Make code checks pass

Makefile

@@ -35,8 +35,7 @@ lint: .venv  ## Check linting
 	. $(VENV_BIN)/activate
 	$(VENV_BIN)/isort --check .
 	$(VENV_BIN)/black --check .
-	$(VENV_BIN)/blackdoc .
-	$(VENV_BIN)/ruff .
+	$(VENV_BIN)/ruff check .
 	$(VENV_BIN)/typos .
 #	$(VENV_BIN)/mypy ranx
 

_typos.toml

@@ -1,4 +1,6 @@
 [default]
 extend-ignore-identifiers-re = [
     ".*Hsi",
+    "relevants",
+    "Comput",
 ]

docs/qrels.md

@@ -69,7 +69,7 @@ You can control the behavior of the underlying `pandas.read_parquet` function by
 
 ```python
 qrels = Qrels.from_parquet(
-    path="/path/to/parquet/file""",
+    path="/path/to/parquet/file",
     q_id_col="q_id",
     doc_id_col="doc_id",
     score_col="score",

docs/report.md

@@ -12,7 +12,7 @@ report = compare(
     qrels=qrels,
     runs=[run_1, run_2, run_3, run_4, run_5],
     metrics=["map@100", "mrr@100", "ndcg@10"],
-    max_p=0.01  # P-value threshold
+    max_p=0.01,  # P-value threshold
 )
 
 print(report)

docs/run.md

@@ -36,7 +36,7 @@ run = Run.from_file("path/to/run.json")  # JSON file
 run = Run.from_file("path/to/run.trec")  # TREC-Style file
 run = Run.from_file("path/to/run.txt")   # TREC-Style file with txt extension
 run = Run.from_file("path/to/run.gz")    # Gzipped TREC-Style file
-run = Run.from_file("path/to/run.lz4")    # lz4 file produced by saving a ranx.Run as lz4
+run = Run.from_file("path/to/run.lz4")   # lz4 file produced by saving a ranx.Run as lz4
 run = Run.from_file("path/to/run.custom", kind="json")  # Loaded as JSON file
 ```
 
@@ -69,7 +69,7 @@ The argument `name` is used to set the name of the run. Default is `None`.
 
 ```python
 run = Run.from_parquet(
-    path="/path/to/parquet/file""",
+    path="/path/to/parquet/file",
     q_id_col="q_id",
     doc_id_col="doc_id",
     score_col="score",

notebooks/2_qrels_and_run.ipynb

@@ -161,11 +161,11 @@
     "os.makedirs(\"notebooks/data\", exist_ok=True)\n",
     "\n",
     "with open(\"notebooks/data/small_qrels.json\", \"w\") as f:\n",
-    "    master = f\"https://raw.githubusercontent.com/AmenRa/ranx/master/notebooks/data/small_qrels.json\"\n",
+    "    master = \"https://raw.githubusercontent.com/AmenRa/ranx/master/notebooks/data/small_qrels.json\"\n",
     "    f.write(requests.get(master).text)\n",
     "\n",
     "with open(\"notebooks/data/small_qrels.trec\", \"w\") as f:\n",
-    "    master = f\"https://raw.githubusercontent.com/AmenRa/ranx/master/notebooks/data/small_qrels.trec\"\n",
+    "    master = \"https://raw.githubusercontent.com/AmenRa/ranx/master/notebooks/data/small_qrels.trec\"\n",
     "    f.write(requests.get(master).text)"
    ]
   },

pyproject.toml

@@ -1,7 +1,13 @@
 [tool.ruff]
 # E501 ignore long comment lines (black should take care of that)
 # E712 ignore == False, needed for numba checks.
+[tool.ruff.lint]
 ignore = ["E501", "E712"]
 
+[tool.black]
+extend-exclude = '''
+\.md$|\.markdown$
+'''
+
 [tool.isort]
 profile = "black"

ranx/data_structures/report.py

@@ -47,7 +47,7 @@ class Report(object):
         qrels=qrels,
         runs=[run_1, run_2, run_3, run_4, run_5],
         metrics=["map@100", "mrr@100", "ndcg@10"],
-        max_p=0.01  # P-value threshold
+        max_p=0.01,  # P-value threshold
     )
 
     print(report)
@@ -253,7 +253,7 @@ def to_latex(self) -> str:
     def to_dict(self) -> Dict:
         """Returns the Report data as a Python dictionary.
 
