Merged v1.0.0 into master

.gitignore

@@ -9,3 +9,6 @@ dist
 variantValidator.egg-info
 VariantValidator/testing/outputs*
 .DS_Store
+
+# backedup files after 2to3 conversion
+*.bak

.travis.yml

@@ -0,0 +1,56 @@
+language: python
+
+matrix:
+  include:
+
+    # Here you can add or remove specific builds, and Python versions. You
+    # should currently be able to use Python 2.6, 2.7, or 3.3 or later. The
+    # NUMPY and SCIPY versions are set here as an example, but you can
+    # add/remove environment variables, and use them below during the install.
+
+    - python: 3.6
+
+services:
+  - mysql
+  - postgresql
+
+addons:
+  postgresql: "9.6"
+
+env:
+  - CODECOV_TOKEN="50dd5c2e-4259-4cfa-97a7-b4429e0d179e"
+
+before_install:
+
+  # Increase size of database drive
+  - sudo mount -o remount,size=50% /var/ramfs
+
+  # Set up the databases - install seqrepo and UTA
+
+  - mysql -e 'CREATE DATABASE validator;'
+  - df -h
+
+  - mkdir "$HOME"/seqrepo
+  - rsync -HavP dl.biocommons.org::seqrepo/2018-08-21/ "$HOME"/seqrepo/2018-08-21/
+
+  # Copy configuration file
+  - cp configuration/travis.ini "$HOME"/.variantvalidator
+
+
+install:
+
+  # Test dependencies
+  - pip install -r requirements_dev.txt
+  - pip install -e .
+
+  # Set up validator database
+  - mysql validator < configuration/empty_vv_db.sql
+#  - update_vdb.py
+  - df -h
+
+script:
+
+  - pytest --cov-report=term --cov=VariantValidator/ # will run all tests in the package
+
+after_script:
+  - codecov

Dockerfile

@@ -0,0 +1,20 @@
+FROM python:3.6
+
+#RUN seqrepo -r ${SEQREPO_DATA_DIR} pull -i ${SEQREPO_DATA_RELEASE}
+#RUN touch ${SEQREPO_DATA_DIR}/testing.txt
+
+#RUN apt update && apt install -y git
+
+WORKDIR /app
+
+COPY . /app
+
+RUN pip install -r requirements_dev.txt
+
+RUN pip install -e .
+
+COPY configuration/docker.ini /root/.variantvalidator
+
+CMD python3 bin/variant_validator.py
+
+

MANIFEST.in

@@ -0,0 +1,3 @@
+recursive-include configuration *
+include README.md
+recursive-include bin *

README.md

@@ -1,4 +1,7 @@
-# About VariantValidator
+# VariantValidator
+[![codecov](https://codecov.io/gh/openvar/variantValidator/branch/restructuring_py3/graph/badge.svg)](https://codecov.io/gh/openvar/variantValidator) [![Build Status](https://travis-ci.org/openvar/variantValidator.png)](https://travis-ci.org/openvar/variantValidator)
+
+## About
 
 VariantValidator is a user-friendly software tool designed to validate the syntax and 
 parameters of DNA variant descriptions according to the HGVS Sequence Variant 
@@ -7,7 +10,7 @@ Nomenclature.
 VariantValidator ensures that users are guided through the intricacies of the HGVS 
 nomenclature, e.g. if the user makes a mistake, VariantValidator automatically corrects 
 the mistake if it can, or provides helpful guidance if it cannot. In addition, 
-VariantValidator accurately interconverts between transcript variant descriptions and 
+VariantValidator accurately inter-converts between transcript variant descriptions and 
 genomic variant descriptions in HGVS and Variant Call Format (VCF)
 
 VariantValidator interfaces with the hgvs package to parse, format, and manipulate 
@@ -31,21 +34,21 @@ For sequence variations falling within the open reading frames of genes, Variant
 
 ## Pre-requisites
 
-VariantValidator will work on Mac OS X or Linux operating systems.
+VariantValidator will work locally on Mac OS X or Linux-compatible computers. It can also work within a [docker container](docs/DOCKER.md).
 
 Required software:
 * MySQL
-* Python 2.7
+* Python 3.6 or above
 * SQLite version 3.8.0 or above
 
 Optional software:
-* Postgres version 9.5 or above
+* Postgres version 9.5 or above, Postgres 10 is not supported.
 
-For installation instructions please see [INSTALLATION.md](INSTALLATION.md)
+For installation instructions please see [INSTALLATION.md](docs/INSTALLATION.md). For the older python 2 version, see previous releases.
 
 # Operation and configuration
 
-Please see [MANUAL.md](MANUAL.md)
+Please see [MANUAL.md](docs/MANUAL.md). Note that the latest version is not compatible with previous releases.
 
 ## License
 
@@ -59,18 +62,19 @@ VariantValidator: Accurate validation, mapping and formatting of sequence variat
 
 Freeman PJ, Hart RK, Gretton LJ, Brookes AJ, Dalgleish R.
 
-> Copyright (C) 2018  Peter Causey-Freeman, University of Leicester
-> 
+> <LICENSE>
+> Copyright (C) 2019 VariantValidator Contributors
+>
 > This program is free software: you can redistribute it and/or modify
 > it under the terms of the GNU Affero General Public License as
 > published by the Free Software Foundation, either version 3 of the
 > License, or (at your option) any later version.
-> 
+>
 > This program is distributed in the hope that it will be useful,
 > but WITHOUT ANY WARRANTY; without even the implied warranty of
 > MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 > GNU Affero General Public License for more details.
-> 
+>
 > You should have received a copy of the GNU Affero General Public License
 > along with this program.  If not, see <https://www.gnu.org/licenses/>.
 > </LICENSE>