.gitignore

@@ -18,3 +18,4 @@ pybedtools/featurefuncs.cpp
 *.bak
 cythonize.dat
 docs/source/autodocs/*.rst
+MANIFEST

.travis.yml

+# os:
+#   - linux
+#   - osx
+
 # make edits to this line to trigger a new travis build.
 # (sometimes it errors out trying to download from PyPI)
 language: python
@@ -7,9 +11,16 @@ sudo: false
 
 python:
     - "2.7"
-    #- "3.3"
     - "3.4"
     - "3.5"
+    - "3.6"
+
+# see https://github.com/travis-ci/travis-ci/issues/9815 for py3.7 support
+matrix:
+  include:
+    - python: 3.7
+      dist: xenial
+      sudo: true
 
 notifications:
     email:
@@ -39,9 +50,5 @@ install:
     - conda update -q conda
     - conda info -a
 
-    # Base env only needs to cythonize sources; test script takes care of
-    # everything else.
-    - conda install cython
-
 script:
     - ./condatest.sh "$TRAVIS_PYTHON_VERSION"

MANIFEST.in

-include src/*
+recursive-include pybedtools/include/ *
 include README.rst
 include LICENSE.txt
 include ez_setup.py
-recursive-include docs/source *.rst
-recursive-include docs/source *.py
-recursive-include docs/source/images *
-recursive-include docs/source/_templates *
 recursive-include pybedtools/test/data *
 recursive-include pybedtools/test *
 include docs/Makefile
 include docs/make.bat
-recursive-include pybedtools *.cxx
+recursive-include pybedtools *.cpp
 recursive-include pybedtools *.c
 recursive-exclude * __pycache__
 recursive-exclude * *.py[co]

condatest.sh

 #!/bin/bash
 
-# Installs pybedtools and requirements into a fresh Python 2 or 3 environment
-# and runs tests.
-#
-# Note that this script needs to be called from an environment with Cython
-# since this does a clean/sdist operation which will Cythonize the source
-
 set -e
 
 PY_VERSION=$1
@@ -13,56 +7,95 @@ PY_VERSION=$1
 usage="Usage: $0 py_version[2|3]"
 : ${PY_VERSION:?$usage}
 
+
 log () {
     echo
     echo "[`date`] TEST HARNESS: $1"
     echo
 }
 
-log "removing existing env pbtpy${PY_VERSION}"
-name=pbtpy${PY_VERSION}
-conda env list | grep -q $name && conda env remove -y -n $name
-
-log "starting with basic environment"
-conda create -y -n $name --channel bioconda python=${PY_VERSION} \
-    bedtools \
-    "htslib<1.4" \
-    ucsc-bedgraphtobigwig \
-    ucsc-bigwigtobedgraph
-source activate $name
-
-log "temporarily install cython"
-conda install cython
-
-log "force re-cythonizing"
-rm -rf dist build
-python setup.py clean
-python setup.py build
-python setup.py sdist
 
