exoplanet-dev · dyahalomi · Feb 9, 2023 · Feb 9, 2023 · Mar 15, 2023 · Mar 15, 2023
diff --git a/docs/tutorials/astrometric.ipynb b/docs/tutorials/astrometric.ipynb
@@ -286,7 +286,6 @@
     "\n",
     "def get_model(parallax=None):\n",
     "    with pm.Model() as model:\n",
-    "\n",
     "        if parallax is None:\n",
     "            # Without an actual parallax measurement, we can model the orbit in units of arcseconds\n",
     "            # by providing a fake_parallax and conversion constant\n",

diff --git a/docs/tutorials/astrometry_rv_case_study.ipynb b/docs/tutorials/astrometry_rv_case_study.ipynb
diff --git a/docs/tutorials/eb.ipynb b/docs/tutorials/eb.ipynb
@@ -191,9 +191,7 @@
     "\n",
     "\n",
     "def build_model(mask):\n",
-    "\n",
     "    with pm.Model() as model:\n",
-    "\n",
     "        # Systemic parameters\n",
     "        mean_lc = pm.Normal(\"mean_lc\", mu=0.0, sd=5.0)\n",
     "        mean_rv = pm.Normal(\"mean_rv\", mu=0.0, sd=50.0)\n",

diff --git a/docs/tutorials/joint.ipynb b/docs/tutorials/joint.ipynb
@@ -311,7 +311,9 @@
    "cell_type": "code",
    "execution_count": null,
    "id": "8000897c",
-   "metadata": {},
+   "metadata": {
+    "lines_to_next_cell": 2
+   },
    "outputs": [],
    "source": [
     "import pymc3 as pm\n",
@@ -330,7 +332,6 @@
     "    if mask is None:\n",
     "        mask = np.ones(len(x), dtype=bool)\n",
     "    with pm.Model() as model:\n",
-    "\n",
     "        # Parameters for the stellar properties\n",
     "        mean_flux = pm.Normal(\"mean_flux\", mu=0.0, sd=10.0)\n",
     "        u_star = xo.QuadLimbDark(\"u_star\")\n",
@@ -487,7 +488,9 @@
   {
    "cell_type": "markdown",
    "id": "d7d02ab9",
-   "metadata": {},
+   "metadata": {
+    "lines_to_next_cell": 2
+   },
    "source": [
     "Now let's plot the map radial velocity model."
    ]
@@ -496,7 +499,9 @@
    "cell_type": "code",
    "execution_count": null,
    "id": "b78425b5",
-   "metadata": {},
+   "metadata": {
+    "lines_to_next_cell": 2
+   },
    "outputs": [],
    "source": [
     "def plot_rv_curve(soln):\n",
@@ -525,7 +530,9 @@
   {
    "cell_type": "markdown",
    "id": "ade1ac5b",
-   "metadata": {},
+   "metadata": {
+    "lines_to_next_cell": 2
+   },
    "source": [
     "That looks pretty similar to what we got in {ref}`rv`.\n",
     "Now let's also plot the transit model."

diff --git a/docs/tutorials/lc-gp-transit.ipynb b/docs/tutorials/lc-gp-transit.ipynb
@@ -140,12 +140,10 @@
     "\n",
     "\n",
     "def build_model(mask=None, start=None):\n",
-    "\n",
     "    if mask is None:\n",
     "        mask = np.ones(len(x), dtype=bool)\n",
     "\n",
     "    with pm.Model() as model:\n",
-    "\n",
     "        # Shared parameters\n",
     "        mean = pm.Normal(\"mean\", mu=0, sd=1, testval=0)\n",
     "\n",
@@ -323,7 +321,6 @@
     "\n",
     "\n",
     "def plot_light_curve(x, y, soln, mask=None):\n",
-    "\n",
     "    if mask is None:\n",
     "        mask = np.ones(len(x), dtype=bool)\n",
     "\n",
@@ -535,7 +532,6 @@
     "RUN_THE_SAMPLING = 0\n",
     "\n",
     "if RUN_THE_SAMPLING:\n",
-    "\n",
     "    with model:\n",
     "        trace = pm.sample(\n",
     "            tune=1500,\n",

