From 7583e76a2909f25000a01fb2f87402ea30e83194 Mon Sep 17 00:00:00 2001 From: Daniel Ecer Date: Thu, 28 Nov 2024 11:15:44 +0000 Subject: [PATCH 1/7] Upgraded to Python 3.9 part of https://github.com/elifesciences/data-hub-issues/issues/1036 --- .python-version | 2 +- Dockerfile | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.python-version b/.python-version index 4351a7e3..27390292 100644 --- a/.python-version +++ b/.python-version @@ -1 +1 @@ -3.8.7 +3.9.17 diff --git a/Dockerfile b/Dockerfile index 0fa116ce..5214729d 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,4 +1,4 @@ -FROM python:3.8-slim +FROM python:3.9-slim ARG install_dev=n USER root From 7cc316e25ea6437293e6e0fbfefc5b23f41aa92e Mon Sep 17 00:00:00 2001 From: Daniel Ecer Date: Thu, 28 Nov 2024 11:29:01 +0000 Subject: [PATCH 2/7] install gcc --- Dockerfile | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/Dockerfile b/Dockerfile index 5214729d..e1c778cc 100644 --- a/Dockerfile +++ b/Dockerfile @@ -3,6 +3,10 @@ ARG install_dev=n USER root +RUN apt-get update \ + && apt-get install gcc \ + && rm -rf /var/lib/apt/lists/* + ENV PIP_NO_CACHE_DIR=1 WORKDIR /peerscout From 1dd1da10706ee8189f2048c60ebb6bd625b3458e Mon Sep 17 00:00:00 2001 From: Daniel Ecer Date: Thu, 28 Nov 2024 11:36:20 +0000 Subject: [PATCH 3/7] Add assume yes flag --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index e1c778cc..327dc20b 100644 --- a/Dockerfile +++ b/Dockerfile @@ -4,7 +4,7 @@ ARG install_dev=n USER root RUN apt-get update \ - && apt-get install gcc \ + && apt-get install --assume-yes --quiet --quiet gcc \ && rm -rf /var/lib/apt/lists/* ENV PIP_NO_CACHE_DIR=1 From a0c4eee4ac8b4c148cf79fe845dd9ba0b9d81d8a Mon Sep 17 00:00:00 2001 From: Daniel Ecer Date: Thu, 28 Nov 2024 11:51:26 +0000 Subject: [PATCH 4/7] Also install g++ --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 327dc20b..2b762037 100644 --- a/Dockerfile +++ b/Dockerfile @@ -4,7 +4,7 @@ ARG install_dev=n USER root RUN apt-get update \ - && apt-get install --assume-yes --quiet --quiet gcc \ + && apt-get install --assume-yes --quiet --quiet gcc g++ \ && rm -rf /var/lib/apt/lists/* ENV PIP_NO_CACHE_DIR=1 From 085a4579fb18a8a945c8a9662c4cb96fa9cdd01e Mon Sep 17 00:00:00 2001 From: Daniel Ecer Date: Thu, 28 Nov 2024 12:07:14 +0000 Subject: [PATCH 5/7] Downgrade setuptools --- requirements.build.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/requirements.build.txt b/requirements.build.txt index 3d259cf8..777b82ff 100644 --- a/requirements.build.txt +++ b/requirements.build.txt @@ -1,2 +1,3 @@ pip==24.3.1 +setuptools==57.5.0 wheel==0.44.0 From 045dc9097f812513bb2d0c0642c7be338df45f94 Mon Sep 17 00:00:00 2001 From: Daniel Ecer Date: Thu, 28 Nov 2024 12:23:10 +0000 Subject: [PATCH 6/7] Upgrade spacy to 2.3.9; revert downgrade of setuptools --- requirements.build.txt | 1 - requirements.spacy.txt | 2 +- 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/requirements.build.txt b/requirements.build.txt index 777b82ff..3d259cf8 100644 --- a/requirements.build.txt +++ b/requirements.build.txt @@ -1,3 +1,2 @@ pip==24.3.1 -setuptools==57.5.0 wheel==0.44.0 diff --git a/requirements.spacy.txt b/requirements.spacy.txt index 7f546809..8420eeb5 100644 --- a/requirements.spacy.txt +++ b/requirements.spacy.txt @@ -1 +1 @@ -spacy==2.2.4 +spacy==2.3.9 From 6d57cf032a1cf6a5bf4f3a7570b8543229646ade Mon Sep 17 00:00:00 2001 From: Daniel Ecer Date: Thu, 28 Nov 2024 12:31:24 +0000 Subject: [PATCH 7/7] Downgrade numpy due to issue with spacy --- requirements.spacy.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/requirements.spacy.txt b/requirements.spacy.txt index 8420eeb5..c08f9853 100644 --- a/requirements.spacy.txt +++ b/requirements.spacy.txt @@ -1 +1,2 @@ +numpy==1.24.4 spacy==2.3.9