CircleCI update of dev docs (build: 14641).

nilearn · Mar 10, 2024 · cd3b3bf · cd3b3bf
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diff --git a/dev/.buildinfo b/dev/.buildinfo
@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 89b80c4660caf02046f5904c4173a858
+config: adc39110db15c93844520c41e0f54bdc
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/dev/_downloads/07fcc19ba03226cd3d83d4e40ec44385/auto_examples_python.zip b/dev/_downloads/07fcc19ba03226cd3d83d4e40ec44385/auto_examples_python.zip
diff --git a/dev/_downloads/6f1e7a639e0699d6164445b55e6c116d/auto_examples_jupyter.zip b/dev/_downloads/6f1e7a639e0699d6164445b55e6c116d/auto_examples_jupyter.zip
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diff --git a/dev/_images/sphx_glr_plot_oasis_vbm_004.png b/dev/_images/sphx_glr_plot_oasis_vbm_004.png
diff --git a/dev/_images/sphx_glr_plot_second_level_association_test_003.png b/dev/_images/sphx_glr_plot_second_level_association_test_003.png
diff --git a/dev/_images/sphx_glr_plot_second_level_one_sample_test_003.png b/dev/_images/sphx_glr_plot_second_level_one_sample_test_003.png
diff --git a/dev/_images/sphx_glr_plot_simulated_data_002.png b/dev/_images/sphx_glr_plot_simulated_data_002.png
diff --git a/dev/_images/sphx_glr_plot_simulated_data_003.png b/dev/_images/sphx_glr_plot_simulated_data_003.png
diff --git a/dev/_images/sphx_glr_plot_simulated_data_004.png b/dev/_images/sphx_glr_plot_simulated_data_004.png
diff --git a/dev/_images/sphx_glr_plot_simulated_data_006.png b/dev/_images/sphx_glr_plot_simulated_data_006.png
diff --git a/dev/_sources/auto_examples/00_tutorials/plot_3d_and_4d_niimg.rst.txt b/dev/_sources/auto_examples/00_tutorials/plot_3d_and_4d_niimg.rst.txt
@@ -74,6 +74,9 @@ from a :term:`Neurovault` repository
  .. code-block:: none
 
 
+    Dataset created in /home/runner/work/nilearn/nilearn/nilearn_data/neurovault
+
+
     ['/home/runner/work/nilearn/nilearn/nilearn_data/neurovault/collection_658/image_10426.nii.gz']
 
 
@@ -126,7 +129,7 @@ statistical map:
  .. code-block:: none
 
 
-    <nilearn.plotting.displays._slicers.OrthoSlicer object at 0x7f6e387b2fc0>
+    <nilearn.plotting.displays._slicers.OrthoSlicer object at 0x7f1bda77e930>
 
 
 
@@ -155,7 +158,7 @@ Visualizing works better with a threshold
  .. code-block:: none
 
 
-    <nilearn.plotting.displays._slicers.OrthoSlicer object at 0x7f6e4419e420>
+    <nilearn.plotting.displays._slicers.OrthoSlicer object at 0x7f1bd9d6ce90>
 
 
 
@@ -183,6 +186,11 @@ correspondence between rest and task
  .. code-block:: none
 
 
+    Dataset created in /home/runner/work/nilearn/nilearn/nilearn_data/smith_2009
+
+    Downloading data from https://www.fmrib.ox.ac.uk/datasets/brainmap+rsns/PNAS_Smith09_rsn10.nii.gz ...
+     ...done. (2 seconds, 0 min)
+
     '/home/runner/work/nilearn/nilearn/nilearn_data/smith_2009/PNAS_Smith09_rsn10.nii.gz'
 
 
@@ -264,7 +272,7 @@ We can then plot it
  .. code-block:: none
 
 
-    <nilearn.plotting.displays._slicers.OrthoSlicer object at 0x7f6e37cbe2d0>
+    <nilearn.plotting.displays._slicers.OrthoSlicer object at 0x7f1bd9c49160>
 
 
 
@@ -475,9 +483,9 @@ image.
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** (0 minutes 17.731 seconds)
+   **Total running time of the script:** (0 minutes 20.948 seconds)
 