diff --git a/docs/tutorials/lc-multi.ipynb b/docs/tutorials/lc-multi.ipynb
@@ -171,7 +171,6 @@
     "# Do several rounds of sigma clipping\n",
     "for i in range(10):\n",
     "    with pm.Model() as model:\n",
-    "\n",
     "        # Shared orbital parameters\n",
     "        log_period = pm.Normal(\"log_period\", mu=np.log(lit_period), sigma=1.0)\n",
     "        period = pm.Deterministic(\"period\", tt.exp(log_period))\n",
@@ -197,7 +196,6 @@
     "        gp_preds = dict()\n",
     "        gp_preds_with_mean = dict()\n",
     "        for n, (name, (x, y, yerr, texp)) in enumerate(datasets.items()):\n",
-    "\n",
     "            # We define the per-instrument parameters in a submodel so that we\n",
     "            # don't have to prefix the names manually\n",
     "            with pm.Model(name=name, model=model):\n",

diff --git a/docs/tutorials/quick-tess.ipynb b/docs/tutorials/quick-tess.ipynb
@@ -169,7 +169,6 @@
     "\n",
     "\n",
     "with pm.Model() as model:\n",
-    "\n",
     "    # Stellar parameters\n",
     "    mean = pm.Normal(\"mean\", mu=0.0, sigma=10.0)\n",
     "    u = xo.QuadLimbDark(\"u\")\n",

diff --git a/docs/tutorials/rv-multi.ipynb b/docs/tutorials/rv-multi.ipynb
@@ -120,7 +120,6 @@
     "t_phase = np.linspace(-0.5, 0.5, 5000)\n",
     "\n",
     "with pm.Model() as model:\n",
-    "\n",
     "    # Parameters describing the orbit\n",
     "    log_K = pm.Normal(\"log_K\", mu=np.log(300), sigma=10)\n",
     "    log_P = pm.Normal(\"log_P\", mu=np.log(2093.07), sigma=10)\n",

diff --git a/docs/tutorials/rv.ipynb b/docs/tutorials/rv.ipynb
@@ -134,7 +134,6 @@
     "import aesara_theano_fallback.tensor as tt\n",
     "\n",
     "with pm.Model() as model:\n",
-    "\n",
     "    # Gaussian priors based on transit data (from Petigura et al.)\n",
     "    t0 = pm.Normal(\"t0\", mu=np.array(t0s), sd=np.array(t0_errs), shape=2)\n",
     "    logP = pm.Normal(\n",

diff --git a/docs/tutorials/stellar-variability.ipynb b/docs/tutorials/stellar-variability.ipynb
@@ -125,7 +125,6 @@
     "from celerite2.theano import terms, GaussianProcess\n",
     "\n",
     "with pm.Model() as model:\n",
-    "\n",
     "    # The mean flux of the time series\n",
     "    mean = pm.Normal(\"mean\", mu=0.0, sigma=10.0)\n",
     "\n",

diff --git a/docs/tutorials/tess.ipynb b/docs/tutorials/tess.ipynb
@@ -159,7 +159,9 @@
    "cell_type": "code",
    "execution_count": null,
    "id": "fbb85aad",
-   "metadata": {},
+   "metadata": {
+    "lines_to_next_cell": 2
+   },
    "outputs": [],
    "source": [
     "import exoplanet as xo\n",
@@ -176,7 +178,6 @@
     "    if mask is None:\n",
     "        mask = np.ones(len(x), dtype=bool)\n",
     "    with pm.Model() as model:\n",
-    "\n",
     "        # Parameters for the stellar properties\n",
     "        mean = pm.Normal(\"mean\", mu=0.0, sd=10.0)\n",
     "        u_star = xo.QuadLimbDark(\"u_star\")\n",
@@ -307,7 +308,9 @@
   {
    "cell_type": "markdown",
    "id": "82a9efd6",
-   "metadata": {},
+   "metadata": {
+    "lines_to_next_cell": 2
+   },
    "source": [
     "Here's how we plot the initial light curve model:"
    ]

diff --git a/docs/tutorials/transit.ipynb b/docs/tutorials/transit.ipynb
@@ -113,7 +113,6 @@
     "import pymc3_ext as pmx\n",
     "\n",
     "with pm.Model() as model:\n",
-    "\n",
     "    # The baseline flux\n",
     "    mean = pm.Normal(\"mean\", mu=0.0, sd=1.0)\n",
     "\n",

diff --git a/docs/tutorials/ttv.ipynb b/docs/tutorials/ttv.ipynb
@@ -119,7 +119,6 @@
     "np.random.seed(9485023)\n",
     "\n",
     "with pm.Model() as model:\n",
-    "\n",
     "    # This part of the model is similar to the model in the `transit` tutorial\n",
     "    mean = pm.Normal(\"mean\", mu=0.0, sd=1.0)\n",
     "    u = xo.QuadLimbDark(\"u\", testval=np.array([0.3, 0.2]))\n",