.coveragerc

+[run]
+branch = True
+omit =
+    */tests*
+    */__init__.py
+    q2_types/_version.py
+    versioneer.py
+
+[report]
+omit =
+    */tests*
+    */__init__.py
+    q2_types/_version.py
+    versioneer.py

.gitattributes

-q2cli/_version.py export-subst
+q2_types/_version.py export-subst

.gitignore

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

.travis.yml

@@ -14,12 +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 -q pytest-cov
+  - pip install -q flake8 coveralls
   - 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
+  - make test-cov
+after_success:
+  - coveralls

MANIFEST.in

 include versioneer.py
-include q2cli/_version.py
+include q2_types/_version.py

Makefile

-.PHONY: all lint test install dev clean distclean
+.PHONY: all lint test test-cov install dev clean distclean
 
 PYTHON ?= python
-PREFIX ?= $(CONDA_PREFIX)
 
 all: ;
 
@@ -10,17 +9,16 @@ lint:
 	flake8
 
 test: all
-	QIIMETEST= nosetests
+	py.test
+
+test-cov: all
+	py.test --cov=q2_types
 
 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).
+# q2-types
 
-## Installation and getting help
+[![Build Status](https://travis-ci.org/qiime2/q2-types.svg?branch=master)](https://travis-ci.org/qiime2/q2-types)
+[![Coverage Status](https://coveralls.io/repos/github/qiime2/q2-types/badge.svg?branch=master)](https://coveralls.io/github/qiime2/q2-types?branch=master)
 
-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
-```
+This is a QIIME 2 plugin. For details on QIIME 2, see https://qiime2.org.

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

@@ -3,16 +3,13 @@
 {% set release = '.'.join(version.split('.')[:2]) %}
 
 package:
-  name: q2cli
+  name: q2-types
   version: {{ version }}
 
 source:
   path: ../..
-
 build:
   script: make install
-  entry_points:
-    - qiime=q2cli.__main__:qiime
 
 requirements:
   host:
@@ -21,16 +18,19 @@ requirements:
 
   run:
     - python {{ python }}
-    - pip
-    - click
+    - scikit-bio >=0.5.4
+    - numpy
+    - blas=*=openblas
+    - pandas
+    - biom-format >=2.1.5,<2.2.0
+    - ijson
+    - h5py
     - qiime2 {{ release }}.*
 
 test:
   imports:
-    - q2cli
-
-  commands:
-    - QIIMETEST= qiime --help
+    - q2_types
+    - qiime2.plugins.types
 
 about:
   home: https://qiime2.org

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

q2_types/__init__.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 importlib
+
+from ._version import get_versions
+
+__version__ = get_versions()['version']
+del get_versions
+
+# feature_data needs to be imported before feature_table to avoid circular
+# import.
+importlib.import_module('q2_types.feature_data')
+importlib.import_module('q2_types.feature_table')
+importlib.import_module('q2_types.distance_matrix')
+importlib.import_module('q2_types.tree')
+importlib.import_module('q2_types.ordination')
+importlib.import_module('q2_types.sample_data')
+importlib.import_module('q2_types.per_sample_sequences')

q2cli/_version.py → q2_types/_version.py

@@ -24,8 +24,8 @@ def get_keywords():
     # each be defined on a line of their own. _version.py will just call
     # get_keywords().
     git_refnames = " (tag: 2019.4.0)"
-    git_full = "dc80fad32777035091692ce1083088380a6ac509"
-    git_date = "2019-05-03 04:14:45 +0000"
+    git_full = "da22ce35c8e3c3740d92867833612d753898c72c"
+    git_date = "2019-05-03 04:14:46 +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 = "q2cli-"
-    cfg.versionfile_source = "q2cli/_version.py"
+    cfg.parentdir_prefix = "q2-types-"
+    cfg.versionfile_source = "q2_types/_version.py"
     cfg.verbose = False
     return cfg
 

q2_types/citations.bib

+@article{mcdonald2012biological,
+  title={The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome},
+  author={McDonald, Daniel and Clemente, Jose C and Kuczynski, Justin and Rideout, Jai Ram and Stombaugh, Jesse and Wendel, Doug and Wilke, Andreas and Huse, Susan and Hufnagle, John and Meyer, Folker and Knight, Rob and Caporaso, J Gregory},
+  journal={GigaScience},
+  volume={1},
+  number={1},
+  pages={7},
+  year={2012},
+  publisher={BioMed Central},
+  doi={10.1186/2047-217X-1-7}
+}
+
+@InProceedings{ mckinney-proc-scipy-2010,
+  author    = { Wes McKinney },
+  title     = { Data Structures for Statistical Computing in Python },
+  booktitle = { Proceedings of the 9th Python in Science Conference },
+  pages     = { 51 -- 56 },
+  year      = { 2010 },
+  editor    = { St{\'e}fan van der Walt and Jarrod Millman }
+}

q2_types/distance_matrix/__init__.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 importlib
+
+from ._format import LSMatFormat, DistanceMatrixDirectoryFormat
+from ._type import DistanceMatrix
+
+__all__ = ['LSMatFormat', 'DistanceMatrixDirectoryFormat', 'DistanceMatrix']
+
+importlib.import_module('q2_types.distance_matrix._transformer')

q2_types/distance_matrix/_format.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 skbio.io
+import qiime2.plugin.model as model
+
+from ..plugin_setup import plugin
+
+
+class LSMatFormat(model.TextFileFormat):
+    def sniff(self):
+        sniffer = skbio.io.io_registry.get_sniffer('lsmat')
+        return sniffer(str(self))[0]
+
+
+DistanceMatrixDirectoryFormat = model.SingleFileDirectoryFormat(
+    'DistanceMatrixDirectoryFormat', 'distance-matrix.tsv', LSMatFormat)
+
+
+plugin.register_formats(LSMatFormat, DistanceMatrixDirectoryFormat)

q2_types/distance_matrix/_transformer.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 skbio
+
+from ..plugin_setup import plugin
+from . import LSMatFormat
+
+
+@plugin.register_transformer
+def _1(data: skbio.DistanceMatrix) -> LSMatFormat:
+    ff = LSMatFormat()
+    with ff.open() as fh:
+        data.write(fh, format='lsmat')
+    return ff
+
+
+@plugin.register_transformer
+def _2(ff: LSMatFormat) -> skbio.DistanceMatrix:
+    return skbio.DistanceMatrix.read(str(ff), format='lsmat', verify=False)

q2_types/distance_matrix/_type.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.
+# ----------------------------------------------------------------------------
+
+from qiime2.plugin import SemanticType
+
+from ..plugin_setup import plugin
+from . import DistanceMatrixDirectoryFormat
+
+
+DistanceMatrix = SemanticType('DistanceMatrix')
+
+plugin.register_semantic_types(DistanceMatrix)
+plugin.register_semantic_type_to_format(
+    DistanceMatrix,
+    artifact_format=DistanceMatrixDirectoryFormat
+)

q2_types/distance_matrix/tests/data/distance-matrix-1x1.tsv

+	s1
+s1	0.0