add small intro text to notebooks

meom-group · Oct 27, 2023 · a93e999 · a93e999
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diff --git a/docs/alboran.sea.rst → docs/alboran_sea.rst b/docs/alboran.sea.rst → docs/alboran_sea.rst
diff --git a/docs/gaussian.eddy.rst → docs/gaussian_eddy.rst b/docs/gaussian.eddy.rst → docs/gaussian_eddy.rst
diff --git a/docs/notebooks.rst b/docs/notebooks.rst
@@ -7,5 +7,5 @@ Notebooks
 .. toctree::
    :maxdepth: 2
 
-   gaussian.eddy
-   alboran.sea
+   gaussian_eddy
+   alboran_sea
diff --git a/notebooks/README.md b/notebooks/README.md
@@ -0,0 +1,5 @@
+# Notebooks
+
+We designed two notebooks, one with the extremely idealised scenario of a [gaussian eddy](gaussian_eddy), and a realistic one focusing on the [Alboran sea](alboran_sea) area.
+
+The goal is both to showcase step-by-step how **jaxparrow** can be used, and to demonstrate the interest of the variational approach we propose.
diff --git a/notebooks/alboran_sea.ipynb b/notebooks/alboran_sea.ipynb
@@ -35,6 +35,8 @@
     "# Input data\n",
     "\n",
     "In this example, we use NEMO model outputs (SSH and velocities), stored in several netCDF files.\n",
+    "Data can be downloaded [here](https://1drv.ms/f/s!Aq7KsFIdmDGepjMT6o77ko-JRRZu?e=hpxeKa), and the files stored inside the `data` folder.\n",
+    "\n",
     "Measurements are located on a C-grid."
    ]
   },
@@ -47,10 +49,7 @@
      "end_time": "2023-10-24T15:29:58.268892996Z",
      "start_time": "2023-10-24T15:29:58.267384387Z"
     },
-    "collapsed": false,
-    "jupyter": {
-     "outputs_hidden": false
-    }
+    "collapsed": false
    },
    "outputs": [],
    "source": [
@@ -66,10 +65,7 @@
    "cell_type": "markdown",
    "id": "31e2b1b4fab206a6",
    "metadata": {
-    "collapsed": false,
-    "jupyter": {
-     "outputs_hidden": false
-    }
+    "collapsed": false
    },
    "source": [
     "#### Alboran sea\n",
@@ -86,10 +82,7 @@
      "end_time": "2023-10-24T15:29:58.269079811Z",
      "start_time": "2023-10-24T15:29:58.267613107Z"
     },
-    "collapsed": false,
-    "jupyter": {
-     "outputs_hidden": false
-    }
+    "collapsed": false
    },
    "outputs": [],
    "source": [
@@ -108,10 +101,7 @@
      "end_time": "2023-10-24T15:29:59.594187826Z",
      "start_time": "2023-10-24T15:29:58.267788417Z"
     },
-    "collapsed": false,
-    "jupyter": {
-     "outputs_hidden": false
-    }
+    "collapsed": false
    },
    "outputs": [],
    "source": [
@@ -156,10 +146,7 @@
    "cell_type": "markdown",
    "id": "1fb1398a5dd8780a",
    "metadata": {
-    "collapsed": false,
-    "jupyter": {
-     "outputs_hidden": false
-    }
+    "collapsed": false
    },
    "source": [
     "We use `masked_array` to restrict the domain to the marine area."
@@ -299,10 +286,7 @@
    "cell_type": "markdown",
    "id": "c8946c6e757a7b15",
    "metadata": {
-    "collapsed": false,
-    "jupyter": {
-     "outputs_hidden": false
-    }
+    "collapsed": false
    },
    "source": [
     "#### Coriolis factor\n",
@@ -388,10 +372,7 @@
      "end_time": "2023-10-24T15:30:01.431995140Z",
      "start_time": "2023-10-24T15:30:00.348815810Z"
     },
-    "collapsed": false,
-    "jupyter": {
-     "outputs_hidden": false
-    }
+    "collapsed": false
    },
    "outputs": [
     {
@@ -465,10 +446,7 @@
    "cell_type": "markdown",
    "id": "c46f9e2e",
    "metadata": {
-    "collapsed": false,
-    "jupyter": {
-     "outputs_hidden": false
-    }
+    "collapsed": false
    },
    "source": [
     "# Cyclogeostrophic balance"
@@ -530,10 +508,7 @@
    "cell_type": "markdown",
