.gitattributes

-q2cli/_version.py export-subst
+q2templates/_version.py export-subst

.gitignore

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

.travis.yml

@@ -14,12 +14,10 @@ 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
+  - conda install -q pytest
   - pip install -q flake8
   - 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

MANIFEST.in

 include versioneer.py
-include q2cli/_version.py
+include q2templates/_version.py

Makefile

 .PHONY: all lint test install dev clean distclean
 
 PYTHON ?= python
-PREFIX ?= $(CONDA_PREFIX)
 
 all: ;
 
@@ -10,17 +9,13 @@ lint:
 	flake8
 
 test: all
-	QIIMETEST= nosetests
+	py.test
 
 install: all
-	$(PYTHON) setup.py install && \
-	mkdir -p $(PREFIX)/etc/conda/activate.d && \
-	cp hooks/50_activate_q2cli_tab_completion.sh $(PREFIX)/etc/conda/activate.d/
+	$(PYTHON) setup.py install
 
 dev: all
-	pip install -e . && \
-	mkdir -p $(PREFIX)/etc/conda/activate.d && \
-	cp hooks/50_activate_q2cli_tab_completion.sh $(PREFIX)/etc/conda/activate.d/
+	pip install -e .
 
 clean: distclean
 

README.md

-# q2cli
-A [click-based](http://click.pocoo.org/) command line interface for [QIIME 2](https://github.com/qiime2/qiime2).
-
-## Installation and getting help
-
-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
-```
+# q2templates
+Design template package for QIIME 2 Plugins

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') or 'placehold' %}
-{% set release = '.'.join(version.split('.')[:2]) %}
+{% set version = data.get('version') %}
 
+# TODO review meta.yml spec and fill in missing fields as necessary (e.g. build number).
 package:
-  name: q2cli
+  name: q2templates
   version: {{ version }}
 
 source:
@@ -11,8 +11,6 @@ source:
 
 build:
   script: make install
-  entry_points:
-    - qiime=q2cli.__main__:qiime
 
 requirements:
   host:
@@ -21,16 +19,13 @@ requirements:
 
   run:
     - python {{ python }}
-    - pip
-    - click
-    - qiime2 {{ release }}.*
+    - setuptools
+    - jinja2
+    - pandas
 
 test:
   imports:
-    - q2cli
-
-  commands:
-    - QIIMETEST= qiime --help
+    - q2templates
 
 about:
   home: https://qiime2.org

debian/changelog

+q2cli (2019.10.0-1) UNRELEASED; urgency=medium
+
+  * Team upload.
+  * New upstream version
+  * Standards-Version: 4.4.1
+  * Drop unneeded patches
+  * (Build-)Depends: python3-jinja2
+  * Upstream seems to have dropped zsh command line completion
+  TODO: The dir q2tamplates is pretty much a copy of package q2templates -
+        specifically its also carrying the third party JS + fonts stuff
+        we just excluded in q2templates.  It might be worth investigating
+        whether this can be removed in q2cli completely
+
+ -- Andreas Tille <tille@debian.org>  Tue, 12 Nov 2019 09:39:41 +0100
+
 q2cli (2019.7.0-1) unstable; urgency=medium
 
   [ Andreas Tille ]

debian/control

@@ -9,8 +9,9 @@ Build-Depends: debhelper-compat (= 12),
                python3-setuptools,
                qiime (>= 2019.7.0),
                python3-click,
-               python3-nose
-Standards-Version: 4.4.0
+               python3-jinja2,
+               python3-nose,
+Standards-Version: 4.4.1
 Vcs-Browser: https://salsa.debian.org/med-team/q2cli
 Vcs-Git: https://salsa.debian.org/med-team/q2cli.git
 Homepage: https://qiime2.org/
@@ -22,6 +23,7 @@ Depends: ${shlibs:Depends},
          ${python3:Depends},
          qiime,
          python3-setuptools,
+         python3-jinja2,
          python3-click
 Description: Click-based command line interface for QIIME 2
  QIIME 2 is a powerful, extensible, and decentralized microbiome analysis

