rsfc 0.0.1__tar.gz

rsfc-0.0.1/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2025 Andrés Montero
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

rsfc-0.0.1/PKG-INFO

@@ -0,0 +1,197 @@
+Metadata-Version: 2.3
+Name: rsfc
+Version: 0.0.1
+Summary: EVERSE Research Software Fairness Checks
+License: MIT
+Author: Andres Montero
+Author-email: andres.montero.martin@upm.es
+Requires-Python: >=3.10,<=3.13
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Requires-Dist: anyascii (==0.3.2)
+Requires-Dist: attrs (==25.3.0)
+Requires-Dist: beautifulsoup4 (==4.13.4)
+Requires-Dist: bibtexparser (==1.4.3)
+Requires-Dist: bs4 (==0.0.1)
+Requires-Dist: build (==1.2.2.post1)
+Requires-Dist: certifi (==2025.6.15)
+Requires-Dist: chardet (==5.2.0)
+Requires-Dist: charset-normalizer (==3.4.2)
+Requires-Dist: click (==8.2.1)
+Requires-Dist: click-option-group (==0.5.7)
+Requires-Dist: contourpy (==1.3.2)
+Requires-Dist: contractions (==0.1.73)
+Requires-Dist: cycler (==0.12.1)
+Requires-Dist: duckdb (==1.3.1)
+Requires-Dist: elementpath (==4.8.0)
+Requires-Dist: falcon (==3.1.3)
+Requires-Dist: fastjsonschema (==2.21.1)
+Requires-Dist: fonttools (==4.58.4)
+Requires-Dist: idna (==3.10)
+Requires-Dist: imbalanced-learn (==0.11.0)
+Requires-Dist: inflect (==7.5.0)
+Requires-Dist: iniconfig (==2.1.0)
+Requires-Dist: jinja2 (==3.1.6)
+Requires-Dist: joblib (==1.5.1)
+Requires-Dist: jsonpath-python (==1.0.6)
+Requires-Dist: jsonschema (==4.24.0)
+Requires-Dist: jsonschema-specifications (==2025.4.1)
+Requires-Dist: jupyter-core (==5.8.1)
+Requires-Dist: kiwisolver (==1.4.8)
+Requires-Dist: lxml (==5.4.0)
+Requires-Dist: markdown (==3.8.1)
+Requires-Dist: markupsafe (==3.0.2)
+Requires-Dist: matplotlib (==3.10.3)
+Requires-Dist: more-itertools (==10.7.0)
+Requires-Dist: morph-kgc (==2.8.1)
+Requires-Dist: nbformat (==5.10.4)
+Requires-Dist: nltk (==3.9.1)
+Requires-Dist: numpy (==1.26.4)
+Requires-Dist: packaging (==25.0)
+Requires-Dist: pandas (==2.3.0)
+Requires-Dist: pillow (==11.2.1)
+Requires-Dist: platformdirs (==4.3.8)
+Requires-Dist: pluggy (==1.6.0)
+Requires-Dist: pyahocorasick (==2.2.0)
+Requires-Dist: pyoxigraph (==0.3.22)
+Requires-Dist: pyparsing (==3.2.3)
+Requires-Dist: pyproject-hooks (==1.2.0)
+Requires-Dist: pystache (>=0.6.8,<0.7.0)
+Requires-Dist: pytest (==7.4.4)
+Requires-Dist: python-dateutil (==2.9.0.post0)
+Requires-Dist: pytz (==2025.2)
+Requires-Dist: pyyaml (==6.0.2)
+Requires-Dist: rdflib (==7.1.4)
+Requires-Dist: rdflib-jsonld (==0.6.2)
+Requires-Dist: referencing (==0.36.2)
+Requires-Dist: regex (==2024.11.6)
+Requires-Dist: requests (==2.32.4)
+Requires-Dist: rpds-py (==0.25.1)
+Requires-Dist: ruamel-yaml (==0.18.14)
+Requires-Dist: ruamel-yaml-clib (==0.2.12)
+Requires-Dist: scikit-learn (==1.3.2)
+Requires-Dist: scipy (==1.15.3)
+Requires-Dist: six (==1.17.0)
+Requires-Dist: somef (==0.9.11)
+Requires-Dist: soupsieve (==2.7)
+Requires-Dist: textblob (==0.17.1)
+Requires-Dist: textsearch (==0.0.24)
+Requires-Dist: threadpoolctl (==3.6.0)
+Requires-Dist: toml (==0.10.2)
+Requires-Dist: tomli (==2.2.1)
+Requires-Dist: tqdm (==4.67.1)
+Requires-Dist: traitlets (==5.14.3)
+Requires-Dist: typeguard (==4.4.4)
+Requires-Dist: typing-extensions (==4.14.0)
+Requires-Dist: tzdata (==2025.2)
+Requires-Dist: urllib3 (==2.5.0)
+Requires-Dist: validators (==0.22.0)
+Requires-Dist: xgboost (==2.1.4)
+Project-URL: Homepage, https://github.com/oeg-upm/rsfc
+Description-Content-Type: text/markdown
+
+# Research Software Fairness Checks (RSFC)
+
+A command line interface to automatically evaluate the quality of a Github or Gitlab repository.
+
+**Authors**: Daniel Garijo, Andrés Montero
+
+
+## Features
+
+Given a repository URL, RSFC will perform a series of checks based on a list of research software quality indicators (RSQI). The RSQIs currently covered by the package are:
+
+- software_has_license
+- software_has_citation
+- has_releases
+- repository_workflows
+- version_control_use
+- requirements_specified
+- software_documentation
+- persistent_and_unique_identifier
+- descriptive_metadata
+
+For more information about these RSQIs, you can check https://github.com/EVERSE-ResearchSoftware/indicators. We have plans to implement all of the RSQIs available in that repository.
+
+
+## Requirements
+
+Python 3.10.8 or higher
+
+Dependencies are available in the requirements.txt or pyproject.toml file located in the root of the repository
+
+## Install from Github with Poetry
+
+To install the package, first clone the repository in your machine.
+This project uses Poetry for dependency and environment management.
+
+```
+git clone https://github.com/oeg-upm/rsfc.git
+```
+
+Go to the project's root directory
+
+```
+cd rsfc
+```
+
+Install Poetry (if you haven’t already)
+
+```
+curl -sSL https://install.python-poetry.org | python3 -
+```
+
+Make sure Poetry is available in your PATH
+
+```
+poetry --version
+```
+
+Create the virtual environment and install dependencies
+
+```
+poetry install
+```
+
+Activate the virtual environment (Optional)
+
+```
+source $(poetry env info --path)/bin/activate
+```
+
+Your terminal prompt should now show something like:
+
+```
+(rsfc-py3.11) your-user@your-machine rsfc %
+```
+
+With virtual environment activated you can tried like this:
+
+```
+rsfc --help
+```
+
+Without poetry virtual environment activated you need to use the poetry run:
+
+```
+poetry run rsfc --help
+```
+
+## Usage
+
+After installation, you can use the package by running if you activated the poetry env
+
+```
+rsfc <repo_url>
+```
+
+or like this without the poetry env
+
+```
+poetry ruyn rsfc <repo_url>
+```
+

