Remove python 3.8 from CI (#2233)

* Update test environments from 3.8 to 3.11

Remove 3.8 python and add 3.11. Move preview mode to 3.10.

* Use 3.10 in benchmarks

* Drop pystan 2 testing and update python to 3.10

* Update python env to 3.10

* Fix naming issue

* Update readthedocs python env to 3.10

* Update and rename .readthedocs.yml to .readthedocs.yaml

* fix typo

* fix rtd config

* Remove 3.11

* fix tsplot np.tile behaviour

* fix np.tile call

* fix pylint

* fix missing tile array change

---------

Co-authored-by: Oriol (ZBook) <oriol.abril.pla@gmail.com>

.azure-pipelines/azure-pipelines-base.yml

@@ -14,18 +14,14 @@ jobs:
         python.version: "3.10"
         PyPIGithub: false
         name: "Python 3.10"
+      Python_310_preview:
+        python.version: "3.10"
+        PyPIGithub: true
+        name: "Python 3.10"
       Python_39:
         python.version: "3.9"
         PyPIGithub: false
         name: "Python 3.9"
-      Python_39_preview:
-        python.version: "3.9"
-        PyPIGithub: true
-        name: "Python 3.9"
-      Python_38:
-        python.version: "3.8"
-        PyPIGithub: false
-        name: "Python 3.8"
 
 
   steps:

.azure-pipelines/azure-pipelines-benchmarks.yml

@@ -5,9 +5,9 @@ jobs:
   timeoutInMinutes: 360
   strategy:
     matrix:
-      Python_39:
-        python.version: "3.9"
-        name: "Python 3.9 - benchmarks"
+      Python_310:
+        python.version: "3.10"
+        name: "Python 3.10 - benchmarks"
 
   steps:
 

.azure-pipelines/azure-pipelines-external.yml

@@ -10,16 +10,14 @@ jobs:
   timeoutInMinutes: 360
   strategy:
     matrix:
-      Python_39_Latest:
-        python.version: "3.9"
-        pystan.version: "latest"
+      Python_310_Latest:
+        python.version: "3.10"
         cmdstanpy.version: "latest"
         emcee.version: "latest"
         name: "External latest"
 
-      Python_39_Special_versions:
-        python.version: "3.9"
-        pystan.version: 2.19.1.1
+      Python_310_Special_versions:
+        python.version: "3.10"
         cmdstanpy.version: "github"
         emcee.version: 2
         name: "External special"
@@ -46,16 +44,6 @@ jobs:
 
       python -m pip --no-cache-dir install torch<2.0 --index-url https://download.pytorch.org/whl/cpu
 
-      if [ "$(pystan.version)" = "latest" ]; then
-          python -m pip --no-cache-dir install pystan
-      else
-          if [ "$(pystan.version)" = "latest" ]; then
-              python -m pip --no-cache-dir install pystan
-          else
-              python -m pip --no-cache-dir install pystan=="$(pystan.version)"
-          fi
-      fi
-
       if [ "$(cmdstanpy.version)" = "latest" ]; then
           python -m pip --no-cache-dir install cmdstanpy
       else
@@ -72,7 +60,7 @@ jobs:
           python -m pip --no-cache-dir install "emcee<3"
       fi
 
-      grep -Ev '^pystan|^cmdstanpy|^emcee' requirements-external.txt | xargs python -m pip install
+      grep -Ev '^cmdstanpy|^emcee' requirements-external.txt | xargs python -m pip install
 
     displayName: 'Install packages'
 
@@ -87,10 +75,6 @@ jobs:
       python -m pip install .
     displayName: 'Install ArviZ package'
 
-  - script: |
-      python -m pip install "setuptools>=48.0,<60" -U
-    displayName: 'Temporary httpstan setuptools fix 2022-11-29'
-
   - script: |
       python -m pip freeze
     displayName: 'Print packages'

.azure-pipelines/azure-pipelines-wheel.yml

@@ -12,9 +12,9 @@ jobs:
   timeoutInMinutes: 360
   strategy:
     matrix:
-      Python_39:
-        python.version: "3.9"
-        name: "Python 3.9 - wheel"
+      Python_310:
+        python.version: "3.10"
+        name: "Python 3.10 - wheel"
 
   steps:
 

.readthedocs.yaml

@@ -0,0 +1,18 @@
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+version: 2
+
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.10"
+
+sphinx:
+  configuration: doc/source/conf.py
+
+python:
+   install:
+   - requirements: requirements.txt
+   - requirements: requirements-docs.txt
+   - method: pip
+     path: .