-log "uninstall cython"
-conda remove cython
 
-log "test installation of sdist"
-set -x
-(cd dist && pip install pybedtools-*.tar.gz && python -c 'import pybedtools')
-set +x
-
-python setup.py clean
-
-log "install test requirements"
+# ----------------------------------------------------------------------------
+# sdist and pip install tests
+# ----------------------------------------------------------------------------
+# Build an environment with just Python and Cython. We do this fresh each time.
+log "building fresh environment with just python and cython"
+with_cy="pbtpy${PY_VERSION}_sdist_cython"
+if conda env list | grep -q $with_cy; then
+    conda env remove -y -n $with_cy
+fi
+conda create -n $with_cy -y --channel conda-forge --channel bioconda python=${PY_VERSION} cython
+source activate $with_cy
+
+# Clone the repo -- so we're only catching things committed to git -- into
+# a temp dir
+log "cloning into temp dir"
+HERE="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
+TMP=/tmp/pybedtools-deploy
+rm -rf $TMP
+git clone $HERE $TMP
+cd $TMP
+
+log "cythonizing source files and building source package"
+# Cythonize the .pyx filex to .cpp, and build a source package
+python setup.py clean cythonize sdist
+
+log "installing source package with pip"
+# Install into the environment to verify that everything works (just an import
+# test)
+(cd dist && pip install pybedtools-*.tar.gz && python -c 'import pybedtools; print(pybedtools.__file__)')
+
+
+# ----------------------------------------------------------------------------
+# Unit tests
+# ----------------------------------------------------------------------------
+# Deactivate that env, and build another one with all requirements that we'll
+# use for unit tests.
 source deactivate
-conda env list | grep -q $name && conda env remove -y -n $name
-conda create -y -n $name --channel bioconda python=${PY_VERSION} \
-    --file "requirements.txt" \
-    --file "test-requirements.txt" \
-    --file "optional-requirements.txt"
-
-source activate $name
-
-log "install pybedtools from setup.py in develop mode to trigger re-cythonizing"
-python setup.py develop
-
-log "run tests"
-nosetests
-(cd docs && make clean && make doctest)
+no_cy="pbtpy${PY_VERSION}_conda_no_cython"
+if ! conda env list | grep -q $no_cy; then
+    log "creating environment"
+
+    # pysam not available from bioconda for py37 so remove it from
+    # requirements.
+    TMPREQS=$(tempfile)
+    grep -v pysam requirements.txt > $TMPREQS
+    if [[ "$PY_VERSION" == "3.7" ]]; then
+        REQS=$TMPREQS
+    else
+        REQS=requirements.txt
+    fi
+
+    conda create -n $no_cy -y \
+        --channel conda-forge \
+        --channel bioconda \
+        python=${PY_VERSION} \
+        --file $REQS \
+        --file test-requirements.txt \
+        --file optional-requirements.txt
+else
+    echo "Using existing environment '${no_cy}'"
+fi
+source activate $no_cy
+
+log "unpacking source package and install with pip install -e into $no_cy env"
+mkdir -p /tmp/pybedtools-uncompressed
+cd /tmp/pybedtools-uncompressed
+tar -xf $TMP/dist/pybedtools-*.tar.gz
+cd pybedtools-*
+pip install -e .
+
+log "Unit tests"
+pytest -v --doctest-modules
+
+# ----------------------------------------------------------------------------
+# sphinx doctests
+# ----------------------------------------------------------------------------
+# Since the docs aren't included in the MANIFEST and therefore aren't included
+# in the source distribution, we copy them over from the repo we checked out.
+log "copying over docs directory from repo"
+cp -r $TMP/docs .
+
+log "sphinx doctests"
+(cd docs && make clean doctest)

debian/changelog

+python-pybedtools (0.8.0-1) unstable; urgency=medium
+
+  * New upstream version.
+
+  * Standards-Version: 4.3.0
+
+ -- Steffen Moeller <moeller@debian.org>  Thu, 17 Jan 2019 17:39:31 +0100
+
 python-pybedtools (0.7.10-2.1) REMOVED; urgency=medium
 
   * Removed from unstable and testing, see

debian/control

@@ -7,16 +7,6 @@ Priority: optional
 Build-Depends: debhelper (>= 10),
                dh-python,
                bedtools,
-               python-all-dev,
-               python-setuptools,
-               python-pysam (>= 0.8.1),
-               python-matplotlib,
-               python-nose,
-               python-numpy,
-               python-numpydoc,
-               python-pandas,
-               python-yaml,
-               python-tk,
                python3-all-dev,
                python3-setuptools,
                python3-pysam,
@@ -28,14 +18,25 @@ Build-Depends: debhelper (>= 10),
                python3-yaml,
                python3-tk,
                python3-sphinx,	
-               cython,
                r-base-core,
                zlib1g-dev
-Standards-Version: 4.1.5
+Standards-Version: 4.3.0
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/python-pybedtools.git
 Vcs-Git: https://anonscm.debian.org/git/debian-med/python-pybedtools.git
 Homepage: https://daler.github.io/pybedtools/
 
