From 8b7714197d15661a64a73631a62b917876178c76 Mon Sep 17 00:00:00 2001
From: Leon Martin <leon_martin@t-online.de>
Date: Wed, 17 Apr 2024 13:52:46 +0200
Subject: [PATCH] Dev (#37)

* added branch dev

* finished license paragraph in readme

* improved logging

* removed obsolete token

* optimized docker configuration

* fixed docker config

* fixed issues with docker compose (issue #3)

* refactored navigation

* styling improvements

* package update

* fixed bug in OWL approach

* prepared interface for verbalization

* removed unnecessary code

* added fair project type

* simplified access to stores; form simplification; navbar improvements

* migrated from rollup to vite

* updated docker config

* jsconfig fix

* updated .gitignore

* ui and code improvments

* mode is now also stored in localStorage

* restructured frontend

* restructured frontend

* improved componentization + refactoring

* minor

* Fix #8 by adding error handling to license retrieval

* Implement FAIR Project Type for Validation (#27)

* Add comments to existing SHACL project shapes #11

* Temporarily fix error when there is no result path #15

* Model FAIR principles as SHACL rules #11

* Fix semantic versioning regex

* Use match-case syntax #20

* Switch from short SHACL notation to more verbose one

* For files, make check in root directory explicit

* Extract the sh:or and sh:and components into node shapes

* Extend repository representation with homepage, tags, and DOIs in readme

* Introduce property shapes

* Split the shapes graph into several files.

* Fix selection and display of project types

* Extend repository representation for FAIR type (#13)

* Add check for valid version increment to repository representation (#13)

* Create separate methods for each repository property (#22)

* Limit repository representation to requirements of project type (#22)

* Remove unnecessary graph returns and process description literal earlier (#22)

* Make check for valid version increment less strict (#13)

* Visualize repository representation ontology (#21)

* Fix cut off letters at the end of words in diagram (#21)

* Adapt verbalized explanation for FAIR project type (#15)

* For sh:or,and,xone: use source shape instead of message (#15)

* Add URLs of IRIs in README.md (#21)

* Replace <repo> "has_default_branch" with <branch> "is_default_branch" (#13, #21, #22)

* Add minCount to qualifiedValueShapes (#11)

Previously, qualifiedValueShape only included qualifiedMinCount. This meant that a graph was valid in which the specified path did not exist at all.

* Add missing minCount constraints (#11)

* Adapt property shapes to changed default branch representation (#11)

* Include number of violations in validation response (#19)

* Show share of fulfilled criteria, v1 (#19)

* Adjust button of progress bar (#19)

* Adapt checks for files in root directory of default branch (#11)

* Use properties from the Software Description Ontology (#24)

* Integration tests for validation of FAIR project type, part 1 (#18)

* Use camelCase for own properties (as in SDO) (#24)

* Replace "has_section" property with more specific ones from SDO (#24)

* Integration tests for validation of FAIR project type, part 2 (#18)

* Introduce mocking (#18)

* Remove OWL part (#25)

* Fix ZeroDivisionError in benchmark.py (#26)

* Adapt FAIR criteria as a result of tests with 26 repos (#14)

* Remove "using" as keyword for usage documentation because of false positives (#14)

* Recognize all keywords per heading (#31) (#33)

* Improve verbalization on validation and specification page (#34)

* Add sh:message to node- and property-shapes (#29)

* Use messages from the validation report in verbalization (#29)

* Add sh:message to node- and property-shapes (#29)

* Use messages from the validation report in verbalization (#29)

* Make check for open issues more precise

* Display verbalized explanation as an unordered list (#29)

* Extract quality criteria from the shapes graph via RDFLib (#30)

* Add descriptions to the node- and property shapes (#30)

* Use Markdown to format descriptions (#30)

* Use adapted Markdown renderer (#30)

* Update Node and package versions

* Add information about SW requirements and citation to README.md

* Organize quality criteria in Markdown tables (#30)

* Correct cardinality in README.md

* Include lower-case letters in the DOI regex

* Add code and resulting files of the quantitative evaluation.

* Add information on how to execute the quantitative evaluation

* benchmark fusion

* change benchmark to scatterplot

* tests with scatter plot

* reran benchmark

* refactored evaluation

* refactored evaluation

* formatting benchmark results

* cleanup

* statistical analysis of runtime benchmark results

* updated benchmark figures

---------

Co-authored-by: Leon Martin <Leon@Home>
Co-authored-by: Leon Martin <lema@work>
Co-authored-by: Tobias Hummel <71486844+Tobias-TH@users.noreply.github.com>
---
 .gitignore                                    |   2 +-
 README.md                                     |  41 +-
 backend/Dockerfile                            |   2 +
 backend/benchmark.py                          |  33 +-
 .../conformity_per_best_practice.pdf          | Bin 0 -> 16738 bytes
 .../evaluation/repos_expected_to_be_fair.json |   1 +
 .../data/evaluation/runtime_benchmark_box.pdf | Bin 0 -> 6309 bytes
 .../evaluation/runtime_benchmark_results.json |   1 +
 .../evaluation/runtime_benchmark_scatter.pdf  | Bin 0 -> 22012 bytes
 backend/data/evaluation/trending_repos.json   |   1 +
 backend/data/shacl/property_shapes.ttl        |   4 +-
 backend/evaluation.py                         | 505 ++++++++++++++++++
 backend/shacl_validator.py                    |   4 +-
 docker-compose.yml                            |   8 +
 14 files changed, 574 insertions(+), 28 deletions(-)
 create mode 100644 backend/data/evaluation/conformity_per_best_practice.pdf
 create mode 100644 backend/data/evaluation/repos_expected_to_be_fair.json
 create mode 100644 backend/data/evaluation/runtime_benchmark_box.pdf
 create mode 100644 backend/data/evaluation/runtime_benchmark_results.json
 create mode 100644 backend/data/evaluation/runtime_benchmark_scatter.pdf
 create mode 100644 backend/data/evaluation/trending_repos.json
 create mode 100644 backend/evaluation.py

