Add bioconda badge and increase test coverage (#78)

clintval · Jan 1, 2019 · 45e2736 · 45e2736
1 parent baac86b
commit 45e2736
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Showing 7 changed files with 47 additions and 45 deletions.
diff --git a/README.md b/README.md
@@ -5,7 +5,6 @@
 [![Code Coverage](https://codecov.io/gh/clintval/sample-sheet/branch/master/graph/badge.svg)](https://codecov.io/gh/clintval/sample-sheet)
 [![PyPi Release](https://badge.fury.io/py/sample_sheet.svg)](https://badge.fury.io/py/sample_sheet)
 [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat-square)](http://bioconda.github.io/recipes/sample-sheet/README.html)
-[![License](https://img.shields.io/pypi/l/sample-sheet.svg)](https://github.com/clintval/sample-sheet/blob/master/LICENSE)
 [![Python Versions](https://img.shields.io/pypi/pyversions/sample-sheet.svg)](https://pypi.python.org/pypi/sample-sheet/)
 [![MyPy Checked](http://www.mypy-lang.org/static/mypy_badge.svg)](http://mypy-lang.org/)
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/ambv/black)

diff --git a/docs/conf.py b/docs/conf.py
@@ -1,4 +1,3 @@
-
 # -*- coding: utf-8 -*-
 #
 # Configuration file for the Sphinx documentation builder.

diff --git a/sample_sheet/__init__.py b/sample_sheet/__init__.py
@@ -10,10 +10,6 @@
 from pathlib import Path
 from string import ascii_letters, digits, punctuation
 from textwrap import wrap
-
-from requests.structures import CaseInsensitiveDict
-from smart_open import smart_open  # type: ignore
-from tabulate import tabulate  # type: ignore
 from typing import (
     Any,
     Generator,
@@ -26,21 +22,17 @@
     Union,
 )
 
+from requests.structures import CaseInsensitiveDict
+from smart_open import smart_open  # type: ignore
+from tabulate import tabulate  # type: ignore
+from terminaltables import SingleTable
+
 from .util import maybe_render_markdown
 
 __all__: List[str] = ['ReadStructure', 'Sample', 'SampleSheet']
 
 __version__ = '0.8.0'
 
-
-try:  # pragma: no cover
-    from terminaltables import SingleTable  # type: ignore
-
-    HAS_TERMINALTABLES = True
-except ImportError:
-    HAS_TERMINALTABLES = False
-
-
 DESIGN_HEADER: List[str] = [
     'Sample_ID',
     'Sample_Name',
@@ -941,7 +933,7 @@ def __str__(self) -> str:
         except OSError:  # pragma: no cover
             in_terminal = False
 
-        if in_terminal and HAS_TERMINALTABLES:
+        if in_terminal:  # pragma: no cover
             return self._repr_tty_()
         else:
             return self.__repr__()

diff --git a/sample_sheet/util.py b/sample_sheet/util.py
@@ -1,7 +1,7 @@
 # pylint: disable=E0401
-from typing import Any, List
+from typing import Any
 
-__all__: List[str] = ['is_ipython_interpreter', 'maybe_render_markdown']
+__all__ = ['is_ipython_interpreter', 'maybe_render_markdown']
 
 
 def is_ipython_interpreter() -> bool:  # pragma: no cover

diff --git a/setup.py b/setup.py
@@ -16,8 +16,12 @@
     license='MIT',
     zip_safe=True,
     packages=find_packages(),
-    install_requires=['click', 'smart_open>=1.5.4', 'tabulate'],
-    extras_requires={'cli': ['terminaltables']},
+    install_requires=[
+        'click',
+        'smart_open>=1.5.4',
+        'tabulate',
+        'terminaltables',
+    ],
     scripts=['scripts/sample-sheet'],
     keywords='illumina samplesheet sample sheet parser bioinformatics',
     classifiers=[

