From 0ebd07bf37b698247f15c0e8d7fc99e4ed7578e2 Mon Sep 17 00:00:00 2001 From: Ben Gyori Date: Wed, 5 Jun 2024 14:39:12 -0400 Subject: [PATCH 1/7] Increase Gilda requirement --- setup.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/setup.py b/setup.py index 14183ece7c..2fde2d2ad8 100755 --- a/setup.py +++ b/setup.py @@ -20,7 +20,7 @@ def main(): 'trips_offline': ['pykqml'], 'reach_offline': ['cython<3', 'pyjnius==1.1.4'], 'eidos_offline': ['cython<3', 'pyjnius==1.1.4'], - 'hypothesis': ['gilda>=0.10.2'], + 'hypothesis': ['gilda>1.0.0'], 'geneways': ['stemming', 'nltk<3.6'], 'bel': ['pybel>=0.15.0,<0.16.0'], 'sbml': ['python-libsbml'], @@ -28,7 +28,7 @@ def main(): 'machine': ['pytz', 'tzlocal', 'tweepy', 'pyyaml>=5.1.0', 'click'], 'explanation': ['kappy==4.1.2', 'paths-graph'], - 'grounding': ['adeft', 'gilda>=0.10.2'], + 'grounding': ['adeft', 'gilda>1.0.0'], # AWS interface and database 'aws': ['boto3', 'reportlab'], # Utilities From 4c6b19d694d464ad71279048383935744a633859 Mon Sep 17 00:00:00 2001 From: kkaris Date: Thu, 6 Jun 2024 11:54:30 -0700 Subject: [PATCH 2/7] Align flask dependency with what's in gilda --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) mode change 100755 => 100644 setup.py diff --git a/setup.py b/setup.py old mode 100755 new mode 100644 index 2fde2d2ad8..50d28c865f --- a/setup.py +++ b/setup.py @@ -35,7 +35,7 @@ def main(): 'graph': ['pygraphviz'], 'plot': ['matplotlib'], 'isi': ['nltk<3.6', 'unidecode'], - 'api': ['flask<2.0', 'flask_restx<0.4', 'flask_cors', + 'api': ['flask>=3.0,4.0', 'flask_restx<0.4', 'flask_cors', 'docstring-parser', 'gunicorn', 'markupsafe<2.1.0'], # scikit-learn 1.5.0 breaks DisambManager.run_adeft_disambiguation From bb1e1b4766db32b4dc14939e8a8cfbae6b7c05d2 Mon Sep 17 00:00:00 2001 From: kkaris Date: Thu, 6 Jun 2024 11:57:31 -0700 Subject: [PATCH 3/7] Remove markupsafe pin --- setup.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/setup.py b/setup.py index 50d28c865f..63b38ba985 100644 --- a/setup.py +++ b/setup.py @@ -36,8 +36,7 @@ def main(): 'plot': ['matplotlib'], 'isi': ['nltk<3.6', 'unidecode'], 'api': ['flask>=3.0,4.0', 'flask_restx<0.4', 'flask_cors', - 'docstring-parser', 'gunicorn', - 'markupsafe<2.1.0'], + 'docstring-parser', 'gunicorn'], # scikit-learn 1.5.0 breaks DisambManager.run_adeft_disambiguation # see: https://github.com/gyorilab/adeft/issues/80 'sklearn_belief': ['scikit-learn<1.5.0'], From 5b23fe072207900db024c5371f5ec6883c90e68f Mon Sep 17 00:00:00 2001 From: kkaris Date: Thu, 6 Jun 2024 12:03:40 -0700 Subject: [PATCH 4/7] Fix typo --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 63b38ba985..028983d0c1 100644 --- a/setup.py +++ b/setup.py @@ -35,7 +35,7 @@ def main(): 'graph': ['pygraphviz'], 'plot': ['matplotlib'], 'isi': ['nltk<3.6', 'unidecode'], - 'api': ['flask>=3.0,4.0', 'flask_restx<0.4', 'flask_cors', + 'api': ['flask>=3.0,<4.0', 'flask_restx<0.4', 'flask_cors', 'docstring-parser', 'gunicorn'], # scikit-learn 1.5.0 breaks DisambManager.run_adeft_disambiguation # see: https://github.com/gyorilab/adeft/issues/80 From 1ae1916bf88bf7f44ea21964ac04364fc8999308 Mon Sep 17 00:00:00 2001 From: kkaris Date: Thu, 6 Jun 2024 12:08:57 -0700 Subject: [PATCH 5/7] Also align flask_restx --- setup.py | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/setup.py b/setup.py index 028983d0c1..211af33177 100644 --- a/setup.py +++ b/setup.py @@ -35,8 +35,11 @@ def main(): 'graph': ['pygraphviz'], 'plot': ['matplotlib'], 'isi': ['nltk<3.6', 'unidecode'], - 'api': ['flask>=3.0,<4.0', 'flask_restx<0.4', 'flask_cors', - 'docstring-parser', 'gunicorn'], + 'api': ['flask>=3.0,<4.0', + 'flask_restx>=1.3.0', + 'flask_cors', + 'docstring-parser', + 'gunicorn'], # scikit-learn 1.5.0 breaks DisambManager.run_adeft_disambiguation # see: https://github.com/gyorilab/adeft/issues/80 'sklearn_belief': ['scikit-learn<1.5.0'], From b9ed436801d9038ae160b6c27891288788dccbf7 Mon Sep 17 00:00:00 2001 From: kkaris Date: Mon, 1 Jul 2024 10:58:01 -0700 Subject: [PATCH 6/7] Try not restricting cython and pyjnius for python 3.10 install --- setup.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/setup.py b/setup.py index 211af33177..785a479e6b 100644 --- a/setup.py +++ b/setup.py @@ -18,8 +18,8 @@ def main(): extras_require = { # Inputs and outputs 'trips_offline': ['pykqml'], - 'reach_offline': ['cython<3', 'pyjnius==1.1.4'], - 'eidos_offline': ['cython<3', 'pyjnius==1.1.4'], + 'reach_offline': ['cython', 'pyjnius'], + 'eidos_offline': ['cython', 'pyjnius'], 'hypothesis': ['gilda>1.0.0'], 'geneways': ['stemming', 'nltk<3.6'], 'bel': ['pybel>=0.15.0,<0.16.0'], From 55ab5403bb20351585601e9f4e3e375599491e20 Mon Sep 17 00:00:00 2001 From: kkaris Date: Tue, 2 Jul 2024 10:27:40 -0700 Subject: [PATCH 7/7] Revert "Try not restricting cython and pyjnius for python 3.10 install" This reverts commit 79ed55b29fcd1a2cec91cf12887c3410983fe07d. --- setup.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/setup.py b/setup.py index 785a479e6b..211af33177 100644 --- a/setup.py +++ b/setup.py @@ -18,8 +18,8 @@ def main(): extras_require = { # Inputs and outputs 'trips_offline': ['pykqml'], - 'reach_offline': ['cython', 'pyjnius'], - 'eidos_offline': ['cython', 'pyjnius'], + 'reach_offline': ['cython<3', 'pyjnius==1.1.4'], + 'eidos_offline': ['cython<3', 'pyjnius==1.1.4'], 'hypothesis': ['gilda>1.0.0'], 'geneways': ['stemming', 'nltk<3.6'], 'bel': ['pybel>=0.15.0,<0.16.0'],