diff --git a/.gitignore b/.gitignore
index d410dc8..5917194 100644
--- a/.gitignore
+++ b/.gitignore
@@ -2,7 +2,7 @@ frontend/node_modules/
 frontend/dist/
 
 backend/__pycache__
-backend/git_access_token
+.github_access_token
 backend/data/benchmarks/
 !backend/data/benchmarks/.gitkeep
 
diff --git a/README.md b/README.md
index 8a59695..2500883 100644
--- a/README.md
+++ b/README.md
@@ -137,13 +137,44 @@ Instead of running frontend and backend using `docker compose up`, you can run b
 
 Note that the frontend depends on the backend. The backend should therefore be started first.
 
-### Benchmarks
+### Evaluation
 
-To reproduce the performance benchmarks shown in the paper, perform the following steps: 
+WARNING: Rerunning the evaluation will overwrite the results that are provided in the repository!
 
-- Create a file called `git_access_token` in the [backend](./backend/) folder. Then enter your GitHub access token in that file and save. 
-- Run `docker compose run --service-ports --entrypoint bash backend` to get a bash that is attached to the frontend container.
-- Run `./benchmark.py` to start the backend in development mode. 
+To reproduce the evaluation results discussed in the SEMANTiCS 2024 paper, perform the following steps: 
+
+- Create a file called `.github_access_token` in the [backend](./backend/) folder. Then, enter your GitHub access token in that file and save. 
+- Run `docker compose run evaluation` to get a bash that is attached to the backend container.
+- Run `./python3 evaluation.py` to rerun the evaluation. This includes the FAIRness assessment of GitHub repositories and the runtime benchmark on the same repositories.
+
+The resulting files are place in the [evaluation](./backend/data/evaluation/) folder.
+
+## Citation
+If you use this software, please cite it as below:
+
+```bibtex
+@inproceedings{DBLP:conf/lwa/MartinH22,
+  author       = {Leon Martin and
+                  Andreas Henrich},
+  editor       = {Pascal Reuss and
+                  Viktor Eisenstadt and
+                  Jakob Michael Sch{\"{o}}nborn and
+                  Jero Sch{\"{a}}fer},
+  title        = {Specification and Validation of Quality Criteria for Git Repositories
+                  using {RDF} and {SHACL}},
+  booktitle    = {Proceedings of the {LWDA} 2022 Workshops: FGWM, FGKD, and FGDB, Hildesheim
+                  (Germany), Oktober 5-7th, 2022},
+  series       = {{CEUR} Workshop Proceedings},
+  volume       = {3341},
+  pages        = {124--135},
+  publisher    = {CEUR-WS.org},
+  year         = {2022},
+  url          = {https://ceur-ws.org/Vol-3341/WM-LWDA\_2022\_CRC\_1149.pdf},
+  timestamp    = {Sat, 30 Sep 2023 09:52:13 +0200},
+  biburl       = {https://dblp.org/rec/conf/lwa/MartinH22.bib},
+  bibsource    = {dblp computer science bibliography, https://dblp.org}
+}
+```
 
 ## Citation
 If you use this software, please cite it as below:
diff --git a/backend/Dockerfile b/backend/Dockerfile
index 616fc46..0d0b060 100644
--- a/backend/Dockerfile
+++ b/backend/Dockerfile
@@ -14,7 +14,9 @@ RUN pip install -U flask-cors
 RUN pip install -U fire
 RUN pip install -U pyshacl
 RUN pip install -U numpy
+RUN pip install -U pandas
 RUN pip install -U matplotlib
+RUN pip install -U brokenaxes
 
 VOLUME [ "/src" ]
 WORKDIR /src
diff --git a/backend/benchmark.py b/backend/benchmark.py
index 449e43b..798b2c1 100644
--- a/backend/benchmark.py
+++ b/backend/benchmark.py
@@ -8,6 +8,7 @@
 
 import matplotlib.pyplot as plt
 
+logging.basicConfig(level=logging.INFO)
 
 def run_benchmark():
     # retrieved 2022/03/22 from https://github.com/trending?since=monthly
@@ -34,12 +35,11 @@ def run_benchmark():
         "vulhub/vulhub"
     ]
 
-    with open("./git_access_token") as file:
+    with open(".github_access_token") as file:
         github_access_token = file.readline().strip()
 
-    benchmark_scenarios = [(github_access_token, repo_name, "FinishedResearchProject") for repo_name in
-                           trending_github_repos] + [(github_access_token, repo_name, "InternalDocumentation")
-                                                     for repo_name in trending_github_repos]
+    benchmark_scenarios = [(github_access_token, repo_name, "FAIRSoftware") for repo_name in
+                           trending_github_repos]
 
     for github_access_token, repo_name, repo_type in benchmark_scenarios:
         file_name = f"{repo_name.split('/')[1]}-{repo_type}"
@@ -47,29 +47,25 @@ def run_benchmark():
         cmd = ["./shacl_validator.py", "--github_access_token", github_access_token, "--repo_name", repo_name,
                "--expected_type", repo_type]
 
-        run(["python3", "-m", "cProfile", "-o",
-             f"data/benchmarks/{file_name}", "-s", "cumulative"] + cmd)
+        run(["python3", "-m", "cProfile", "-o", f"data/benchmarks/{file_name}", "-s", "cumulative"] + cmd)
 
         sleep(3)
 
 
 def process_results():
-    all_finished = []
-    all_internal = []
+    all_fair = []
 
     step_durations = [0, 0, 0]
 
