From cc6c7be87d87c09bcb7c90025f2a6fe0a7038c58 Mon Sep 17 00:00:00 2001
From: deepsidhu85 <deepsidhu85@gmail.com>
Date: Fri, 10 Feb 2023 11:03:50 -0600
Subject: [PATCH] Updated version number (#31)

* Updated version number

* Updated wording of changelog entry

* Updated branch names from master to main
---
 .github/workflows/ci-tests.yml                      | 10 +++++-----
 CHANGELOG.md                                        |  3 +++
 Makefile                                            |  2 +-
 README.md                                           |  6 +++---
 irida_import/irida_import.xml.sample                |  2 +-
 irida_import/tests/integration/irida_data_setup.py  |  2 +-
 irida_import/tests/integration/tests_integration.py |  2 +-
 setup.py                                            |  2 +-
 8 files changed, 16 insertions(+), 13 deletions(-)

diff --git a/.github/workflows/ci-tests.yml b/.github/workflows/ci-tests.yml
index 9924e9e5..d496f823 100644
--- a/.github/workflows/ci-tests.yml
+++ b/.github/workflows/ci-tests.yml
@@ -3,14 +3,14 @@ name: Integration Tests
 on:
   pull_request: # Run on all pull requests
   push:
-    branches:   # Run on any push to development or master
+    branches:   # Run on any push to development or main
       - development
-      - master
-  schedule:     # Run weekly on development and master
+      - main
+  schedule:     # Run weekly on development and main
     - cron: 0 2 * * 1
       branches: development
     - cron: 0 2 * * 1
-      branches: master
+      branches: main
 
 
 jobs:
@@ -45,7 +45,7 @@ jobs:
     strategy:
       fail-fast: False #Setting so that if one of the test suites fail, the other will continue
       matrix:
-        branch: ['master','development'] # IRIDA Branches to test against
+        branch: ['main','development'] # IRIDA Branches to test against
 
     steps:
       - uses: actions/checkout@v2 #Checkout the project from git
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 53ce1333..ead0412b 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -2,6 +2,9 @@
 
 All notable changes to irida-galaxy-importer will be documeted in this file.
 
+## 2.1.0
+* Added in support for importing IRIDA files that are not available locally (i.e. in the cloud)
+
 ## 2.0.1
 * Switched from travisCI tests to Github Actions
 * Switched integration tests to launch irida via gradle
diff --git a/Makefile b/Makefile
index f23bf182..0504e310 100644
--- a/Makefile
+++ b/Makefile
@@ -1,5 +1,5 @@
 SHELL=/bin/bash
-IRIDA_VERSION?=master
+IRIDA_VERSION?=main
 
 requirements: clean env
 	source .virtualenv/bin/activate
diff --git a/README.md b/README.md
index d7c51331..09c5e716 100644
--- a/README.md
+++ b/README.md
@@ -68,7 +68,7 @@ The Galaxy [tools/][galaxy-tools] directory contains tools that come with the Ga
 ```bash
 cd galaxy/tools/
 
-git clone -b master https://github.com/phac-nml/irida-galaxy-importer.git
+git clone -b main https://github.com/phac-nml/irida-galaxy-importer.git
 cd irida-galaxy-importer
 
 # Optional. Checkout specific release from https://github.com/phac-nml/irida-galaxy-importer/releases
@@ -277,9 +277,9 @@ make unittests
 Integration tests can be run with
 
 ```bash
-make integrationtests branch=master
+make integrationtests branch=main
 ```
-This tests against the `master` branch of IRIDA
+This tests against the `main` branch of IRIDA
 
 [galaxy]: https://galaxyproject.org/
 [irida]: https://www.irida.ca/
diff --git a/irida_import/irida_import.xml.sample b/irida_import/irida_import.xml.sample
index 7f140d9d..ffa3a303 100644
--- a/irida_import/irida_import.xml.sample
+++ b/irida_import/irida_import.xml.sample
@@ -1,4 +1,4 @@
-<tool add_galaxy_url="False" force_history_refresh="True" id="TOOL_ID" name="IRIDA" tool_type="data_source" version="2.0.0">
+<tool add_galaxy_url="False" force_history_refresh="True" id="TOOL_ID" name="IRIDA" tool_type="data_source" version="2.1.0">
     <description>server</description>
     <command detect_errors="exit_code"><![CDATA[
         PYTHONPATH="$__tool_directory__"
diff --git a/irida_import/tests/integration/irida_data_setup.py b/irida_import/tests/integration/irida_data_setup.py
index 8536f592..2d2ba9fe 100644
--- a/irida_import/tests/integration/irida_data_setup.py
+++ b/irida_import/tests/integration/irida_data_setup.py
@@ -20,7 +20,7 @@ def __init__(self, base_url, user, password, branch, db_host, db_port, repo_dir)
         :param base_url: url of the IRIDA instance's API
         :param user: default admin username
         :param password: default admin password
-        :param branch: the github branch to run the integration tests on (e.g. 'master' or 'development')
+        :param branch: the github branch to run the integration tests on (e.g. 'main' or 'development')
         :param db_host: mysql database host
         :param db_port: mysql database port
         :param repo_dir: where to download and install irida
diff --git a/irida_import/tests/integration/tests_integration.py b/irida_import/tests/integration/tests_integration.py
index 94b26717..4faa877c 100644
--- a/irida_import/tests/integration/tests_integration.py
+++ b/irida_import/tests/integration/tests_integration.py
@@ -82,7 +82,7 @@ def create_test_suite():
     return suite
 
 
-def start(irida_branch="master", db_host="localhost", db_port="3306"):
+def start(irida_branch="main", db_host="localhost", db_port="3306"):
     """
     Start running the integration tests
 
diff --git a/setup.py b/setup.py
index fc7512fa..b68cb270 100644
--- a/setup.py
+++ b/setup.py
@@ -25,7 +25,7 @@ def readme():
 
 
 setup(name='irida_import',
-      version='2.0.0',
+      version='2.1.0',
       description='A tool for importing data from IRIDA into Galaxy',
       url='https://github.com/phac-nml/irida-galaxy-importer',
       author='NML Bioinformatics',