From 199d77490ea4ac1e3bba495f1439838b536d35f4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Miguel=20Gonz=C3=A1lez=20Duque?= Date: Mon, 8 Jul 2024 14:31:51 +0200 Subject: [PATCH] Relaxes numpy requirements --- environment.yml | 2 +- .../a_simple_objective_function_registration/environment.yml | 2 +- pyproject.toml | 2 +- requirements.txt | 2 +- src/poli/core/chemistry/environment.yml | 2 +- src/poli/objective_repository/aloha/environment.yml | 2 +- src/poli/objective_repository/foldx_rfp_lambo/environment.yml | 2 +- src/poli/objective_repository/foldx_sasa/environment.yml | 2 +- src/poli/objective_repository/foldx_stability/environment.yml | 2 +- .../foldx_stability_and_sasa/environment.yml | 2 +- src/poli/objective_repository/gfp_cbas/environment.yml | 2 +- src/poli/objective_repository/gfp_select/environment.yml | 2 +- .../objective_repository/penalized_logp_lambo/environment.yml | 2 +- src/poli/objective_repository/rasp/environment.yml | 2 +- src/poli/objective_repository/rdkit_logp/environment.yml | 2 +- src/poli/objective_repository/rdkit_qed/environment.yml | 2 +- .../rfp_foldx_stability_and_sasa/environment.yml | 2 +- src/poli/objective_repository/sa_tdc/environment.yml | 2 +- src/poli/objective_repository/super_mario_bros/environment.yml | 2 +- .../objective_repository/toy_continuous_problem/environment.yml | 2 +- src/poli/objective_repository/white_noise/environment.yml | 2 +- 21 files changed, 21 insertions(+), 21 deletions(-) diff --git a/environment.yml b/environment.yml index 45b09709..4c3deed0 100644 --- a/environment.yml +++ b/environment.yml @@ -5,7 +5,7 @@ dependencies: - python=3.9 - pip - pip: - - numpy<2 + - numpy - rdkit - biopython - selfies diff --git a/examples/the_basics/a_simple_objective_function_registration/environment.yml b/examples/the_basics/a_simple_objective_function_registration/environment.yml index 77d338fb..8ccd9ade 100644 --- a/examples/the_basics/a_simple_objective_function_registration/environment.yml +++ b/examples/the_basics/a_simple_objective_function_registration/environment.yml @@ -5,5 +5,5 @@ dependencies: - python=3.9 - pip - pip: - - numpy<2 + - numpy - "git+https://github.com/MachineLearningLifeScience/poli.git@dev" diff --git a/pyproject.toml b/pyproject.toml index f479db96..f4a157b5 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -22,7 +22,7 @@ classifiers = [ ] keywords = ["optimization", "molecular", "discrete", "proteins"] dependencies = [ - "numpy<2", + "numpy", "rdkit", "selfies" ] diff --git a/requirements.txt b/requirements.txt index e4628f72..fae4145b 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,3 +1,3 @@ -numpy<2 +numpy rdkit selfies diff --git a/src/poli/core/chemistry/environment.yml b/src/poli/core/chemistry/environment.yml index e9348d00..8ac5ade4 100644 --- a/src/poli/core/chemistry/environment.yml +++ b/src/poli/core/chemistry/environment.yml @@ -11,7 +11,7 @@ dependencies: - openbabel - openmm - pip: - - numpy<2 + - numpy - "git+https://github.com/MachineLearningLifeScience/poli.git@dev" - biopython - python-levenshtein diff --git a/src/poli/objective_repository/aloha/environment.yml b/src/poli/objective_repository/aloha/environment.yml index 182d5ec8..ec43cb53 100644 --- a/src/poli/objective_repository/aloha/environment.yml +++ b/src/poli/objective_repository/aloha/environment.yml @@ -5,7 +5,7 @@ dependencies: - python=3.9 - pip - pip: - - numpy<2 + - numpy - selfies - rdkit - "git+https://github.com/MachineLearningLifeScience/poli.git@dev" diff --git