From 3d6f0cd5ee301e65549f084467a2ab2c68b87a46 Mon Sep 17 00:00:00 2001 From: Sebastien Besson Date: Wed, 8 Jun 2022 14:38:22 +0100 Subject: [PATCH 1/9] Bump omero-blitz, omero-common-test and omero-gateway versions --- etc/omero.properties | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/etc/omero.properties b/etc/omero.properties index b0a06895f69..24b9bb84e67 100644 --- a/etc/omero.properties +++ b/etc/omero.properties @@ -208,9 +208,9 @@ versions.omero-scripts-url=${versions.omero-pypi} ### ## Internal dependencies -versions.omero-blitz=5.5.10 -versions.omero-common-test=5.5.9 -versions.omero-gateway=5.6.9 +versions.omero-blitz=5.5.12 +versions.omero-common-test=5.5.10 +versions.omero-gateway=5.6.10 versions.omero-scripts=5.6.2 versions.OMEZarrReader=0.2.0 ## Global overrides, if empty ignored From e4753ffb7a014cffca3f930b27ef82d79028f896 Mon Sep 17 00:00:00 2001 From: Sebastien Besson Date: Wed, 8 Jun 2022 15:25:43 +0100 Subject: [PATCH 2/9] Add new changelog entry for OMERO.server 5.6.5 release --- history.rst | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) diff --git a/history.rst b/history.rst index 57317cff23a..9c62a8d9359 100644 --- a/history.rst +++ b/history.rst @@ -5,6 +5,35 @@ OMERO version history ===================== +5.6.5 (June 2022) +------------------ + +This release includes the following upgrade of the OMERO.server Java components: + +- omero-gateway-java 5.6.10 +- omero-blitz 5.5.12 +- omero-server 5.6.4 +- omero-renderer 5.5.12 +- omero-romio 5.5.12 +- omero-common 5.5.12 +- omero-model 5.5.12 + + +Improvements include: + +- a new server configuration allowing to control the pyramidal requirement for floating-point images +- an upgrade of Bio-Formats to version 6.10.0 +- the inclusion of the experimental OMEZarrReader version 0.2.0 for reading OME-NGFF data + +**Note:** This upgrade will invalidate the Bio-Formats Memoizer cache. Please +see the upgrade guide for further information. + +This version of the OMERO.server has been tested with: + +- OMERO.py 5.11.2 +- OMERO.web 5.14.1 +- OMERO.dropbox 5.6.2 + 5.6.4 (April 2022) ------------------ From 572355e2a71ce18e5586131f393746b5400ac4d7 Mon Sep 17 00:00:00 2001 From: Sebastien Besson Date: Wed, 8 Jun 2022 15:31:12 +0100 Subject: [PATCH 3/9] Adjust versions of omero-* components --- history.rst | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/history.rst b/history.rst index 9c62a8d9359..ab082e6489a 100644 --- a/history.rst +++ b/history.rst @@ -13,10 +13,10 @@ This release includes the following upgrade of the OMERO.server Java components: - omero-gateway-java 5.6.10 - omero-blitz 5.5.12 - omero-server 5.6.4 -- omero-renderer 5.5.12 -- omero-romio 5.5.12 -- omero-common 5.5.12 -- omero-model 5.5.12 +- omero-renderer 5.5.10 +- omero-romio 5.7.0 +- omero-common 5.5.10 +- omero-model 5.6.7 Improvements include: From b0b58f929015ea50b1e8fe06b41464a41d316973 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Wed, 22 Jun 2022 12:22:58 +0100 Subject: [PATCH 4/9] fix name --- .github/workflows/source_build.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/source_build.yml b/.github/workflows/source_build.yml index 4f97849a152..3e6329ab2cf 100644 --- a/.github/workflows/source_build.yml +++ b/.github/workflows/source_build.yml @@ -6,7 +6,7 @@ on: - cron: '0 0 * * 0' jobs: - buil: + build: name: Build OMERO from source runs-on: ubuntu-20.04 steps: From efa512b787fd8635c7cb4f3275e35e067feb7332 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Wed, 22 Jun 2022 12:24:37 +0100 Subject: [PATCH 5/9] test rebuild with various combinations --- .github/workflows/source_build.yml | 23 ++++++++++++++++++++++- 1 file changed, 22 insertions(+), 1 deletion(-) diff --git a/.github/workflows/source_build.yml b/.github/workflows/source_build.yml index 