Vamos24 replication

INSTALL.md

@@ -1,16 +1,11 @@
 # Installation
 ## Installation Instructions
-In the following, we describe how to replicate the validation from our paper (Section 5) step-by-step.
+In the following, we describe how to replicate the evaluation from our paper step-by-step.
 The instructions explain how to build the Docker image and run the validation in a Docker container.
 
-### 1. Install Docker (if required)
-How to install Docker depends on your operating system:
+### 1. Start Docker
 
-- _Windows or Mac_: You can find download and installation instructions [here](https://www.docker.com/get-started).
-- _Linux Distributions_: How to install Docker on your system, depends on your distribution. The chances are high that Docker is part of your distributions package database.
-Docker's [documentation](https://docs.docker.com/engine/install/) contains instructions for common distributions.
-
-Then, start the docker deamon.
+Start the docker daemon.
 
 ### 2. Open a Suitable Terminal
 ```
@@ -31,10 +26,18 @@ Clone this repository to a directory of your choice using git:
 ```shell
 git clone https://github.com/VariantSync/DiffDetective.git
 ```
-Then, navigate to the root of your local clone of this repository:
+Then, navigate to the root of your local clone of this repository
 ```shell
 cd DiffDetective
 ```
+and checkout the branch of the replication:
+```shell
+git checkout vamos24_explanations
+```
+Finally, navigate to the replication directory
+```shell
+cd replication/VaMoS24-explanations
+```
 
 ### 3. Build the Docker Container
 To build the Docker container you can run the `build` script corresponding to your operating system:
@@ -45,9 +48,9 @@ To build the Docker container you can run the `build` script corresponding to yo
   ./build.sh
 ```
 
-## 4. Verification & Replication
+## 4. Replication
 
-### Running the Replication or Verification
+### Running the Replication
 To execute the replication you can run the `execute` script corresponding to your operating system with `replication` as first argument.
 
 #### Windows:
@@ -57,10 +60,9 @@ To execute the replication you can run the `execute` script corresponding to you
 
 > WARNING!
 > The replication will at least require an hour and might require up to a day depending on your system.
-> Therefore, we offer a short verification (5-10 minutes) which runs DiffDetective on only four of the datasets.
-> You can run it by providing "verification" as argument instead of "replication" (i.e., `.\execute.bat verification`,  `./execute.sh verification`).
 > If you want to stop the execution, you can call the provided script for stopping the container in a separate terminal.
 > When restarted, the execution will continue processing by restarting at the last unfinished repository.
+> If you want to replicate parts of the evaluation on a subset of the datasets, run the replication on a custom dataset (see below for instructions).
 > #### Windows:
 > `.\stop-execution.bat`
 > #### Linux/Mac (bash):
@@ -69,61 +71,11 @@ To execute the replication you can run the `execute` script corresponding to you
 You might see warnings or errors reported from SLF4J like `Failed to load class "org.slf4j.impl.StaticLoggerBinder"` which you can safely ignore.
 Further troubleshooting advice can be found at the bottom of this file.
 
-The results of the verification will be stored in the [results](results) directory.
+The results of the verification will be stored in the [results](../../results) directory.
 
 ### Expected Output of the Verification
-The aggregated results of the verification/replication can be found in the following files.
-The example file content shown below should match your results when running the _verification_.
-(Note that the links below only have a target _after_ running the replication or verification.)
-
-- The [speed statistics](results/validation/current/speedstatistics.txt) contain information about the total runtime, median runtime, mean runtime, and more:
-  ```
-  #Commits: 24701
-  Total   commit process time is: 14.065916666666668min
-  Fastest commit process time is: d86e352859e797f6792d6013054435ae0538ef6d___xfig___0ms
-  Slowest commit process time is: 9838b7032ea9792bec21af424c53c07078636d21___xorg-server___7996ms
-  Median  commit process time is: f77ffeb9b26f49ef66f77929848f2ac9486f1081___tcl___13ms
-  Average commit process time is: 34.166835350795516ms
-  ```
-- The [classification results](results/validation/current/ultimateresult.metadata.txt) contain information about how often each pattern was matched, and more.
-  ```
-  repository: <NONE>
-  total commits: 42323
-  filtered commits: 7425
-  failed commits: 0
-  empty commits: 10197
-  processed commits: 24701
-  tree diffs: 80751
-  fastestCommit: 518e205b06d0dc7a0cd35fbc2c6a4376f2959020___xorg-server___0ms
-  slowestCommit: 9838b7032ea9792bec21af424c53c07078636d21___xorg-server___7996ms
-  runtime in seconds: 853.9739999999999
-  runtime with multithreading in seconds: 144.549
-  treeformat: org.variantsync.diffdetective.diff.difftree.serialize.treeformat.CommitDiffDiffTreeLabelFormat
-  nodeformat: org.variantsync.diffdetective.mining.formats.ReleaseMiningDiffNodeFormat
-  edgeformat: org.variantsync.diffdetective.mining.formats.DirectedEdgeLabelFormat with org.variantsync.diffdetective.mining.formats.ReleaseMiningDiffNodeFormat
-  analysis: org.variantsync.diffdetective.validation.PatternValidationTask
-  #NON nodes: 0
-  #ADD nodes: 0
-  #REM nodes: 0
-  filtered because not (is not empty): 212
-  AddToPC: { total = 443451; commits = 22470 }
-  AddWithMapping: { total = 51036; commits = 2971 }
-  RemFromPC: { total = 406809; commits = 21384 }
-  RemWithMapping: { total = 36622; commits = 2373 }
-  Specialization: { total = 7949; commits = 1251 }
-  Generalization: { total = 11057; commits = 955 }
-  Reconfiguration: { total = 3186; commits = 381 }
-  Refactoring: { total = 4862; commits = 504 }
-  Untouched: { total = 0; commits = 0 }
-  #Error[conditional macro without expression]: 2
-  #Error[#else after #else]: 2
-  #Error[#else or #elif without #if]: 11
-  #Error[#endif without #if]: 12
-  #Error[not all annotations closed]: 8
-  ```
-
-Moreover, the results comprise the (LaTeX) tables that are part of our paper and appendix.
-The processing times might deviate because performance depends on your hardware.
+
+The [results](../../results) directory contains a folder relationshipEdges. This folder contains the statistics for every repository, i.e., total run time, run times per commit, fastest/slowest commit, and statistics about the constructed edge-typed variation diffs, and all analysed variation diffs in linegraph format.
 
