Merge pull request #481 from HajimeKawahara/releasev1.5

Release v1.5

MANIFEST.in

@@ -3,14 +3,14 @@ include src/exojax/data/atom/barklem_collet_2016_pff.txt
 include src/exojax/data/atom/iso_mn.txt
 include src/exojax/data/atom/HITRAN_molparam.txt
 include src/exojax/data/clouds/drag_force.txt
+include src/exojax/data/clouds/ammonia_liquid_density.csv
 include src/exojax/data/abundance/AAG2021.dat
 include src/exojax/data/atom/NIST_Atomic_Ionization_Energies.txt
 
 include src/exojax/data/testdata/spectrum.txt
 include src/exojax/data/testdata/spectrum_ch4.txt
 include src/exojax/data/testdata/spectrum_ch4_new.txt
 include src/exojax/data/testdata/spectrum_co.txt
-include src/exojax/data/testdata/moldb_h2o_exomol.pickle
 include src/exojax/data/testdata/moldb_vald.pickle
 include src/exojax/data/testdata/lpf_test_ref.txt
 include src/exojax/data/testdata/modit_test_ref.txt
@@ -43,6 +43,10 @@ include src/exojax/data/testdata/CO/12C-16O/SAMPLE/12C-16O__SAMPLE.trans.bz2
 include src/exojax/data/testdata/CO/12C-16O/SAMPLE/12C-16O__SAMPLE.trans.hdf5
 
 include src/exojax/data/premodit/elower_grid_trange.npz
+include src/exojax/data/premodit/elower_grid_trange_v2.npz
+
+include src/exojax/data/testdata/test.refrind
+include src/exojax/data/testdata/miegrid_lognorm_test.mg.npz
 
 graft tests
 graft examples

README.md

@@ -5,17 +5,30 @@
  [![paper](https://img.shields.io/badge/paper-ApJS_258_31_(2022)-orange)](https://iopscience.iop.org/article/10.3847/1538-4365/ac3b4d) 
  <a href="https://codeclimate.com/github/HajimeKawahara/exojax/maintainability"><img src="https://api.codeclimate.com/v1/badges/97c5e8835f3ef9c4ad7c/maintainability" /></a>
 
-Auto-differentiable line-by-line spectral modelling of exoplanets/brown dwarfs/M dwarfs using JAX. Read [the docs](http://secondearths.sakura.ne.jp/exojax) 🐕. 
-In short, ExoJAX allows you to do gradient based optimisation and HMC NUTS fitting using the latest database.
+Differentiable spectral modelling of exoplanets/brown dwarfs/M dwarfs using JAX!
+Read [the docs](http://secondearths.sakura.ne.jp/exojax/develop) 🐕. 
+In short, ExoJAX allows you to do gradient based optimizations and HMC-NUTS samplings using the latest database.
 
 ExoJAX is at least compatible with
 
-- [NumPyro](https://github.com/pyro-ppl/numpyro) (PPL)
-- BlackJAX
-- [JAXopt](https://github.com/google/jaxopt) (differentiable optimizer)
+- PPLs: [NumPyro](https://github.com/pyro-ppl/numpyro), [blackjax](https://github.com/blackjax-devs/blackjax) 
+- Optimizers: [JAXopt](https://github.com/google/jaxopt), [optax](https://github.com/google-deepmind/optax), [bayeux](https://github.com/jax-ml/bayeux)
+
+<img src="https://github.com/HajimeKawahara/exojax/assets/15956904/8aa9673b-b64b-4b65-a76c-2966ef1edbc7" Titie="exojax" Width=850px>
+
+<details><summary>ExoJAX Classes</summary>
+
+- Databases: *db (mdb: molecular, adb: atomic, cdb:continuum, pdb: particulates)
+- Opacity Calculators: opa  (i.e. Voigt profile)
+- Atmospheric Radiative Transfer: art (emission w, w/o scattering, refelction, transmission)
+- Atompsheric Microphysics: amp (clouds etc)
+
+</details>
+
+## Get Started 
+
+See [this page](http://secondearths.sakura.ne.jp/exojax/develop/tutorials/get_started.html) for the first step!
 
