From 13488238fdbd070aaaf04e8a58b79b3b3d7afd30 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?S=C3=A9bastien=20Besson?= Date: Tue, 25 Mar 2025 08:28:44 +0000 Subject: [PATCH 1/7] Install Python 3.11 in the base Docker images --- server/Dockerfile | 2 +- slave/Dockerfile | 2 +- web/Dockerfile | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/server/Dockerfile b/server/Dockerfile index 3290deb1..73d40bb0 100644 --- a/server/Dockerfile +++ b/server/Dockerfile @@ -9,7 +9,7 @@ RUN chmod +x /home/settings.env WORKDIR /tmp/omero-install/linux -RUN dnf install -y python3 python3-pip +RUN dnf install -y python3.11 python3.11-pip RUN pip install build # Ice dependencies diff --git a/slave/Dockerfile b/slave/Dockerfile index 9aa7052d..fb7ccd05 100644 --- a/slave/Dockerfile +++ b/slave/Dockerfile @@ -14,7 +14,7 @@ RUN chmod +x /home/settings.env RUN dnf install -y make # Python job -RUN dnf install -y python3-setuptools python3-pip +RUN dnf install -y python3.11 python3.11-pip RUN pip install build # Ice dependencies diff --git a/web/Dockerfile b/web/Dockerfile index daed2cd7..18b4b698 100644 --- a/web/Dockerfile +++ b/web/Dockerfile @@ -19,7 +19,7 @@ ADD ./run.sh /tmp/run.sh RUN chown omero:omero /tmp/run.sh RUN chmod a+x /tmp/run.sh -RUN dnf install -y python3 openssl python3-pip +RUN dnf install -y python3.11 openssl python3.11-pip RUN pip install build RUN dnf clean all From 1f2ab3fecbc11c21aac29f0492e473a90e6373a2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?S=C3=A9bastien=20Besson?= Date: Tue, 25 Mar 2025 08:29:09 +0000 Subject: [PATCH 2/7] Update job configuration to create Python 3.11 environments Use the appropriate pre-built manylinux Ice wheel package Remove unnecessary future dependency --- home/jobs/BIOFORMATS-build/config.xml | 2 +- home/jobs/BIOFORMATS-push/config.xml | 2 +- home/jobs/OMERO-build/config.xml | 4 ++-- home/jobs/OMERO-docs/config.xml | 2 +- home/jobs/OMERO-push/config.xml | 2 +- home/jobs/OMERO-server/config.xml | 6 +++--- home/jobs/OMERO-test-integration/config.xml | 6 +++--- home/jobs/OMERO-training/config.xml | 6 +++--- home/jobs/OMERO-web/config.xml | 6 +++--- 9 files changed, 18 insertions(+), 18 deletions(-) diff --git a/home/jobs/BIOFORMATS-build/config.xml b/home/jobs/BIOFORMATS-build/config.xml index 74991e48..88bc4381 100644 --- a/home/jobs/BIOFORMATS-build/config.xml +++ b/home/jobs/BIOFORMATS-build/config.xml @@ -73,7 +73,7 @@ - python3 -mvenv venv + python3.11 -mvenv venv source $WORKSPACE/venv/bin/activate cd bio-formats-build diff --git a/home/jobs/BIOFORMATS-push/config.xml b/home/jobs/BIOFORMATS-push/config.xml index 67b1da5e..728ff2a3 100644 --- a/home/jobs/BIOFORMATS-push/config.xml +++ b/home/jobs/BIOFORMATS-push/config.xml @@ -72,7 +72,7 @@ false - python3 -mvenv venv + python3.11 -mvenv venv source $WORKSPACE/venv/bin/activate pip install -U pip pip install -U scc diff --git a/home/jobs/OMERO-build/config.xml b/home/jobs/OMERO-build/config.xml index 90df658c..03ad0b58 100644 --- a/home/jobs/OMERO-build/config.xml +++ b/home/jobs/OMERO-build/config.xml @@ -75,9 +75,9 @@ export OMERO_BRANCH=$MERGE_PUSH_BRANCH