-**Estimated memory usage:**  213 MB
+**Estimated memory usage:**  222 MB
 
 
 .. _sphx_glr_download_auto_examples_00_tutorials_plot_3d_and_4d_niimg.py:

diff --git a/dev/_sources/auto_examples/00_tutorials/plot_decoding_tutorial.rst.txt b/dev/_sources/auto_examples/00_tutorials/plot_decoding_tutorial.rst.txt
diff --git a/dev/_sources/auto_examples/00_tutorials/plot_nilearn_101.rst.txt b/dev/_sources/auto_examples/00_tutorials/plot_nilearn_101.rst.txt
@@ -77,7 +77,7 @@ Let's quickly plot this file:
  .. code-block:: none
 
 
-    <nilearn.plotting.displays._slicers.OrthoSlicer object at 0x7f6e48af23f0>
+    <nilearn.plotting.displays._slicers.OrthoSlicer object at 0x7f1bd45e0680>
 
 
 
@@ -125,7 +125,7 @@ Here we give as inputs the image filename and the smoothing value in mm
  .. code-block:: none
 
 
-    <nibabel.nifti1.Nifti1Image object at 0x7f6e48814050>
+    <nibabel.nifti1.Nifti1Image object at 0x7f1bdd6069c0>
 
 
 
@@ -154,7 +154,7 @@ instance to look at it
  .. code-block:: none
 
 
-    <nilearn.plotting.displays._slicers.OrthoSlicer object at 0x7f6e4886fce0>
+    <nilearn.plotting.displays._slicers.OrthoSlicer object at 0x7f1bd9c02e10>
 
 
 
@@ -183,7 +183,7 @@ We could also pass it to the smoothing function
  .. code-block:: none
 
 
-    <nilearn.plotting.displays._slicers.OrthoSlicer object at 0x7f6e48817dd0>
+    <nilearn.plotting.displays._slicers.OrthoSlicer object at 0x7f1bd9c18b30>
 
 
 
@@ -249,9 +249,9 @@ passed on to other nilearn tools, or saved to disk.
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** (0 minutes 3.898 seconds)
+   **Total running time of the script:** (0 minutes 3.799 seconds)
 
-**Estimated memory usage:**  177 MB
+**Estimated memory usage:**  188 MB
 
 
 .. _sphx_glr_download_auto_examples_00_tutorials_plot_nilearn_101.py:

diff --git a/dev/_sources/auto_examples/00_tutorials/plot_python_101.rst.txt b/dev/_sources/auto_examples/00_tutorials/plot_python_101.rst.txt
@@ -67,14 +67,14 @@ A simple example of basic Python numerics and how to plot it.
  .. code-block:: none
 
 
-    [<matplotlib.lines.Line2D object at 0x7f6e3ae272f0>]
+    [<matplotlib.lines.Line2D object at 0x7f1bdcda34d0>]
 
 
 
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** (0 minutes 0.232 seconds)
+   **Total running time of the script:** (0 minutes 0.230 seconds)
 
 **Estimated memory usage:**  10 MB
 

diff --git a/dev/_sources/auto_examples/00_tutorials/plot_single_subject_single_run.rst.txt b/dev/_sources/auto_examples/00_tutorials/plot_single_subject_single_run.rst.txt
@@ -81,6 +81,13 @@ Retrieving the data
 
