From ba07624307852dea433490d24a5f48b82bbb4a3a Mon Sep 17 00:00:00 2001 From: Steffen Graber Date: Mon, 17 Jun 2024 08:26:39 +0200 Subject: [PATCH 1/3] Fix pipeline (#231) * Merge build and deploy to fix deploy problems * Add nest-server requirements * Fix nest-desktop and compose file * Add v3.7 * Remove test * Add v3.7 to readme * Fix nestml version and add pygsl * Set pygsl to fix version --- src/3.7/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/3.7/Dockerfile b/src/3.7/Dockerfile index f2877d9..d0b4fca 100644 --- a/src/3.7/Dockerfile +++ b/src/3.7/Dockerfile @@ -116,7 +116,7 @@ RUN apt-get update && apt-get install -y --no-install-recommends \ python3 -m pip install --upgrade pip && \ python3 -m pip install -r ${SRC_PATH}/nest-simulator-${NEST_VERSION}/requirements_testing.txt && \ python3 -m pip install -r ${SRC_PATH}/nest-simulator-${NEST_VERSION}/requirements_nest_server.txt && \ - python3 -m pip install --upgrade pygsl && \ + python3 -m pip install pygsl==2.3.3 && \ python3 -m pip install --upgrade nest-desktop && \ python3 -m pip install --upgrade nestml && \ python3 -m pip install --force-reinstall --upgrade scipy From 550dfdcb256fdf25cdbc3c4ebcdaf55f8d4ade33 Mon Sep 17 00:00:00 2001 From: Steffen Graber Date: Wed, 19 Jun 2024 11:51:00 +0200 Subject: [PATCH 2/3] Fix pipeline issue with pygsl and numpy v2 (#232) * Merge build and deploy to fix deploy problems * Add nest-server requirements * Fix nest-desktop and compose file * Add v3.7 * Remove test * Add v3.7 to readme * Fix nestml version and add pygsl * Set pygsl to fix version * Fix pygsl problems with numpy v2 --- src/3.7/Dockerfile | 13 ++++++------- 1 file changed, 6 insertions(+), 7 deletions(-) diff --git a/src/3.7/Dockerfile b/src/3.7/Dockerfile index d0b4fca..99f1d26 100644 --- a/src/3.7/Dockerfile +++ b/src/3.7/Dockerfile @@ -62,7 +62,6 @@ RUN apt-get update && apt-get install -y --no-install-recommends \ python3-jupyter-core \ python3-mpi4py \ python3-nose \ - python3-numpy \ python3-pandas \ python3-path \ python3-pip \ @@ -91,7 +90,7 @@ RUN apt-get update && apt-get install -y --no-install-recommends \ wget "https://github.com/nest/nest-simulator/archive/refs/tags/v${NEST_VERSION}.tar.gz" -P ${SRC_PATH} && \ tar -xzf v${NEST_VERSION}.tar.gz && \ python3 -m pip install -r ${SRC_PATH}/nest-simulator-${NEST_VERSION}/doc/requirements.txt && \ - python3 -m pip install sphinx_gallery==0.10.1 && \ + python3 -m pip install sphinx_gallery==0.10.1 numpy<2.0dev0 && \ chmod +x ${SRC_PATH}/nest-simulator-${NEST_VERSION}/build_support/install_music.sh && \ ${SRC_PATH}/nest-simulator-${NEST_VERSION}/build_support/install_music.sh && \ mkdir ${SRC_PATH}/nest-build && cd $_ && \ @@ -113,13 +112,13 @@ RUN apt-get update && apt-get install -y --no-install-recommends \ ${SRC_PATH}/nest-simulator-${NEST_VERSION} && \ make && \ make install && \ - python3 -m pip install --upgrade pip && \ - python3 -m pip install -r ${SRC_PATH}/nest-simulator-${NEST_VERSION}/requirements_testing.txt && \ - python3 -m pip install -r ${SRC_PATH}/nest-simulator-${NEST_VERSION}/requirements_nest_server.txt && \ - python3 -m pip install pygsl==2.3.3 && \ + python3 -m pip install --upgrade pip setuptools wheel && \ + python3 -m pip install -r ${SRC_PATH}/nest-simulator-${NEST_VERSION}/requirements.txt && \ + python3 -m pip install --upgrade numpy<2.0dev0 && \ python3 -m pip install --upgrade nest-desktop && \ python3 -m pip install --upgrade nestml && \ - python3 -m pip install --force-reinstall --upgrade scipy + python3 -m pip install --upgrade scipy && \ + python3 -m pip install --upgrade pygsl COPY entrypoint.sh /usr/local/bin/entrypoint.sh RUN chmod +x /usr/local/bin/entrypoint.sh From 3a9d430c3eecb22cd6541f8d96cbe2d89cfe18e2 Mon Sep 17 00:00:00 2001 From: Steffen Graber Date: Thu, 20 Jun 2024 12:40:58 +0200 Subject: [PATCH 3/3] Fix the pipeline to install pygsl (#233) * Merge build and deploy to fix deploy problems * Add nest-server requirements * Fix nest-desktop and compose file * Add v3.7 * Remove test * Add v3.7 to readme * Fix nestml version and add pygsl * Set pygsl to fix version * Fix pygsl problems with numpy v2 * Fix pygsl install --- src/3.7/Dockerfile | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/src/3.7/Dockerfile b/src/3.7/Dockerfile index 99f1d26..8b2d3ac 100644 --- a/src/3.7/Dockerfile +++ b/src/3.7/Dockerfile @@ -21,6 +21,7 @@ RUN apt-get update && apt-get install -y --no-install-recommends \ curl \ cython3 \ freeglut3-dev \ + git \ gosu \ jq \ junitparser \ @@ -90,7 +91,7 @@ RUN apt-get update && apt-get install -y --no-install-recommends \ wget "https://github.com/nest/nest-simulator/archive/refs/tags/v${NEST_VERSION}.tar.gz" -P ${SRC_PATH} && \ tar -xzf v${NEST_VERSION}.tar.gz && \ python3 -m pip install -r ${SRC_PATH}/nest-simulator-${NEST_VERSION}/doc/requirements.txt && \ - python3 -m pip install sphinx_gallery==0.10.1 numpy<2.0dev0 && \ + python3 -m pip install sphinx_gallery==0.10.1 'numpy<=1.26' && \ chmod +x ${SRC_PATH}/nest-simulator-${NEST_VERSION}/build_support/install_music.sh && \ ${SRC_PATH}/nest-simulator-${NEST_VERSION}/build_support/install_music.sh && \ mkdir ${SRC_PATH}/nest-build && cd $_ && \ @@ -114,12 +115,12 @@ RUN apt-get update && apt-get install -y --no-install-recommends \ make install && \ python3 -m pip install --upgrade pip setuptools wheel && \ python3 -m pip install -r ${SRC_PATH}/nest-simulator-${NEST_VERSION}/requirements.txt && \ - python3 -m pip install --upgrade numpy<2.0dev0 && \ python3 -m pip install --upgrade nest-desktop && \ python3 -m pip install --upgrade nestml && \ python3 -m pip install --upgrade scipy && \ - python3 -m pip install --upgrade pygsl - + python3 -m pip install --upgrade gsl wheel setuptools swig && \ + python3 -m pip install --upgrade pygsl@git+https://github.com/pygsl/pygsl@v2.3.3 + COPY entrypoint.sh /usr/local/bin/entrypoint.sh RUN chmod +x /usr/local/bin/entrypoint.sh