Implementing Ruff for code consistency and coverage to asses test coverage

.coveragerc

@@ -0,0 +1,11 @@
+[run]
+branch = True
+source = brukerapi
+
+[report]
+# Ignore lines matching this regex in coverage report
+exclude_lines =
+    # Ignore raise statements (intentional exceptions)
+    raise
+    # Ignore debug-only code
+    if __name__ == .__main__.:

.github/workflows/assets/zenodo.py

@@ -1,14 +1,15 @@
-import requests
 import json
 import sys
 from pathlib import Path
+
 import pkg_resources
-import docutils
+import requests
 
 PARENT_ID = 698342
-BASE_URL = 'https://sandbox.zenodo.org/api/deposit/depositions/'
+BASE_URL = "https://sandbox.zenodo.org/api/deposit/depositions/"
 
-def publish(path_dist, access_token, verbose=False):
+
+def publish(path_dist, access_token, *, verbose=False):
     """Publish a new version of software to Zenodo
 
     Parameters:
@@ -18,75 +19,75 @@ def publish(path_dist, access_token, verbose=False):
 
     """
 
-    params = {'access_token': access_token}
+    params = {"access_token": access_token}
     headers = {"Content-Type": "application/json"}
 
     # Create a new version of the deposition
-    r = requests.post(BASE_URL + '{}/actions/newversion'.format(PARENT_ID),
-                        params=params,
-                        json={},
-                        headers=headers)
-
+    r = requests.post(BASE_URL + f"{PARENT_ID}/actions/newversion", params=params, json={}, headers=headers)
+
     if verbose:
-        print('Create a new version of the deposition: {}'.format(r.status_code))
+        print(f"Create a new version of the deposition: {r.status_code}")
 
     # Get the new version, its id and bucket_url
-    r = requests.get(r.json()['links']['latest_draft'], params=params)
-    deposition_id = r.json()['id']
+    r = requests.get(r.json()["links"]["latest_draft"], params=params)
+    deposition_id = r.json()["id"]
     bucket_url = r.json()["links"]["bucket"]
 
     if verbose:
-        print('Get the new version: {}'.format(r.status_code))
-        print('id: {}'.format(deposition_id))
-        print('bucket_url: {}'.format(bucket_url))
+        print(f"Get the new version: {r.status_code}")
+        print(f"id: {deposition_id}")
+        print(f"bucket_url: {bucket_url}")
 
     # Delete existing files
-    for file in r.json()['files']:
-        requests.delete(BASE_URL + '%s/files/%s' % (deposition_id, file['id']), params=params)
+    for file in r.json()["files"]:
+        requests.delete(BASE_URL + "{}/files/{}".format(deposition_id, file["id"]), params=params)
 
     # Locate distributuon file
-    files = [file for file in Path(path_dist).glob('**/*') if file.name.endswith('tar.gz')]
+    files = [file for file in Path(path_dist).glob("**/*") if file.name.endswith("tar.gz")]
 
     # Put distribution file
     with files[0].open(mode="rb") as fp:
         r = requests.put(
-            '{}/{}'.format(bucket_url, files[0].name),
+            f"{bucket_url}/{files[0].name}",
             data=fp,
             params=params,
         )
 
     if verbose:
-        print('Put distribution file: {}'.format(r.status_code))
+        print(f"Put distribution file: {r.status_code}")
 
     # Load metadata
     metadata = load_metadata()
 
     # Put metadata
-    r = requests.put(BASE_URL + '%s' % deposition_id, params=params, data=json.dumps(metadata), headers=headers)
+    r = requests.put(BASE_URL + f"{deposition_id}", params=params, data=json.dumps(metadata), headers=headers)
 
     if verbose:
-        print('Put metadata: {}'.format(r.status_code))
+        print(f"Put metadata: {r.status_code}")
 
     # Publish new version
-    r = requests.post(BASE_URL + '%s/actions/publish' % deposition_id, params=params )
+    r = requests.post(BASE_URL + f"{deposition_id}/actions/publish", params=params)
 
     if verbose:
-        print('Publish new version: {}'.format(r.status_code))
+        print(f"Publish new version: {r.status_code}")
+
 
 def get_version():
     return pkg_resources.get_distribution("brukerapi").version
 
+
 def load_metadata():
-    with open(Path(__file__).parent / 'fixed.json') as f:
+    with open(Path(__file__).parent / "fixed.json") as f:
         data = json.load(f)
 
-    data['metadata']['version'] = get_version()
+    data["metadata"]["version"] = get_version()
 
     return data
 
+
 def append_changelog():
     pass
 
+
 if __name__ == "__main__":
     publish(sys.argv[0], sys.argv[1])
-

.github/workflows/python-ci.yml

@@ -65,7 +65,7 @@ jobs:
       run: |
         git clone https://github.com/isi-nmr/brukerapi-python.git
         cd brukerapi-python
-        pip install pytest zenodo_get
+        pip install pytest zenodo_get pytest-cov
         pip install -e .[dev] --use-pep517
 
