Change sunbather structure to make it packageable

.flake8

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+[flake8]
+max-line-length = 88
+per-file-ignores =
+    # imported but unused
+    __init__.py: F401
+

.github/workflows/pylint.yml

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+name: Pylint
+
+on: [push]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.9", "3.10", "3.11"]
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install pylint
+        pip install -e .
+    - name: Analysing the code with pylint
+      run: |
+        pylint -d C0301,C0103,C0209 --fail-under 8.5 $(git ls-files '*.py')

.gitignore

@@ -1,12 +1,11 @@
 .DS_Store
-src/.DS_Store
-src/RT_tables/.DS_Store
-examples/.DS_Store
-examples/materials/.DS_Store
-tests/.DS_Store
-tests/materials/.DS_Store
-src/__pycache__/
-examples/.ipynb_checkpoints
+__pycache__/
+*.ipynb_checkpoints
+*.egg-info
+*.swp
 examples/WASP52b_dT.csv
 examples/WASP52b_sigmaT.csv
 examples/WASP52b_nsig_fit.csv
+env/
+dist/
+src/sunbather/cloudy

.readthedocs.yaml

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+# Read the Docs configuration file for Sphinx projects
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the OS, Python version and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.12"
+    # You can also specify other tool versions:
+    # nodejs: "20"
+    # rust: "1.70"
+    # golang: "1.20"
+
+# Build documentation in the "docs/" directory with Sphinx
+sphinx:
+  configuration: docs/conf.py
+  # You can configure Sphinx to use a different builder, for instance use the dirhtml builder for simpler URLs
+  # builder: "dirhtml"
+  # Fail on all warnings to avoid broken references
+  # fail_on_warning: true
+
+# Optionally build your docs in additional formats such as PDF and ePub
+# formats:
+#   - pdf
+#   - epub
+
+# Optional but recommended, declare the Python requirements required
+# to build your documentation
+# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
+python:
+  install:
+    - requirements: docs/requirements.txt

MANIFEST.in

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+recursive-include src/sunbather *

docs/Makefile

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+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/api.rst

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+API
+===
+
+.. autosummary::
+   :toctree: generated
+
+   sunbather
+   sunbather.construct_parker
+   sunbather.convergeT_parker
+   sunbather.install_cloudy
+   sunbather.solveT
+   sunbather.tools

docs/conf.py

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+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+import sys
+import os
+from pathlib import Path
+
+sys.path.insert(0, str(Path('..', 'src').resolve()))
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+project = "sunbather"
+copyright = "2024, Dion Linssen"
+author = "Dion Linssen"
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = [
+    "sphinx_rtd_theme",
+    "sphinx.ext.autodoc",
+    "sphinx.ext.autosummary",
+    "myst_parser",
+]
+
+templates_path = ["_templates"]
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
+
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+# html_theme = 'alabaster'
+html_theme = "sphinx_rtd_theme"
+html_static_path = ["_static"]
+
+
+# Configuration for Read the Docs
+html_baseurl = os.environ.get("READTHEDOCS_CANONICAL_URL", "/")

