.gitattributes

-qiime2/_version.py export-subst
+q2cli/_version.py export-subst

.gitignore

@@ -63,5 +63,3 @@ target/
 
 # vi
 .*.swp
-
-.DS_Store

.travis.yml

@@ -14,10 +14,12 @@ install:
   - wget -q https://raw.githubusercontent.com/qiime2/environment-files/master/latest/staging/qiime2-latest-py36-linux-conda.yml
   - conda env create -q -n test-env --file qiime2-latest-py36-linux-conda.yml
   - source activate test-env
+  - conda install -q nose
   - pip install -q flake8
-  - conda install nose
   - pip install -q https://github.com/qiime2/q2lint/archive/master.zip
   - make install
 script:
   - make lint
   - make test
+  - QIIMETEST= source tab-qiime
+  - QIIMETEST= qiime info

CONTRIBUTING.md

-Contributing to QIIME 2
------------------------
-
-QIIME 2 is an open-source project, and we are very interested in contributions from the community. Please get in touch through the [QIIME 2 Forum](https://forum.qiime2.org) if you'd like to get involved.

MANIFEST.in

 include versioneer.py
-include qiime2/_version.py
+include q2cli/_version.py

Makefile

@@ -15,12 +15,12 @@ test: all
 install: all
 	$(PYTHON) setup.py install && \
 	mkdir -p $(PREFIX)/etc/conda/activate.d && \
-	cp hooks/00_activate_qiime2_envs.sh $(PREFIX)/etc/conda/activate.d/ && \
-	mkdir -p $(PREFIX)/etc/conda/deactivate.d && \
-	cp hooks/00_deactivate_qiime2_envs.sh $(PREFIX)/etc/conda/deactivate.d/
+	cp hooks/50_activate_q2cli_tab_completion.sh $(PREFIX)/etc/conda/activate.d/
 
 dev: all
-	pip install -e .
+	pip install -e . && \
+	mkdir -p $(PREFIX)/etc/conda/activate.d && \
+	cp hooks/50_activate_q2cli_tab_completion.sh $(PREFIX)/etc/conda/activate.d/
 
 clean: distclean
 

README.md

-# QIIME 2
+# q2cli
+A [click-based](http://click.pocoo.org/) command line interface for [QIIME 2](https://github.com/qiime2/qiime2).
 
-[![Build Status](https://travis-ci.org/qiime2/qiime2.svg?branch=master)](https://travis-ci.org/qiime2/qiime2)
+## Installation and getting help
 
-Source code repository for the QIIME 2 framework. Visit [https://qiime2.org](https://qiime2.org) to learn more about the QIIME 2 project.
+Visit https://qiime2.org to learn more about q2cli and the QIIME 2 project.
+
+## Enabling tab completion
+
+### Bash
+
+To enable tab completion in Bash, run the following command or add it to your `.bashrc`/`.bash_profile`:
+
+```bash
+source tab-qiime
+```
+
+### ZSH
+
+To enable tab completion in ZSH, run the following commands or add them to your `.zshrc`:
+
+```bash
+autoload bashcompinit && bashcompinit && source tab-qiime
+```

bin/tab-qiime

+#!/usr/bin/env bash
+
+# Bash completion script that defers to a cached completion script representing
+# the state of the current QIIME 2 deployment.
+#
+# This script is intended to be executed on the command-line or in
+# .bashrc/.bash_profile:
+#
+#     source tab-qiime
+#
+
+_qiime_completion()
+{
+  # Attempt to find the cached completion script. If q2cli isn't installed, or
+  # is an incompatible version, don't attempt completion.
+  local completion_path="$(python -c "import q2cli.util; print(q2cli.util.get_completion_path())" 2> /dev/null)"
+
+  if [[ $? != 0 ]]; then
+    unset COMPREPLY
+    return 0
+  fi
+
+  # If the completion script exists, attempt completion by invoking the script
+  # in a subshell, supplying COMP_WORDS and COMP_CWORD. Capture the output as
+  # the completion reply. If the completion script failed, don't attempt
+  # completion.
+  if [[ -f "$completion_path" ]] ; then
+    COMPREPLY=( $(COMP_WORDS="${COMP_WORDS[*]}" COMP_CWORD="${COMP_CWORD}" "$completion_path" 2> /dev/null) )
+
+    if [[ $? != 0 ]]; then
+      unset COMPREPLY
+      return 0
+    fi
+  else
+    unset COMPREPLY
+    return 0
+  fi
+
+  return 0
+}
+
+# Enable default readline and bash completion behavior when `_qiime_completion`
+# doesn't have a reply.
+complete -F _qiime_completion -o default -o bashdefault qiime
+
+# Execute a `qiime` command (any command will do) so that tab-completion will
+# work out-of-the-box (e.g. with a fresh installation of q2cli). Running a
+# command will create or refresh the cache if necessary, which contains the
+# actual completion script.
+#
+# Ignore stdout to avoid displaying help text to users enabling tab-completion.
+# stderr displays the note about cache refreshing, as that can take a few
+# moments to complete.
+qiime > /dev/null

