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[WIP] Add github actions to run test and publish to pypi (#72)
* Add github actions to run test and update to pypi * Fix some tests. * Skips were added to the tests relying on the mannheim drugbank sparql endpoint. * Updated ttl urls to the fhir examples. * Updated cli help file. * Update json-ld text used in the schemaorg tests. * Fix error on setup.cfg file * Fix errors when importing library on changelog * Fetch tags on actions to obtain correct version in tests and rerun test_n3_mapper * Fix run of n3 mapper tests * Use pipenv for n3 mapper * Final adjustments to github action
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‎.github/workflows/main.yaml‎

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name: Build
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on:
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push:
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branches: [ master ]
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jobs:
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unittests-n-commits:
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runs-on: ubuntu-latest
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strategy:
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matrix:
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python-version: [3.7]
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steps:
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- uses: actions/checkout@v2
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with:
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fetch-depth: 0
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v2
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install dependencies
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run: |
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python setup.py install
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pip install -r requirements.txt
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pip install pbr
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- name: Build test files
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run: |
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echo `python tests/test_utils/test_n3_mapper.py`
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- name: Test with unittest
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run: python -m unittest discover -p 'test_*.py'
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- name: Check in requirements.txt and requirements-dev.txt
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run: |
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git add requirements*.txt
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if [[ ! -z $(git status -s requirements*.txt) ]]
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then
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git config --local user.email "[email protected]"
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git config --local user.name "GitHub Action"
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git commit -m 'Automatically generated requirements.txt and requirements-dev.txt' requirements*.txt
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git push
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fi

‎.github/workflows/pr-test.yaml‎

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name: unittests
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on:
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pull_request:
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branches: [ master ]
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jobs:
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build-pipenv:
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runs-on: ubuntu-latest
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strategy:
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matrix:
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python-version: [3.8]
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steps:
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- uses: actions/checkout@v2
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with:
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fetch-depth: 0
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v2
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install pipenv
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uses: dschep/install-pipenv-action@v1
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- name: Install dependencies
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run: |
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python setup.py install
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pip install -r requirements.txt
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pip install pbr
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- name: Build test files
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run: |
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echo `python tests/test_utils/test_n3_mapper.py`
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- name: Test with unittest
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run: python -m unittest discover -p 'test_*.py'

‎.github/workflows/pypi-publish.yaml‎

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name: Publish Python Package
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on:
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push:
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branches: [ master ]
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jobs:
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build-n-publish:
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name: Build and publish Python 🐍 distributions 📦 to PyPI and TestPyPI
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runs-on: ubuntu-latest
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strategy:
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matrix:
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python-version: [3.7]
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steps:
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- uses: actions/checkout@v2
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v2
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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pip install wheel
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- name: build a binary wheel dist
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run: |
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rm -fr dist
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python setup.py bdist_wheel sdist
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- name: Publish distribution 📦 to Test PyPI
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if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
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uses: pypa/[email protected]
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with:
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user: __token__
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password: ${{ secrets.test_pypi_password }}
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repository_url: https://test.pypi.org/legacy/
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- name: Publish distribution 📦 to PyPI
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if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
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uses: pypa/[email protected]
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with:
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user: __token__
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password: ${{ secrets.pypi_password }}

‎.gitignore‎

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# Do not submit Pipfile.lock (https://pypi.org/project/pipenv-to-requirements/)
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Pipfile.lock
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# mac os specific files
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.DS_Store

‎AUTHORS‎

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Alejandro González Hevia <[email protected]>
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Egon Willighagen <[email protected]>
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Harold Solbrig <[email protected]>
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Harold Solbrig <[email protected]>

‎ChangeLog‎

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CHANGES
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=======
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* Fix error on setup.cfg file
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* Fix some tests
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* Add github actions to run test and update to pypi
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* Update slurper notebook to use agent
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v0.7.15
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-------
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* Pull the help call out of it
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* First cut at Biohackathon2020 slurper
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* Update requirements.txt
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* Update prefixlib to support rdflib 5.x behavior
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* Added the "tortoise" serializer that replicates rdflib 4.x prefix behavior
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* Checkpoint on outstanding unit tests
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* Fix for issue #67 and issue #65
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* Checkpoint
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* Checkpoint
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* Checkpoint
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* Passes
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* First cut on SDO example
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* First cut at schemaorg example
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* Remove unused imports and uncomment code in test\_issue\_41
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* Fix for issue #42
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* Added GraphDB specific tag to use the GraphDB BNode solution
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* ChangeLog
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* Update change log

‎tests/test_cli/clitests.py‎

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"""
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testfile_path = os.path.join(self.testdir_path, testfile)
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if text_filter is None:
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text_filter = lambda txt: txt.replace('\r\n', '\n').strip()
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text_filter = lambda txt: "".join(txt.replace('\r\n', '\n').strip().split())
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outf = StringIO()
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arg_list = args.split() if isinstance(args, str) else args

‎tests/test_cli/output/evaluate/help‎

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-pb, --persistbnodes Treat BNodes as persistent in SPARQL endpoint
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--useragent USERAGENT
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Use this user agent in the SPARQL Queries (Default:
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"PyShEx/0.7.14 (https://github.com/hsolbrig/PyShEx;
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"PyShEx/0.7.16 (https://github.com/hsolbrig/PyShEx;
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[email protected])")

‎tests/test_cli/test_evaluate.py‎

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failexpected=True)
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self.assertFalse(update_test_files, "Updating test files")
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@unittest.skipIf(True, "SPARQL query, sometimes URL is down. Need to look for an alternative.")
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def test_sparql_query(self):
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""" Test a sample DrugBank sparql query """
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shex = os.path.join(datadir, 't1.shex')

‎tests/test_cli/test_sparql_options.py‎

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def prog_ep(self, argv: List[str]) -> bool:
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return bool(evaluate_cli(argv, prog=self.testprog))
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@unittest.skipIf(True, "SPARQL query, sometimes URL is down. Need to look for an alternative.")
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def test_sparql_query(self):
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""" Test a sample DrugBank sparql query """
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shex = os.path.join(datadir, 't1.shex')
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sparql = os.path.join(datadir, 't1.sparql')
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rdf = 'http://wifo5-04.informatik.uni-mannheim.de/drugbank/sparql'
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self.do_test([rdf, shex, '-sq', sparql], 'dbsparql1')
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@unittest.skipIf(True, "SPARQL query, sometimes URL is down. Need to look for an alternative.")
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def test_print_queries(self):
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""" Test a sample DrugBank sparql query printing queries"""
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shex = os.path.join(datadir, 't1.shex')
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sparql = os.path.join(datadir, 't1.sparql')
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rdf = 'http://wifo5-04.informatik.uni-mannheim.de/drugbank/sparql'
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self.do_test([rdf, shex, '-sq', sparql, '-ps'], 'dbsparql2', text_filter=elapsed_filter)
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@unittest.skipIf(True, "SPARQL query, sometimes URL is down. Need to look for an alternative.")
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def test_print_results(self):
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""" Test a sample DrugBank sparql query printing results"""
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shex = os.path.join(datadir, 't1.shex')
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sparql = os.path.join(datadir, 't1.sparql')
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rdf = 'http://wifo5-04.informatik.uni-mannheim.de/drugbank/sparql'
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self.do_test([rdf, shex, '-sq', sparql, '-pr', "--stopafter", "1"], 'dbsparql3', text_filter=elapsed_filter)
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@unittest.skipIf(True, "SPARQL query, sometimes URL is down. Need to look for an alternative.")
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def test_named_graph(self):
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""" Test a sample DrugBank using any named graph """
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