From 178888f09bb8e609c5dacd2d4bfc1650c25cea1b Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Mon, 13 Jan 2020 15:21:52 +0000 Subject: [PATCH 1/9] make file py3 compabitle --- .omeroci/bump-version | 25 +++++++++++++------------ 1 file changed, 13 insertions(+), 12 deletions(-) diff --git a/.omeroci/bump-version b/.omeroci/bump-version index 6bcbdc9..1553630 100755 --- a/.omeroci/bump-version +++ b/.omeroci/bump-version @@ -10,25 +10,26 @@ from datetime import date desc_file = join(dirname(__file__), pardir, "DESCRIPTION") pom_file = join(dirname(__file__), pardir, "pom.xml") + def processDesc(version, omeroversion): today = date.today() try: f = input(files=(desc_file), inplace=1) for line in f: if line.startswith("Date:"): - print "Date: %s" % today + print("Date: %s" % today) elif line.startswith("Version:") \ and version is not None: - print "Version: %s" % version + print("Version: %s" % version) elif line.startswith("OMERO_Version:") \ and omeroversion is not None: - print "OMERO_Version: %s" % omeroversion + print("OMERO_Version: %s" % omeroversion) else: - print line, - + print(line,) finally: f.close() + def processPom(version, omeroversion): inVersion = False inOmeroVersion = False @@ -37,24 +38,24 @@ def processPom(version, omeroversion): for line in f: if inVersion and version is not None\ and "version" in line: - print " %s" % version + print(" %s" % version) inVersion = False elif inOmeroVersion and omeroversion is not None\ and "version" in line: - print " %s" % omeroversion + print(" %s" % omeroversion) inOmeroVersion = False elif "pom-omero-client" in line: inOmeroVersion = True - print line, + print(line,) elif "romero-gateway" in line: inVersion = True - print line, + print(line,) else: - print line, - + print(line,) finally: f.close() + if __name__ == "__main__": parser = ArgumentParser() parser.add_argument("-v", nargs='?') @@ -62,6 +63,6 @@ if __name__ == "__main__": args = parser.parse_args() if args.v is None and args.o is None: print("Usage: ./bumpversion [-v VERSION] [-o OMERO_VERSION]") - else: + else: processDesc(args.v, args.o) processPom(args.v, args.o) From ffb1273c246124decdbdf24f50085a5b2b438398 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Mon, 13 Jan 2020 15:22:31 +0000 Subject: [PATCH 2/9] update travis to use py3 --- .travis.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.travis.yml b/.travis.yml index ff1311d..4a692f4 100644 --- a/.travis.yml +++ b/.travis.yml @@ -1,12 +1,12 @@ env: - - OMERO_SERVER_VERSION=5.5 + - OMERO_SERVER_VERSION=5.6 sudo: required language: python python: - - "2.7" + - "3.6" services: - docker From cb455f8f722ed458b78592a01e31788d6bc687ce Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Mon, 13 Jan 2020 15:34:04 +0000 Subject: [PATCH 3/9] bump to 5.6 --- DESCRIPTION | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 521907d..c93cdab 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,11 +1,11 @@ Package: romero.gateway Type: Package -Version: 0.4.7 -Date: 2019-06-25 +Version: 0.4.8 +Date: 2020-01-14 Title: OMERO R Gateway Description: R Wrapper around the OMERO Java Gateway, which enables access to an OMERO server within R. - Supported OMERO version: 5.5 . + Supported OMERO version: 5.6 . Maintainer: Dominik Lindner Authors@R: c(person("Dominik", "Lindner", role = c("aut", "cre", "ctb"), email = "d.lindner@dundee.ac.uk"), From c625879ff7452a666b4a1509cd4e6b6f78139d85 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Mon, 13 Jan 2020 15:34:23 +0000 Subject: [PATCH 4/9] add entry --- CHANGELOG.md | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 4976e3e..7b6cca3 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,10 +1,17 @@ +0.4.8 (January 2020) +-------------------- + +- updated to OMERO 5.6 + 0.4.7 (June 2019) ----------------- + - updated to OMERO 5.5 - preserved backward compatibility to OMERO 5.4 0.4.6 (June 2019) ----------------- + - fixed bug in Image.getPixelValues() method which returned distorted array of pixel values for images with non-square dimensions (PR #66) From a944eafaf6ccf32295e72c39b0365108cccadce4 Mon Sep 17 00:00:00 2001 From: Dominik Lindner Date: Tue, 14 Jan 2020 10:23:24 +0000 Subject: [PATCH 5/9] Add OMERO 5.6 to Readme --- README.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 315219f..d30e23c 100644 --- a/README.md +++ b/README.md @@ -26,8 +26,9 @@ Download the latest romero.gateway version which is compatible with your OMERO s OMERO version | romero.gateway version --- | --- +5.6 | 0.4.8 5.5 | 0.4.7 -5.4 | all +5.4 | <= 0.4.7 ### Windows From d2f1d6d7846974d88a678a808611ded63826dd8c Mon Sep 17 00:00:00 2001 From: Dominik Lindner Date: Wed, 15 Jan 2020 09:50:34 +0000 Subject: [PATCH 6/9] Update Readme again --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index d30e23c..92600d9 100644 --- a/README.md +++ b/README.md @@ -26,7 +26,7 @@ Download the latest romero.gateway version which is compatible with your OMERO s OMERO version | romero.gateway version --- | --- -5.6 | 0.4.8 +5.6, 5.5 | 0.4.8 5.5 | 0.4.7 5.4 | <= 0.4.7 From 2f3ace973b91e38116277ce1fbdf03dfe534e674 Mon Sep 17 00:00:00 2001 From: Dominik Lindner Date: Thu, 16 Jan 2020 10:07:24 +0000 Subject: [PATCH 7/9] Update changelog --- CHANGELOG.md | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 7b6cca3..0066d5d 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -2,6 +2,10 @@ -------------------- - updated to OMERO 5.6 +- attachDataframe method supports setting the namespace +- OMERO_LIBS_DOWNLOAD environment variable can be used to specify + a custom URL from where to download the OMERO Java libs +- OMEROServer supports the 'sudo' functionality 0.4.7 (June 2019) ----------------- From f7fc7991ac252255dddf444f93c50255f496e014 Mon Sep 17 00:00:00 2001 From: Dominik Lindner Date: Thu, 16 Jan 2020 10:08:14 +0000 Subject: [PATCH 8/9] Update date in Description --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index c93cdab..1cfb666 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: romero.gateway Type: Package Version: 0.4.8 -Date: 2020-01-14 +Date: 2020-01-16 Title: OMERO R Gateway Description: R Wrapper around the OMERO Java Gateway, which enables access to an OMERO server within R. From 7ff84c3b1e58d4b029b9ea4926de43a2263ccb4d Mon Sep 17 00:00:00 2001 From: Dominik Lindner Date: Wed, 22 Jan 2020 13:12:54 +0000 Subject: [PATCH 9/9] Update release date --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 1cfb666..728e5c9 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: romero.gateway Type: Package Version: 0.4.8 -Date: 2020-01-16 +Date: 2020-01-22 Title: OMERO R Gateway Description: R Wrapper around the OMERO Java Gateway, which enables access to an OMERO server within R.