run tests on Python 3.8

.travis.yml

@@ -12,6 +12,7 @@ matrix:
     - python: 2.7
     - python: 3.6
     - python: 3.7
+    - python: 3.8
       dist: xenial
       sudo: true
 

condatest.sh

@@ -57,14 +57,18 @@ 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.
+    # conflicts with pysam in bioconda for py37 or py38 so remove it from
+    # conda requirements; allow to install from pip
     TMPREQS=$(tempfile)
-    grep -v pysam requirements.txt > $TMPREQS
+    REQS=requirements.txt
     if [[ "$PY_VERSION" == "3.7" ]]; then
+        grep -v pysam requirements.txt > $TMPREQS
+        REQS=$TMPREQS
+    fi
+
+    if [[ "$PY_VERSION" == "3.8" ]]; then
+        grep -v pysam requirements.txt > $TMPREQS
         REQS=$TMPREQS
-    else
-        REQS=requirements.txt
     fi
 
     # genomepy>=0.8 not available for py27
@@ -76,7 +80,6 @@ if ! conda env list | grep -q $no_cy; then
         OPTREQS=optional-requirements.txt
     fi
 
-
     conda create -n $no_cy -y \
         --channel conda-forge \
         --channel bioconda \
@@ -100,8 +103,8 @@ pip install -e .
 # manipulation in test_helpers and test_issues. So run in its own separate
 # pytests process.
 log "Unit tests"
-pytest -v --doctest-modules --ignore pybedtools/test/test_genomepy_integration.py
-pytest -v pybedtools/test/test_genomepy_integration.py
+pytest -v --doctest-modules
+pytest -v pybedtools/test/genomepy_integration.py
 
 # ----------------------------------------------------------------------------
 # sphinx doctests

pybedtools/bedtool.py

@@ -2794,7 +2794,7 @@ def percentileofscore(a, score):
                 a_len = np.array(list(range(len(a)))) + 1.0
 
             a = np.sort(a)
-            idx = [a == score]
+            idx = tuple([a == score])
             pct = (np.mean(a_len[idx]) / n) * 100.0
             return pct
 

pybedtools/helpers.py

@@ -25,7 +25,7 @@
 from .logger import logger
 from .cbedtools import create_interval_from_list
 
-BUFSIZE = 1
+BUFSIZE = -1
 
 _tags = {}
 
@@ -744,7 +744,7 @@ def get_chromsizes_from_ucsc(
     d = {}
     try:
         p = subprocess.Popen(
-            cmds, stdout=subprocess.PIPE, stderr=subprocess.PIPE, bufsize=1
+            cmds, stdout=subprocess.PIPE, stderr=subprocess.PIPE, bufsize=BUFSIZE
         )
         stdout, stderr = p.communicate()
         if stderr:
@@ -770,7 +770,7 @@ def get_chromsizes_from_ucsc(
     try:
         cmds = [fetchchromsizes, genome]
         p = subprocess.Popen(
-            cmds, stdout=subprocess.PIPE, stderr=subprocess.PIPE, bufsize=1
+            cmds, stdout=subprocess.PIPE, stderr=subprocess.PIPE, bufsize=BUFSIZE
         )
         stdout, stderr = p.communicate()
         if stderr:

pybedtools/scripts/intron_exon_reads.py

@@ -80,31 +80,31 @@ def count_reads_in_features(features):
     g = pybedtools.BedTool(gff).remove_invalid().saveas()
 
     # Set up pool of workers
-    pool = multiprocessing.Pool(processes=args.processes)
+    with multiprocessing.Pool(processes=args.processes) as pool:
 
-    # Get separate files for introns and exons in parallel
-    featuretypes = ["intron", "exon"]
-    introns, exons = pool.map(subset_featuretypes, featuretypes)
+        # Get separate files for introns and exons in parallel
+        featuretypes = ["intron", "exon"]
+        introns, exons = pool.map(subset_featuretypes, featuretypes)
 
-    # Since `subset_featuretypes` returns filenames, we convert to BedTool objects
-    # to do intersections below.
-    introns = pybedtools.BedTool(introns)
-    exons = pybedtools.BedTool(exons)
+        # Since `subset_featuretypes` returns filenames, we convert to BedTool objects
+        # to do intersections below.
+        introns = pybedtools.BedTool(introns)
+        exons = pybedtools.BedTool(exons)
 
-    # Identify unique and shared regions using bedtools commands subtract, merge,
-    # and intersect.
-    exon_only = exons.subtract(introns).merge()
-    intron_only = introns.subtract(exons).merge()
-    intron_and_exon = exons.intersect(introns).merge()
+        # Identify unique and shared regions using bedtools commands subtract, merge,
+        # and intersect.
+        exon_only = exons.subtract(introns).merge()
+        intron_only = introns.subtract(exons).merge()
+        intron_and_exon = exons.intersect(introns).merge()
 
-    # Do intersections with BAM file in parallel. Note that we're passing filenames
-    # to multiprocessing.Pool rather than BedTool objects.
-    features = (exon_only.fn, intron_only.fn, intron_and_exon.fn)
+        # Do intersections with BAM file in parallel. Note that we're passing filenames
+        # to multiprocessing.Pool rather than BedTool objects.
+        features = (exon_only.fn, intron_only.fn, intron_and_exon.fn)
 
-    # Run count_reads_in_features in parallel over features
-    results = pool.map(count_reads_in_features, features)
+        # Run count_reads_in_features in parallel over features
+        results = pool.map(count_reads_in_features, features)
 
-    labels = ("exon_only", "intron_only", "intron_and_exon")
+        labels = ("exon_only", "intron_only", "intron_and_exon")
 
     for label, reads in zip(labels, results):
         print("{0}\t{1}".format(label, reads))

pybedtools/test/test_1.py

@@ -144,7 +144,7 @@ def test_tuple_creation():
 def test_tabix():
     try:
         a = pybedtools.example_bedtool("a.bed")
-        t = a.tabix()
+        t = a.tabix(force=True)
         assert t._tabixed()
         results = t.tabix_intervals("chr1:99-200")
         results = str(results)

pybedtools/test/test_issues.py

@@ -690,10 +690,11 @@ def test_issue_251():
 def test_issue_257():
     try:
         import pandas
+        import numpy as np
     except ImportError:
         pytest.mark.skip("Pandas not installed; skipping")
     df = pybedtools.example_bedtool("a.bed").to_dataframe()
-    df.iloc[-1, -3:] = pandas.np.nan
+    df.iloc[-1, -3:] = np.nan
     b = pybedtools.BedTool.from_dataframe(df)
     assert str(b) == fix(
         """

pybedtools/test/test_scripts.py

@@ -1,4 +1,5 @@
 import pybedtools
+import six
 from textwrap import dedent
 from .tfuncs import setup_module, teardown_module
 from pybedtools.scripts import annotate, venn_mpl, venn_gchart
@@ -188,7 +189,7 @@ def test_venn_gchart_main():
     sys.stderr = orig_stderr
     os.unlink("gcharttmp")
 
-
+@pytest.mark.skipif(six.PY2, reason="multiprocessing pool context manager does not work for py2")
 def test_intron_exon_reads():
     gff = pybedtools.example_filename("gdc.gff")
     bam = pybedtools.example_filename("gdc.bam")