  .. code-block:: none
 
+
+    Dataset created in /home/runner/work/nilearn/nilearn/nilearn_data/spm_auditory
+
+    Data absent, downloading...
+    Downloading data from https://www.fil.ion.ucl.ac.uk/spm/download/data/MoAEpilot/MoAEpilot.zip ...
+    Downloaded 1327104 of 34212021 bytes (3.9%,   26.4s remaining)    Downloaded 2121728 of 34212021 bytes (6.2%,   32.2s remaining)    Downloaded 2727936 of 34212021 bytes (8.0%,   36.9s remaining)    Downloaded 3325952 of 34212021 bytes (9.7%,   39.4s remaining)    Downloaded 3989504 of 34212021 bytes (11.7%,   39.7s remaining)    Downloaded 4554752 of 34212021 bytes (13.3%,   40.7s remaining)    Downloaded 5234688 of 34212021 bytes (15.3%,   40.5s remaining)    Downloaded 5660672 of 34212021 bytes (16.5%,   42.2s remaining)    Downloaded 6152192 of 34212021 bytes (18.0%,   42.7s remaining)    Downloaded 6782976 of 34212021 bytes (19.8%,   42.1s remaining)    Downloaded 7503872 of 34212021 bytes (21.9%,   40.7s remaining)    Downloaded 8224768 of 34212021 bytes (24.0%,   39.4s remaining)    Downloaded 8863744 of 34212021 bytes (25.9%,   38.5s remaining)    Downloaded 9461760 of 34212021 bytes (27.7%,   37.9s remaining)    Downloaded 10141696 of 34212021 bytes (29.6%,   36.8s remaining)    Downloaded 10756096 of 34212021 bytes (31.4%,   36.1s remaining)    Downloaded 11190272 of 34212021 bytes (32.7%,   36.2s remaining)    Downloaded 11640832 of 34212021 bytes (34.0%,   36.1s remaining)    Downloaded 12206080 of 34212021 bytes (35.7%,   35.4s remaining)    Downloaded 12861440 of 34212021 bytes (37.6%,   34.3s remaining)    Downloaded 13492224 of 34212021 bytes (39.4%,   33.3s remaining)    Downloaded 14188544 of 34212021 bytes (41.5%,   32.0s remaining)    Downloaded 14688256 of 34212021 bytes (42.9%,   31.5s remaining)    Downloaded 15155200 of 34212021 bytes (44.3%,   31.1s remaining)    Downloaded 15695872 of 34212021 bytes (45.9%,   30.3s remaining)    Downloaded 16326656 of 34212021 bytes (47.7%,   29.3s remaining)    Downloaded 16719872 of 34212021 bytes (48.9%,   29.0s remaining)    Downloaded 17088512 of 34212021 bytes (49.9%,   28.8s remaining)    Downloaded 17522688 of 34212021 bytes (51.2%,   28.4s remaining)    Downloaded 17989632 of 34212021 bytes (52.6%,   27.8s remaining)    Downloaded 18464768 of 34212021 bytes (54.0%,   27.1s remaining)    Downloaded 18923520 of 34212021 bytes (55.3%,   26.5s remaining)    Downloaded 19456000 of 34212021 bytes (56.9%,   25.7s remaining)    Downloaded 20086784 of 34212021 bytes (58.7%,   24.5s remaining)    Downloaded 20832256 of 34212021 bytes (60.9%,   23.0s remaining)    Downloaded 21544960 of 34212021 bytes (63.0%,   21.7s remaining)    Downloaded 22077440 of 34212021 bytes (64.5%,   20.8s remaining)    Downloaded 22700032 of 34212021 bytes (66.4%,   19.7s remaining)    Downloaded 23420928 of 34212021 bytes (68.5%,   18.4s remaining)    Downloaded 24174592 of 34212021 bytes (70.7%,   17.0s remaining)    Downloaded 24731648 of 34212021 bytes (72.3%,   16.1s remaining)    Downloaded 25329664 of 34212021 bytes (74.0%,   15.1s remaining)    Downloaded 26034176 of 34212021 bytes (76.1%,   13.8s remaining)    Downloaded 26836992 of 34212021 bytes (78.4%,   12.4s remaining)    Downloaded 27729920 of 34212021 bytes (81.1%,   10.8s remaining)    Downloaded 28491776 of 34212021 bytes (83.3%,    9.5s remaining)    Downloaded 29097984 of 34212021 bytes (85.1%,    8.5s remaining)    Downloaded 29499392 of 34212021 bytes (86.2%,    7.8s remaining)    Downloaded 29990912 of 34212021 bytes (87.7%,    7.1s remaining)    Downloaded 30580736 of 34212021 bytes (89.4%,    6.1s remaining)    Downloaded 31236096 of 34212021 bytes (91.3%,    5.0s remaining)    Downloaded 31793152 of 34212021 bytes (92.9%,    4.0s remaining)    Downloaded 32317440 of 34212021 bytes (94.5%,    3.2s remaining)    Downloaded 32948224 of 34212021 bytes (96.3%,    2.1s remaining)    Downloaded 33677312 of 34212021 bytes (98.4%,    0.9s remaining) ...done. (58 seconds, 0 min)
+    Extracting data from /home/runner/work/nilearn/nilearn/nilearn_data/spm_auditory/sub001/MoAEpilot.zip..... done.
     /home/runner/work/nilearn/nilearn/nilearn_data/spm_auditory/sub001/fM00223/fM00223_004.img
     /home/runner/work/nilearn/nilearn/nilearn_data/spm_auditory/sub001/fM00223/fM00223_005.img
     /home/runner/work/nilearn/nilearn/nilearn_data/spm_auditory/sub001/fM00223/fM00223_006.img
@@ -129,7 +136,7 @@ We can display the first functional image and the subject's anatomy:
  .. code-block:: none
 
