From 775f0a6f90108d49d209b6e9cdbe6bab1b9ff36d Mon Sep 17 00:00:00 2001 From: jmenglund Date: Fri, 5 Aug 2016 23:17:39 +0200 Subject: [PATCH 01/10] Add Zenodo DOI badge --- README.rst | 61 +++++++++++++++++++++++++++--------------------------- 1 file changed, 30 insertions(+), 31 deletions(-) diff --git a/README.rst b/README.rst index 4b36111..2f3fab4 100644 --- a/README.rst +++ b/README.rst @@ -1,7 +1,7 @@ predsim ======= -|Build-Status| |License| +|Build-Status| |License| |DOI-URI| ``predsim`` is a command-line tool for simulating predictive datasets from `MrBayes `_ output files. @@ -112,37 +112,34 @@ License ``predsim`` is distributed under the `MIT license `_. -.. .. - +Citing +------ + +If you use results produced with this package in a scientific +publication, please just mention the package name in the text and +cite the Zenodo DOI of this project: + +|DOI-URI| + +You can select a citation style from the dropdown menu in the +*"Cite as"* section on the Zenodo page. + +``predsim`` relies on other software that also should be cited. Below are +suggested citations for Seq-Gen, DendroPy and pandas, +respectively: + +* Rambaut A., Grassly NC 1997. Seq-Gen: an application for the Monte + Carlo simulation of DNA sequence evolution along phylogenetic trees. + Comput. Appl. Biosci. 13:235–238. + +* Sukumaran J, Holder MT. 2010. DendroPy: a Python library for + phylogenetic computing. Bioinformatics 26:1569–1571. + +* McKinney W. 2010. Data structures for statistical computing in python. + *In* Proceedings of the 9th Python in Science Conference + (van der Walt S, Millman J, editors), pages 51–56. + Author ------ @@ -153,3 +150,5 @@ Markus Englund, `orcid.org/0000-0003-1688-7112 Date: Fri, 5 Aug 2016 23:18:20 +0200 Subject: [PATCH 02/10] Add patch release --- CHANGELOG.rst | 7 +++++++ predsim.py | 2 +- setup.py | 2 +- 3 files changed, 9 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.rst b/CHANGELOG.rst index 306f2b3..1c2cc69 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -1,6 +1,13 @@ Changelog ========= +v0.1.1 +------ + +Release date: YYYY-MM-DD + +`View commits `_ + v0.1.0 ------ diff --git a/predsim.py b/predsim.py index 3f2df2a..7ddef67 100755 --- a/predsim.py +++ b/predsim.py @@ -16,7 +16,7 @@ __authors__ = 'Markus Englund' __license__ = 'MIT' -__version__ = '0.1.0' +__version__ = '0.1.1' def _get_skiprows(cnt): diff --git a/setup.py b/setup.py index bfaab0e..b7216ab 100755 --- a/setup.py +++ b/setup.py @@ -8,7 +8,7 @@ setup( name='predsim', - version='0.1.0', + version='0.1.1', description=( 'Command-line tool for simulating predictive ' 'datasets from MrBayes\' output.'), From 28fbed29571a94fda5f7997e747ffeb073fe75db Mon Sep 17 00:00:00 2001 From: jmenglund Date: Sun, 7 Aug 2016 09:16:36 +0200 Subject: [PATCH 03/10] Add PyPI badge --- README.rst | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/README.rst b/README.rst index 2f3fab4..6491c1e 100644 --- a/README.rst +++ b/README.rst @@ -1,7 +1,7 @@ predsim ======= -|Build-Status| |License| |DOI-URI| +|Build-Status| |PyPI-Status| |License| |DOI-URI| ``predsim`` is a command-line tool for simulating predictive datasets from `MrBayes `_ output files. @@ -148,6 +148,8 @@ Markus Englund, `orcid.org/0000-0003-1688-7112 Date: Sun, 7 Aug 2016 18:40:43 +0200 Subject: [PATCH 04/10] Fix typo --- README.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.rst b/README.rst index 6491c1e..c64495d 100644 --- a/README.rst +++ b/README.rst @@ -129,7 +129,7 @@ You can select a citation style from the dropdown menu in the suggested citations for Seq-Gen, DendroPy and pandas, respectively: -* Rambaut A., Grassly NC 1997. Seq-Gen: an application for the Monte +* Rambaut A., Grassly NC. 1997. Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comput. Appl. Biosci. 