## Setting up
+> To get set up using _only_ the Eclipse IDE (<https://www.eclipse.org/>) then please see the section [Setting up in Eclipse IDE](#setting-up-in-eclipse-ide)
+
The method here is described in terms of using a command line. You can easily do this on linux or in a Terminal window in macOS. You can do it in Windows.
* Java 11 compliant JDK
Sign up at <http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev>.
-## Building in Eclipse
-
-We develop in Eclipse, and support settings to develop and save Jalview source code
-in our preferred style. We also support running the Jalview application, debugging
-and running tests with TestNG from within Eclipse.
-
-To get Jalview set up as a project in Eclipse, we recommend using at least the 2019-03
-version of Eclipse IDE for Java Developers which you can download from the Eclipse
-website: <https://www.eclipse.org/downloads/>
-
-Once installed, we also recommend installing several plugins from the Eclipse Marketplace.
-
-To do so, launch Eclipse, and go to Help->Eclipse Marketplace...
-
-Search for and install:
-
-1. Buildship Gradle Integration 3.0 (or greater)
-1. Groovy Development Tools 3.4.0 (or greater)
-1. TestNG for Eclipse (optional -- only needed if you want to run tests from Eclipse)
-
-> At time of writing, TestNG for Eclipse does not show up in the Eclipse Marketplace
-as the latest released version does not install in Eclipse 2019-03.
-However, you can install a working beta of TestNG for Eclipse by going to
->
-Help->Install New Software...
->
-and entering
->
-`TestNG Eclipse Composite P2 Repo - http://beust.com/eclipse-beta`
->
-into the *Work with* box and click on the *Add...* button.
->
-Eclipse might pause for a bit with the word *Pending* in the table below at this point, but it will eventually list TestNG with
-a selection box under the *Name* column.
->
-Select *TestNG* and carry on through the
-install process to install the TestNG plugin.
-
-After installing the plugins, it is a good to get Java 11 set up in Eclipse as the default JRE.
-
-To do this go to Preferences (Eclipse->Preferences in macOS, File->Preferences
-on Windows or Window->Preferences on Linux) and find
-
-Java -> Installed JREs
-
-If your Java 11 installation is not listed, click on
-
-*Add* -> Standard VM -> *Next*
-
-and enter the JRE home. You can browse to where it was installed. Give it a name (like "AdoptOpenJDK 11"). Select this JDK
-as the default JRE and click on *Apply and Close*.
-
-
-You can now import Jalview. It is important to import
-Jalview as a Gradle project (not as a Java project), so go to
-
-File->Import...
-
-find and select
-
-Gradle->Existing Gradle Project
-
-and then click on the *Next >* button.
-
-In the following options, it is the *Project Root Directory* you should set to be the
-`jalview` folder that git downloaded. Then you can click on the *Finish* button.
## Gradle properties
```
in the `jalview` root folder.
-
## Enabling Code Coverage with OpenClover
Bytecode instrumentation tasks are enabled by specifying 'true' (or just a non-whitespace non-numeric word) in the 'clover' property. This adds the 'openclover' plugin to the build script's classpath, making it possible to track code execution during test which can be viewed as an HTML report published at build/reports/clover/index.html.
_Note_ do not forget to include the -Dfile.encoding=UTF-8 option: this is essential for some platforms in order for Clover to correctly parse some Jalview source files that contain characters that are UTF-8 encoded.
+## Setting up in Eclipse IDE
+
+### Installing Eclipse IDE
+
+We develop in Eclipse, and support settings to develop and save Jalview source code
+in our preferred style. We also support running the Jalview application, debugging
+and running tests with TestNG from within Eclipse.
+
+To get Jalview set up as a project in Eclipse, we recommend using at least the 2019-12
+version of Eclipse IDE for Java Developers which you can download from the Eclipse
+website: <https://www.eclipse.org/downloads/>. Since Eclipse 2020-03 you are encouraged to use the Eclipse Installer (see the Eclipse Downloads page).
+In the installer, when given a choice of packages for Eclipse you should choose the "Eclipse IDE for Enterprise Java Developers" package.
+
+
+
+Once Eclipse is installed, we also recommend installing several plugins from the Eclipse Marketplace.
+
+Some of these should already be installed with the Enterprise Java Developer package:
+
+1. Buildship Gradle Integration 3.0 (or greater)
+1. EclEmma Java Code Coverage
+1. Egit - Git Integration for Eclipse
+
+To install the others, launch Eclipse, and go to Help->Eclipse Marketplace...
+
+Search for and install:
+
+1. Groovy Development Tools 3.4.0 (or greater)
+1. Checkstyle Plug-in (optional)
+1. TestNG for Eclipse (optional -- only needed if you want to run tests from Eclipse)
+
+> At time of writing, TestNG for Eclipse does not show up in the Eclipse Marketplace
+as the latest released version does not install in Eclipse 2019-03.
+However, you can install a working release of TestNG for Eclipse by going to
+>
+Help->Install New Software...
