Modifies the docs to account for the api change

Author: miguelgondu

docs/poli-docs/contributing/a_new_problem.md

@@ -233,7 +233,7 @@ If you can find your problem in this list, then you're set! You should be able t
 ```python
 from poli import objective_factory
 
-problem_info, f, x0, y0, _ = objective_factory.create(
+f, x0, y0 = objective_factory.create(
     name="your_problem",
     ...,
     your_arg_1=...,      # <-- Keywords you (maybe) needed

docs/poli-docs/getting_started/getting_started.md

@@ -128,7 +128,7 @@ Let's write a small script that creates an instance of `white_noise` from the re
 import numpy as np
 from poli import objective_factory
 
-problem_info, f, x0, y0, run_info = objective_factory.create(name="white_noise")
+f, x0, y0 = objective_factory.create(name="white_noise")
 
 x = np.array([["1", "2", "3"]])  # must be of shape [b, L], in this case [1, 3].
 for _ in range(5):

docs/poli-docs/using_poli/objective_repository/RaSP.md

@@ -36,7 +36,7 @@ Follow that with
 conda activate poli__rasp
 ```
 
-Supposing you have [`3ned.pdb`](https://www.rcsb.org/structure/3ned) in the same directory as this script:
+Assuming you have [`3ned.pdb`](https://www.rcsb.org/structure/3ned) in the same directory as this script:
 
 ```python
 from pathlib import Path
@@ -53,7 +53,7 @@ if __name__ == "__main__":
         # You could have more if you want.
     ]
 
-    problem_info, f_rasp, x0, y0, _ = objective_factory.create(
+    f_rasp, x0, y0 = objective_factory.create(
         name="rasp",
         wildtype_pdb_path=wildtype_pdb_paths_for_rasp,
     )
@@ -79,7 +79,7 @@ if __name__ == "__main__":
 
 :::{tab-item} In isolation
 
-Supposing you have [`3ned.pdb`](https://www.rcsb.org/structure/3ned) in the same directory as this script:
+Assuming you have [`3ned.pdb`](https://www.rcsb.org/structure/3ned) in the same directory as this script:
 
 ```python
 from pathlib import Path
@@ -96,7 +96,7 @@ if __name__ == "__main__":
         # You could have more if you want.
     ]
 
-    problem_info, f_rasp, x0, y0, _ = objective_factory.create(
+    f_rasp, x0, y0 = objective_factory.create(
         name="rasp",
         wildtype_pdb_path=wildtype_pdb_paths_for_rasp,
     )

docs/poli-docs/using_poli/objective_repository/aloha.md

@@ -19,7 +19,7 @@ import numpy as np
 from poli import objective_factory
 
 # How to create
-problem_info, f, x0, y0, run_info = objective_factory.create(name="aloha")
+f, x0, y0 = objective_factory.create(name="aloha")
 
 # Example input:
 x = np.array([["A", "L", "O", "O", "F"]])  # must be of shape [b, L], in this case [1, 5].

docs/poli-docs/using_poli/objective_repository/dockstring.md

@@ -76,7 +76,7 @@ import numpy as np
 from poli import objective_factory
 
 if __name__ == "__main__":
-    problem_info, f, x0, y0, _ = objective_factory.create(
+    f, x0, y0 = objective_factory.create(
         name="dockstring",
         target_name="DRD2",
         string_representation="SMILES",

docs/poli-docs/using_poli/objective_repository/drd3_docking.md

@@ -85,15 +85,15 @@ Running this objective function will create an `./oracle` folder on your working
 
 ::::{tab-set}
 
-:::{tab-item} (Isolated) in the `poli__lambo` environment
+:::{tab-item} (Isolated) in the `poli__tdc` environment
 