debian/patches/call_py3.patch

-Description: call python3 in the tab-qiime script, as the package is python3 only
-From: Alex Mestiashvili <amestia@rsh2.donotuse.de>
---- q2cli.orig/bin/tab-qiime
-+++ q2cli/bin/tab-qiime
-@@ -13,7 +13,7 @@
- {
-   # Attempt to find the cached completion script. If q2cli isn't installed, or
-   # is an incompatible version, don't attempt completion.
--  local completion_path="$(python -c "import q2cli.util; print(q2cli.util.get_completion_path())" 2> /dev/null)"
-+  local completion_path="$(python3 -c "import q2cli.util; print(q2cli.util.get_completion_path())" 2> /dev/null)"
- 
-   if [[ $? != 0 ]]; then
-     unset COMPREPLY

debian/patches/inform_zsh_users_howto_set_autocompletion.patch

-Author: Liubov Chuprikova <chuprikovalv@gmail.com>
-Last-Update: Sat, 23 Mar 2019 14:43:01 +0100
-Description: Bash users will have a working completion, but we also need to
- inform zsh users how they can enable completion.
-
---- a/q2cli/__main__.py
-+++ b/q2cli/__main__.py
-@@ -17,15 +17,10 @@
- 
- To get help with QIIME 2, visit https://qiime2.org.
- 
--To enable tab completion in Bash, run the following command or add it to your \
--.bashrc/.bash_profile:
--
--    source tab-qiime
--
- To enable tab completion in ZSH, run the following commands or add them to \
- your .zshrc:
- 
--    autoload bashcompinit && bashcompinit && source tab-qiime
-+    autoload bashcompinit && bashcompinit && source /usr/share/bash-completion/completions/qiime
- 
- """
- 

debian/patches/series

-call_py3.patch
-inform_zsh_users_howto_set_autocompletion.patch

debian/qiime.1

@@ -11,11 +11,6 @@ QIIME 2 command\-line interface (q2cli)
 \fB\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\fR
 .IP
 To get help with QIIME 2, visit https://qiime2.org.
-.IP
-To enable tab completion in ZSH, run the following commands or add them to
-your .zshrc:
-.IP
-autoload bashcompinit && bashcompinit && source \fI\,/usr/share/bashcompletion/completions/qiime\/\fP
 .SH OPTIONS
 .TP
 \fB\-\-version\fR

debian/rules

 #!/usr/bin/make -f
 
 # DH_VERBOSE := 1
-export LC_ALL=C.UTF-8
-
-include /usr/share/dpkg/default.mk
-# this provides:
-# DEB_SOURCE: the source package name
-# DEB_VERSION: the full version of the package (epoch + upstream vers. + revision)
-# DEB_VERSION_EPOCH_UPSTREAM: the package's version without the Debian revision
-# DEB_VERSION_UPSTREAM_REVISION: the package's version without the Debian epoch
-# DEB_VERSION_UPSTREAM: the package's upstream version
-# DEB_DISTRIBUTION: the distribution(s) listed in the current entry of debian/changelog
-# SOURCE_DATE_EPOCH: the source release date as seconds since the epoch, as
-#                    specified by <https://reproducible-builds.org/specs/source-date-epoch/>
-
-# for hardening you might like to uncomment this:
-# export DEB_BUILD_MAINT_OPTIONS=hardening=+all
 
 %:
 	dh $@ --with python3 --buildsystem=pybuild
@@ -24,8 +9,3 @@ override_dh_auto_test:
 ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
 	LC_ALL=C.UTF-8 dh_auto_test -- -s custom --test-args='cd {build_dir}; HOME=${CURDIR} QIIMETEST= nosetests3'
 endif
-
-override_dh_install:
-	dh_install
-	mkdir -p debian/$(DEB_SOURCE)/usr/share/bash-completion/completions
-	mv debian/$(DEB_SOURCE)/usr/bin/tab-qiime debian/$(DEB_SOURCE)/usr/share/bash-completion/completions/qiime

