bump version to v1.3.5

MikkelSchubert · Oct 12, 2021 · 50a8a54 · 50a8a54
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diff --git a/CHANGES.md b/CHANGES.md
@@ -1,5 +1,11 @@
 # Changelog
 
+## [1.3.5] - 2021-10-12
+
+### Added
+  - Added command-line option to reduce/turn off validation with picard ValidateSamFile.
+
+
 ## [1.3.4] - 2021-09-23
 
 ### Added
@@ -752,8 +758,8 @@ the (partially) updated documentation now hosted on ReadTheDocs.
   - Switching to more traditional version-number tracking.
 
 
-[Unreleased]: https://github.com/MikkelSchubert/paleomix/compare/v1.3.4...HEAD
-[1.3.3]: https://github.com/MikkelSchubert/paleomix/compare/v1.3.3...v1.3.4
+[1.3.5]: https://github.com/MikkelSchubert/paleomix/compare/v1.3.4...v1.3.5
+[1.3.4]: https://github.com/MikkelSchubert/paleomix/compare/v1.3.3...v1.3.4
 [1.3.3]: https://github.com/MikkelSchubert/paleomix/compare/v1.3.2...v1.3.3
 [1.3.2]: https://github.com/MikkelSchubert/paleomix/compare/v1.3.1...v1.3.2
 [1.3.1]: https://github.com/MikkelSchubert/paleomix/compare/v1.3.0...v1.3.1

diff --git a/docs/conf.py b/docs/conf.py
@@ -26,7 +26,7 @@
 # The short X.Y version
 version = "1.3"
 # The full version, including alpha/beta/rc tags
-release = "1.3.4"
+release = "1.3.5"
 
 
 # -- General configuration ---------------------------------------------------

diff --git a/docs/installation.rst b/docs/installation.rst
@@ -17,13 +17,13 @@ In addition, some libraries used by PALEOMIX may require additional development
 
 Once all requirements have been installed, PALEOMIX may be installed using `pip`::
 
-    $ python3 -m pip install paleomix==1.3.4
+    $ python3 -m pip install paleomix==1.3.5
 
 To verify that the installation was carried out correctly, run the command `paleomix`::
 
     $ paleomix
     PALEOMIX - pipelines and tools for NGS data analyses
-    Version: v1.3.4
+    Version: v1.3.5
 
     ...
 
@@ -45,7 +45,7 @@ This installation method requires the `venv` module. On Debian based systems, th
 Once `venv` is installed, creation of a virtual environment and installation of PALEOMIX may be carried out as shown here::
 
     $ python3 -m venv venv
-    $ ./venv/bin/pip install paleomix==v1.3.4
+    $ ./venv/bin/pip install paleomix==v1.3.5
 
 Following successful completion of these commands, the `paleomix` executable will be accessible in the `./venv/bin/` folder. However, as this folder also contains a copy of Python itself, it is not recommended to add it to your `PATH`. Instead, simply link the `paleomix` executable to a folder in your `PATH`. This can be accomplished as follows::
 
@@ -78,7 +78,7 @@ To install `conda` and also set it up so it can use the `bioconda`_ bioinformati
 
 Next, run the following commands to download the conda environment template for this release of PALEOMIX and to create a new conda environment named `paleomix` using that template::
 
-    $ curl -fL https://github.com/MikkelSchubert/paleomix/releases/download/v1.3.4/paleomix_environment.yaml > paleomix_environment.yaml
+    $ curl -fL https://github.com/MikkelSchubert/paleomix/releases/download/v1.3.5/paleomix_environment.yaml > paleomix_environment.yaml
     $ conda env create -n paleomix -f paleomix_environment.yaml
 
 You can now activate the paleomix environment with::

diff --git a/paleomix/__init__.py b/paleomix/__init__.py
@@ -21,5 +21,5 @@
 # SOFTWARE.
 #
 
-__version_info__ = (1, 3, 4)
+__version_info__ = (1, 3, 5)
 __version__ = "%i.%i.%i" % __version_info__
diff --git a/paleomix_environment.yaml b/paleomix_environment.yaml
@@ -17,4 +17,4 @@ dependencies:
   - r-gam
   - r-inline
   - pip:
-    - paleomix==1.3.4
+    - paleomix==1.3.5