ci/recipe/meta.yaml

 {% set data = load_setup_py_data() %}
-{% set version = data.get('version') %}
+{% set version = data.get('version') or 'placehold' %}
+{% set release = '.'.join(version.split('.')[:2]) %}
 
 package:
-  name: qiime2
+  name: q2cli
   version: {{ version }}
 
 source:
@@ -10,6 +11,8 @@ source:
 
 build:
   script: make install
+  entry_points:
+    - qiime=q2cli.__main__:qiime
 
 requirements:
   host:
@@ -18,23 +21,16 @@ requirements:
 
   run:
     - python  {{ python }}
-    - pyyaml
-    - decorator
-    - pandas
-    - tzlocal
-    - python-dateutil
-    - pyparsing ==2.3.0
-    - bibtexparser
-    - networkx
+    - pip
+    - click
+    - qiime2 {{ release }}.*
 
 test:
   imports:
-    - qiime2
+    - q2cli
 
   commands:
-    # TODO don't require devs to remember setting this env var before running
-    # tests. The value can be anything.
-    - QIIMETEST= python -c "import qiime2.plugins.dummy_plugin"
+    - QIIMETEST= qiime --help
 
 about:
   home: https://qiime2.org

debian/changelog

+qiime (2019.7.0-1) UNRELEASED; urgency=medium
+
+  * New upstream version
+  * debhelper-compat 12
+  * Standards-Version: 4.4.0
+  * Respect DEB_BUILD_OPTIONS in override_dh_auto_test target
+  * Remove trailing whitespace in debian/changelog
+  * Remove trailing whitespace in debian/control
+  * Trim trailing whitespace.
+  * (Build-)Depends: python3-click
+  TODO: Build-time test failure
+    ModuleNotFoundError: No module named 'qiime2'
+
+ -- Andreas Tille <tille@debian.org>  Fri, 02 Aug 2019 23:15:44 +0200
+
 qiime (2019.4.0-1) unstable; urgency=medium
 
   * Team upload.
@@ -476,4 +491,3 @@ qiime (1.1.0-1) experimental; urgency=low
   * Initial release.
 
  -- Sri Girish Srinivasa Murthy <srigirish@evolbio.mpg.de>  Tue, 20 Jul 2010 00:03:02 +0200
-

debian/compat

-12

debian/control

@@ -5,18 +5,19 @@ Uploaders: Steffen Moeller <moeller@debian.org>,
            Andreas Tille <tille@debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 12~),
+Build-Depends: debhelper-compat (= 12),
                dh-python,
                python3,
                python3-setuptools,
                python3-nose,
                python3-bibtexparser,
+               python3-click,
                python3-decorator,
                python3-pandas,
                python3-tzlocal,
                python3-yaml,
                python3-networkx
-Standards-Version: 4.3.0
+Standards-Version: 4.4.0
 Vcs-Browser: https://salsa.debian.org/med-team/qiime
 Vcs-Git: https://salsa.debian.org/med-team/qiime.git
 Homepage: https://qiime2.org
@@ -27,6 +28,7 @@ Depends: ${shlibs:Depends},
          ${misc:Depends},
          ${python3:Depends},
          python3-bibtexparser,
+         python3-click,
          python3-decorator,
          python3-pandas,
          python3-tzlocal,

debian/rules

@@ -18,4 +18,6 @@ export PYBUILD_AFTER_TEST=rm -rf {build_dir}/qiime2.egg-* {build_dir}/site.py {b
 	dh $@ --with python3 --buildsystem=pybuild
 
 override_dh_auto_test:
+ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
 	LC_ALL=C.UTF-8 dh_auto_test -- -s custom --test-args="cd {build_dir}; QIIMETEST= nosetests3"
+endif

