From fb737d1dab478f7ad90c038108fe4afb74a8e5cd Mon Sep 17 00:00:00 2001 From: mihailefter Date: Fri, 12 Mar 2021 10:11:30 +0100 Subject: [PATCH 1/8] Mention dev --- mutalyzer/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/mutalyzer/__init__.py b/mutalyzer/__init__.py index f20c120..47ca65b 100644 --- a/mutalyzer/__init__.py +++ b/mutalyzer/__init__.py @@ -21,7 +21,7 @@ # [1] http://peak.telecommunity.com/DevCenter/setuptools#specifying-your-project-s-version # [2] http://semver.org/ -__version_info__ = ('2', '0', '33') +__version_info__ = ('2', '0', '34' 'dev') __date__ = '24 November 2020' From ce6650342f12277ae963c7b2abeeea79edbda7f3 Mon Sep 17 00:00:00 2001 From: mihailefter Date: Fri, 12 Mar 2021 10:12:08 +0100 Subject: [PATCH 2/8] Update paper link --- mutalyzer/website/templates/about.html | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/mutalyzer/website/templates/about.html b/mutalyzer/website/templates/about.html index e027c92..aa3de6c 100644 --- a/mutalyzer/website/templates/about.html +++ b/mutalyzer/website/templates/about.html @@ -100,11 +100,9 @@

Development

Since references to WWW-sites are not yet acknowledged as citations, please mention - - "Wildeman M et al. (2008). Improving sequence variant - descriptions in mutation databases and literature using the - Mutalyzer sequence variation nomenclature checker. Hum Mutat 29, - 6-13" (direct + + "Lefter M et al. (2021). Mutalyzer2: Next Generation HGVS Nomenclature Checker. + Bioinformatics, 2021 Feb 4." (direct link) when referring to these pages.

From 73c6b9c9b0b7dd41bafed7ff8247b262d43a8276 Mon Sep 17 00:00:00 2001 From: mihailefter Date: Fri, 12 Mar 2021 10:12:33 +0100 Subject: [PATCH 3/8] Add link to version 3 --- mutalyzer/website/templates/base.html | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/mutalyzer/website/templates/base.html b/mutalyzer/website/templates/base.html index c279d3a..c32926e 100644 --- a/mutalyzer/website/templates/base.html +++ b/mutalyzer/website/templates/base.html @@ -150,6 +150,14 @@ {% endif %} +
+

