Add new notebooks (#61)

Author: dirmeier

docs/_static/theme.css

@@ -35,7 +35,7 @@ h1 {
     margin-bottom: 50px;
 }
 h3, h2, h1 {
-    font-weight: 300 !important;
+
 }
 
 nav > li > a > code.literal {

docs/index.rst

@@ -110,12 +110,10 @@ License
     :maxdepth: 1
     :hidden:
 
-    Getting started <notebooks/introduction>
-    SBI with sbijax <notebooks/sbi_with_sbijax>
-    Neural networks <notebooks/neural_networks>
-    Density estimators <notebooks/density_estimators>
-    High-dimensional inference <notebooks/high_dimensional_inference>
-    Figure styling <notebooks/figure_styling>
+    Getting started <notebooks/getting_started>
+    A more detailed intro  <notebooks/more_detailed_intro>
+    Examples <notebooks/examples>
+    Inference using EEG data  <notebooks/eeg_data_example>
 
 ..  toctree::
     :caption: 🚀 Examples

docs/notebooks/density_estimators.ipynb

@@ -29,7 +29,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.15"
+   "version": "3.11.9"
   }
  },
  "nbformat": 4,

…mental_code/chp5-real_data_example.ipynb docs/notebooks/eeg_data_example.ipynbmanuscript+supplement/experimental_code/chp5-real_data_example.ipynb renamed to docs/notebooks/eeg_data_example.ipynb manuscript+supplement/experimental_code/chp5-real_data_example.ipynb renamed to docs/notebooks/eeg_data_example.ipynb

@@ -216,9 +216,6 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "if not os.path.exists(\"figs\"):\n",
-    "    os.mkdir(\"figs\")\n",
-    "\n",
     "color_closed = \"#700e01\"\n",
     "color_open = \"#c79999\""
    ]
@@ -275,8 +272,7 @@
     "    laxes[1].spines['left'].set_color('black')\n",
     "    laxes[1].set_xlabel(\"Time\", fontsize=18)\n",
     "    laxes[0].set_ylabel(\"Amplitude\", fontsize=18)\n",
-    "    laxes[0].yaxis.set_label_coords(-0.1, -0.1)    \n",
-    "    plt.savefig(\"figs/real_data-data.pdf\", dpi=200)\n",
+    "    laxes[0].yaxis.set_label_coords(-0.1, -0.1)        \n",
     "    plt.show()\n",
     "\n",
     "with plt.style.context(\"sbijax\"):\n",
@@ -291,8 +287,7 @@
     "    raxes.set_xlabel(\"Frequency [Hz]\", fontsize=18)\n",
     "    raxes.set_ylabel(\"Power spectral density [dB]\", fontsize=18)\n",
     "    raxes.legend(frameon=False, fontsize=18)\n",
-    "    raxes.grid(linewidth=0.5)\n",
-    "    plt.savefig(\"figs/real_data-periodogram.pdf\", dpi=200)\n",
+    "    raxes.grid(linewidth=0.5)    \n",
     "    plt.show()"
    ]
   },
@@ -365,7 +360,6 @@
     "    raxes.legend(frameon=False, fontsize=18)\n",
     "    raxes.grid(linewidth=0.5)\n",
     "    raxes.tick_params(axis='both',labelsize=13)\n",
-    "plt.savefig(\"figs/real_data-all_data.pdf\", dpi=200)\n",
     "plt.show()"
    ]
   },
@@ -864,7 +858,6 @@
     "    fontsize=15,\n",
     "    title_fontsize=16\n",
     ")\n",
-    "plt.savefig(\"figs/real_data-real_data_posteriors.pdf\", dpi=200)\n",
     "plt.show()"
    ]
   },
@@ -938,7 +931,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.7"
+   "version": "3.11.9"
   }
  },
  "nbformat": 4,

…nt/experimental_code/chp4-examples.ipynb docs/notebooks/examples.ipynbmanuscript+supplement/experimental_code/chp4-examples.ipynb renamed to docs/notebooks/examples.ipynb manuscript+supplement/experimental_code/chp4-examples.ipynb renamed to docs/notebooks/examples.ipynb

@@ -7,7 +7,7 @@
    "source": [
     "# Examples\n",
     "\n",
-    "Here we implement the models given in the `Examples` section."
+    "In the following, we demonstrate several `sbijax` methods using the complex \"Simple Liklelihood Complex Posterior\" model."
    ]
   },
   {
@@ -47,9 +47,7 @@
    "outputs": [],
    "source": [
     "import warnings\n",
-    "warnings.filterwarnings(\"ignore\")\n",
-    "\n",
-    "if not os.path.exists(\"figs\"): os.mkdir(\"figs\")"
+    "warnings.filterwarnings(\"ignore\")"
    ]
   },
   {
@@ -345,7 +343,6 @@
     "    ax.yaxis.label.set_size(20)\n",
     "    ax.tick_params(axis='both',labelsize=13)\n",
     "plt.tight_layout()\n",
-    "plt.savefig(\"./figs/example-rhat_ress-slice.pdf\", dpi=200)\n",
     "plt.show()"
    ]
   },
@@ -418,7 +415,6 @@
     "\n",
     "plot_ess_and_trace(slice_inference_data)\n",
     "plt.tight_layout()\n",
-    "plt.savefig(\"./figs/example-triple_plot-slice.pdf\", dpi=200)\n",
     "plt.show()"
    ]
   },
@@ -442,7 +438,6 @@
    "source": [
     "plot_posteriors(slice_samples.reshape(-1, 5))\n",
     "plt.tight_layout()\n",
-    "plt.savefig(\"./figs/example-pair_plot-slice.pdf\", dpi=200)\n",
     "plt.show()"
    ]
   },
@@ -562,7 +557,6 @@
     "    inference_data_as_dictionary(snle_inference_results.posterior)[\"theta\"],\n",
     ")\n",
     "plt.tight_layout()\n",
-    "plt.savefig(\"./figs/example-pair_plot-snle.pdf\", dpi=200)\n",
     "plt.show()"
    ]
   },
@@ -664,7 +658,6 @@
     "    inference_data_as_dictionary(fmpe_inference_results.posterior)[\"theta\"],\n",
     ")\n",
     "plt.tight_layout()\n",
-    "plt.savefig(\"./figs/example-pair_plot-fmpe.pdf\", dpi=200)\n",
     "plt.show()"
    ]
   },
@@ -780,7 +773,6 @@
     "    inference_data_as_dictionary(smc_inference_results.posterior)[\"theta\"],\n",
     ")\n",
     "plt.tight_layout()\n",
-    "plt.savefig(\"./figs/example-pair_plot-smc.pdf\", dpi=200)\n",
     "plt.show()"
    ]
   },
@@ -852,7 +844,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.7"
+   "version": "3.11.9"
   }
  },
  "nbformat": 4,

docs/notebooks/figure_styling.ipynb

@@ -356,7 +356,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.15"
+   "version": "3.11.9"
   }
  },
  "nbformat": 4,