hooks/00_activate_qiime2_envs.sh

-#!/bin/sh
-
-export MPLBACKEND='Agg'
-export R_LIBS_USER=$CONDA_PREFIX/lib/R/library/
-export PYTHONNOUSERSITE=$CONDA_PREFIX/lib/python*/site-packages/

hooks/00_deactivate_qiime2_envs.sh

-#!/bin/sh
-
-unset MPLBACKEND
-unset R_LIBS_USER
-unset PYTHONNOUSERSITE

hooks/50_activate_q2cli_tab_completion.sh

+if [ -n "${ZSH_VERSION-}" ]; then
+  autoload bashcompinit && bashcompinit && source tab-qiime
+elif [ -n "${BASH_VERSION-}" ]; then
+  source tab-qiime
+fi

qiime2/core/exceptions.py → q2cli/__init__.py

@@ -6,6 +6,7 @@
 # The full license is in the file LICENSE, distributed with this software.
 # ----------------------------------------------------------------------------
 
+from ._version import get_versions
 
-class ValidationError(Exception):
-    pass
+__version__ = get_versions()['version']
+del get_versions

qiime2/core/tests/test_path.py → q2cli/__main__.py

@@ -6,37 +6,39 @@
 # The full license is in the file LICENSE, distributed with this software.
 # ----------------------------------------------------------------------------
 
-import os
-import unittest
+import click
 
-from qiime2.core.path import OutPath
+import q2cli.commands
 
 
-class TestOutPath(unittest.TestCase):
-    def test_new_outpath(self):
-        f = OutPath()
-        self.assertIsInstance(f, OutPath)
-        self.assertTrue(f.is_file())
+ROOT_COMMAND_HELP = """\
+QIIME 2 command-line interface (q2cli)
+--------------------------------------
 
-        g = OutPath(dir=True)
-        self.assertIsInstance(g, OutPath)
-        self.assertTrue(g.is_dir())
+To get help with QIIME 2, visit https://qiime2.org.
 
-    def test_new_outpath_context_mgr(self):
-        with OutPath() as f:
-            path = str(f)
-            self.assertIsInstance(f, OutPath)
-            self.assertTrue(os.path.isfile(path))
-        self.assertFalse(os.path.isfile(path))
+To enable tab completion in Bash, run the following command or add it to your \
+.bashrc/.bash_profile:
 
-    def test_destructor(self):
-        f = OutPath()
-        path = str(f)
+    source tab-qiime
 
-        self.assertTrue(os.path.isfile(path))
-        f._destructor()
-        self.assertFalse(os.path.isfile(path))
+To enable tab completion in ZSH, run the following commands or add them to \
+your .zshrc:
+
+    autoload bashcompinit && bashcompinit && source tab-qiime
+
+"""
+
+
+# Entry point for CLI
+@click.command(cls=q2cli.commands.RootCommand, invoke_without_command=True,
+               no_args_is_help=True, help=ROOT_COMMAND_HELP)
+@click.version_option(prog_name='q2cli',
+                      message='%(prog)s version %(version)s\nRun `qiime info` '
+                              'for more version details.')
+def qiime():
+    pass
 
 
 if __name__ == '__main__':
-    unittest.main()
+    qiime()

qiime2/_version.py → q2cli/_version.py

@@ -23,9 +23,9 @@ def get_keywords():
     # setup.py/versioneer.py will grep for the variable names, so they must
     # each be defined on a line of their own. _version.py will just call
     # get_keywords().
-    git_refnames = " (tag: 2019.4.0)"
-    git_full = "f60a7d43a97f065d4e3248e3df93703aa48d95ab"
-    git_date = "2019-05-03 04:14:45 +0000"
+    git_refnames = " (tag: 2019.7.0)"
+    git_full = "06b978c96c8efce8be0c8213e744cb4b389f2bc6"
+    git_date = "2019-07-30 18:15:53 +0000"
     keywords = {"refnames": git_refnames, "full": git_full, "date": git_date}
     return keywords
 
@@ -42,8 +42,8 @@ def get_config():
     cfg.VCS = "git"
     cfg.style = "pep440"
     cfg.tag_prefix = ""
-    cfg.parentdir_prefix = "qiime2-"
-    cfg.versionfile_source = "qiime2/_version.py"
+    cfg.parentdir_prefix = "q2cli-"
+    cfg.versionfile_source = "q2cli/_version.py"
     cfg.verbose = False
     return cfg