CircleCI update of dev docs (3214).

benchopt · Jul 12, 2024 · e937ffb · e937ffb
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diff --git a/_downloads/07fcc19ba03226cd3d83d4e40ec44385/auto_examples_python.zip b/_downloads/07fcc19ba03226cd3d83d4e40ec44385/auto_examples_python.zip
diff --git a/_downloads/6f1e7a639e0699d6164445b55e6c116d/auto_examples_jupyter.zip b/_downloads/6f1e7a639e0699d6164445b55e6c116d/auto_examples_jupyter.zip
diff --git a/_images/sphx_glr_plot_run_benchmark_001.png b/_images/sphx_glr_plot_run_benchmark_001.png
diff --git a/_images/sphx_glr_plot_run_benchmark_002.png b/_images/sphx_glr_plot_run_benchmark_002.png
diff --git a/_images/sphx_glr_plot_run_benchmark_003.png b/_images/sphx_glr_plot_run_benchmark_003.png
diff --git a/_images/sphx_glr_plot_run_benchmark_004.png b/_images/sphx_glr_plot_run_benchmark_004.png
diff --git a/_images/sphx_glr_plot_run_benchmark_005.png b/_images/sphx_glr_plot_run_benchmark_005.png
diff --git a/_images/sphx_glr_plot_run_benchmark_python_R_001.png b/_images/sphx_glr_plot_run_benchmark_python_R_001.png
diff --git a/_images/sphx_glr_plot_run_benchmark_python_R_002.png b/_images/sphx_glr_plot_run_benchmark_python_R_002.png
diff --git a/_images/sphx_glr_plot_run_benchmark_python_R_003.png b/_images/sphx_glr_plot_run_benchmark_python_R_003.png
diff --git a/_images/sphx_glr_plot_run_benchmark_python_R_004.png b/_images/sphx_glr_plot_run_benchmark_python_R_004.png
diff --git a/_images/sphx_glr_plot_run_benchmark_python_R_005.png b/_images/sphx_glr_plot_run_benchmark_python_R_005.png
diff --git a/_images/sphx_glr_plot_run_benchmark_python_R_006.png b/_images/sphx_glr_plot_run_benchmark_python_R_006.png
diff --git a/_images/sphx_glr_plot_run_benchmark_python_R_thumb.png b/_images/sphx_glr_plot_run_benchmark_python_R_thumb.png
diff --git a/_images/sphx_glr_plot_run_benchmark_thumb.png b/_images/sphx_glr_plot_run_benchmark_thumb.png
diff --git a/_sources/auto_examples/plot_run_benchmark.rst b/_sources/auto_examples/plot_run_benchmark.rst
@@ -78,7 +78,7 @@ Run benchmark from a script
         |--sklearn: not installed
         |--sklearn: not installed
         |--Lightning: initialization (1 / 15 reps)        |--Lightning:   0.0% (1 / 15 reps)        |--Lightning:   1.0% (1 / 15 reps)        |--Lightning:   2.0% (1 / 15 reps)        |--Lightning:   3.0% (1 / 15 reps)        |--Lightning:  16.2% (1 / 15 reps)        |--Lightning:  21.3% (1 / 15 reps)        |--Lightning:  25.4% (1 / 15 reps)        |--Lightning:  28.8% (1 / 15 reps)        |--Lightning:  35.8% (1 / 15 reps)        |--Lightning:  43.2% (1 / 15 reps)        |--Lightning:  50.9% (1 / 15 reps)        |--Lightning:  61.6% (1 / 15 reps)        |--Lightning:  76.9% (1 / 15 reps)        |--Lightning: initialization (2 / 15 reps)        |--Lightning:   0.0% (2 / 15 reps)        |--Lightning:   1.0% (2 / 15 reps)        |--Lightning:   2.0% (2 / 15 reps)        |--Lightning:   3.0% (2 / 15 reps)        |--Lightning:  16.2% (2 / 15 reps)        |--Lightning:  21.3% (2 / 15 reps)        |--Lightning:  25.4% (2 / 15 reps)        |--Lightning:  28.8% (2 / 15 reps)        |--Lightning:  35.8% (2 / 15 reps)        |--Lightning:  43.2% (2 / 15 reps)        |--Lightning:  50.9% (2 / 15 reps)        |--Lightning:  61.6% (2 / 15 reps)        |--Lightning:  76.9% (2 / 15 reps)        |--Lightning: initialization (3 / 15 reps)        |--Lightning:   0.0% (3 / 15 reps)        |--Lightning:   1.0% (3 / 15 reps)        |--Lightning:   2.0% (3 / 15 reps)        |--Lightning:   3.0% (3 / 15 reps)        |--Lightning:  16.2% (3 / 15 reps)        |--Lightning:  21.3% (3 / 15 reps)        |--Lightning:  25.4% (3 / 15 reps)        |--Lightning:  28.8% (3 / 15 reps)        |--Lightning:  35.8% (3 / 15 reps)        |--Lightning:  43.2% (3 / 15 reps)        |--Lightning:  50.9% (3 / 15 