Merge branch 'radis:develop' into develop

.github/ISSUE_TEMPLATE/bug_report.yaml

@@ -1,6 +1,6 @@
-name: "💩Bug Report"
+name: "Bug Report"
 description: "Create a bug report to help us improve Radis \U0001F331"
-title: "💩 Bug Report: "
+title: "Bug Report: "
 labels: [bug]
 body:
   - type: markdown
@@ -24,15 +24,12 @@ body:
       label: "💡 Possible solutions"
       description: "Not obligatory, but suggest an idea for implementing addition or change"
       placeholder: "It actually ..."
-  - type: dropdown
+  - type: input
     id: radis-version
     attributes:
       label: "🎲 Radis version"
       description: "What version of Radis are you running?(radis.get_version())"
-      options:
-        - Version 1.0.0
-        - Version 0.9.18
-        - Version 0.9.19
+
     validations:
       required: true
   - type: dropdown

.travis.yml

@@ -23,7 +23,9 @@ jobs:
         # Install Micromamba
         # We do this conditionally because it saves us some downloading if the
         # version is the same.
-        - wget -qO- https://micromamba.snakepit.net/api/micromamba/linux-64/latest | tar -xvj bin/micromamba
+        # For now use http instead of https according to this comment:
+        # https://github.com/mamba-org/mamba/issues/1675#issuecomment-1127160021
+        - wget -qO- http://micromamba.snakepit.net/api/micromamba/linux-64/latest | tar -xvj bin/micromamba
         - ./bin/micromamba shell init -s bash -p ~/micromamba
         - source ~/.bashrc
         - micromamba activate base
@@ -44,14 +46,20 @@ jobs:
         # Your test script goes here
         - echo ">>> Run tests"
         # use XVFB to have headless display port, and still run the Matplotlib tests.
-        - xvfb-run pytest --cov=./
+        - xvfb-run -a pytest --cov=./
         # lookup 'addopts' in setup.cfg>[tools:pytest] for default tests
 
+      services:
+        - xvfb
+
       after_success:
         # codecoverage
         - pip install codecov
         - codecov
 
+      before_script:
+        - export MPLBACKEND=Agg
+
     - stage: lint
       name: Code Quality Checks
       install:

docs/_templates/buttons.html

@@ -10,6 +10,12 @@
 
 
 <p>
+</a>
+<a href="https://radis.github.io/radis-lab/">
+    <img class="circle-icon"
+         src="{{ pathto('radis_ico.png', 1) }}"
+         alt="Radis-Website">
+</a>
 <a href="https://github.com/radis/radis">
     <img class="circle-icon"
          src="{{ pathto('_static/assets/general/button_github.svg', 1) }}"
@@ -31,4 +37,9 @@
          src="{{ pathto('_static/assets/general/radislab.png', 1) }}"
          alt="Radis-Lab">
 </a>
+<a href="https://radis.github.io/">
+    <img class="circle-icon"
+         src="{{ pathto('_static/assets/general/radisicon.png', 1) }}"
+         alt="Radis-Lab">
+</a>
 </p>

docs/conf.py

@@ -263,6 +263,7 @@ def setup(app):
     "fixed_sidebar": True,
     "analytics_id": "UA-113616205-1",
     "link": "#7A306C",
+    "extra_nav_links": {"RADIS Website": "https://radis.github.io/"},
 }
 
 # Add any paths that contain custom themes here, relative to this directory.
@@ -436,7 +437,7 @@ def setup(app):
         "RADIS Documentation",
         author,
         "RADIS",
-        "A fast line-by-line code for high resolution infrared molecular spectra",
+        "A fast line-by-line code for high resolution infrared molecular spectra: https://radis.github.io/",
         "Miscellaneous",
     ),
 ]

docs/dev/_architecture.rst

@@ -8,6 +8,7 @@ The RADIS modules are organized with the following flow chart
 .. image:: RADIS_flow_chart.*
     :alt: https://radis.readthedocs.io/en/latest/_images/RADIS_flow_chart.svg
     :scale: 100 %
+    :height: 500px
 
 -------------------------------------------------------------------------
 

docs/features/features.rst

@@ -15,7 +15,7 @@ It includes:
 
