070 python3

.dockerignore

@@ -3,3 +3,6 @@ tests/*/output/*
 tests/*/temp.fasta
 tests/hrefpkg-build/hrefpkg
 *.ssi
+*-env
+deenurp.egg-info
+build

.travis.yml

@@ -1,6 +1,7 @@
-sudo: false
 language: python
-python: 2.7
+python:
+  - 3.8
+  - 3.9
 
 cache:
   # must specify pip dir
@@ -11,13 +12,6 @@ cache:
 
 env:
   global:
-    # These two environment variables could be set by Travis itself, or Travis
-    # could configure itself in /etc/, ~/, or inside of the virtual
-    # environments. In any case if these two values get configured then end
-    # users only need to enable the pip cache and manually run pip wheel before
-    # running pip install.
-    - PIP_WHEEL_DIR=$HOME/.cache/pip/wheels
-    - PIP_FIND_LINKS=file://$HOME/.cache/pip/wheels
     - VIRTUAL_ENV=deenurp-env
 
 addons:
@@ -32,7 +26,7 @@ install:
   - "bin/bootstrap.sh $VIRTUAL_ENV"
 
 script:
-  - python setup.py test
+  - python3 -m deenurp.test
   - tests/run.sh
 
 notifications:

CHANGES.rst

@@ -2,6 +2,11 @@
  Changes for deenurp
 =====================
 
+0.3.0
+=====
+
+* Python 3 support and other dependency upgrades and bug fixes
+
 0.2.7
 =====
 

Dockerfile

@@ -1,48 +1,34 @@
-FROM ubuntu:18.04
-MAINTAINER [email protected]
+FROM python:3.9
+LABEL org.opencontainers.image.authors="[email protected],[email protected],[email protected]"
 
 # Install prerequisites
-RUN apt-get update && apt-get install --assume-yes --no-install-recommends \
-    build-essential \
-    gfortran \
-    git \
-    liblapack-dev \
-    libopenblas-dev \
-    make \
-    python-dev \
-    python-pip \
-    python2.7 \
-    unzip \
-    wget
+RUN apt-get update && \
+apt-get upgrade --assume-yes && \
+apt-get install --assume-yes --no-install-recommends git wget
 
 # Add files
 RUN mkdir /usr/local/share/deenurp/
 ADD bin /usr/local/share/deenurp/bin
 ADD tests /usr/local/share/deenurp/tests
 ADD deenurp /usr/local/share/deenurp/deenurp
-ADD deenurp.py setup.py requirements.txt MANIFEST.in /usr/local/share/deenurp/
+ADD deenurp.py setup.py requirements.txt /usr/local/share/deenurp/
 
 # Install deenurp and dependencies
 RUN cd /usr/local/share/deenurp/ && \
-    PYTHON=/usr/bin/python2.7 \
+    PYTHON=/usr/local/bin/python3 \
     DEENURP=/usr/local/share/deenurp/ \
     bin/bootstrap.sh /usr/local/
 
 # clean up sources apt packages
 RUN rm -rf /var/lib/apt/lists/* && \
     rm -rf /root/.cache/pip && \
     rm -rf /usr/local/share/deenurp/src && \
-    apt-get purge -y --auto-remove \
-      build-essential \
-      unzip \
-      git \
-      python-dev \
-      make
+    apt-get purge -y --auto-remove git
 
 # create some mount points
 RUN mkdir -p /app /fh /mnt /run/shm
 
 # Run tests
-RUN python -m deenurp.test && \
+RUN python3 -m deenurp.test && \
     cd /usr/local/share/deenurp && \
     tests/run.sh

README.rst

@@ -12,9 +12,13 @@ The Easy Way
 
 * confirm availability of necessary libraries to compile dependencies
   (on Ubuntu: ``sudo apt-get install gfortran libopenblas-dev liblapack-dev``)
-* Install Python 2.7
-* run `bin/bootstrap.sh`
-* run `source bin-env/bin/activate`
+* Install Python >= 3.8 or Python 3 Virtual Environment 
+::
+
+  % python3 -m venv bin-env
+  % source bin-env/bin/activate
+  % bin/bootstrap.sh
+
 
 the `deenurp` executable should now be on your `$PATH`
 
@@ -25,7 +29,7 @@ See required system libraries above.
 