reps)        |--Lightning:  61.6% (3 / 15 reps)        |--Lightning:  76.9% (3 / 15 reps)        |--Lightning: initialization (4 / 15 reps)        |--Lightning:   0.0% (4 / 15 reps)        |--Lightning:   1.0% (4 / 15 reps)        |--Lightning:   2.0% (4 / 15 reps)        |--Lightning:   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|--Lightning: initialization (6 / 15 reps)        |--Lightning:   0.0% (6 / 15 reps)        |--Lightning:   1.0% (6 / 15 reps)        |--Lightning:   2.0% (6 / 15 reps)        |--Lightning:   3.0% (6 / 15 reps)        |--Lightning:  16.2% (6 / 15 reps)        |--Lightning:  21.3% (6 / 15 reps)        |--Lightning:  25.4% (6 / 15 reps)        |--Lightning:  28.8% (6 / 15 reps)        |--Lightning:  35.8% (6 / 15 reps)        |--Lightning:  43.2% (6 / 15 reps)        |--Lightning:  50.9% (6 / 15 reps)        |--Lightning:  61.6% (6 / 15 reps)        |--Lightning:  76.9% (6 / 15 reps)        |--Lightning: initialization (7 / 15 reps)        |--Lightning:   0.0% (7 / 15 reps)        |--Lightning:   1.0% (7 / 15 reps)        |--Lightning:   2.0% (7 / 15 reps)        |--Lightning:   3.0% (7 / 15 reps)        |--Lightning:  16.2% (7 / 15 reps)        |--Lightning:  21.3% (7 / 15 reps)        |--Lightning:  25.4% (7 / 15 reps)        |--Lightning:  28.8% (7 / 15 reps)        |--Lightning:  35.8% (7 / 15 reps)        |--Lightning:  43.2% (7 / 15 reps)        |--Lightning:  50.9% (7 / 15 reps)        |--Lightning:  61.6% (7 / 15 reps)        |--Lightning:  76.9% (7 / 15 reps)        |--Lightning: initialization (8 / 15 reps)        |--Lightning:   0.0% (8 / 15 reps)        |--Lightning:   1.0% (8 / 15 reps)        |--Lightning:   2.0% (8 / 15 reps)        |--Lightning:   3.0% (8 / 15 reps)        |--Lightning:  16.2% (8 / 15 reps)        |--Lightning:  21.3% (8 / 15 reps)        |--Lightning:  25.4% (8 / 15 reps)        |--Lightning:  28.8% (8 / 15 reps)        |--Lightning:  35.8% (8 / 15 reps)        |--Lightning:  43.2% (8 / 15 reps)        |--Lightning:  50.9% (8 / 15 reps)        |--Lightning:  61.6% (8 / 15 reps)        |--Lightning:  76.9% (8 / 15 reps)        |--Lightning: initialization (9 / 15 reps)        |--Lightning:   0.0% (9 / 15 reps)        |--Lightning:   1.0% (9 / 15 reps)        |--Lightning:   2.0% (9 / 15 reps)        |--Lightning:   3.0% (9 / 15 reps)        |--Lightning:  16.2% (9 / 15 reps)        |--Lightning:  21.3% (9 / 15 reps)        |--Lightning:  25.4% (9 / 15 reps)        |--Lightning:  28.8% (9 / 15 reps)        |--Lightning:  35.8% (9 / 15 reps)        |--Lightning:  43.2% (9 / 15 reps)        |--Lightning:  50.9% (9 / 15 reps)        |--Lightning:  61.6% (9 / 15 reps)        |--Lightning:  76.9% (9 / 15 reps)        |--Lightning: initialization (10 / 15 reps)        |--Lightning:   0.0% (10 / 15 reps)        |--Lightning:   1.0% (10 / 15 reps)        |--Lightning:   2.0% (10 / 15 reps)        |--Lightning:   3.0% (10 / 15 reps)        |--Lightning:  16.2% (10 / 15 reps)        |--Lightning:  21.3% (10 / 15 reps)        |--Lightning:  25.4% (10 / 15 reps)        |--Lightning:  28.8% (10 / 15 reps)        |--Lightning:  35.8% (10 / 15 reps)        |--Lightning:  43.2% (10 / 15 reps)        |--Lightning:  50.9% (10 / 15 reps)        |--Lightning:  61.6% (10 / 15 reps)        |--Lightning:  76.9% (10 / 15 reps)        |--Lightning: initialization (11 / 15 reps)        |--Lightning:   0.0% (11 / 15 reps)        |--Lightning:   1.0% (11 / 15 reps)        |--Lightning:   2.0% (11 / 15 reps)        |--Lightning:   3.0% (11 / 15 reps)        |--Lightning:  16.2% (11 / 15 reps)        |--Lightning:  21.3% (11 / 15 reps)        |--Lightning:  25.4% (11 / 15 reps)        |--Lightning:  28.8% (11 / 15 reps)        |--Lightning:  35.8% (11 / 15 reps)        |--Lightning:  43.2% (11 / 15 reps)        |--Lightning:  50.9% (11 / 15 reps)        |--Lightning:  61.6% (11 / 15 reps)        |--Lightning:  76.9% (11 / 15 reps)        |--Lightning: initialization (12 / 15 reps)        |--Lightning:   0.0% (12 / 15 reps)        |--Lightning:   1.0% (12 / 15 reps)        |--Lightning:   2.0% (12 / 15 reps)        |--Lightning:   3.0% (12 / 15 reps)        |--Lightning:  16.2% (12 / 15 reps)        |--Lightning:  21.3% (12 / 15 reps)        |--Lightning:  25.4% (12 / 15 reps)        |--Lightning:  28.8% (12 / 15 reps)        |--Lightning:  35.8% (12 / 15 reps)        |--Lightning:  43.2% (12 / 15 reps)        |--Lightning:  50.9% (12 / 15 reps)        |--Lightning:  61.6% (12 / 15 reps)        |--Lightning:  76.9% (12 / 15 reps)        |--Lightning: initialization (13 / 15 reps)        |--Lightning:   0.0% (13 / 15 reps)        |--Lightning:   1.0% (13 / 15 reps)        |--Lightning:   2.0% (13 / 15 reps)        |--Lightning:   3.0% (13 / 15 reps)        |--Lightning:  16.2% (13 / 15 reps)        |--Lightning:  21.3% (13 / 15 reps)        |--Lightning:  25.4% (13 / 15 reps)        |--Lightning:  28.8% (13 / 15 reps)        |--Lightning:  35.8% (13 / 15 reps)        |--Lightning:  43.2% (13 / 15 reps)        |--Lightning:  50.9% (13 / 15 reps)        |--Lightning:  61.6% (13 / 15 reps)        |--Lightning:  76.9% (13 / 15 reps)        |--Lightning: initialization (14 / 15 reps)        |--Lightning:   0.0% (14 / 15 reps)        |--Lightning:   1.0% (14 / 15 reps)        |--Lightning:   2.0% (14 / 15 reps)        |--Lightning:   3.0% (14 / 15 reps)        |--Lightning:  16.2% (14 / 15 reps)        |--Lightning:  21.3% (14 / 15 reps)        |--Lightning:  25.4% (14 / 15 reps)        |--Lightning:  28.8% (14 / 15 reps)        |--Lightning:  35.8% (14 / 15 reps)        |--Lightning:  43.2% (14 / 15 reps)        |--Lightning:  50.9% (14 / 15 reps)        |--Lightning:  61.6% (14 / 15 reps)        |--Lightning:  76.9% (14 / 15 reps)        |--Lightning: initialization (15 / 15 reps)        |--Lightning:   0.0% (15 / 15 reps)        |--Lightning:   1.0% (15 / 15 reps)        |--Lightning:   2.0% (15 / 15 reps)        |--Lightning:   3.0% (15 / 15 reps)        |--Lightning:  16.2% (15 / 15 reps)        |--Lightning:  21.3% (15 / 15 reps)        |--Lightning:  25.4% (15 / 15 reps)        |--Lightning:  28.8% (15 / 15 reps)        |--Lightning:  35.8% (15 / 15 reps)        |--Lightning:  43.2% (15 / 15 reps)        |--Lightning:  50.9% (15 / 15 reps)        |--Lightning:  61.6% (15 / 15 reps)        |--Lightning:  76.9% (15 / 15 reps)        |--Lightning: done (timeout)
-    Saving result in: /home/circleci/project/benchmarks/benchmark_logreg_l2/outputs/benchopt_run_2024-07-12_12h33m32.parquet
+    Saving result in: /home/circleci/project/benchmarks/benchmark_logreg_l2/outputs/benchopt_run_2024-07-12_13h34m20.parquet
     Save objective_curve plot of objective_value for Simulated[n_features=500,n_samples=200] and L2 Logistic Regression[lmbd=1.0] as: /home/circleci/project/benchmarks/benchmark_logreg_l2/outputs/9348ade1e8f5682bfd9864f3fd1919ae_objective_value_objective_curve.pdf
     Save objective_curve plot of objective_Test loss for Simulated[n_features=500,n_samples=200] and L2 Logistic Regression[lmbd=1.0] as: /home/circleci/project/benchmarks/benchmark_logreg_l2/outputs/9348ade1e8f5682bfd9864f3fd1919ae_objective_Test loss_objective_curve.pdf
     Save suboptimality_curve plot of objective_value for Simulated[n_features=500,n_samples=200] and L2 Logistic Regression[lmbd=1.0] as: /home/circleci/project/benchmarks/benchmark_logreg_l2/outputs/9348ade1e8f5682bfd9864f3fd1919ae_objective_value_suboptimality_curve.pdf
@@ -137,7 +137,7 @@ Run benchmark from a script
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** (0 minutes 26.665 seconds)
+   **Total running time of the script:** (0 minutes 27.741 seconds)
 