arviz/plots/backends/bokeh/lmplot.py

@@ -80,7 +80,6 @@ def plot_lm(
     y_model_mean_kwargs.setdefault("line_width", 2)
 
     for i, ax_i in enumerate((item for item in axes.flatten() if item is not None)):
-
         _, _, _, y_plotters = y[i]
         _, _, _, x_plotters = x[i]
         legend_it = []
@@ -124,9 +123,8 @@ def plot_lm(
         if y_model is not None:
             _, _, _, y_model_plotters = y_model[i]
             if kind_model == "lines":
-
                 model_legend = ax_i.multi_line(
-                    [np.tile(x_plotters, (num_samples, 1))],
+                    [np.tile(np.array(x_plotters, dtype=object), (num_samples, 1))],
                     [np.transpose(y_model_plotters)],
                     **y_model_plot_kwargs,
                 )

arviz/plots/tsplot.py

@@ -284,8 +284,8 @@ def plot_ts(
     length_plotters = len_x * len_y
     # TODO: Incompatible types in assignment (expression has type "ndarray[Any, dtype[Any]]",
     # TODO: variable has type "List[Any]")  [assignment]
-    y_plotters = np.tile(y_plotters, (len_x, 1))  # type: ignore[assignment]
-    x_plotters = np.tile(x_plotters, (len_y, 1))  # type: ignore[assignment]
+    y_plotters = np.tile(np.array(y_plotters, dtype=object), (len_x, 1))  # type: ignore[assignment]
+    x_plotters = np.tile(np.array(x_plotters, dtype=object), (len_y, 1))  # type: ignore[assignment]
 
     # Generate plotters for all the available data
     y_mean_plotters = None
@@ -317,8 +317,12 @@ def plot_ts(
         # If there are multiple x and multidimensional y, we need total of len(x)*len(y) graphs
         # TODO: Incompatible types in assignment (expression has type "ndarray[Any, dtype[Any]]",
         # TODO: variable has type "List[Any]")  [assignment]
-        y_hat_plotters = np.tile(y_hat_plotters, (len_x, 1))  # type: ignore[assignment]
-        y_mean_plotters = np.tile(y_mean_plotters, (len_x, 1))  # type: ignore[assignment]
+        y_hat_plotters = np.tile(
+            np.array(y_hat_plotters, dtype=object), (len_x, 1)
+        )  # type: ignore[assignment]
+        y_mean_plotters = np.tile(
+            np.array(y_mean_plotters, dtype=object), (len_x, 1)
+        )  # type: ignore[assignment]
 
     y_holdout_plotters = None
     x_holdout_plotters = None
@@ -344,8 +348,12 @@ def plot_ts(
         # If there are multiple x and multidimensional y, we need total of len(x)*len(y) graphs
         # TODO: Incompatible types in assignment (expression has type "ndarray[Any, dtype[Any]]",
         # TODO: variable has type "List[Any]")  [assignment]
-        y_holdout_plotters = np.tile(y_holdout_plotters, (len_x, 1))  # type: ignore[assignment]
-        x_holdout_plotters = np.tile(x_holdout_plotters, (len_y, 1))  # type: ignore[assignment]
+        y_holdout_plotters = np.tile(
+            np.array(y_holdout_plotters, dtype=object), (len_x, 1)
+        )  # type: ignore[assignment]
+        x_holdout_plotters = np.tile(
+            np.array(x_holdout_plotters, dtype=object), (len_y, 1)
+        )  # type: ignore[assignment]
 
     y_forecasts_plotters = None
     y_forecasts_mean_plotters = None
@@ -386,10 +394,14 @@ def plot_ts(
         # TODO: Incompatible types in assignment (expression has type "ndarray[Any, dtype[Any]]",
         # TODO: variable has type "List[Any]")  [assignment]
         y_forecasts_mean_plotters = np.tile(
-            y_forecasts_mean_plotters, (len_x, 1)
+            np.array(y_forecasts_mean_plotters, dtype=object), (len_x, 1)
+        )  # type: ignore[assignment]
+        y_forecasts_plotters = np.tile(
+            np.array(y_forecasts_plotters, dtype=object), (len_x, 1)
+        )  # type: ignore[assignment]
+        x_holdout_plotters = np.tile(
+            np.array(x_holdout_plotters, dtype=object), (len_y, 1)
         )  # type: ignore[assignment]
-        y_forecasts_plotters = np.tile(y_forecasts_plotters, (len_x, 1))  # type: ignore[assignment]
-        x_holdout_plotters = np.tile(x_holdout_plotters, (len_y, 1))  # type: ignore[assignment]
 
     rows, cols = default_grid(length_plotters)