Merge branch 'master' into ExoMol

.github/workflows/publish.yaml

@@ -0,0 +1,72 @@
+name: Publish on PyPI
+
+on:
+  release:
+    types: [published]
+  workflow_dispatch:
+
+
+jobs:
+  fix_release_deps:
+    permissions: write-all
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+    - uses: actions/setup-python@v4
+      with:
+        python-version: '3.12'
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip pip-tools setuptools
+
+    - name: Set configuration
+      run: |
+        git config --global user.name "${GITHUB_ACTOR}"
+        git config --global user.email "${GITHUB_ACTOR_ID}+${GITHUB_ACTOR}@users.noreply.github.com"
+
+    - name: Create requirements files
+      run: |
+        python tools/generate_requirements_txt.py
+        pip-compile -o requirements_full.txt pyproject.toml
+        git add requirements_full.txt requirements.txt
+        git commit -m "Updated requirements.txt files" || true
+
+    - name: Bump version to new tag
+      run: |
+        python -m pip install bump-my-version
+        bump-my-version bump --new-version $GITHUB_REF_NAME patch
+        git commit -am "Bump version to: $GITHUB_REF_NAME"
+
+    - name: Push back changes to master and tag
+      run: |
+        git tag --force $GITHUB_REF_NAME HEAD
+        git push --force --tags
+        git switch -C master
+        git push --set-upstream -f origin master
+
+  deploy:
+    needs: fix_release_deps
+    runs-on: ubuntu-latest
+    environment: release
+    permissions:
+      # IMPORTANT: this permission is mandatory for trusted publishing
+      id-token: write
+
+    steps:
+    - uses: actions/checkout@v3
+      with:
+        ref: ${{ github.ref_name }}
+
+    - uses: actions/setup-python@v4
+      with:
+        python-version: '3.12'
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install build setuptools>=61.2 wheel
+        python -m build --no-isolation
+
+    - name: Publish package
+      uses: pypa/gh-action-pypi-publish@release/v1

.github/workflows/tests.yaml

@@ -0,0 +1,53 @@
+name: Tests for JANUS
+
+on:
+  push:
+  pull_request:
+  workflow_dispatch:
+
+jobs:
+  test:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.10', '3.11', '3.12']
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Get SOCRATES
+        uses: actions/checkout@v4
+        with:
+          repository: 'FormingWorlds/SOCRATES'
+          path: 'SOCRATES'
+
+      - name: Setup system
+        run: |
+          sudo apt update
+          sudo apt-get install libnetcdff-dev netcdf-bin gfortran gcc
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Build SOCRATES
+        run: |
+          export LD_LIBRARY_PATH=""
+          cd SOCRATES
+          ./configure
+          ./build_code 
+          source set_rad_env
+          cd ..
+
+      - name: Build JANUS
+        run: |
+          pip install -e .
+
+      - name: Test with pytest
+        run: |
+          pip install pytest
+          export FWL_DATA="./fwl_data"
+          source SOCRATES/set_rad_env
+          pytest

.gitignore

@@ -17,22 +17,15 @@ Tprofile.pdf
 .DS_Store
 .vscode
 __pycache__/
-rad_trans/socrates_code/*
-!rad_trans/socrates_code/.gitkeep
 nogit_*
-spectral_files/shared
+src/janus/data/spectral_files/shared
 fwl_janus.egg-info
 
-# Ignore SOCRATES code files
-rad_trans/socrates_code/*
-
 # Video files
 *.mp4
-spectral_files/sp_b318_HITRAN_a16_gen_original
-spectral_files/sp_b318_HITRAN_a16_2203/temp
-spectral_files/sp_b318_HITRAN_a16_2203
-socrates_2002.tar.xz
-set_rad_env
+src/janus/data/spectral_files/sp_b318_HITRAN_a16_gen_original
+src/janus/data/spectral_files/sp_b318_HITRAN_a16_2203/temp
+src/janus/data/spectral_files/sp_b318_HITRAN_a16_2203
 
 output/
 utils/*.ipynb*

README.md

@@ -17,17 +17,12 @@ https://proteus-code.readthedocs.io
 * LS - Laurent Soucasse ([email protected])
 
