Release v1.2

.github/workflows/main.yml

@@ -0,0 +1,61 @@
+name: Run pytest
+on:
+  # Triggers the workflow on push or pull request events but only for the "develop" and "master" branch
+  push:
+    branches: [ "develop" , "master"]
+  pull_request:
+    branches: [ "develop" , "master"]
+
+
+jobs:
+  pytest:
+    runs-on: ubuntu-latest
+
+    steps:
+      # Checkout repository
+      - name: Checkout
+        uses: actions/checkout@v2
+
+      # Setup Python
+      - name: Set up Python 3.8
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.8
+
+      # install package	  
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python setup.py install
+
+      # install pytest
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install pytest
+
+      # pytest -> JUnit xml
+      - name: PyTest
+        run: |
+          python -m pytest tests/unittests --junit-xml results/pytest.xml
+        continue-on-error: true
+
+      # show the results
+      - name: Upload Unit Test Results
+        if: ${{ always() }}
+        uses: actions/upload-artifact@v2
+        with:
+          name: Unit Test Results (Python 3.8)
+          path: results/*.xml
+
+      - name: Download Artifacts
+        if: success() || failure()
+        uses: actions/download-artifact@v2
+        with:
+          path: artifacts
+
+      - name: Publish Unit Test Results
+        uses: EnricoMi/publish-unit-test-result-action@v1
+        with:
+          files: artifacts/**/*.xml
+

CONTRIBUTING.md

@@ -15,25 +15,18 @@ We adopt a simple git-flow model, consisting of master, develop, contributor-def
 
 ## Issues and Discussion
 
-You can ask anything about exojax in Issue tracker and Discussion. 
+You can ask anything about ExoJAX in Issue tracker and Discussion. 
 
 ## Tests
 
 As proposed by @gully #86, we now have unit tests using pytest. 
-Please consider to include unit tests if your update gives new functionality to ExoJAX.
-Some external files are needed to complete all the tests. Check [here](http://secondearths.sakura.ne.jp/exojax/data/).
 
-## TIPS
-
-### pyformat
-
-Pyformat formats the code to follow a consistent style that used in ExoJAX.
+- tests/unittests: Unit tests, fast and independent from other databases as possible
+- tests/integration: mildly fast, it can include external databases
+- tests/endtoend: kind of samples including examples with PPLs 
 
-At minimum, you can use it as
 
-```sh
-pyformat -i your_code.py
-```
+## TIPS
 
 ### How to include data into exojax
 

LICENSES_bundled.txt

@@ -0,0 +1,34 @@
+Name: scipy
+Files: optimal_div_length
+TakenFrom: scipy.signal._signaltools._oa_calc_oalens
+License:
+Copyright (c) 2001-2002 Enthought, Inc. 2003-2022, SciPy Developers.
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions
+are met:
+
+1. Redistributions of source code must retain the above copyright
+   notice, this list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above
+   copyright notice, this list of conditions and the following
+   disclaimer in the documentation and/or other materials provided
+   with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived
+   from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

MANIFEST.in

@@ -1,10 +1,28 @@
 include src/exojax/data/atom/atomic.txt
 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/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_co_exomol.pickle
+include src/exojax/data/testdata/moldb_co_hitemp.pickle
+include src/exojax/data/testdata/moldb_co_hitemp_single_isotope.pickle
+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
+include src/exojax/data/testdata/premodit_test_ref.txt
+include src/exojax/data/testdata/premodit_test_hitemp_ref.txt
+include src/exojax/data/testdata/modit_rt_test_ref.txt
+include src/exojax/data/testdata/premodit_rt_test_ref.txt
+include src/exojax/data/testdata/premodit_rt_test_hitemp_ref.txt
+include src/exojax/data/testdata/modit_rt_test_vald_ref.txt
 
 graft tests
 graft examples

README.md

@@ -3,6 +3,7 @@
  [![Docs](https://img.shields.io/badge/docs-exojax-brightgreen)](http://secondearths.sakura.ne.jp/exojax/)
  [![arxiv](https://img.shields.io/badge/arxiv-2105.14782-blue)](http://arxiv.org/abs/2105.14782)
  [![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 modeling of exoplanets/brown dwarfs/M dwarfs using JAX. Read [the docs](http://secondearths.sakura.ne.jp/exojax) 🐕. 
 In a nutshell, ExoJAX enables you to do a HMC-NUTS fitting using the latest database.
@@ -52,7 +53,7 @@ autoxs.mdb is the [moldb.MdbExomol class](http://secondearths.sakura.ne.jp/exoja
 <details><summary>Emission Spectrum :heavy_check_mark: </summary>
 
 ```python
-from exojax.spec.rtransfer import nugrid
+from exojax.utils.grids import wavenumber_grid
 from exojax.spec import AutoRT
 nus,wav,res=nugrid(1900.0,2300.0,200000,"cm-1")
 Parr=numpy.logspace(-8,2,100) #100 layers from 10^-8 bar to 10^2 bar
@@ -127,9 +128,8 @@ nvcc -V
 Install such as
 
 ```
-sudo dpkg -i cudnn-local-repo-ubuntu2004-8.3.1.22_1.0-1_amd64.deb
-pip uninstall jax
-pip install "jax[cuda11_cudnn82]" -f https://storage.googleapis.com/jax-releases/jax_releases.html
+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.