 First, install binary dependencies:
 
-* Python 2.7
+* Python 3
 
     - pip, for installing python dependencies (http://www.pip-installer.org/)
     - Python packages:
@@ -46,6 +50,12 @@ Finally, install::
 
     python setup.py install
 
+The Docker Way
+==============
+
+Deenurp can be run from a Docker image which can be built locally from the Dockerfile
+or pulled ``docker pull nghoffman/deenurp:v0.3.0``
+
 De-novo reference set creation
 ==============================
 

bin/bootstrap.sh

@@ -14,23 +14,9 @@ set -e
 # installs deenurp and dependencies to $VIRTUAL_ENV if defined;
 # otherwise creates a virtualenv locally.
 
-# Will attempt to install python packages from wheels if $PIP_FIND_LINKS is defined
-# and pip --use-wheel is specified
-
-# set $PIP_WHEEL_DIR and $PIP_FIND_LINKS in the parent environment if
-# desired
-
-# Will attempt to create wheels if $PIP_WHEEL_DIR is defined
-# see https://pip.pypa.io/en/latest/user_guide.html#environment-variables
-
-
 mkdir -p src
 SRCDIR=$(readlink -f src)
 
-if [[ -n "$PIP_WHEEL_DIR" ]]; then
-    mkdir -p "$PIP_WHEEL_DIR"
-fi
-
 srcdir(){
     tar -tf $1 | head -1
 }
@@ -44,7 +30,7 @@ else
 fi
 
 if [[ -z $PYTHON ]]; then
-    PYTHON=$(which python2)
+    PYTHON=$(which python3)
 fi
 
 # Defines the default source directory for deenurp as the parent of
@@ -55,65 +41,24 @@ fi
 
 VENV_VERSION=15.1.0
 PPLACER_BUILD=1.1.alpha19
-INFERNAL_VERSION=1.1.2
+INFERNAL_VERSION=1.1.4
 RAXML_VERSION=8.0.5
 MUSCLE_VERSION=3.8.31
 VSEARCH_VERSION=2.6.2
 
-check_version(){
-    # usage: check_version module version-string
-    "$PYTHON" <<EOF 2> /dev/null
-import $1
-from distutils.version import LooseVersion
-assert LooseVersion($1.__version__) >= LooseVersion("$2")
-EOF
-}
-
-# create virtualenv if necessary, downloading source if available
-# version is not up to date.
-VENV_URL="https://github.com/pypa/virtualenv/archive/${VENV_VERSION}"
+# create virtualenv
 if [[ ! -f "${venv:?}/bin/activate" ]]; then
-    # if the system virtualenv is up to date, use it
-    if check_version virtualenv $VENV_VERSION; then
-      echo "using $(which virtualenv) (version $(virtualenv --version))"
-	    virtualenv "$venv"
-    else
-	echo "downloading virtualenv version $VENV_VERSION"
-	if [[ ! -f src/virtualenv-${VENV_VERSION}/virtualenv.py ]]; then
-	    mkdir -p src
-	    (cd src && \
-		wget --quiet -nc ${VENV_URL}.tar.gz && \
-		tar -xf ${VENV_VERSION}.tar.gz)
-	fi
-	"$PYTHON" src/virtualenv-${VENV_VERSION}/virtualenv.py "$venv"
-    fi
+    $PYTHON -m venv $venv
 else
     echo "virtualenv $venv already exists"
 fi
 
