.github/ISSUE_TEMPLATE/6-where-to-go.md

@@ -14,9 +14,6 @@ Sorted alphabetically by repo name.
 - A Concourse resource for working with conda
   https://github.com/qiime2/conda-channel-resource/issues
 
-- Old conda recipes (repo is mostly unused now)
-  https://github.com/qiime2/conda-recipes/issues
-
 - Web app for vanity URLs for QIIME 2 data assets
   https://github.com/qiime2/data.qiime2.org/issues
 
@@ -71,6 +68,9 @@ Sorted alphabetically by repo name.
 - The q2-feature-table plugin
   https://github.com/qiime2/q2-feature-table/issues
 
+- The q2-fragment-insertion plugin
+  https://github.com/qiime2/q2-fragment-insertion/issues
+
 - The q2-gneiss plugin
   https://github.com/qiime2/q2-gneiss/issues
 
@@ -92,6 +92,9 @@ Sorted alphabetically by repo name.
 - The q2-sample-classifier plugin
   https://github.com/qiime2/q2-sample-classifier/issues
 
+- The q2-shogun plugin
+  https://github.com/qiime2/q2-shogun/issues
+
 - The q2-taxa plugin
   https://github.com/qiime2/q2-taxa/issues
 

.github/SUPPORT.md

@@ -22,8 +22,6 @@ Sorted alphabetically by repo name.
   | The CI automation engine that builds and distributes QIIME 2
 - [conda-channel-resource](https://github.com/qiime2/conda-channel-resource/issues)
   | A Concourse resource for working with conda
-- [conda-recipes](https://github.com/qiime2/conda-recipes/issues)
-  | Old conda recipes (repo is mostly unused now)
 - [data.qiime2.org](https://github.com/qiime2/data.qiime2.org/issues)
   | Web app for vanity URLs for QIIME 2 data assets
 - [dev-docs](https://github.com/qiime2/dev-docs/issues)
@@ -60,6 +58,8 @@ Sorted alphabetically by repo name.
   | The q2-feature-classifier plugin
 - [q2-feature-table](https://github.com/qiime2/q2-feature-table/issues)
   | The q2-feature-table plugin
+- [q2-fragment-insertion](https://github.com/qiime2/q2-fragment-insertion/issues)
+  | The q2-fragment-insertion plugin
 - [q2-gneiss](https://github.com/qiime2/q2-gneiss/issues)
   | The q2-gneiss plugin
 - [q2-longitudinal](https://github.com/qiime2/q2-longitudinal/issues)
@@ -74,6 +74,8 @@ Sorted alphabetically by repo name.
   | The q2-quality-filter plugin
 - [q2-sample-classifier](https://github.com/qiime2/q2-sample-classifier/issues)
   | The q2-sample-classifier plugin
+- [q2-shogun](https://github.com/qiime2/q2-shogun/issues)
+  | The q2-shogun plugin
 - [q2-taxa](https://github.com/qiime2/q2-taxa/issues)
   | The q2-taxa plugin
 - [q2-types](https://github.com/qiime2/q2-types/issues)

.travis.yml

@@ -11,8 +11,8 @@ before_install:
   - conda update -q conda
   - conda info -a
 install:
-  - wget -q https://raw.githubusercontent.com/qiime2/environment-files/master/latest/staging/qiime2-latest-py35-linux-conda.yml
-  - conda env create -q -n test-env --file qiime2-latest-py35-linux-conda.yml
+  - 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
   - pip install -q flake8
   - conda install nose

LICENSE

 BSD 3-Clause License
 
-Copyright (c) 2016-2018, QIIME 2 development team.
+Copyright (c) 2016-2019, QIIME 2 development team.
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

Makefile

 .PHONY: all lint test install dev clean distclean
 
+PYTHON ?= python
+PREFIX ?= $(CONDA_PREFIX)
+
 all: ;
 
 lint:
@@ -10,11 +13,11 @@ test: all
 	QIIMETEST= nosetests
 
 install: all
-	python setup.py install && \
-	mkdir -p $(CONDA_PREFIX)/etc/conda/activate.d && \
-	cp hooks/00_activate_qiime2_envs.sh $(CONDA_PREFIX)/etc/conda/activate.d/ && \
-	mkdir -p $(CONDA_PREFIX)/etc/conda/deactivate.d && \
-	cp hooks/00_deactivate_qiime2_envs.sh $(CONDA_PREFIX)/etc/conda/deactivate.d/
+	$(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/
 
 dev: all
 	pip install -e .

