new readme

README.md

@@ -1,35 +1,48 @@
 # 21cmCAST
 
-[![PyPI - Python Version](https://img.shields.io/pypi/pyversions/py21cmcast)](https://pypi.org/project/py21cmcast/)
-[![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
 [![Build Status](https://github.com/gaetanfacchinetti/21cmCAST/actions/workflows/python-package.yml/badge.svg?branch=main)](https://github.com/gaetanfacchinetti/21cmCAST/actions/workflows/CI.yml?query=branch%3Amain)
 
+[![PyPI - Python Version](https://img.shields.io/pypi/pyversions/py21cmcast)](https://pypi.org/project/py21cmcast/)
+[![PyPi Version](https://img.shields.io/pypi/v/py21cmcast.svg)](https://pypi.python.org/pypi/py21cmcast/)
+[![License: GPL v3](https://img.shields.io/badge/license-GPLv3-green.svg)](https://www.gnu.org/licenses/gpl-3.0)
+
+[![Static Badge](https://img.shields.io/badge/physics-cosmology-darkblue)](https://en.wikipedia.org/wiki/Cosmology)
+[![Static Badge](https://img.shields.io/badge/physics-21cm-yellow)](https://en.wikipedia.org/wiki/Hydrogen_line)
+[![Static Badge](https://img.shields.io/badge/stats-fisher-green)](https://en.wikipedia.org/wiki/Fisher_information)
+
+
 
-This package provides tools to perform Fisher fore**CAST**s from 21cmFAST outputs. It has been built on / complementarily to the [21cmFish](https://21cmfish.readthedocs.io/en/latest/) package[^1]. A detailed example of how it works can be found in [**scripts/exec/fisher.ipynb**](./scripts/exec/fisher.ipynb). 
+This lightweight package provides tools to perform automated analysis of [21cmFAST](https://21cmfast.readthedocs.io/en/latest/)[^1][^2] outputs and in particular run Fisher fore**CAST**s. It has initially been built on / complementarily to the [21cmFish](https://21cmfish.readthedocs.io/en/latest/) package[^3]. 
 
-In order to work properly, the codes requires to have a working installation of
-- [**21cmFAST**](https://21cmfast.readthedocs.io/en/latest/)[^2][^3]
-- [**21cmSense**](https://21cmsense.readthedocs.io/en/latest/)[^4]
+---
+ ⚠️ **If you are using this code**, please cite the following work for which it has been developped
+> *Gaétan Facchinetti, Laura Lopez-Honorez, Yuxiang Qin, Andrei Mesinger*, 21cm signal sensitivity to dark matter decay [[JCAP 01 (2024) 005]](https://iopscience.iop.org/article/10.1088/1475-7516/2024/01/005) [[arXiv:2308.16656]](https://arxiv.org/abs/2308.16656)
 
-If you are considering using this code, please cite the following work for which it has been developped
-- *G. Facchinetti, L. Lopez-Honorez, Y. Qin, A. Mesinger*, 21cm signal sensitivity to dark matter decay [[arXiv:2308.16656]](https://arxiv.org/abs/2308.16656)
+</br>
+
+<p align="center">
+  <img src="illustration.png" width="430" height="450" />
+</p>
 
 
 ## Installation
 
-In order to install the code you can install it with pip running
+In order to install the code you can install it with pip, running
 ```
 pip install py21cmcast
 ```
-In order to use and modify the code clone this repository and run
+To install a modified version of the code (or the latest version, available on github) clone this repository and run
 ```
 pip install -e .
 ```
-in the main folder.
+in the main folder. In addition, `meta.yaml` and `build.sh` files are provided for a manual installation with conda. However, the conda install is not garanteed to succeed since it has not been tested.
+
+Although the installation should proceed and you should be able to import the package into your python environement, in order to analyse 21cmFAST raw data, the codes requires to have a working installation of 21cmFAST. For Fisher forcasts, you will need to install [21cmSense](https://21cmsense.readthedocs.io/en/latest/)[^4] in order to evaluate the sensitivity of instruments (current version works with 21cmSense version 2.0.0).
+
 
 ## Quick start guide
 
-Examples on how to run the code are available [here](./examples/) along with an example of input config file.
+Examples on how to run the code are available [here](./examples/) along with an minimal example of input config file.
 
 
 ## Ongoing work
@@ -39,10 +52,12 @@ To do list:
 - [ ] uniformely use astropy units throughout the entire code
 - [ ] add docstrings to the classes
 
-[^1]: *Charlotte A. Mason, Julian B. Muñoz, Bradley Greig, Andrei Mesinger, and Jaehong Park*, 21cmfish: Fisher-matrix framework for fast parameter forecasts from the cosmic 21-cm signal [[arXiv:2212.09797]](https://arxiv.org/abs/2212.09797)
 
-[^2]: *Andrei Mesinger, Steven Furlanetto, and Renyue Cen*, 21cmFAST: A Fast, Semi-Numerical Simulation of the High-Redshift 21-cm Signal [[arXiv:1003.3878]](https://arxiv.org/abs/1003.3878)
+--- 
+[^1]: *Andrei Mesinger, Steven Furlanetto, and Renyue Cen*, 21cmFAST: A Fast, Semi-Numerical Simulation of the High-Redshift 21-cm Signal [[arXiv:1003.3878]](https://arxiv.org/abs/1003.3878)
+
+[^2]: *Andrei Mesinger and Steven Furlanetto*, Efficient Simulations of Early Structure Formation and Reionization [[arXiv:0704.0946]](https://arxiv.org/abs/0704.0946)
 
