Add ruff action and format (#110)

* Ruff format

* Add ruff action; use uv

.github/workflows/python-test.yml

@@ -1,4 +1,4 @@
-# This workflow will install Python dependencies, run tests and lint with a single version of Python
+# This workflow will install Python dependencies, run tests, and lint with multiple version of Python
 # For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
 
 name: Python test
@@ -12,21 +12,44 @@ on:
 permissions:
   contents: read
 
+env:
+  UV_SYSTEM_PYTHON: true
+
 jobs:
   test:
-
     runs-on: ubuntu-latest
-
+    strategy:
+      fail-fast: false
+      matrix:
+        python_version: ["3.9", "3.10", "3.11"]
     steps:
-    - uses: actions/checkout@v3
-    - name: Set up Python 3.9
-      uses: actions/setup-python@v3
+    - uses: actions/checkout@v4
+    - name: Set up Python ${{matrix.python_version}}
+      uses: actions/setup-python@v5
       with:
-        python-version: "3.9"
+        python-version: ${{matrix.python_version}}
+    - name: Install uv
+      run: |
+        curl -LsSf https://astral.sh/uv/install.sh | sh
     - name: Install dependencies
       run: |
-        python -m pip install --upgrade pip
-        pip install -e .[dev] --index-url https://gitlab.mpcdf.mpg.de/api/v4/projects/2187/packages/pypi/simple
+        uv pip install -e '.[dev]'
     - name: Test with pytest
       run: |
         pytest
+
+  ruff-linting:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: chartboost/ruff-action@v1
+        with:
+          args: "check ."
+
+  ruff-formatting:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: chartboost/ruff-action@v1
+        with:
+          args: "format . --check"

pyproject.toml

@@ -31,7 +31,7 @@ dependencies = [
 [project.optional-dependencies]
 dev = [
     "pytest",
-    "ruff==0.1.8",
+    "ruff",
     "structlog==22.3.0",
 ]
 
@@ -42,8 +42,18 @@ file = "LICENSE"
 "Homepage" = "https://github.com/FAIRmat-NFDI/nomad-measurements"
 "Bug Tracker" = "https://github.com/FAIRmat-NFDI/nomad-measurements/issues"
 
+[tool.uv]
+index-url = "https://gitlab.mpcdf.mpg.de/api/v4/projects/2187/packages/pypi/simple"
+
 [tool.ruff]
 include = ["src/*.py", "tests/*.py"]
+exclude = ["dependencies"]
+
+# Same as Black.
+line-length = 88
+indent-width = 4
+
+[tool.ruff.lint]
 select = [
     "E", # pycodestyle
     "W", # pycodestyle
@@ -65,11 +75,6 @@ ignore = [
     "PLR5501", # else-if-used
 ]
 fixable = ["ALL"]
-exclude = ["dependencies"]
-
-# Same as Black.
-line-length = 88
-indent-width = 4
 
 [tool.ruff.format]
 # use single quotes for strings.

src/nomad_measurements/__init__.py

@@ -15,9 +15,7 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 #
-from typing import (
-    TYPE_CHECKING
-)
+from typing import TYPE_CHECKING
 from nomad.metainfo.metainfo import (
     Category,
 )
@@ -44,17 +42,20 @@
         BoundLogger,
     )
 
+
 class NOMADMeasurementsCategory(EntryDataCategory):
-    '''
+    """
     A category for all measurements defined in the `nomad-measurements` plugin.
-    '''
+    """
+
     m_def = Category(label='NOMAD Measurements', categories=[EntryDataCategory])
 
 
 class ActivityReference(SectionReference):
-    '''
+    """
     A section used for referencing an Activity.
-    '''
+    """
+
     reference = Quantity(
         type=Activity,
         description='A reference to a NOMAD `Activity` entry.',
@@ -65,58 +66,57 @@ class ActivityReference(SectionReference):
     )
     lab_id = Quantity(
         type=str,
-        description='''
+        description="""
         The readable identifier for the activity.
-        ''',
+        """,
         a_eln=ELNAnnotation(
             component=ELNComponentEnum.StringEditQuantity,
         ),
     )
 
     def normalize(self, archive, logger: 'BoundLogger') -> None:
-        '''
+        """
         The normalizer for the `EntityReference` class.
         Will attempt to fill the `reference` from the `lab_id` or vice versa.
 