docs/faq.md

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+# FAQ
+
+## How do I create Parker wind profiles?
+
+Add the parameters of the planet/star system to the *$SUNBATHER_PROJECT_PATH/planets.txt* file. Make sure the SED you specify in _planets.txt_ is present in the _$CLOUDY_PATH/data/SED/_ folder in the right format. Then run the `construct_parker.py` module in your terminal (use `-help` to see the arguments). 
+
+## How do I choose the composition of the atmosphere?
+
+The composition usually has to be specified at two stages:  
+
+1. When creating the Parker wind profiles with the `construct_parker.py` module: You can choose to use a pure H/He composition (which uses `p-winds` standalone) by specifying the hydrogen fraction by number with the `-fH` argument. You can also choose an arbitrary composition that includes metal species (which uses `p-winds` and _Cloudy_ in tandem) with the `-z` and `-zelem` arguments. In this case, `-z` specifies a metallicity relative to solar and is thus a scaling factor for all metal species. `-zelem` can be used to scale the abundance of individual elements, for example as `-zelem Na=3 Mg+=10 Fe+2=0.5 K=0`. Note that `-z` and `-zelem` can be used together and are **multiplicative**. In `construct_parker.py`, the composition only affects the wind structure through the mean molecular weight. Therefore, using `-z` and `-zelem` is only needed for (highly) supersolar metallicities; using `-fH 0.9` will usually suffice for a solar composition atmosphere.
+
+2. When simulating Parker wind profiles with _Cloudy_ with the `convergeT_parker.py` module: You can specify the composition with the `-z` and `-zelem` arguments as explained under point 1. The default is a solar composition, so `-z 1`. If you want to simulate a pure H/He composition with _Cloudy_, you can pass `-z 0` (and specify the He abundance through `-zelem He=...)`. Contrary to point 1 however, in `convergeT_parker.py`, the metal content directly affects the thermal structure and XUV absorption, so we recommend using `-z 1` even when you only make hydrogen and helium spectra.
+
+## How do I calculate the transmission spectrum?
+
+Create the Parker wind profile with `construct_parker.py` and simulate it with _Cloudy_ with `convergeT_parker.py` while making sure you specify for which species you want to save output with the `-save_sp` argument (if unsure, just pass `-save_sp all`). Then, load the _Cloudy_ output in your Python script with the `tools.Sim` class (see FAQ below), and use the `RT.FinFout()` function to make the transit spectrum. At minimum, `RT.FinFout()` expects the `Sim` object, a wavelength array, and a list of species for which to calculate the spectrum. See the _sunbather/examples/fit_helium.ipynb_ notebook for an example.
+
+## How do I simulate one planet with different stellar SEDs?
+
+The safest way is to add another entry in the *$SUNBATHER_PROJECT_PATH/planets.txt* file, with the same parameter values, but a different "name" and "SEDname" (the "full name" can be the same). 
+
+Alternatively and more prone to mistakes, the `construct_parker.py` and `convergeT_parker.py` modules also has the `-SEDname` argument which allows you to specify a different name of the SED file without making a new entry in the _planets.txt_ file. In this case, it is **strongly advised** to use a different `-pdir` and `-dir` (that references the SED type) as well. 
+
+## Why do I have to specify a `-pdir` and a `-dir`?
+
+Generally, for one planet you may want to create Parker wind profiles with different temperatures, mass-loss rates, but also different atmospheric compositions. The `-pdir` and `-dir` correspond to actual folders on your machine. Each folder groups together profiles with different $T$ and $\dot{M}$, so the `-pdir` and `-dir` effectively allow you to separate the profiles by composition. `-pdir` corresponds to the folder where the Parker wind **structure** (i.e. density and velocity as a function of radius) is stored: *$SUNBATHER_PROJECT_PATH/parker_profiles/planetname/pdir/*, and `-dir` corresponds to the folder where the _Cloudy_ simulations of the profiles are stored: *$SUNBATHER_PROJECT_PATH/sims/1D/planetname/dir/*.
+
+For example, you can make one `-pdir` which stores a grid of $T-\dot{M}$ profiles at a H/He ratio of 90/10, and another which stores a grid of profiles at a ratio of 99/01. The reason that the  `-dir` argument is not the exact same as the `-pdir` argument, is that you may want to create your Parker wind structure profile only once (in one `-pdir` folder) but then run it multiple times with _Cloudy_ while changing the abundance of one particular trace element (in multiple `-dir` folders). The latter would usually not really change the atmospheric structure, but could produce a very different spectral feature.
+
+## How do I read / plot the output of Cloudy in Python?