 
-    <nilearn.plotting.displays._slicers.OrthoSlicer object at 0x7f6e489dbbc0>
+    <nilearn.plotting.displays._slicers.OrthoSlicer object at 0x7f1bd45e35c0>
 
 
 
@@ -1264,9 +1271,9 @@ Oops, there is a lot of non-neural signal in there (ventricles, arteries)...
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** (0 minutes 16.005 seconds)
+   **Total running time of the script:** (1 minutes 14.764 seconds)
 
-**Estimated memory usage:**  276 MB
+**Estimated memory usage:**  271 MB
 
 
 .. _sphx_glr_download_auto_examples_00_tutorials_plot_single_subject_single_run.py:

diff --git a/dev/_sources/auto_examples/00_tutorials/sg_execution_times.rst.txt b/dev/_sources/auto_examples/00_tutorials/sg_execution_times.rst.txt
@@ -6,7 +6,7 @@
 
 Computation times
 =================
-**01:13.290** total execution time for 5 files **from auto_examples/00_tutorials**:
+**02:19.568** total execution time for 5 files **from auto_examples/00_tutorials**:
 
 .. container::
 
@@ -32,18 +32,18 @@ Computation times
    * - Example
      - Time
      - Mem (MB)
+   * - :ref:`sphx_glr_auto_examples_00_tutorials_plot_single_subject_single_run.py` (``plot_single_subject_single_run.py``)
+     - 01:14.764
+     - 271.2
    * - :ref:`sphx_glr_auto_examples_00_tutorials_plot_decoding_tutorial.py` (``plot_decoding_tutorial.py``)
-     - 00:35.424
-     - 903.4
+     - 00:39.826
+     - 904.6
    * - :ref:`sphx_glr_auto_examples_00_tutorials_plot_3d_and_4d_niimg.py` (``plot_3d_and_4d_niimg.py``)
-     - 00:17.731
-     - 213.1
-   * - :ref:`sphx_glr_auto_examples_00_tutorials_plot_single_subject_single_run.py` (``plot_single_subject_single_run.py``)
-     - 00:16.005
-     - 275.7
+     - 00:20.948
+     - 221.6
    * - :ref:`sphx_glr_auto_examples_00_tutorials_plot_nilearn_101.py` (``plot_nilearn_101.py``)
-     - 00:03.898
-     - 176.7
+     - 00:03.799
+     - 187.6
    * - :ref:`sphx_glr_auto_examples_00_tutorials_plot_python_101.py` (``plot_python_101.py``)
-     - 00:00.232
+     - 00:00.230
      - 9.8
diff --git a/dev/_sources/auto_examples/01_plotting/plot_3d_map_to_surface_projection.rst.txt b/dev/_sources/auto_examples/01_plotting/plot_3d_map_to_surface_projection.rst.txt
diff --git a/dev/_sources/auto_examples/01_plotting/plot_atlas.rst.txt b/dev/_sources/auto_examples/01_plotting/plot_atlas.rst.txt
@@ -52,6 +52,15 @@ Retrieving the atlas data
 
