Merge pull request #537 from HajimeKawahara/releasev1_6

Release v1_6

.github/workflows/main.yml

@@ -17,10 +17,10 @@ jobs:
         uses: actions/checkout@v4
 
       # Setup Python
-      - name: Set up Python 3.10
+      - name: Set up Python 3.11
         uses: actions/setup-python@v4
         with:
-          python-version: '3.10'
+          python-version: '3.11'
 
       # install package	  
       - name: Install dependencies

MANIFEST.in

@@ -5,11 +5,13 @@ 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/abundance/xspec_abundance.txt
 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_ch4_trans.txt
 include src/exojax/data/testdata/spectrum_co.txt
 include src/exojax/data/testdata/moldb_vald.pickle
 include src/exojax/data/testdata/lpf_test_ref.txt

README.md

@@ -7,20 +7,21 @@
 
 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.
+In short, ExoJAX allows you to do gradient based optimizations, HMC-NUTS, and SVI using the latest database.
 
 ExoJAX is at least compatible with
 
-- 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)
+- PPLs: [NumPyro](https://github.com/pyro-ppl/numpyro), [blackjax](https://github.com/blackjax-devs/blackjax), [bayeux](https://github.com/jax-ml/bayeux) 
+- Optimizers: [JAXopt](https://github.com/google/jaxopt), [optax](https://github.com/google-deepmind/optax)
 
-<img src="https://github.com/HajimeKawahara/exojax/assets/15956904/8aa9673b-b64b-4b65-a76c-2966ef1edbc7" Titie="exojax" Width=850px>
+<img src="https://github.com/user-attachments/assets/70d4291b-f818-4204-ab96-b3bd6c99c48f" 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)
+- Opacity Calculators: opa  (Voigt profile, CIA, Mie, Rayleigh scattering etc)
 - Atmospheric Radiative Transfer: art (emission w, w/o scattering, refelction, transmission)
+- Spectral Operator: sop (planet rotation, instrumental boradening)
 - Atompsheric Microphysics: amp (clouds etc)
 
 </details>
@@ -29,87 +30,19 @@ ExoJAX is at least compatible with
 
 See [this page](http://secondearths.sakura.ne.jp/exojax/develop/tutorials/get_started.html) for the first step!
 
-## Functions
+## Real Examples (external)
 
-<details open><summary>Voigt Profile :heavy_check_mark: </summary>
-
-```python3
-from exojax.spec import voigt
-nu=numpy.linspace(-10,10,100)
-voigt(nu,1.0,2.0) #sigma_D=1.0, gamma_L=2.0
-```
-
-</details>
-
-<details><summary>Cross Section using HITRAN/HITEMP/ExoMol :heavy_check_mark: </summary>
-
-```python
-from exojax.utils.grids import wavenumber_grid
-from exojax.spec.api import MdbExomol
-from exojax.spec.opacalc import OpaPremodit
-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",)
-mdb = MdbExomol(".database/CO/12C-16O/Li2015",nu_grid)
-opa = OpaPremodit(mdb,nu_grid,auto_trange=[900.0,1100.0])
-xsv = opa.xsvector(1000.0, 1.0) # cross section for 1000K, 1 bar
-```
-
- <img src="https://user-images.githubusercontent.com/15956904/111430765-2eedf180-873e-11eb-9740-9e1a313d590c.png" Titie="exojax auto cross section" Width=850px> 
-
-</details>
-
-
-
-<details><summary>Do you just want to plot the line strength at T=1000K? </summary>
-
-```python
-mdb.change_reference_temperature(1000.) # at 1000K
-plt.plot(mdb.nu_lines,mdb.line_strength_ref,".")
-```
-
-</details>
-
-<details><summary>Emission Spectrum :heavy_check_mark: </summary>
-
-```python
-art = ArtEmisPure(nu_grid=nu_grid, pressure_btm=1.e2, pressure_top=1.e-8, nlayer=100)
-F = art.run(dtau, Tarr)
-```
-
-<img src="https://user-images.githubusercontent.com/15956904/116488770-286ea000-a8ce-11eb-982d-7884b423592c.png" Titie="exojax auto \emission spectrum" Width=850px> 
-
-</details>
-
-<details><summary>Transmission Spectrum :heavy_check_mark: </summary></details>
-<details><summary>Reflection Spectrum :heavy_check_mark: </summary></details>
-
-## Installation
-
-```
-pip install exojax
-```
-
-or
-
-```
-python setup.py install
-```
-
-<details><summary>Note on installation w/ GPU support</summary>
-
-:books: You need to install CUDA, JAX w/ NVIDIA GPU support.
-
-Visit [here](https://github.com/google/jax) for the installation of GPU supported JAX.
-
-</details>
+- :star: [exojaxample_WASP39b](https://github.com/sh-tada/exojaxample_WASP39b) : An example of HMC-NUTS for actual hot Saturn (JWST/ERS, NIRSPEC/G395H)
+- :star: [exojaxample_jupiter](https://github.com/HajimeKawahara/exojaxample_jupiter) : An example of HMC-NUTS for actual Jupiter reflection spectrum
 
