Commit 970d3394 authored by Liubov Chuprikova's avatar Liubov Chuprikova
Browse files

New upstream version 2019.10.0

parent 2b3d3033

README.md

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@@ -23,4 +23,4 @@ Please visit the [contributing page](https://github.com/qiime2/qiime2/blob/maste 
## Citing QIIME 2

If you use QIIME 2 for any published research, please include the following citation:



> Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, Alexander H, Alm EJ, Arumugam M, Asnicar F, Bai Y, Bisanz JE, Bittinger K, Brejnrod A, Brislawn CJ, Brown CT, Callahan BJ, Caraballo-Rodríguez AM, Chase J, Cope EK, Da Silva R, Diener C, Dorrestein PC, Douglas GM, Durall DM, Duvallet C, Edwardson CF, Ernst M, Estaki M, Fouquier J, Gauglitz JM, Gibbons SM, Gibson DL, Gonzalez A, Gorlick K, Guo J, Hillmann B, Holmes S, Holste H, Huttenhower C, Huttley GA, Janssen S, Jarmusch AK, Jiang L, Kaehler BD, Kang KB, Keefe CR, Keim P, Kelley ST, Knights D, Koester I, Kosciolek T, Kreps J, Langille MGI, Lee J, Ley R, Liu YX, Loftfield E, Lozupone C, Maher M, Marotz C, Martin BD, McDonald D, McIver LJ, Melnik AV, Metcalf JL, Morgan SC, Morton JT, Naimey AT, Navas-Molina JA, Nothias LF, Orchanian SB, Pearson T, Peoples SL, Petras D, Preuss ML, Pruesse E, Rasmussen LB, Rivers A, Robeson MS, Rosenthal P, Segata N, Shaffer M, Shiffer A, Sinha R, Song SJ, Spear JR, Swafford AD, Thompson LR, Torres PJ, Trinh P, Tripathi A, Turnbaugh PJ, Ul-Hasan S, van der Hooft JJJ, Vargas F, Vázquez-Baeza Y, Vogtmann E, von Hippel M, Walters W, Wan Y, Wang M, Warren J, Weber KC, Williamson CHD, Willis AD, Xu ZZ, Zaneveld JR, Zhang Y, Zhu Q, Knight R, and Caporaso JG. 2019. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nature Biotechnology. https://doi.org/10.1038/s41587-019-0209-9
 
> Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, Alexander H, Alm EJ, Arumugam M, Asnicar F, Bai Y, Bisanz JE, Bittinger K, Brejnrod A, Brislawn CJ, Brown CT, Callahan BJ, Caraballo-Rodríguez AM, Chase J, Cope EK, Da Silva R, Diener C, Dorrestein PC, Douglas GM, Durall DM, Duvallet C, Edwardson CF, Ernst M, Estaki M, Fouquier J, Gauglitz JM, Gibbons SM, Gibson DL, Gonzalez A, Gorlick K, Guo J, Hillmann B, Holmes S, Holste H, Huttenhower C, Huttley GA, Janssen S, Jarmusch AK, Jiang L, Kaehler BD, Kang KB, Keefe CR, Keim P, Kelley ST, Knights D, Koester I, Kosciolek T, Kreps J, Langille MGI, Lee J, Ley R, Liu YX, Loftfield E, Lozupone C, Maher M, Marotz C, Martin BD, McDonald D, McIver LJ, Melnik AV, Metcalf JL, Morgan SC, Morton JT, Naimey AT, Navas-Molina JA, Nothias LF, Orchanian SB, Pearson T, Peoples SL, Petras D, Preuss ML, Pruesse E, Rasmussen LB, Rivers A, Robeson MS, Rosenthal P, Segata N, Shaffer M, Shiffer A, Sinha R, Song SJ, Spear JR, Swafford AD, Thompson LR, Torres PJ, Trinh P, Tripathi A, Turnbaugh PJ, Ul-Hasan S, van der Hooft JJJ, Vargas F, Vázquez-Baeza Y, Vogtmann E, von Hippel M, Walters W, Wan Y, Wang M, Warren J, Weber KC, Williamson CHD, Willis AD, Xu ZZ, Zaneveld JR, Zhang Y, Zhu Q, Knight R, and Caporaso JG. 2019. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nature Biotechnology 37:852–857. https://doi.org/10.1038/s41587-019-0209-9

ci/recipe/meta.yaml

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    - python {{ python }}

    - pyyaml

    - decorator

    # TODO: unset this pin once pandas 0.25.x is sorted out

    - pandas 0.24.2

    - pandas

    - tzlocal

    - python-dateutil

    - pyparsing ==2.3.0

    - bibtexparser

    - networkx

qiime2/_version.py

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@@ -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: 2019.7.0)"

    git_full = "a7d3da5a733aa14749c21ddda969e7ccd403c311"

    git_date = "2019-07-30 18:15:55 +0000"

    git_refnames = " (tag: 2019.10.0)"

    git_full = "1ef06fd6c0c78b41777afc7688d45e69d22a693b"

    git_date = "2019-11-01 01:04:24 +0000"

    keywords = {"refnames": git_refnames, "full": git_full, "date": git_date}

    return keywords

qiime2/citations.bib

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  title={Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2},

  journal={Nature Biotechnology},

  year={2019},

  volume={37},

  number={8},

  pages={852-857},

  issn={1546-1696},

  doi={10.1038/s41587-019-0209-9},

  url={https://doi.org/10.1038/s41587-019-0209-9}

qiime2/core/type/primitive.py

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@@ -419,12 +419,12 @@ class _MetadataColumn(_PrimitiveTemplateBase): 
            raise TypeError("Unsupported type in field: %r"

                            % (field.get_name(),))



    def decode(self, metadata):

    def decode(self, value):

        # This interface should have already retrieved this object.

        if not self.is_element(metadata):

        if not isinstance(value, metadata.MetadataColumn):

            raise TypeError("`Metadata` must be provided by the interface"

                            " directly.")

        return metadata

        return value



    def encode(self, value):

        # TODO: Should this be the provenance representation? Does that affect