upgrade version

xadupre · xadupre · commit 7e94de4b2824 · 2025-12-04T01:21:44.000+01:00
diff --git a/.local.jenkins.lin.yml b/.local.jenkins.lin.yml
diff --git a/_doc/index.rst b/_doc/index.rst
@@ -78,4 +78,5 @@ Xavier Dupré
 Older versions
 ++++++++++++++
 
+* `0.5.0 <../v0.5.0/index.html>`_
 * `0.4.0 <../v0.4.0/index.html>`_
diff --git a/_doc/notebooks/dsgarden/correlation_non_lineaire.ipynb b/_doc/notebooks/dsgarden/correlation_non_lineaire.ipynb
@@ -940,7 +940,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 49,
+   "execution_count": null,
    "metadata": {
     "scrolled": false
    },
@@ -962,7 +962,7 @@
     "\n",
     "def pairplot_cross_val(data, model=None, ax=None, **params):\n",
     "    if ax is None:\n",
-    "        fig, ax = plt.subplots(\n",
+    "        _fig, ax = plt.subplots(\n",
     "            data.shape[1], data.shape[1], figsize=params.get(\"figsize\", (10, 10))\n",
     "        )\n",
     "    if \"figsize\" in params:\n",
diff --git a/_doc/notebooks/metric/pvalues_examples.ipynb b/_doc/notebooks/metric/pvalues_examples.ipynb
@@ -1045,7 +1045,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": null,
    "metadata": {},
    "outputs": [
     {
@@ -1087,7 +1087,7 @@
     "    if ax is None:\n",
     "        import matplotlib.pyplot as plt\n",
     "\n",
-    "        fig, ax = plt.subplots(1, 1, figsize=figsize)\n",
+    "        _fig, ax = plt.subplots(1, 1, figsize=figsize)\n",
     "\n",
     "    smarker = {\n",
     "        (True, True): \"o-\",\n",
@@ -1262,4 +1262,4 @@
  },
  "nbformat": 4,
  "nbformat_minor": 2
-}
+}
diff --git a/_doc/notebooks/ml/logreg_voronoi.ipynb b/_doc/notebooks/ml/logreg_voronoi.ipynb
@@ -167,7 +167,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
+   "execution_count": null,
    "metadata": {},
    "outputs": [
     {
@@ -233,7 +233,7 @@
     "    cmap = plt.cm.tab20\n",
     "    Z = Z.reshape(xx.shape)\n",
     "    if ax is None:\n",
-    "        fig, ax = plt.subplots(1, 1, figsize=figsize or (4, 3))\n",
+    "        _fig, ax = plt.subplots(1, 1, figsize=figsize or (4, 3))\n",
     "    ax.pcolormesh(xx, yy, Z, cmap=cmap)\n",
     "\n",
     "    # Plot also the training points\n",
diff --git a/_unittests/ut_nlp/test_completion.py b/_unittests/ut_nlp/test_completion.py
@@ -184,7 +184,7 @@ def cmks(trie):
                 nb += 1
             return nb, gmks, gmksd, size
 
-        nb, gmks, gmksd, size = cmks(trie)
+        nb, gmks, gmksd, _size = cmks(trie)
         # print(nb, size, gmks / nb, gmksd / nb, gmks / size, gmksd / size)
         if gmks > gmksd:
             raise AssertionError(f"gmks={gmks} gmksd={gmksd}")
@@ -198,7 +198,7 @@ def cmks(trie):
             raise AssertionError("should not happen")
 
         trie = CompletionTrieNode.build(titles)
-        nb2, gmks2, gmksd2, size = cmks(trie)
+        nb2, gmks2, gmksd2, _size = cmks(trie)
         self.assertEqual(nb, nb2)
         self.assertEqual(gmks, gmks2)
         self.assertEqual(gmksd, gmksd2)
@@ -207,7 +207,7 @@ def cmks(trie):
         # print("-----")
         for i in range(1, 20):
             trie = CompletionTrieNode.build(titles[:i])
-            nb, gmks, gmksd, size = cmks(trie)
+            nb, gmks, gmksd, _size = cmks(trie)
             if i == 1:
                 self.assertEqual(gmks, 30)
             # print(i, nb, size, gmks / nb, gmksd / nb, gmks / size, gmksd / size, gmks)
@@ -231,14 +231,14 @@ def cmks(trie):
             (None, '"contra el gang del chicharron"', '"Contra el gang del chicharron')
         ]
         trie = CompletionTrieNode.build(titles)
-        nb, gmks, gmksd, size = cmks(trie)
+        _nb, gmks, _gmksd, _size = cmks(trie)
         # print("***", 1, nb, size, gmks / nb, gmksd / nb,
         #       gmks / size, gmksd / size, gmks)
         self.assertEqual(gmks, 30)
 