  .. code-block:: none
 
+
+    Dataset created in /home/runner/work/nilearn/nilearn/nilearn_data/fsl
+
+    Downloading data from https://www.nitrc.org/frs/download.php/9902/HarvardOxford.tgz ...
+     ...done. (1 seconds, 0 min)
+    Extracting data from /home/runner/work/nilearn/nilearn/nilearn_data/fsl/c4d84bbdf5c3325f23e304cdea1e9706/HarvardOxford.tgz..... done.
+    Downloading data from https://www.nitrc.org/frs/download.php/12096/Juelich.tgz ...
+     ...done. (0 seconds, 0 min)
+    Extracting data from /home/runner/work/nilearn/nilearn/nilearn_data/fsl/ab1b53038e13028e55f691a69003c208/Juelich.tgz..... done.
     Atlas ROIs are located at: /home/runner/work/nilearn/nilearn/nilearn_data/fsl/data/atlases/HarvardOxford/HarvardOxford-cort-maxprob-thr25-2mm.nii.gz
     Atlas ROIs are located at: /home/runner/work/nilearn/nilearn/nilearn_data/fsl/data/atlases/Juelich/Juelich-maxprob-thr0-1mm.nii.gz
 
@@ -86,7 +95,7 @@ Visualizing the Harvard-Oxford atlas
  .. code-block:: none
 
 
-    <nilearn.plotting.displays._slicers.OrthoSlicer object at 0x7f6e44137710>
+    <nilearn.plotting.displays._slicers.OrthoSlicer object at 0x7f1bd42ca300>
 
 
 
@@ -116,7 +125,7 @@ Visualizing the Juelich atlas
  .. code-block:: none
 
 
-    <nilearn.plotting.displays._slicers.OrthoSlicer object at 0x7f6e488feff0>
+    <nilearn.plotting.displays._slicers.OrthoSlicer object at 0x7f1bd59a8b30>
 
 
 
@@ -184,9 +193,9 @@ Visualizing the Juelich atlas with contours
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** (0 minutes 59.243 seconds)
+   **Total running time of the script:** (0 minutes 57.240 seconds)
 
-**Estimated memory usage:**  436 MB
+**Estimated memory usage:**  409 MB
 
 
 .. _sphx_glr_download_auto_examples_01_plotting_plot_atlas.py:

diff --git a/dev/_sources/auto_examples/01_plotting/plot_carpet.rst.txt b/dev/_sources/auto_examples/01_plotting/plot_carpet.rst.txt
@@ -206,9 +206,9 @@ Visualizing global patterns, separated by tissue type
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** (0 minutes 6.087 seconds)
+   **Total running time of the script:** (0 minutes 5.909 seconds)
 
-**Estimated memory usage:**  941 MB
+**Estimated memory usage:**  1000 MB
 
 
 .. _sphx_glr_download_auto_examples_01_plotting_plot_carpet.py:

diff --git a/dev/_sources/auto_examples/01_plotting/plot_colormaps.rst.txt b/dev/_sources/auto_examples/01_plotting/plot_colormaps.rst.txt
@@ -113,7 +113,7 @@ Plot matplotlib color maps
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** (0 minutes 2.956 seconds)
+   **Total running time of the script:** (0 minutes 2.910 seconds)
 
 **Estimated memory usage:**  18 MB
 

diff --git a/dev/_sources/auto_examples/01_plotting/plot_demo_glass_brain.rst.txt b/dev/_sources/auto_examples/01_plotting/plot_demo_glass_brain.rst.txt
@@ -72,7 +72,7 @@ Glass brain plotting: whole brain sagittal cuts
  .. code-block:: none
 
 
-    <nilearn.plotting.displays._projectors.OrthoProjector object at 0x7f6e3af834d0>
+    <nilearn.plotting.displays._projectors.OrthoProjector object at 0x7f1bd9c79160>
 
 
 
@@ -109,7 +109,7 @@ the z view (option "display_mode").
  .. code-block:: none
 
 
-    <nilearn.plotting.displays._projectors.XZProjector object at 0x7f6e4872f500>
+    <nilearn.plotting.displays._projectors.XZProjector object at 0x7f1bd5a39160>
 
 
 