a/src/poli/objective_repository/foldx_rfp_lambo/environment.yml b/src/poli/objective_repository/foldx_rfp_lambo/environment.yml index 8e457e43..9cc3a5ee 100644 --- a/src/poli/objective_repository/foldx_rfp_lambo/environment.yml +++ b/src/poli/objective_repository/foldx_rfp_lambo/environment.yml @@ -11,7 +11,7 @@ dependencies: - openbabel - openmm - pip: - - numpy<2 + - numpy - "git+https://github.com/MachineLearningLifeScience/poli.git@dev" - biopython==1.81 - botorch==0.8.5 diff --git a/src/poli/objective_repository/foldx_sasa/environment.yml b/src/poli/objective_repository/foldx_sasa/environment.yml index b4e8149f..fec10a51 100644 --- a/src/poli/objective_repository/foldx_sasa/environment.yml +++ b/src/poli/objective_repository/foldx_sasa/environment.yml @@ -8,6 +8,6 @@ dependencies: - pip: - biopython - python-levenshtein - - numpy<2 + - numpy - pdb-tools - "git+https://github.com/MachineLearningLifeScience/poli.git@dev" diff --git a/src/poli/objective_repository/foldx_stability/environment.yml b/src/poli/objective_repository/foldx_stability/environment.yml index b4e8149f..fec10a51 100644 --- a/src/poli/objective_repository/foldx_stability/environment.yml +++ b/src/poli/objective_repository/foldx_stability/environment.yml @@ -8,6 +8,6 @@ dependencies: - pip: - biopython - python-levenshtein - - numpy<2 + - numpy - pdb-tools - "git+https://github.com/MachineLearningLifeScience/poli.git@dev" diff --git a/src/poli/objective_repository/foldx_stability_and_sasa/environment.yml b/src/poli/objective_repository/foldx_stability_and_sasa/environment.yml index b4e8149f..fec10a51 100644 --- a/src/poli/objective_repository/foldx_stability_and_sasa/environment.yml +++ b/src/poli/objective_repository/foldx_stability_and_sasa/environment.yml @@ -8,6 +8,6 @@ dependencies: - pip: - biopython - python-levenshtein - - numpy<2 + - numpy - pdb-tools - "git+https://github.com/MachineLearningLifeScience/poli.git@dev" diff --git a/src/poli/objective_repository/gfp_cbas/environment.yml b/src/poli/objective_repository/gfp_cbas/environment.yml index 9f90ca9a..a8217319 100644 --- a/src/poli/objective_repository/gfp_cbas/environment.yml +++ b/src/poli/objective_repository/gfp_cbas/environment.yml @@ -7,7 +7,7 @@ dependencies: - pip: - biopython - python-levenshtein - - numpy<2 + - numpy - pandas - scipy - "git+https://github.com/MachineLearningLifeScience/poli.git@dev" diff --git a/src/poli/objective_repository/gfp_select/environment.yml b/src/poli/objective_repository/gfp_select/environment.yml index 1c89b49c..dedfcfa2 100644 --- a/src/poli/objective_repository/gfp_select/environment.yml +++ b/src/poli/objective_repository/gfp_select/environment.yml @@ -7,6 +7,6 @@ dependencies: - pip: - biopython - python-levenshtein - - numpy<2 + - numpy - pandas - "git+https://github.com/MachineLearningLifeScience/poli.git@master" diff --git a/src/poli/objective_repository/penalized_logp_lambo/environment.yml b/src/poli/objective_repository/penalized_logp_lambo/environment.yml index 87b5813a..eb871189 100644 --- a/src/poli/objective_repository/penalized_logp_lambo/environment.yml +++ b/src/poli/objective_repository/penalized_logp_lambo/environment.yml @@ -11,7 +11,7 @@ dependencies: - openbabel - openmm - pip: - - numpy<2 + - numpy - "git+https://github.com/MachineLearningLifeScience/poli.git@dev" - biopython==1.81 - botorch==0.8.5 diff --git a/src/poli/objective_repository/rasp/environment.yml b/src/poli/objective_repository/rasp/environment.yml index 2e3160f8..43b843a4 100644 --- a/src/poli/objective_repository/rasp/environment.yml +++ b/src/poli/objective_repository/rasp/environment.yml @@ -15,7 +15,7 @@ dependencies: - make - pip - pip: - - numpy<2 + - numpy - "git+https://github.com/MachineLearningLifeScience/poli.git@dev" - biopython==1.72 - torch diff --git a/src/poli/objective_repository/rdkit_logp/environment.yml b/src/poli/objective_repository/rdkit_logp/environment.yml index be65926c..02f189c9 100644 --- a/src/poli/objective_repository/rdkit_logp/environment.yml +++ b/src/poli/objective_repository/rdkit_logp/environment.yml @@ -5,7 +5,7 @@ dependencies: - python=3.9 - pip - pip: - - numpy<2 + - numpy - rdkit - selfies - "git+https://github.com/MachineLearningLifeScience/poli.git@dev" diff --git a/src/poli/objective_repository/rdkit_qed/environment.yml b/src/poli/objective_repository/rdkit_qed/environment.yml index be65926c..02f189c9 100644 --- a/src/poli/objective_repository/rdkit_qed/environment.yml +++ b/src/poli/objective_repository/rdkit_qed/environment.yml @@ -5,7 +5,7 @@ dependencies: - python=3.9 - pip - pip: - - numpy<2 + - numpy - rdkit - selfies - "git+https://github.com/MachineLearningLifeScience/poli.git@dev" diff --git a/src/poli/objective_repository/rfp_foldx_stability_and_sasa/environment.yml b/src/poli/objective_repository/rfp_foldx_stability_and_sasa/environment.yml index b4e8149f..fec10a51 100644 --- a/src/poli/objective_repository/rfp_foldx_stability_and_sasa/environment.yml +++ b/src/poli/objective_repository/rfp_foldx_stability_and_sasa/environment.yml @@ -8,6 +8,6 @@ dependencies: - pip: - biopython - python-levenshtein - - numpy<2 + - numpy - pdb-tools - "git+https://github.com/MachineLearningLifeScience/poli.git@dev" diff --git a/src/poli/objective_repository/sa_tdc/environment.yml b/src/poli/objective_repository/sa_tdc/environment.yml index 02060d38..5545e4b0 100644 --- a/src/poli/objective_repository/sa_tdc/environment.yml +++ b/src/poli/objective_repository/sa_tdc/environment.yml @@ -11,7 +11,7 @@ dependencies: - openbabel - openmm - pip: - - numpy<2 + - numpy - "git+https://github.com/MachineLearningLifeScience/poli.git@dev" - biopython==1.81 - python-levenshtein==0.12.2 diff --git a/src/poli/objective_repository/super_mario_bros/environment.yml b/src/poli/objective_repository/super_mario_bros/environment.yml index 74413eed..3cccc5c0 100644 --- a/src/poli/objective_repository/super_mario_bros/environment.yml +++ b/src/poli/objective_repository/super_mario_bros/environment.yml @@ -7,5 +7,5 @@ dependencies: - conda-forge::openjdk - pip - pip: - - numpy<2 + - numpy - "git+https://github.com/MachineLearningLifeScience/poli.git@dev" diff --git a/src/poli/objective_repository/toy_continuous_problem/environment.yml b/src/poli/objective_repository/toy_continuous_problem/environment.yml index 1dd675c9..2da33a9f 100644 --- a/src/poli/objective_repository/toy_continuous_problem/environment.yml +++ b/src/poli/objective_repository/toy_continuous_problem/environment.yml @@ -5,5 +5,5 @@ dependencies: - python=3.9 - pip - pip: - - numpy<2 + - numpy - "git+https://github.com/MachineLearningLifeScience/poli.git@dev" diff --git a/src/poli/objective_repository/white_noise/environment.yml b/src/poli/objective_repository/white_noise/environment.yml index 182d5ec8..ec43cb53 100644 --- a/src/poli/objective_repository/white_noise/environment.yml +++ b/src/poli/objective_repository/white_noise/environment.yml @@ -5,7 +5,7 @@ dependencies: - python=3.9 - pip - pip: - - numpy<2 + - numpy - selfies - rdkit - "git+https://github.com/MachineLearningLifeScience/poli.git@dev"