 
 ## 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)
+- Paper II: in prep
+
+
 
 ## License
 

documents/conf.py

@@ -13,49 +13,53 @@
 import sphinx_rtd_theme
 import os
 import sys
-sys.path.insert(0, os.path.abspath('~/exojax'))
+
+sys.path.insert(0, os.path.abspath("~/exojax"))
 
 
 # -- Project information -----------------------------------------------------
 
-project = 'ExoJAX'
-copyright = '2020-2024, ExoJAX contributors'
-author = 'ExoJAX contributors'
+project = "ExoJAX"
+copyright = "2020-2024, ExoJAX contributors"
+author = "ExoJAX contributors"
 
 # The full version, including alpha/beta/rc tags
-release = '1.5.0'
+release = "1.6.0"
 
 
 # -- General configuration ---------------------------------------------------
 
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
-extensions = ['sphinx.ext.autodoc', 'sphinx.ext.napoleon', 'sphinxemoji.sphinxemoji',
-              ]
+extensions = [
+    "sphinx.ext.autodoc",
+    "sphinx.ext.napoleon",
+    "sphinxemoji.sphinxemoji",
+]
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path.
-exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
 
 
 # -- Options for HTML output -------------------------------------------------
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'sphinx_rtd_theme'
+html_theme = "sphinx_rtd_theme"
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
-html_logo = '_static/logo.png'
+html_static_path = ["_static"]
+html_logo = "_static/logo.png"
 
-#html_theme_options = {
+# html_theme_options = {
 #    'style_nav_header_background': '#333',
-#}
-html_css_files = ['header.css']
+# }
+html_css_files = ["header.css"]

documents/developers/doc.rst

@@ -23,9 +23,11 @@ Generates the up-to-date documents of tutorials
 
 The following commands automatically run the tutorial notebooks and generate rst:
 
+``documents/tutorials/``
+
+
 .. code:: sh
 
-	cd documents/tutorials/
     python jupyter2rst.py exe
 
 If you just want to generate rst without executing notebooks, try this:

documents/developers/pytest.rst

@@ -1,35 +1,31 @@
 Test codes for developers
 ==============================
 
-ExoJAX has many test codes in the ``tests`` directory. The ``test`` directory contains several types of the collection of ``pytest`` code.
+ExoJAX has many test codes in the ``tests`` directory. ExoJAX has three test categories. 
+
+Unit Tests
+-----------------
+``tests/unittests``: Tests in this category are automatically executed by GitHub Actions 
+when a pull request is made to the develop or master branch. 
+Therefore, items that need to be downloaded from external sites or take more than 10 seconds to run should not be included in this category. 
+Tests that take a long time but are considered unit tests should be placed in ``integrations/unittests_long``.
+
+Integration Tests
+-----------------
+``tests/integration``:　This category is for testing the behavior of multiple integrated functions. Tests that have a long execution time, 
+involve external downloads, or depend on the status of external servers should be included here if they are to be part of automated testing.
+ntegration tests also include comparisons with other codes or outputs, ensuring higher reliability. 
+However, since changes in the counterpart code can occur, the tests do not always succeed. 
+
+- ``tests/integration/comparison/transmission`` : An example of a transmission comparison with calculations done by Y. Kawashima using a different method.
+- ``tests/integration/comparison/twostream``: A comparison code with the radiative spectrum calculations performed by petitRADTRANS.
+- ``tests/integration/comparison/clouds``: A comparison with cloud models from VIRGA.
+
+End-to-end Tests
+-----------------
+``tests/endtoend``: In ExoJAX, codes like HMC-NUTS that require long execution times are often used in the final application. 
+Therefore, such tests belong to the end-to-end category. However, due to the long execution times, these tests are not run frequently.
 
-- ``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``.
-
-test/unittests
----------------------
-
-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
-
-   cd exojax/test/unittests
-   pytest 
-
-
-test/integration/unittest_long
-----------------------------------
-
-In essence, these are the unit tests that need longer time than the code in ``unittest``, sometimes including downloading the data.  
-
-test/integration/comparison
----------------------------
-
-The code for the comparison with external data, packages, etc 
-
-- ``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``
 
 
 

documents/index.rst

@@ -6,7 +6,9 @@
 ExoJAX
 ==================================
 
-Version 1.5 (:doc:`userguide/history`)
+Version 1.6 (:doc:`userguide/history`) 
+
+Note: Paper II will be under peer review. We plan to release version 2.0 at the time of acceptance of the paper II.
 