 - Absorption and emission spectra of all [HITRAN-2020]_ and [ExoMol-2020]_ species under equilibrium calculations (:py:data:`~radis.db.MOLECULES_LIST_EQUILIBRIUM`)
 - Absorption and emission spectra of CO2 and CO for non-LTE calculations (see :py:data:`~radis.db.MOLECULES_LIST_NONEQUILIBRIUM` )
-- Different Line Databases: support of [HITRAN-2020]_, [HITEMP-2010]_ and [CDSD-4000]_ line databases (see :py:data:`~radis.lbl.loader.KNOWN_DBFORMAT`)
+- Different Line Databases: support of [HITRAN-2020]_, [HITEMP-2010]_, [CDSD-4000]_, [ExoMol-2020]_, [GEISA-2020]_ line databases (see :py:data:`~radis.lbl.loader.KNOWN_DBFORMAT`)
 - Calculation of :ref:`Rovibrational Energies of molecules <label_examples_rovibrational_energies>`.
 - Calculation of equilibrium and nonequilibrium :ref:`Partition Functions <label_examples_partition_functions>`.
 - Spatially heterogeneous spectra (see :ref:`see line-of-sight <label_los_index>`)

docs/index.rst

@@ -50,7 +50,7 @@ using Astroquery (based on [HAPI]_). Output is a
                       Tgas=700,           # K
                       mole_fraction=0.1,
                       path_length=1,      # cm
-                      databank='hitran',  # or use 'hitemp'
+                      databank='hitran',  # or 'hitemp', 'geisa', 'exomol'
                       )
     s.apply_slit(0.5, 'nm')       # simulate an experimental slit
     s.plot('radiance')
@@ -71,7 +71,7 @@ store the CO(X) rovibrational energies): ::
                       Trot=300 * u.K,
                       mole_fraction=0.1,
                       path_length=1 * u.cm,
-                      databank='hitran',  # or use 'hitemp'
+                      databank='hitran',  # or 'hitemp', 'geisa', 'exomol'
                       )
     s2.apply_slit(0.5, 'nm')
     s2.plot('radiance', nfig='same')    # compare with previous

docs/references/_bibliography.rst

@@ -69,10 +69,21 @@ The latest HITEMP database version is automatically downloaded if using ``databa
                spectroscopic databank, Journal of Quantitative Spectroscopy and Radiative Transfer 112 (9) (2011)
                1403–1410, ISSN 00224073, `doi:10.1016/j.jqsrt.2011.03.005 <https://www.sciencedirect.com/science/article/pii/S0022407311001154>`__
 
+The latest ExoMol database is automatically downloaded if using ``databank='exomol'``. ExoMol contains
+multiple sub-databases per molecule. See :py:func:`~radis.io.exomol.fetch_exomol`
+
 .. [ExoMol-2020] Tennyson et al., The 2020 release of the ExoMol database: Molecular line lists for
                 exoplanet and other hot atmospheres, Journal of Quantitative Spectroscopy and Radiative Transfer 255,
                 (2020), 107228,  `doi:10.1016/j.jqsrt.2020.107228 <https://www.sciencedirect.com/science/article/abs/pii/S002240732030491X>`__
 
+.. [ExoMol-2016] Tennyson et al.,  The ExoMol database: molecular line lists for exoplanet and other hot atmospheres,
+                J. Molec. Spectrosc., 327, 73-94 (2016), `doi:10.1016/j.jms.2016.05.002 <https://arxiv.org/abs/1603.05890>`__
+
+The GEISA 2020 database is automatically downloaded with ``databank='geisa'``.
+
+.. [GEISA-2020] Delahaye et al, The 2020 edition of the GEISA spectroscopic database,
+                J. Molec. Spectrosc., 380, 111510 (2021) `doi:10.1016/j.jms.2021.111510 <https://www.sciencedirect.com/science/article/pii/S0022285221000928>`
+
 For download and configuration of line databases, see the :ref:`Line Databases section <label_line_databases>`
 
 

docs/references/references.rst

@@ -60,6 +60,13 @@ Research papers using RADIS and the associated algorithms :
 
 - Papers citing |badge_article2| : https://scholar.google.fr/scholar?cites=17363432006874800849
 
+Spectroscopy Tutorials
+=====================
+Tutorials for molecular spectroscopy can be found here at https://github.com/radis/spectro101
+
+- Lab Spectroscopy: https://github.com/radis/spectro101/blob/main/102_lab_spectroscopy.ipynb
+
+- Line Broadening : https://github.com/radis/spectro101/blob/main/103_lineshape_broadening.ipynb
 
 Useful Links
 ============

docs/spectrum/spectrum.rst

@@ -338,6 +338,11 @@ method to retrieve the quantity un the units you want::
     _, R = s.get('radiance_noslit', wunit='nm', Iunit='W/cm2/sr/nm',
                  medium='air')
 
+Use with `return_units` to get dimensioned Astropy Quantities ::
+
+    w, R  = s.get('radiance_noslit', return_units=True)
+    # w, R are astropy quantities
+
 See :ref:`spectral arrays <label_spectral _arrays>` for the list
 of spectral arrays.
 