-[^3]: *Andrei Mesinger and Steven Furlanetto*, Efficient Simulations of Early Structure Formation and Reionization [[arXiv:0704.0946]](https://arxiv.org/abs/0704.0946)
+[^3]: *Charlotte A. Mason, Julian B. Muñoz, Bradley Greig, Andrei Mesinger, and Jaehong Park*, 21cmfish: Fisher-matrix framework for fast parameter forecasts from the cosmic 21-cm signal [[arXiv:2212.09797]](https://arxiv.org/abs/2212.09797)
 
 [^4]: *Jonathan C. Pober, Adrian Liu, Joshua S. Dillon, James E. Aguirre, Judd D. Bowman et al.*, What Next-Generation 21 cm Power Spectrum Measurements Can Teach Us About the Epoch of Reionization [[arXiv:1310.7031]](https://arxiv.org/abs/1310.7031)

build.sh

@@ -0,0 +1 @@
+$PYTHON setup.py install     # Python command to install the script.

examples/fisher.ipynb

@@ -12,10 +12,7 @@
     "from astropy import units\n",
     "\n",
     "import warnings\n",
-    "warnings.filterwarnings(\"ignore\", category=np.VisibleDeprecationWarning)\n",
-    "\n",
-    "%load_ext autoreload\n",
-    "%autoreload 2"
+    "warnings.filterwarnings(\"ignore\", category=np.VisibleDeprecationWarning)"
    ]
   },
   {
@@ -66,7 +63,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "z_bins, z_centers, k_bins = p21c.define_grid_modes_redshifts(6., 8 * units.MHz, z_max = 22, k_min = 0.1 / units.Mpc, k_max = 1 / units.Mpc)\n",
+    "z_bins, z_array, k_bins = p21c.define_grid_modes_redshifts(6., 8 * units.MHz, z_max = 22, k_min = 0.1 / units.Mpc, k_max = 1 / units.Mpc)\n",
     "print(\"The redshift bin edges are:\", z_bins)\n",
     "print(\"The mode bin edges are:\", k_bins)"
    ]
@@ -78,7 +75,7 @@
    "source": [
     "## III. Define the fiducial model and get its power spectrum\n",
     "\n",
-    "A **Fiducial** object can be defined by specifying the path where the lightcones are saved (depends on what was set on the config file) as well as  the redshifts and modes bin edges. Note that we must set by hand whether the mode bins are linearly of logarithmically spaced with the option **logk**  that is by default **False** as the output mode bin deges returned by **define\\_grid\\_modes\\_redshits()** are linearly spaced. Further options can be specified, such as an **observation**  and a fraction of modeling error **frac\\_mod** (see below)."
+    "A **Fiducial** object can be defined by specifying the path where the lightcones are saved (depends on what was set on the config file) as well as  the redshifts and modes bin edges. Note that we must set by hand whether the mode bins are linearly of logarithmically spaced with the option **logk**  that is by default **False** as the output mode bin deges returned by **define\\_grid\\_modes\\_redshits()** are linearly spaced. Further options can be specified, such as a fraction of modeling error **frac\\_mod** (see below)."
    ]
   },
   {
@@ -87,7 +84,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "fiducial = p21c.Fiducial(\"../runs/CONSTRAINT_BKR_MINIHALOS\", z_bins, z_centers, k_bins, False, load=True)"
+    "fiducial = p21c.Fiducial(\"../runs/CONSTRAINT_BKR_MINIHALOS\", z_bins, z_array, k_bins, False, load=True)"
    ]
   },
   {
@@ -123,7 +120,7 @@
    "source": [
     "## IV. Evaluate experimental noise\n",
     "\n",
-    "The experimental noise is derived using **21cmSense**. To that end one simply has to fix the 'observation' attribute of the fiducial object. The only valid input for now is 'HERA' but other can be added straightforwardly."
+    "The experimental noise is derived using **21cmSense**. To that end one simply has to pass an 'observation_set' attribute to the compute_sensitivity() method of the fiducial object. If none are passed the default is used `default_HERA`. To use a custom instrument create a list of 21cmSense Observations objects the length of 'fiducial.z_array' (each observation corresponding to the redshift in `fiducial.z_array`)."
    ]
   },
   {

meta.yaml

@@ -0,0 +1,49 @@
+{% set name = "py21cmcast" %}
+{% set version = "1.0.2" %}
+
+package:
+  name: {{ name|lower }}
+  version: {{ version }}
+
+source:
+  url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/py21cmcast-{{ version }}.tar.gz
+  sha256: ac4716cf9817bd9d11ef4a3217b5c6825c1f683f2dc716d6f28e21cb9dbc8cf4
+
+build:
+  noarch: python
+  script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation
+  number: 0
+
+requirements:
+  host:
+    - python >=3.6
+    - setuptools >=61.0.0
+    - wheel
+    - pip
+  run:
+    - python >=3.6
+    - numpy >=1.16.5
+    - matplotlib-base >=3.4.3
+    - powerbox >=0.7.3
+    - configparser >=6.0.0
+    - astropy >=5.0.0
+    - scipy
+
+test:
+  imports:
+    - py21cmcast
+  commands:
+    - pip check
+  requires:
+    - pip
+
+about:
+  summary: Fisher forecasts with 21cm experiments
+  license: GPL-3.0
+  license_file: LICENSE
+  home:
+    dev_url: https://github.com/gaetanfacchinetti/21cmCAST
+
+extra:
+  recipe-maintainers:
+    - gaetanfacchinetti