-    for result_file in glob.glob("./data/benchmarks/*"):
+    for result_file in glob.glob("./data/benchmarks/*FAIRSoftware"):
         stats = pstats.Stats(result_file)
 
         for k, v in stats.stats.items():
             _, _, function = k
 
             if function == "validate_repo_against_specs":
-                if "FinishedResearchProject" in result_file:
-                    all_finished.append(v[3])
-                else:
-                    all_internal.append(v[3])
+                if "FAIRSoftware" in result_file:
+                    all_fair.append(v[3])
 
             elif function == "create_project_type_representation":
                 step_durations[0] += v[3]
@@ -86,16 +82,14 @@ def process_results():
         ylabel='Seconds',
     )
 
-    ax.boxplot([all_finished, all_internal])
+    ax.boxplot([all_fair])
 
-    ax.set_xticklabels(
-        ["$T_{F}$", "$T_{I}$"])
+    ax.set_xticklabels(["$T_{FAIRSoftware}$"])
 
     plt.tight_layout(pad=0)
-
     plt.savefig("./data/benchmarks/benchmark_results.pdf")
 
-    total = sum(all_finished) + sum(all_internal)
+    total = sum(all_fair)
 
     step_one_percent = '{:.2f}%'.format(
         step_durations[0] / total * 100)
@@ -109,5 +103,8 @@ def process_results():
 