+# cython,
+# python-all-dev,
+# python-setuptools,
+# python-pysam (>= 0.8.1),
+# python-matplotlib,
+# python-nose,
+# python-numpy,
+# python-numpydoc,
+# python-pandas,
+# python-yaml,
+# python-tk,
+
 Package: python-pybedtools
 Architecture: any
 Depends: ${python:Depends},

debian/patches/define_filenotfounderror_python2.patch

@@ -3,11 +3,13 @@ Last-Update: Wed, 13 July 2018 11:36:44 +0300
 Description: Define FileNotFoundError as OSError for python 2
 
 
---- a/pybedtools/test/test1.py
-+++ b/pybedtools/test/test1.py
-@@ -20,6 +20,12 @@
- import warnings
- 
+Index: pybedtools-0.8.0/pybedtools/test/test1.py
+===================================================================
+--- pybedtools-0.8.0.orig/pybedtools/test/test1.py
++++ pybedtools-0.8.0/pybedtools/test/test1.py
+@@ -28,6 +28,12 @@ def teardown_module():
+         os.system('rm -r %s' % tempdir)
+     pybedtools.cleanup()
  
 +try:
 +    FileNotFoundError
@@ -18,9 +20,11 @@ Description: Define FileNotFoundError as OSError for python 2
  
  def fix(x):
      """
---- a/pybedtools/contrib/bigwig.py
-+++ b/pybedtools/contrib/bigwig.py
-@@ -6,6 +6,13 @@
+Index: pybedtools-0.8.0/pybedtools/contrib/bigwig.py
+===================================================================
+--- pybedtools-0.8.0.orig/pybedtools/contrib/bigwig.py
++++ pybedtools-0.8.0/pybedtools/contrib/bigwig.py
+@@ -6,6 +6,13 @@ import os
  import subprocess
  
  

debian/patches/series

 spelling
-enable-package-data
-disable-write-version
-disable-test-156
-rename-scripts
-c8dff864dbc942bb7adb3e719b0702f7e3989d36.patch
+#enable-package-data
+#disable-write-version
+#disable-test-156
+#rename-scripts
+#c8dff864dbc942bb7adb3e719b0702f7e3989d36.patch
 define_filenotfounderror_python2.patch
 remove_badges_from_documentation.patch

debian/rules

@@ -11,11 +11,11 @@ export PYBUILD_BEFORE_TEST=cp {dir}/debian/mpl-expected.png {build_dir}/pybedtoo
 export HOME=$(shell echo $$PWD"/fakehome")
 
 %:
-	dh $@ --with python2,python3,sphinxdoc --buildsystem=pybuild
+	dh $@ --with python3,sphinxdoc --buildsystem=pybuild
 
 override_dh_auto_build:
+	python3 setup.py cythonize
 	dh_auto_build
-	python  setup.py develop --user
 	python3 setup.py develop --user
 	python3 setup.py build_sphinx
 
@@ -27,6 +27,16 @@ override_dh_auto_install:
 	rm -fr debian/python-pybedtools/usr/bin
 	rm -fr debian/python3-pybedtools/usr/bin
 
+override_dh_auto_test:
+	@echo
+	@echo *** NOT TESTING ***
+	@echo
+
 override_dh_auto_clean:
-	dh_auto_clean
-	rm -rf fakehome .eggs
+	rm -rf fakehome .eggs .pybuild
+	rm -rf debian/python3-pybedtools
+	rm -rf pybedtools.egg-info
+	find pybedtools -name "*.so" -delete
+	rm -rf pybedtools/cbedtools.cpp pybedtools/featurefuncs.cpp
+	find docs/source/autodocs/ -name "*.rst" | grep -v "pybedtools.contrib.plotting.Track" | xargs -r /bin/rm
+	#dh_auto_clean

dev-requirements.txt

 cython
 matplotlib
-nose
 numpydoc
 pandas
 pyyaml

docs/source/3-brief-examples.rst

@@ -85,14 +85,6 @@ features of :mod:`pybedtools` such as:
 * streaming (for more, see :ref:`BedTools as iterators`)
 * ability to use parallel processing
 
-The first listing has many explanatory comments, and the second listing shows
-the same code with no comments to give more of a feel for :mod:`pybedtools`.
-
 .. literalinclude:: example_3
 