-<img src="https://user-images.githubusercontent.com/15956904/222950543-6de25bb2-48f2-4bc7-a588-77daa105442e.png" Titie="exojax" Width=850px>
-
 ## Functions
 
 <details open><summary>Voigt Profile :heavy_check_mark: </summary>
@@ -34,8 +47,7 @@ voigt(nu,1.0,2.0) #sigma_D=1.0, gamma_L=2.0
 from exojax.utils.grids import wavenumber_grid
 from exojax.spec.api import MdbExomol
 from exojax.spec.opacalc import OpaPremodit
-
-from jax.config import config
+from jax import config
 config.update("jax_enable_x64", True)
 
 nu_grid,wav,res=wavenumber_grid(1900.0,2300.0,200000,xsmode="premodit",unit="cm-1",)
@@ -48,6 +60,8 @@ xsv = opa.xsvector(1000.0, 1.0) # cross section for 1000K, 1 bar
 
 </details>
 
+
+
 <details><summary>Do you just want to plot the line strength at T=1000K? </summary>
 
 ```python
@@ -68,7 +82,8 @@ F = art.run(dtau, Tarr)
 
 </details>
 
-See http://secondearths.sakura.ne.jp/exojax/develop/tutorials/get_started.html for the first step!
+<details><summary>Transmission Spectrum :heavy_check_mark: </summary></details>
+<details><summary>Reflection Spectrum :heavy_check_mark: </summary></details>
 
 ## Installation
 
@@ -82,38 +97,20 @@ or
 python setup.py install
 ```
 
-<details><summary> Note on installation w/ GPU support</summary>
-
-:books: You need to install CUDA, NumPyro, JAX w/ NVIDIA GPU support, and cuDNN. 
+<details><summary>Note on installation w/ GPU support</summary>
 
-- NumPyro
+:books: You need to install CUDA, JAX w/ NVIDIA GPU support.
 
-ExoJAX supports NumPyro >=0.7.0. Please check the required JAX version by NumPyro. In May 2021, it seems the recent version of [NumPyro](https://github.com/pyro-ppl/numpyro) requires jaxlib>=0.1.62 (see [setup.py](https://github.com/pyro-ppl/numpyro/blob/master/setup.py) of NumPyro for instance). 
-
-- JAX
-
-Check you cuda version:
-
-```
-nvcc -V
-```
-
-Install such as
-
-```
-pip install --upgrade pip
-pip install --upgrade "jax[cuda]" -f https://storage.googleapis.com/jax-releases/jax_releases.html
-```
-
-Please visit [here](https://github.com/google/jax) for details.
+Visit [here](https://github.com/google/jax) for the installation of GPU supported JAX.
 
 </details>
 
+
 ## References
 [![paper](https://img.shields.io/badge/paper_I-ApJS_258_31_(2022)-orange)](https://iopscience.iop.org/article/10.3847/1538-4365/ac3b4d) 
 
 - Paper I: Kawahara, Kawashima, Masuda, Crossfield, Pannier, van den Bekerom, [ApJS 258, 31 (2022)](https://iopscience.iop.org/article/10.3847/1538-4365/ac3b4d)
 
 ## License
 
-🐈 Copyright 2020-2023 ExoJAX contributors. exojax is publicly available under the MIT license.
+🐈 Copyright 2020-2024 ExoJAX contributors. ExoJAX is publicly available under the MIT license.

documents/conf.py

@@ -19,11 +19,11 @@
 # -- Project information -----------------------------------------------------
 
 project = 'ExoJAX'
-copyright = '2020-2023, ExoJAX contributors'
+copyright = '2020-2024, ExoJAX contributors'
 author = 'ExoJAX contributors'
 
 # The full version, including alpha/beta/rc tags
-release = '1.4.1'
+release = '1.5.0'
 
 
 # -- General configuration ---------------------------------------------------

documents/developers/doc.rst

@@ -1,10 +1,10 @@
-Generating Documents
+Generates documents
 ==============================
 
 We use the google style of the sphinx document.
 
 .. code:: sh
-	  
+	
     pip install sphinx_rtd_theme sphinxemoji
 
 This is an example to generate the sphinx doc.
@@ -18,10 +18,10 @@ This is an example to generate the sphinx doc.
     make clean
     make html
 
-Generating up-to-date documents of tutorials
+Generates the up-to-date documents of tutorials
 ------------------------------------------------
 
-The below commands automatically run the tutorial notebooks and generate rst:
+The following commands automatically run the tutorial notebooks and generate rst:
 
 .. code:: sh
 
@@ -34,3 +34,9 @@ If you just want to generate rst without executing notebooks, try this:
 
     python jupyter2rst.py none
 
+One by One:
+
+.. code:: sh
+
+    python jupyter2rst_each.py (python filename)
+

documents/developers/pytest.rst

@@ -1,61 +1,47 @@
 Test codes for developers
 ==============================
 
-ExoJAX has many test codes in 'tests' directory.
-We recommend to write the unit test code in 'tests' directory before pull-request and to perform the unit tests before your submission of the pull-request:
+ExoJAX has many test codes in the ``tests`` directory. The ``test`` directory contains several types of the collection of ``pytest`` code.
 