OMERO_VEN=$WORKSPACE/omero-virtualenv source $HOME/settings.env -python3 -m venv $OMERO_VEN +python3.11 -m venv $OMERO_VEN -$OMERO_VEN/bin/pip install https://github.com/glencoesoftware/zeroc-ice-py-rhel9-x86_64/releases/download/20230830/zeroc_ice-3.6.5-cp39-cp39-linux_x86_64.whl +$OMERO_VEN/bin/pip install https://github.com/glencoesoftware/zeroc-ice-py-linux-x86_64/releases/download/20240202/zeroc_ice-3.6.5-cp311-cp311-manylinux_2_28_x86_64.whl $OMERO_VEN/bin/pip install -U setuptools omero-py source docs/hudson/OMERO.sh diff --git a/home/jobs/OMERO-docs/config.xml b/home/jobs/OMERO-docs/config.xml index bfc37c6b..9949b856 100644 --- a/home/jobs/OMERO-docs/config.xml +++ b/home/jobs/OMERO-docs/config.xml @@ -61,7 +61,7 @@ false - python3 -mvenv venv + python3.11 -mvenv venv source $WORKSPACE/venv/bin/activate pip install -U pip pip install -U scc diff --git a/home/jobs/OMERO-push/config.xml b/home/jobs/OMERO-push/config.xml index b0c258d6..efab0947 100644 --- a/home/jobs/OMERO-push/config.xml +++ b/home/jobs/OMERO-push/config.xml @@ -85,7 +85,7 @@ false - python3 -mvenv venv + python3.11 -mvenv venv source $WORKSPACE/venv/bin/activate pip install -U pip pip install -U scc diff --git a/home/jobs/OMERO-server/config.xml b/home/jobs/OMERO-server/config.xml index 740dcc22..5cbe66ae 100644 --- a/home/jobs/OMERO-server/config.xml +++ b/home/jobs/OMERO-server/config.xml @@ -54,7 +54,7 @@ if [ -e $OMERO_DIST ]; then fi rm -rf $WORKSPACE/.venv3 -python3 -m venv $WORKSPACE/.venv3 +python3.11 -m venv $WORKSPACE/.venv3 if [ "$PURGE_DATA" = "true" ]; then dropdb -h $OMERO_DB_HOST -U $OMERO_DB_USER $OMERO_DB_NAME || echo "First run or already exists" @@ -123,8 +123,8 @@ mv $WORKSPACE/$DIST $OMERO_DIST source $WORKSPACE/.venv3/bin/activate -pip install https://github.com/glencoesoftware/zeroc-ice-py-rhel9-x86_64/releases/download/20230830/zeroc_ice-3.6.5-cp39-cp39-linux_x86_64.whl -pip install -U pip future +pip install -U pip +pip install https://github.com/glencoesoftware/zeroc-ice-py-linux-x86_64/releases/download/20240202/zeroc_ice-3.6.5-cp311-cp311-manylinux_2_28_x86_64.whl pip install markdown pip install reportlab # For figure pip install omego diff --git a/home/jobs/OMERO-test-integration/config.xml b/home/jobs/OMERO-test-integration/config.xml index dd480de5..4fefcac2 100644 --- a/home/jobs/OMERO-test-integration/config.xml +++ b/home/jobs/OMERO-test-integration/config.xml @@ -15,11 +15,11 @@ rm -rf $WORKSPACE/.venv3 -python3 -m venv $WORKSPACE/.venv3 +python3.11 -m venv $WORKSPACE/.venv3 source $WORKSPACE/.venv3/bin/activate -pip install https://github.com/glencoesoftware/zeroc-ice-py-rhel9-x86_64/releases/download/20230830/zeroc_ice-3.6.5-cp39-cp39-linux_x86_64.whl -pip install -U pip future setuptools +pip install -U pip setuptools +pip install https://github.com/glencoesoftware/zeroc-ice-py-linux-x86_64/releases/download/20240202/zeroc_ice-3.6.5-cp311-cp311-manylinux_2_28_x86_64.whl pip install markdown pip install mox3 pytest pytest-django pytest-xdist pytest-mock pip install tables diff --git a/home/jobs/OMERO-training/config.xml b/home/jobs/OMERO-training/config.xml