examples/plot_compare_CO_exomol_hitemp.py

@@ -27,7 +27,7 @@
     "wmin": 2002 / u.cm,
     "wmax": 2300 / u.cm,
     "molecule": "CO",
-    "isotope": "2",
+    "isotope": "1",
     "pressure": 1.01325,  # bar
     "Tgas": 1000,  # K
     "mole_fraction": 0.1,
@@ -37,7 +37,7 @@
 }
 
 s_exomol = calc_spectrum(
-    **conditions, databank="exomol", name="ExoMol's HITEMP (H2 broadened)"
+    **conditions, databank="exomol", name="ExoMol's HITEMP (default broadening)"
 )
 s_hitemp = calc_spectrum(
     **conditions,

examples/plot_compare_CO_geisa_hitran.py

@@ -0,0 +1,52 @@
+# -*- coding: utf-8 -*-
+"""
+=========================================================
+Compare CO spectrum from the GEISA and HITRAN database
+=========================================================
+
+GEISA Database has been newly implemented in RADIS 0.13 release on May 15, 2022. This is among
+the very first attemps to compare the spectra generated from the two databases.
+
+Auto-download and calculate CO spectrum from the GEISA database, and the HITRAN database.
+
+Output should be similar, but not exactly! By default these two databases provide different
+broadening coefficients. However, the Einstein coefficients & linestrengths should be
+approximately the same, therefore the integrals under the lines should be similar.
+
+You can see it by running the code below.
+
+For your interest, GEISA and HITRAN lines can be downloaded and accessed separately using
+:py:func:`~radis.io.geisa.fetch_geisa` and :py:func:`~radis.io.hitran.fetch_hitran`
+
+"""
+import astropy.units as u
+
+from radis import calc_spectrum, plot_diff
+
+conditions = {
+    "wmin": 2002 / u.cm,
+    "wmax": 2300 / u.cm,
+    "molecule": "CO",
+    "pressure": 1.01325,  # bar
+    "Tgas": 1000,  # K
+    "mole_fraction": 0.1,
+    "path_length": 1,  # cm
+    "verbose": True,
+}
+
+s_geisa = calc_spectrum(**conditions, databank="geisa", name="GEISA's CO")
+
+s_hitran = calc_spectrum(
+    **conditions,
+    databank="hitran",
+    name="HITRAN's CO",
+)
+
+"""
+
+In :py:func:`~radis.io.geisa.fetch_geisa`, you can choose to additionally plot the
+absolute difference (method='diff') by default, or the ratio (method='ratio'), or both.
+
+"""
+
+plot_diff(s_geisa, s_hitran, method=["diff", "ratio"])

examples/plot_exomol_spectrum.py

@@ -6,9 +6,6 @@
 
 Auto-download and compute a SiO spectrum from the ExoMol database ([ExoMol-2020]_)
 
-ExoMol lines can be downloaded and accessed separately using
-:py:func:`~radis.io.exomol.fetch_exomol`
-
 """
 
 from radis import calc_spectrum
@@ -29,14 +26,21 @@
 s.plot("radiance")
 
 
-#%% See line data:
+#%%
+
+"""ExoMol lines can be downloaded and accessed separately using
+:py:func:`~radis.io.exomol.fetch_exomol`
+"""
+
+# See line data:
 from radis.io.exomol import fetch_exomol
 
 df = fetch_exomol("SiO", database="EBJT", isotope="1", load_wavenum_max=5000)
 print(df)
 
 
-#%% See the list of recommended databases for the 1st isotope of SiO :
+#%%
+# See the list of recommended databases for the 1st isotope of SiO :
 from radis.io.exomol import get_exomol_database_list, get_exomol_full_isotope_name
 
 databases, recommended = get_exomol_database_list(

radis/__version__.txt

@@ -1 +1 @@
-0.12.1
+0.13.0

radis/db/classes.py

@@ -248,7 +248,7 @@ def get_molecule_identifier(molecule_name):
     except KeyError:
         raise NotImplementedError(
             "Molecule '{0}' not supported. Choose one of {1}".format(
-                molecule_name, list(trans2.keys())
+                molecule_name, sorted(list(trans2.keys()))
             )
         )
 

radis/db/references.py

@@ -14,6 +14,7 @@
     "HITRAN-2016": "10.1016/j.jqsrt.2017.06.038",
     "HITRAN-2020": "10.1016/j.jqsrt.2021.107949",
     "HITEMP-2010": "10.1016/j.jqsrt.2010.05.001",
+    "GEISA-2020": "10.1016/j.jms.2021.111510",
     "CDSD-4000": "10.1016/j.jqsrt.2011.03.005",
     "ExoMol-2020": "10.1016/j.jqsrt.2020.107228",
     # Tabulated Partition functions

radis/io/__init__.py

@@ -8,6 +8,7 @@
 
 from .cdsd import cdsd2df
 from .exomol import fetch_exomol
+from .geisa import fetch_geisa
 from .hitemp import fetch_hitemp
 from .hitran import fetch_hitran, hit2df
 from .query import fetch_astroquery
@@ -19,4 +20,5 @@
     "fetch_hitran",
     "fetch_exomol",
     "fetch_astroquery",
+    "fetch_geisa",
 ]