3e6329ab2cf..d3c43bcb87b 100644 --- a/.github/workflows/source_build.yml +++ b/.github/workflows/source_build.yml @@ -7,6 +7,10 @@ on: jobs: build: + strategy: + matrix: + build_bf: [true] + build_zarr: [true] name: Build OMERO from source runs-on: ubuntu-20.04 steps: @@ -16,5 +20,22 @@ jobs: run: | pip install flake8 flake8 . - - name: Build + - name: install dependencies + run: | + sudo apt-get install -y git maven wget + - name: Build Bio-Formats + if: matrix.build_bf + run: | + git clone https://github.com/ome/bioformats /tmp/bioformats --depth 1 + cd /tmp/bioformats + mvn install -DskipTests + - name: Build ZarrReader + if: matrix.build_zarr + run: | + git clone https://github.com/ome/ZarrReader /tmp/ZarrReader + cd /tmp/ZarrReader + mvn install -DskipTests + - name: Build OMERO run: ./build.py + - name: Rebuild + run: ./build.py clean && ./build.py From ab5bfe3fef782260b25e6311b6eddf1cb4be5a3c Mon Sep 17 00:00:00 2001 From: Sebastien Besson Date: Thu, 23 Jun 2022 11:38:13 +0100 Subject: [PATCH 6/9] Remove mention of OMEZarrReader in the release notes --- history.rst | 1 - 1 file changed, 1 deletion(-) diff --git a/history.rst b/history.rst index ab082e6489a..2b7db513148 100644 --- a/history.rst +++ b/history.rst @@ -23,7 +23,6 @@ Improvements include: - a new server configuration allowing to control the pyramidal requirement for floating-point images - an upgrade of Bio-Formats to version 6.10.0 -- the inclusion of the experimental OMEZarrReader version 0.2.0 for reading OME-NGFF data **Note:** This upgrade will invalidate the Bio-Formats Memoizer cache. Please see the upgrade guide for further information. From 413e7b2aa6c54dbb5115ec840e977d5fafa8bb67 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Thu, 23 Jun 2022 11:42:43 +0100 Subject: [PATCH 7/9] build without bf and zarr --- .github/workflows/source_build.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/source_build.yml b/.github/workflows/source_build.yml index d3c43bcb87b..9b52ccecf9a 100644 --- a/.github/workflows/source_build.yml +++ b/.github/workflows/source_build.yml @@ -9,8 +9,8 @@ jobs: build: strategy: matrix: - build_bf: [true] - build_zarr: [true] + build_bf: [false] + build_zarr: [false] name: Build OMERO from source runs-on: ubuntu-20.04 steps: From 8c00f6b3636fd7da7e97e7c00f9d0d748de321e5 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Thu, 23 Jun 2022 11:45:18 +0100 Subject: [PATCH 8/9] build using david's branch --- .github/workflows/source_build.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/source_build.yml b/.github/workflows/source_build.yml index 9b52ccecf9a..f9499e3687b 100644 --- a/.github/workflows/source_build.yml +++ b/.github/workflows/source_build.yml @@ -10,7 +10,7 @@ jobs: strategy: matrix: build_bf: [false] - build_zarr: [false] + build_zarr: [true] name: Build OMERO from source runs-on: ubuntu-20.04 steps: @@ -32,7 +32,7 @@ jobs: - name: Build ZarrReader if: matrix.build_zarr run: | - git clone https://github.com/ome/ZarrReader /tmp/ZarrReader + git clone -b dependency-updates https://github.com/dgault/ZarrReader /tmp/ZarrReader cd /tmp/ZarrReader mvn install -DskipTests - name: Build OMERO From a19a0b5cb28b3020ecbf756debb58eaa00faa4bc Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Thu, 23 Jun 2022 11:54:11 +0100 Subject: [PATCH 9/9] use snapshot --- etc/omero.properties | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/etc/omero.properties b/etc/omero.properties index 24b9bb84e67..bec594ab64d 100644 --- a/etc/omero.properties +++ b/etc/omero.properties @@ -212,6 +212,6 @@ versions.omero-blitz=5.5.12 versions.omero-common-test=5.5.10 versions.omero-gateway=5.6.10 versions.omero-scripts=5.6.2 -versions.OMEZarrReader=0.2.0 +versions.OMEZarrReader=0.2.1-SNAPSHOT ## Global overrides, if empty ignored versions.bioformats=