ci/recipe/conda_build_config.yaml

+python:
+  - 3.6

ci/recipe/meta.yaml

@@ -12,18 +12,18 @@ build:
   script: make install
 
 requirements:
-  build:
-    - python 3.5*
+  host:
+    - python {{ python }}
     - setuptools
 
   run:
-    - python 3.5*
-    - setuptools
+    - python {{ python }}
     - pyyaml
     - decorator
     - pandas
     - tzlocal
     - python-dateutil
+    - pyparsing ==2.3.0
     - bibtexparser
 
 test:

debian/changelog

-qiime (2018.8.0-1) UNRELEASED; urgency=medium
+qiime (2019.1.0-1) unstable; urgency=medium
 
   [ Andreas Tille ]
   * Switch to Qiime2
+    Closes: #820308
      - Adapt watch file
      - Point Homepage to Qiime2
+  * debhelper 12
+  * Architecture: all
 
   [ Liubov Chuprikova ]
   * Make .egg-info available for build time tests
   * Adapt d/copyright to Qiime2
-  * Standards-Version: 4.2.1
+  * Standards-Version: 4.3.0
 
- -- Andreas Tille <tille@debian.org>  Fri, 19 Oct 2018 15:20:48 +0200
+ -- Andreas Tille <tille@debian.org>  Mon, 04 Feb 2019 11:37:46 +0100
 
 qiime (1.9.1+dfsg-3) unstable; urgency=medium
 

debian/compat

-11
+12

debian/control

@@ -5,9 +5,9 @@ Uploaders: Steffen Moeller <moeller@debian.org>,
            Andreas Tille <tille@debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 11~),
+Build-Depends: debhelper (>= 12~),
                dh-python,
-               python3-dev,
+               python3,
                python3-setuptools,
                python3-nose,
                python3-bibtexparser,
@@ -15,13 +15,13 @@ Build-Depends: debhelper (>= 11~),
                python3-pandas,
                python3-tzlocal,
                python3-yaml
-Standards-Version: 4.2.1
+Standards-Version: 4.3.0
 Vcs-Browser: https://salsa.debian.org/med-team/qiime
 Vcs-Git: https://salsa.debian.org/med-team/qiime.git
 Homepage: https://qiime2.org
 
 Package: qiime
-Architecture: any
+Architecture: all
 Depends: ${shlibs:Depends},
          ${misc:Depends},
          ${python3:Depends},

debian/patches/0000_fixme_hack_around_UnicodeDecodeError_in_bibtex.patch

---- a/qiime2/citations.bib
-+++ b/qiime2/citations.bib
-@@ -1,6 +1,6 @@
- @article{caporaso2010qiime,
-   title={QIIME allows analysis of high-throughput community sequencing data},
--  author={Caporaso, J Gregory and Kuczynski, Justin and Stombaugh, Jesse and Bittinger, Kyle and Bushman, Frederic D and Costello, Elizabeth K and Fierer, Noah and Peña, Antonio Gonzalez and Goodrich, Julia K and Gordon, Jeffrey I and Huttley, Gavin A and Kelley, Scott T and Knights, Dan and Koenig, Jeremy E and Ley, Ruth E and Lozupone, Catherine A and McDonald, Daniel and Muegge, Brian D and Pirrung, Meg and Reeder, Jens and Sevinsky, Joel R and Turnbaugh, Peter J and Walters, William A and Widmann, Jeremy and Yatsunenko, Tanya and Zaneveld, Jesse and Knight, Rob},
-+  author={Caporaso, J Gregory and Kuczynski, Justin and Stombaugh, Jesse},
-   journal={Nature methods},
-   volume={7},
-   number={5},

debian/patches/series

-0000_fixme_hack_around_UnicodeDecodeError_in_bibtex.patch

qiime2/__init__.py

 # ----------------------------------------------------------------------------
-# Copyright (c) 2016-2018, QIIME 2 development team.
+# Copyright (c) 2016-2019, QIIME 2 development team.
 #
 # Distributed under the terms of the Modified BSD License.
 #

