Fix Path instance file name when dealing with xtiff.

BodenmillerGroup · Aug 14, 2020 · 4bb23c3 · 4bb23c3
1 parent bd05f6b
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Showing 9 changed files with 17 additions and 20 deletions.
diff --git 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
@@ -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
@@ -27,7 +27,6 @@ <h1 class="title">Module <code>imctools.data.acquisitiondata</code></h1>
 <span>Expand source code</span>
 </summary>
 <pre><code class="python">import logging
-import os
 import re
 from pathlib import Path
 from typing import Optional, Sequence, Union
@@ -164,7 +163,7 @@ <h1 class="title">Module <code>imctools.data.acquisitiondata</code></h1>
         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 @@ <h2 class="section-title" id="header-classes">Classes</h2>
         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 @@ <h2 id="parameters">Parameters</h2>
     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
@@ -49,7 +49,7 @@ <h2 id="prerequisites">Prerequisites</h2>
 </ul>
 <h2 id="installation">Installation</h2>
 <p>Preferable way to install <code><a title="imctools" href="#imctools">imctools</a></code> is via official PyPI registry. Please define package version explicitly in order to avoid incompatibilities between v1.x and v2.x versions:</p>
-<pre><code>pip install imctools==2.0.0
+<pre><code>pip install imctools==2.0.1
 </code></pre>
 <p>In old IMC segmentation pipelines versions 1.x should be used!</p>
 <pre><code>pip install imctools==1.0.8
@@ -140,7 +140,7 @@ <h3 id="usage-of-previous-version-1x">Usage of previous version 1.x</h3>
 
 __author__ = &#34;&#34;&#34;Vito Zanotelli, Anton Rau&#34;&#34;&#34;
 __email__ = &#34;[email protected], [email protected]&#34;
-__version__ = &#34;2.0.0&#34;</code></pre>
+__version__ = &#34;2.0.1&#34;</code></pre>
 </details>
 </section>
 <section>

diff --git a/imctools/__init__.py b/imctools/__init__.py
@@ -6,4 +6,4 @@
 
 __author__ = """Vito Zanotelli, Anton Rau"""
 __email__ = "[email protected], [email protected]"
-__version__ = "2.0.0"
+__version__ = "2.0.1"
diff --git 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
diff --git 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 <[email protected]>", "Anton Rau <[email protected]>"]

diff --git 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