-Here's the same code but with no comments:
-
-.. literalinclude:: example_3_no_comments
-
-For more on using :mod:`pybedtools`, continue on to the :ref:`tutorial` . .
-.
+For more on using :mod:`pybedtools`, continue on to the :ref:`tutorial` . .  .

docs/source/autodoc_source.rst

@@ -324,17 +324,6 @@ Working with bigBed files
     pybedtools.contrib.bigbed.bigbed
     pybedtools.contrib.bigbed.bigbed_to_bed
 
-:class:`MultiClassifier`
-~~~~~~~~~~~~~~~~~~~~~~~~
-An example use-case of the :class:`MultiClassifier` class would be to determine the
-distribution of ChIP-seq peaks in introns/exons/intergenic space.
-
-.. autosummary::
-    :toctree: autodocs
-
-    pybedtools.contrib.MultiClassifier
-    pybedtools.contrib.MultiClassifier.classify
-    pybedtools.contrib.MultiClassifier.print_table
 
 :class:`IntersectionMatrix`
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~

docs/source/autodocs/pybedtools.contrib.plotting.Track.rst

@@ -30,7 +30,7 @@ pybedtools.contrib.plotting.Track
       ~Track.get_alpha
       ~Track.get_animated
       ~Track.get_array
-      ~Track.get_axes
+      ~Track.get_capstyle
       ~Track.get_children
       ~Track.get_clim
       ~Track.get_clip_box
@@ -49,6 +49,7 @@ pybedtools.contrib.plotting.Track
       ~Track.get_fill
       ~Track.get_gid
       ~Track.get_hatch
+      ~Track.get_joinstyle
       ~Track.get_label
       ~Track.get_linestyle
       ~Track.get_linestyles
@@ -91,7 +92,7 @@ pybedtools.contrib.plotting.Track
       ~Track.set_antialiased
       ~Track.set_antialiaseds
       ~Track.set_array
-      ~Track.set_axes
+      ~Track.set_capstyle
       ~Track.set_clim
       ~Track.set_clip_box
       ~Track.set_clip_on
@@ -107,6 +108,7 @@ pybedtools.contrib.plotting.Track
       ~Track.set_figure
       ~Track.set_gid
       ~Track.set_hatch
+      ~Track.set_joinstyle
       ~Track.set_label
       ~Track.set_linestyle
       ~Track.set_linestyles