 ### Repository structure
-* `README.md`                          - This file
-* `JANUS.env`                          - Sets environment flags to run the code
-* `src/janus/SocRadConv.py`            - Main JANUS Python script
-* `src/janus/data/luminosity_tracks/`  - Stellar evolution data
-* `src/janus/data/spectral_files/`     - Spectral files for SOCRATES
-* `src/janus/modules/`                 - Utility python scripts
-* `src/janus/plotting_tools/`          - Plotting scripts
-* `src/janus/utils/`                   - Utility python scripts
-* `tests/demo_runaway_greenhouse.py`   - Demonstrate pure-steam runaway greenhouse OLR curve
-* `tests/demo_instellation.py`         - Calculate fluxes (and temperatures) for different instellations
-* `tools/`                             - Useful tools
+* `README.md`           - This file
+* `src/janus/data/`     - Janus data files
+* `src/janus/modules/`  - Utility python scripts
+* `src/janus/utils/`    - Utility python scripts
+* `examples/`           - Typical use scripts
+* `tools/`              - Useful tools
 
 ### Developer installation instructions
 1. Download and install Socrates
@@ -36,14 +31,19 @@ https://proteus-code.readthedocs.io
     * `./configure`
     * `./build-code`
     * `source set_rad_env`
+    * `cd ..`
 2. Download and install Janus
     * `git clone [email protected]:FormingWorlds/JANUS.git`
     * `cd JANUS`
     * `pip install -e .`
+3. Download spectral files from the [OSF repository](https://osf.io/vehxg/)
+    * Set the environment variable FWL_DATA to define where the spectral data files will be stored
+        * `export FWL_DATA=...`
+    * Run the following commands within a python environment (or script) to download all basic spectral files
+        * `from janus.utils.data import DownloadSpectralFiles`
+        * `DownloadSpectralFiles()`
+    * Alternatively, you can specify which spectral data you want to download, and optionally the number of bands
+    * `DownloadSpectralFiles("/Frostflow", 4096)`
 
 ### Run instructions
-Only attempt to run JANUS after you have followed all of the instructions in INSTALL.md    
-If using a fresh shell, it is necessary to perform the following steps:     
-1. `source JANUS.env`    
-2. `conda activate janus`    
-Then you can run the code by running: `python SocRadConv.py`      
+In the examples folder you can find python scripts showing typical usecases/workflows of atmosphere modelling with Janus.

