Can now pass urls to commandline fairtally with progressbar

.githooks/pre-commit

@@ -0,0 +1,28 @@
+#!/bin/sh
+
+echo "Script $0 triggered ..."
+echo "Starting prospector analysis ..."
+
+# quietly run prospector
+prospector 1>/dev/null
+
+# use return code to abort commit if necessary
+if [ $? != "0" ]; then
+    echo "Commit aborted. Run 'prospector' to see the errors."
+    exit 1
+fi
+
+
+echo "Starting isort analysis ..."
+
+# recursively run isort on fairtally/ directory, don't try to automatically fix anything
+isort --recursive --check-only fairtally
+
+if [ $? != "0" ]; then
+    echo "Commit aborted."
+    exit 1
+fi
+
+echo "Pre-commit checks completed successfully."
+exit 0
+

fairtally/__init__.py

@@ -1,10 +1,13 @@
-# -*- coding: utf-8 -*-
-
 import logging
-
 from .__version__ import __version__
 
+
 logging.getLogger(__name__).addHandler(logging.NullHandler())
 
 __author__ = "FAIR Software"
 __email__ = '[email protected]'
+
+
+__all__ = [
+    "__version__"
+]

fairtally/__version__.py

@@ -1,9 +1,3 @@
-import os
-import sys
 
-# To update the package version number, edit CITATION.cff
-citationfile = os.path.join(sys.exec_prefix, 'citation/fairtally', 'CITATION.cff')
-with open(citationfile, 'r') as cff:
-    for line in cff:
-        if 'version:' in line:
-            __version__ = line.replace('version:', '').strip().strip('"')
+
+__version__ = "0.1.0"

fairtally/cli.py

@@ -0,0 +1,76 @@
+import io
+import json
+from pathlib import Path
+import click
+from howfairis import Checker
+from howfairis import Compliance
+from howfairis import Repo
+from jinja2 import Template
+from tqdm import tqdm
+from fairtally.get_badge_color import get_badge_color
+from fairtally.redirect_stdout_stderr import RedirectStdStreams
+
+
+@click.command()
+@click.argument("urls", nargs=-1)
+@click.option("--html", "output_file_html",
+              help="Filename of where to write the results as HTML.",
+              default=None, type=click.File("wt"))
+@click.option("--json", "output_file_json",
+              help="Filename of where to write the results as JSON.",
+              default=None, type=click.File("wt"))
+def cli(urls=None, output_file_html=None, output_file_json=None):
+
+    def write_as_json():
+        with output_file_json:
+            json.dump(results, output_file_json, sort_keys=True)
+
+    def write_as_html():
+        parent = Path(__file__).parent
+        template_file = parent / "data" / "index.html.template"
+        with open(template_file) as f:
+            template = Template(f.read())
+        s = template.render(results=results)
+        with output_file_html:
+            output_file_html.write(s)
+
+    if len(urls) == 0:
+        print("No URLs provided, aborting.")
+        return
+
+    results = list()
+
+    url_progressbar = tqdm(urls, bar_format="fairtally progress: |{bar}| {n_fmt}/{total_fmt}", ncols=70, position=0)
+    current_value = tqdm(total=0, bar_format="{desc}", position=1)
+    for url in url_progressbar:
+        stderr_buffer = io.StringIO()
+        stdout_buffer = io.StringIO()
+        with RedirectStdStreams(stdout=stdout_buffer, stderr=stderr_buffer):
+            try:
+                current_value.set_description_str("currently checking " + url)
+                repo = Repo(url)
+                compliance = Checker(repo, ignore_repo_config=True, is_quiet=True).check_five_recommendations()
+            except Exception:
+                compliance = Compliance(False, False, False, False, False)
+            finally:
+                badge = "https://img.shields.io/badge/fair--software.eu-{0}-{1}"\
+                        .format(compliance.urlencode(), get_badge_color(compliance))
+                d = dict(url=url, badge=badge, repository=compliance.repository, license=compliance.license,
+                         registry=compliance.registry, citation=compliance.citation, checklist=compliance.checklist,
+                         count=compliance.count(), stdout=stdout_buffer.getvalue(), stderr=stderr_buffer.getvalue())
+
+        current_value.set_description_str()
+        results.append(d)
+
+    if output_file_json is None and output_file_html is None:
+        print(json.dumps(results))
+
+    if output_file_json is not None:
+        write_as_json()
+
+    if output_file_html is not None:
+        write_as_html()
+
+
+if __name__ == "__main__":
+    cli()

fairtally/data/index.html.template

@@ -0,0 +1,36 @@
+<html>
+
+<head>
+</head>
+
+<body>
+
+<table>
+  <tr>
+    <th>URL</th>
+    <th>repository</th>
+    <th>license</th>
+    <th>registry</th>
+    <th>citation</th>
+    <th>checklist</th>
+    <th>count</th>
+    <th>badge</th>
+
+  </tr>
+
+  {% for item in results %}
+  <tr>
+    <td><a href="{{item.url}}">{{item.url}}</a></td>
+    <td>{{item.repository}}</td>
+    <td>{{item.license}}</td>
+    <td>{{item.registry}}</td>
+    <td>{{item.citation}}</td>
+    <td>{{item.checklist}}</td>
+    <td>{{item.count}}</td>
+    <td><a href="https://fair-software.eu"><img src="{{item.badge}}"></a></td>
+  </tr>
+  {% endfor %}
+
+</body>
+
+</html>

fairtally/get_badge_color.py

@@ -0,0 +1,17 @@
+from howfairis import Compliance
+
+
+def get_badge_color(compliance: Compliance) -> str:
+
+    score = compliance.count(True)
+
+    if score in [0, 1]:
+        return "red"
+    if score in [2, 3]:
+        return "orange"
+    if score in [4]:
+        return "yellow"
+    if score == 5:
+        return "green"
+
+    raise Exception("should not happen")