 ### (Optional) Running DiffDetective on Custom Datasets
 You can also run DiffDetective on other datasets by providing the path to the dataset file as first argument to the execution script:
@@ -133,27 +85,27 @@ You can also run DiffDetective on other datasets by providing the path to the da
 #### Linux/Mac (bash):
 `./execute.sh path/to/custom/dataset.md`
 
-The input file must have the same format as the other dataset files (i.e., repositories are listed in a Markdown table). You can find [dataset files](docs/datasets.md) in the [docs](docs) folder.
+The input file must have the same format as the other dataset files (i.e., repositories are listed in a Markdown table). You can find [dataset files](../../docs/datasets/all.md) in the [docs/datasets](../../docs/datasets) folder.
 
 ## Troubleshooting
 
 ### 'Got permission denied while trying to connect to the Docker daemon socket'
-`Problem:` This is a common problem under Linux, if the user trying to execute Docker commands does not have the permissions to do so. 
+`Problem:` This is a common problem under Linux, if the user trying to execute Docker commands does not have the permissions to do so.
 
 `Fix:` You can fix this problem by either following the [post-installation instructions](https://docs.docker.com/engine/install/linux-postinstall/), or by executing the scripts in the replication package with elevated permissions (i.e., `sudo`).
 
 ### 'Unable to find image 'replication-package:latest' locally'
-`Problem:` The Docker container could not be found. This either means that the name of the container that was built does not fit the name of the container that is being executed (this only happens if you changed the provided scripts), or that the Docker container was not built yet. 
+`Problem:` The Docker container could not be found. This either means that the name of the container that was built does not fit the name of the container that is being executed (this only happens if you changed the provided scripts), or that the Docker container was not built yet.
 
 `Fix:` Follow the instructions described above in the section `Build the Docker Container`.
 
 ### No results after verification, or 'cannot create directory '../results/validation/current': Permission denied'
-`Problem:` This problem can occur due to how permissions are managed inside the Docker container. More specifically, it will appear, if Docker is executed with elevated permissions (i.e., `sudo`) and if there is no [results](results) directory because it was deleted manually. In this case, Docker will create the directory with elevated permissions, and the Docker user has no permissions to access the directory.
+`Problem:` This problem can occur due to how permissions are managed inside the Docker container. More specifically, it will appear, if Docker is executed with elevated permissions (i.e., `sudo`) and if there is no [results](../../results) directory because it was deleted manually. In this case, Docker will create the directory with elevated permissions, and the Docker user has no permissions to access the directory.
 
-`Fix:` If there is a _results_ directory, delete it with elevated permission (e.g., `sudo rm -r results`). 
+`Fix:` If there is a _results_ directory, delete it with elevated permission (e.g., `sudo rm -r results`).
 Then, create a new _results_ directory without elevated permissions, or execute `git restore .` to restore the deleted directory.
 
 ### Failed to load class "org.slf4j.impl.StaticLoggerBinder"
 `Problem:` An operation within the initialization phase of the logger library we use (tinylog) failed.
 
-`Fix:` Please ignore this warning. Tinylog will fall back onto a default implementation (`Defaulting to no-operation (NOP) logger implementation`) and logging will work as expected.
+`Fix:` Please ignore this warning. Tinylog will fall back onto a default implementation (`Defaulting to no-operation (NOP) logger implementation`) and logging will work as expected.