[GH-15608] Replace Jira links with GH issue equivalent [nocheck] (#15610

)

* [GH-15608] - Replace Jira links with GH issue equivalent

* [GH-15608] Replace Jira links with GH issue equivalent [nocheck]

* Fix bindings

* Address Wendy's comment.

* Fix typo

* Change tests

* exclude demos

* Update flow items

CONTRIBUTING.md

@@ -26,47 +26,14 @@ If you're an Open Source community member you should send these to one of:
 
 ### How to File Bugs and Feature Requests
 
-You can file a bug report or feature request directly in the H2O-3 JIRA tracking system at [https://0xdata.atlassian.net/projects/PUBDEV](https://0xdata.atlassian.net/projects/PUBDEV). Anyone can create a JIRA ticket as long as you create a JIRA account using your email address.  
+You can file a bug report or feature request directly on the [GitHub issues](https://github.com/h2oai/h2o-3/issues) page.
 
-Log in to the [H2O JIRA tracking system](https://0xdata.atlassian.net/projects/PUBDEV). (Create an account if necessary.)
+Once inside the Github issues page, click the **New issue** button.
 
-Once inside the home page, click the **Create** button.
-
- ![create](h2o-docs/src/product/images/jira_create.png)
+ ![create](h2o-docs/src/product/images/issue_create.png)
 
 A form will display allowing you to enter information about the bug or feature request.
 
- ![new issue](h2o-docs/src/product/images/jira_new_issue.png)
-
-* Select the Project that you want to file the issue under. For example, if this is an open source public bug, you should file it under **Public H2O 3 (PUBDEV)**.
-* Specify the Issue Type. For example, if you believe you've found a bug, then select **Bug**, or if you want to request a new feature, then select **New Feature**.
-* Provide a short but concise summar about the issue. The summary will be shown when engineers organize, filter, and search for Jira tickets.
-* Specify the urgency of the issue using the Priority dropdown menu. 
-* If there is a due date specify it with the Due Date.
-* The Components drop down refers to the API or language that the issue relates to. (See the drop down menu for available options.)
-* You can leave Affects Version/s, Fix Version\s, and Assignee fields blank. Our engineering team will fill this in.
-* Add a detailed description of your bug in the Description section. Best practice for descriptions include:
-
-  	* A summary of what the issue is
-  	* What you think is causing the issue
-  	* Reproducible code that can be run end to end without requiring an engineer to edit your code. Use {code} {code} around your code to make it appear in code format.
-  	* Any scripts or necessary documents. Add by dragging and dropping your files into the create issue dialogue box.
-
-You can leave the rest of the ticket blank. When you are done with your ticket, simply click on the **Create** button at the bottom of the page.
-
- ![new issue](h2o-docs/src/product/images/jira_finished_create.png)
-
-After you click **Create**, a pop up will appear on the right side of your screen with a link to your Jira ticket. It will have the form https://0xdata.atlassian.net/browse/PUBDEV-####. You can use this link to later edit your ticket. 
-
-Please note that your Jira ticket number along with its summary will appear in one of the Jira ticket slack channels, and anytime you update the ticket anyone associated with that ticket, whether as the assignee or a watcher will receive an email with your changes.
-
-### How to Vote for or Comment on JIRA Issues
-
-You can also vote for or comment on existing bugs and feature requests that are already in the H2O-3 JIRA. To vote for a JIRA issue, log in the the H2O JIRA tracking system (create an account if necessary), find or create the issue that you want to vote for, then click the **Vote for this issue** link (upper right portion of the issue). Voting can help H2O prioritize the features that are included in each release. 
-
->***Note***: JIRA issues for customers with Enterprise Support contracts go into a private project so that customer information is kept secure. Contact [email protected] for more information.
-
-
 ## Help and Documentation
 
 You can help others directly and help improve the resources that others read to learn and use H2O by contributing to the formal documentation or the forums.
@@ -115,12 +82,12 @@ For Scala tests see the Sparkling Water GitHub repo.
 
 You can contribute R, Python, Java or Scala code for H2O, either for bug fixes or new features.  If you have your own idea about what to work on a good place to begin is to discuss it with us on [Gitter](https://gitter.im/h2oai/h2o-3) so that we can help point you in the right direction.
 
-For ideas about what to work on see the H2O-3 [JIRA ticket system](https://0xdata.atlassian.net/projects/PUBDEV).
+For ideas about what to work on see the H2O-3 [Github issues](https://github.com/h2oai/h2o-3/issues).
 
