From ab9ac5369b7726d15772e80a3c27a548b0bd18b4 Mon Sep 17 00:00:00 2001
From: Ko <ko.sugawara@riken.jp>
Date: Sat, 25 Jan 2025 19:02:20 +0900
Subject: [PATCH 1/2] keep updated with the latest version of tifffile

---
 Dockerfile                       | 1 -
 elephant-core/elephant/common.py | 4 ++--
 2 files changed, 2 insertions(+), 3 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index df22079..812cae1 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -42,7 +42,6 @@ RUN ln -sf /dev/stdout /var/log/nginx/access.log \
 # install pypi packages
 COPY requirements.txt /tmp/requirements.txt
 RUN python -m pip install -r /tmp/requirements.txt && rm /tmp/requirements.txt
-RUN python -m pip install "tifffile<2022.4.22"
 # RUN pip install memory_profiler line_profiler
 # RUN pip install --no-deps stardist==0.8.3 csbdeep==0.7.2 numba==0.56.0 llvmlite==0.39.0 natsort==8.1.0
 
diff --git a/elephant-core/elephant/common.py b/elephant-core/elephant/common.py
index 9a84710..fc4c4ad 100644
--- a/elephant-core/elephant/common.py
+++ b/elephant-core/elephant/common.py
@@ -1324,7 +1324,7 @@ def export_ctc_labels(config, spots_dict):
             os.path.join(savedir, f'mask{t:0{digits}d}.tif'),
             label[:, None] if n_dims == 3 else label,
             imagej=True,
-            compress=6,
+            compression=("zlib", 6),
         )
         timepoints.discard(t)
     # Save blank images for unlabeled frames
@@ -1334,7 +1334,7 @@ def export_ctc_labels(config, spots_dict):
             os.path.join(savedir, f'mask{t:0{digits}d}.tif'),
             label[:, None] if n_dims == 3 else label,
             imagej=True,
-            compress=6,
+            compression=("zlib", 6),
         )
     if is_zip:
         zip_path = shutil.make_archive('/tmp/archive', 'zip', savedir)

From 3fcb21cdc823b23832aed4f09b9396a8445575d6 Mon Sep 17 00:00:00 2001
From: Ko <ko.sugawara@riken.jp>
Date: Sat, 25 Jan 2025 19:02:38 +0900
Subject: [PATCH 2/2] update version to 0.6.2

---
 Dockerfile-test                   | 2 +-
 Makefile                          | 2 +-
 elephant-core/elephant/version.py | 2 +-
 elephant_server.ipynb             | 2 +-
 4 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/Dockerfile-test b/Dockerfile-test
index 9a96b15..a2f0ecf 100644
--- a/Dockerfile-test
+++ b/Dockerfile-test
@@ -1,4 +1,4 @@
-FROM elephant-server:0.6.0
+FROM elephant-server:0.6.2
 
 LABEL maintainer="Ko Sugawara <ko.sugawara@ens-lyon.fr>"
 
diff --git a/Makefile b/Makefile
index 6ed1461..0a347a7 100755
--- a/Makefile
+++ b/Makefile
@@ -5,7 +5,7 @@ help:
 
 ELEPHANT_GPU?=all
 ELEPHANT_WORKSPACE?=${PWD}/workspace
-ELEPHANT_IMAGE_NAME?=elephant-server:0.6.0
+ELEPHANT_IMAGE_NAME?=elephant-server:0.6.2
 ELEPHANT_NVIDIA_GID?=$$(ls -n /dev/nvidia0 2>/dev/null | awk '{print $$4}')
 ELEPHANT_DOCKER?=docker
 ELEPHANT_RABBITMQ_NODENAME?=rabbit@localhost
diff --git a/elephant-core/elephant/version.py b/elephant-core/elephant/version.py
index 1b796b8..51fd1de 100644
--- a/elephant-core/elephant/version.py
+++ b/elephant-core/elephant/version.py
@@ -24,4 +24,4 @@
 # ==============================================================================
 """Version definition."""
 
-__version__ = "0.6.0"
+__version__ = "0.6.2"
diff --git a/elephant_server.ipynb b/elephant_server.ipynb
index c497b74..e2be0f1 100644
--- a/elephant_server.ipynb
+++ b/elephant_server.ipynb
@@ -39,7 +39,7 @@
       },
       "outputs": [],
       "source": [
-        "%env ELEPHANT_SERVER_VERSION = v0.6.0"
+        "%env ELEPHANT_SERVER_VERSION = v0.6.2"
       ]
     },
     {