fairtally/redirect_stdout_stderr.py

@@ -0,0 +1,21 @@
+import sys
+
+
+# from https://stackoverflow.com/a/6796752
+class RedirectStdStreams():
+
+    def __init__(self, stdout=None, stderr=None):
+        self._stdout = stdout or sys.stdout
+        self._stderr = stderr or sys.stderr
+
+    def __enter__(self):
+        self.old_stdout, self.old_stderr = sys.stdout, sys.stderr
+        self.old_stdout.flush()
+        self.old_stderr.flush()
+        sys.stdout, sys.stderr = self._stdout, self._stderr
+
+    def __exit__(self, exc_type, exc_value, traceback):
+        self._stdout.flush()
+        self._stderr.flush()
+        sys.stdout = self.old_stdout
+        sys.stderr = self.old_stderr

setup.cfg

@@ -1,21 +1,29 @@
-[metadata]
-description-file = README.rst
-
 [aliases]
 # Define `python setup.py test`
 test=pytest
 
+# Define `python setup.py build_sphinx`
+[build_sphinx]
+source-dir = docs
+build-dir = docs/_build
+all_files = 1
+builder = html
+
 [coverage:run]
 branch = True
 source = fairtally
 
+[metadata]
+description-file = README.rst
+
 [tool:pytest]
 testpaths = tests
 addopts = --cov --cov-report xml --cov-report term --cov-report html
 
-# Define `python setup.py build_sphinx`
-[build_sphinx]
-source-dir = docs
-build-dir = docs/_build
-all_files = 1
-builder = html
+[tool:isort]
+lines_after_imports = 2
+force_single_line = 1
+no_lines_before = FUTURE,STDLIB,THIRDPARTY,FIRSTPARTY,LOCALFOLDER
+known_first_party = fairtally
+src_paths = fairtally,tests,livetests
+line_length = 120

setup.py

@@ -1,62 +1,72 @@
 #!/usr/bin/env python
-# -*- coding: utf-8 -*-
 import os
-
+from fairtally.__version__ import __version__
 from setuptools import setup
 
 here = os.path.abspath(os.path.dirname(__file__))
 
-# To update the package version number, edit CITATION.cff
-with open('CITATION.cff', 'r') as cff:
-    for line in cff:
-        if 'version:' in line:
-            version = line.replace('version:', '').strip().strip('"')
 
-with open('README.rst') as readme_file:
+with open("README.rst") as readme_file:
     readme = readme_file.read()
 
 setup(
-    name='fairtally',
-    version=version,
+    name="fairtally",
+    entry_points={
+        "console_scripts": ["fairtally=fairtally.cli:cli"],
+    },
+    version=__version__,
     description="Make a report based on howfairis results",
-    long_description=readme + '\n\n',
+    long_description=readme + "\n\n",
     author="FAIR Software",
-    author_email='[email protected]',
-    url='https://github.com/fair-software/fairtally',
+    author_email="[email protected]",
+    url="https://github.com/fair-software/fairtally",
     packages=[
-        'fairtally',
+        "fairtally",
     ],
     include_package_data=True,
     license="Apache Software License 2.0",
     zip_safe=False,
-    keywords='fairtally',
+    keywords="fairtally",
     classifiers=[
-        'Development Status :: 2 - Pre-Alpha',
-        'Intended Audience :: Developers',
-        'License :: OSI Approved :: Apache Software License',
-        'Natural Language :: English',
-        'Programming Language :: Python :: 3',
-        'Programming Language :: Python :: 3.5',
-        'Programming Language :: Python :: 3.6',
-        'Programming Language :: Python :: 3.7',
+        "Development Status :: 2 - Pre-Alpha",
+        "Intended Audience :: Developers",
+        "License :: OSI Approved :: Apache Software License",
+        "Natural Language :: English",
+        "Programming Language :: Python :: 3",
+        "Programming Language :: Python :: 3.6",
+        "Programming Language :: Python :: 3.7",
+        "Programming Language :: Python :: 3.8",
+        "Programming Language :: Python :: 3.9"
+    ],
+    test_suite="tests",
+    install_requires=[
+        "click == 7.*",
+        "howfairis == 0.14.*",
+        "jinja2 == 2.*",
+        "tqdm == 4.*"
     ],
-    test_suite='tests',
-    install_requires=[],  # FIXME: add your package's dependencies to this list
     setup_requires=[
-        # dependency for `python setup.py test`
-        'pytest-runner',
-        # dependencies for `python setup.py build_sphinx`
-        'sphinx',
-        'sphinx_rtd_theme',
-        'recommonmark'
     ],
     tests_require=[
-        'pytest',
-        'pytest-cov',
-        'pycodestyle',
     ],
     extras_require={
-        'dev':  ['prospector[with_pyroma]', 'yapf', 'isort'],
+        "dev": [
+            "bumpversion",
+            "prospector[with_pyroma]",
+            "pycodestyle",
+            "pytest-cov",
+            "pytest-runner",
+            "pytest",
+            "recommonmark",
+            "sphinx_rtd_theme",
+            "sphinx-click",
+            "sphinx",
+            "yapf"
+        ],
+        "publishing": [
+            "twine",
+            "wheel"
+        ]
     },
-    data_files=[('citation/fairtally', ['CITATION.cff'])]
+    data_files=[("citation/fairtally", ["CITATION.cff"])]
 )

tests/test_fairtally.py

@@ -5,8 +5,6 @@
 """
 import pytest
 
-from fairtally import fairtally
-
 
 def test_something():
     assert True