 To contribute code, fork the H2O-3 GitHub repo, create a branch for your work and when you're done, create a pull request.  Once a PR has been created, it will trigger the H2O-3 Jenkins test system and should start automatically running tests (this will show up in the comment history on the PR).  Make sure all the tests pass.  A few notes:
 
-* If there's not already a JIRA ticket associated with this task, please create one.
-* If there is a JIRA ticket associated with your changes, choose a branch name that includes that JIRA number.  e.g. `PUBDEV-1234_new_pca`
+* If there's not already a GitHub issue associated with this task, please create one.
+* If there is a GitHub issue associated with your changes, choose a branch name that includes that  number.  e.g. `gh-1234_new_pca`
 * New code must come with unit tests.  Here are some examples of [runits](https://github.com/h2oai/h2o-3/tree/master/h2o-r/tests), [pyunits](https://github.com/h2oai/h2o-3/tree/master/h2o-py/tests) and [junits](https://github.com/h2oai/h2o-3/tree/master/h2o-algos/src/test/java/hex) to help get you started.
-* Use the JIRA number in the PR title.  e.g. "PUBDEV-1234: Added new `pca_method` option in the PCA algorithm".
-* Write a summary of all changes & additions to the code in the PR description and add a link to the JIRA.
+* Use the GitHub number in the PR title.  e.g. "GH-1234: Added new `pca_method` option in the PCA algorithm".
+* Write a summary of all changes & additions to the code in the PR description and add a link to the GitHub issue.

README.md

@@ -47,36 +47,27 @@ More info on downloading & installing H2O is available in the [H2O User Guide](h
 <a name="Resources"></a>
 ## 2. Open Source Resources
 
-Most people interact with three or four primary open source resources:  **GitHub** (which you've already found), **JIRA** (for bug reports and issue tracking), **Stack Overflow** for H2O code/software-specific questions, and **h2ostream** (a Google Group / email discussion forum) for questions not suitable for Stack Overflow.  There is also a **Gitter** H2O developer chat group, however for archival purposes & to maximize accessibility, we'd prefer that standard H2O Q&A be conducted on Stack Overflow.
+Most people interact with three or four primary open source resources:  **GitHub** (which you've already found), **GitHub issues** (for bug reports and issue tracking), **Stack Overflow** for H2O code/software-specific questions, and **h2ostream** (a Google Group / email discussion forum) for questions not suitable for Stack Overflow.  There is also a **Gitter** H2O developer chat group, however for archival purposes & to maximize accessibility, we'd prefer that standard H2O Q&A be conducted on Stack Overflow.
 
 <a name="IssueTracking"></a>
 ### 2.1 Issue Tracking and Feature Requests
 
-> (Note: There is only one issue tracking system for the project.  GitHub issues are not enabled; you must use JIRA.)
+You can browse and create new issues in our GitHub repository:  <https://github.com/h2oai/h2o-3>
 
-You can browse and create new issues in our open source **JIRA**:  <http://jira.h2o.ai>
+*  You can **browse** and search for **issues** without logging in to Github:
+    1. Click the `Issues` tab on the top of the page
+    2. Apply filter to search for particular issues 
+*  To **create** an **issue** (either a bug or a feature request):
+    *  Create H2O-3 issues on the page [https://github.com/h2oai/h2o-3/issues/new/choose](https://github.com/h2oai/h2o-3/issues/new/choose).  (Note: Sparkling Water questions should be addressed under the [Sparkling Water](https://github.com/h2oai/sparkling-water/issues) repository.)
 
-*  You can **browse** and search for **issues** without logging in to JIRA:
-    1.  Click the `Issues` menu
-    1.  Click `Search for issues`
-*  To **create** an **issue** (either a bug or a feature request), please create yourself an account first:
-    1.  Click the `Log In` button on the top right of the screen
-    1.  Click `Create an acccount` near the bottom of the login box
-    1.  Once you have created an account and logged in, use the `Create` button on the menu to create an issue
-    1.  Create H2O-3 issues in the [PUBDEV](https://0xdata.atlassian.net/projects/PUBDEV/issues) project.  (Note: Sparkling Water questions should be filed under the [SW](https://0xdata.atlassian.net/projects/SW/issues) project.)
-*	You can also vote for feature requests and/or other issues. Voting can help H2O prioritize the features that are included in each release.
-	1. Go to the [H2O JIRA page](https://0xdata.atlassian.net/).
-	2. Click **Log In** to either log in or create an account if you do not already have one.
-	3. Search for the feature that you want to prioritize, or create a new feature.
-	4. Click on the **Vote for this issue** link. This is located on the right side of the issue under the **People** section.
 
