Merge pull request #90 from TRON-Bioinformatics/develop

Release v2.0.0

.github/ISSUE_TEMPLATE/bug_report.md

@@ -13,8 +13,8 @@ A clear and concise description of what the bug is.
 **To Reproduce**
 Steps to reproduce the behavior:
 1. Go to '...'
-2. Click on '....'
-3. Scroll down to '....'
+2. Click on '...'
+3. Scroll down to '...'
 4. See error
 
 **Expected behavior**

.github/workflows/documentation.yml

@@ -0,0 +1,23 @@
+name: Documentation
+on: [push]
+jobs:
+  run:
+    runs-on: ubuntu-20.04
+    env:
+      OS: ubuntu-20.04
+      PYTHON: '3.8'
+
+    steps:
+    - uses: actions/checkout@v3
+    - uses: actions/setup-python@v4
+      with:
+        python-version: '3.8'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install setuptools wheel coverage
+        pip install -r docs/requirements.txt
+
+    - name: Build documentation
+      run: |
+        cd docs; make clean html

.github/workflows/unit_tests.yml

@@ -1,10 +1,11 @@
 name: Unit tests
-
 on: [push]
-
 jobs:
-  test:
+  run:
     runs-on: ubuntu-20.04
+    env:
+      OS: ubuntu-20.04
+      PYTHON: '3.8'
 
     # Service containers to run with `container-job`
     services:
@@ -21,15 +22,16 @@ jobs:
         options: --health-cmd pg_isready --health-interval 10s --health-timeout 5s --health-retries 5
 
     steps:
-    - uses: actions/checkout@v2
-    - uses: actions/setup-python@v2
+    - uses: actions/checkout@v3
+    - uses: actions/setup-python@v4
       with:
         python-version: '3.8'
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install setuptools wheel
-    - name: Build, install and run unit tests
+        pip install setuptools wheel coverage
+
+    - name: Generate Report
       env:
         # The hostname used to communicate with the PostgreSQL service container
         POSTGRES_HOST: localhost
@@ -44,4 +46,7 @@ jobs:
         python setup.py bdist_wheel
         pip install numpy==1.21.0
         pip install dist/covigator*.whl
-        python -m unittest discover covigator.tests.unit_tests
+        coverage run -m unittest discover covigator.tests.unit_tests
+
+    - name: Upload Coverage to Codecov
+      uses: codecov/codecov-action@v3

README.md

@@ -6,10 +6,14 @@
 
 [![PyPI version](https://badge.fury.io/py/covigator.svg)](https://badge.fury.io/py/covigator)
 [![Run unit tests](https://github.com/TRON-Bioinformatics/covigator/actions/workflows/unit_tests.yml/badge.svg?branch=main)](https://github.com/TRON-Bioinformatics/covigator/actions/workflows/unit_tests.yml)
+[![codecov](https://codecov.io/gh/TRON-Bioinformatics/covigator/branch/main/graph/badge.svg?token=J5Q8UV65PD)](https://codecov.io/gh/TRON-Bioinformatics/covigator)
+[![Codacy Badge](https://app.codacy.com/project/badge/Grade/d6735b902b7b42e0a7cd423cebff69d2)](https://www.codacy.com/gh/TRON-Bioinformatics/covigator/dashboard?utm_source=github.com&utm_medium=referral&utm_content=TRON-Bioinformatics/covigator&utm_campaign=Badge_Grade)
 [![Powered by Dash](https://img.shields.io/badge/powered%20by-Dash-orange.svg?style=flat&colorA=E1523D&colorB=007D8A)](https://dash.plotly.com/)
 [![License](https://img.shields.io/badge/license-MIT-green)](https://opensource.org/licenses/MIT)
 [![Documentation Status](https://readthedocs.org/projects/covigator/badge/?version=latest)](https://covigator.readthedocs.io/en/latest/?badge=latest)
 
+![CoVigator art](covigator/dashboard/assets/wordcloud.png)
+
 **CoVigator dashboard**: [https://covigator.tron-mainz.de](https://covigator.tron-mainz.de)
 
 **CoVigator documentation**: [https://covigator.readthedocs.io/](https://covigator.readthedocs.io)
@@ -69,5 +73,5 @@ The project was kindly supported by
 ## How to cite
 
 * Schrörs, B., Riesgo-Ferreiro, P., Sorn, P., Gudimella, R., Bukur, T., Rösler, T., Löwer, M., & Sahin, U. (2021). 
-  Large-scale analysis of SARS-CoV-2 spike-glycoprotein mutants demonstrates the need for continuous screening of virus 
-  isolates. PLOS ONE, 16(9), e0249254. [10.1371/journal.pone.0249254](https://doi.org/10.1371/journal.pone.0249254)
+Large-scale analysis of SARS-CoV-2 spike-glycoprotein mutants demonstrates the need for continuous screening of virus 
+isolates. PLOS ONE, 16(9), e0249254. [10.1371/journal.pone.0249254](https://doi.org/10.1371/journal.pone.0249254)

covigator/__init__.py

@@ -1,5 +1,5 @@
-VERSION = "v1.1.0"
-ANALYSIS_PIPELINE_VERSION = "v0.14.0"
+VERSION = "v2.0.0"
+ANALYSIS_PIPELINE_VERSION = "v0.15.0"
 
 MISSENSE_VARIANT = "missense_variant"
 SYNONYMOUS_VARIANT = "synonymous_variant"

covigator/accessor/abstract_accessor.py

@@ -1,4 +1,4 @@
-from datetime import date, datetime
+from datetime import date
 from typing import Union
 import requests
 from covigator.misc.country_parser import CountryParser
@@ -7,13 +7,21 @@
 from covigator.exceptions import CovigatorExcludedSampleTooEarlyDateException
 from covigator.misc import backoff_retrier
 
-NUMBER_RETRIES = 5
+NUMBER_RETRIES = -1
 
 
 class SampleCovid19:
     pass
 
 
+def _parse_abstract(value, _type):
+    try:
+        value = _type(value)
+    except (ValueError, TypeError):
+        value = None
+    return value
+
+
 class AbstractAccessor:
 
     def __init__(self):
@@ -33,15 +41,10 @@ def _parse_country(self, sample: Union[SampleEna, SampleCovid19]):
         sample.continent_alpha_2 = parsed_country.continent_alpha_2
         sample.continent = parsed_country.continent
 
-    def _parse_dates(self, sample: Union[SampleEna, SampleCovid19]):
-        sample.collection_date = self._parse_abstract(sample.collection_date, date.fromisoformat)
-        sample.first_created = self._parse_abstract(sample.first_created, date.fromisoformat)
+
+    @staticmethod
+    def _parse_dates(sample: Union[SampleEna, SampleCovid19]):
+        sample.collection_date = _parse_abstract(sample.collection_date, date.fromisoformat)
+        sample.first_created = _parse_abstract(sample.first_created, date.fromisoformat)
         if sample.collection_date is not None and sample.collection_date < MINIMUM_DATE:
             raise CovigatorExcludedSampleTooEarlyDateException
-
-    def _parse_abstract(self, value, type):
-        try:
-            value = type(value)
-        except (ValueError, TypeError):
-            value = None
-        return value