index 9e265d4c..e41a118e 100644 --- a/home/jobs/OMERO-training/config.xml +++ b/home/jobs/OMERO-training/config.xml @@ -15,11 +15,11 @@ rm -rf $WORKSPACE/.venv3 -python3 -m venv $WORKSPACE/.venv3 +python3.11 -m venv $WORKSPACE/.venv3 source $WORKSPACE/.venv3/bin/activate -pip install https://github.com/glencoesoftware/zeroc-ice-py-rhel9-x86_64/releases/download/20230830/zeroc_ice-3.6.5-cp39-cp39-linux_x86_64.whl -pip install -U pip future setuptools +pip install -U pip setuptools +pip install https://github.com/glencoesoftware/zeroc-ice-py-linux-x86_64/releases/download/20240202/zeroc_ice-3.6.5-cp311-cp311-manylinux_2_28_x86_64.whl pip install markdown # Avoid installing psutil for now # https://github.com/pytest-dev/pytest-xdist/issues/585 diff --git a/home/jobs/OMERO-web/config.xml b/home/jobs/OMERO-web/config.xml index 6c479d3a..bcc6c06f 100644 --- a/home/jobs/OMERO-web/config.xml +++ b/home/jobs/OMERO-web/config.xml @@ -26,11 +26,11 @@ rm -rf $WORKSPACE/.venv3 -python3 -m venv $WORKSPACE/.venv3 +python3.11 -m venv $WORKSPACE/.venv3 source $WORKSPACE/.venv3/bin/activate -pip install https://github.com/glencoesoftware/zeroc-ice-py-rhel9-x86_64/releases/download/20230830/zeroc_ice-3.6.5-cp39-cp39-linux_x86_64.whl -pip install -U pip future +pip install -U pip +pip install https://github.com/glencoesoftware/zeroc-ice-py-linux-x86_64/releases/download/20240202/zeroc_ice-3.6.5-cp311-cp311-manylinux_2_28_x86_64.whl pip install markdown pip install omero-py omero-web # Latest in order to stop server. NB: Re-installed from python-superbuild below From 75e1cc9624749d45ad2aebf131da7906209f79c7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?S=C3=A9bastien=20Besson?= Date: Tue, 25 Mar 2025 08:36:46 +0000 Subject: [PATCH 3/7] Use versioned pip executable --- server/Dockerfile | 2 +- slave/Dockerfile | 2 +- web/Dockerfile | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/server/Dockerfile b/server/Dockerfile index 73d40bb0..d13129e2 100644 --- a/server/Dockerfile +++ b/server/Dockerfile @@ -10,7 +10,7 @@ WORKDIR /tmp/omero-install/linux RUN dnf install -y python3.11 python3.11-pip -RUN pip install build +RUN pip3.11 install build # Ice dependencies RUN dnf install -y 'dnf-command(config-manager)' && \ diff --git a/slave/Dockerfile b/slave/Dockerfile index fb7ccd05..9ac6298a 100644 --- a/slave/Dockerfile +++ b/slave/Dockerfile @@ -15,7 +15,7 @@ RUN dnf install -y make # Python job RUN dnf install -y python3.11 python3.11-pip -RUN pip install build +RUN pip3.11 install build # Ice dependencies RUN dnf install -y 'dnf-command(config-manager)' && \ diff --git a/web/Dockerfile b/web/Dockerfile index 18b4b698..9d807f98 100644 --- a/web/Dockerfile +++ b/web/Dockerfile @@ -20,7 +20,7 @@ RUN chown omero:omero /tmp/run.sh RUN chmod a+x /tmp/run.sh RUN dnf install -y python3.11 openssl python3.11-pip -RUN pip install build +RUN pip3.11 install build RUN dnf clean all From 612027530171041990009e43c2469598d241dcc4 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Thu, 27 Mar 2025 22:12:22 +0000 Subject: [PATCH 4/7] Update robot job --- home/jobs/OMERO-robot/config.xml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/home/jobs/OMERO-robot/config.xml b/home/jobs/OMERO-robot/config.xml index b564e608..373a47a2 100644 --- a/home/jobs/OMERO-robot/config.xml +++ b/home/jobs/OMERO-robot/config.xml @@ -55,11 +55,11 @@ rm -rf $WORKSPACE/.venv3 -python -m venv $WORKSPACE/.venv3 +python3.11 -m venv $WORKSPACE/.venv3 source $WORKSPACE/.venv3/bin/activate -pip install https://github.com/glencoesoftware/zeroc-ice-py-rhel9-x86_64/releases/download/20230830/zeroc_ice-3.6.5-cp39-cp39-linux_x86_64.whl -pip install -U pip future setuptools +pip install -U pip setuptools +pip install https://github.com/glencoesoftware/zeroc-ice-py-linux-x86_64/releases/download/20240202/zeroc_ice-3.6.5-cp311-cp311-manylinux_2_28_x86_64.whl pip install omero-py omero-web # Latest in order to stop server. From 08fb36d6dedb43dd42a4586f89ac41c19de59d71 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?S=C3=A9bastien=20Besson?= Date: Fri, 28 Mar 2025 08:05:46 +0000 Subject: [PATCH 5/7] Activate the virtual environment before building OMERO --- home/jobs/OMERO-build/config.xml | 1 + 1 file changed, 1 insertion(+) diff --git a/home/jobs/OMERO-build/config.xml b/home/jobs/OMERO-build/config.xml index 03ad0b58..367b6917 100644 --- a/home/jobs/OMERO-build/config.xml +++ b/home/jobs/OMERO-build/config.xml @@ -79,6 +79,7 @@ python3.11 -m venv $OMERO_VEN $OMERO_VEN/bin/pip install https://github.com/glencoesoftware/zeroc-ice-py-linux-x86_64/releases/download/20240202/zeroc_ice-3.6.5-cp311-cp311-manylinux_2_28_x86_64.whl $OMERO_VEN/bin/pip install -U setuptools omero-py +source $OMERO_VEN/bin/activate source docs/hudson/OMERO.sh From 98a582c92c2de127a53c760048235de7c9df7744 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Fri, 28 Mar 2025 08:31:08 +0000 Subject: [PATCH 6/7] Delete the env --- home/jobs/OMERO-build/config.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/home/jobs/OMERO-build/config.xml b/home/jobs/OMERO-build/config.xml index 367b6917..87b5b5aa 100644 --- a/home/jobs/OMERO-build/config.xml +++ b/home/jobs/OMERO-build/config.xml @@ -73,7 +73,7 @@ cd src export OMERO_BRANCH=$MERGE_PUSH_BRANCH OMERO_VEN=$WORKSPACE/omero-virtualenv - +rm -rf $OMERO_VEN source $HOME/settings.env python3.11 -m venv $OMERO_VEN From 2191ed958a311639a09ca77b9932f4fc128c7fbf Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Fri, 28 Mar 2025 09:30:11 +0000 Subject: [PATCH 7/7] cap setuptools --- home/jobs/OMERO-build/config.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/home/jobs/OMERO-build/config.xml b/home/jobs/OMERO-build/config.xml index 87b5b5aa..04d88c36 100644 --- a/home/jobs/OMERO-build/config.xml +++ b/home/jobs/OMERO-build/config.xml @@ -78,7 +78,7 @@ source $HOME/settings.env python3.11 -m venv $OMERO_VEN $OMERO_VEN/bin/pip install https://github.com/glencoesoftware/zeroc-ice-py-linux-x86_64/releases/download/20240202/zeroc_ice-3.6.5-cp311-cp311-manylinux_2_28_x86_64.whl -$OMERO_VEN/bin/pip install -U setuptools omero-py +$OMERO_VEN/bin/pip install -U 'setuptools<66' omero-py source $OMERO_VEN/bin/activate source docs/hudson/OMERO.sh