 
 .. _sphx_glr_download_auto_examples_plot_run_benchmark.py:

diff --git a/_sources/auto_examples/plot_run_benchmark_python_R.rst b/_sources/auto_examples/plot_run_benchmark_python_R.rst
@@ -80,7 +80,7 @@ Demo benchmark with R/Python
       |--Lasso Regression[fit_intercept=False,reg=0.5]
         |--Python-PGD[use_acceleration=False]: done
         |--R-PGD: done (timeout)
-    Saving result in: /home/circleci/project/benchmarks/benchmark_lasso/outputs/benchopt_run_2024-07-12_12h33m04.parquet
+    Saving result in: /home/circleci/project/benchmarks/benchmark_lasso/outputs/benchopt_run_2024-07-12_13h33m51.parquet
     Save objective_curve plot of objective_value for Simulated[n_features=5000,n_samples=100,rho=0] and Lasso Regression[fit_intercept=False,reg=0.5] as: /home/circleci/project/benchmarks/benchmark_lasso/outputs/3ebdde1738d5255ff1b6b4a7ea598289_objective_value_objective_curve.pdf
     Save objective_curve plot of objective_support_size for Simulated[n_features=5000,n_samples=100,rho=0] and Lasso Regression[fit_intercept=False,reg=0.5] as: /home/circleci/project/benchmarks/benchmark_lasso/outputs/3ebdde1738d5255ff1b6b4a7ea598289_objective_support_size_objective_curve.pdf
     Save objective_curve plot of objective_duality_gap for Simulated[n_features=5000,n_samples=100,rho=0] and Lasso Regression[fit_intercept=False,reg=0.5] as: /home/circleci/project/benchmarks/benchmark_lasso/outputs/3ebdde1738d5255ff1b6b4a7ea598289_objective_duality_gap_objective_curve.pdf
@@ -137,7 +137,7 @@ Demo benchmark with R/Python
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** (2 minutes 5.532 seconds)
+   **Total running time of the script:** (2 minutes 12.575 seconds)
 