@@ -146,7 +146,7 @@ Glass brain plotting: Hemispheric sagittal cuts
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** (0 minutes 3.340 seconds)
+   **Total running time of the script:** (0 minutes 3.199 seconds)
 
 **Estimated memory usage:**  15 MB
 

diff --git a/dev/_sources/auto_examples/01_plotting/plot_demo_glass_brain_extensive.rst.txt b/dev/_sources/auto_examples/01_plotting/plot_demo_glass_brain_extensive.rst.txt
@@ -104,7 +104,7 @@ a :class:`~nilearn.plotting.displays.OrthoProjector` is returned.
  .. code-block:: none
 
 
-    <nilearn.plotting.displays._projectors.OrthoProjector object at 0x7f6e48a37620>
+    <nilearn.plotting.displays._projectors.OrthoProjector object at 0x7f1bd44a0a40>
 
 
 
@@ -135,7 +135,7 @@ setting ``colorbar=True``.
  .. code-block:: none
 
 
-    <nilearn.plotting.displays._projectors.OrthoProjector object at 0x7f6e47d2a540>
+    <nilearn.plotting.displays._projectors.OrthoProjector object at 0x7f1bd44a35c0>
 
 
 
@@ -173,7 +173,7 @@ axial projections by setting ``display_mode='xz'``, which returns a
  .. code-block:: none
 
 
-    <nilearn.plotting.displays._projectors.XZProjector object at 0x7f6e548b0710>
+    <nilearn.plotting.displays._projectors.XZProjector object at 0x7f1bd998b4a0>
 
 
 
@@ -208,7 +208,7 @@ Additionally, we only visualize coronal and axial projections by setting
  .. code-block:: none
 
 
-    <nilearn.plotting.displays._projectors.YZProjector object at 0x7f6e387b26f0>
+    <nilearn.plotting.displays._projectors.YZProjector object at 0x7f1bd9561370>
 
 
 
@@ -240,7 +240,7 @@ Setting ``plot_abs=True`` and ``display_mode='yx'`` (returns a
  .. code-block:: none
 
 
-    <nilearn.plotting.displays._projectors.YXProjector object at 0x7f6e38734530>
+    <nilearn.plotting.displays._projectors.YXProjector object at 0x7f1be5c77b30>
 
 
 
@@ -282,7 +282,7 @@ colorbar will not be centered around zero.
  .. code-block:: none
 
 
-    <nilearn.plotting.displays._projectors.YZProjector object at 0x7f6e4889db20>
+    <nilearn.plotting.displays._projectors.YZProjector object at 0x7f1bd59aac60>
 
 
 
@@ -321,7 +321,7 @@ losing colours due to the thresholding.
  .. code-block:: none
 
 
-    <nilearn.plotting.displays._projectors.YZProjector object at 0x7f6e387b3e30>
+    <nilearn.plotting.displays._projectors.YZProjector object at 0x7f1bd95fe600>
 
 
 
@@ -365,7 +365,7 @@ enables an hemispheric sagittal view. The display object returned is then a
  .. code-block:: none
 
 
-    <nilearn.plotting.displays._projectors.LZRProjector object at 0x7f6e481486b0>
+    <nilearn.plotting.displays._projectors.LZRProjector object at 0x7f1bd4474650>
 
 
 
@@ -403,7 +403,7 @@ enables an hemispheric sagittal view. The display object returned is then a
  .. code-block:: none
 
 
-    <nilearn.plotting.displays._projectors.LYRZProjector object at 0x7f6e3aec1fd0>
+    <nilearn.plotting.displays._projectors.LYRZProjector object at 0x7f1bea7cd310>
 
 
 
@@ -446,7 +446,7 @@ If you are only interested in single projections, you can set
  .. code-block:: none
 
 
-    <nilearn.plotting.displays._projectors.XProjector object at 0x7f6e4871efc0>
+    <nilearn.plotting.displays._projectors.XProjector object at 0x7f1bd97bcec0>
 
 
 
@@ -830,7 +830,7 @@ Next, using the same display object, we plot positive sign of activation.
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** (0 minutes 27.074 seconds)
+   **Total running time of the script:** (0 minutes 25.834 seconds)
 
 **Estimated memory usage:**  9 MB