 
 if __name__ == "__main__":
+    # fairness assessment
     run_benchmark()
     process_results()
+
+    # runtime
diff --git a/backend/data/evaluation/conformity_per_best_practice.pdf b/backend/data/evaluation/conformity_per_best_practice.pdf
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new file mode 100644
index 0000000..4e4e20e
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new file mode 100644
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diff --git a/backend/data/evaluation/runtime_benchmark_scatter.pdf b/backend/data/evaluation/runtime_benchmark_scatter.pdf
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index 0000000..9f20ade
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+++ b/backend/data/evaluation/trending_repos.json
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"ExplicitCitation": false, "DescriptionOrAtLeastOneTopic": true, "InstallationInstructionsInReadme": false, "SoftwareRequirements": false}, "shadcn-ui/ui": {"DescriptionOrReadme": true, "PersistentId": false, "PublicRepository": true, "SemanticVersioning": false, "UsageNotesInReadme": false, "ExactlyOneLicense": true, "ExplicitCitation": false, "DescriptionOrAtLeastOneTopic": true, "InstallationInstructionsInReadme": false, "SoftwareRequirements": true}, "civitai/civitai": {"DescriptionOrReadme": true, "PersistentId": false, "PublicRepository": true, "SemanticVersioning": false, "UsageNotesInReadme": false, "ExactlyOneLicense": true, "ExplicitCitation": false, "DescriptionOrAtLeastOneTopic": true, "InstallationInstructionsInReadme": true, "SoftwareRequirements": true}, "mrsked/mrsk": {"DescriptionOrReadme": true, "PersistentId": true, "PublicRepository": true, "SemanticVersioning": false, "UsageNotesInReadme": false, "ExactlyOneLicense": true, "ExplicitCitation": false, "DescriptionOrAtLeastOneTopic": true, "InstallationInstructionsInReadme": false, "SoftwareRequirements": false}, "AppFlowy-IO/AppFlowy": {"DescriptionOrReadme": true, "PersistentId": false, "PublicRepository": true, "SemanticVersioning": false, "UsageNotesInReadme": false, "ExactlyOneLicense": true, "ExplicitCitation": false, "DescriptionOrAtLeastOneTopic": true, "InstallationInstructionsInReadme": true, "SoftwareRequirements": false}, "servo/servo": {"DescriptionOrReadme": true, "PersistentId": false, "PublicRepository": true, "SemanticVersioning": false, "UsageNotesInReadme": false, "ExactlyOneLicense": true, "ExplicitCitation": false, "DescriptionOrAtLeastOneTopic": true, "InstallationInstructionsInReadme": true, "SoftwareRequirements": true}, "stanfordnlp/dspy": {"DescriptionOrReadme": true, "PersistentId": true, "PublicRepository": true, "SemanticVersioning": true, "UsageNotesInReadme": false, "ExactlyOneLicense": true, "ExplicitCitation": false, "DescriptionOrAtLeastOneTopic": true, "InstallationInstructionsInReadme": false, "SoftwareRequirements": true}, "jwasham/coding-interview-university": {"DescriptionOrReadme": true, "PersistentId": false, "PublicRepository": true, "SemanticVersioning": false, "UsageNotesInReadme": true, "ExactlyOneLicense": true, "ExplicitCitation": false, "DescriptionOrAtLeastOneTopic": true, "InstallationInstructionsInReadme": false, "SoftwareRequirements": false}, "chat2db/Chat2DB": {"DescriptionOrReadme": true, "PersistentId": true, "PublicRepository": true, "SemanticVersioning": false, "UsageNotesInReadme": false, "ExactlyOneLicense": true, "ExplicitCitation": false, "DescriptionOrAtLeastOneTopic": true, "InstallationInstructionsInReadme": true, "SoftwareRequirements": false}, "opentofu/opentofu": {"DescriptionOrReadme": true, "PersistentId": true, "PublicRepository": true, "SemanticVersioning": true, "UsageNotesInReadme": false, "ExactlyOneLicense": true, "ExplicitCitation": false, "DescriptionOrAtLeastOneTopic": true, "InstallationInstructionsInReadme": false, "SoftwareRequirements": false}, "microsoft/guidance": {"DescriptionOrReadme": true, "PersistentId": false, "PublicRepository": true, "SemanticVersioning": false, "UsageNotesInReadme": false, "ExactlyOneLicense": true, "ExplicitCitation": false, "DescriptionOrAtLeastOneTopic": true, "InstallationInstructionsInReadme": true, "SoftwareRequirements": false}, "nlpxucan/WizardLM": {"DescriptionOrReadme": true, "PersistentId": false, "PublicRepository": true, "SemanticVersioning": false, "UsageNotesInReadme": false, "ExactlyOneLicense": false, "ExplicitCitation": false, "DescriptionOrAtLeastOneTopic": true, "InstallationInstructionsInReadme": false, "SoftwareRequirements": false}, "makeplane/plane": {"DescriptionOrReadme": true, "PersistentId": false, "PublicRepository": true, "SemanticVersioning": false, "UsageNotesInReadme": false, "ExactlyOneLicense": true, "ExplicitCitation": false, "DescriptionOrAtLeastOneTopic": true, "InstallationInstructionsInReadme": true, "SoftwareRequirements": true}, "cbh123/narrator": {"DescriptionOrReadme": true, "PersistentId": false, "PublicRepository": true, "SemanticVersioning": false, "UsageNotesInReadme": false, "ExactlyOneLicense": false, "ExplicitCitation": false, "DescriptionOrAtLeastOneTopic": true, "InstallationInstructionsInReadme": true, "SoftwareRequirements": true}, "gkamradt/langchain-tutorials": {"DescriptionOrReadme": true, "PersistentId": false, "PublicRepository": true, "SemanticVersioning": false, "UsageNotesInReadme": false, "ExactlyOneLicense": false, "ExplicitCitation": false, "DescriptionOrAtLeastOneTopic": true, "InstallationInstructionsInReadme": false, "SoftwareRequirements": false}, "documenso/documenso": {"DescriptionOrReadme": true, "PersistentId": false, "PublicRepository": true, "SemanticVersioning": false, "UsageNotesInReadme": false, "ExactlyOneLicense": true, "ExplicitCitation": false, "DescriptionOrAtLeastOneTopic": true, "InstallationInstructionsInReadme": true, "SoftwareRequirements": true}, "CompVis/stable-diffusion": {"DescriptionOrReadme": true, "PersistentId": false, "PublicRepository": true, "SemanticVersioning": false, "UsageNotesInReadme": false, "ExactlyOneLicense": true, "ExplicitCitation": false, "DescriptionOrAtLeastOneTopic": true, "InstallationInstructionsInReadme": false, "SoftwareRequirements": true}, "Vaibhavs10/insanely-fast-whisper": {"DescriptionOrReadme": true, "PersistentId": false, "PublicRepository": true, "SemanticVersioning": false, "UsageNotesInReadme": true, "ExactlyOneLicense": true, "ExplicitCitation": false, "DescriptionOrAtLeastOneTopic": false, "InstallationInstructionsInReadme": false, "SoftwareRequirements": false}, "Z4nzu/hackingtool": {"DescriptionOrReadme": true, "PersistentId": false, "PublicRepository": true, "SemanticVersioning": false, "UsageNotesInReadme": false, "ExactlyOneLicense": true, "ExplicitCitation": false, "DescriptionOrAtLeastOneTopic": true, "InstallationInstructionsInReadme": true, "SoftwareRequirements": true}, "tiann/KernelSU": {"DescriptionOrReadme": true, "PersistentId": true, "PublicRepository": true, "SemanticVersioning": false, "UsageNotesInReadme": true, "ExactlyOneLicense": true, "ExplicitCitation": false, "DescriptionOrAtLeastOneTopic": true, "InstallationInstructionsInReadme": false, "SoftwareRequirements": false}, "coqui-ai/TTS": {"DescriptionOrReadme": true, "PersistentId": false, "PublicRepository": true, "SemanticVersioning": false, "UsageNotesInReadme": false, "ExactlyOneLicense": true, "ExplicitCitation": true, "DescriptionOrAtLeastOneTopic": true, "InstallationInstructionsInReadme": true, "SoftwareRequirements": true}}