-        ```python
+        ```
         {
             "stat_test": "fisher"
             # metrics and model_names allows to read the report without

ranx/fusion/isr.py

@@ -45,7 +45,7 @@ def isr(runs: List[Run], name: str = "isr") -> Run:
                         Fl{\'{a}}vio Martins and
                         Jo{\~{a}}o Magalh{\~{a}}es},
             title     = {Multimodal medical information retrieval with unsupervised rank fusion},
-            journal   = {Comput. Medical Imaging Graph.},
+            journal   = {Computerized Medical Imaging and Graphics},
             volume    = {39},
             pages     = {35--45},
             year      = {2015},

ranx/fusion/log_isr.py

@@ -51,7 +51,7 @@ def log_isr(runs: List[Run], name: str = "log_isr") -> Run:
                         Fl{\'{a}}vio Martins and
                         Jo{\~{a}}o Magalh{\~{a}}es},
             title     = {Multimodal medical information retrieval with unsupervised rank fusion},
-            journal   = {Comput. Medical Imaging Graph.},
+            journal   = {Computerized Medical Imaging and Graphics},
             volume    = {39},
             pages     = {35--45},
             year      = {2015},

ranx/fusion/logn_isr.py

@@ -51,7 +51,7 @@ def logn_isr(runs: List[Run], sigma: float = 0.01, name: str = "logn_isr") -> Ru
                         Fl{\'{a}}vio Martins and
                         Jo{\~{a}}o Magalh{\~{a}}es},
             title     = {Multimodal medical information retrieval with unsupervised rank fusion},
-            journal   = {Comput. Medical Imaging Graph.},
+            journal   = {Computerized Medical Imaging and Graphics},
             volume    = {39},
             pages     = {35--45},
             year      = {2015},

ranx/meta/compare.py

@@ -32,7 +32,7 @@ def compare(
         qrels=qrels,
         runs=[run_1, run_2, run_3, run_4, run_5],
         metrics=["map@100", "mrr@100", "ndcg@10"],
-        max_p=0.01  # P-value threshold
+        max_p=0.01,  # P-value threshold
     )
 
     print(report)

ranx/meta/evaluate.py

@@ -41,15 +41,15 @@ def extract_metric_and_params(metric):
 
 
 def convert_qrels(qrels):
-    if type(qrels) == Qrels:
+    if isinstance(qrels, Qrels):
         return qrels.to_typed_list()
     elif isinstance(qrels, dict):
         return python_dict_to_typed_list(qrels, sort=True)
     return qrels
 
 
 def convert_run(run):
-    if type(run) == Run:
+    if isinstance(run, Run):
         return run.to_typed_list()
     elif isinstance(run, dict):
         return python_dict_to_typed_list(run, sort=True)
@@ -128,10 +128,10 @@ def evaluate(
     if not return_mean:
         return_std = False
 
-    if make_comparable and type(qrels) == Qrels and type(run) == Run:
+    if make_comparable and isinstance(qrels, Qrels) and isinstance(run, Run):
         run = run.make_comparable(qrels)
 
-    if type(qrels) in [Qrels, dict] and type(run) in [Run, dict]:
+    if isinstance(qrels, (Qrels, dict)) and isinstance(run, (Run, dict)):
         check_keys(qrels, run)
 
     _qrels = convert_qrels(qrels)
@@ -146,7 +146,7 @@ def evaluate(
         metric_scores_dict[metric] = metric_switch(m)(_qrels, _run, k, rel_lvl)
 
     # Save results in Run ------------------------------------------------------
-    if type(run) == Run and save_results_in_run:
+    if isinstance(run, Run) and save_results_in_run:
         for m, scores in metric_scores_dict.items():
             run.mean_scores[m] = np.mean(scores)
             if return_std: