotations import (
-    ELNAnnotation,
-    ELNComponentEnum,
 )
 from nomad.datamodel.metainfo.workflow import (
     Link,
 )
 from nomad.metainfo import (
-    SectionProxy,
+    MEnum,
+    Quantity,
     Reference,
+    SchemaPackage,
+    Section,
+    SectionProxy,
+    SubSection,
 )
 
-from nomad.config import config
-
 m_package = SchemaPackage(name='Material Processing')
 
 configuration = config.get_plugin_entry_point('nomad_material_processing:schema')

diff --git a/src/nomad_material_processing/solution/__init__.py b/src/nomad_material_processing/solution/__init__.py
@@ -3,7 +3,7 @@
 
 class SolutionSchemaPackageEntryPoint(SchemaPackageEntryPoint):
     def load(self):
-        from nomad_material_processing.solution.schema import m_package
+        from nomad_material_processing.solution.general import m_package
 
         return m_package
 

diff --git a/...ad_material_processing/solution/schema.py → ...d_material_processing/solution/general.py b/...ad_material_processing/solution/schema.py → ...d_material_processing/solution/general.py
@@ -1,42 +1,44 @@
 from typing import TYPE_CHECKING, Union
-from nomad.units import ureg
+
 import numpy as np
 from nomad.datamodel.data import (
     ArchiveSection,
     EntryData,
 )
 from nomad.datamodel.metainfo.annotations import (
     ELNAnnotation,
-    SectionProperties,
     Filter,
+    SectionProperties,
 )
 from nomad.datamodel.metainfo.basesections import (
     Component,
     CompositeSystem,
     CompositeSystemReference,
-    SystemComponent,
     InstrumentReference,
     Process,
     ProcessStep,
-    PureSubstanceComponent,
     PubChemPureSubstanceSection,
+    PureSubstanceComponent,
+    SystemComponent,
 )
 from nomad.metainfo import (
-    SchemaPackage,
     Datetime,
     MEnum,
     Quantity,
+    SchemaPackage,
     Section,
     SubSection,
 )
+from nomad.units import ureg
+
 from nomad_material_processing.solution.utils import (
     create_archive,
     create_unique_filename,
 )
 
 if TYPE_CHECKING:
-    from structlog.stdlib import BoundLogger
     from nomad.datamodel import EntryArchive
+    from structlog.stdlib import BoundLogger
 
 from nomad.config import config
 
@@ -599,14 +601,13 @@ def normalize(self, archive: 'EntryArchive', logger: 'BoundLogger') -> None:
             if not self.volume:
                 # assume entire volume of the solution is used
                 self.volume = available_volume
-            else:
-                if self.volume > available_volume:
-                    logger.warning(
-                        f'The volume used for the "{self.name}" is greater than the '
-                        'available volume of the solution. Setting it to the available '
-                        'volume.'
-                    )
-                    self.volume = available_volume
+            elif self.volume > available_volume:
+                logger.warning(
+                    f'The volume used for the "{self.name}" is greater than the '
+                    'available volume of the solution. Setting it to the available '
+                    'volume.'
+                )
+                self.volume = available_volume
             if self.system.density:
                 self.mass = self.system.density * self.volume
         super().normalize(archive, logger)

diff --git a/src/nomad_material_processing/solution/utils.py b/src/nomad_material_processing/solution/utils.py
@@ -15,13 +15,10 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 #
-from typing import TYPE_CHECKING
-
 import json
 import math
-import re
+from typing import TYPE_CHECKING
 
-import pandas as pd
 import yaml
 
 if TYPE_CHECKING:
@@ -84,7 +81,6 @@ def create_archive(
     entry_dict, context, filename, file_type, logger, *, overwrite: bool = False
 ):
     from nomad.datamodel.context import ClientContext
-    from nomad.datamodel import EntryArchive
 
     file_exists = context.raw_path_exists(filename)
     dicts_are_equal = None