+ Check out the + Mutalyzer 3 Alpha + release! +

+
+
{% if page_title %}

{{ page_title }}

{% endif %} From 26bbf41cd9949b99d5c158136933c6d6409ba6f3 Mon Sep 17 00:00:00 2001 From: mihailefter Date: Fri, 12 Mar 2021 10:20:26 +0100 Subject: [PATCH 4/8] Update dependencies --- requirements.txt | 32 ++++++++++++++++---------------- 1 file changed, 16 insertions(+), 16 deletions(-) diff --git a/requirements.txt b/requirements.txt index 57eda11..575cf57 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,30 +1,30 @@ -e git+https://github.com/mutalyzer/magic-python.git@centos6-fix#egg=Magic_file_extensions -Flask==1.1.1 -Jinja2==2.10.1 +Flask==1.1.2 +Jinja2==2.11.3 MySQL-python==1.2.5 -PyYAML==5.2 -SQLAlchemy==1.3.11 +PyYAML==5.4.1 +SQLAlchemy==1.3.23 Sphinx==1.8.5 -Werkzeug==0.16.0 -alembic==1.3.1 +Werkzeug==1.0.1 +alembic==1.5.7 backtranslate==0.0.5 biopython==1.75 -chardet==3.0.4 +chardet==4.0.0 cssselect==1.1.0 -e git+https://github.com/mutalyzer/crossmapper-legacy.git#egg=crossmapper description-extractor==2.3.5 interval-binning==1.0.0 -lxml==4.4.2 +lxml==4.6.2 mock==3.0.5 mockredispy==2.9.3 pyparsing==2.0.5 -pytest==4.6.7 -pytz==2019.3 -redis==3.3.11 -requests==2.22.0 -simplejson==3.17.0 -sphinx-rtd-theme==0.4.3 -spyne==2.12.16 +pytest==4.6.11 +pytz==2021.1 +redis==3.5.3 +requests==2.25.1 +simplejson==3.17.2 +sphinx-rtd-theme==0.5.1 +spyne==2.13.16 suds==0.4 wsgiref==0.1.2 -xlrd==1.2.0 +xlrd==2.0.1 From a6a6f35cb6b89076835494a0109154b1f7a0df81 Mon Sep 17 00:00:00 2001 From: mihailefter Date: Fri, 12 Mar 2021 13:00:26 +0100 Subject: [PATCH 5/8] Downgrade xlrd --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 575cf57..269a0a3 100644 --- a/requirements.txt +++ b/requirements.txt @@ -27,4 +27,4 @@ sphinx-rtd-theme==0.5.1 spyne==2.13.16 suds==0.4 wsgiref==0.1.2 -xlrd==2.0.1 +xlrd==1.2.0 From 77b28e1446b841418f7ae7ad6323c2fc934cfef4 Mon Sep 17 00:00:00 2001 From: mihailefter Date: Fri, 12 Mar 2021 13:05:12 +0100 Subject: [PATCH 6/8] Reduce padding --- mutalyzer/website/templates/base.html | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/mutalyzer/website/templates/base.html b/mutalyzer/website/templates/base.html index c32926e..1b34d4f 100644 --- a/mutalyzer/website/templates/base.html +++ b/mutalyzer/website/templates/base.html @@ -150,7 +150,9 @@
{% endif %} -
+

Check out the Mutalyzer 3 Alpha From 2d04bcba7bc928e979589ff83bbafc3b7105e16a Mon Sep 17 00:00:00 2001 From: mihailefter Date: Fri, 12 Mar 2021 13:23:21 +0100 Subject: [PATCH 7/8] Open external links in new tabs --- mutalyzer/website/templates/base.html | 18 ++++++++++-------- 1 file changed, 10 insertions(+), 8 deletions(-) diff --git a/mutalyzer/website/templates/base.html b/mutalyzer/website/templates/base.html index 1b34d4f..da8367a 100644 --- a/mutalyzer/website/templates/base.html +++ b/mutalyzer/website/templates/base.html @@ -93,11 +93,13 @@

  • External links
    • @@ -106,16 +108,16 @@ @@ -127,7 +129,7 @@
    • -
    From 9bd1cffe551282120fa65a7790f968ba3b43326d Mon Sep 17 00:00:00 2001 From: mihailefter Date: Mon, 15 Mar 2021 12:52:36 +0100 Subject: [PATCH 8/8] Update links --- mutalyzer/website/templates/about.html | 9 +++++---- mutalyzer/website/templates/base.html | 2 +- 2 files changed, 6 insertions(+), 5 deletions(-) diff --git a/mutalyzer/website/templates/about.html b/mutalyzer/website/templates/about.html index aa3de6c..d20b497 100644 --- a/mutalyzer/website/templates/about.html +++ b/mutalyzer/website/templates/about.html @@ -98,11 +98,12 @@

    Development

    -Since references to WWW-sites are not yet acknowledged as citations, -please mention +Please mention + - "Lefter M et al. (2021). Mutalyzer2: Next Generation HGVS Nomenclature Checker. - Bioinformatics, 2021 Feb 4." (direct + "Lefter M et al. (2021). Mutalyzer 2: Next Generation HGVS + Nomenclature Checker. Bioinformatics, btab051" + (direct link) when referring to these pages.

    diff --git a/mutalyzer/website/templates/base.html b/mutalyzer/website/templates/base.html index da8367a..c75760f 100644 --- a/mutalyzer/website/templates/base.html +++ b/mutalyzer/website/templates/base.html @@ -157,7 +157,7 @@ style="background-color: #d9edf7; padding-top:20px; padding-bottom:20px;">

    Check out the - Mutalyzer 3 Alpha + Mutalyzer 3 Alpha release!