    "id": "d3e2c5e5e0da2dea",
    "metadata": {
-    "collapsed": false,
-    "jupyter": {
-     "outputs_hidden": false
-    }
+    "collapsed": false
    },
    "source": [
     "#### Comparison to NEMO's velocities"
@@ -548,10 +523,7 @@
      "end_time": "2023-10-24T15:30:06.300383524Z",
      "start_time": "2023-10-24T15:30:05.259525231Z"
     },
-    "collapsed": false,
-    "jupyter": {
-     "outputs_hidden": false
-    }
+    "collapsed": false
    },
    "outputs": [
     {
@@ -664,10 +636,7 @@
      "end_time": "2023-10-24T15:30:06.831692322Z",
      "start_time": "2023-10-24T15:30:06.789372115Z"
     },
-    "collapsed": false,
-    "jupyter": {
-     "outputs_hidden": false
-    }
+    "collapsed": false
    },
    "outputs": [],
    "source": [
@@ -679,10 +648,7 @@
    "cell_type": "markdown",
    "id": "eb3c62eac7e2b973",
    "metadata": {
-    "collapsed": false,
-    "jupyter": {
-     "outputs_hidden": false
-    }
+    "collapsed": false
    },
    "source": [
     "#### Comparison to NEMO's velocities"
@@ -697,10 +663,7 @@
      "end_time": "2023-10-24T15:30:07.967620399Z",
      "start_time": "2023-10-24T15:30:06.831499573Z"
     },
-    "collapsed": false,
-    "jupyter": {
-     "outputs_hidden": false
-    }
+    "collapsed": false
    },
    "outputs": [
     {
@@ -762,10 +725,7 @@
    "cell_type": "markdown",
    "id": "2b64d8ebac4a31ba",
    "metadata": {
-    "collapsed": false,
-    "jupyter": {
-     "outputs_hidden": false
-    }
+    "collapsed": false
    },
    "source": [
     "## Ioannou method\n",
@@ -782,10 +742,7 @@
      "end_time": "2023-10-24T15:30:08.872891446Z",
      "start_time": "2023-10-24T15:30:07.967248383Z"
     },
-    "collapsed": false,
-    "jupyter": {
-     "outputs_hidden": false
-    }
+    "collapsed": false
    },
    "outputs": [
     {
@@ -827,10 +784,7 @@
      "end_time": "2023-10-24T15:30:08.919845144Z",
      "start_time": "2023-10-24T15:30:08.876337674Z"
     },
-    "collapsed": false,
-    "jupyter": {
-     "outputs_hidden": false
-    }
+    "collapsed": false
    },
    "outputs": [],
    "source": [
@@ -842,10 +796,7 @@
    "cell_type": "markdown",
    "id": "ba21c56a0c967d4f",
    "metadata": {
-    "collapsed": false,
-    "jupyter": {
-     "outputs_hidden": false
-    }
+    "collapsed": false
    },
    "source": [
     "#### Comparison to NEMO's velocities"
@@ -860,10 +811,7 @@
      "end_time": "2023-10-24T15:30:09.913220224Z",
      "start_time": "2023-10-24T15:30:08.919576667Z"
     },
-    "collapsed": false,
-    "jupyter": {
-     "outputs_hidden": false
-    }
+    "collapsed": false
    },
    "outputs": [
     {
@@ -925,10 +873,7 @@
    "cell_type": "markdown",
    "id": "7953c74e27d1e5d",
    "metadata": {
-    "collapsed": false,
-    "jupyter": {
-     "outputs_hidden": false
-    }
+    "collapsed": false
    },
    "source": [
     "#### Comparison to Penven velocities"
@@ -943,10 +888,7 @@
      "end_time": "2023-10-24T15:30:10.810287931Z",
      "start_time": "2023-10-24T15:30:09.913500587Z"
     },
-    "collapsed": false,
-    "jupyter": {
-     "outputs_hidden": false
-    }
+    "collapsed": false
    },
    "outputs": [
     {

diff --git a/notebooks/alboran_sea/alboran_sea.md b/notebooks/alboran_sea/alboran_sea.md
@@ -3,6 +3,8 @@
 ## Input data
 
 In this example, we use NEMO model outputs (SSH and velocities), stored in several netCDF files.
+Data can be downloaded [here](https://1drv.ms/f/s!Aq7KsFIdmDGepjMT6o77ko-JRRZu?e=hpxeKa), and the files stored inside the `data` folder.
+
 Measurements are located on a C-grid.
 
 ```python