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

q2cli/__main__.py

-# ----------------------------------------------------------------------------
-# Copyright (c) 2016-2019, QIIME 2 development team.
-#
-# Distributed under the terms of the Modified BSD License.
-#
-# The full license is in the file LICENSE, distributed with this software.
-# ----------------------------------------------------------------------------
-
-import click
-
-import q2cli.commands
-
-
-ROOT_COMMAND_HELP = """\
-QIIME 2 command-line interface (q2cli)
---------------------------------------
-
-To get help with QIIME 2, visit https://qiime2.org.
-
-To enable tab completion in Bash, run the following command or add it to your \
-.bashrc/.bash_profile:
-
-    source tab-qiime
-
-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__':
-    qiime()

q2cli/builtin/dev.py

-# ----------------------------------------------------------------------------
-# Copyright (c) 2016-2019, QIIME 2 development team.
-#
-# Distributed under the terms of the Modified BSD License.
-#
-# The full license is in the file LICENSE, distributed with this software.
-# ----------------------------------------------------------------------------
-
-import click
-
-from q2cli.click.command import ToolCommand, ToolGroupCommand
-
-
-@click.group(help='Utilities for developers and advanced users.',
-             cls=ToolGroupCommand)
-def dev():
-    pass
-
-
-@dev.command(name='refresh-cache',
-             short_help='Refresh CLI cache.',
-             help="Refresh the CLI cache. Use this command if you are "
-                  "developing a plugin, or q2cli itself, and want your "
-                  "changes to take effect in the CLI. A refresh of the cache "
-                  "is necessary because package versions do not typically "
-                  "change each time an update is made to a package's code. "
-                  "Setting the environment variable Q2CLIDEV to any value "
-                  "will always refresh the cache when a command is run.",
-             cls=ToolCommand)
-def refresh_cache():
-    import q2cli.core.cache
-    q2cli.core.cache.CACHE.refresh()
-
-
-import_theme_help = \
-    ("Allows for customization of q2cli's command line styling based on an "
-     "imported .theme (INI formatted) file. If you are unfamiliar with .ini "
-     "formatted files look here https://en.wikipedia.org/wiki/INI_file."
-     "\n"
-     "\n"
-     "The .theme file allows you to customize text on the basis of what that "
-     "text represents with the following supported text types: command, "
-     "option, type, default_arg, required, emphasis, problem, warning, error, "
-     "and success. These will be your headers in the '[]' brackets. "
-     "\n"
-     "\n"
-     "`command` refers to the name of the command you issued. `option` refers "
-     "to the arguments you give to the command when running it. `type` refers "
-     "to the QIIME 2 semantic typing of these arguments (where applicable). "
-     "`default_arg` refers to the label next to the argument indicating its "
-     "default value (where applicable), and if it is required (where "
-     "applicable). `required` refers to any arguments that must be passed to "
-     "the command for it to work and gives them special formatting on top of "
-     "your normal `option` formatting. `emphasis` refers to any emphasized "
-     "pieces of text within help text. `problem` refers to the text informing "
-     "you there were issues with the command. `warning` refers to the text "
-     "for non-fatal issues while `error` refers to the text for fatal issues."
-     "`success` refers to text indicating a process completed as expected."
-     "\n"
-     "\n"
-     "Depending on what your terminal supports, some or all of the following "
-     "pieces of the text's formatting may be customized: bold, dim (if true "
-     "the text's brightness is reduced), underline, blink, reverse (if true "
-     "foreground and background colors are reversed), and finally fg "
-     "(foreground color) and bg (background color). The first five may each "
-     "be either true or false, while the colors may be set to any of the "
-     "following: black, red, green, yellow, blue, magenta, cyan, white, "
-     "bright_black, bright_red, bright_green, bright_yellow, bright_blue, "
-     "bright_magenta, bright_cyan, or bright_white.")
-
-
-@dev.command(name='import-theme',
-             short_help='Install new command line theme.',
-             help=import_theme_help,
-             cls=ToolCommand)
-@click.option('--theme', required=True,
-              type=click.Path(exists=True, file_okay=True,
-                              dir_okay=False, readable=True),
-              help='Path to file containing new theme info')
-def import_theme(theme):
-    import os
-    import shutil
-    from configparser import Error
-
-    import q2cli.util
-    from q2cli.core.config import CONFIG
-
-    try:
-        CONFIG.parse_file(theme)
-    except Error as e:
-        # If they tried to change [error] in a valid manner before we hit our
-        # parsing error, we don't want to use their imported error settings
-        CONFIG.styles = CONFIG.get_default_styles()
-        header = 'Something went wrong while parsing your theme: '
-        q2cli.util.exit_with_error(e, header=header, traceback=None)
-    shutil.copy(theme, os.path.join(q2cli.util.get_app_dir(),
-                'cli-colors.theme'))
-
-
-@dev.command(name='export-default-theme',
-             short_help='Export the default settings.',
-             help='Create a .theme (INI formatted) file from the default '
-             'settings at the specified filepath.',
-             cls=ToolCommand)
-@click.option('--output-path', required=True,
-              type=click.Path(exists=False, file_okay=True,
-                              dir_okay=False, readable=True),
-              help='Path to output the config to')
-def export_default_theme(output_path):
-    import configparser
-    from q2cli.core.config import CONFIG
-
-    parser = configparser.ConfigParser()
-    parser.read_dict(CONFIG.get_default_styles())
-    with open(output_path, 'w') as fh:
-        parser.write(fh)
-
-
-def abort_if_false(ctx, param, value):
-    if not value:
-        ctx.abort()
-
-
-@dev.command(name='reset-theme',
-             short_help='Reset command line theme to default.',
-             help="Reset command line theme to default. Requres the '--yes' "
-             "parameter to be passed asserting you do want to reset.",
-             cls=ToolCommand)
-@click.option('--yes', is_flag=True, callback=abort_if_false,
-              expose_value=False,
-              prompt='Are you sure you want to reset your theme?')
-def reset_theme():
-    import os
-    import q2cli.util
-
-    path = os.path.join(q2cli.util.get_app_dir(), 'cli-colors.theme')
-    if os.path.exists(path):
-        os.unlink(path)
-        click.echo('Theme reset.')
-    else:
-        click.echo('Theme was already default.')