\ No newline at end of file
diff --git a/backend/data/shacl/property_shapes.ttl b/backend/data/shacl/property_shapes.ttl
index e987982..6b5eb25 100644
--- a/backend/data/shacl/property_shapes.ttl
+++ b/backend/data/shacl/property_shapes.ttl
@@ -85,8 +85,8 @@ propertyShapes:DoiAsHomepage
 		# The homepage link is internally mapped via the "website" property.
 		sh:path     sd:website ;
 		# https://www.crossref.org/blog/dois-and-matching-regular-expressions/
-		# Put into the right format with the help of ChatGPT.
-		sh:pattern  "^https://doi\\.org/10\\.[0-9]{4,}/[-._;()/:A-Z0-9]+$" ;
+		# Put into the right format with the help of ChatGPT, adapted.
+		sh:pattern  "^https://doi\\.org/10\\.[0-9]{4,}/[-._;()/:A-Za-z0-9]+$" ;
 		sh:minCount 1 ;
 		sh:message  "The homepage attribute is not set or its value is not a DOI. Make sure this attribute is filled with a DOI." ;
 		sh:description
diff --git a/backend/evaluation.py b/backend/evaluation.py
new file mode 100644
index 0000000..a063495
--- /dev/null
+++ b/backend/evaluation.py
@@ -0,0 +1,505 @@
+#!/usr/bin/env python3
+
+import json
+import logging
+import pstats
+from subprocess import run
+
+import pandas as pd 
+import numpy as np
+from github import UnknownObjectException, Github, Auth
+from matplotlib import pyplot as plt
+from brokenaxes import brokenaxes
+
+import validation_interface, verbalization_interface
+
+logging.basicConfig(level=logging.INFO)
+
+def perform_evaluation() -> None:
+    with open(".github_access_token") as file:
+        github_access_token = file.readline().strip()
+
+    repos_expected_to_be_fair = get_repos_expected_to_be_fair()
+    trending_repos = get_trending_repo_set()
+
+    results_per_criterion_fair = get_validation_result_per_criterion(repos_expected_to_be_fair, github_access_token)
+    with open("./data/evaluation/repos_expected_to_be_fair.json", "w") as file:
+        json.dump(results_per_criterion_fair, file)
+
+    results_per_criterion_trending = get_validation_result_per_criterion(trending_repos, github_access_token)
+    with open("./data/evaluation/trending_repos.json", "w") as file:
+        json.dump(results_per_criterion_trending, file)
+
+    runtime_benchmark_results = execute_runtime_benchmark(repos_expected_to_be_fair, trending_repos, github_access_token)
+    with open("./data/evaluation/runtime_benchmark_results.json", "w") as file:
+        json.dump(runtime_benchmark_results, file)
+
+
+def get_repos_expected_to_be_fair() -> list[str]:
+    return ["oeg-upm/oeg-software-graph", "zenodraft/zenodraft",
+            "comses-education/wolf-sheep", "fair-software/howfairis",
+            "GrainLearning/grainLearning", "online-behaviour/machine-learning"]
+
+
+def get_trending_repo_set() -> list[str]:
+    # First 20 repositories on the 15th of each month from https://github.com/trending?since=monthly (via Web Archive)
+    trending_github_repos = {
+        "march_2023": [
+            "lllyasviel/ControlNet",
+            "hpcaitech/ColossalAI",
+            "AUTOMATIC1111/stable-diffusion-webui",
+            "amazon-science/mm-cot",
+            "usememos/memos",
+            "civitai/civitai",
+            "ggerganov/whisper.cpp",
+            "zhayujie/chatgpt-on-wechat",
+            "openai/openai-python",
+            "f/awesome-chatgpt-prompts",
+            "mrsked/mrsk",
+            "yt-dlp/yt-dlp",
+            "zloirock/core-js",
+            "Asabeneh/30-Days-Of-Python",
+            "jaymody/picoGPT",
+            "bmaltais/kohya_ss",
+            "ytdl-org/youtube-dl",
+            "alibaba/lowcode-engine",
+            "NAStool/nas-tools",
+            "CompVis/stable-diffusion"
+        ], "april_2023": [
+            "tloen/alpaca-lora",
+            "cocktailpeanut/dalai",
+            "THUDM/ChatGLM-6B",
+            "ggerganov/llama.cpp",
+            "tatsu-lab/stanford_alpaca",
+            "GaiZhenbiao/ChuanhuChatGPT",
+            "hwchase17/langchain",
+            "microsoft/DeepSpeed",
+            "Chanzhaoyu/chatgpt-web",
+            "oobabooga/text-generation-webui",
+            "gencay/vscode-chatgpt",
+            "PlexPt/awesome-chatgpt-prompts-zh",
+            "shadcn/taxonomy",
+            "apple/ml-stable-diffusion",
+            "ConnectAI-E/Feishu-OpenAI",
+            "ztjhz/BetterChatGPT",
+            "kaixindelele/ChatPaper",
+            "AUTOMATIC1111/stable-diffusion-webui",
+            "comfyanonymous/ComfyUI",
+            "chathub-dev/chathub"
+        ], "may_2023": [
+            "Significant-Gravitas/Auto-GPT",
+            "voicepaw/so-vits-svc-fork",
+            "reworkd/AgentGPT",
+            "Ryujinx/Ryujinx",
+            "LAION-AI/Open-Assistant",
+            "imClumsyPanda/langchain-ChatGLM",
+            "svc-develop-team/so-vits-svc",
+            "pengzhile/pandora",
+            "hwchase17/langchain",
+            "lllyasviel/ControlNet-v1-1-nightly",
+            "facebookresearch/AnimatedDrawings",
+            "qdrant/qdrant",
+            "gkamradt/langchain-tutorials",
+            "RVC-Project/Retrieval-based-Voice-Conversion-WebUI",
+            "l15y/wenda",
+            "TheRamU/Fay",
+            "Yidadaa/ChatGPT-Next-Web",
+            "bluesky-social/atproto",
+            "shadcn/ui",
+            "calcom/cal.com"
+        ], "june_2023": [
+            "microsoft/guidance",
+            "smol-ai/developer",
+            "sunner/ChatALL",
+            "google/comprehensive-rust",
+            "makeplane/plane",
+            "facebookresearch/fairseq",
+            "imartinez/privateGPT",
+            "pengzhile/pandora",
+            "xiangsx/gpt4free-ts",
+            "csunny/DB-GPT",
+            "FlowiseAI/Flowise",
+            "geohot/tinygrad",
+            "iperov/DeepFaceLive",
+            "steven-tey/dub",
+            "langgenius/dify",
+            "alibaba/Chat2DB",
+            "go-skynet/LocalAI",
+            "JushBJJ/Mr.-Ranedeer-AI-Tutor",
+            "iv-org/invidious",
+            "RVC-Project/Retrieval-based-Voice-Conversion-WebUI"
+        ], "july_2023": [
+            "AntonOsika/gpt-engineer",
+            "AI4Finance-Foundation/FinGPT",
+            "alibaba/ali-dbhub",
+            "baichuan-inc/Baichuan-7B",
+            "tinygrad/tinygrad",
+            "StanGirard/quivr",
+            "h2oai/h2ogpt",
+            "CodeEditApp/CodeEdit",
+            "vercel/platforms",
+            "toeverything/AFFiNE",
+            "Uniswap/v4-core",
+            "LemmyNet/lemmy",
+            "sveltejs/svelte",
+            "facebookresearch/ijepa",
+            "hiyouga/ChatGLM-Efficient-Tuning",
+            "mastodon/mastodon",
+            "Mintplex-Labs/anything-llm",
+            "996icu/996.ICU",
+            "RVC-Project/Retrieval-based-Voice-Conversion-WebUI",
+            "loft-sh/devpod"
+        ], "august_2023": [
+            "facebookresearch/llama",
+            "geekan/MetaGPT",