+>
+and entering
+>
+`TestNG Release - https://dl.bintray.com/testng-team/testng-eclipse-release`
+>
+into the *Work with* box and click on the *Add...* button.
+>
+Eclipse might pause for a bit with the word *Pending* in the table below at this point, but it will eventually list TestNG with
+a selection box under the *Name* column.
+>
+Select *TestNG* and carry on through the
+install process to install the TestNG plugin.
+
+After installing the plugins, check that Java 11 is set up in Eclipse as the default JRE (see section [Java 11 compliant JDK](#java-11-compliant-jdk)).
+
+To do this go to Preferences (Eclipse->Preferences in macOS, File->Preferences
+on Windows or Window->Preferences on Linux) and find
+
+Java -> Installed JREs
+
+If your Java 11 installation is not listed, click on
+
+*Add* -> Standard VM -> *Next*
+
+and enter the JRE home. You can browse to where it is installed. Give it a name (like "AdoptOpenJDK 11"). Select this JDK
+as the default JRE and click on *Apply and Close*.
+
+
+You can now import Jalview.
+
+### Importing Jalview as an Eclipse project
+
+#### Importing an already downloaded git repo
+
+If you have already downloaded Jalview using `git clone` then you can import this folder into Eclipse directly.
+
+It is important to import
+Jalview as a Gradle project (not as a Java project), so go to
+
+File->Import...
+
+find and select
+
+Gradle->Existing Gradle Project
+
+and then click on the *Next* button.
+
+In the following options, it is the __Project Root Directory__ you should set to be the
+`jalview` folder that git downloaded. Then you can click on the *Finish* button.
+
+#### Using Eclipse IDE to download the git repo
+
+If you don't have git as a command line tool or would prefer to work entirely within Eclipse IDE then
+Eclipse's eGit plugin can set up a git repo of the jalview source. Go to
+
+File->Import...
+
+Find and select
+
+Git->Projects from Git
+
+and then click on the *Next* button.
+
+Then select Clone URI and click on *Next*.
+
+In the next window (Source Git Repository) you should put the `git clone` URL in the text box labelled `URI`. If you have a Jalview developer account (with a username and password for the Jalview git repository) then you should enter
+`https://source.jalview.org/git/jalview.git`.
+If you do not have a Jalview developer account then you should enter
+`http://source.jalview.org/git/jalview.git`.
+You will not be able to push any of your changes back to the Jalview git repository. However you can still pull all branches of the Jalview source code to your computer and develop the code there.
+> You can sign up for a Jalview developer account at <https://source.jalview.org/crucible/>
+
+If you have a Jalview developer account, enter the username and password and decide if you want to use Eclipse's secure storage. If you don't have an account you can leave the Authentication section blank.
+
+
+
+Click on the *Next* button.
+
+The next window (Branch Selection) gives a list of the many Jalview branches, which by default will be all checked. You probably only want to download one branch (you can always download others at a later time). This is likely to be the `develop` branch so you can click on the *Deselect All* button, find the `develop` branch (the filter text helps), select that, and then click on the *Next* button.
+
+Choose a directory to your copy of the git repo in, and leave the other options as they are and click on the *Next* button. The next stage may take a minute or two as it checks out the selected branch(es) from the Jalview git repository.
+
+When it has finished it is important to select __Import as general project__ and then click on *Next*.
+> Ideally there would be an _Import as gradle project_ here but there isn't -- we'll sort that out later.
+
+
+
+Click on the *Next* button.
+
+You can change the project name here. By default it will show as __jalview__ which is fine unless you have another instance of the a Jalview project also called jalview, in which case you could change this project's name now to avoid a conflict within Eclipse.
+
+Click on *Finish*!
+
+However, we haven't finished...
+
+You should now see, and be able to expand, the jalview project in the Project Explorer. We need to tell eclipse that this is a Gradle project, which will then allow the Eclipse Buildship plugin to automatically configure almost everything else!
+
+Right click on the project name (jalview) in the Project Explorer and find Configure towards the bottom of this long context menu, then choose Add Gradle Nature.
+
+
+
+The project should now reconfigure itself using the `build.gradle` file to dynamically set various aspects of the project including classpath.
+
+#### Additional views
+
+Some views that are automatically added when Importing a Gradle Project are not added when simply Adding a Gradle Nature, but we can add these manually by clicking on
+Window->Show View->Console
+and
+Window->Show View->Other...
+Filter with the word "gradle" and choose both __Gradle Executions__ and __Gradle Tasks__ and then click on the *Open* button.
+
+
+Okay, ready to code! Use of Eclipse is beyond the scope of this document, but you can find more information about developing jalview and our developer workflow in the google doc <https://docs.google.com/document/d/1lZo_pZRkazDBJGNachXr6qCVlw8ByuMYG6e9SZlPUlQ/edit?usp=sharing>
---
[Jalview Development Team](mailto:help@jalview.org)
git://source.jalview.org / jalview.git / blobdiff