q2cli/builtin/info.py

-# ----------------------------------------------------------------------------
-# Copyright (c) 2016-2019, QIIME 2 development team.
-#
-# Distributed under the terms of the Modified BSD License.
-#
-# The full license is in the file LICENSE, distributed with this software.
-# ----------------------------------------------------------------------------
-
-import click
-
-from q2cli.click.command import ToolCommand
-
-
-def _echo_version():
-    import sys
-    import qiime2
-    import q2cli
-
-    pyver = sys.version_info
-    click.echo('Python version: %d.%d.%d' %
-               (pyver.major, pyver.minor, pyver.micro))
-    click.echo('QIIME 2 release: %s' % qiime2.__release__)
-    click.echo('QIIME 2 version: %s' % qiime2.__version__)
-    click.echo('q2cli version: %s' % q2cli.__version__)
-
-
-def _echo_plugins():
-    import q2cli.core.cache
-
-    plugins = q2cli.core.cache.CACHE.plugins
-    if plugins:
-        for name, plugin in sorted(plugins.items()):
-            click.echo('%s: %s' % (name, plugin['version']))
-    else:
-        click.secho('No plugins are currently installed.\nYou can browse '
-                    'the official QIIME 2 plugins at https://qiime2.org')
-
-
-@click.command(help='Display information about current deployment.',
-               cls=ToolCommand)
-def info():
-    import q2cli.util
-    # This import improves performance for repeated _echo_plugins
-    import q2cli.core.cache
-
-    click.secho('System versions', fg='green')
-    _echo_version()
-    click.secho('\nInstalled plugins', fg='green')
-    _echo_plugins()
-
-    click.secho('\nApplication config directory', fg='green')
-    click.secho(q2cli.util.get_app_dir())
-
-    click.secho('\nGetting help', fg='green')
-    click.secho('To get help with QIIME 2, visit https://qiime2.org')