     - name: Cache Zenodo data
@@ -75,4 +75,22 @@ jobs:
         key: zenodo-4522220
 
     - name: Run all dataset tests
-      run: python -m pytest test -v
+      run: |
+        python -m pytest test -v --cov=brukerapi --cov-branch --cov-report=xml --cov-report=term-missing --cov-report=html
+
+    - name: Upload coverage HTML
+      uses: actions/upload-artifact@v4
+      with:
+        name: coverage-report
+        path: htmlcov/
+
+    - name: Print total coverage
+      run: |
+        echo "Total coverage:"
+        python - <<EOF
+        import xml.etree.ElementTree as ET
+        tree = ET.parse('coverage.xml')
+        root = tree.getroot()
+        line_rate = float(root.attrib['line-rate']) * 100
+        print(f"{line_rate:.2f}%")
+        EOF

.github/workflows/ruff.yml

@@ -0,0 +1,18 @@
+name: Ruff Lint
+
+on: [push, pull_request]
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with:
+          python-version: "3.13"
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install ruff
+      - name: Run Ruff
+        run: ruff check .

README.rst

@@ -11,6 +11,9 @@ brukerapi-python
     :target: https://bruker-api.readthedocs.io/en/latest/?badge=latest
     :alt: Documentation Status
 
+.. image:: https://codecov.io/gh/isi-nmr/brukerapi-python/branch/main/graph/badge.svg
+   :target: https://codecov.io/gh/isi-nmr/brukerapi-python
+   :alt: Test coverage
 A Python package providing I/O interface for Bruker data sets.
 
 tl;dr

brukerapi/cli.py

@@ -1,18 +1,17 @@
-from argparse import ArgumentParser
-from brukerapi.splitters import *
-from brukerapi.folders import *
 import sys
+from argparse import ArgumentParser
 
+from brukerapi.folders import Dataset, Filter, Folder, Path
+from brukerapi.splitters import FrameGroupSplitter, SlicePackageSplitter
 
-def main():
-    """
 
-    """
-    parser = ArgumentParser(prog='bruker')
+def main():
+    """ """
+    parser = ArgumentParser(prog="bruker")
     subparsers = parser.add_subparsers()
 
     # report sub-command
-    parser_report = subparsers.add_parser('report', help='export properties of data sets to json, or yaml file')
+    parser_report = subparsers.add_parser("report", help="export properties of data sets to json, or yaml file")
     parser_report.add_argument(
         "-i",
         "--input",
@@ -27,27 +26,22 @@ def main():
     parser_report.add_argument(
         "-f",
         "--format",
-        choices=['json', 'yml'],
-        default='json',
+        choices=["json", "yml"],
+        default="json",
         help="Format of report files",
     )
     parser_report.add_argument(
         "-p",
         "--props",
         type=str,
-        nargs='+',
+        nargs="+",
         help="List of properties to include",
     )
-    parser_report.add_argument(
-        "-v",
-        "--verbose",
-        help="make verbose",
-        action="store_true"
-    )
+    parser_report.add_argument("-v", "--verbose", help="make verbose", action="store_true")
     parser_report.set_defaults(func=report)
 
     # report sub-command
-    parser_split = subparsers.add_parser('split', help='split dataset into several sub-datasets')
+    parser_split = subparsers.add_parser("split", help="split dataset into several sub-datasets")
     parser_split.add_argument(
         "-i",
         "--input",
@@ -68,7 +62,7 @@ def main():
         "-s",
         "--slice_package",
         dest="slice_package",
-        action='store_true',
+        action="store_true",
         help="Split by slice package",
     )
     parser_split.add_argument(
@@ -81,7 +75,7 @@ def main():
     parser_split.set_defaults(func=split)
 
     # filter sub-command
-    parser_filter = subparsers.add_parser('filter', help='get files based on query')
+    parser_filter = subparsers.add_parser("filter", help="get files based on query")
     parser_filter.add_argument(
         "-i",
         "--input",
@@ -108,8 +102,6 @@ def main():
     func(args)
 
 
-
-
 def split(args):
     """
     split sub-command
@@ -145,13 +137,12 @@ def report(args):
         elif output.is_dir():
             # folder to folder
             Folder(input).report(path_out=output, format_=args.format, props=args.props, verbose=args.verbose)
-    else:
-        # dataset in-place
-        if output is None:
-            Dataset(input, add_parameters=['subject']).report(props=args.props, verbose=args.verbose)
-        # dataset to folder, or dataset to file
-        elif output.is_dir():
-            Dataset(input, add_parameters=['subject']).report(path=output, props=args.props, verbose=args.verbose)
+    # dataset in-place
+    elif output is None:
+        Dataset(input, add_parameters=["subject"]).report(props=args.props, verbose=args.verbose)
+    # dataset to folder, or dataset to file
+    elif output.is_dir():
+        Dataset(input, add_parameters=["subject"]).report(path=output, props=args.props, verbose=args.verbose)
 
 
 def filter(args):

brukerapi/data.py

@@ -1,8 +1,7 @@
-class DataRandomAccess():
-
+class DataRandomAccess:
     def __init__(self, dataset):
         self._dataset = dataset
         self._scheme = dataset._scheme
 
     def __getitem__(self, slice):
-        return self._scheme.ra(slice)
+        return self._scheme.ra(slice)