lint/format, update pytest action and add failing test

.github/workflows/ci.yml

@@ -60,7 +60,7 @@ jobs:
       - run: poetry install --with dev
       - run: echo "$(poetry env info --path)/bin" >> $GITHUB_PATH
 
-      - uses: jakebailey/pyright-action@v1
+      - uses: jakebailey/pyright-action@v2
         with:
           version: ${{ matrix.pyright-version }}
 

python/mdvtools/conversions.py

@@ -193,8 +193,10 @@ def create_regulamentary_project(
         # trying to avoid unbound variables - but not convinced this is correct
         # what is supposed to happen if bigwig_folder is not a URL?
         # >> need tests for this function... <<
-        beds = bigwigs = ['' for _ in all_names]
-        print("bigwig_folder is not a URL - using empty URLs for tracks, may well be wrong.")
+        beds = bigwigs = ["" for _ in all_names]
+        print(
+            "bigwig_folder is not a URL - using empty URLs for tracks, may well be wrong."
+        )
         pass
     # get the reference
 

python/mdvtools/mdvproject.py

@@ -413,7 +413,7 @@ def add_annotations(
                 f"index column {index_col} not found in {datasource} datasource"
             )
         # py-right: dictionary key must be hashable
-        newdf = pandas.DataFrame({index_col: self.get_column(datasource, index_col)}) # type: ignore
+        newdf = pandas.DataFrame({index_col: self.get_column(datasource, index_col)})  # type: ignore
         h5 = self._get_h5_handle()
         gr = h5[datasource]
         assert isinstance(gr, h5py.Group)
@@ -1202,7 +1202,9 @@ def get_subgroup_bytes(grp, index, sparse=False):
         return numpy.array(grp["x"][offset : offset + _len], numpy.float32).tobytes()
 
 
-def add_column_to_group(col: dict, data: pandas.Series | pandas.DataFrame, group: h5py.Group, length: int):
+def add_column_to_group(
+    col: dict, data: pandas.Series | pandas.DataFrame, group: h5py.Group, length: int
+):
     """
     col (dict): The column metadata (may be modified e.g. to add values)
     data (pandas.Series): The data to add
@@ -1230,7 +1232,10 @@ def add_column_to_group(col: dict, data: pandas.Series | pandas.DataFrame, group
                 col["values"] = [x for x in values.index if values[x] != 0]
             vdict = {k: v for v, k in enumerate(col["values"])}
             group.create_dataset(
-                col["field"], length, dtype=dtype, data=data.map(vdict) # type: ignore
+                col["field"],
+                length,
+                dtype=dtype,
+                data=data.map(vdict),  # type: ignore
             )
             # convert to string
             col["values"] = [str(x) for x in col["values"]]

python/mdvtools/server.py

@@ -206,7 +206,9 @@ def get_binary_data():
                 return "Request must contain JSON with 'datasource' and 'name'", 400
             if project.dir is None or not os.path.exists(project.dir):
                 return "Project directory not found", 404
-            path = safe_join(project.dir, "binarydata", req["datasource"], f"{req['name']}.gz")
+            path = safe_join(
+                project.dir, "binarydata", req["datasource"], f"{req['name']}.gz"
+            )
             if path is None or not os.path.exists(path):
                 return "Binary data not found", 404
             with open(path, "rb") as f:

python/mdvtools/tests/test_column_groups.py

@@ -3,15 +3,12 @@
 import pandas as pd
 
 # make a project in local temp directory, which is ignored by git
-path = os.path.join(os.path.dirname(__file__), 'temp', 'test_column_groups')
+path = os.path.join(os.path.dirname(__file__), "temp", "test_column_groups")
 if not os.path.exists(path):
     os.makedirs(path)
 p = MDVProject(path, delete_existing=True)
 
-df = pd.DataFrame({
-    'a': [1, 2, 3],
-    'b': [4, 5, 6],
-    'c': [7, 8, 9]
-})
+df = pd.DataFrame({"a": [1, 2, 3], "b": [4, 5, 6], "c": [7, 8, 9]})
 
-p.add_datasource('test', df)
+p.add_datasource("test", df)
+assert False  ## making a test that fails, to see if it runs properly etc.