From c93a59c4c2cb1da736d070be7cb9faa7f7006eca Mon Sep 17 00:00:00 2001 From: Alexis Hill Date: Thu, 19 Nov 2020 13:10:18 -0500 Subject: [PATCH 1/5] increment package version number for release --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index cf72eb9..9611c91 100755 --- a/setup.py +++ b/setup.py @@ -14,7 +14,7 @@ from shutil import copyfile, copymode PROJECT_NAME = "pinetree" -VERSION = "0.2.0" +VERSION = "0.3.0" class CMakeExtension(Extension): def __init__(self, name, sourcedir=''): From 37043e97e87783ddf34698b47e0bf6a33bd159d5 Mon Sep 17 00:00:00 2001 From: Alexis Hill Date: Thu, 19 Nov 2020 13:38:47 -0500 Subject: [PATCH 2/5] update documentation --- src/pinetree/python_bindings.cpp | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/src/pinetree/python_bindings.cpp b/src/pinetree/python_bindings.cpp index a1ac5fb..e825d6f 100644 --- a/src/pinetree/python_bindings.cpp +++ b/src/pinetree/python_bindings.cpp @@ -407,8 +407,9 @@ PYBIND11_MODULE(core, m) { .. note:: - At this time, overlapping genes or genes that overlap with - ribosome binding sites are not supported. + Overlapping genes, or genes that overlap with + ribosome binding sites, are supported as of version + 0.3.0. Args: name (str): Name of gene. Name may be referenced by From ba07cbff4863527a638211e1e49ea08aedbeda4a Mon Sep 17 00:00:00 2001 From: Alexis Hill Date: Thu, 19 Nov 2020 13:50:15 -0500 Subject: [PATCH 3/5] more documentation updates --- src/pinetree/python_bindings.cpp | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/src/pinetree/python_bindings.cpp b/src/pinetree/python_bindings.cpp index e825d6f..6c9bbfe 100644 --- a/src/pinetree/python_bindings.cpp +++ b/src/pinetree/python_bindings.cpp @@ -408,8 +408,10 @@ PYBIND11_MODULE(core, m) { .. note:: Overlapping genes, or genes that overlap with - ribosome binding sites, are supported as of version - 0.3.0. + ribosome binding sites, are supported as of release + 0.3.0. If using an ealier version, specifing overlapping + genes is not recommended, and could cause the program + to crash. Args: name (str): Name of gene. Name may be referenced by From 0710f0902674e0671bb0d60d4ce34a61b6a3551c Mon Sep 17 00:00:00 2001 From: Alexis Hill Date: Thu, 19 Nov 2020 16:09:10 -0500 Subject: [PATCH 4/5] hopefully travis will actually use python3.7 now --- .travis.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index a42f53e..8949100 100644 --- a/.travis.yml +++ b/.travis.yml @@ -1,6 +1,6 @@ language: cpp python: - - "3.7" + - 3.7 matrix: include: - os: linux From b23cfb6606a962b1eddd11f27db62be6f55a722d Mon Sep 17 00:00:00 2001 From: Alexis Hill Date: Mon, 23 Nov 2020 18:22:37 -0500 Subject: [PATCH 5/5] add release updates up to release 0.3.0 --- NEWS.md | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 NEWS.md diff --git a/NEWS.md b/NEWS.md new file mode 100644 index 0000000..21f80bf --- /dev/null +++ b/NEWS.md @@ -0,0 +1,21 @@ +# Changelog + +## Pinetree 0.3.0 + +- Support for site-specific RNase binding constants. +- Overlapping genes and genes that overlap with ribosome binding sites are now fully supported. +- Bug fixes. + +## Pinetree 0.2.0 + +- It is now possible to simulate transcript degradation from internal and external cleavage sites. +- Fixed transcript abundances for simulating translation without transcription. +- Minor bug fixes and more informative error messages. + +## Pinetree 0.1.4 + +- More informative error message message when installation fails because cmake is not installed. + +## Pinetree 0.1.0 + +First initial release. \ No newline at end of file