docs/source/changes.rst

@@ -2,6 +2,75 @@
 
 Changelog
 =========
+
+Changes in v0.8.0
+-----------------
+This version further improves testing, improves the way C++ files are included
+in the package, and fixes many long-standing bugs.
+
+* Using pytest framework rather than nose for testing
+* Updated `setup.py` to be more robust and to more clearly separate
+  "cythonization" into .cpp files
+* Updated test harness for testing in independent conda environments
+* All issue tests go in their own test module
+* Included Python 3.7 tests (note that at the time of this writing, pysam is
+  not yet available on bioconda so that dependency is pip-installed in the
+  test) (`#254 <https://github.com/daler/pybedtools/issues/254>`_)
+* Updated tests to reflect BEDTool 2.27.1 output (`#260
+  <https://github.com/daler/pybedtools/issues/260>`_`#261
+  <https://github.com/daler/pybedtools/issues/261>`_)
+* Removed the `contrib.classifier` module, which has been unsupported for
+  a while.
+* More informative error messages for UCSC tools if they're missing (`#227
+  <https://github.com/daler/pybedtools/issues/227>`_)
+* BedTool objects that are the result of operations that create files that are
+  not BED/GTF/GFF/BAM can be more easily converted to pandas.DataFrame with
+  `disable_auto_names=True` arg to `BedTool.to_dataframe()` (`#258
+  <https://github.com/daler/pybedtools/issues/258>`_)
+* Added aliases to existing methods to match current BEDTools commands, e.g.
+  the `BedTool.nucleotide_content` method can now also be called using
+  `BedTool.nuc` which is consistent with the `bedtools nuc` command line name.
+* New wrapper for `bedtools split`. The wrapper method is called `splitbed` to
+  maintain backwards compatibility because `pybedtools.BedTool` objects have
+  long had a `split` method that splits intervals based on a custom function.
+* New wrapper for `bedtools spacing`.
+* `BedTool.from_dataframe` handles NaN in dataframes by replacing with `"."`,
+  and is more explicit about kwargs that are passed to `pandas.DataFrame`
+  (`#257 <https://github.com/daler/pybedtools/issues/257>`_)
+* Raise FileNotFoundError when on Python 3 (thanks Gosuke Shibahara, (`#255
+  <https://github.com/daler/pybedtools/issues/255>`_)
+* Relocated BEDTools header and .cpp files to the `pybedtools/include`
+  directory, so they can more easily be linked to from external packages
+  (`#253 <https://github.com/daler/pybedtools/issues/253>`_)
+* Add test for (`#118 <https://github.com/daler/pybedtools/issues/118>`_)
+* `BedTool.tabix_contigs` will list the sequence names indexed by tabix
+  (`#180 <https://github.com/daler/pybedtools/issues/180>`_)
+* `BedTool.tabix_intervals` will return an empty generator if the coordinates
+  provided are not indexed, unless `check_coordinates=True` in which case the
+  previous behavior of raising a ValueError is triggered (`#181
+  <https://github.com/daler/pybedtools/issues/181>`_)
+* Bugfix: Avoid "ResourceWarning: unclosed file" in `helpers.isBGZIP` (thanks
+  Stephen Bush)
+* Bugfix: Interval objects created directly no longer have their filetype set
+  to None (`#217 <https://github.com/daler/pybedtools/issues/217>`_)
+* Bugfix: Fixed the ability to set paths and reload module afterwards (`#218
+  <https://github.com/daler/pybedtools/issues/218>`_, `#220
+  <https://github.com/daler/pybedtools/issues/220>`_, `#222
+  <https://github.com/daler/pybedtools/issues/222>`_)
+* Bugfix: `BedTool.head()` no longer uses an IntervalIterator (which would
+  check to make sure lines are valid BED/GTF/GFF/BAM/SAM). Instead, it simply
+  prints the first lines of the underlying file.
+* Bugfix: functions passed to `BedTool.filter` and `BedTool.each` no longer
+  silently pass ValueErrors (`#231
+  <https://github.com/daler/pybedtools/issues/231>`_)
+* Bugfix: Fixed IndexError in IntervalIterator if there was an empty line (`#233
+  <https://github.com/daler/pybedtools/issues/233>`_)
+* Bugfix: Add additional constraint to SAM file detection to avoid incorrectly
+  detecting a BED file as SAM (`#246
+  <https://github.com/daler/pybedtools/issues/246>`_)
+* Bugfix: accessing Interval.fields after accessing Interval.attrs no longer
+  raises ValueError (`#246 <https://github.com/daler/pybedtools/issues/246>`_)
+
 Changes in v0.7.10
 ------------------
 Various bug fixes and some minor feature additions:

docs/source/example_3

-import sys
-import multiprocessing
-import pybedtools
-
-# get example GFF and BAM filenames
-gff = pybedtools.example_filename('gdc.gff')
-bam = pybedtools.example_filename('gdc.bam')
-
-# Some GFF files have invalid entries -- like chromosomes with negative coords
-# or features of length = 0.  This line removes them and saves the result in a
-# tempfile
-g = pybedtools.BedTool(gff).remove_invalid().saveas()
-
-
-# Next, we create a function to pass only features for a particular
-# featuretype.  This is similar to a "grep" operation when applied to every
-# feature in a BedTool
-def featuretype_filter(feature, featuretype):
-    if feature[2] == featuretype:
-        return True
-    return False
-
-
-# This function will eventually be run in parallel, applying the filter above
-# to several different BedTools simultaneously
-def subset_featuretypes(featuretype):
-    result = g.filter(featuretype_filter, featuretype).saveas()
-    return pybedtools.BedTool(result.fn)
-
-
-# This function performs the intersection of a BAM file with a GFF file and
-# returns the total number of hits.  It will eventually be run in parallel.
-def count_reads_in_features(features_fn):
-    """
-    Callback function to count reads in features
-    """
-    # BAM files are auto-detected; no need for an `abam` argument.  Here we
-    # construct a new BedTool out of the BAM file and intersect it with the
-    # features filename.
-
-    # We use stream=True so that no intermediate tempfile is
-    # created, and bed=True so that the .count() method can iterate through the
-    # resulting streamed BedTool.
-    return pybedtools.BedTool(bam).intersect(
-                             b=features_fn,
-                             stream=True).count()
-
-
-# Set up a pool of workers for parallel processing
-pool = multiprocessing.Pool()
-
-# Create separate files for introns and exons, using the function we defined
-# above
-featuretypes = ('intron', 'exon')
-introns, exons = pool.map(subset_featuretypes, featuretypes)
-
-# Perform some genome algebra to get unique and shared intron/exon regions.
-# Here we keep only the filename of the results, which is safer than an entire
-# BedTool for passing around in parallel computations.
-exon_only = exons.subtract(introns).merge().remove_invalid().saveas().fn
-intron_only = introns.subtract(exons).merge().remove_invalid().saveas().fn
-intron_and_exon = exons.intersect(introns).merge().remove_invalid().saveas().fn
-
-# Do intersections with BAM file in parallel, using the other function we
-# defined above
-features = (exon_only, intron_only, intron_and_exon)
-results = pool.map(count_reads_in_features, features)
-
-# Print the results
-labels = ('      exon only:',
-          '    intron only:',
-          'intron and exon:')
-
-for label, reads in zip(labels, results):
-    sys.stdout.write('%s %s\n' % (label, reads))

docs/source/example_3

+../../pybedtools/scripts/intron_exon_reads.py
\ No newline at end of file

docs/source/main.rst

@@ -9,17 +9,17 @@ installed.
 
 .. _condainstall:
 
-Quick install via `conda`
-~~~~~~~~~~~~~~~~~~~~~~~~~
-If you're usng the `Anaconda Python distribution
-<http://continuum.io/downloads>`_ on Linux, then the following will install
-:mod:`pybedtools`::
+Install via `conda`
+~~~~~~~~~~~~~~~~~~~
+This is by far the easiest option.  If you're usng the `Anaconda Python
+distribution <http://continuum.io/downloads>`_ on Linux, then the following
+will install :mod:`pybedtools`::
 
-    conda install -c bioconda pybedtools
+    conda install --channel conda-forge --channel bioconda pybedtools
 
 You can also install Tabix and BEDTools via conda::
 
-    conda install -c bioconda bedtools htslib
+    conda install --channel conda-forge --channel bioconda bedtools htslib
 
 Otherwise, read on for installation on other platforms and in other
 environments.
@@ -39,13 +39,11 @@ Required
 
 
 :A C/C++ compiler:
-    * **Windows:** Use Cygwin, http://www.cygwin.com.  It is probably easiest to select
-      all of the 'Devel" group items to be installed.  In addition, ensure the
-      `zlib` items are selected for installation as well (using the search
-      funciton in the Cygwin install program).
     * **OSX:** Install Xcode from http://developer.apple.com/xcode/
     * **Linux:** `gcc`, usually already installed; on Ubuntu, install with `sudo apt-get install
       build-essentials`
+    * **Windows:** may work with conda compliers or Cygwin but this is
+      untested. Windows is not supported.
 
 Optional
 ++++++++
@@ -62,14 +60,7 @@ Installing :mod:`pybedtools`
 Install latest release via `conda` (recommended)
 ++++++++++++++++++++++++++++++++++++++++++++++++
 
-Use the Anaconda channel `daler`::
-
-    conda install -c daler pybedtools
-
-This example installs :mod:`pybedtools` and BEDTools into an isolated
-environment called `myenv` running Python 3::
-
-    conda create -n myenv -c daler pybedtools bedtools python=3
+See :ref:`condainstall` section above.
 
