From 8e06d5b0a38e5579e55f1678d73925c305daaece Mon Sep 17 00:00:00 2001 From: Goran Jelic-Cizmek Date: Tue, 23 Jul 2024 11:38:45 +0200 Subject: [PATCH 01/14] Pin NumPy again --- scripts/buildNeuron.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scripts/buildNeuron.sh b/scripts/buildNeuron.sh index 77e96b5..c3b72f2 100755 --- a/scripts/buildNeuron.sh +++ b/scripts/buildNeuron.sh @@ -32,7 +32,7 @@ else pip install --upgrade plotly "ipywidgets>=7.0.0" fi if [[ -f external/nmodl/requirements.txt ]]; then - pip install --upgrade -r external/nmodl/requirements.txt + pip install --upgrade -r external/nmodl/requirements.txt 'numpy<2' fi # Needed for installation of older NEURON versions with Python 12 pip install --upgrade setuptools From a56a47db519f157fa755cf47acf427c901d71472 Mon Sep 17 00:00:00 2001 From: Goran Jelic-Cizmek Date: Tue, 23 Jul 2024 11:56:53 +0200 Subject: [PATCH 02/14] Debugging CentOS 7 CI --- .github/workflows/build-neuron.yml | 20 -------------------- 1 file changed, 20 deletions(-) diff --git a/.github/workflows/build-neuron.yml b/.github/workflows/build-neuron.yml index a384446..7f743f8 100644 --- a/.github/workflows/build-neuron.yml +++ b/.github/workflows/build-neuron.yml @@ -78,28 +78,8 @@ jobs: strategy: matrix: os: - # GitHub Actions MacOS 13 runner - - { vm: macos-13, flavour: macOS } - # GitHub Actions MacOS 12 runner - - { vm: macos-12, flavour: macOS } # CentOS7 Docker image - { vm: ubuntu-latest, container: "centos:7", flavour: redhat } - # Alma Linux 8 Docker image - - { vm: ubuntu-latest, container: "almalinux:8.10", flavour: redhat } - # CentOS Stream 9 Docker image - - { vm: ubuntu-latest, container: "quay.io/centos/centos:stream9", flavour: redhat } - # Fedora 37 Docker image - - { vm: ubuntu-latest, container: "fedora:37", flavour: redhat } - # Fedora Latest (38, at time of writing) Docker image - - { vm: ubuntu-latest, container: "fedora:latest", flavour: redhat } - # Ubuntu 20.04 Docker image - - { vm: ubuntu-latest, container: "ubuntu:20.04", flavour: debian } - # Ubuntu Latest (22.04, at time of writing) Docker image - - { vm: ubuntu-latest, container: "ubuntu:latest", flavour: debian } - # Debian Bullseye (11) Docker image - - { vm: ubuntu-latest, container: "debian:bullseye", flavour: debian } - # At the time of writing, Debian Bookworm (12) Docker image - - { vm: ubuntu-latest, container: "debian:stable", flavour: debian } branch_or_tag_and_default_wheel: ${{ fromJson(needs.provide_version_matrix.outputs.matrix) }} fail-fast: false From 78c23b65f81fed5102bb3e29ab21bfb2b53ae14f Mon Sep 17 00:00:00 2001 From: Goran Jelic-Cizmek Date: Tue, 23 Jul 2024 12:01:15 +0200 Subject: [PATCH 03/14] Maybe change checkout action version? --- .github/workflows/build-neuron.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/build-neuron.yml b/.github/workflows/build-neuron.yml index 7f743f8..235fa29 100644 --- a/.github/workflows/build-neuron.yml +++ b/.github/workflows/build-neuron.yml @@ -85,7 +85,7 @@ jobs: steps: # Checkout the dedicated repository that steers the CI build - - uses: actions/checkout@v3 + - uses: actions/checkout@v2 # Install required packages using the system package manager. This # includes installing or updating the git client to a sufficiently From 06d29dcaf3f94dc82ddde97bb60278ffa002978b Mon Sep 17 00:00:00 2001 From: Goran Jelic-Cizmek Date: Tue, 23 Jul 2024 12:03:55 +0200 Subject: [PATCH 04/14] Try again --- .github/workflows/build-neuron.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/build-neuron.yml b/.github/workflows/build-neuron.yml index 235fa29..808575f 100644 --- a/.github/workflows/build-neuron.yml +++ b/.github/workflows/build-neuron.yml @@ -85,7 +85,7 @@ jobs: steps: # Checkout the dedicated repository that steers the CI build - - uses: actions/checkout@v2 + - uses: actions/checkout@v4 # Install required packages using the system package manager. This # includes installing or updating the git client to a sufficiently From 2c1f14d4f7785b20d326a80a6c5ee68b6adbdcaf Mon Sep 17 00:00:00 2001 From: Goran Jelic-Cizmek Date: Tue, 23 Jul 2024 12:08:12 +0200 Subject: [PATCH 05/14] Revert "Try again" This reverts commit 06d29dcaf3f94dc82ddde97bb60278ffa002978b. --- .github/workflows/build-neuron.