q2cli/builtin/tools.py

-# ----------------------------------------------------------------------------
-# Copyright (c) 2016-2019, QIIME 2 development team.
-#
-# Distributed under the terms of the Modified BSD License.
-#
-# The full license is in the file LICENSE, distributed with this software.
-# ----------------------------------------------------------------------------
-
-import os
-
-import click
-
-import q2cli.util
-from q2cli.click.command import ToolCommand, ToolGroupCommand
-
-
-_COMBO_METAVAR = 'ARTIFACT/VISUALIZATION'
-
-
-@click.group(help='Tools for working with QIIME 2 files.',
-             cls=ToolGroupCommand)
-def tools():
-    pass
-
-
-@tools.command(name='export',
-               short_help='Export data from a QIIME 2 Artifact '
-               'or a Visualization',
-               help='Exporting extracts (and optionally transforms) data '
-               'stored inside an Artifact or Visualization. Note that '
-               'Visualizations cannot be transformed with --output-format',
-               cls=ToolCommand)
-@click.option('--input-path', required=True, metavar=_COMBO_METAVAR,
-              type=click.Path(exists=True, file_okay=True,
-                              dir_okay=False, readable=True),
-              help='Path to file that should be exported')
-@click.option('--output-path', required=True,
-              type=click.Path(exists=False, file_okay=True, dir_okay=True,
-                              writable=True),
-              help='Path to file or directory where '
-              'data should be exported to')
-@click.option('--output-format', required=False,
-              help='Format which the data should be exported as. '
-              'This option cannot be used with Visualizations')
-def export_data(input_path, output_path, output_format):
-    import qiime2.util
-    import qiime2.sdk
-    import distutils
-    from q2cli.core.config import CONFIG
-    result = qiime2.sdk.Result.load(input_path)
-    if output_format is None:
-        if isinstance(result, qiime2.sdk.Artifact):
-            output_format = result.format.__name__
-        else:
-            output_format = 'Visualization'
-        result.export_data(output_path)
-    else:
-        if isinstance(result, qiime2.sdk.Visualization):
-            error = '--output-format cannot be used with visualizations'
-            click.echo(CONFIG.cfg_style('error', error), err=True)
-            click.get_current_context().exit(1)
-        else:
-            source = result.view(qiime2.sdk.parse_format(output_format))
-            if os.path.isfile(str(source)):
-                if os.path.isfile(output_path):
-                    os.remove(output_path)
-                else:
-                    # create directory (recursively) if it doesn't exist yet
-                    os.makedirs(os.path.dirname(output_path), exist_ok=True)
-                qiime2.util.duplicate(str(source), output_path)
-            else:
-                distutils.dir_util.copy_tree(str(source), output_path)
-
-    output_type = 'file' if os.path.isfile(output_path) else 'directory'
-    success = 'Exported %s as %s to %s %s' % (input_path, output_format,
-                                              output_type, output_path)
-    click.echo(CONFIG.cfg_style('success', success))
-
-
-def show_importable_types(ctx, param, value):
-    if not value or ctx.resilient_parsing:
-        return
-
-    import qiime2.sdk
-
-    importable_types = sorted(qiime2.sdk.PluginManager().importable_types,
-                              key=repr)
-
-    if importable_types:
-        for name in importable_types:
-            click.echo(name)
-    else:
-        click.echo('There are no importable types in the current deployment.')
-
-    ctx.exit()
-
-
-def show_importable_formats(ctx, param, value):
-    if not value or ctx.resilient_parsing:
-        return
-
-    import qiime2.sdk
-
-    importable_formats = sorted(qiime2.sdk.PluginManager().importable_formats)
-
-    if importable_formats:
-        for format in importable_formats:
-            click.echo(format)
-    else:
-        click.echo('There are no importable formats '
-                   'in the current deployment.')
-
-    ctx.exit()
-
-
-@tools.command(name='import',
-               short_help='Import data into a new QIIME 2 Artifact.',
-               help="Import data to create a new QIIME 2 Artifact. See "
-                    "https://docs.qiime2.org/ for usage examples and details "
-                    "on the file types and associated semantic types that can "
-                    "be imported.",
-                    cls=ToolCommand)
-@click.option('--type', required=True,
-              help='The semantic type of the artifact that will be created '
-                   'upon importing. Use --show-importable-types to see what '
-                   'importable semantic types are available in the current '
-                   'deployment.')