 After the setup described above, you can simply run the following code from 
 
 ```python
 from poli import objective_factory
 
 # How to create
-problem_info, f, x0, y0, run_info = objective_factory.create(
+f, x0, y0 = objective_factory.create(
     name="drd3_docking",
     force_register=True
 )

docs/poli-docs/using_poli/objective_repository/foldx_rfp_lambo.md

@@ -16,7 +16,7 @@ We need you to have `foldx` installed, and available in your home directory. We
 
 ### Python environment
 
-We expect you to have [cloned and installed the `lambo` repository](https://github.com/samuelstanton/lambo). Since there are some files we can't install automatically using `pip install git+...`, we ask you to create a `conda` environment for the lambo tasks:
+We recommend that you have [cloned and installed the `lambo` repository](https://github.com/samuelstanton/lambo). Since there are some files we can't install automatically using `pip install git+...`, we recommend that you create a `conda` environment for the lambo tasks:
 
 ```
 # From the root of the poli repository
@@ -44,6 +44,13 @@ In particular, we need
 
 Make sure the data is avaliable.
 
+:::{admonition} We can install `lambo` automatically
+:class: dropdown
+
+These steps can be skipped. If so, we will install LaMBO automatically and download the relevant files using `PyGithub`. That being said, the API of GitHub limits queries if you are doing anonymous queries. If you decide to skip installing lambo, we recommend that you add an environment variable called `GITHUB_TOKEN_FOR_POLI` whose value is a personal token. [See how to create one here.](https://docs.github.com/en/authentication/keeping-your-account-and-data-secure/managing-your-personal-access-tokens#creating-a-fine-grained-personal-access-token)
+
+:::
+
 ## How to run
 
 You can only run this objective function either in the `poli__lambo` environment, or as an isolated process (which runs this environment underneath).
@@ -62,8 +69,8 @@ import numpy as np
 from poli import objective_factory
 
 # How to create
-problem_info, f, x0, y0, run_info = objective_factory.create(
-    name="foldx_rfp",
+f, x0, y0 = objective_factory.create(
+    name="foldx_rfp_lambo",
 )
 
 # Example input:

docs/poli-docs/using_poli/objective_repository/foldx_sasa.md

@@ -62,7 +62,7 @@ from poli import objective_factory
 wildtype_pdb_file = Path("path/to/wildtype.pdb")
 
 # How to create
-problem_info, f, x0, y0, run_info = objective_factory.create(
+f, x0, y0 = objective_factory.create(
     name="foldx_sasa",
     wildtype_pdb_file=wildtype_pdb_file
 )
@@ -91,7 +91,7 @@ from poli import objective_factory
 wildtype_pdb_file = Path("path/to/wildtype.pdb")
 
 # How to create
-problem_info, f, x0, y0, run_info = objective_factory.create(
+f, x0, y0 = objective_factory.create(
     name="foldx_sasa",
     wildtype_pdb_file=wildtype_pdb_file,
     force_register=True,

docs/poli-docs/using_poli/objective_repository/foldx_stability.md

@@ -61,7 +61,7 @@ from poli import objective_factory
 wildtype_pdb_file = Path("path/to/wildtype.pdb")
 
 # How to create
-problem_info, f, x0, y0, run_info = objective_factory.create(
+f, x0, y0 = objective_factory.create(
     name="foldx_stability",
     wildtype_pdb_file=wildtype_pdb_file
 )
@@ -90,7 +90,7 @@ from poli import objective_factory
 wildtype_pdb_file = Path("path/to/wildtype.pdb")
 
 # How to create
-problem_info, f, x0, y0, run_info = objective_factory.create(
+f, x0, y0 = objective_factory.create(
     name="foldx_stability",
     wildtype_pdb_file=wildtype_pdb_file,
     force_register=True,

docs/poli-docs/using_poli/objective_repository/penalized_logp_lambo.md

@@ -57,7 +57,7 @@ import numpy as np
 from poli import objective_factory
 
 # Using create
-problem_info, f, x0, y0, _ = objective_factory.create(name="penalized_logp_lambo")
+f, x0, y0 = objective_factory.create(name="penalized_logp_lambo")
 
 # An example input
 print(x0)
@@ -77,10 +77,3 @@ f.terminate()
 
 - `penalized: bool = True`. Whether we are evaluating penalized logP or not.
 - `string_representation: str = "SMILES"`. Can be either `"SMILES"` or `"SELFIES"`.
-
-<!-- ## References
-
-:::{bibliography}
-:style: alpha
-
-::: -->