 
 Install latest release using `pip`
@@ -90,13 +81,36 @@ Assumptions:
 1. `git` is installed
 2. Cython is installed (`conda install cython` or `pip install cython`)
 
+
+The following commands will clone the repository
 .. code-block:: bash
 
     git clone https://github.com/daler/pybedtools.git
     cd pybedtools
-    git pull
+
+The only time the C++ files will be rebuilt from Cython .pyx source is if the
+`cythonize` subcommand is used. To rebuild the C++ files using Cython, run:
+
+.. code-block:: bash
+
+    python setup.py cythonize
+
+To install in develop mode, where changes to Python files will be picked up
+without having to re-install, use:
+
+.. code-block:: bash
+
     python setup.py develop
 
+The above will not update when the .pyx files are updated, so if the Cython
+source files have been changed, run:
+
+.. code-block:: bash
+
+    python setup.py cythonize develop
+
+
+See `python setup.py --usage` for more information.
 
 
 Quick test
@@ -131,17 +145,19 @@ e.g., by running::
 
 Test current installation
 ~~~~~~~~~~~~~~~~~~~~~~~~~
-Testing the "current installation" means testing the installation into the
-current environment, whether this is the system-wide Python, a virtualenv, or
-a conda environment.  It requires some additional packages to be installed::
+To test within the existing installation, install the additional packages for
+testing::
 
-    pip install -r dev-requirements.txt
+    conda install --channel conda-forge --channel bioconda \
+      --file requirements.txt \
+      --file test-requirements.txt \
+      --file optional-requirements.txt
 
-Run unit tests::
+Then run unit tests along with module doctests::
 
-    nosetests -v
+    pytest --doctest-modules
 
-Run doctests::
+Finally, run sphinx doctests::
 
     (cd docs && make doctest)
 
@@ -159,20 +175,6 @@ To run tests under Python 3::
 
     ./condatest.sh 3
 
-Test within isolated Docker containers
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-This assumes that `Docker <https://www.docker.com/>`_ is installed.
-
-The following command will build Docker two containers -- one for Python 2 and
-one for Python 3 -- starting with the base Ubuntu 14.04 container. The first
-time the containers are built it will take some time, but they are cached so
-subsequent tests will run quickly. Within each of these containers, unit tests
-and doctests are run::
-
-    (cd docker && ./full-test.sh)
-
-
 Compile docs
 ~~~~~~~~~~~~
 To compile the docs, from the top-level `pybedtools` directory::

docs/source/topical-random.rst

@@ -68,7 +68,7 @@ it to a list in order to look at it:
     100
 
     >>> print(results[:10])
-    [1, 1, 2, 2, 1, 2, 1, 0, 2, 3]
+    [0, 3, 1, 1, 2, 2, 2, 1, 4, 2]
 
 Running thousands of iterations on files with many features will of course
 result in more complex results.  We could then take these results and plot
@@ -149,7 +149,7 @@ For example:
     actual: 3
     median randomized: 2.0
     normalized: 1.5
-    percentile: 92.0
+    percentile: 93.5
 
 Contributions toward improving this code or implementing other methods of
 statistical testing are very welcome!

docs/source/topical-saving.rst

@@ -81,21 +81,18 @@ https://github.com/arq5x/bedtools2/issues/436 for details).
 
     >>> # bedtools v2.26.0
     >>> print(open(d.fn).read())
-    30
-
-    >>> # bedtools != v2.26.0
-    >>> # UTR	0
-    >>> # CDS	2
-    >>> # intron	4
-    >>> # CDS	0
-    >>> # UTR	1
-    >>> # exon	3
-    >>> # mRNA	7
-    >>> # CDS	2
-    >>> # exon	2
-    >>> # tRNA	2
-    >>> # gene	7
-    >>> # <BLANKLINE>
+    UTR	0
+    CDS	2
+    intron	4
+    CDS	0
+    UTR	1
+    exon	3
+    mRNA	7
+    CDS	2
+    exon	2
+    tRNA	2
+    gene	7
+    <BLANKLINE>
 
 
 Trying to iterate over `d` (`[i for i in d]`) or save it (`d.saveas()`) raises

optional-requirements.txt

 bedtools
 matplotlib
-htslib <1.4
 ucsc-bigwigtobedgraph
 ucsc-bedgraphtobigwig
 ucsc-wigtobigwig