+            "bregman-arie/devops-exercises",
+            "comfyanonymous/ComfyUI",
+            "nextui-org/nextui",
+            "OpenBMB/ToolBench",
+            "Stability-AI/generative-models",
+            "EbookFoundation/free-programming-books",
+            "facebookresearch/audiocraft",
+            "invoke-ai/InvokeAI",
+            "Codium-ai/pr-agent",
+            "kenjihiranabe/The-Art-of-Linear-Algebra",
+            "Dao-AILab/flash-attention",
+            "DioxusLabs/dioxus",
+            "reflex-dev/reflex",
+            "bazingagin/npc_gzip",
+            "oobabooga/text-generation-webui",
+            "vercel/commerce",
+            "krahets/hello-algo",
+            "songquanpeng/one-api"
+        ], "september_2023": [
+            "oven-sh/bun",
+            "opentffoundation/manifesto",
+            "krahets/hello-algo",
+            "lllyasviel/Fooocus",
+            "hehonghui/awesome-english-ebooks",
+            "kuafuai/DevOpsGPT",
+            "graphdeco-inria/gaussian-splatting",
+            "modelscope/facechain",
+            "zanfranceschi/rinha-de-backend-2023-q3",
+            "Z4nzu/hackingtool",
+            "a16z-infra/ai-town",
+            "phoboslab/wipeout-rewrite",
+            "organicmaps/organicmaps",
+            "NVlabs/neuralangelo",
+            "pedroslopez/whatsapp-web.js",
+            "documenso/documenso",
+            "prasanthrangan/hyprdots",
+            "IceWhaleTech/CasaOS",
+            "nlpxucan/WizardLM",
+            "ymcui/Chinese-LLaMA-Alpaca-2"
+        ], "october_2023": [
+            "OpenBMB/ChatDev",
+            "opentofu/opentofu",
+            "Pythagora-io/gpt-pilot",
+            "godotengine/godot",
+            "appwrite/appwrite",
+            "coqui-ai/TTS",
+            "spacedriveapp/spacedrive",
+            "novuhq/novu",
+            "krahets/hello-algo",
+            "jwasham/coding-interview-university",
+            "massgravel/Microsoft-Activation-Scripts",
+            "haotian-liu/LLaVA",
+            "EbookFoundation/free-programming-books",
+            "graphdeco-inria/gaussian-splatting",
+            "bevyengine/bevy",
+            "harness/gitness",
+            "airbnb/javascript",
+            "TabbyML/tabby",
+            "fishaudio/Bert-VITS2",
+            "TheAlgorithms/JavaScript"
+        ], "november_2023": [
+            "ByteByteGoHq/system-design-101",
+            "zzzgydi/clash-verge",
+            "cpacker/MemGPT",
+            "localsend/localsend",
+            "2dust/v2rayN",
+            "yangshun/tech-interview-handbook",
+            "SagerNet/sing-box",
+            "XTLS/Xray-core",
+            "public-apis/public-apis",
+            "PWhiddy/PokemonRedExperiments",
+            "chat2db/Chat2DB",
+            "v2fly/v2ray-core",
+            "2dust/v2rayNG",
+            "lyswhut/lx-music-desktop",
+            "OpenTalker/video-retalking",
+            "MatsuriDayo/nekoray",
+            "apache/incubator-answer",
+            "apernet/hysteria",
+            "danielgross/localpilot",
+            "donnemartin/system-design-primer"
+        ], "december_2023": [
+            "abi/screenshot-to-code",
+            "BuilderIO/gpt-crawler",
+            "Stability-AI/generative-models",
+            "lllyasviel/Fooocus",
+            "microsoft/generative-ai-for-beginners",
+            "facebookresearch/seamless_communication",
+            "tldraw/tldraw",
+            "microsoft/ML-For-Beginners",
+            "lobehub/lobe-chat",
+            "dotnet/eShop",
+            "microsoft/AI-For-Beginners",
+            "comfyanonymous/ComfyUI",
+            "ollama-webui/ollama-webui",
+            "cbh123/narrator",
+            "Vaibhavs10/insanely-fast-whisper",
+            "biomejs/biome",
+            "google-deepmind/graphcast",
+            "AppFlowy-IO/AppFlowy",
+            "langgenius/dify",
+            "danny-avila/LibreChat"
+        ], "january_2024": [
+            "Stirling-Tools/Stirling-PDF",
+            "Pythagora-io/gpt-pilot",
+            "mckaywrigley/chatbot-ui",
+            "jzhang38/TinyLlama",
+            "tachiyomiorg/tachiyomi",
+            "Hillobar/Rope",
+            "jianchang512/clone-voice",
+            "shadcn-ui/ui",
+            "anoma/namada",
+            "DataTalksClub/data-engineering-zoomcamp",
+            "jmorganca/ollama",
+            "AmruthPillai/Reactive-Resume",
+            "ruanyf/weekly",
+            "danswer-ai/danswer",
+            "karanpratapsingh/system-design",
+            "tiann/KernelSU",
+            "lobehub/lobe-chat",
+            "practical-tutorials/project-based-learning",
+            "apache/incubator-answer",
+            "labring/FastGPT"
+        ], "february_2024": [
+            "maybe-finance/maybe",
+            "netease-youdao/QAnything",
+            "TencentARC/PhotoMaker",
+            "KRTirtho/spotube",
+            "stanfordnlp/dspy",
+            "vanna-ai/vanna",
+            "xiaolai/everyone-can-use-english",
+            "usememos/memos",
+            "DataTalksClub/data-engineering-zoomcamp",
+            "joaomdmoura/crewAI",
+            "SerenityOS/serenity",
+            "EbookFoundation/free-programming-books",
+            "MooreThreads/Moore-AnimateAnyone",
+            "expo/expo",
+            "backstage/backstage",
+            "servo/servo",
+            "Dooy/chatgpt-web-midjourney-proxy",
+            "NvChad/NvChad",
+            "rails/rails",
+            "nushell/nushell"
+        ]}
+
+    repo_list: list = []
+
+    for key in trending_github_repos:
+        repo_list.extend(trending_github_repos[key])
+
+    return list(set(repo_list))
+
+
+def get_validation_result_per_criterion(repos: list, github_access_token: str) -> dict[str, dict[str, bool]]:
+    results_per_criterion: dict[str, dict[str, bool]] = {}
+
+    for repo_name in repos:
+        try:
+            _, _, report = validation_interface.run_validator(github_access_token, repo_name, "FAIRSoftware")
+        except UnknownObjectException as e:
+            logging.exception(f"Could not validate {repo_name} against the FAIRSoftware project type. {e}")
+            continue
+        verbalized_explanation = verbalization_interface.run_verbalizer(report)
+        result_per_criterion = process_verbalized_explanation(verbalized_explanation)
+        results_per_criterion[repo_name] = result_per_criterion
+
+    return results_per_criterion
+
+
+def process_verbalized_explanation(verbalized_explanation: list[str]) -> dict[str, bool]:
+    possible_messages_with_mapping: dict[str, str] = {
+        "The repository has no description and no README file.": "DescriptionOrReadme",
+        "No persistent ID was found.": "PersistentId",
+        "The repository is private.": "PublicRepository",
+        "There are no releases or Semantic Versioning is violated.": "SemanticVersioning",
+        "There is no README file or it does not contain usage instructions for the software.": "UsageNotesInReadme",
+        "No license information was found.": "ExactlyOneLicense",
+        "No citation information was found.": "ExplicitCitation",
+        "The repository has no description and no topics assigned.": "DescriptionOrAtLeastOneTopic",
