Merge pull request #109 from nvictus/develop

Switch to pytest and add coverage reporting

.gitignore

@@ -1,31 +1,47 @@
-COMMANDS
-old
-npm-debug.log
-.DS_Store
-clodius/fast.cpython-35m-darwin.so
-clodius/fast.so
-tmp
-checkpoint
+*.py[cod]
+__pycache__
 *~
 *.swn
 *.swo
 *.swp
 *.tiles
-*.pyc
-/data
+
+# setup and build artifacts
+*.egg-info/
+.eggs/
+dist/
+build/
+MANIFEST
+docs/_templates
+docs/_static
+docs/_build
+clodius/*.c
+*.so
+
+# test and coverage artifacts
+.cache
+.pytest_cache
+.coverage
+coverage.xml
+htmlcov/
+
+# OS-generated files
+.DS_Store
+.Spotlight-V100
+.Trashes
+ehthumbs.db
+Thumbs.db
+
+.ipynb_checkpoints/
+.idea/
+old
+tmp
+checkpoint
+data/
+output/
+COMMANDS
+npm-debug.log
 output.tar
 profile.dat
 profile.png
-output/
 aws_keys.py
-.ipynb_checkpoints/
-/build
-/dist
-.idea/
-clodius.egg-info
-.eggs
-clodius/*.c
-*.so
-docs/_templates
-docs/_static
-docs/_build

.travis.yml

@@ -14,8 +14,6 @@ before_install:
   - wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
   - bash miniconda.sh -b -p $HOME/miniconda
   - export PATH="$HOME/miniconda/bin:$PATH"
-  # Prefer stability to having the latest
-  # - conda update --yes conda
 install:
   - conda install --yes python=$TRAVIS_PYTHON_VERSION numpy
   - pip install -r requirements-dev.txt

CHANGELOG

@@ -1,3 +1,7 @@
+?
+
+- Maintenance: Swicthed from nose to pytest and added coverage reporting.
+
 v0.11.1
 
 - Added `max_tile_width` parameter to ct.bam.tiles() so that users can set a

README.md

@@ -1,4 +1,7 @@
-# Clodius <img src="https://travis-ci.org/hms-dbmi/clodius.svg?branch=develop"/>
+# Clodius
+
+[![Build Status](https://travis-ci.org/higlass/clodius.svg?branch=develop)](https://travis-ci.org/higlass/clodius)
+[![Docs](https://img.shields.io/badge/docs-📖-red.svg?colorB=6680ff)](https://docs.higlass.io/data_preparation.html)
 
 Displaying large amounts of data often requires first turning it into
 not-so-large amounts of data. Clodius is a program and library designed
@@ -45,30 +48,23 @@ The recommended way to develop `clodius` is to use a [conda](https://conda.io/do
 install `clodius` with develop mode:
 
 ```shell
-python setup.py develop
-```
-
-Note that making changes to the `clodius/fast.pyx` [cython](http://docs.cython.org/en/latest/src/quickstart/cythonize.html) module requires an
-explicit recompile step:
-
-```shell
-python setup.py build_ext --inplace
+pip install -e .
 ```
 
 ## Testing
 
 
-The unit tests for clodius can be run using [nosetests](http://nose.readthedocs.io/en/latest/):
+The unit tests for clodius can be run using [pytest](https://docs.pytest.org/en/latest/):
 
 ```shell
-nosetests test
+pytest
 ```
 
 Individual unit tests can be specified by indicating the file and function
 they are defined in:
 
 ```shell
-nosetests test/cli_test.py:test_clodius_aggregate_bedgraph
+pytest test/cli_test.py:test_clodius_aggregate_bedgraph
 ```
 
 ## Quick start with Docker

requirements-dev.txt

@@ -1,5 +1,6 @@
 -r requirements.txt
 flake8
-nose==1.3.7
+pytest
+pytest-cov
 autopep8
 bumpversion

scripts/pyprof.sh

@@ -1,7 +1,7 @@
 #!/bin/bash
-# https://github.com/martinxyz/config/blob/master/scripts/pyprof
-set - e  # exit on error
-rm - f profile.png profile.dat
-python - m cProfile - o profile.dat $@
-gprof2dot.py - f pstats profile.dat | dot - Tpng - o profile.png
-open profile.png
+#https://github.com/martinxyz/config/blob/master/scripts/pyprof
+set -e # exit on error
+rm -f profile.png profile.dat
+python -m cProfile -o profile.dat $@
+gprof2dot.py -f pstats profile.dat | dot -Tpng -o profile.png
+eog profile.png

setup.cfg

@@ -0,0 +1,39 @@
+[wheel]
+universal = 1
+
+[flake8]
+exclude =
+  __init__.py
+  src/* # src directory is generated during build, and then cleared.
+  src/**/*
+
+max-line-length = 80
+
+ignore =
+  E501 # Line too long
+  E722 # do not use bare 'except'
+  W503 # line break before binary operator
+  W504 # line break after binary operator
+
+select = 
+  C # mccabe code complexity
+  E # pycodestyle error
+  W # pycodestyle warning
+  F # pyflakes fatals
+  # B # bugbear default checks
+  # B950 # bugbear opinonated warning (Line too long: max-line-length + 10%)
+
+[tool:pytest]
+addopts = --cov=clodius --cov-report=term-missing --cov-report=html --cov-report=xml
+testpaths =
+    test
+
+[coverage:run]
+source =
+    clodius/
+
+[coverage:report]
+exclude_lines =
+    pragma: no cover
+    return NotImplemented
+    raise NotImplementedError

test/tiles/bigwig_test.py

@@ -4,10 +4,6 @@
 import base64
 
 
-def arr_eq_nan(a, b):
-    return ((a == b) | (np.isnan(a) & np.isnan(b))).all()
-
-
 def test_bigwig_tiles():
     filename = op.join(
         'data',
@@ -60,14 +56,14 @@ def test_bigwig_tiles():
     )
 
     assert min_max_val.shape[0] == 2 * mean_val.shape[0]
-    assert arr_eq_nan(min_max_val[::2], min_val)
-    assert arr_eq_nan(min_max_val[1::2], max_val)
+    assert np.allclose(min_max_val[::2], min_val, equal_nan=True)
+    assert np.allclose(min_max_val[1::2], max_val, equal_nan=True)
 
     assert whisker_val.shape[0] == 4 * mean_val.shape[0]
-    assert arr_eq_nan(whisker_val[::4], min_val)
-    assert arr_eq_nan(whisker_val[1::4], max_val)
-    assert arr_eq_nan(whisker_val[2::4], mean_val)
-    assert arr_eq_nan(whisker_val[3::4], std_val)
+    assert np.allclose(whisker_val[::4], min_val, equal_nan=True)
+    assert np.allclose(whisker_val[1::4], max_val, equal_nan=True)
+    assert np.allclose(whisker_val[2::4], mean_val, equal_nan=True)
+    assert np.allclose(whisker_val[3::4], std_val, equal_nan=True)
 
 
 def test_tileset_info():

travis_test.sh

@@ -16,5 +16,5 @@ start download
 end download
 
 start test
-nosetests test
+pytest
 end test