examples/SocRadConv.py

@@ -0,0 +1,133 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Created on Mon Jan 23 12:20:27 2023
+
+@authors: 
+Mark Hammond (MH)
+Tim Lichtenberg (TL)    
+Ryan Boukrouche (RB)
+Harrison Nicholls (HN)
+
+JANUS radiative-convective model, using SOCRATES for radiative-transfer.
+"""
+
+import matplotlib as mpl
+mpl.use('Agg')
+
+import time as t
+import os, shutil, toml
+import numpy as np
+from importlib.resources import files
+
+from janus.modules.stellar_luminosity import InterpolateStellarLuminosity
+from janus.modules.solve_pt import RadConvEqm
+from janus.modules.solve_pt import *
+from janus.modules.plot_flux_balance import plot_fluxes
+from janus.modules.plot_emission_spectrum import plot_emission
+from janus.utils.socrates import CleanOutputDir
+
+import janus.utils.GeneralAdiabat as ga # Moist adiabat with multiple condensibles
+from janus.utils.atmosphere_column import atmos
+import janus.utils.StellarSpectrum as StellarSpectrum
+from janus.utils.ReadSpectralFile import ReadBandEdges
+from janus.utils.data import DownloadSpectralFiles
+
+####################################
+##### Stand-alone initial conditions
+####################################
+if __name__ == "__main__":
+
+    print("Start JANUS")
+
+    # Set up dirs
+    if os.environ.get('RAD_DIR') == None:
+        raise Exception("Socrates environment variables not set! Have you installed Socrates and sourced set_rad_env?")
+    if os.environ.get('FWL_DATA') == None:
+        raise Exception("The FWL_DATA environment variable where spectral data will be downloaded needs to be set up!")
+    dirs = {
+            "janus": str(files("janus"))+"/",
+            "output": os.path.abspath(os.getcwd())+"/output/"
+            }
+
+    start = t.time()
+    ##### Settings
+    cfg_file =  dirs["janus"]+"data/tests/config_janus.toml"
+    with open(cfg_file, 'r'):
+          cfg = toml.load(cfg_file)  
+
+    # Planet
+    time = { "planet": cfg['planet']['time'], "star": cfg['star']['time']}
+    star_mass = cfg['star']['star_mass']
+    mean_distance = cfg['star']['mean_distance']
+
+    # Define volatiles by partial pressures
+    vol_mixing = {}
+    vol_partial = {
+        "H2O" : 9.0e5,
+        "CO2" : 2.0e5,
+        "CH4" : 3.0e5,
+        "CO" :  5.0e5,
+        "N2" :  4.0e5,
+        "H2" :  1.0e5,
+        }
+
+    # Tidy directory
+    if os.path.exists(dirs["output"]):
+        shutil.rmtree(dirs["output"])
+    os.mkdir(dirs["output"])
+
+    #Download required spectral files
+    DownloadSpectralFiles("/Dayspring")
+    DownloadSpectralFiles("/stellar_spectra")
+
+    # Move/prepare spectral file
+    print("Inserting stellar spectrum")
+    StellarSpectrum.InsertStellarSpectrum(
+        os.environ.get('FWL_DATA')+"/spectral_files/Dayspring/256/Dayspring.sf",
+        os.environ.get('FWL_DATA')+"/spectral_files/stellar_spectra/Sun_t4_4Ga_claire_12.txt",
+        dirs["output"]
+    )
+
+    band_edges = ReadBandEdges(dirs["output"]+"star.sf")
+
+    # Create atmosphere object
+    atm = atmos.from_file(cfg_file, band_edges, vol_mixing=vol_mixing, vol_partial=vol_partial)
+
+    # Set stellar heating on or off
+    if cfg['star']['stellar_heating'] == False: 
+        atm.instellation = 0.
+    else:
+        atm.instellation = InterpolateStellarLuminosity(star_mass, time, mean_distance)
+        print("Instellation:", round(atm.instellation), "W/m^2")
+
+    # Set up atmosphere with general adiabat
+    atm_dry, atm = RadConvEqm(dirs,
+                              time,
+                              atm,
+                              standalone=True,
+                              cp_dry=False,
+                              trppD=False, # Calculate dynamically?
+                              rscatter=False, # Rayleigh scattering on/off
+                              pure_steam_adj=False, # Pure steam convective adjustment
+                              surf_dt=False, # Surface temperature time-stepping
+                              # Options activated by surf_dt
+                              cp_surf=1e5, # Heat capacity of the ground [J.kg^-1.K^-1],
+                              mix_coeff_atmos=1e6, # mixing coefficient of the atmosphere [s]
+                              mix_coeff_surf=1e6 # mixing coefficient at the surface [s]
+                              )
+
+    # Plot abundances w/ TP structure
+    ga.plot_adiabats(atm,filename= dirs["output"]+"moist_ga.png")
+    atm.write_PT(filename= dirs["output"]+"moist_pt.tsv")
+    atm.write_ncdf( dirs["output"]+"moist_atm.nc")
+    plot_fluxes(atm,filename= dirs["output"]+"moist_fluxes.png")
+    plot_emission(atm, dirs["output"]+"toa_emission.png", planck_surface=True, show_bands=True)
+
+    # Tidy
+    CleanOutputDir(os.getcwd())
+    CleanOutputDir(dirs['output'])
+
+    end = t.time()
+    print("Runtime:", round(end - start,2), "s")
+