-.. code:: sh
-
-   cd exojax
-   pytest tests
+- ``tests/unittests``: the collection of the unit tests. The GitHub action runs the test code in this directory.
+- ``tests/integration``: the collection of the test codes that need longer time to run than the code in ``unittest``.
 
-You might need some files. 
+test/unittests
+---------------------
 
-- VALD data 
-
-You can download them from `here <http://secondearths.sakura.ne.jp/exojax/data/>`_, but see the following warning.
-
-.. warning::
-
-   Note that if you use Windows or Mac, .gz might be unziped when downloading despite no renaming. I mean, the same name with .gz, but unziped!  In this case, download ``extradata.tar`` and untar it.
-
-
-Unit test using pytest
-----------------------------
-
-Before starting the unit test, install pytest:
+We recommend to write the unit test code in ``tests/unittests`` directory before pull-request and to perform the unit tests before your submission of the pull-request:
 
 .. code:: sh
 
-   pip install pytest
+   cd exojax/test/unittests
+   pytest 
 
 
-To test all of the unit tests, perform
+test/integration/unittest_long
+----------------------------------
 
-.. code:: sh
+In essence, these are the unit tests that need longer time than the code in ``unittest``, sometimes including downloading the data.  
 
-   cd exojax
-   pytest tests
+test/integration/comparison
+---------------------------
 
-or you can test one by one 
+The code for the comparison with external data, packages, etc 
 
-.. code:: sh
+- ``transmission/comparison_with_kawashima_transmission.py``: comparison with Yui Kawashima's computation of the transmission spectrum
+- ``twostream/comparison_petitRADTRANS_*.py``: comparison with pRT
+- ``nonair/nonair_co_hitran_comp.py``: non-air broadening comparison with ``radis``
 
-   cd tests/auto
-   pytest autoxs_test.py
 
 
-Tests for the reverse modeling (retrieval)
------------------------------------------------
+Others
+--------------
 
-The unit test is not appropriate for the reverse modeling because it takes a lot of time.
-For the tests of the reverse modeling, use code in 'tests/reverse' directory.
+VALD data 
+^^^^^^^^^^^^^^^^
 
-- reverse_lpf.py simple test for HMC-NUTS using LPF
-- reverse_methane.py simple test for HMC-NUTS using MODIT
+You can download them from `here <http://secondearths.sakura.ne.jp/exojax/data/>`_, but see the following warning.
 
- .. code:: sh
+.. warning::
+
+   Note that if you use Windows or Mac, .gz might be unziped when downloading despite no renaming. I mean, the same name with .gz, but unziped!  In this case, download ``extradata.tar`` and untar it.
 
-   cd tests/reverse
-   python reverse_lpf.py
-   python reverse_methane.py

documents/index.rst

@@ -6,16 +6,22 @@
 ExoJAX
 ==================================
 
-version 1.4 (:doc:`userguide/history`)
+Version 1.5 (:doc:`userguide/history`)
 
-`ExoJAX <https://github.com/HajimeKawahara/exojax>`_ provides an auto-differentiable high-resolution spectrum model for exoplanets/brown dwarfs using `JAX <https://github.com/google/jax>`_. ExoJAX enables a fully Bayesian inference of the high-dispersion data to fit the line-by-line spectral computation to the observed spectrum, from end-to-end (i.e. from molecular/atomic databases to real spectra), by combining it with `the Hamiltonian Monte Carlo <https://en.wikipedia.org/wiki/Hamiltonian_Monte_Carlo>`_ in recent probabilistic programming languages such as `NumPyro <https://github.com/pyro-ppl/numpyro>`_. So, the notable features of ExoJAX are summarized as 
+`ExoJAX <https://github.com/HajimeKawahara/exojax>`_ provides an auto-differentiable high-resolution spectrum model for exoplanets/brown dwarfs using `JAX <https://github.com/google/jax>`_. 
+ExoJAX enables a fully Bayesian inference of the high-dispersion data to fit the line-by-line spectral computation to the observed spectrum, 
+from end-to-end (i.e. from molecular/atomic databases to real spectra), 
+by combining it with `the Hamiltonian Monte Carlo <https://en.wikipedia.org/wiki/Hamiltonian_Monte_Carlo>`_ 
+in recent probabilistic programming languages such as `NumPyro <https://github.com/pyro-ppl/numpyro>`_. 
+So, the notable features of ExoJAX are summarized as 
 
