Fixes 'popper workflow' issue with missing stage files

The command assumed that a stage file always exist. We know skip
generating a call graph for missing stage files.

docs/ci/popperci.md

@@ -127,34 +127,6 @@ status' is `GOLD`, the status of all validations is `PASS`. When the
 pipeline runs correctly but one or more validations fail (pipeline's 
 status is `PASS`), the status of one or more validations is `FAIL`.
 
-## Popper Badges
-
-We maintain a badging service that can be used to keep track of the 
-status of a pipeline. In order to enable this, the `--enable-badging` 
-flag has to be passed to the `popper ci` subcommand.
-
-![Badging service.](/figures/cibadges.png)
-
-Badges are commonly used to denote the status of a software project 
-with respect to certain aspect, e.g. whether the latest version can be 
-built without errors, or the percentage of code that unit tests cover 
-(code coverage). Badges available for Popper are shown in the above 
-figure. If badging is enabled, after the execution of a pipeline, the 
-status of a pipeline is recorded in the badging server, which keeps 
-track of statuses for every revision of ever pipeline.
-
-Users can include a link to the badge in the `README` page of a 
-pipeline, which can be displayed on the web interface of the version 
-control system (GitHub in this case). The CLI tool can generate links 
-for pipelines:
-
-```bash
-popper badge <exp>
-```
-
-Which prints to `stdout` the text that should be added to the `README` 
-file of the pipeline.
-
 ## Testing Locally
 
 The 
@@ -193,3 +165,47 @@ popper_logs/
 ├── validate.sh.out
 └── validate.sh.err
 ```
+
+These files are added to the 
+[`.gitignore`](https://help.github.com/articles/ignoring-files/) file 
+so they won't be committed to the git repository when doing `git add`. 
+To quickly remove them, one can clean the working tree:
+
+```bash
+# get list of files that would be deleted
+# include directories (-d)
+# include ignored files (-x)
+git clean -dx --dry-run
+
+# remove --dry-run and add --force to actually delete files
+git clean -dx --force
+```
+
+## Popper Badges
+
+We maintain a badging service that can be used to keep track of the 
+status of a pipeline. In order to enable this, the `--enable-badging` 
+flag has to be passed to the `popper ci` subcommand.
+
+![Badging service.](/figures/cibadges.png)
+
+Badges are commonly used to denote the status of a software project 
+with respect to certain aspect, e.g. whether the latest version can be 
+built without errors, or the percentage of code that unit tests cover 
+(code coverage). Badges available for Popper are shown in the above 
+figure. If badging is enabled, after the execution of a pipeline, the 
+status of a pipeline is recorded in the badging server, which keeps 
+track of statuses for every revision of ever pipeline.
+
+Users can include a link to the badge in the `README` page of a 
+pipeline, which can be displayed on the web interface of the version 
+control system (GitHub in this case). The CLI tool can generate links 
+for pipelines:
+
+```bash
+popper badge <exp>
+```
+
+Which prints to `stdout` the text that should be added to the `README` 
+file of the pipeline.
+

docs/protocol/getting_started.md

@@ -5,8 +5,6 @@ artifacts following a [DevOps](https://en.wikipedia.org/wiki/DevOps)
 approach, with the goal of making it easy for others (and yourself!) 
 to repeat an experiment or analysis pipeline.
 
-## Quickstart Guide
-
 We first need to install the CLI tool by following [these 
 instructions](https://github.com/systemslab/popper/tree/master/popper#install). 
 Show the available commands:
@@ -21,7 +19,7 @@ Show which version you installed:
 popper version
 ```
 
-> **NOTE**: this exercise was written using 0.4.1.
+> **NOTE**: this exercise was written using 0.5
 
 Create a project repository (if you are not familiar with git, look [here](https://www.learnenough.com/git-tutorial)):
 
@@ -34,7 +32,8 @@ git add .
 git commit -m 'first commit'
 ```
 
-Initialize the popper repository and add the commit file to git:
+Initialize the popper repository and add the `.popper.yml` file to 
+git:
 
 ```bash
 popper init

popper/common.go

@@ -94,7 +94,7 @@ func getPipelineName() (expName string, err error) {
 
 func ensureInRootFolder() {
 	if !sh.Test("dir", "pipelines") {
-		log.Fatalln("Can't find pipelines/ folder in current directory.")
+		log.Fatalln("Can't find pipelines/ folder in current directory. 'cd' to root of project.")
 	}
 }
 

popper/graph.go

@@ -8,6 +8,7 @@ import (
 	"log"
 	"strings"
 
+	sh "github.com/codeskyblue/go-sh"
 	"github.com/spf13/cobra"
 	"mvdan.cc/sh/syntax"
 )
@@ -68,7 +69,7 @@ func getDotGraphForStage(pipelinePath, stageFile, previousStageFile string) (dot
 
 			// first comment in a script goes in the root of that stage
 			if _, present := nodesInGraph[hashIt(stage)]; !present {
-				dot += fmt.Sprintf("  %s [shape=record,label=\"{%s|%s}\"];\n", stage, stageFile, label)
+				dot += fmt.Sprintf("  %s [shape=record,style=filled,label=\"{%s|%s}\"];\n", stage, stageFile, label)
 
 				if len(previousStageFile) > 0 {
 					previous := strings.Replace(previousStageFile, ".sh", "", -1)
@@ -97,7 +98,7 @@ func getDotGraphForStage(pipelinePath, stageFile, previousStageFile string) (dot
 					}
 					break
 				}
-				label = cmdValue + ":" + label
+				label = cmdValue + ": " + label
 			case *syntax.ForClause:
 				label = "loop: " + label
 			case *syntax.WhileClause:
@@ -145,6 +146,9 @@ func getDotGraph(pipelinePath string, stages []string) (dot string, err error) {
 
 	for _, stage := range stages {
 
+		if !sh.Test("f", pipelinePath+"/"+stage) {
+			continue
+		}
 		if subdot, err := getDotGraphForStage(pipelinePath, stage, previousStage); err != nil {
 			return "", err
 		} else {

popper/version.go

@@ -6,7 +6,7 @@ import (
 	"github.com/spf13/cobra"
 )
 
-var versionId = "0.5"
+var versionId = "0.5.1"
 
 var versionCmd = &cobra.Command{
 	Use:   "version",