rsfc-0.0.1/README.md

@@ -0,0 +1,100 @@
+# Research Software Fairness Checks (RSFC)
+
+A command line interface to automatically evaluate the quality of a Github or Gitlab repository.
+
+**Authors**: Daniel Garijo, Andrés Montero
+
+
+## Features
+
+Given a repository URL, RSFC will perform a series of checks based on a list of research software quality indicators (RSQI). The RSQIs currently covered by the package are:
+
+- software_has_license
+- software_has_citation
+- has_releases
+- repository_workflows
+- version_control_use
+- requirements_specified
+- software_documentation
+- persistent_and_unique_identifier
+- descriptive_metadata
+
+For more information about these RSQIs, you can check https://github.com/EVERSE-ResearchSoftware/indicators. We have plans to implement all of the RSQIs available in that repository.
+
+
+## Requirements
+
+Python 3.10.8 or higher
+
+Dependencies are available in the requirements.txt or pyproject.toml file located in the root of the repository
+
+## Install from Github with Poetry
+
+To install the package, first clone the repository in your machine.
+This project uses Poetry for dependency and environment management.
+
+```
+git clone https://github.com/oeg-upm/rsfc.git
+```
+
+Go to the project's root directory
+
+```
+cd rsfc
+```
+
+Install Poetry (if you haven’t already)
+
+```
+curl -sSL https://install.python-poetry.org | python3 -
+```
+
+Make sure Poetry is available in your PATH
+
+```
+poetry --version
+```
+
+Create the virtual environment and install dependencies
+
+```
+poetry install
+```
+
+Activate the virtual environment (Optional)
+
+```
+source $(poetry env info --path)/bin/activate
+```
+
+Your terminal prompt should now show something like:
+
+```
+(rsfc-py3.11) your-user@your-machine rsfc %
+```
+
+With virtual environment activated you can tried like this:
+
+```
+rsfc --help
+```
+
+Without poetry virtual environment activated you need to use the poetry run:
+
+```
+poetry run rsfc --help
+```
+
+## Usage
+
+After installation, you can use the package by running if you activated the poetry env
+
+```
+rsfc <repo_url>
+```
+
+or like this without the poetry env
+
+```
+poetry ruyn rsfc <repo_url>
+```

