From 1043feffd463d7c54211772e12bdfa8b79e7eccc Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Joan=20H=C3=A9risson?= Date: Mon, 23 Oct 2023 17:22:52 +0200 Subject: [PATCH 1/5] build(environment.yaml): update --- environment.yaml | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/environment.yaml b/environment.yaml index f515346..703145f 100644 --- a/environment.yaml +++ b/environment.yaml @@ -2,7 +2,7 @@ name: rptools channels: - conda-forge dependencies: - - python >=3.9 + - python <=3.11 - brs_utils # rpcompletion, rpfba, Args - cobra # rpfba, rpextractsink, rplibs - timeout-decorator # rpextractsink @@ -17,9 +17,10 @@ dependencies: - colored # rplibs - networkx >=2.5 # rplibs - filetype # rplibs (conda-forge) - - rr_cache>=3.1.1 # rpcompletion + - rr_cache >=3.1.1 # rpcompletion - rxn_rebuild # rpcompletion - chemlite # rpcompletion ,rpfba, rpthermo - h5py # rpscore - xgboost # rpscore - - sqlalchemy =1.4.31 # (for pandas requirements) + - sqlalchemy # (for pandas requirements) + - bs4 # rpviz From e90254030eda72b0c056531c1e203a983905fc8e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Joan=20H=C3=A9risson?= Date: Mon, 23 Oct 2023 17:47:09 +0200 Subject: [PATCH 2/5] build(environment.yaml): rm pkgs --- environment.yaml | 2 -- 1 file changed, 2 deletions(-) diff --git a/environment.yaml b/environment.yaml index 703145f..5469afb 100644 --- a/environment.yaml +++ b/environment.yaml @@ -13,7 +13,6 @@ dependencies: - scipy # rpthermo - equilibrator-api # rpthermo - equilibrator-cache >=0.5.4 # rpthermo - - openbabel # rpthermo (equilibrator-assets) - colored # rplibs - networkx >=2.5 # rplibs - filetype # rplibs (conda-forge) @@ -22,5 +21,4 @@ dependencies: - chemlite # rpcompletion ,rpfba, rpthermo - h5py # rpscore - xgboost # rpscore - - sqlalchemy # (for pandas requirements) - bs4 # rpviz From 97629d543594049382f57b6215e97c7623b456b1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Joan=20H=C3=A9risson?= Date: Tue, 24 Oct 2023 17:31:16 +0200 Subject: [PATCH 3/5] fix(rprank): fix import --- rptools/rprank/__main__.py | 15 ++------------- 1 file changed, 2 insertions(+), 13 deletions(-) diff --git a/rptools/rprank/__main__.py b/rptools/rprank/__main__.py index 9f8712d..82274e5 100644 --- a/rptools/rprank/__main__.py +++ b/rptools/rprank/__main__.py @@ -1,16 +1,5 @@ -from typing import ( - Dict, - List -) -from logging import ( - Logger, - getLogger -) -from os import ( - path as os_path, - makedirs -) -from .rpRank import rank +from os import path as os_path +from .rprank import rank from .Args import add_arguments from rptools.rplibs import rpPathway from rptools import build_args_parser From 6066d0d12326a5862895859246a82066bb25d5bd Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Joan=20H=C3=A9risson?= Date: Tue, 24 Oct 2023 19:04:44 +0200 Subject: [PATCH 4/5] build(environment): cobra >=0.26.3 --- environment.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/environment.yaml b/environment.yaml index 5469afb..5331ab2 100644 --- a/environment.yaml +++ b/environment.yaml @@ -4,7 +4,7 @@ channels: dependencies: - python <=3.11 - brs_utils # rpcompletion, rpfba, Args - - cobra # rpfba, rpextractsink, rplibs + - cobra >=0.26.3 # rpfba, rpextractsink, rplibs - timeout-decorator # rpextractsink - rdkit # rpextractsink, rplibs - python-libsbml # rplibs, rpfba From 6e761e1f3bdd28a29cfad7a929b22ed56fa54f26 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Joan=20H=C3=A9risson?= Date: Tue, 24 Oct 2023 19:10:38 +0200 Subject: [PATCH 5/5] fix(rprank): import --- rptools/rprank/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/rptools/rprank/__init__.py b/rptools/rprank/__init__.py index f85f5f1..3de14ee 100644 --- a/rptools/rprank/__init__.py +++ b/rptools/rprank/__init__.py @@ -4,4 +4,4 @@ @author: Joan Hérisson, Jean_Loup Faulon """ -from .rprank import rank +from rptools.rprank.rprank import rank