added wkhtmltopdf to CI script

.github/workflows/tests.yml

@@ -26,6 +26,11 @@ jobs:
           python -m pip install --upgrade pip
           python -m pip install flake8 pytest pytest-cov pylint 
           if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+      - name: Install wkthtmltopdf
+        run: |
+          sudo apt-get install -y xfonts-base xfonts-75dpi
+          wget https://github.com/wkhtmltopdf/packaging/releases/download/0.12.6-1/wkhtmltox_0.12.6-1.bionic_amd64.deb
+          sudo dpkg -i wkhtmltox_0.12.6-1.bionic_amd64.deb
       - name: Lint with flake8
         run: |
           # stop the build if there are Python syntax errors or undefined names

README.md

@@ -75,7 +75,7 @@ To install Vaxrank for local development, you may do the below:
 
 ```
 git clone git@github.com:openvax/vaxrank.git
-conda create -q -n vaxrank-dev-env python=3.5.2 numpy scipy nose pandas pylint
+conda create -q -n vaxrank-dev-env python=3.5.2 numpy scipy pandas pylint
 source activate vaxrank-dev-env
 pip install -r requirements.txt
 pip install .
@@ -86,8 +86,7 @@ pyensembl install --release 87 --species mouse
 You should run the linter and the test suite as you work on Vaxrank (and these will be run automatically by our continuous integration server up on a PR being made).
 
 ```
-./lint.sh
-nosetests test
+./lint.sh && ./test.sh 
 ```
 
 The first run of the tests may take a while (8 minutes on a 2016 Macbook Pro) to create the FM index of the proteome, but subsequent tests should take only a few seconds.

tests/test_cancer_driver_gene.py

@@ -19,7 +19,8 @@
     _DRIVER_VARIANT_COLUMN_NAME
 )
 from varcode import Variant
-from nose.tools import eq_
+
+from .common import eq_
 
 
 def test_HRAS_G13C_in_cancer_driver_genes():

tests/test_epitope_prediction.py

@@ -10,17 +10,15 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from __future__ import absolute_import, print_function, division
-
-from nose.tools import eq_, ok_
-
 from mhctools import RandomBindingPredictor
 from pyensembl import genome_for_reference_name
 from varcode import Variant
 from vaxrank.epitope_prediction import predict_epitopes, EpitopePrediction
 from vaxrank.mutant_protein_fragment import MutantProteinFragment
 from vaxrank.vaccine_peptide import VaccinePeptide
 
+from .common import eq_, ok_
+
 mouse_genome = genome_for_reference_name("GRCm38")
 
 def test_reference_peptide_logic():

tests/test_manufacturability.py

@@ -12,7 +12,6 @@
 
 from vaxrank.manufacturability import ManufacturabilityScores
 
-
 def test_c_terminal_proline():
     scores = ManufacturabilityScores.from_amino_acids("A" * 6 + "P")
     assert scores.c_terminal_proline

tests/test_mutant_protein_sequence.py

@@ -10,13 +10,12 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from __future__ import absolute_import, print_function, division
+from mhctools import RandomBindingPredictor
 
-from nose.tools import eq_, assert_almost_equal
 from vaxrank.cli import make_vaxrank_arg_parser, run_vaxrank_from_parsed_args
 from vaxrank.mutant_protein_fragment import MutantProteinFragment
-from mhctools import RandomBindingPredictor
 
+from .common import eq_, almost_eq_
 from .testing_helpers import data_path
 
 random_binding_predictor = RandomBindingPredictor(["H-2-Kb", "H-2-Db"])
@@ -119,7 +118,7 @@ def test_keep_top_k_epitopes():
         # propagated as expected
         mutant_epitope_score = sum(
             p.logistic_epitope_score() for p in vaccine_peptide.mutant_epitope_predictions)
-        assert_almost_equal(mutant_epitope_score, vaccine_peptide.mutant_epitope_score)
+        almost_eq_(mutant_epitope_score, vaccine_peptide.mutant_epitope_score)
 
 def test_mutant_protein_fragment_serialization():
     arg_parser = make_vaxrank_arg_parser()

tests/test_shell_script.py

@@ -13,7 +13,7 @@
 
 from os.path import getsize
 from mock import patch
-from nose.plugins.attrib import attr
+
 from tempfile import NamedTemporaryFile
 
 import pandas as pd
@@ -129,7 +129,6 @@ def test_html_report():
         assert len(lines) > 1
 
 
-@attr('skip')  # want the ability to skip this test on some machines
 def test_pdf_report():
     with NamedTemporaryFile(mode="rb") as f:
         pdf_args = cli_args_for_b16_seqdata + ["--output-pdf-report", f.name]
@@ -148,7 +147,3 @@ def test_report_no_peptides(mock_vaccine_peptides_for_variant):
         contents = f.read()
         assert contents == ''
 
-
-if __name__ == "__main__":
-    test_csv_report()
-    test_html_report()

vaxrank/report.py

@@ -35,7 +35,7 @@
 
 JINJA_ENVIRONMENT = jinja2.Environment(
     loader=jinja2.FileSystemLoader(os.path.dirname(__file__)),
-    extensions=['jinja2.ext.autoescape'],
+    extensions=[],
     autoescape=False,
     trim_blocks=True,
     lstrip_blocks=True,