 - **HMC-NUTS, gradient-based optimizer available**
 - **Easy to use the latest molecular/atomic data in** :doc:`userguide/api`,  **and** :doc:`userguide/atomll` 
 - **A transparent open-source project; anyone who wants to participate can join the development!**
 
-|:green_circle:| If you have an error and/or want to know the up-to-date info, visit `ExoJAX wiki <https://github.com/HajimeKawahara/exojax/wiki>`_. Or use `the discussions form <https://github.com/HajimeKawahara/exojax/discussions>`_ on github or directly raise `issues <https://github.com/HajimeKawahara/exojax/issues>`_.
-
+|:green_circle:| If you have an error and/or want to know the up-to-date info, visit `ExoJAX wiki <https://github.com/HajimeKawahara/exojax/wiki>`_. 
+Or use `the discussions form <https://github.com/HajimeKawahara/exojax/discussions>`_ on github or directly raise `issues <https://github.com/HajimeKawahara/exojax/issues>`_.
+
 Contents
 ==================================
 
@@ -59,7 +65,7 @@ License & Attribution
 Copyright 2021-2023, Contributors
 
 - `Hajime Kawahara <http://secondearths.sakura.ne.jp/en/index.html>`_ (@HajimeKawahara, maintainer)
-- Yui Kawashima (@ykawashima)
+- `Yui Kawashima <https://sites.google.com/view/yuikawashima/home>`_ (@ykawashima, co-maintainer)
 - Kento Masuda (@kemasuda)
 - Ian Crossfield
 - Dirk van den Bekerom (@dcmvdbekerom)
@@ -69,6 +75,7 @@ Copyright 2021-2023, Contributors
 - Stevanus Nugroho (@astrostevanus)
 - Tako Ishikawa (@chonma0ctopus)
 - Yui Kasagi (@YuiKasagi)
+- Shotaro Tada (@sh-tada)
 
 ExoJAX is free software made available under the MIT License. See the ``LICENSE``.
 

documents/tutorials.rst

@@ -5,21 +5,23 @@ Basics
    :maxdepth: 1
 
    tutorials/get_started.rst
-   tutorials/optimize_spectrum_JAXopt.rst
+   tutorials/optimize_spectrum.rst
    tutorials/reverse_premodit.rst
 
 
 Applications
 ====================
 
-
-Retrieval More
---------------------------
+Tips for Real Analysis
+-------------------------
 
 .. toctree::
    :maxdepth: 1
 
+   tutorials/Fitting_Telluric_Lines.rst
    tutorials/reverse_precompute_grid.rst
+   userguide/memorysetting.rst	
+   tutorials/elower_setting.rst
 
 
 Transmission Spectra
@@ -30,6 +32,14 @@ Transmission Spectra
 
    tutorials/Transmission_beta.rst
 
+Reflection Spectrum
+------------------------------------
+
+.. toctree::
+   :maxdepth: 1
+
+   tutorials/Jupiter_cloud_model_using_amp.rst
+   tutorials/Jupiter_Hires_Modeling.rst
 
 Molecular/Atomic/Continuum Databases
 ---------------------------------------
@@ -42,14 +52,6 @@ Molecular/Atomic/Continuum Databases
    tutorials/Fortrat.rst
    tutorials/CIA_opacity.rst
 
-Tuning ExoJAX
-===========================
-
-.. toctree::
-   :maxdepth: 1
-
-   userguide/memorysetting.rst	
-   tutorials/elower_setting.rst
 
 Multi Molecule/Segments Mdb and Opa Handler
 =============================================
@@ -79,6 +81,15 @@ Cross Section using Various Opacity Calculators
 Others
 ================
 
+Scattering
+--------------------
+
+.. toctree::
+   :maxdepth: 1
+
+   userguide/rayleigh.rst
+
+
 Micro Chemical/Physical Processes
 --------------------------------------