         titles.append((None, '"la sequestree"', '"La séquestrée'))
         trie = CompletionTrieNode.build(titles)
-        nb, gmks, gmksd, size = cmks(trie)
+        _nb, gmks, _gmksd, _size = cmks(trie)
         # print("***", 2, nb, size, gmks / nb, gmksd / nb,
         #       gmks / size, gmksd / size, gmks)
         # for n in trie.leaves():
diff --git a/_unittests/ut_nlp/test_completion_mks.py b/_unittests/ut_nlp/test_completion_mks.py
@@ -56,8 +56,8 @@ def gain_dynamique_moyen_par_mot(queries, weights):
             titles = [_.strip(" \n\r\t") for _ in f.readlines()]
         # print(titles[:5])
         trie = CompletionTrieNode.build([(None, q) for q in titles])
-        nb, gmks, gmksd, gmksd2, size = cmks(trie)
-        gain, gain_dyn, gain_dyn2, ave_length = gain_dynamique_moyen_par_mot(
+        nb, _gmks, _gmksd, _gmksd2, _size = cmks(trie)
+        _gain, _gain_dyn, _gain_dyn2, _ave_length = gain_dynamique_moyen_par_mot(
             titles, [1.0] * len(titles)
         )
         # print("***", 1, nb, size, "*", gmks / size, gmksd / size, gmksd2 / size)
diff --git a/_unittests/ut_nlp/test_completion_simple.py b/_unittests/ut_nlp/test_completion_simple.py
@@ -185,8 +185,8 @@ def gain_dynamique_moyen_par_mot(queries, weights):
         # print(titles[:5])
         trie = CompletionSystem([(None, q) for q in titles])
         trie.compute_metrics(details=True)
-        nb, gmks, gmksd, gmksd2, size = cmks(trie)
-        gain, gain_dyn, gain_dyn2, ave_length = gain_dynamique_moyen_par_mot(
+        nb, _gmks, _gmksd, _gmksd2, _size = cmks(trie)
+        _gain, _gain_dyn, _gain_dyn2, _ave_length = gain_dynamique_moyen_par_mot(
             titles, [1.0] * len(titles)
         )
         # print("***", 1, nb, size, "*", gmks / size, gmksd / size, gmksd2 / size)
diff --git a/_unittests/ut_xrun_doc/test_documentation_examples.py b/_unittests/ut_xrun_doc/test_documentation_examples.py
@@ -40,7 +40,7 @@ def run_test(self, fold: str, name: str, verbose=0) -> int:
             cmds = [sys.executable, "-u", os.path.join(fold, name)]
             p = subprocess.Popen(cmds, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
             res = p.communicate()
-            out, err = res
+            _out, err = res
             st = err.decode("ascii", errors="ignore")
             if "No such file or directory" in st:
                 raise FileNotFoundError(st)  # noqa: B904
diff --git a/_unittests/ut_xrun_doc/test_documentation_notebook.py b/_unittests/ut_xrun_doc/test_documentation_notebook.py
@@ -76,7 +76,7 @@ def run_test(self, nb_name: str, verbose=0) -> int:
                     cmds, stdout=subprocess.PIPE, stderr=subprocess.PIPE
                 )
                 res = p.communicate()
-                out, err = res
+                _out, err = res
                 st = err.decode("ascii", errors="ignore")
                 if "No such file or directory" in st:
                     raise FileNotFoundError(st)  # noqa: B904
diff --git a/mlstatpy/ext_test_case.py b/mlstatpy/ext_test_case.py
@@ -50,7 +50,6 @@ def get_url_content_timeout(
     The function raises the exception :class:`InternetException`.
     """
     import gzip
-    import socket
     import urllib.error as urllib_error
     import urllib.request as urllib_request
     import http.client as http_client
@@ -110,7 +109,7 @@ def _local_loop(ur):
         urllib_error.HTTPError,
         urllib_error.URLError,
         ConnectionRefusedError,
-        socket.timeout,
+        TimeoutError,
         ConnectionResetError,
         http_client.BadStatusLine,
         http_client.IncompleteRead,
@@ -384,7 +383,9 @@ def assertAlmostEqual(
             value = numpy.array(value).astype(expected.dtype)
         self.assertEqualArray(expected, value, atol=atol, rtol=rtol)
 
-    def assertRaise(self, fct: Callable, exc_type: Optional[Exception] = None):
+    def assertRaise(
+        self, fct: Callable, exc_type: Optional[Exception] = None
+    ):  # noqa: UP045
         exct = exc_type or Exception
         try:
             fct()
diff --git a/mlstatpy/graph/graph_distance.py b/mlstatpy/graph/graph_distance.py
@@ -758,7 +758,7 @@ def private_kruskal_matrix(self, matrix, reverse):
             max(sum(_.values()) for _ in countLeft.values()),
         )
         while count > 1:
-            k, v = matrix.pop()
+            _k, v = matrix.pop()
             i, j = v
             countRight[i][j] -= 1
             countLeft[j][i] -= 1
@@ -915,7 +915,7 @@ def distance_matching_graphs_paths(
 
         if verbose > 0:
             print("[distance_matching_graphs_paths] private_count_left_right")
-        count_edge_left, count_edge_right = self.private_count_left_right(
+        _count_edge_left, count_edge_right = self.private_count_left_right(
             reduction_edge
         )
         count_vertex_left, count_vertex_right = self.private_count_left_right(
diff --git a/mlstatpy/image/detection_segment/detection_segment.py b/mlstatpy/image/detection_segment/detection_segment.py
@@ -233,7 +233,7 @@ def detect_segments(
     # on calcule les tables de la binomiale pour eviter d'avoir a le fait a
     # chaque fois qu'on en a besoin
     yy, xx = grad.shape[:2]
-    nbbin = int(math.ceil(math.sqrt(xx * xx + yy * yy)))
+    nbbin = int(math.ceil(math.sqrt(xx * xx + yy * yy)))  # noqa: RUF046
     binomiale = tabule_queue_binom(nbbin, proba_bin)
 