 <a name="OpenSourceResources"></a>
 ### 2.2 List of H2O Resources
 
 *  GitHub
     * <https://github.com/h2oai/h2o-3>
-*  JIRA -- file bug reports / track issues here
-    * The [PUBDEV](https://0xdata.atlassian.net/projects/PUBDEV/issues) project contains issues for the current H2O-3 project)
+*  GitHub issues -- file bug reports / track issues here
+    * The <https://github.com/h2oai/h2o-3/issues> page contains issues for the current H2O-3 project)
 *  Stack Overflow -- ask all code/software questions here
     * <http://stackoverflow.com/questions/tagged/h2o>
 *  Cross Validated (Stack Exchange) -- ask algorithm/theory questions here
@@ -709,7 +700,7 @@ Click, C., Lanford, J., Malohlava, M., Parmar, V., and Roark, H. (Oct. 2016). _G
 <a name="Community"></a>
 ## 10. Community
 
-H2O has been built by a great many number of contributors over the years both within H2O.ai (the company) and the greater open source community.  You can begin to contribute to H2O by answering [Stack Overflow](http://stackoverflow.com/questions/tagged/h2o) questions or [filing bug reports](https://0xdata.atlassian.net/projects/PUBDEV/issues).  Please join us!  
+H2O has been built by a great many number of contributors over the years both within H2O.ai (the company) and the greater open source community.  You can begin to contribute to H2O by answering [Stack Overflow](http://stackoverflow.com/questions/tagged/h2o) questions or [filing bug reports](https://github.com/h2oai/h2o-3/issues).  Please join us!  
 
 
 ### Team & Committers

docker/jenkins-images/Dockerfile-graalvm

@@ -1,4 +1,4 @@
-# This is not part of the automated system (Will be fixed by https://h2oai.atlassian.net/browse/ITA-1506)
+# This is not part of the automated system.
 # The corresponding image harbor.h2o.ai/opsh2oai/h2o-3/dev-r-3.5.3-graalvm-17:42 was build manually from this file
 
 

docker/scripts/install_R_version

@@ -100,7 +100,7 @@ checkRInstallLog R.install.2.log
   )) \
 " 2>&1 | tee R.install.3.log
 checkRInstallLog R.install.3.log
-# Latest XGBoost (from source) does not compile; see https://0xdata.atlassian.net/browse/PUBDEV-7812
+# Latest XGBoost (from source) does not compile; see https://github.com/h2oai/h2o-3/issues/7830
 #/usr/local/R/current/bin/R -e "chooseCRANmirror(graphics=FALSE, ind=1); \
 #  install.packages(c('xgboost'), type='source') \
 #" 2>&1 | tee R.install.2.log

gradle/publish.gradle

@@ -98,11 +98,10 @@ publishing {
                       connection 'scm:git:https://github.com/h2oai/h2o-dev.git'
                       developerConnection 'scm:git:[email protected]:h2oai/h2o-dev.git'
                   }
-
-                  // Public H2O JIRA for issue management
+
                   issueManagement {
-                      system 'Jira'
-                      url    'http://jira.h2o.ai'
+                      system 'GitHub issues'
+                      url    'https://github.com/h2oai/h2o-3/issues'
                   }
                   // Developer information
                   developers {

h2o-admissibleml/src/main/java/hex/Infogram/Infogram.java

@@ -511,8 +511,8 @@ private void buildInfoGramsNRelevance(boolean validPresent) {
 
     /***
      * This method basically go through all the predictors and calculate the cmi associated with each predictor.  For
-     * core infogram, refer to https://h2oai.atlassian.net/browse/PUBDEV-8075 section I.  For fair infogram, refer to
-     * https://h2oai.atlassian.net/browse/PUBDEV-8075 section II.
+     * core infogram, refer to https://github.com/h2oai/h2o-3/issues/7830 section I.  For fair infogram, refer to
+     * https://github.com/h2oai/h2o-3/issues/7830 section II.
      * 
      * @param modelCount : current model count to build
      * @param numModel : total number of models to build
@@ -571,7 +571,7 @@ else if (frameInd == lastModelInd)// add all predictors
     }
 