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/build-neuron.yml b/.github/workflows/build-neuron.yml index 808575f..235fa29 100644 --- a/.github/workflows/build-neuron.yml +++ b/.github/workflows/build-neuron.yml @@ -85,7 +85,7 @@ jobs: steps: # Checkout the dedicated repository that steers the CI build - - uses: actions/checkout@v4 + - uses: actions/checkout@v2 # Install required packages using the system package manager. This # includes installing or updating the git client to a sufficiently From 1fa89e2e4a08a372f6a7917bdbb86e4bc11dbb7a Mon Sep 17 00:00:00 2001 From: Goran Jelic-Cizmek Date: Tue, 23 Jul 2024 12:08:27 +0200 Subject: [PATCH 06/14] Go back to the default --- .github/workflows/build-neuron.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/build-neuron.yml b/.github/workflows/build-neuron.yml index 235fa29..7f743f8 100644 --- a/.github/workflows/build-neuron.yml +++ b/.github/workflows/build-neuron.yml @@ -85,7 +85,7 @@ jobs: steps: # Checkout the dedicated repository that steers the CI build - - uses: actions/checkout@v2 + - uses: actions/checkout@v3 # Install required packages using the system package manager. This # includes installing or updating the git client to a sufficiently From 05997d3fb9a243772e16fe02a5237a6b7e78322d Mon Sep 17 00:00:00 2001 From: Goran Jelic-Cizmek Date: Tue, 23 Jul 2024 12:09:15 +0200 Subject: [PATCH 07/14] Try fix from that one GH comment --- .github/workflows/build-neuron.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/build-neuron.yml b/.github/workflows/build-neuron.yml index 7f743f8..62a48ee 100644 --- a/.github/workflows/build-neuron.yml +++ b/.github/workflows/build-neuron.yml @@ -74,6 +74,7 @@ jobs: UNPRIVILEGED_USER: runner # User created+used inside Docker containers # Extra software collections to be installed and enabled on CentOS7 SOFTWARE_COLLECTIONS_centos_7: devtoolset-9 rh-git218 rh-python38 + ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION: 'true' strategy: matrix: From 7364025d3efc092d53a6c5cd289df7291db9a1cf Mon Sep 17 00:00:00 2001 From: Goran Jelic-Cizmek Date: Tue, 23 Jul 2024 12:16:49 +0200 Subject: [PATCH 08/14] =?UTF-8?q?Try=20fixes=20suggested=20by=20?= =?UTF-8?q?=F0=9F=A4=96=F0=9F=A4=96=F0=9F=A4=96?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- scripts/install_redhat_centos_7.sh | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/scripts/install_redhat_centos_7.sh b/scripts/install_redhat_centos_7.sh index 65e645b..f25fc9d 100755 --- a/scripts/install_redhat_centos_7.sh +++ b/scripts/install_redhat_centos_7.sh @@ -2,6 +2,14 @@ # Use MPICH instead of OpenMPI on CentOS7, see #51. # This variable will be read by install_redhat.sh mpi_lib=mpich-devel + +# CentOS 7 is EOL as of 2024-06-30, so we need to use the vault +sed -i 's|mirrorlist.centos.org|vault.centos.org|g' /etc/yum.repos.d/CentOS-Base.repo +sed -i 's|#baseurl=http://vault.centos.org|baseurl=http://vault.centos.org|g' /etc/yum.repos.d/CentOS-Base.repo +yum clean all +yum makecache + +# actually install the packages # EPEL is needed to get CMake 3 in CentOS7 # SCL is needed to get a modern toolchain in CentOS7 yum install -y epel-release centos-release-scl centos-release-scl-rh From 45611809c0851d67d0979e26576e7146097aea56 Mon Sep 17 00:00:00 2001 From: Goran Jelic-Cizmek Date: Tue, 23 Jul 2024 12:18:50 +0200 Subject: [PATCH 09/14] Try another URL? --- scripts/install_redhat_centos_7.sh | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/scripts/install_redhat_centos_7.sh b/scripts/install_redhat_centos_7.sh index f25fc9d..8dec39d 100755 --- a/scripts/install_redhat_centos_7.sh +++ b/scripts/install_redhat_centos_7.sh @@ -4,8 +4,7 @@ mpi_lib=mpich-devel # CentOS 7 is EOL as of 2024-06-30, so we need to use the vault -sed -i 's|mirrorlist.centos.org|vault.centos.org|g' /etc/yum.repos.d/CentOS-Base.repo -sed -i 's|#baseurl=http://vault.centos.org|baseurl=http://vault.centos.org|g' /etc/yum.repos.d/CentOS-Base.repo +sed -i 's,^mirrorlist=,#,; s,^#baseurl=http://mirror\.centos\.org/centos/$releasever,baseurl=https://vault.centos.org/7.9.2009,' /etc/yum.repos.d/CentOS-Base.repo yum clean all yum makecache From f5bb23e7ed05657b940fbb4103a02b2886cb596b Mon Sep 17 00:00:00 2001 From: Goran Jelic-Cizmek Date: Tue, 23 Jul 2024 12:26:03 +0200 Subject: [PATCH 10/14] Try the nuclear option --- scripts/install_redhat_centos_7.sh | 44 +++++++++++++++++++++++++++++- 1 file changed, 43 insertions(+), 1 deletion(-) diff --git a/scripts/install_redhat_centos_7.sh b/scripts/install_redhat_centos_7.sh index 8dec39d..80a62cd 100755 --- a/scripts/install_redhat_centos_7.sh +++ b/scripts/install_redhat_centos_7.sh @@ -4,7 +4,49 @@ mpi_lib=mpich-devel # CentOS 7 is EOL as of 2024-06-30, so we need to use the vault -sed -i 's,^mirrorlist=,#,; s,^#baseurl=http://mirror\.centos\.org/centos/$releasever,baseurl=https://vault.centos.org/7.9.2009,' /etc/yum.repos.d/CentOS-Base.repo +contents=$(cat << EOF +[base] +name=CentOS-$releasever - Base +baseurl=http://vault.centos.org/7.9.2009/os/$basearch/ +gpgcheck=1 +gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-CentOS-7 + +[updates] +name=CentOS-$releasever - Updates +baseurl=http://vault.centos.org/7.9.2009/updates/$basearch/ +gpgcheck=1 +gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-CentOS-7 + +[extras] +name=CentOS-$releasever - Extras +baseurl=http://vault.centos.org/7.9.2009/extras/$basearch/ +gpgcheck=1 +gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-CentOS-7 + +[centosplus] +name=CentOS-$releasever - Plus +baseurl=http://vault.centos.org/7.9.2009/centosplus/$basearch/ +gpgcheck=1 +enabled=0 +gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-CentOS-7 + +[centos-sclo-rh] +name=CentOS-$releasever - SCLo rh +baseurl=http://vault.centos.org/7.9.2009/sclo/$basearch/rh/ +gpgcheck=1 +enabled=1 +gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-CentOS-7 + +[centos-sclo-sclo] +name=CentOS-$releasever - SCLo sclo +baseurl=http://vault.centos.org/7.9.2009/sclo/$basearch/sclo/ +gpgcheck=1 +enabled=1 +gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-CentOS-7 +EOF +) +echo "${contents}" > /etc/yum.repos.d/CentOS-Base.repo + yum clean all yum makecache From 1b4ab5d0eeac61d701321cd38680c31ca40daf41 Mon Sep 17 00:00:00 2001 From: Goran Jelic-Cizmek Date: Tue, 23 Jul 2024 12:29:48 +0200 Subject: [PATCH 11/14] Escape the dollars --- scripts/install_redhat_centos_7.sh | 24 ++++++++++++------------ 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/scripts/install_redhat_centos_7.sh b/scripts/install_redhat_centos_7.sh index 80a62cd..9622eab 100755 --- a/scripts/install_redhat_centos_7.sh +++ b/scripts/install_redhat_centos_7.sh @@ -6,40 +6,40 @@ mpi_lib=mpich-devel # CentOS 7 is EOL as of 2024-06-30, so we need to use the vault contents=$(cat << EOF [base] -name=CentOS-$releasever - Base -baseurl=http://vault.centos.org/7.9.2009/os/$basearch/ +name=CentOS-\$releasever - Base +baseurl=http://vault.centos.org/7.9.2009/os/\$basearch/ gpgcheck=1 gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-CentOS-7 [updates] -name=CentOS-$releasever - Updates -baseurl=http://vault.centos.org/7.9.2009/updates/$basearch/ +name=CentOS-\$releasever - Updates +baseurl=http://vault.centos.org/7.9.2009/updates/\$basearch/ gpgcheck=1 gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-CentOS-7 [extras] -name=CentOS-$releasever - Extras -baseurl=http://vault.centos.org/7.9.2009/extras/$basearch/ +name=CentOS-\$releasever - Extras +baseurl=http://vault.centos.org/7.9.2009/extras/\$basearch/ gpgcheck=1 gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-CentOS-7 [centosplus] -name=CentOS-$releasever - Plus -baseurl=http://vault.centos.org/7.9.2009/centosplus/$basearch/ +name=CentOS-\$releasever - Plus +baseurl=http://vault.centos.org/7.9.2009/centosplus/\$basearch/ gpgcheck=1 enabled=0 gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-CentOS-7 [centos-sclo-rh] -name=CentOS-$releasever - SCLo rh -baseurl=http://vault.centos.org/7.9.2009/sclo/$basearch/rh/ +name=CentOS-\$releasever - SCLo rh +baseurl=http://vault.centos.org/7.9.2009/sclo/\$basearch/rh/ gpgcheck=1 enabled=1 gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-CentOS-7 [centos-sclo-sclo] -name=CentOS-$releasever - SCLo sclo -baseurl=http://vault.centos.org/7.9.2009/sclo/$basearch/sclo/ +name=CentOS-\$releasever - SCLo sclo +baseurl=http://vault.centos.org/7.9.2009/sclo/\$basearch/sclo/ gpgcheck=1 enabled=1 gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-CentOS-7 From d89067ee64a949294cb984ec794aaf76179ecb10 Mon Sep 17 00:00:00 2001 From: Goran Jelic-Cizmek Date: Tue, 23 Jul 2024 12:34:37 +0200 Subject: [PATCH 12/14] Something to do with keys --- scripts/install_redhat_centos_7.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scripts/install_redhat_centos_7.sh b/scripts/install_redhat_centos_7.sh index 9622eab..6c5bafc 100755 --- a/scripts/install_redhat_centos_7.sh +++ b/scripts/install_redhat_centos_7.sh @@ -46,7 +46,7 @@ gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-CentOS-7 EOF ) echo "${contents}" > /etc/yum.repos.d/CentOS-Base.repo - +rpm --import /etc/pki/rpm-gpg/RPM-GPG-KEY-CentOS-7 yum clean all yum makecache From d89660bcd60d78c5e9d94252a87a0e53bc067d51 Mon Sep 17 00:00:00 2001 From: Goran Jelic-Cizmek Date: Tue, 23 Jul 2024 12:47:53 +0200 Subject: [PATCH 13/14] Actually download the vault key and register it --- scripts/install_redhat_centos_7.sh | 1 + 1 file changed, 1 insertion(+) diff --git a/scripts/install_redhat_centos_7.sh b/scripts/install_redhat_centos_7.sh index 6c5bafc..cbd482f 100755 --- a/scripts/install_redhat_centos_7.sh +++ b/scripts/install_redhat_centos_7.sh @@ -46,6 +46,7 @@ gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-CentOS-7 EOF ) echo "${contents}" > /etc/yum.repos.d/CentOS-Base.repo +curl -o /etc/pki/rpm-gpg/RPM-GPG-KEY-CentOS-7 https://vault.centos.org/RPM-GPG-KEY-CentOS-7 rpm --import /etc/pki/rpm-gpg/RPM-GPG-KEY-CentOS-7 yum clean all yum makecache From a1373912fc072144b89c671cb8c72c6c8c7a32bd Mon Sep 17 00:00:00 2001 From: Goran Jelic-Cizmek Date: Tue, 23 Jul 2024 12:50:54 +0200 Subject: [PATCH 14/14] Try without verification? --- scripts/install_redhat_centos_7.sh | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/scripts/install_redhat_centos_7.sh b/scripts/install_redhat_centos_7.sh index cbd482f..2b09838 100755 --- a/scripts/install_redhat_centos_7.sh +++ b/scripts/install_redhat_centos_7.sh @@ -14,33 +14,33 @@ gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-CentOS-7 [updates] name=CentOS-\$releasever - Updates baseurl=http://vault.centos.org/7.9.2009/updates/\$basearch/ -gpgcheck=1 +gpgcheck=0 gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-CentOS-7 [extras] name=CentOS-\$releasever - Extras baseurl=http://vault.centos.org/7.9.2009/extras/\$basearch/ -gpgcheck=1 +gpgcheck=0 gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-CentOS-7 [centosplus] name=CentOS-\$releasever - Plus baseurl=http://vault.centos.org/7.9.2009/centosplus/\$basearch/ -gpgcheck=1 +gpgcheck=0 enabled=0 gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-CentOS-7 [centos-sclo-rh] name=CentOS-\$releasever - SCLo rh baseurl=http://vault.centos.org/7.9.2009/sclo/\$basearch/rh/ -gpgcheck=1 +gpgcheck=0 enabled=1 gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-CentOS-7 [centos-sclo-sclo] name=CentOS-\$releasever - SCLo sclo baseurl=http://vault.centos.org/7.9.2009/sclo/\$basearch/sclo/ -gpgcheck=1 +gpgcheck=0 enabled=1 gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-CentOS-7 EOF