From 4bb23c3c3b712fa08ceb7e99436442ed31951b8a Mon Sep 17 00:00:00 2001 From: Anton Rau Date: Fri, 14 Aug 2020 14:56:35 +0200 Subject: [PATCH] Fix Path instance file name when dealing with `xtiff`. --- CHANGELOG.md | 9 ++++----- README.md | 2 +- docs/data/acquisitiondata.html | 7 +++---- docs/index.html | 4 ++-- imctools/__init__.py | 2 +- imctools/data/acquisitiondata.py | 3 +-- poetry.lock | 6 +++--- pyproject.toml | 2 +- setup.cfg | 2 +- 9 files changed, 17 insertions(+), 20 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index faaee2d..c11b1cd 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,9 +5,8 @@ All notable changes to this project will be documented in this file. The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## [Unreleased] +## [2.0.1] - 2020-08-14 +- Fix Path instance file name when dealing with `xtiff` -## [2.0.dev1] - 2019-11-22 - -### Added -- Blah-blah +## [2.0.0] - 2020-08-12 +- Initial release diff --git a/README.md b/README.md index b7a76bb..f56cc23 100755 --- a/README.md +++ b/README.md @@ -32,7 +32,7 @@ Version 1.x documentation (deprecated): https://imctools.readthedocs.io Preferable way to install `imctools` is via official PyPI registry. Please define package version explicitly in order to avoid incompatibilities between v1.x and v2.x versions: ``` -pip install imctools==2.0.0 +pip install imctools==2.0.1 ``` In old IMC segmentation pipelines versions 1.x should be used! ``` diff --git a/docs/data/acquisitiondata.html b/docs/data/acquisitiondata.html index 4050dd0..ad95e3b 100644 --- a/docs/data/acquisitiondata.html +++ b/docs/data/acquisitiondata.html @@ -27,7 +27,6 @@

Module imctools.data.acquisitiondata

Expand source code 
import logging
-import os
 import re
 from pathlib import Path
 from typing import Optional, Sequence, Union
@@ -164,7 +163,7 @@ 
Module imctools.data.acquisitiondata

         data = np.array(self._get_image_stack_cyx(order), dtype=dtype)
         to_tiff(
             data,
-            filename,
+            str(filename),
             ome_xml_fun=get_ome_xml,
             channel_names=channel_labels,
             channel_fluors=channel_names,
@@ -389,7 +388,7 @@ 
Classes

         data = np.array(self._get_image_stack_cyx(order), dtype=dtype)
         to_tiff(
             data,
-            filename,
+            str(filename),
             ome_xml_fun=get_ome_xml,
             channel_names=channel_labels,
             channel_fluors=channel_names,
@@ -715,7 +714,7 @@ 
Parameters

     data = np.array(self._get_image_stack_cyx(order), dtype=dtype)
     to_tiff(
         data,
-        filename,
+        str(filename),
         ome_xml_fun=get_ome_xml,
         channel_names=channel_labels,
         channel_fluors=channel_names,
diff --git a/docs/index.html b/docs/index.html
index 33b610a..ce499b2 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -49,7 +49,7 @@ 
Prerequisites

 
 
Installation

 
Preferable way to install imctools is via official PyPI registry. Please define package version explicitly in order to avoid incompatibilities between v1.x and v2.x versions:

-
pip install imctools==2.0.0
+
pip install imctools==2.0.1
 

 
In old IMC segmentation pipelines versions 1.x should be used!

 
pip install imctools==1.0.8
@@ -140,7 +140,7 @@ 
Usage of previous version 1.x

 
 __author__ = """Vito Zanotelli, Anton Rau"""
 __email__ = "vito.zanotelli@uzh.ch, anton.rau@uzh.ch"
-__version__ = "2.0.0"

+__version__ = "2.0.1"

 
 
 

diff --git a/imctools/__init__.py b/imctools/__init__.py
index f85bfbc..8cfd016 100644
--- a/imctools/__init__.py
+++ b/imctools/__init__.py
@@ -6,4 +6,4 @@
 
 __author__ = """Vito Zanotelli, Anton Rau"""
 __email__ = "vito.zanotelli@uzh.ch, anton.rau@uzh.ch"
-__version__ = "2.0.0"
+__version__ = "2.0.1"
diff --git a/imctools/data/acquisitiondata.py b/imctools/data/acquisitiondata.py
index 511023c..e6d0b14 100644
--- a/imctools/data/acquisitiondata.py
+++ b/imctools/data/acquisitiondata.py
@@ -1,5 +1,4 @@
 import logging
-import os
 import re
 from pathlib import Path
 from typing import Optional, Sequence, Union
@@ -136,7 +135,7 @@ def save_ome_tiff(
         data = np.array(self._get_image_stack_cyx(order), dtype=dtype)
         to_tiff(
             data,
-            filename,
+            str(filename),
             ome_xml_fun=get_ome_xml,
             channel_names=channel_labels,
             channel_fluors=channel_names,
diff --git a/poetry.lock b/poetry.lock
index c7d85a8..cd4e21b 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -468,7 +468,7 @@ description = "Read and write TIFF(r) files"
 name = "tifffile"
 optional = false
 python-versions = ">=3.6"
-version = "2020.7.24"
+version = "2020.8.13"
 
 [package.dependencies]
 numpy = ">=1.15.1"
@@ -890,8 +890,8 @@ six = [
     {file = "six-1.15.0.tar.gz", hash = "sha256:30639c035cdb23534cd4aa2dd52c3bf48f06e5f4a941509c8bafd8ce11080259"},
 ]
 tifffile = [
-    {file = "tifffile-2020.7.24-py3-none-any.whl", hash = "sha256:73cd17d8df01fed38b9000c9b209eb7c894fde5abc616c5ff7b1f476e38cf07f"},
-    {file = "tifffile-2020.7.24.tar.gz", hash = "sha256:cd8549d6f0742c3c95a856744a26064a1aad1c132fbab95dc9e5dce891a62c17"},
+    {file = "tifffile-2020.8.13-py3-none-any.whl", hash = "sha256:d4505ed63982367781a88a2c53fcab41d7fa4f298e99235e769f0fa6ca6f68e2"},
+    {file = "tifffile-2020.8.13.tar.gz", hash = "sha256:60043e50adab5a1b9f13c3fb1a23992b9af00e1ada13d7ffe48c1ad7e0062cb8"},
 ]
 toml = [
     {file = "toml-0.10.1-py2.py3-none-any.whl", hash = "sha256:bda89d5935c2eac546d648028b9901107a595863cb36bae0c73ac804a9b4ce88"},
diff --git a/pyproject.toml b/pyproject.toml
index 78c3470..ad1c847 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -4,7 +4,7 @@ build-backend = "poetry.masonry.api"
 
 [tool.poetry]
 name = "imctools"
-version = "2.0.0"
+version = "2.0.1"
 description = "Tools to handle Fluidigm IMC data"
 license = "MIT"
 authors = ["Vito Zanotelli ", "Anton Rau "]
diff --git a/setup.cfg b/setup.cfg
index de69216..2edb76f 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 2.0.0
+current_version = 2.0.1
 commit = False
 tag = False