Updated readme with the missing parameters for python scripts

code/README.md

@@ -28,23 +28,23 @@ The figure shows a suggested workflow consisting of four steps. Step 1 and Step
 To get issues one needs a bug tracking system. As an example the project Jenkins uses [JIRA](https://issues.jenkins-ci.org).
 From here it is possible to fetch issues that we then can link to bug fixing commits.
 
-We have provided an example script that can be used to fetch issues from Jenkins issues (see 1) in the [figure](#workflow)). In the directory fetch_jira_bugs, one can find the **fetch.py** script. The script has a jql string which is used as a filter to get certain issues. JIRA provides a neat way to test these jql strings directly in the [web page](https://issues.jenkins-ci.org/browse/JENKINS-41020?jql=). Change to the advanced view and then enter the search creiterias. Notice that the jql string is generated in the browsers url bar once enter is hit.
+We have provided an example script that can be used to fetch issues from Jenkins issues (see 1) in the [figure](#workflow). In the directory fetch_jira_bugs, one can find the **fetch.py** script. The script has a jql string which is used as a filter to get certain issues. JIRA provides a neat way to test these jql strings directly in the [web page](https://issues.jenkins-ci.org/browse/JENKINS-41020?jql=). Change to the advanced view and then enter the search criteria. Notice that the jql string is generated in the browser's url bar once enter is hit.
 
 To fetch issues from Jenkins JIRA, just run:
 ```python
-python fetch.py
+python fetch.py --issue-code <issue_code> --jira-project <jira_project_base_url>
 ```
-It creates a directory with issues (see issues folder in the [figure](#workflow)). These issues will later on be used by the `find_bug_fixes.py` script. 
+passing as parameters the code used for the project issues on JIRA and the name of the JIRA repository of the project (e.g., _issues.jenkins-ci.org_). The script creates a directory with issues (see issues folder in the [figure](#workflow)). These issues will later on be used by the `find_bug_fixes.py` script. 
 
 ### Step 2. Preprocess the git log output (SZZ pre-step) ###
-Second we need to convert the `git log` output to something that can be processed. That requires a local copy of the repository that we aim to analyze, [Jenkins Core Repository](https://github.com/jenkinsci/jenkins). Onced cloned, one can now run the **git_log_to_array.py** script (see 2) in the [figure](#workflow)). The script requires an absolute path to the cloned repository and optionally a SHA-1 for an initial commit.
+Second we need to convert the `git log` output to something that can be processed. That requires a local copy of the repository that we aim to analyze, [Jenkins Core Repository](https://github.com/jenkinsci/jenkins). Onced cloned, one can now run the **git_log_to_array.py** script (see 2 in the [figure](#workflow)). The script requires an absolute path to the cloned repository and a SHA-1 for an initial commit.
 ```python
-python git_log_to_array.py --repo-path <path_to_local_repo>
+python git_log_to_array.py --from-commit <SHA-1_of_initial_commit> --repo-path <path_to_local_repo>
 ```
 Once executed, this creates a file `gitlog.json` that can be used together with issues that we created with `fetch.py` script. 
 
 ### Step 3. Identify bug-fixing commits (SZZ Phase 1) ###
-Now using the `find_bug_fixes.py` (see 3) in the [figure](#workflow)) and this file, we can get a json file
+Now using the `find_bug_fixes.py` (see 3 in the [figure](#workflow)) and this file, we can get a json file
 that contains the Issue and its corresponding commit SHA-1, the commit date, the creation date and the resolution date. Just run:
 ```python
 python find_bug_fixes.py --gitlog <path_to_gitlog_file> --issue-list <path_to_issues_directory>
@@ -62,7 +62,7 @@ like:
 gradle build && gradle fatJar
 ```
 
-Or if the algorithm should be runned without building a jar:
+Or if the algorithm should be run without building a jar:
 
 ```shell
 gradle build && gradle runJar
@@ -71,7 +71,7 @@ gradle build && gradle runJar
 The algorithm tries to use as many cores as possible during runtime.
 
 To get the bug introducing commits from a repository using the file produced
-by the previous issue to bug fix commit step, run (see 4) in the [figure](#workflow)):
+by the previous issue to bug fix commit step, run (see 4 in the [figure](#workflow)):
 
 ```shell
 java -jar szz_find_bug_introducers-<version_number>.jar -i <path_to_issue_list.json> -r <path_to_local_repo>
@@ -157,7 +157,7 @@ The features are:
 1. Overall experience.
 2. Recent experience.
 
-The script builds a graph to keep track of each authors experience. The intial
+The script builds a graph to keep track of each authors experience. The initial
 run is:
 `python assemble_experience_features.py --repository <repo_path> --branch <branch> --save-graph`