 
 .. _sphx_glr_download_auto_examples_plot_run_benchmark_python_R.py:

diff --git a/_sources/auto_examples/sg_execution_times.rst b/_sources/auto_examples/sg_execution_times.rst
@@ -6,7 +6,7 @@
 
 Computation times
 =================
-**02:32.198** total execution time for 2 files **from auto_examples**:
+**02:40.316** total execution time for 2 files **from auto_examples**:
 
 .. container::
 
@@ -33,8 +33,8 @@ Computation times
      - Time
      - Mem (MB)
    * - :ref:`sphx_glr_auto_examples_plot_run_benchmark_python_R.py` (``plot_run_benchmark_python_R.py``)
-     - 02:05.532
+     - 02:12.575
      - 0.0
    * - :ref:`sphx_glr_auto_examples_plot_run_benchmark.py` (``plot_run_benchmark.py``)
-     - 00:26.665
+     - 00:27.741
      - 0.0
diff --git a/_sources/benchmark_workflow/config_benchopt.rst b/_sources/benchmark_workflow/config_benchopt.rst
@@ -10,7 +10,7 @@ There are two configuration levels. The first level is the global config for the
 
 To get the BenchOpt global config file used by the benchopt command, you can run ``benchopt config``. Using the option ``--benchmark,-b <benchmark>`` allows to display the config file for a specific benchmark. See :ref:`config_file` for more details on how the config file path is resolved.
 
-The structure of the files follows the Microsoft Windows INI files structure and is described in :ref:`config_structure`. The available settings are listed in :ref:`config_settings`.
+The structure of the files follows the Yaml files structure and is described in :ref:`config_structure`. The available settings are listed in :ref:`config_settings`.
 
 The value of each setting can be accessed with the CLI using ``benchopt config [-b <benchmark>] get <name>``. Similarly, the setting value can be set using ``benchopt config [-b <benchmark>] set <name> <value>``.
 
@@ -22,34 +22,37 @@ Config File Location
 For the global configuration file, the resolution order is the following:
 
 1. The environment variable ``BENCHOPT_CONFIG`` is set to an existing file,
-2. A file ``benchopt.ini`` in the current directory,
-3. The default file is ``$HOME/.config/benchopt.ini``.
+2. A file ``benchopt.yml`` in the current directory,
+3. The default file is ``$HOME/.config/benchopt.yml``.
 
-For benchmark configuration files, they are usually located in the benchmark folder, and named ``benchopt.ini``. If it does not exist, the default is to use the global config file.
+For benchmark configuration files, they are usually located in the benchmark folder, and named ``benchopt.yml``. If it does not exist, the default is to use the global config file.
 
 .. _config_structure:
 
 Config File Structure
 ---------------------
 
-The config files for benchopt follow the Microsoft Windows INI files structure. The global settings are grouped in a ``[benchopt]`` section:
+The config files for benchopt follow the YAML files structure:
 
-.. code-block:: ini
+.. code-block:: yml
 
-    [benchopt]
-    debug = true  # Activate or not debug logs
-    raise_install_error = no  # Raise/ignore install error. Default is ignore.
-    github_token = 0...0  # Token used to publish results on benchopt/results
+    debug: true  # Activate or not debug logs. Default is false.
+    conda_cmd: mamba  # Command to use to install packages. Default is conda.
+    github_token: 0...0  # Token used to publish results on benchopt/results
 
 For benchmark settings, they are grouped in a section with the same name as the benchmark. For a benchmark named ``benchmark_bench``, the config structure is:
 
-.. code-block:: ini
+.. code-block:: yml
 
-    [benchmark_bench]
-    plots =
-        suboptimality_curve
-        bar_chart
-        objective_curve
+    benchmark_bench:
+        plots:
+            - suboptimality_curve
+            - bar_chart
+            - objective_curve
+        data_paths:
+            imagenet: /path/to/imagenet
+
+Note that specific benchmark config can also be set into the config file of the benchmark, located in the benchmark folder. The global config file is used as a fallback if the benchmark config file does not exist.
 