-@click.option('--input-path', required=True,
-              type=click.Path(exists=True, file_okay=True, dir_okay=True,
-                              readable=True),
-              help='Path to file or directory that should be imported.')
-@click.option('--output-path', required=True, metavar='ARTIFACT',
-              type=click.Path(exists=False, file_okay=True, dir_okay=False,
-                              writable=True),
-              help='Path where output artifact should be written.')
-@click.option('--input-format', required=False,
-              help='The format of the data to be imported. If not provided, '
-                   'data must be in the format expected by the semantic type '
-                   'provided via --type.')
-@click.option('--show-importable-types', is_flag=True, is_eager=True,
-              callback=show_importable_types, expose_value=False,
-              help='Show the semantic types that can be supplied to --type '
-                   'to import data into an artifact.')
-@click.option('--show-importable-formats', is_flag=True, is_eager=True,
-              callback=show_importable_formats, expose_value=False,
-              help='Show formats that can be supplied to --input-format to '
-                   'import data into an artifact.')
-def import_data(type, input_path, output_path, input_format):
-    import qiime2.sdk
-    import qiime2.plugin
-    from q2cli.core.config import CONFIG
-    try:
-        artifact = qiime2.sdk.Artifact.import_data(type, input_path,
-                                                   view_type=input_format)
-    except qiime2.plugin.ValidationError as e:
-        header = 'There was a problem importing %s:' % input_path
-        q2cli.util.exit_with_error(e, header=header, traceback=None)
-    except Exception as e:
-        header = 'An unexpected error has occurred:'
-        q2cli.util.exit_with_error(e, header=header)
-    artifact.save(output_path)
-    if input_format is None:
-        input_format = artifact.format.__name__
-
-    success = 'Imported %s as %s to %s' % (input_path,
-                                           input_format,
-                                           output_path)
-    click.echo(CONFIG.cfg_style('success', success))
-
-
-@tools.command(short_help='Take a peek at a QIIME 2 Artifact or '
-                          'Visualization.',
-               help="Display basic information about a QIIME 2 Artifact or "
-                    "Visualization, including its UUID and type.",
-               cls=ToolCommand)
-@click.argument('path', type=click.Path(exists=True, file_okay=True,
-                                        dir_okay=False, readable=True),
-                metavar=_COMBO_METAVAR)
-def peek(path):
-    import qiime2.sdk
-    from q2cli.core.config import CONFIG
-
-    metadata = qiime2.sdk.Result.peek(path)
-
-    click.echo(CONFIG.cfg_style('type', "UUID")+":        ", nl=False)
-    click.echo(metadata.uuid)
-    click.echo(CONFIG.cfg_style('type', "Type")+":        ", nl=False)
-    click.echo(metadata.type)
-    if metadata.format is not None:
-        click.echo(CONFIG.cfg_style('type', "Data format")+": ", nl=False)
-        click.echo(metadata.format)
-
-
-@tools.command('inspect-metadata',
-               short_help='Inspect columns available in metadata.',
-               help='Inspect metadata files or artifacts viewable as metadata.'
-                    ' Providing multiple file paths to this command will merge'
-                    ' the metadata.',
-               cls=ToolCommand)
-@click.option('--tsv/--no-tsv', default=False,
-              help='Print as machine-readable TSV instead of text.')
-@click.argument('paths', nargs=-1, required=True, metavar='METADATA...',
-                type=click.Path(exists=True, file_okay=True, dir_okay=False,
-                                readable=True))
-@q2cli.util.pretty_failure(traceback=None)
-def inspect_metadata(paths, tsv, failure):
-    m = [_load_metadata(p) for p in paths]
-    metadata = m[0]
-    if m[1:]:
-        metadata = metadata.merge(*m[1:])
-
-    # we aren't expecting errors below this point, so set traceback to default
-    failure.traceback = 'stderr'
-    failure.header = "An unexpected error has occurred:"
-
-    COLUMN_NAME = "COLUMN NAME"
-    COLUMN_TYPE = "TYPE"
-    max_name_len = max([len(n) for n in metadata.columns]
-                       + [len(COLUMN_NAME)])
-    max_type_len = max([len(p.type) for p in metadata.columns.values()]
-                       + [len(COLUMN_TYPE)])
-
-    if tsv:
-        import csv
-        import io
-
-        def formatter(*row):
-            # This is gross, but less gross than robust TSV writing.
-            with io.StringIO() as fh:
-                writer = csv.writer(fh, dialect='excel-tab', lineterminator='')
-                writer.writerow(row)
-                return fh.getvalue()
-    else:
-        formatter = ("{0:>%d}  {1:%d}" % (max_name_len, max_type_len)).format
-
-    click.secho(formatter(COLUMN_NAME, COLUMN_TYPE), bold=True)
-    if not tsv:
-        click.secho(formatter("=" * max_name_len, "=" * max_type_len),
-                    bold=True)
-
-    for name, props in metadata.columns.items():
-        click.echo(formatter(name, props.type))
-
-    if not tsv:
-        click.secho(formatter("=" * max_name_len, "=" * max_type_len),
-                    bold=True)
-        click.secho(("{0:>%d}  " % max_name_len).format("IDS:"),
-                    bold=True, nl=False)
-        click.echo(metadata.id_count)
-        click.secho(("{0:>%d}  " % max_name_len).format("COLUMNS:"),
-                    bold=True, nl=False)
-        click.echo(metadata.column_count)
-
-
-def _load_metadata(path):
-    import qiime2
-    import qiime2.sdk
-
-    # TODO: clean up duplication between this and the metadata handlers.
-    try:
-        artifact = qiime2.sdk.Result.load(path)
-    except Exception:
-        metadata = qiime2.Metadata.load(path)
-    else:
-        if isinstance(artifact, qiime2.Visualization):
-            raise Exception("Visualizations cannot be viewed as QIIME 2"
-                            " metadata:\n%r" % path)
-        elif artifact.has_metadata():
-            metadata = artifact.view(qiime2.Metadata)
-        else:
-            raise Exception("Artifacts with type %r cannot be viewed as"
-                            " QIIME 2 metadata:\n%r" % (artifact.type, path))
-
-    return metadata
-
-
-@tools.command(short_help='View a QIIME 2 Visualization.',
-               help="Displays a QIIME 2 Visualization until the command "
-                    "exits. To open a QIIME 2 Visualization so it can be "
-                    "used after the command exits, use 'qiime tools extract'.",
-               cls=ToolCommand)
-@click.argument('visualization-path', metavar='VISUALIZATION',
-                type=click.Path(exists=True, file_okay=True, dir_okay=False,
-                                readable=True))
-@click.option('--index-extension', required=False, default='html',
-              help='The extension of the index file that should be opened. '
-                   '[default: html]')
-def view(visualization_path, index_extension):
-    # Guard headless envs from having to import anything large
-    import sys
-    from q2cli.core.config import CONFIG
-    if not os.getenv("DISPLAY") and sys.platform != "darwin":
-        raise click.UsageError(
-            'Visualization viewing is currently not supported in headless '
-            'environments. You can view Visualizations (and Artifacts) at '
-            'https://view.qiime2.org, or move the Visualization to an '
-            'environment with a display and view it with `qiime tools view`.')
-
-    import zipfile
-    import qiime2.sdk
-
-    if index_extension.startswith('.'):
-        index_extension = index_extension[1:]
-    try:
-        visualization = qiime2.sdk.Visualization.load(visualization_path)
-    # TODO: currently a KeyError is raised if a zipped file that is not a
-    # QIIME 2 result is passed. This should be handled better by the framework.
-    except (zipfile.BadZipFile, KeyError, TypeError):
-        raise click.BadParameter(
-            '%s is not a QIIME 2 Visualization. Only QIIME 2 Visualizations '
-            'can be viewed.' % visualization_path)
-
-    index_paths = visualization.get_index_paths(relative=False)
-
-    if index_extension not in index_paths:
-        raise click.BadParameter(
-            'No index %s file is present in the archive. Available index '
-            'extensions are: %s' % (index_extension,
-                                    ', '.join(index_paths.keys())))
-    else:
-        index_path = index_paths[index_extension]
-        launch_status = click.launch(index_path)
-        if launch_status != 0:
-            click.echo(CONFIG.cfg_style('error', 'Viewing visualization '
-                                        'failed while attempting to open '
-                                        f'{index_path}'), err=True)
-        else:
-            while True:
-                click.echo(
-                    "Press the 'q' key, Control-C, or Control-D to quit. This "
-                    "view may no longer be accessible or work correctly after "
-                    "quitting.", nl=False)
-                # There is currently a bug in click.getchar where translation
-                # of Control-C and Control-D into KeyboardInterrupt and
-                # EOFError (respectively) does not work on Python 3. The code
-                # here should continue to work as expected when the bug is
-                # fixed in Click.
-                #
-                # https://github.com/pallets/click/issues/583
-                try:
-                    char = click.getchar()
-                    click.echo()
-                    if char in {'q', '\x03', '\x04'}:
-                        break
-                except (KeyboardInterrupt, EOFError):
-                    break
-
-
-@tools.command(short_help="Extract a QIIME 2 Artifact or Visualization "
-                          "archive.",
-               help="Extract all contents of a QIIME 2 Artifact or "
-                    "Visualization's archive, including provenance, metadata, "
-                    "and actual data. Use 'qiime tools export' to export only "
-                    "the data stored in an Artifact or Visualization, with "
-                    "the choice of exporting to different formats.",
-               cls=ToolCommand)
-@click.option('--input-path', required=True, metavar=_COMBO_METAVAR,
-              type=click.Path(exists=True, file_okay=True, dir_okay=False,
-                              readable=True),
-              help='Path to file that should be extracted')
-@click.option('--output-path', required=False,
-              type=click.Path(exists=False, file_okay=False, dir_okay=True,
-                              writable=True),
-              help='Directory where archive should be extracted to '
-                   '[default: current working directory]',
-              default=os.getcwd())
-def extract(input_path, output_path):
-    import zipfile
-    import qiime2.sdk
-    from q2cli.core.config import CONFIG
-
-    try:
-        extracted_dir = qiime2.sdk.Result.extract(input_path, output_path)
-    except (zipfile.BadZipFile, ValueError):
-        raise click.BadParameter(
-            '%s is not a valid QIIME 2 Result. Only QIIME 2 Artifacts and '
-            'Visualizations can be extracted.' % input_path)
-    else:
-        success = 'Extracted %s to directory %s' % (input_path, extracted_dir)
-        click.echo(CONFIG.cfg_style('success', success))
-
-
-@tools.command(short_help='Validate data in a QIIME 2 Artifact.',
-               help='Validate data in a QIIME 2 Artifact. QIIME 2 '
-                    'automatically performs some basic validation when '
-                    'managing your data; use this command to perform explicit '
-                    'and/or more thorough validation of your data (e.g. when '
-                    'debugging issues with your data or analyses).\n\nNote: '
-                    'validation can take some time to complete, depending on '
-                    'the size and type of your data.',
-               cls=ToolCommand)
-@click.argument('path', type=click.Path(exists=True, file_okay=True,
-                                        dir_okay=False, readable=True),
-                metavar=_COMBO_METAVAR)
-@click.option('--level', required=False, type=click.Choice(['min', 'max']),
-              help='Desired level of validation. "min" will perform minimal '
-                   'validation, and "max" will perform maximal validation (at '
-                   'the potential cost of runtime).',
-              default='max', show_default=True)
-def validate(path, level):
-    import qiime2.sdk
-    from q2cli.core.config import CONFIG
-
-    try:
-        result = qiime2.sdk.Result.load(path)
-    except Exception as e:
-        header = 'There was a problem loading %s as a QIIME 2 Result:' % path
-        q2cli.util.exit_with_error(e, header=header)
-
-    try:
-        result.validate(level)
-    except qiime2.plugin.ValidationError as e:
-        header = 'Result %s does not appear to be valid at level=%s:' % (
-                path, level)
-        q2cli.util.exit_with_error(e, header=header, traceback=None)
-    except Exception as e:
-        header = ('An unexpected error has occurred while attempting to '
-                  'validate result %s:' % path)
-        q2cli.util.exit_with_error(e, header=header)
-    else:
-        click.echo(CONFIG.cfg_style('success', f'Result {path} appears to be '
-                                    f'valid at level={level}.'))
-
-
-@tools.command(short_help='Print citations for a QIIME 2 result.',
-               help='Print citations as a BibTex file (.bib) for a QIIME 2'
-                    ' result.',
-               cls=ToolCommand)
-@click.argument('path', type=click.Path(exists=True, file_okay=True,
-                                        dir_okay=False, readable=True),
-                metavar=_COMBO_METAVAR)
-def citations(path):
-    import qiime2.sdk
-    import io
-    from q2cli.core.config import CONFIG
-    ctx = click.get_current_context()
-
-    try:
-        result = qiime2.sdk.Result.load(path)
-    except Exception as e:
-        header = 'There was a problem loading %s as a QIIME 2 result:' % path
-        q2cli.util.exit_with_error(e, header=header)
-
-    if result.citations:
-        with io.StringIO() as fh:
-            result.citations.save(fh)
-            click.echo(fh.getvalue(), nl=False)
-        ctx.exit(0)
-    else:
-        click.echo(CONFIG.cfg_style('problem', 'No citations found.'),
-                   err=True)
-        ctx.exit(1)