+        "There is no README file or it does not contain installation instructions.": "InstallationInstructionsInReadme",
+        "No information on the requirements of the software was found.": "SoftwareRequirements"
+    }
+
+    result_per_criterion: dict[str, bool] = {}
+    for possible_message, mapping in possible_messages_with_mapping.items():
+        if any(actual_message.startswith(possible_message) for actual_message in verbalized_explanation):
+            result_per_criterion[mapping] = False
+        else:
+            result_per_criterion[mapping] = True
+
+    return result_per_criterion
+
+
+def execute_runtime_benchmark(repos_expected_to_be_fair: list, trending_repos: list, github_access_token: str) -> None:
+    auth = Auth.Token(github_access_token)
+    g = Github(auth=auth)
+
+    runtime_benchmark_results = dict()
+
+    runtime_per_repo = []
+    step_durations = [0, 0, 0]
+
+    for repo_name in trending_repos + repos_expected_to_be_fair:
+        # skip repo for evaluation if relevant data cannot be fetched
+        try:
+            repo = g.get_repo(repo_name)
+            # compute repo size as the sum of releases branches and issues
+            repo_size = repo.get_releases().totalCount + repo.get_branches().totalCount + repo.get_issues().totalCount
+        except:
+            continue
+
+        # perform fairness assessment with profiler
+        file_name = f"{repo_name.split('/')[1]}"
+        
+        logging.info(f"{repo_name} has in total {repo_size} releases, branches, and issues.")
+
+        cmd = ["./shacl_validator.py", "--github_access_token", github_access_token, "--repo_name", repo_name,
+               "--expected_type", "FAIRSoftware"]
+
+        run(["python3", "-m", "cProfile", "-o", f"data/benchmarks/{file_name}", "-s", "cumulative"] + cmd)
+        
+        # process stats of fairness assessment runtime
+        stats = pstats.Stats(f"data/benchmarks/{file_name}")
+
+        for k, v in stats.stats.items():
+            _, _, function = k
+
+            if function == "validate_repo_against_specs":
+                runtime = v[3]
+
+            elif function == "create_project_type_representation":
+                step_durations[0] += v[3]
+
+            elif function == "create_repository_representation":
+                step_durations[1] += v[3]
+
+            elif function == "run_validation":
+                step_durations[2] += v[3]
+
+        runtime_per_repo.append(runtime)
+        origin = "trending" if repo_name in trending_repos else "expected"
+        runtime_benchmark_results[file_name] = (repo_size, runtime, origin)
+
+    total_runtime = sum(runtime_per_repo)
+    step_durations = ["{:.2f}%".format(duration / total_runtime * 100) for duration in step_durations]
+
+    logging.info(
+        f"Shapes graph composition/repository representation generation/validation account for {'/'.join(step_durations)} of the total runtime.")
+
+    return runtime_benchmark_results
+
+def visualize_results() -> None:
+
+    def get_results_in_percent(results_per_criterion: dict[str, dict[str, bool]]) -> dict[str, float]:
+        first_inner_dict = list(results_per_criterion.values())[0]
+        numeric_results: dict[str, int] = {key: 0 for key in first_inner_dict}
+
+        for _, result_per_criterion in results_per_criterion.items():
+            for criterion, value in result_per_criterion.items():
+                if value:
+                    numeric_results[criterion] += 1
+
+        return {key: value / len(results_per_criterion) * 100 for key, value in numeric_results.items()}
+
+    # plot FAIRness assessment
+    with open("./data/evaluation/repos_expected_to_be_fair.json") as file_fair:
+        results_per_criterion_fair: dict[str, dict[str, bool]] = json.load(file_fair)
+
+    with open("./data/evaluation/trending_repos.json") as file_trending:
+        results_per_criterion_trending: dict[str, dict[str, bool]] = json.load(file_trending)
+
+    normalized_numeric_results_fair = get_results_in_percent(results_per_criterion_fair)
+    normalized_numeric_results_trending = get_results_in_percent(results_per_criterion_trending)
+
+    best_practices = ("BP1", "BP2", "BP3", "BP4", "BP5", "BP6", "BP7", "BP8", "BP9", "BP10")
+    scores_fair = list(normalized_numeric_results_fair.values())
+    scores_trending = list(normalized_numeric_results_trending.values())
+
+    x = np.arange(len(best_practices))
+    width = 0.35
+    fig, ax = plt.subplots(figsize=(6, 4))
+
+    ax.bar(x - width / 2, scores_fair, width, label="Repositories Expected to be FAIR (N=6)", color="#00407A")
+    ax.bar(x + width / 2, scores_trending, width, label="Trending Repositories (N=217)", color="#8ed7d7")
+    ax.legend(loc="lower left", ncol=1, bbox_to_anchor=(0, 1, 1, 0))
+
+    ax.set_ylabel("Percentage of Conform Repositories")
+
+    ax.set_yticks(np.arange(0, 101, 10))
+    ax.set_yticks(np.arange(5, 100, 5), minor=True)
+    ax.set_xticks(x)
+    ax.set_xticklabels(best_practices)
+
+    ax.set_axisbelow(True)
+    ax.yaxis.grid(which="major", linestyle="dashed", linewidth=0.5, color="black")
+    ax.yaxis.grid(which="minor", linestyle="dashed", linewidth=0.5)
+
+    fig.tight_layout()
+
+    plt.savefig("./data/evaluation/conformity_per_best_practice.pdf")
+
+    # plot runtime benchmark
+    x_trending = []
+    y_trending = []
+
+    x_expected = []
+    y_expected = []
+
+    with open("./data/evaluation/runtime_benchmark_results.json") as file_benchmark:
+        runtime_benchmark_results: dict[str, dict[str, bool]] = json.load(file_benchmark)
+
+    for size, runtime, origin in runtime_benchmark_results.values():
+        if origin == "trending":
+            x_trending.append(size)
+            y_trending.append(runtime)
+
+        else:
+            x_expected.append(size)
+            y_expected.append(runtime)
+
+    fig = plt.figure(figsize=(6, 4))
+
+    bax = brokenaxes(xlims=((0, 5000), (12000, 12500)), ylims=((0, 30), (50, 55)))
+
+    bax.scatter(x_trending, y_trending, c="#8ed7d7", s=15, label="Trending Repositories\n(N=217)")
+    bax.scatter(x_expected, y_expected, c="#00407A", s=15, label="Repositories Expected to\nbe FAIR (N=6)")
+
+    bax.set_xlabel("Repository Size")
+    bax.set_ylabel("Runtime Duration in Seconds")
+
+    bax.legend(loc=1, ncol=1)
+
+    bax.grid(axis='y', which='major', ls="dashed")
+    bax.grid(axis='y', which='minor', ls="dashed", linewidth=0.5)
+
+    plt.savefig("./data/evaluation/runtime_benchmark_scatter.pdf")
+
+    data = {'size': x_expected,
+            'runtime': y_expected}
+    df_expected = pd.DataFrame(data)
+
+    data = {'size': x_trending,
+            'runtime': y_trending}
+    df_trending = pd.DataFrame(data)
+
+    print(df_expected.describe(), df_trending.describe())
+
+if __name__ == "__main__":
+    perform_evaluation()
+    visualize_results()
diff --git a/backend/shacl_validator.py b/backend/shacl_validator.py
index b484b4e..0fd9f2e 100644
--- a/backend/shacl_validator.py
+++ b/backend/shacl_validator.py
@@ -204,7 +204,7 @@ def versions_have_valid_increment(release_list: PaginatedList | list[dict]) -> b
 