+
+The `Sim` class in the `tools.py` module can be used to read in simulations by giving the full path to the simulation. _Cloudy_ output is separated into different output files, which all have the same name but a different extension. The bulk structure of the atmosphere (including temperature and density) is stored in the ".ovr" file. The radiative heating and cooling rates as a function of radius are stored in the ".heat" and ".cool" files. The densities of different energy levels of different atomic/ionic species are stored in the ".den" file. These files are all read in as a Pandas dataframe and can be accessed as follows:
+
+``` python
+import sys
+sys.path.append("/path/to/sunbather/src/")
+import tools
+
+mysimulation = tools.Sim(tools.projectpath+"/sims/1D/planetname/dir/parker_T_Mdot/converged")
+
+#to get the planet parameters of this simulation:
+mysimulation.p.R #radius
+mysimulation.p.Mstar #mass of host star
+
+#to get Cloudy output
+mysimulation.ovr.alt #radius grid of the following profiles:
+mysimulation.ovr.rho #density profile
+mysimulation.ovr.Te #temperature profile
+mysimulation.ovr.v #velocity profile
+mysimulation.cool.ctot #total radiative cooling
+mysimulation.den['H[1]'] #density of ground-state atomic hydrogen
+mysimulation.den['He[2]'] #density of metastable helium
+mysimulation.den['Fe+2[10]'] #density of the tenth energy level of Fe 2+
+```
+
+## Can I run a Parker wind profile through Cloudy while using the isothermal temperature profile?
+
+Yes, you can pass the `-constantT` flag to `convergeT_parker.py` to simulate the Parker wind profile without converging on a nonisothermal temperature structure. This will save a _Cloudy_ simulation called "constantT" and the folder structure works the same way as for converged simulations: you again need to pass a `-dir` where the simulation is saved, and you can in principle use the same directory that you use for converged profiles (but you will need to pass the `-overwrite` flag if the converged nonisothermal simulation already exists - nothing will be overwritten in this case though!).
+
+## I forgot to specify for which species I want Cloudy output with the `-save_sp` argument. Do I need to run `convergeT_parker.py` again from scratch?
+
+You can use the `tools.insertden_Cloudy_in()` function to add species to a (converged) Cloudy simulation file and run it again, without having to go through the temperature convergence scheme again. If you want to do this for a grid of Parker wind models, you will have to set up a loop over the correct filepaths yourself.
+
+## Can I run an atmospheric profile other than an (isothermal) Parker wind?
+
+You can "trick" the code into running an arbitrary outflow profile by saving your density and velocity profile in the expected file format in the *$SUNBATHER_PROJECT_PATH/parker_profiles/* folder. For example, you can create a simple density and velocity profile in Python:
+
+``` python
+p = tools.Planet('generic_planet') #make sure you add the parameters in planets.txt
+
+r = np.linspace(1, 10, num=1000) * p.R #in cm
+rho = 1e-15 / np.linspace(1, 10, num=1000)**3 #falls with r^3
+v = 5e4 * np.linspace(1, 10, num=1000) #starts at 0.5km/s, increases linearly with r so that Mdot = 4 pi rho v r^2 is constant
+mu = np.repeat(np.nan, 1000) #mu is not used by convergeT_parker.py
+
+print("log(Mdot) =", np.log10(4*np.pi*r[0]**2*rho[0]*v[0]))
+
+np.savetxt(tools.projectpath+'/parker_profiles/'+p.name+'/geometric/pprof_'+p.name+'_T=0_M=0.000.txt', np.column_stack((r, rho, v, mu)), delimiter='\t')
+```
+
+You can then solve the temperature structure of this profile with: `python convergeT_parker.py -plname generic_planet -pdir geometric -dir geometric -T 0 -Mdot 0`
+
+Similarly, you could for example postprocess the density and velocity profile of an _ATES_ simulation (Caldiroli et al. 2021) with _sunbather_ to produce a transmission spectrum.
+
+## How do I stop the simulation at the Roche radius / choose the maximum radius?
+
+The `construct_parker.py` module always creates a profile up until 20 $R_p$ and this can only be changed by editing the source code. 
+
+The `convergeT_parker.py` module by default simulates the atmosphere with *Cloudy* up until 8 $R_p$ and this can be changed with the `-altmax` argument. 
+
+The `RT.FinFout()` function by default makes a transit spectrum based on the full *Cloudy* simulation (so up until 8 $R_p$), but you can give an upper boundary in cm with the `cut_at` argument. For example, if you want to include only material up until the planet's Roche radius when making the transit spectrum, it generally doesn't hurt to leave `construct_parker.py` and `convergeT_parker.py` at the default values, and just pass `cut_at=mysimulation.p.Rroche` to `RT.FinFout()` (assuming `mysimulation` is the `tools.Sim` object of your *Cloudy* simulation).