rsfc-0.0.1/pyproject.toml

@@ -0,0 +1,99 @@
+[tool.poetry]
+name = "rsfc"
+version = "0.0.1"
+description = "EVERSE Research Software Fairness Checks"
+authors = ["Andres Montero <andres.montero.martin@upm.es>"]
+license = "MIT"
+readme = "README.md"
+packages = [{ include = "rsfc", from = "src" }]
+homepage = "https://github.com/oeg-upm/rsfc"
+
+[tool.poetry.dependencies]
+python = ">=3.10,<=3.13"
+somef = "0.9.11"
+regex = "2024.11.6"
+requests = "2.32.4"
+anyascii = "0.3.2"
+attrs = "25.3.0"
+beautifulsoup4 = "4.13.4"
+bibtexparser = "1.4.3"
+bs4 = "0.0.1"
+build = "1.2.2.post1"
+certifi = "2025.6.15"
+chardet = "5.2.0"
+charset-normalizer = "3.4.2"
+click = "8.2.1"
+click-option-group = "0.5.7"
+contourpy = "1.3.2"
+contractions = "0.1.73"
+cycler = "0.12.1"
+duckdb = "1.3.1"
+elementpath = "4.8.0"
+falcon = "3.1.3"
+fastjsonschema = "2.21.1"
+fonttools = "4.58.4"
+idna = "3.10"
+imbalanced-learn = "0.11.0"
+inflect = "7.5.0"
+iniconfig = "2.1.0"
+jinja2 = "3.1.6"
+joblib = "1.5.1"
+jsonpath-python = "1.0.6"
+jsonschema = "4.24.0"
+jsonschema-specifications = "2025.4.1"
+jupyter-core = "5.8.1"
+kiwisolver = "1.4.8"
+lxml = "5.4.0"
+markdown = "3.8.1"
+markupsafe = "3.0.2"
+matplotlib = "3.10.3"
+more-itertools = "10.7.0"
+morph-kgc = "2.8.1"
+nbformat = "5.10.4"
+nltk = "3.9.1"
+numpy = "1.26.4"
+packaging = "25.0"
+pandas = "2.3.0"
+pillow = "11.2.1"
+platformdirs = "4.3.8"
+pluggy = "1.6.0"
+pyahocorasick = "2.2.0"
+pyoxigraph = "0.3.22"
+pyparsing = "3.2.3"
+pyproject-hooks = "1.2.0"
+pytest = "7.4.4"
+python-dateutil = "2.9.0.post0"
+pytz = "2025.2"
+pyyaml = "6.0.2"
+rdflib = "7.1.4"
+rdflib-jsonld = "0.6.2"
+referencing = "0.36.2"
+rpds-py = "0.25.1"
+ruamel-yaml = "0.18.14"
+ruamel-yaml-clib = "0.2.12"
+scikit-learn = "1.3.2"
+scipy = "1.15.3"
+six = "1.17.0"
+soupsieve = "2.7"
+textblob = "0.17.1"
+textsearch = "0.0.24"
+threadpoolctl = "3.6.0"
+toml = "0.10.2"
+tomli = "2.2.1"
+tqdm = "4.67.1"
+traitlets = "5.14.3"
+typeguard = "4.4.4"
+typing-extensions = "4.14.0"
+tzdata = "2025.2"
+urllib3 = "2.5.0"
+validators = "0.22.0"
+xgboost = "2.1.4"
+pystache = "^0.6.8"
+
+[tool.poetry.scripts]
+rsfc = "rsfc.main:main"
+
+[build-system]
+requires = ["poetry-core"]
+build-backend = "poetry.core.masonry.api"
+

rsfc-0.0.1/src/rsfc/__init__.py

@@ -0,0 +1,3 @@
+# -*- coding: utf-8 -*-
+
+__version__ = "0.0.1"

rsfc-0.0.1/src/rsfc/main.py

@@ -0,0 +1,13 @@
+import argparse
+
+def main():
+    parser = argparse.ArgumentParser(description="RSFC - EVERSE Research Software Fairness Checks")
+    parser.add_argument("repo_url", help="URL of the Github repository to be analyzed")
+
+    args = parser.parse_args()
+    
+    from rsfc.rsfc_core import build_assessment
+    build_assessment(args.repo_url)
+
+if __name__ == "__main__":
+    main()

