Merge pull request #132 from hammerlab/update-travis-config

Copied new travis config from Varcode

.travis.yml

@@ -3,24 +3,38 @@ language: python
 python:
   - "2.7"
   - "3.4"
-# Setup anaconda; see https://gist.github.com/dan-blanchard/7045057
 before_install:
-  - wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O miniconda.sh
-  - chmod +x miniconda.sh
-  - ./miniconda.sh -b
-  - export PATH=/home/travis/miniconda/bin:$PATH
-  - conda update --yes conda
+  # Commands below copied from: http://conda.pydata.org/docs/travis.html
+  # We do this conditionally because it saves us some downloading if the
+  # version is the same.
+  - if [[ "$TRAVIS_PYTHON_VERSION" == "2.7" ]]; then
+      wget https://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O miniconda.sh;
+    else
+      wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
+    fi
+  - bash miniconda.sh -b -p $HOME/miniconda
+  - export PATH="$HOME/miniconda/bin:$PATH"
+  # reset the shell's lookup table for program name to path mappings
+  - hash -r
+  - conda config --set always_yes yes --set changeps1 no
+  - conda update -q conda
+  # Useful for debugging any issues with conda
+  - conda info -a
 addons:
   apt:
     packages:
+    # install pandoc for use with pypandoc for converting the README
+    # from markdown to RST
     - pandoc
 install:
-  - conda install --yes python=$TRAVIS_PYTHON_VERSION numpy scipy nose pandas matplotlib
+  - >
+      conda create -q -n test-environment python=$TRAVIS_PYTHON_VERSION
+      numpy scipy nose pandas matplotlib
+  - source activate test-environment
+  - pip install pypandoc
   - pip install -r requirements.txt
   - pip install .
   - pip install coveralls
-  # required for generating reStructuredText README
-  - pip install pypandoc
 script:
   # human releases
   - pyensembl install --release 54 --species human

lint.sh

@@ -1,9 +1,15 @@
 #!/bin/bash
 set -o errexit
 
+
+# disabling several categories of errors due to false positives in pylint,
+# see these issues:
+# - https://bitbucket.org/logilab/pylint/issues/701/false-positives-with-not-an-iterable-and
+# - https://bitbucket.org/logilab/pylint/issues/58
+
 find . -name '*.py' \
   | xargs pylint \
   --errors-only \
-  --disable=print-statement
+  --disable=print-statement,unsubscriptable-object,not-an-iterable,no-member
 
 echo 'Passes pylint check'

pyensembl/ensembl_url_templates.py

@@ -24,7 +24,7 @@
 from __future__ import print_function, division, absolute_import
 from os.path import join
 
-from six.moves.urllib_parse import urljoin
+from six.moves import urllib_parse
 
 from .species import Species, find_species_by_name
 from .ensembl_release_versions import check_release_number
@@ -36,6 +36,7 @@
 # GTF annotation files: /pub/release-78/gtf/homo_sapiens/
 SPECIES_SUBDIR_TEMPLATE = "/pub/release-%(release)d/%(filetype)s/%(species)s/"
 
+
 def _species_subdir(
         ensembl_release,
         species="homo_sapiens",
@@ -51,6 +52,7 @@ def _species_subdir(
         "species": species,
     }
 
+
 def _normalize_release_properties(ensembl_release, species):
     """
     Make sure a given release is valid, normalize it to be an integer,
@@ -65,6 +67,7 @@ def _normalize_release_properties(ensembl_release, species):
 # GTF annotation file example: Homo_sapiens.GTCh38.gtf.gz
 GTF_FILENAME_TEMPLATE = "%(Species)s.%(reference)s.%(release)d.gtf.gz"
 
+
 def make_gtf_url(ensembl_release, species, server=ENSEMBL_FTP_SERVER):
     """
     Returns a URL and a filename, which can be joined together.
@@ -78,7 +81,7 @@ def make_gtf_url(ensembl_release, species, server=ENSEMBL_FTP_SERVER):
         filetype="gtf",
         server=server)
 
-    url_subdir = urljoin(server, subdir)
+    url_subdir = urllib_parse.urljoin(server, subdir)
 
     filename = GTF_FILENAME_TEMPLATE % {
         "Species": species.capitalize(),
@@ -91,6 +94,7 @@ def make_gtf_url(ensembl_release, species, server=ENSEMBL_FTP_SERVER):
 FASTA_DNA_CHROMOSOME_FILENAME_TEMPLATE = \
     "%(Species)s.%(reference)s.%(release)d.%(sequence_type)s.chromosome.%(contig)s.fa.gz"
 
+
 def make_fasta_dna_url(
         ensembl_release,
         species,
@@ -107,7 +111,7 @@ def make_fasta_dna_url(
         species=species,
         filetype="fasta",
         server=server,)
-    server_subdir = urljoin(server, subdir)
+    server_subdir = urllib_parse.urljoin(server, subdir)
 
     server_sequence_subdir = join(server_subdir, "dna")
     filename = FASTA_DNA_CHROMOSOME_FILENAME_TEMPLATE % {
@@ -130,6 +134,7 @@ def make_fasta_dna_url(
 NEW_FASTA_FILENAME_TEMPLATE = \
     "%(Species)s.%(reference)s.%(sequence_type)s.all.fa.gz"
 
+
 def make_fasta_url(
         ensembl_release,
         species,
@@ -150,7 +155,7 @@ def make_fasta_url(
         filetype="fasta",
         server=server)
 
-    server_subdir = urljoin(server, subdir)
+    server_subdir = urllib_parse.urljoin(server, subdir)
     server_sequence_subdir = join(server_subdir, sequence_type)
     if ensembl_release <= 75:
         filename = OLD_FASTA_FILENAME_TEMPLATE % {