   /***
-   * Calculate the CMI for each predictor.  Refer to https://h2oai.atlassian.net/browse/PUBDEV-8075 section I step 2 
+   * Calculate the CMI for each predictor.  Refer to https://github.com/h2oai/h2o-3/issues/7830 section I step 2 
    * for core infogram, or section II step 3 for fair infogram 
    *
    */

h2o-admissibleml/src/main/java/hex/Infogram/InfogramUtils.java

@@ -207,7 +207,7 @@ public static void removeFromDKV(Key<Frame>[] generatedFrameKeys) {
   }
 
   /***
-   * To calculate the CMI, refer to https://h2oai.atlassian.net/browse/PUBDEV-8075 section I step 2 for core infogram,
+   * To calculate the CMI, refer to https://github.com/h2oai/h2o-3/issues/7830 section I step 2 for core infogram,
    * section II step 2 for fair infogram.  Note that the last model is built with all predictors for core infogram or
    * built with protected columns for fair infogram.
    */

h2o-algos/src/main/java/hex/anovaglm/ANOVAGLM.java

@@ -185,7 +185,7 @@ public final void buildModel() {
 
     /***
      * This method will transform the training frame such that the constraints on the GLM parameters will be satisfied.  
-     * Refer to ANOVAGLMTutorial https://h2oai.atlassian.net/browse/PUBDEV-8088 section III.II.
+     * Refer to ANOVAGLMTutorial https://github.com/h2oai/h2o-3/issues/7561 section III.II.
      */
     void generateTransformedColumns() {
       _allTransformedColNames = flat(_transformedColNames);

h2o-algos/src/main/java/hex/anovaglm/ANOVAGLMModel.java

@@ -253,7 +253,7 @@ public void fillOutput(String[] modelNames, int[] degreeOfFreedom) {
   /**
    * The Type III SS calculation, degree of freedom, F-statistics and p-values will be included in the model
    * summary.  For details on how those are calculated, refer to ANOVAGLMTutorial  
-   * https://h2oai.atlassian.net/browse/PUBDEV-8088 section V.
+   * https://github.com/h2oai/h2o-3/issues/7561 section V.
    * 
    * @return a {@link TwoDimTable} representation of the result frame
    */

h2o-algos/src/main/java/hex/anovaglm/ANOVAGLMUtils.java

@@ -42,7 +42,7 @@ public static String[] extractPredNames(DataInfo dinfo,  int numOfPredictors) {
 
   /**
    * In order to calculate Type III SS, we need the individual predictors and their interactions.  For details, refer
-   * to ANOVAGLMTutorial https://h2oai.atlassian.net/browse/PUBDEV-8088 section IV
+   * to ANOVAGLMTutorial https://github.com/h2oai/h2o-3/issues/7561 section IV
    * 
    * @param predNamesIndividual: string containing individual predictor names
    * @param maxPredInt: maximum number of predictors allowed in interaction term generation
@@ -250,7 +250,7 @@ public static GLMParameters[] buildGLMParameters(Frame[] trainingFrames, ANOVAGL
 
   /***
    * This method is used to generate Model SS for all models built except the full model.  Refer to AnovaGLMTutorial
-   *  https://h2oai.atlassian.net/browse/PUBDEV-8088 section V.
+   *  https://github.com/h2oai/h2o-3/issues/7561 section V.
    * 
    * @param glmModels
    * @param family
@@ -359,7 +359,7 @@ public static String[] transformMultipleCols(Frame vec2Transform, String[][] pre
 
   /**
    * Generate frame transformation on two interacting columns.  Refer to AnovaGLMTutorial 
-   * https://h2oai.atlassian.net/browse/PUBDEV-8088 sectinos III.II. and IV.
+   * https://github.com/h2oai/h2o-3/issues/7561 sectinos III.II. and IV.
    * 
    * @param vec2Transform: frame containing the two predictors to transform
    * @param vecNames: name of the predictors
@@ -395,7 +395,7 @@ public static String[] transformTwoCols(Frame vec2Transform, String[] vecNames,
   }
 
   /**
-   * perform data transformation described in AnovaGLMTutorial https://h2oai.atlassian.net/browse/PUBDEV-8088 
+   * perform data transformation described in AnovaGLMTutorial https://github.com/h2oai/h2o-3/issues/7561
    * section III.II on one predictor.
    * 
    * @param vec2Transform: frame containing that one predictor to transform.