13:235–238. From 58fa93fcec853c2179c535410a6eadcd9f36cdd3 Mon Sep 17 00:00:00 2001 From: jmenglund Date: Mon, 8 Aug 2016 08:15:14 +0200 Subject: [PATCH 05/10] Update introduction --- README.rst | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/README.rst b/README.rst index c64495d..c9541f1 100644 --- a/README.rst +++ b/README.rst @@ -5,9 +5,9 @@ predsim ``predsim`` is a command-line tool for simulating predictive datasets from `MrBayes `_ output files. -Datasets can be simulated under the GTR+G+I substitution model or any of -its nested variants available in MrBayes (JC69, HKY85 etc.). The script -uses `Seq-Gen `_ for +Datasets can be simulated under the GTR+G+I substitution model or any nested +variant available in MrBayes (JC69, HKY85 etc.). The script uses +`Seq-Gen `_ for simulating the DNA-sequences and builds on the third-party libraries `DendroPy `_ and `pandas `_. From 5fec65653a434bb6ee91bd1eb67e53ab2255c8ba Mon Sep 17 00:00:00 2001 From: jmenglund Date: Mon, 8 Aug 2016 08:15:35 +0200 Subject: [PATCH 06/10] Update usage notes --- README.rst | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/README.rst b/README.rst index c9541f1..5caa862 100644 --- a/README.rst +++ b/README.rst @@ -86,10 +86,13 @@ Usage -p FILE, --seqgen-path FILE path to a Seq-Gen executable (default: "seq-gen") -It is strongly recommended that you use the ``-c FILE`` option to check the +Usage notes +~~~~~~~~~~~ + +* It is strongly recommended that you use the ``-c FILE`` option to check the commands run by Seq-Gen. -Depending on your Python version, you might need to specify the full path to +* Depending on your Python version, you might need to specify the full path to your Seq-Gen executable with the ``-p FILE`` option. From d66c52be42f80c77a332f27491ff5cf291dfb8ac Mon Sep 17 00:00:00 2001 From: jmenglund Date: Mon, 8 Aug 2016 08:16:51 +0200 Subject: [PATCH 07/10] Fix typo --- README.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.rst b/README.rst index 5caa862..5589150 100644 --- a/README.rst +++ b/README.rst @@ -90,10 +90,10 @@ Usage notes ~~~~~~~~~~~ * It is strongly recommended that you use the ``-c FILE`` option to check the -commands run by Seq-Gen. + commands run by Seq-Gen. * Depending on your Python version, you might need to specify the full path to -your Seq-Gen executable with the ``-p FILE`` option. + your Seq-Gen executable with the ``-p FILE`` option. Running tests From e53af38b51575dfa17430008a8a3e3465bc6aac8 Mon Sep 17 00:00:00 2001 From: jmenglund Date: Mon, 8 Aug 2016 08:19:34 +0200 Subject: [PATCH 08/10] Remove heading "Usage notes" --- README.rst | 2 -- 1 file changed, 2 deletions(-) diff --git a/README.rst b/README.rst index 5589150..e76f197 100644 --- a/README.rst +++ b/README.rst @@ -86,8 +86,6 @@ Usage -p FILE, --seqgen-path FILE path to a Seq-Gen executable (default: "seq-gen") -Usage notes -~~~~~~~~~~~ * It is strongly recommended that you use the ``-c FILE`` option to check the commands run by Seq-Gen. From b402da1b63fd1b4898b792c9a30904c61c2831ab Mon Sep 17 00:00:00 2001 From: jmenglund Date: Mon, 8 Aug 2016 08:21:43 +0200 Subject: [PATCH 09/10] Fix typo --- README.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.rst b/README.rst index e76f197..f143d64 100644 --- a/README.rst +++ b/README.rst @@ -124,13 +124,13 @@ cite the Zenodo DOI of this project: |DOI-URI| You can select a citation style from the dropdown menu in the -*"Cite as"* section on the Zenodo page. +"Cite as" section on the Zenodo page. ``predsim`` relies on other software that also should be cited. Below are suggested citations for Seq-Gen, DendroPy and pandas, respectively: -* Rambaut A., Grassly NC. 1997. Seq-Gen: an application for the Monte +* Rambaut A, Grassly NC. 1997. Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comput. Appl. Biosci. 13:235–238. From 09209baeea26da9e81f863cedc33f4f5a3728d1b Mon Sep 17 00:00:00 2001 From: jmenglund Date: Thu, 11 Aug 2016 16:00:19 +0200 Subject: [PATCH 10/10] Update release info --- CHANGELOG.rst | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.rst b/CHANGELOG.rst index 1c2cc69..4543e93 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -4,7 +4,9 @@ Changelog v0.1.1 ------ -Release date: YYYY-MM-DD +* Updates to the documentation in *README.rst* + +Release date: 2016-08-11 `View commits `_