From 86c17b190d64e1754cb49c4c29aa4c56a11c3034 Mon Sep 17 00:00:00 2001
From: Guillaume Gay <guillaume@damcb.com>
Date: Wed, 24 Jan 2024 09:53:34 +0100
Subject: [PATCH] update .omero, some test failing

---
 .omero                            |  1 -
 .omeroci/cli-build                | 10 +---------
 .omeroci/py-setup                 |  6 +++++-
 LICENSE                           |  0
 README.md                         |  0
 requirements.txt                  |  0
 setup.py                          |  0
 test/integration/test_transfer.py |  2 +-
 8 files changed, 7 insertions(+), 12 deletions(-)
 delete mode 160000 .omero
 mode change 100644 => 100755 LICENSE
 mode change 100644 => 100755 README.md
 mode change 100644 => 100755 requirements.txt
 mode change 100644 => 100755 setup.py

diff --git a/.omero b/.omero
deleted file mode 160000
index 3824e85..0000000
--- a/.omero
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit 3824e8568d3eb1352eca3a413811b7d665fb3aef
diff --git a/.omeroci/cli-build b/.omeroci/cli-build
index ed09e48..32bf677 100755
--- a/.omeroci/cli-build
+++ b/.omeroci/cli-build
@@ -11,15 +11,7 @@ cd $TARGET
 GUESS=${PWD#*omero-cli-*}
 PLUGIN=${PLUGIN:-$GUESS}
 
-export JAVA_HOME=$(readlink -f /usr/bin/java | sed "s:/bin/java::")
-export JAVA_LD_LIBRARY_PATH="$JAVA_HOME/lib/:$JAVA_HOME/lib/server"
-export CONDA_BACKUP_JAVA_HOME=$JAVA_HOME
-export CONDA_BACKUP_JAVA_LD_LIBRARY_PATH=$JAVA_LD_LIBRARY_PATH
-
-source /tmp/miniconda/bin/activate
-conda init
-conda activate omero
-
 export OMERO_DIST=${OMERO_DIST:-/opt/omero/server/OMERO.server}
 omero $PLUGIN -h
+
 python setup.py test -t test -i ${OMERO_DIST}/etc/ice.config -vs
diff --git a/.omeroci/py-setup b/.omeroci/py-setup
index cfcd089..a743327 100755
--- a/.omeroci/py-setup
+++ b/.omeroci/py-setup
@@ -8,6 +8,7 @@ set -x
 TARGET=${TARGET:-..}
 PLUGIN=${PLUGIN:-}
 
+<<<<<<< HEAD:.omeroci/py-setup
 export JAVA_HOME=$(readlink -f /usr/bin/java | sed "s:/bin/java::")
 export JAVA_LD_LIBRARY_PATH="$JAVA_HOME/lib/:$JAVA_HOME/lib/server"
 export CONDA_BACKUP_JAVA_HOME=$JAVA_HOME
@@ -21,8 +22,11 @@ conda activate omero
 conda install -c conda-forge zeroc-ice=3.6.5
 conda install -c bioconda bftools
 
+=======
+>>>>>>> be5209a (update .omero, some test failing):.omero/py-setup
 cd $TARGET
 cd $(setup_dir)
-pip install .
+python setup.py sdist
+pip install -U dist/*.tar.gz
 python setup.py clean
 rm -rf dist *egg-info src/*egg-info
diff --git a/LICENSE b/LICENSE
old mode 100644
new mode 100755
diff --git a/README.md b/README.md
old mode 100644
new mode 100755
diff --git a/requirements.txt b/requirements.txt
old mode 100644
new mode 100755
diff --git a/setup.py b/setup.py
old mode 100644
new mode 100755
diff --git a/test/integration/test_transfer.py b/test/integration/test_transfer.py
index 68d969c..e609055 100644
--- a/test/integration/test_transfer.py
+++ b/test/integration/test_transfer.py
@@ -205,7 +205,7 @@ def test_pack_metadata_only(self, target_name, tmpdir):
         args = self.args + ["pack", target, "--binaries", "none", "--simple",
                             str(tmpdir)]
         with pytest.raises(ValueError):
-                self.cli.invoke(args, strict=True)
+            self.cli.invoke(args, strict=True)
         self.delete_all()
 
     @pytest.mark.parametrize('folder_name', TEST_FOLDERS)