 `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, 
@@ -19,6 +21,11 @@ So, the notable features of ExoJAX are summarized as
 - **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!**
 
+.. admonition:: For a more geek-oriented explanation
+
+   ExoJAX is a spectral model based on the `Differentiable Programming (DP) <https://arxiv.org/abs/2403.14606>`_ paradigm!
+   ExoJAX aims to provide building blocks for retrieval code, much like Minecraft |:bricks:|.
+
 |: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>`_.
 
@@ -49,6 +56,13 @@ Contents
 
    exojax/exojax.rst
 
+ExoJAX example (exojaxample)
+---------------------------------
+
+- |:ringed_planet:| `exojaxample_WASP39b <https://github.com/sh-tada/exojaxample_WASP39b>`_ : An example of HMC-NUTS for actual hot Saturn (JWST/ERS, NIRSPEC/G395H)
+
+- |:ringed_planet:| `exojaxample_jupiter <https://github.com/HajimeKawahara/exojaxample_jupiter>`_ : An example of HMC-NUTS for actual Jupiter reflection spectrum
+
 
 References 
 ---------------------
@@ -57,12 +71,12 @@ References
   `ApJS 258, 31 (2022) <https://iopscience.iop.org/article/10.3847/1538-4365/ac3b4d>`_
   (Paper I)
 
+- Kawahara et al., 2024, in prep. (Paper II)
 
-
 License & Attribution
 ---------------------
 
-Copyright 2021-2023, Contributors
+Copyright 2021-2024, Contributors
 
 - `Hajime Kawahara <http://secondearths.sakura.ne.jp/en/index.html>`_ (@HajimeKawahara, maintainer)
 - `Yui Kawashima <https://sites.google.com/view/yuikawashima/home>`_ (@ykawashima, co-maintainer)
@@ -71,11 +85,13 @@ Copyright 2021-2023, Contributors
 - Dirk van den Bekerom (@dcmvdbekerom)
 - Daniel Kitzmann (@daniel-kitzmann)
 - Brett Morris (@bmorris3)
-- Erwan Pannier (@erwanp) and `RADIS <https://github.com/radis/radis>`_ community
+- Erwan Pannier (@erwanp) and Nicolas Minesi (@minouHub) from `RADIS <https://github.com/radis/radis>`_ community
 - Stevanus Nugroho (@astrostevanus)
 - Tako Ishikawa (@chonma0ctopus)
 - Yui Kasagi (@YuiKasagi)
 - Shotaro Tada (@sh-tada)
+- Ko Hosokawa (@KoHosokawa)
+- Hibiki Yama 
 
 ExoJAX is free software made available under the MIT License. See the ``LICENSE``.
 

documents/tutorials.rst

@@ -32,14 +32,19 @@ Transmission Spectra
 
    tutorials/Transmission_beta.rst
 
+|:ringed_planet:| An example of HMC-NUTS for actual hot Saturn (JWST/ERS, NIRSPEC/G395H) can be found `here <https://github.com/sh-tada/exojaxample_WASP39b>`_ .
+
+
 Reflection Spectrum
 ------------------------------------
 
 .. toctree::
    :maxdepth: 1
 
-   tutorials/Jupiter_cloud_model_using_amp.rst
-   tutorials/Jupiter_Hires_Modeling.rst
+   tutorials/jupiters/Jupiter_cloud_model_using_amp.rst
+   tutorials/jupiters/Jupiter_Hires_Modeling.rst
+
+|:ringed_planet:| An example of HMC-NUTS for actual Jupiter reflection spectrum can be found `here <https://github.com/HajimeKawahara/exojaxample_jupiter>`_ .
 
 Molecular/Atomic/Continuum Databases
 ---------------------------------------
@@ -51,6 +56,7 @@ Molecular/Atomic/Continuum Databases
    tutorials/branch.rst
    tutorials/Fortrat.rst
    tutorials/CIA_opacity.rst
+   tutorials/Forward_modeling_for_Fe_I_lines_of_Kurucz.rst
 
 
 Multi Molecule/Segments Mdb and Opa Handler
@@ -118,5 +124,7 @@ Others
    tutorials/hjerting.rst
    tutorials/pure_absorption_rt.rst
    tutorials/voigt_function.rst
+   tutorials/Cross_Section_using_Discrete_Integral_Transform.rst
+   tutorials/Cross_Section_using_Modified_Discrete_Integral_Transform.rst