rsfc-0.0.1/src/rsfc/model/assessedSoftware.py

@@ -0,0 +1,117 @@
+import urllib
+from urllib.parse import unquote
+import requests
+from datetime import datetime
+
+class AssessedSoftware:
+    def __init__(self, repo_url, repo_type):
+        self.software_url = repo_url
+        base_url = self.get_repo_base_url(repo_url, repo_type)
+        self.software_name = self.get_soft_name(unquote(base_url))
+        self.software_version = self.get_soft_version(base_url, repo_type)
+        self.software_id = None
+        
+        
+    def get_repo_base_url(self, repo_url, repo_type):
+        parsed_url = urllib.parse.urlparse(repo_url)
+        path_parts = parsed_url.path.strip("/").split("/")
+        if len(path_parts) < 2:
+            raise ValueError("Error when getting repository API URL")
+
+        owner, repo = path_parts[-2], path_parts[-1]
+
+        if repo_type == 'GITHUB':
+            url = f"https://api.github.com/repos/{owner}/{repo}"
+        elif repo_type == "GITLAB":
+            project_path = urllib.parse.quote(f"{owner}/{repo}", safe="")
+            url = f"https://gitlab.com/api/v4/projects/{project_path}"
+        else:
+            raise ValueError("URL not within supported types (Github and Gitlab)")
+
+        return url
+        
+    '''def get_base_url(self, repo_url, repo_type):
+        parsed_url = urllib.parse.urlparse(repo_url)
+        path_parts = parsed_url.path.strip("/").split("/")
+        if len(path_parts) < 2:
+            raise ValueError("Error when getting Github API URL")
+        owner, repo = path_parts[-2], path_parts[-1]
+        
+        url = f"https://api.github.com/repos/{owner}/{repo}"
+        
+        return url'''
+        
+        
+    def get_soft_name(self, base_url):
+        name = base_url.rstrip("/").split("/")[-1]
+        return name
+
+
+    def get_soft_version(self, url, repo_type):
+        try:
+            releases_url = f"{url}/releases"
+
+            response = requests.get(releases_url)
+            response.raise_for_status()
+            releases = response.json()
+
+            latest_release = None
+            latest_date = None
+
+            for release in releases:
+                if repo_type == "GITHUB":
+                    date_str = release.get("published_at")
+                    tag = release.get("tag_name")
+                elif repo_type == "GITLAB":
+                    date_str = release.get("released_at")
+                    tag = release.get("tag_name")
+                else:
+                    raise ValueError("Unsupported repository type")
+
+                if date_str and tag:
+                    try:
+                        dt = datetime.fromisoformat(date_str.rstrip("Z"))
+                    except ValueError:
+                        continue
+
+                    if latest_release is None or dt > latest_date:
+                        latest_release = tag
+                        latest_date = dt
+
+            return latest_release
+
+        except Exception as e:
+            print(f"Error fetching releases from {repo_type} at {releases_url}: {e}")
+            return None
+
+
+
+    '''def get_soft_version(self, url):
+        try:
+            releases_url = f"{url}/releases"
+            response = requests.get(releases_url)
+            response.raise_for_status()
+            releases = response.json()
+
+            latest_release = None
+            latest_date = None
+            for release in releases:
+                date_str = release.get("published_at")
+                tag = release.get("tag_name")
+                if date_str and tag:
+                    try:
+                        dt = datetime.fromisoformat(date_str.rstrip("Z"))
+                    except ValueError:
+                        continue
+
+                    if latest_release is None or dt > latest_date:
+                        latest_release = tag
+                        latest_date = dt
+
+            return latest_release
+
+        except Exception as e:
+            print(f"Error fetching releases from GitHub: {e}")
+            return None'''
+
+

rsfc-0.0.1/src/rsfc/model/check.py

@@ -0,0 +1,28 @@
+from rsfc.utils import constants
+
+class Check:
+    def __init__(self, indicator_id, process, output, evidence):
+        self.checkers_info = constants.CHECKERS_DICT
+        
+        self.indicator_id = indicator_id
+        self.process = process
+        self.output = output
+        self.evidence = evidence
+
+    def convert(self):
+        return {
+            "@type": "CheckResult",
+            "assessesIndicator": {
+                "@id": self.indicator_id
+            },
+            "checkingSoftware": {
+                "@type": "schema:SoftwareApplication",
+                "name": self.checkers_info['rsfc']['name'],
+                "@id": self.checkers_info['rsfc']['id'],
+                "softwareVersion": self.checkers_info['rsfc']['version']
+            },
+            "process": self.process,
+            "status": { "@id": "schema:CompletedActionStatus" },
+            "output": self.output,
+            "evidence": self.evidence
+        }