## 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
`utils/install4j/` | files used by the packaging tool, install4j
`build.gradle` | the build file used by gradle
`gradle.properties` | configurable properties for the build process
+ `RELEASE` | propertyfile configuring JALVIEW_VERSION (from jalview.version) and the release branch (from jalview.release). An alternative file can be specified via JALVIEW_RELEASE_FILE property
Note that you need a Java 11 JDK to compile Jalview whether your target build is Java 1.8 or Java 11.
We have made significant customisations to the `getdown` launcher which you can find
in `getdown/src/getdown`.
-> You don't need to build this afresh as the required `gradle-core.jar`
-and `gradle-launcher.jar` files are already distributed in `j11lib` and `getdown/lib` but if you want to, then
+> You don't need to build this afresh as the required `getdown-core.jar`
+and `getdown-launcher.jar` files are already distributed in `j11lib` and `getdown/lib` but if you want to, then
you'll need a working Maven and also a Java 8 JDK. Ensure the Java 8 `javac` is forefront
in your path and do
>
>cd getdown/src/getdown
>mvn clean package -Dgetdown.host.whitelist="jalview.org,*.jalview.org"
>```
-> and you will find the required `.jar` files in `core/target/gradle-core-XXX.jar`
-and `launcher/target/gradle-launcher-XXX.jar`. The `gradle-core.jar` should then be copied
-to all three of the `j8lib`, `j11lib` and `getdown/lib` folders, whilst the `gradle-launcher.jar` only
+> and you will find the required `.jar` files in `core/target/getdown-core-XXX.jar`
+and `launcher/target/getdown-launcher-XXX.jar`. The `getdown-core.jar` should then be copied
+to all three of the `j8lib`, `j11lib` and `getdown/lib` folders, whilst the `getdown-launcher.jar` only
needs to be copied to `getdown/lib`.
>
>The `mvn` command should ideally include the `-Dgetdown.host.whitelist=*.jalview.org` setting.
getdown, and the final argument, "`jalview`", is a getdown application id (only "`jalview`"
is defined here).
+The command line sequence for building and relocating the getdown artifacts can be executed as a script via `getdown/src/getdown/mvn_cmd`. Please make sure this script is kept up to date should the getdown build instructions change.
### Running tests
gradle test -PtestngGroups=Network
```
-Available groups are Functional (default), Network, External.
+Available groups include Functional (default), Network, External.
+
+#### Excluding some tests
+
+Some of Jalview's Functional tests don't pass reliably in all environments. We tag these tests with a group like 'Not-bamboo' to mark them for exclusion when we run tests as part of continuous integration.
+
+To exclude one or more groups of tests, add them as a comma separated list in testngExcludedGroups.
+
+```bash
+gradle test -PtestngExcludedGroups=Not-bamboo
+```
### Installer packaging with *install4j*
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
Note that bamboo_planKey should be set by the build plan with `-Pbamboo_planKey=${bamboo.planKey}`
- application subdir as `alt`
- Getdown launcher cannot use a `file://` scheme appbase.
-* `DEVELOP`: This is for creating a `develop` appbase channel on the main web server. This won't become live until the actual getdown artefact is synced to the web server.
+* `DEVELOP`: This is for creating a `develop` appbase channel on the main web server. This won't become live until the actual getdown artefact is synced to the web server.
It will set
- `appbase` as `http://www.jalview.org/getdown/develop/JAVA_VERSION`
- application subdir as `alt`
- `appbase` as `http://www.jalview.org/getdown/SCRATCH-NAME/JAVA_VERSION`
- application subdir as `alt`
- Getdown launcher cannot use a `file://` scheme appbase.
+* `TEST-LOCAL`: Like `SCRATCH` but with a specific `test-local` channel name and a local filesystem appbase. This is meant for testing an over-the-air update on the local filesystem. An extra property `LOCALDIR` must be given (e.g. `-PLOCALDIR=/home/user/tmp/test`)
+ It will set
+ - `appbase` as `file://${LOCALDIR}`
+ - application subdir as `alt`
+ - Getdown launcher can use a `file://` scheme appbase.
* `TEST-RELEASE`: Like `SCRATCH` but with a specific `test-release` channel name. This won't become live until the actual getdown artefact is synced to the web server. This is meant for testing an over-the-air update without interfering with the live `release` or `develop` channels.
It will set
- `appbase` as `http://www.jalview.org/getdown/test-release/JAVA_VERSION`
gradle getdown -PCHANNEL=SCRATCH-my_test_version
```
+#### JALVIEW_VERSION and the RELEASE file
+Any Jalview build will include the value of JALVIEW_VERSION in various places, including the 'About' and Jalview Desktop window title, and in filenames for the stand-alone executable jar. You can specify a custom version for a build via the JALVIEW_VERSION property, but for most situations, JALVIEW_VERSION will be automatically configured according to the value of the CHANNEL property, using the `jalview.version` property specified in the RELEASE file:
+ - `CHANNEL=RELEASE` will set version to jalview.version
+ - `CHANNEL=TEST or DEVELOP` will append '-test' or '-develop' to jalview.version
+
+It is also possible to specify a custom location for the RELEASE file via an optional JALVIEW_RELEASE_FILE property.
+
#### `install4jMediaTypes`
If you are building *install4j* installers (requires *install4j* to be installed) then this property specifies a comma-separated
list of media types (i.e. platform specific installers) *install4j* should actually build.
```
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