Updated type annotations, testing of tutorial notebooks with Python 3.11

tomasstolker · Sep 26, 2023 · 4a56512 · 4a56512
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Showing 12 changed files with 691 additions and 509 deletions.
diff --git a/docs/tutorials/atmospheric_retrieval.ipynb b/docs/tutorials/atmospheric_retrieval.ipynb
diff --git a/docs/tutorials/companion_data.ipynb b/docs/tutorials/companion_data.ipynb
@@ -61,7 +61,7 @@
      "output_type": "stream",
      "text": [
       "==============\n",
-      "species v0.6.0\n",
+      "species v0.7.1\n",
       "==============\n",
       "Working folder: /Users/tomasstolker/applications/species/docs/tutorials\n",
       "Creating species_config.ini... [DONE]\n",
@@ -77,7 +77,7 @@
     {
      "data": {
       "text/plain": [
-       "<species.core.init.SpeciesInit at 0x145baaa50>"
+       "<species.core.init.SpeciesInit at 0x14b07d790>"
       ]
      },
      "execution_count": 2,
@@ -164,7 +164,7 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "100%|████████████████████████████████████████| 288k/288k [00:00<00:00, 241MB/s]"
+      "100%|████████████████████████████████████████| 288k/288k [00:00<00:00, 158MB/s]"
      ]
     },
     {
@@ -181,22 +181,8 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      " [DONE]\n",
-      "Adding filter: MKO/NSFCam.K..."
-     ]
-    },
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "/Users/tomasstolker/applications/species/species/data/database.py:1329: UserWarning: Found 33 fluxes with NaN in the data of GPI_YJHK. Removing the spectral fluxes that contain a NaN.\n",
+      "\n",
+      "/Users/tomasstolker/applications/species/species/data/database.py:1341: UserWarning: Found 33 fluxes with NaN in the data of GPI_YJHK. Removing the spectral fluxes that contain a NaN.\n",
       "  warnings.warn(\n"
      ]
     },
@@ -205,6 +191,7 @@
      "output_type": "stream",
      "text": [
       " [DONE]\n",
+      "Adding filter: MKO/NSFCam.K... [DONE]\n",
       "Adding object: beta Pic c [DONE]\n",
       "Adding filter: Paranal/SPHERE.IRDIS_D_H23_2... [DONE]\n",
       "Adding filter: Paranal/SPHERE.IRDIS_D_H23_3... [DONE]\n",
@@ -218,14 +205,15 @@
       "Adding filter: Keck/NIRC2.Ms... [DONE]\n",
       "Adding object: 51 Eri b [DONE]\n",
       "Adding filter: Subaru/CIAO.z... [DONE]\n",
-      "Adding filter: Paranal/SPHERE.IRDIS_B_J..."
+      "Adding filter: Paranal/SPHERE.IRDIS_B_J... [DONE]\n",
+      "Adding filter: Keck/NIRC2.H..."
      ]
     },
     {
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "/Users/tomasstolker/applications/species/species/data/filters.py:209: UserWarning: The minimum transmission value of Subaru/CIAO.z is smaller than zero (-1.80e-03). Wavelengths with negative transmission values will be removed.\n",
+      "/Users/tomasstolker/applications/species/species/data/filters.py:222: UserWarning: The minimum transmission value of Subaru/CIAO.z is smaller than zero (-1.80e-03). Wavelengths with negative transmission values will be removed.\n",
       "  warnings.warn(\n"
      ]
     },
@@ -234,7 +222,6 @@
      "output_type": "stream",
      "text": [
       " [DONE]\n",
-      "Adding filter: Keck/NIRC2.H... [DONE]\n",
       "Adding filter: Keck/NIRC2.Ks... [DONE]\n",
       "Adding object: HR 8799 b [DONE]\n",
       "Adding object: HR 8799 c [DONE]\n",

diff --git a/docs/tutorials/data_model.ipynb b/docs/tutorials/data_model.ipynb
diff --git a/docs/tutorials/emission_line.ipynb b/docs/tutorials/emission_line.ipynb