diff --git a/test-requirements.txt b/test-requirements.txt
@@ -1,11 +1,18 @@
-black==18.6b2
-coverage==4.5
-flake8==3.5.0
-mypy==0.620
-nose==1.3.7
-pylint==2.0.0
-pytest==3.6.3
-pytest-cov==2.5.1
-pytest-remotedata==0.3.0
-pytest-doctestplus==0.1.3
-pytest-parallel==0.0.2
+black
+coverage
+flake8
+flake8-eradicate
+flake8-blind-except
+flake8-builtins
+flake8-bugbear
+flake8-import-order
+flake8-logging-format
+flake8-rst-docstrings
+hypothesis
+mypy
+nose
+pylint
+pytest
+pytest-cov
+pytest-doctestplus
+pytest-parallel
diff --git a/tests/test_sample_sheet.py b/tests/test_sample_sheet.py
@@ -18,7 +18,6 @@
 from requests.exceptions import HTTPError
 
 from sample_sheet import *  # Test import of __all__
-from sample_sheet import HAS_TERMINALTABLES
 
 RESOURCES = Path(__file__).absolute().resolve().parent / 'resources'
 
@@ -129,6 +128,13 @@ def test_add_samples(self):
         eq_(len(sample_sheet.samples), 2)
         eq_(sample_sheet.samples[0], sample1)
 
+    def test_add_sample_without_sample_id(self):
+        """Test adding a sample without a sample ID"""
+        sample = Sample()
+        sample_sheet = SampleSheet()
+        with pytest.raises(ValueError):
+            sample_sheet.add_sample(sample)
+
     def test_add_sample_with_index(self):
         """Test that the SampleSheet sets a sample with attribute ``index``"""
         sample = Sample({'Sample_ID': 0, 'index': 'ACGTTNAT'})
@@ -718,33 +724,28 @@ def test_repr(self):
             'SampleSheet(\'{}\')'.format(infile),
         )
 
-    @pytest.mark.xfail(reasion="Not sure if multi-line diff is correct")
-    @pytest.mark.skipif(
-        not HAS_TERMINALTABLES,
-        reason="We need `terminaltables` installed here",
-    )
     def test_repr_tty(self):
         """Test ``_repr_tty_()``"""
         self.maxDiff = 3000
         sample_sheet = SampleSheet(RESOURCES / 'paired-end-single-index.csv')
         source = '\n' + ''.join(decode_vt_100(sample_sheet._repr_tty_()))
         target = (
             '\n┌Header─────────────┬─────────────────────────────────┐'
-            '\n│ IEM1_File_Version │ 4                               │'
-            '\n│ Investigator_Name │ jdoe                            │'
-            '\n│ Experiment_Name   │ exp001                          │'
+            '\n│ IEM1FileVersion   │ 4                               │'
+            '\n│ Investigator Name │ jdoe                            │'
+            '\n│ Experiment Name   │ exp001                          │'
             '\n│ Date              │ 11/16/2017                      │'
             '\n│ Workflow          │ SureSelectXT                    │'
             '\n│ Application       │ NextSeq FASTQ Only              │'
             '\n│ Assay             │ SureSelectXT                    │'
             '\n│ Description       │ A description of this flow cell │'
             '\n│ Chemistry         │ Default                         │'
             '\n└───────────────────┴─────────────────────────────────┘'
-            '\n┌Settings──────────────────────┬──────────┐'
-            '\n│ create_fastq_for_index_reads │ 1        │'
-            '\n│ barcode_mismatches           │ 2        │'
-            '\n│ reads                        │ 151, 151 │'
-            '\n└──────────────────────────────┴──────────┘'
+            '\n┌Settings──────────────────┬──────────┐'
+            '\n│ CreateFastqForIndexReads │ 1        │'
+            '\n│ BarcodeMismatches        │ 2        │'
+            '\n│ Reads                    │ 151, 151 │'
+            '\n└──────────────────────────┴──────────┘'
             '\n┌Identifiers┬──────────────┬────────────┬──────────┬────────┐'
             '\n│ Sample_ID │ Sample_Name  │ Library_ID │ index    │ index2 │'
             '\n├───────────┼──────────────┼────────────┼──────────┼────────┤'