 def version_pair_has_valid_version_increment(pair: tuple[Version, Version]) -> bool:
     # If the first number (major) is increased, the second (minor) and third (micro) must be set to zero.
-    if (pair[0].major + 1 == pair[1].major) & (pair[1].minor == 0) & (pair[1].micro == 0):
+    if (pair[0].major >= pair[1].major) & (pair[1].minor == 0) & (pair[1].micro == 0):
         return True
 
     # If minor is increased, micro must be set to zero.
@@ -303,7 +303,7 @@ def include_readme(graph: Graph, repo_entity: URIRef, repo: Repository, include_
     if include_check_for_doi:
         # Check whether there is at least one DOI in the README file (as text or link href).
         # Regex adapted from https://www.crossref.org/blog/dois-and-matching-regular-expressions/
-        doi_pattern = re.compile(r"https://doi\.org/10\.\d{4,}/[-._;()/:A-Z0-9]+")
+        doi_pattern = re.compile(r"https://doi\.org/10\.\d{4,}/[-._;()/:A-Za-z0-9]+")
         if soup.find_all(string=doi_pattern) or soup.find_all(href=doi_pattern):
             graph.add((readme_entity, props["containsDoi"], Literal("true")))
         else:
diff --git a/docker-compose.yml b/docker-compose.yml
index cafcf58..95fa4c6 100644
--- a/docker-compose.yml
+++ b/docker-compose.yml
@@ -17,3 +17,11 @@ services:
     ports:
       - "3000:3000"
     command: bash -c "npm install && npm run dev"
+  evaluation:
+    build: ./backend
+    container_name: evaluation
+    volumes:
+      - ./backend:/src
+    ports:
+      - "5000:5000"
+    entrypoint: bash