JAL-3248 Added step to create the eclipse files before project import. Noted non...

Cherry pick from release, generated new building.html as it's a different process. Also added in a "**/*.md" into build.gradle (wasn't finding anything with "*.md")

diff --git a/build.gradle b/build.gradle
index f298bd7..c3e89e5 100644 (file)
--- a/build.gradle
+++ b/build.gradle
@@ -1084,6 +1084,7 @@ def convertMdToHtml (FileTree mdFiles, File cssFile) {
 
     def htmlFilePath = mdFile.getPath().replaceAll(/\..*?$/, ".html")
     def htmlFile = file(htmlFilePath)
+    println("Creating ${htmlFilePath}")
     htmlFile.text = htmlText
   }
 }
@@ -1121,7 +1122,7 @@ task copyDocs(type: Copy) {
 
 task convertMdFiles {
   dependsOn copyDocs
-  def mdFiles = fileTree(dir: docBuildDir, include: "*.md")
+  def mdFiles = fileTree(dir: docBuildDir, include: "**/*.md")
   def cssFile = file("${jalviewDir}/${flexmark_css}")
 
   doLast {

diff --git a/doc/building.html b/doc/building.html
index 2ca2641..44ffd5e 100644 (file)
--- a/doc/building.html
+++ b/doc/building.html
@@ -727,7 +727,7 @@ java -jar getdown-launcher.jar . jalview
 <p>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.</p>
 <ul>
 <li>Java 11 compliant JDK</li>
-<li>gradle 5.2 or above</li>
+<li>gradle 5.2 or above <em>(NB gradle 6.6 and above currently produces NullPointerExceptions during the build. This is non-fatal and does not affect the build. Use gradle 6.5.1 to avoid this)</em></li>
 <li>git</li>
 </ul>
 <blockquote>
@@ -1121,7 +1121,7 @@ list of media types (i.e. platform specific installers) <em>install4j</em> shoul
 <p>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.</p>
-<p>To get Jalview set up as a project in Eclipse, we recommend using at least the 2019-12
+<p>To get Jalview set up as a project in Eclipse, we recommend using at least the 2020-03
 version of Eclipse IDE for Java Developers which you can download from the Eclipse
 website: <a href="https://www.eclipse.org/downloads/">https://www.eclipse.org/downloads/</a>.  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 &quot;Eclipse IDE for Enterprise Java Developers&quot; package.</p>
@@ -1142,7 +1142,7 @@ In the installer, when given a choice of packages for Eclipse you should choose
 </ol>
 <blockquote>
 <p>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.
+as the latest released version does not install in Eclipse 2020-03.
 However, you can install a working release of TestNG for Eclipse by going to</p>
 <p>Help-&gt;Install New Software...</p>
 <p>and entering</p>
@@ -1165,6 +1165,10 @@ as the default JRE and click on <em>Apply and Close</em>.</p>
 <h3 id="importing-jalview-as-an-eclipse-project"><a href="#importing-jalview-as-an-eclipse-project" name="importing-jalview-as-an-eclipse-project" class="anchor"><span class="octicon octicon-link"></span>Importing Jalview as an Eclipse project</a></h3>
 <h4 id="importing-an-already-downloaded-git-repo"><a href="#importing-an-already-downloaded-git-repo" name="importing-an-already-downloaded-git-repo" class="anchor"><span class="octicon octicon-link"></span>Importing an already downloaded git repo</a></h4>
 <p>If you have already downloaded Jalview using <code>git clone</code> then you can import this folder into Eclipse directly.</p>
+<p><strong>Before importing the cloned git repo you must create the Eclipse project files.</strong> You can do this by either running</p>
+<p><code>gradle eclipse</code></p>
+<p>or</p>
+<p>Unzipping the file <code>utils/eclipse/eclipse_startup_files.zip</code> in the base repo directory (<code>jalview</code>)</p>
 <p>It is important to import
 Jalview as a Gradle project (not as a Java project), so go to</p>
 <p>File-&gt;Import...</p>

diff --git a/doc/building.md b/doc/building.md
index 06e796d..e8328d2 100644 (file)
--- a/doc/building.md
+++ b/doc/building.md
@@ -26,7 +26,7 @@ java -jar getdown-launcher.jar . jalview
 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
-* gradle 5.2 or above
+* gradle 5.2 or above *(NB gradle 6.6 and above currently produces NullPointerExceptions during the build. This is non-fatal and does not affect the build. Use gradle 6.5.1 to avoid this)*
 * git
 
 > The versions and installation methods here are just suggestions (which we have tested 
@@ -536,7 +536,7 @@ We develop in Eclipse, and support settings to develop and save Jalview source c
 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 
+To get Jalview set up as a project in Eclipse, we recommend using at least the 2020-03
 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.
@@ -560,7 +560,7 @@ Search for and install:
 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.
+as the latest released version does not install in Eclipse 2020-03.
 However, you can install a working release of TestNG for Eclipse by going to
 >
 > Help->Install New Software...
@@ -600,6 +600,14 @@ You can now import Jalview.
 
 If you have already downloaded Jalview using `git clone` then you can import this folder into Eclipse directly.
 
+__Before importing the cloned git repo you must create the Eclipse project files.__ You can do this by either running
+
+`gradle eclipse`
+
+or
+
+Unzipping the file `utils/eclipse/eclipse_startup_files.zip` in the base repo directory (`jalview`)
+
 It is important to import 
 Jalview as a Gradle project (not as a Java project), so go to