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Merge branch 'release-v1.0.0-RC1'
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# Conflicts:
#	README.md
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Daniel Danis committed Oct 12, 2020
2 parents ef11208 + db9797b commit ae65c8a
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132 changes: 7 additions & 125 deletions .gitignore
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.idea
*.iml

### The empty Squirls database meant to be used with IDE to provide autocompletion etc.
1710_splicing_empty.mv.db
1710_splicing_empty.trace.db

### Java template
# Compiled class file
*.class
# Compiled class files and resources
target/

# Log file
*.log
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.mtj.tmp/

# Package Files #
!maven-wrapper.jar
*.jar
*.war
*.nar
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# virtual machine crash logs, see http://www.java.com/en/download/help/error_hotspot.xml
hs_err_pid*

### Python template
# Byte-compiled / optimized / DLL files
__pycache__/
*.py[cod]
*$py.class

# C extensions
*.so

# Distribution / packaging
.Python
build/
develop-eggs/
dist/
downloads/
eggs/
.eggs/
lib/
lib64/
parts/
sdist/
var/
wheels/
pip-wheel-metadata/
share/python-wheels/
*.egg-info/
.installed.cfg
*.egg
MANIFEST

# PyInstaller
# Usually these files are written by a python script from a template
# before PyInstaller builds the exe, so as to inject date/other infos into it.
*.manifest
*.spec

# Installer logs
pip-log.txt
pip-delete-this-directory.txt

# Unit test / coverage reports
htmlcov/
.tox/
.nox/
.coverage
.coverage.*
.cache
nosetests.xml
coverage.xml
*.cover
.hypothesis/
.pytest_cache/

# Translations
*.mo
*.pot

# Django stuff:
*.log
local_settings.py
db.sqlite3

# Flask stuff:
instance/
.webassets-cache

# Scrapy stuff:
.scrapy

# Sphinx documentation
docs/_build/

# PyBuilder
target/

# Jupyter Notebook
.ipynb_checkpoints

# IPython
profile_default/
ipython_config.py

# pyenv
.python-version

# pipenv
# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
# However, in case of collaboration, if having platform-specific dependencies or dependencies
# having no cross-platform support, pipenv may install dependencies that don't work, or not
# install all needed dependencies.
#Pipfile.lock

# celery beat schedule file
celerybeat-schedule

# SageMath parsed files
*.sage.py

# Environments
.env
.venv
env/
venv/
ENV/
env.bak/
venv.bak/

# Spyder project settings
.spyderproject
.spyproject

# Rope project settings
.ropeproject

# mkdocs documentation
/site

# mypy
.mypy_cache/
.dmypy.json
dmypy.json

# Pyre type checker
.pyre/

117 changes: 117 additions & 0 deletions .mvn/wrapper/MavenWrapperDownloader.java
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/*
* Copyright 2007-present the original author or authors.
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
import java.net.*;
import java.io.*;
import java.nio.channels.*;
import java.util.Properties;

public class MavenWrapperDownloader {

private static final String WRAPPER_VERSION = "0.5.6";
/**
* Default URL to download the maven-wrapper.jar from, if no 'downloadUrl' is provided.
*/
private static final String DEFAULT_DOWNLOAD_URL = "https://repo.maven.apache.org/maven2/io/takari/maven-wrapper/"
+ WRAPPER_VERSION + "/maven-wrapper-" + WRAPPER_VERSION + ".jar";

/**
* Path to the maven-wrapper.properties file, which might contain a downloadUrl property to
* use instead of the default one.
*/
private static final String MAVEN_WRAPPER_PROPERTIES_PATH =
".mvn/wrapper/maven-wrapper.properties";

/**
* Path where the maven-wrapper.jar will be saved to.
*/
private static final String MAVEN_WRAPPER_JAR_PATH =
".mvn/wrapper/maven-wrapper.jar";

/**
* Name of the property which should be used to override the default download url for the wrapper.
*/
private static final String PROPERTY_NAME_WRAPPER_URL = "wrapperUrl";

public static void main(String args[]) {
System.out.println("- Downloader started");
File baseDirectory = new File(args[0]);
System.out.println("- Using base directory: " + baseDirectory.getAbsolutePath());

// If the maven-wrapper.properties exists, read it and check if it contains a custom
// wrapperUrl parameter.
File mavenWrapperPropertyFile = new File(baseDirectory, MAVEN_WRAPPER_PROPERTIES_PATH);
String url = DEFAULT_DOWNLOAD_URL;
if(mavenWrapperPropertyFile.exists()) {
FileInputStream mavenWrapperPropertyFileInputStream = null;
try {
mavenWrapperPropertyFileInputStream = new FileInputStream(mavenWrapperPropertyFile);
Properties mavenWrapperProperties = new Properties();
mavenWrapperProperties.load(mavenWrapperPropertyFileInputStream);
url = mavenWrapperProperties.getProperty(PROPERTY_NAME_WRAPPER_URL, url);
} catch (IOException e) {
System.out.println("- ERROR loading '" + MAVEN_WRAPPER_PROPERTIES_PATH + "'");
} finally {
try {
if(mavenWrapperPropertyFileInputStream != null) {
mavenWrapperPropertyFileInputStream.close();
}
} catch (IOException e) {
// Ignore ...
}
}
}
System.out.println("- Downloading from: " + url);

File outputFile = new File(baseDirectory.getAbsolutePath(), MAVEN_WRAPPER_JAR_PATH);
if(!outputFile.getParentFile().exists()) {
if(!outputFile.getParentFile().mkdirs()) {
System.out.println(
"- ERROR creating output directory '" + outputFile.getParentFile().getAbsolutePath() + "'");
}
}
System.out.println("- Downloading to: " + outputFile.getAbsolutePath());
try {
downloadFileFromURL(url, outputFile);
System.out.println("Done");
System.exit(0);
} catch (Throwable e) {
System.out.println("- Error downloading");
e.printStackTrace();
System.exit(1);
}
}

private static void downloadFileFromURL(String urlString, File destination) throws Exception {
if (System.getenv("MVNW_USERNAME") != null && System.getenv("MVNW_PASSWORD") != null) {
String username = System.getenv("MVNW_USERNAME");
char[] password = System.getenv("MVNW_PASSWORD").toCharArray();
Authenticator.setDefault(new Authenticator() {
@Override
protected PasswordAuthentication getPasswordAuthentication() {
return new PasswordAuthentication(username, password);
}
});
}
URL website = new URL(urlString);
ReadableByteChannel rbc;
rbc = Channels.newChannel(website.openStream());
FileOutputStream fos = new FileOutputStream(destination);
fos.getChannel().transferFrom(rbc, 0, Long.MAX_VALUE);
fos.close();
rbc.close();
}

}
2 changes: 2 additions & 0 deletions .mvn/wrapper/maven-wrapper.properties
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distributionUrl=https://repo.maven.apache.org/maven2/org/apache/maven/apache-maven/3.6.3/apache-maven-3.6.3-bin.zip
wrapperUrl=https://repo.maven.apache.org/maven2/io/takari/maven-wrapper/0.5.6/maven-wrapper-0.5.6.jar
5 changes: 5 additions & 0 deletions CHANGELOG.md
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# Changelog

## v1.3.0
✈ re-brand to Squirls, restructure code
✈ implement prototype SVG graphics generation using VMVT
✈ add splicing features

## v1.2.0
✈ rename API class `SplicingEvaluator` to `SplicingAnnotator`

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