 
 .. _config_settings:

diff --git a/_sources/sg_execution_times.rst b/_sources/sg_execution_times.rst
@@ -6,7 +6,7 @@
 
 Computation times
 =================
-**02:32.198** total execution time for 2 files **from all galleries**:
+**02:40.316** total execution time for 2 files **from all galleries**:
 
 .. container::
 
@@ -33,8 +33,8 @@ Computation times
      - Time
      - Mem (MB)
    * - :ref:`sphx_glr_auto_examples_plot_run_benchmark_python_R.py` (``../examples/plot_run_benchmark_python_R.py``)
-     - 02:05.532
+     - 02:12.575
      - 0.0
    * - :ref:`sphx_glr_auto_examples_plot_run_benchmark.py` (``../examples/plot_run_benchmark.py``)
-     - 00:26.665
+     - 00:27.741
      - 0.0
diff --git a/_sources/whats_new.rst b/_sources/whats_new.rst
@@ -13,8 +13,9 @@ Version 1.6 - In development
 API
 ~~~
 
-- Add a `save_final_results` method to Objective. If implemented it is run after the last solver iteration, to get desired outputs to be saved to file system.
-  By `Pierre-Antoine Comby`_ (:gh:`722`)
+- Add a `save_final_results` method to Objective. If implemented it is run
+  after the last solver iteration, to get desired outputs to be saved to file
+  system. By `Pierre-Antoine Comby`_ (:gh:`722`)
 
 - Add native way to do cross-validation in a benchmark with
   ``Objective.cv`` attribute that change split for each repetition.
@@ -24,7 +25,8 @@ API
   potentially non-trivial structures (like dictionaries).
   By `Thomas Moreau`_ (:gh:`706`).
 
-- Raise error when an invalid install_cmd is provided. By `Jad Yehya` (:gh:`714`).
+- Raise error when an invalid install_cmd is provided.
+  By `Jad Yehya` (:gh:`714`).
 
 CLI
 ~~~
@@ -38,6 +40,9 @@ CLI
 - Add ``--no-timeout`` option in ``benchopt run`` to allow solvers to bypass
   timeout. By `Célestin Eve`_ (:gh:`725`)
 
+- Remove support for deprecated ``.ini`` config files. All config files should
+  now use the ``yaml`` format. By `Thomas Moreau`_ (:gh:`699`)
+
 FIX
 ~~~
 

diff --git a/_static/documentation_options.js b/_static/documentation_options.js
@@ -1,5 +1,5 @@
 const DOCUMENTATION_OPTIONS = {
-    VERSION: '1.5.2.dev54',
+    VERSION: '1.5.2.dev55',
     LANGUAGE: 'en',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',

diff --git a/auto_examples/index.html b/auto_examples/index.html
@@ -8,7 +8,7 @@
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
-    <title>Examples Gallery &#8212; benchopt 1.5.2.dev54 documentation</title>
+    <title>Examples Gallery &#8212; benchopt 1.5.2.dev55 documentation</title>
 
 
 
@@ -43,7 +43,7 @@
 <link rel="preload" as="script" href="../_static/scripts/pydata-sphinx-theme.js?digest=dfe6caa3a7d634c4db9b" />
   <script src="../_static/vendor/fontawesome/6.5.2/js/all.min.js?digest=dfe6caa3a7d634c4db9b"></script>
 
-    <script src="../_static/documentation_options.js?v=6a4a99ec"></script>
+    <script src="../_static/documentation_options.js?v=d1b61bf1"></script>
     <script src="../_static/doctools.js?v=9a2dae69"></script>
     <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../_static/clipboard.min.js?v=a7894cd8"></script>
@@ -151,7 +151,7 @@
     <script>document.write(`<img src="../_static/logo_benchopt.png" class="logo__image only-dark" alt="benchopt logo"/>`);</script>
 
 
-    <p class="title logo__title">1.5.2.dev54</p>
+    <p class="title logo__title">1.5.2.dev55</p>
 
 </a></div>
         <div class="sidebar-primary-item">