     # nb_seg est le nombre total de segment de l'image
diff --git a/mlstatpy/nlp/completion_simple.py b/mlstatpy/nlp/completion_simple.py
@@ -139,7 +139,9 @@ def str_all_completions(self, maxn=10, use_precompute=True) -> str:
         return "\n".join(rows)
 
     def init_metrics(
-        self, position: int, completions: Optional[List["CompletionElement"]] = None
+        self,
+        position: int,
+        completions: Optional[List["CompletionElement"]] = None,  # noqa: UP045
     ):
         """
         Initializes the metrics.
@@ -198,7 +200,7 @@ def update_metrics(
         position: int,
         improved: dict,
         delta: float,
-        completions: Optional[List["CompletionElement"]] = None,
+        completions: Optional[List["CompletionElement"]] = None,  # noqa: UP045
         iteration=-1,
     ):
         """
diff --git a/pyproject.toml b/pyproject.toml
@@ -1,3 +1,39 @@
+[project]
+authors = [{name="Xavier Dupré", email="xavier.dupre@gmail.com"}]
+classifiers = [
+    "Intended Audience :: Science/Research",
+    "Intended Audience :: Developers",
+    "License :: OSI Approved :: MIT License",
+    "Programming Language :: C",
+    "Programming Language :: Python",
+    "Topic :: Software Development",
+    "Topic :: Scientific/Engineering",
+    "Development Status :: 5 - Production/Stable",
+    "Operating System :: Microsoft :: Windows",
+    "Operating System :: POSIX",
+    "Operating System :: Unix",
+    "Operating System :: MacOS",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+]
+dependencies = ["numpy>=2", "scikit-learn>=1.5", "scipy"]
+description = "Points de détails liés au machine learning"
+keywords = ["cython", "scikit-learn", "machine-learning"]
+license = {file = "LICENSE.txt"}
+name = "mlstatpy"
+readme = "README.rst"
+requires-python = ">=3.10"
+version = "0.5.0"
+
+[project.urls]
+homepage = "https://sdpython.github.io/doc/mlstatpy/dev/"
+documentation = "https://sdpython.github.io/doc/mlstatpy/dev/"
+repository = "https://github.com/sdpython/mlstatpy/"
+changelog = "https://sdpython.github.io/doc/mlstatpy/dev/CHANGELOGS.html"
+
 [tool.rstcheck]
 report_level = "INFO"
 ignore_directives = [
@@ -81,8 +117,8 @@ select = [
     "B905",
     "C401", "C408", "C413",
     "RUF012", "RUF100", "RUF010",
-    "SIM108", "SIM910", "SIM110", "SIM102", "SIM114", "SIM103",
-    "UP015", "UP027", "UP031", "UP034", "UP032", "UP006", "UP035", "UP007", "UP030", "UP038"
+    "SIM905", "SIM108", "SIM910", "SIM110", "SIM102", "SIM114", "SIM103",
+    "UP015", "UP027", "UP031", "UP034", "UP032", "RUF051", "UP006", "UP035", "UP045", "UP007", "UP030", "UP038"
 ]
 "_unittests/**" = ["SIM113", "RUF005", "E402"]
 "**/plot*.py" = ["B018"]
diff --git a/requirements.txt b/requirements.txt
@@ -1,3 +1,3 @@
-mlinsights>=0.2
-onnxruntime>=1.12
-skl2onnx
+mlinsights>=0.4
+onnxruntime>=1.23
+skl2onnx>=1.14
diff --git a/setup.py b/setup.py
@@ -58,8 +58,9 @@
         "Development Status :: 5 - Production/Stable",
         "Operating System :: OS Independent",
         "Programming Language :: Python :: 3",
-        "Programming Language :: Python :: 3.9",
         "Programming Language :: Python :: 3.10",
         "Programming Language :: Python :: 3.11",
+        "Programming Language :: Python :: 3.12",
+        "Programming Language :: Python :: 3.13",
     ],
 )

Original file line number	Diff line number	Diff line change
`@@ -76,7 +76,7 @@ def run_test(self, nb_name: str, verbose=0) -> int:`
`76`	`76`	`cmds, stdout=subprocess.PIPE, stderr=subprocess.PIPE`
`77`	`77`	`)`
`78`	`78`	`res = p.communicate()`
`79`		`- out, err = res`
	`79`	`+ _out, err = res`
`80`	`80`	`st = err.decode("ascii", errors="ignore")`
`81`	`81`	`if "No such file or directory" in st:`
`82`	`82`	`raise FileNotFoundError(st) # noqa: B904`