 source $venv/bin/activate
-
 # full path; set by activate
 venv=$VIRTUAL_ENV
-
-# Preserve the order of installation. The requirements are sorted so
-# that secondary (and higher-order) dependencies appear first. See
-# bin/pipdeptree2requirements.py. We use --no-deps to prevent various
-# packages from being repeatedly installed, uninstalled, reinstalled,
-# etc. Also, enfoprcing the order of installation ensures that
-# install-time dependencies are met (`pip install -r requirements.txt`
-# fails due to a install-time dependency that cogent has for numpy)
-pip2 install -U pip
-
-# install pysqlite and updated sqlite3 libraries
-wget --quiet -O - \
-     https://raw.githubusercontent.com/fhcrc/taxtastic/master/dev/install_pysqlite.sh | bash
-
-while read pkg; do
-    pip2 install "$pkg" --no-deps --upgrade
-done < <(/bin/grep -v -E '^#|^$' "$DEENURP/requirements.txt")
-
-pip2 install "$DEENURP"
+pip install -U pip wheel
+pip install -r requirements.txt
+pip install .
 
 # install pplacer and accompanying python scripts
 PPLACER_DIR=pplacer-Linux-v${PPLACER_BUILD}
@@ -128,11 +73,12 @@ if pplacer_is_installed; then
     $venv/bin/pplacer --version
 else
     mkdir -p src && \
-	(cd src && \
-	wget -nc --quiet https://github.com/matsen/pplacer/releases/download/v$PPLACER_BUILD/$PPLACER_ZIP && \
-	unzip -o $PPLACER_ZIP && \
-	cp $PPLACER_DIR/{pplacer,guppy,rppr} $venv/bin && \
-	pip2 install -U $PPLACER_DIR/scripts)
+	(cd src \
+	     && wget -nc --quiet https://github.com/matsen/pplacer/releases/download/v$PPLACER_BUILD/$PPLACER_ZIP \
+	     && unzip -o $PPLACER_ZIP \
+	     && cp $PPLACER_DIR/{pplacer,guppy,rppr} $venv/bin \
+	     # && pip2 install -U $PPLACER_DIR/scripts \
+	)
     # confirm that we have installed the requested build
     if ! pplacer_is_installed; then
 	echo -n "Error: you requested pplacer build $PPLACER_BUILD "
@@ -218,4 +164,3 @@ else
 	    cd muscle${MUSCLE_VERSION}/src && \
 	    ./mk && cp muscle $venv/bin)
 fi
-

bin/pipdeptree2requirements.py

@@ -21,5 +21,5 @@
 deps = set()
 for __, pkg in sorted(lines):
     if pkg not in deps:
-        print pkg
+        print(pkg)
         deps.add(pkg)

deenurp/__init__.py

@@ -24,7 +24,7 @@
 import os
 import pkgutil
 import sys
-import util
+from . import util
 
 log = logging.getLogger(__name__)
 
@@ -89,9 +89,8 @@ def setup_logging(namespace):
                   '%(funcName)s %(lineno)s %(message)s')
     datefmt = '%Y-%m-%d %H:%M:%S'
 
-    logging.basicConfig(stream=namespace.log, format=log_format,
-                        level=loglevel, log_format=log_format,
-                        datefmt=datefmt)
+    logging.basicConfig(
+        stream=namespace.log, format=log_format, level=loglevel, datefmt=datefmt)
 
 
 def parse_version(parser):
@@ -105,7 +104,7 @@ def parse_args(parser):
     parser.add_argument('-l', '--log',
                         metavar='FILE',
                         default=sys.stdout,
-                        type=util.file_opener('a', buffering=0),  # append
+                        type=util.file_opener('a'),  # append
                         help='Send logging to a file')
 
     parser.add_argument('-v', '--verbose',
@@ -128,7 +127,7 @@ def parse_subcommands(parser, argv):
     """
     Setup all sub-commands
     """
-    import subcommands
+    from . import subcommands
 
     subparsers = parser.add_subparsers(dest='subparser_name')
 
@@ -158,7 +157,7 @@ def parse_subcommands(parser, argv):
         try:
             imp = '{}.{}'.format(subcommands.__name__, name)
             mod = importlib.import_module(imp)
-        except Exception, e:
+        except Exception as e:
             log.error('error importing subcommand {}'.format(name))
             log.error(e)
             continue