update readme (#103)

* update readme

* update notebook

.gitignore

@@ -1,8 +1,8 @@
-notebooks/.ipynb_checkpoints/
-notebooks/*.ipynb
+.ipynb_checkpoints
+*.ipynb
+*.png
 lace.egg-info/
-*/__pycache__/
-*/*/__pycache__/
+__pycache__
 .github/workflows/.python-tests.yml.swn
 .github/workflows/.python-tests.yml.swo
 .github/workflows/.python-tests.yml.swp

README.md

@@ -41,6 +41,14 @@ pip install -e .
 but there may be some issues.
 
 
+#### Notebooks:
+
+- All notebooks in the repository are in .py format. To generate the .ipynb version, run:
+
+```
+jupytext --to ipynb notebooks/*.py
+```
+
 - If you want to use notebooks via JupyterHub, you'll also need to download `ipykernel`:
 
 ```
@@ -104,7 +112,7 @@ The current version of the emulator, relased in this repo, does not emulate `alp
 
 In the `Notebooks` folder, there are several tutorials one can run to learn how to use the archives and emulators.
 
-- Archive tutorial: notebooks/Tutorial_bookkeeping.ipynb
-- Emulator tutorial: notebooks/Tutorial_emulator.ipynb
+- Archive tutorial: notebooks/Tutorial_bookkeeping.py
+- Emulator tutorial: notebooks/Tutorial_emulator.py
 
-In the `tests` folder, there are four scripts that you can run to open a Gadget or Nyx archive and run the G^and NN emulators.
+In the `tests` folder, there is a script that you can run to check that the package is working properly.

notebooks/Tutorial_emulator.py

@@ -59,6 +59,49 @@
 plt.ylabel(r'$\pi^{-1} \, k_\parallel \, P_\mathrm{1D}$')
 plt.xscale('log')
 
+# %% [markdown]
+# To get the amplitude and slope of the linear power spectrum from a target cosmology (input of emulator)
+
+# %%
+from lace.cosmo.camb_cosmo import get_cosmology
+from lace.cosmo.fit_linP import get_linP_Mpc_zs
+
+# %%
+h = 0.6778216034931903
+H0 = 100 * h
+omch2 = 0.11762521740991255
+ombh2 = 0.022239961079792658
+ns = 0.9628958142411611
+As = np.exp(3.0151299559643365)*1e-10
+
+cosmo = get_cosmology(H0=H0, omch2=omch2, ombh2=ombh2, ns=ns, As=As)
+
+zs = [3]
+kp_Mpc = 0.7
+get_linP_Mpc_zs(cosmo, zs, kp_Mpc)
+
+# %% [markdown]
+# To get the amplitude and slope of the linear power spectrum on kms units at z=3 for a target cosmology (output of cup1d)
+
+# %%
+from lace.cosmo.fit_linP import parameterize_cosmology_kms
+
+# %%
+h = 0.6778216034931903
+H0 = 100 * h
+omch2 = 0.11762521740991255
+ombh2 = 0.022239961079792658
+ns = 0.9628958142411611
+As = np.exp(3.0151299559643365)*1e-10
+
+cosmo = get_cosmology(H0=H0, omch2=omch2, ombh2=ombh2, ns=ns, As=As)
+
+zstar = 3
+kp_kms = 0.009
+camb_results = None
+parameterize_cosmology_kms(cosmo, camb_results, zstar, kp_kms)
+
+
 # %% [markdown]
 # #### nyx simulations
 
@@ -87,7 +130,7 @@
 plt.xscale('log')
 
 # %% [markdown]
-# ## For developers
+# ## A general user should stop here. For developers below
 
 # %%
 import os, sys