qiime2/_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: 2018.8.0)"
-    git_full = "d29dc72666a15730d5f73bfe15fe2093228ccd33"
-    git_date = "2018-08-31 15:55:45 +0000"
+    git_refnames = " (tag: 2019.1.0)"
+    git_full = "58cb1e54f57e10fdbf9b032d8192e6089123fed4"
+    git_date = "2019-01-29 14:00:34 +0000"
     keywords = {"refnames": git_refnames, "full": git_full, "date": git_date}
     return keywords
 

qiime2/citations.bib

-@article{caporaso2010qiime,
-  title={QIIME allows analysis of high-throughput community sequencing data},
-  author={Caporaso, J Gregory and Kuczynski, Justin and Stombaugh, Jesse and Bittinger, Kyle and Bushman, Frederic D and Costello, Elizabeth K and Fierer, Noah and Peña, Antonio Gonzalez and Goodrich, Julia K and Gordon, Jeffrey I and Huttley, Gavin A and Kelley, Scott T and Knights, Dan and Koenig, Jeremy E and Ley, Ruth E and Lozupone, Catherine A and McDonald, Daniel and Muegge, Brian D and Pirrung, Meg and Reeder, Jens and Sevinsky, Joel R and Turnbaugh, Peter J and Walters, William A and Widmann, Jeremy and Yatsunenko, Tanya and Zaneveld, Jesse and Knight, Rob},
-  journal={Nature methods},
-  volume={7},
-  number={5},
-  pages={335},
-  year={2010},
-  publisher={Nature Publishing Group},
-  doi={10.1038/nmeth.f.303}
+@article{10.7287/peerj.preprints.27295v1,
+ title = {QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science},
+ author = {Bolyen, Evan and Rideout, Jai Ram and Dillon, Matthew R and Bokulich, Nicholas A and Abnet, Christian and Al-Ghalith, Gabriel A and Alexander, Harriet and Alm, Eric J and Arumugam, Manimozhiyan and Asnicar, Francesco and Bai, Yang and Bisanz, Jordan E and Bittinger, Kyle and Brejnrod, Asker and Brislawn, Colin J and Brown, C Titus and Callahan, Benjamin J and Caraballo-Rodríguez, Andrés Mauricio and Chase, John and Cope, Emily and Da Silva, Ricardo and Dorrestein, Pieter C and Douglas, Gavin M and Durall, Daniel M and Duvallet, Claire and Edwardson, Christian F and Ernst, Madeleine and Estaki, Mehrbod and Fouquier, Jennifer and Gauglitz, Julia M and Gibson, Deanna L and Gonzalez, Antonio and Gorlick, Kestrel and Guo, Jiarong and Hillmann, Benjamin and Holmes, Susan and Holste, Hannes and Huttenhower, Curtis and Huttley, Gavin and Janssen, Stefan and Jarmusch, Alan K and Jiang, Lingjing and Kaehler, Benjamin and Kang, Kyo Bin and Keefe, Christopher R and Keim, Paul and Kelley, Scott T and Knights, Dan and Koester, Irina and Kosciolek, Tomasz and Kreps, Jorden and Langille, Morgan GI and Lee, Joslynn and Ley, Ruth and Liu, Yong-Xin and Loftfield, Erikka and Lozupone, Catherine and Maher, Massoud and Marotz, Clarisse and Martin, Bryan and McDonald, Daniel and McIver, Lauren J and Melnik, Alexey V and Metcalf, Jessica L and Morgan, Sydney C and Morton, Jamie and Naimey, Ahmad Turan and Navas-Molina, Jose A and Nothias, Louis Felix and Orchanian, Stephanie B and Pearson, Talima and Peoples, Samuel L and Petras, Daniel and Preuss, Mary Lai and Pruesse, Elmar and Rasmussen, Lasse Buur and Rivers, Adam and Robeson, II, Michael S and Rosenthal, Patrick and Segata, Nicola and Shaffer, Michael and Shiffer, Arron and Sinha, Rashmi and Song, Se Jin and Spear, John R and Swafford, Austin D and Thompson, Luke R and Torres, Pedro J and Trinh, Pauline and Tripathi, Anupriya and Turnbaugh, Peter J and Ul-Hasan, Sabah and van der Hooft, Justin JJ and Vargas, Fernando and Vázquez-Baeza, Yoshiki and Vogtmann, Emily and von Hippel, Max and Walters, William and Wan, Yunhu and Wang, Mingxun and Warren, Jonathan and Weber, Kyle C and Williamson, Chase HD and Willis, Amy D and Xu, Zhenjiang Zech and Zaneveld, Jesse R and Zhang, Yilong and Knight, Rob and Caporaso, J Gregory},
+ year = 2018,
+ month = {oct},
+ volume = 6,
+ pages = {e27295v1},
+ journal = {PeerJ Preprints},
+ issn = {2167-9843},
+ url = {https://doi.org/10.7287/peerj.preprints.27295v1},
+ doi = {10.7287/peerj.preprints.27295v1}
 }

