Merge pull request #3181 from antgonza/docs-improvements

fix #3170 + others

Author: charles-cowart

qiita_pet/support_files/doc/source/checklist-for-ebi-ena-submission.rst

@@ -15,6 +15,16 @@ applies for studies in sandbox state that will become private or public.
 .. warning::
    direct BIOM uploads cannot become private or public
 
+.. note::
+    The EBI-ENA submission returns two accessions - the primary starts with PRJ
+    and the secondary with ERP; they can be used interchangeably. We suggest that
+    you add at least one of them to your manuscript, together with the Qiita Study id.
+    Please do not forget to cite Qiita (https://doi.org/10.1038/s41592-018-0141-9).
+    This information should be sufficient for your manuscript but if you would like
+    to add direct links to your data, once they are public, you can use the EBI-ENA:
+    `https://www.ebi.ac.uk/ena/browser/view/[accession]` or the Qiita Study
+    id: `https://qiita.ucsd.edu/public/?study_id=[study-id]`
+
 `Here <https://knightlab.ucsd.edu/wordpress/wp-content/uploads/2016/04/QiitaTemplate_20181218.xlsx>`__ you will find a document outlining these requirements, with examples, when possible.
 
 Note that submissions are time consuming and need full collaboration from the user.
@@ -140,6 +150,7 @@ Remember, metadata is the most important part for an analysis, without it we onl
 
       .. note::
         The current valid values for instrument_model per platform are - please contact us if you would like to add yours to this list:
+
         +---------------------+----------------------------------------------------------------------------------------------------------+
         | Platform            | Valid instrument_model options                                                                           |
         +=====================+==========================================================================================================+
@@ -150,7 +161,7 @@ Remember, metadata is the most important part for an analysis, without it we onl
         |                     |  ``Illumina Genome Analyzer IIx``, ``Illumina HiScanSQ``, ``Illumina HiSeq 1000``,                       |
         |                     |  ``Illumina HiSeq 1500``,, ``Illumina HiSeq 2000``, ``Illumina HiSeq 2500``, ``Illumina HiSeq 3000``,    |
         |                     |  ``Illumina HiSeq 4000``, ``Illumina MiSeq``, ``Illumina MiniSeq``, ``Illumina NovaSeq 6000``,           |
-        |                     |  ``NextSeq 500``, ``NextSeq 550``, ``Illumina NovaSeq 6000`` or ``unspecified``                          |
+        |                     |  ``NextSeq 500``, ``NextSeq 550``, or ``unspecified``                                                    |
         +---------------------+----------------------------------------------------------------------------------------------------------+
         | ``Ion_Torrent``     |  ``Ion Torrent PGM``, ``Ion Torrent Proton``, ``Ion Torrent S5``, ``Ion Torrent S5 XL``                  |
         +---------------------+----------------------------------------------------------------------------------------------------------+

qiita_pet/support_files/doc/source/conf.py

@@ -23,6 +23,7 @@
 
 import sys
 import os
+from qiita_db import __version__ as qiita_version
 
 import sphinx_bootstrap_theme
 
@@ -64,9 +65,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = '0.1.0-dev'
+version = qiita_version
 # The full version, including alpha/beta/rc tags.
-release = '0.1.0-dev'
+release = qiita_version
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

qiita_pet/support_files/doc/source/downloading.rst

@@ -14,8 +14,17 @@ artifacts public and select "Allow Qiita users to download raw data files" from
 the main study page.
 
 .. note::
-   Note that all Qiita downloads are zip files but the name of the file will change based on the tool you use to download them. For example if you are using wget, we recommend adding the URL in quotes and using the -O flag to save the file with a correct name; like this: wget "your-qiita-URL" -O your_filename.zip
-
+   - All Qiita downloads are zip files but the name of the file will change based
+     on the tool you use to download them. For example if you are using wget,
+     we recommend adding the URL in quotes and using the -O flag to save the
+     file with a correct name; like this:
+     `wget "your-qiita-URL" -O your_filename.zip`.
+   - The downloaded zip file is a dump of our storage with the data you requested
+     organized by the data type. This is, when unzipped the contents will be
+     in folders by the type (`mapping_file, BIOM, per_sample_FASTQ, processed_data,
+     etc`) and within each you will have (a) folder(s) with the artifact id(s) download;
+     each of these folders will have the files of that artifact: `biom, txt, fastq.gz,
+     index.html, etc.`
 
 Downloading All Public Data in BIOM format
 ------------------------------------------

setup.py

@@ -105,8 +105,8 @@
       install_requires=['psycopg2', 'click', 'bcrypt', 'pandas',
                         'biom-format', 'tornado<6.0', 'toredis', 'redis',
                         'scp', 'pyparsing', 'h5py',  'natsort', 'nose', 'pep8',
-                        'networkx', 'humanize', 'wtforms<3.0.0',
-                        'openpyxl', 'sphinx-bootstrap-theme', 'Sphinx', 'nltk',
+                        'networkx', 'humanize', 'wtforms<3.0.0', 'nltk',
+                        'openpyxl', 'sphinx-bootstrap-theme', 'Sphinx<3.0',
                         'gitpython', 'redbiom', 'pyzmq', 'sphinx_rtd_theme',
                         'paramiko', 'seaborn',  'matplotlib', 'scipy', 'nose',
                         'flake8', 'six', 'qiita-files @ https://github.com/'