h2o-algos/src/main/java/hex/ensemble/StackedEnsembleModel.java

@@ -366,7 +366,7 @@ void doScoreOrCopyMetrics(Job job) {
     // cross-validation metrics -- the true k-fold cv metrics for the ensemble would require training k sets of
     // cross-validated base models (rather than a single set of cross-validated base models), which is extremely
     // computationally expensive and awkward from the standpoint of the existing Stacked Ensemble API.
-    // More info: https://0xdata.atlassian.net/browse/PUBDEV-3971
+    // More info: https://github.com/h2oai/h2o-3/issues/10864
     // Need to do DeepClone because otherwise framekey is incorrect (metalearner train is levelone not train)
     if (null != this._output._metalearner._output._cross_validation_metrics) {
       this._output._cross_validation_metrics = this._output._metalearner._output._cross_validation_metrics

h2o-algos/src/main/java/hex/gam/GamSplines/NBSplinesTypeIDerivative.java

@@ -10,9 +10,9 @@ public class NBSplinesTypeIDerivative {
     /***
      * This class implements the first or second derivative of NBSpline Type I (derivative of Mi,k(t)) in order to 
      * generate the penalty function described in Section VI.I equation 16 of doc in 
-     * JIRA: https://h2oai.atlassian.net/browse/PUBDEV-8398.
+     * the GitHub issue: https://github.com/h2oai/h2o-3/issues/7261.
      * Doc 2 is the doc for M-spline implementation and can be found here: 
-     * https://h2oai.atlassian.net/browse/PUBDEV-8835
+     * https://github.com/h2oai/h2o-3/issues/6926
      */
     private final int _order; // order k as in derivative of Mi,k(t)
     private final int _basisIndex; // index i

h2o-algos/src/main/java/hex/gam/GamSplines/ThinPlateDistanceWithKnots.java

@@ -18,7 +18,7 @@
 
 /**
  * Implementation details of this class can be found in GamThinPlateRegressionH2O.doc attached to this 
- * JIRA: https://h2oai.atlassian.net/browse/PUBDEV-7860
+ * GitHub issue: https://github.com/h2oai/h2o-3/issues/7783
  **/
 public class ThinPlateDistanceWithKnots extends MRTask<ThinPlateDistanceWithKnots> {
   final double[][] _knots;  // store knot values for the spline class

h2o-algos/src/main/java/hex/gam/MatrixFrameUtils/AddISGamColumns.java

@@ -9,7 +9,7 @@
 
 /**
  * class to gamified all gam_columns with bs set to 2.  For details regarding I-spline, please refer to doc I in 
- * JIRA: https://h2oai.atlassian.net/browse/PUBDEV-8398.  This one performs gamification only.
+ * the GitHub issue: https://github.com/h2oai/h2o-3/issues/7261.  This one performs gamification only.
  */
 public class AddISGamColumns extends MRTask<AddISGamColumns> {
     double[][][] _knotsMat; // knots without duplication for I-spline

h2o-algos/src/main/java/hex/gam/MatrixFrameUtils/GenISplineGamOneColumn.java

@@ -11,7 +11,7 @@
 import static hex.gam.GamSplines.NBSplinesTypeIDerivative.genISPenaltyMatrix;
 
 /**
- * Gamified one gam column at a time using I-spline.  See doc in JIRA: https://h2oai.atlassian.net/browse/PUBDEV-8398.
+ * Gamified one gam column at a time using I-spline. See doc in the GH issue: https://github.com/h2oai/h2o-3/issues/7261.
  * This one is different from AddISGamColumns because it generates the penalty matrix, zTranform if applicable and
  * perform scaling of the penalty matrix apart from performing gamification.
  */

h2o-algos/src/main/java/hex/glm/DispersionUtils.java

@@ -18,7 +18,7 @@
 public class DispersionUtils {
     /***
      * Estimate dispersion factor using maximum likelihood.  I followed section IV of the doc in 
-     * https://h2oai.atlassian.net/browse/PUBDEV-8683 . 
+     * https://github.com/h2oai/h2o-3/issues/7013. 
      */
     public static double estimateGammaMLSE(GLMTask.ComputeGammaMLSETsk mlCT, double seOld, double[] beta, 
                                            GLMModel.GLMParameters parms, ComputationState state, Job job, GLMModel model) {