qiime2/core/__init__.py

 # ----------------------------------------------------------------------------
-# Copyright (c) 2016-2018, QIIME 2 development team.
+# Copyright (c) 2016-2019, QIIME 2 development team.
 #
 # Distributed under the terms of the Modified BSD License.
 #

qiime2/core/archive/__init__.py

 # ----------------------------------------------------------------------------
-# Copyright (c) 2016-2018, QIIME 2 development team.
+# Copyright (c) 2016-2019, QIIME 2 development team.
 #
 # Distributed under the terms of the Modified BSD License.
 #

qiime2/core/archive/archiver.py

 # ----------------------------------------------------------------------------
-# Copyright (c) 2016-2018, QIIME 2 development team.
+# Copyright (c) 2016-2019, QIIME 2 development team.
 #
 # Distributed under the terms of the Modified BSD License.
 #
@@ -17,6 +17,8 @@ import io
 import qiime2
 import qiime2.core.cite as cite
 
+from qiime2.core.util import md5sum_directory, from_checksum_format
+
 _VERSION_TEMPLATE = """\
 QIIME 2
 archive: %s
@@ -27,6 +29,9 @@ ArchiveRecord = collections.namedtuple(
     'ArchiveRecord', ['root', 'version_fp', 'uuid', 'version',
                       'framework_version'])
 
+ChecksumDiff = collections.namedtuple(
+    'ChecksumDiff', ['added', 'removed', 'changed'])
+
 
 class _Archive:
     """Abstraction layer over the archive filesystem.
@@ -223,7 +228,7 @@ class _ZipArchive(_Archive):
 
 
 class Archiver:
-    CURRENT_FORMAT_VERSION = '4'
+    CURRENT_FORMAT_VERSION = '5'
     CURRENT_ARCHIVE = _ZipArchive
     _FORMAT_REGISTRY = {
         # NOTE: add more archive formats as things change
@@ -232,6 +237,7 @@ class Archiver:
         '2': 'qiime2.core.archive.format.v2:ArchiveFormat',
         '3': 'qiime2.core.archive.format.v3:ArchiveFormat',
         '4': 'qiime2.core.archive.format.v4:ArchiveFormat',
+        '5': 'qiime2.core.archive.format.v5:ArchiveFormat'
     }
 
     @classmethod
@@ -346,6 +352,25 @@ class Archiver:
     def save(self, filepath):
         self.CURRENT_ARCHIVE.save(self.path, filepath)
 
+    def validate_checksums(self):
+        if not isinstance(self._fmt, self.get_format_class('5')):
+            return ChecksumDiff({}, {}, {})
+
+        obs = dict(x for x in md5sum_directory(str(self.root_dir)).items()
+                   if x[0] != self._fmt.CHECKSUM_FILE)
+        exp = dict(from_checksum_format(line) for line in
+                   (self.root_dir / self._fmt.CHECKSUM_FILE).open().readlines()
+                   )
+        obs_keys = set(obs)
+        exp_keys = set(exp)
+
+        added = {x: obs[x] for x in obs_keys - exp_keys}
+        removed = {x: exp[x] for x in exp_keys - obs_keys}
+        changed = {x: (exp[x], obs[x]) for x in exp_keys & obs_keys
+                   if exp[x] != obs[x]}
+
+        return ChecksumDiff(added=added, removed=removed, changed=changed)
+
     @property
     def _destructor(self):
         return self.path._destructor

qiime2/core/archive/format/__init__.py

 # ----------------------------------------------------------------------------
-# Copyright (c) 2016-2018, QIIME 2 development team.
+# Copyright (c) 2016-2019, QIIME 2 development team.
 #
 # Distributed under the terms of the Modified BSD License.
 #

qiime2/core/archive/format/tests/__init__.py

 # ----------------------------------------------------------------------------
-# Copyright (c) 2016-2018, QIIME 2 development team.
+# Copyright (c) 2016-2019, QIIME 2 development team.
 #
 # Distributed under the terms of the Modified BSD License.
 #