Merge pull request #605 from jeffjennings/broken_notebooks

[WIP] Broken notebooks

Author: adrn

requirements.txt

@@ -1,12 +1,12 @@
 astropy
-astroquery
+astroquery>=0.4.8.dev9474  # 2024-09-24 pinned for Gaia column capitalization issue
 IPython
 matplotlib
-numpy
+numpy==1.26.4 # temporary for build test
 jupyter
 scipy
 notebook
-spectral-cube @ git+https://github.com/radio-astro-tools/spectral-cube  # as of: 2021-09-21
+spectral-cube
 radio-beam
 reproject
 dust_extinction

tutorials/color-excess/color-excess.ipynb

@@ -201,7 +201,7 @@
    "outputs": [],
    "source": [
     "download_dir = pathlib.Path('~/.astropy/cache/astroquery/Mast').expanduser()\n",
-    "download_dir.mkdir(exist_ok=True)\n",
+    "download_dir.mkdir(exist_ok=True, parents=True)\n",
     "\n",
     "obsTable = Observations.query_object(\"HD 147933\", radius=\"1 arcsec\")\n",
     "obsTable_spec = obsTable[obsTable['dataproduct_type'] == 'spectrum']\n",
@@ -214,7 +214,10 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "obsids = obsTable_spec[39]['obsid']\n",
+    "# retrieve a specific 'obs_id' corresponding to the IUE spectrum\n",
+    "obsTable_spec.add_index('obs_id')\n",
+    "obsids = obsTable_spec.loc['lwr05639']['obsid']\n",
+    "\n",
     "dataProductsByID = Observations.get_product_list(obsids)\n",
     "manifest = Observations.download_products(dataProductsByID, \n",
     "                                          download_dir=str(download_dir))"
@@ -268,11 +271,11 @@
    "outputs": [],
    "source": [
     "custom_query = Simbad()\n",
-    "custom_query.add_votable_fields('fluxdata(U)','fluxdata(B)','fluxdata(V)')\n",
+    "custom_query.add_votable_fields('U','B','V')\n",
     "phot_table=custom_query.query_object('HD 147933')\n",
-    "Umag=phot_table['FLUX_U']\n",
-    "Bmag=phot_table['FLUX_B']\n",
-    "Vmag=phot_table['FLUX_V']"
+    "Umag=phot_table['U']\n",
+    "Bmag=phot_table['B']\n",
+    "Vmag=phot_table['V']"
    ]
   },
   {

tutorials/spectral-cube-reprojection/SpectralCubeReprojectExample.ipynb

@@ -523,7 +523,14 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "cube2vel_reproj = cube2vel_spatialspectralsmooth.reproject(cube1vel.header)\n",
+    "# first we make a copy of the target (cube1vel) header and set its rest frequency \n",
+    "# to that of the cube we're reprojecting (cube2vel_spatialspectralsmooth)\n",
+    "# (see https://github.com/radio-astro-tools/spectral-cube/issues/874)\n",
+    "tgthdr = cube1vel.header\n",
+    "tgthdr['RESTFRQ'] = cube2vel_spatialspectralsmooth.header['RESTFRQ']\n",
+    "\n",
+    "# now we continue with the reprojection\n",
+    "cube2vel_reproj = cube2vel_spatialspectralsmooth.reproject(tgthdr)\n",
     "cube2vel_reproj"
    ]
   },
@@ -615,7 +622,7 @@
     "        cube2daskvel_spectralresample = cube2daskvel_smooth.spectral_interpolate(cube1vel.spectral_axis,\n",
     "                                                                             suppress_smooth_warning=True)\n",
     "        cube2daskvel_spatialspectralsmooth = cube2daskvel_spectralresample.convolve_to(common_beam)\n",
-    "        cube2daskvel_reproj = cube2daskvel_spatialspectralsmooth.reproject(cube1vel.header)\n",
+    "        cube2daskvel_reproj = cube2daskvel_spatialspectralsmooth.reproject(tgthdr) # as above, tgthdr is altered cube1vel header\n",
     "cube2daskvel_reproj"
    ]
   },

tutorials/vo/conesearch.ipynb

@@ -243,7 +243,10 @@
    "outputs": [],
    "source": [
     "my_db = vos_catalog.get_remote_catalog_db(conf.conesearch_dbname)\n",
-    "my_cat = my_db.get_catalog_by_url(result.url + '&')\n",
+    "try:\n",
+    "    my_cat = my_db.get_catalog_by_url(result.url)\n",
+    "except AttributeError:\n",
+    "    my_cat = my_db.get_catalog_by_url(result.url + '&')\n",
     "print(my_cat.dumps())"
    ]
   },