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   "source": [
    "# What do I reference? \n",
    "\n",
    "This notebook shows you how to get the references you need based on:\n",
    "- your `full_output` data bundle\n",
    "- specified molecules\n",
    "- specified methods (e.g. 1d spectra vs climate) "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "b13c9271",
   "metadata": {},
   "outputs": [],
   "source": [
    "import picaso.justdoit as jdi\n",
    "import picaso.references as pref"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "4a7c4a03",
   "metadata": {},
   "source": [
    "Let's set up a quick little model run so that we can see how the reference function works"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "000e4824",
   "metadata": {},
   "outputs": [],
   "source": [
    "opa = jdi.opannection(wave_range=[0.3,1]) #lets just use all defaults\n",
    "planet=jdi.inputs()\n",
    "planet.phase_angle(0) #radians\n",
    "planet.gravity(gravity=25, gravity_unit=jdi.u.Unit('m/(s**2)')) #any astropy units available\n",
    "planet.star(opa, 5000,0,4.0) #opacity db, pysynphot database, temp, metallicity, logg\n",
    "planet.atmosphere(filename=jdi.jupiter_pt(), sep='\\s+')\n",
    "full_output=planet.spectrum(opa, full_output=True)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "978a1928",
   "metadata": {},
   "source": [
    "## Get opacity data references based on model output"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "7b54700d",
   "metadata": {},
   "outputs": [],
   "source": [
    "refs = pref.References() \n",
    "opa_latex, bibdb = refs.get_opa(full_output=full_output['full_output'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "c88e3e0f",
   "metadata": {},
   "outputs": [],
   "source": [
    "print(opa_latex)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "f7a50176",
   "metadata": {},
   "outputs": [],
   "source": [
    "bibdb.entries[0:2]"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "dc01bb22",
   "metadata": {},
   "source": [
    "### Write to bibtex file"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "5c5e75f0",
   "metadata": {},
   "outputs": [],
   "source": [
    "pref.create_bib(bibdb, 'molecule.bib')"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "ae01ca41",
   "metadata": {},
   "source": [
    "## Get opacity data references for certain molecules"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "d19ea5fd",
   "metadata": {},
   "outputs": [],
   "source": [
    "opa_latex, bibdb = refs.get_opa(molecules=['H2O','CO2'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "29078324",
   "metadata": {},
   "outputs": [],
   "source": [
    "print(opa_latex)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "138fa680",
   "metadata": {},
   "outputs": [],
   "source": [
    "bibdb.entries"
   ]
  }
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