         Args:
             archive (EntryArchive): The archive containing the section that is being
             normalized.
             logger ('BoundLogger'): A structlog logger.
-        '''
+        """
         super(ActivityReference, self).normalize(archive, logger)
         if self.reference is None and self.lab_id is not None:
             from nomad.search import search, MetadataPagination
-            query = {
-                'results.eln.lab_ids': self.lab_id
-            }
+
+            query = {'results.eln.lab_ids': self.lab_id}
             search_result = search(
                 owner='all',
                 query=query,
                 pagination=MetadataPagination(page_size=1),
-                user_id=archive.metadata.main_author.user_id)
+                user_id=archive.metadata.main_author.user_id,
+            )
             if search_result.pagination.total > 0:
-                entry_id = search_result.data[0]["entry_id"]
-                upload_id = search_result.data[0]["upload_id"]
+                entry_id = search_result.data[0]['entry_id']
+                upload_id = search_result.data[0]['upload_id']
                 self.reference = f'../uploads/{upload_id}/archive/{entry_id}#data'
                 if search_result.pagination.total > 1:
                     logger.warn(
                         f'Found {search_result.pagination.total} entries with lab_id: '
                         f'"{self.lab_id}". Will use the first one found.'
                     )
             else:
-                logger.warn(
-                    f'Found no entries with lab_id: "{self.lab_id}".'
-                )
+                logger.warn(f'Found no entries with lab_id: "{self.lab_id}".')
         elif self.lab_id is None and self.reference is not None:
             self.lab_id = self.reference.lab_id
         if self.name is None and self.lab_id is not None:
             self.name = self.lab_id
 
 
 class ProcessReference(ActivityReference):
-    '''
+    """
     A section used for referencing a Process.
-    '''
+    """
+
     reference = Quantity(
         type=Process,
         description='A reference to a NOMAD `Process` entry.',
@@ -128,10 +128,11 @@ class ProcessReference(ActivityReference):
 
 
 class InSituMeasurement(Measurement):
-    '''
+    """
     A section used for a measurement performed in-situ during a process.
-    '''
+    """
+
     process = SubSection(
         section_def=ProcessReference,
         description='A reference to the process during which the measurement occurred.',
-    )
+    )

src/nomad_measurements/transmission/__init__.py

@@ -1,2 +1,2 @@
 from .schema import *
-from .parser import *
+from .parser import *

src/nomad_measurements/transmission/parser.py

@@ -15,9 +15,7 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 #
-from typing import (
-    TYPE_CHECKING
-)
+from typing import TYPE_CHECKING
 from nomad.metainfo import (
     Quantity,
 )
@@ -43,12 +41,11 @@ class RawFileTransmissionData(EntryData):
         type=ELNTransmission,
         a_eln=ELNAnnotation(
             component='ReferenceEditQuantity',
-        )
+        ),
     )
 
 
 class TransmissionParser(MatchingParser):
-
     def __init__(self):
         super().__init__(
             code_name='XRD Parser',
@@ -59,5 +56,7 @@ def parse(self, mainfile: str, archive: 'EntryArchive', logger) -> None:
         entry = ELNTransmission.m_from_dict(ELNTransmission.m_def.a_template)
         entry.data_file = data_file
         file_name = f'{data_file[:-6]}.archive.json'
-        archive.data = RawFileTransmissionData(measurement=create_archive(entry,archive,file_name))
-        archive.metadata.entry_name = data_file[:-4] + ' data file'
+        archive.data = RawFileTransmissionData(
+            measurement=create_archive(entry, archive, file_name)
+        )
+        archive.metadata.entry_name = data_file[:-4] + ' data file'

src/nomad_measurements/transmission/schema.py

@@ -18,9 +18,7 @@
 import re
 import os
 import json
-from typing import (
-    TYPE_CHECKING
-)
+from typing import TYPE_CHECKING
 from nomad.datamodel.metainfo.basesections import (
     Measurement,
     ReadableIdentifiers,
@@ -57,25 +55,25 @@
 
 
 class Operator(ArchiveSection):
-    name=Quantity(
+    name = Quantity(
         type=str,
         a_eln=ELNAnnotation(
             component=ELNComponentEnum.StringEditQuantity,
         ),
     )
-    affiliation=Quantity(
+    affiliation = Quantity(
         type=str,
         a_eln=ELNAnnotation(
             component=ELNComponentEnum.StringEditQuantity,
         ),
     )
-    address=Quantity(
+    address = Quantity(
         type=str,
         a_eln=ELNAnnotation(
             component=ELNComponentEnum.StringEditQuantity,
         ),
     )
-    email=Quantity(
+    email = Quantity(
         type=str,
         a_eln=ELNAnnotation(
             component=ELNComponentEnum.StringEditQuantity,
@@ -107,7 +105,9 @@ def normalize(self, archive: 'EntryArchive', logger: 'BoundLogger') -> None:
             if self.operator.name:
                 eln_dict['/ENTRY[entry]/operator/name'] = self.name
             if self.operator.affiliation:
-                eln_dict['/ENTRY[entry]/operator/affiliation'] = self.operator.affiliation
+                eln_dict['/ENTRY[entry]/operator/affiliation'] = (
+                    self.operator.affiliation
+                )
             if self.operator.address:
                 eln_dict['/ENTRY[entry]/operator/address'] = self.operator.address
             if self.operator.email:
@@ -128,7 +128,7 @@ def normalize(self, archive: 'EntryArchive', logger: 'BoundLogger') -> None:
                 os.path.join(raw_path, self.data_file),
                 os.path.join(raw_path, eln_filename),
             ],
-            'output': os.path.join(raw_path, output)
+            'output': os.path.join(raw_path, output),
         }
         try:
             convert(**converter_params)