2021.03 (#3084)

antgonza · web-flow · commit e9f6190b734b · 2021-03-18T17:29:06.000-07:00
* 2021.03

* add Command.processing_jobs to changelog

* codecov

* codecov required

* codecov token
diff --git a/.github/workflows/qiita-ci.yml b/.github/workflows/qiita-ci.yml
@@ -187,8 +187,8 @@ jobs:
 
       - uses: codecov/codecov-action@v1
         with:
+         token: ${{ secrets.CODECOV_TOKEN }}
          file: codecov.yml
-         fail_ci_if_error: true
 
   lint:
     runs-on: ubuntu-latest
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,6 +1,19 @@
 # Qiita changelog
 
 
+Version 2021.03
+---------------
+
+* Fixed [issue](https://github.com/qiita-spots/qtp-target-gene/issues/32) that left behind non gz per sample FASTQ files.
+* [Recommended Workflows](https://qiita-rc.ucsd.edu/workflows/) are now stored in the database.
+* Added a new button only for owners and admins within the Study page to display a list of all the Analyses generated with that study; helpful to clean up Studies and for general information.
+* The Qiita CI now runs as [GitHub Actions](https://github.com/qiita-spots/qiita/actions); moving away from Travis CI.
+* Prep information file object now stores its creation and modification timestamps.
+* Improved creation time for all information files via the to_dataframe() method.
+* Split the "other" category of the storage stats plot (https://qiita.ucsd.edu/stats/) into "other" and "biom" so biom can be its own category.
+* Added a processing_jobs property to qiita_db.software.Command to easily retrieve all jobs in the system that have ran the given command.
+* Fixed the following issues: [#3068](https://github.com/qiita-spots/qiita/issues/3068), [#3072](https://github.com/qiita-spots/qiita/issues/3072), [#3076](https://github.com/qiita-spots/qiita/issues/3076), and [#3070](https://github.com/qiita-spots/qiita/issues/3070).
+
 Version 2021.01
 ---------------
 
diff --git a/codecov.yml b/codecov.yml
@@ -1,2 +1,6 @@
 ignore:
-  - "qiita_db/support_files/**/*"
+    - "qiita_db/support_files/**/*"
+
+codecov:
+    max_report_age: off
+    require_ci_to_pass: yes
diff --git a/qiita_core/__init__.py b/qiita_core/__init__.py
@@ -6,4 +6,4 @@
 # The full license is in the file LICENSE, distributed with this software.
 # -----------------------------------------------------------------------------
 
-__version__ = "2021.01"
+__version__ = "2021.03"
diff --git a/qiita_db/__init__.py b/qiita_db/__init__.py
@@ -27,7 +27,7 @@
 from . import user
 from . import processing_job
 
-__version__ = "2021.01"
+__version__ = "2021.03"
 
 __all__ = ["analysis", "artifact",  "archive", "base", "commands",
            "environment_manager", "exceptions", "investigation", "logger",
diff --git a/qiita_pet/__init__.py b/qiita_pet/__init__.py
@@ -6,4 +6,4 @@
 # The full license is in the file LICENSE, distributed with this software.
 # -----------------------------------------------------------------------------
 
-__version__ = "2021.01"
+__version__ = "2021.03"
diff --git a/qiita_pet/handlers/api_proxy/__init__.py b/qiita_pet/handlers/api_proxy/__init__.py
@@ -38,7 +38,7 @@
 from .user import (user_jobs_get_req)
 from .util import check_access, check_fp
 
-__version__ = "2021.01"
+__version__ = "2021.03"
 
 __all__ = ['prep_template_summary_get_req', 'data_types_get_req',
            'study_get_req', 'sample_template_filepaths_get_req',
diff --git a/qiita_pet/support_files/doc/source/checklist-for-ebi-ena-submission.rst b/qiita_pet/support_files/doc/source/checklist-for-ebi-ena-submission.rst
@@ -1,14 +1,18 @@
 .. role:: red
 
-Send data to EBI-ENA
-====================
+Making data Public in Qiita and/or send data to EBI-ENA
+=======================================================
 
 Qiita allows users to deposit their study, sample, experiment and sequence data to the
 `European Nucleotide Archive (ENA) <https://www.ebi.ac.uk/ena>`__, which is the permanent data
 repository of the `European Bioinformatics Institute (EBI) <https://www.ebi.ac.uk/>`__. Submitting to
 this repository will provide you with a unique identifier for your study, which is generally a
 requirement for publications. Your study will be housed with all other Qiita submissions
-and so we require adherence to the `MiXs standard <http://gensc.org/mixs/>`__.
+and so we require adherence to the `MiXs standard <http://gensc.org/mixs/>`__. Note that this also
+applies for studies in sandbox state that will become private or public.
+
+.. warning::
+   direct BIOM uploads cannot become private or public
 
 `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.
 
diff --git a/qiita_pet/support_files/doc/source/faq.rst b/qiita_pet/support_files/doc/source/faq.rst
@@ -209,6 +209,8 @@ To correct this issue, simply add a column to your preparation information file
 "run_prefix". In this column, add the sample names from your BIOM table that matches the sample
 names listed in the sample_name column in your preparation information file.
 
+As a reminder, direct BIOM uploads cannot become public in the system.
+
 
 What's a Qiita Artifact?
 ------------------------
diff --git a/qiita_pet/support_files/doc/source/index.rst b/qiita_pet/support_files/doc/source/index.rst
@@ -26,6 +26,7 @@ Looking for information about getting started? Please see the document here:
 .. toctree::
 
    gettingstartedguide/index.rst
+   qiita-philosophy/index.rst
    qiimp.rst
 
 Looking for information about how to process your data? Please see the document here:
@@ -73,6 +74,5 @@ If you intend to deploy or develop Qiita we recommend that you have a look at th
 
 .. toctree::
 
-   qiita-philosophy/index.rst
    admin/index.rst
    dev/index.rst
diff --git a/qiita_pet/support_files/doc/source/qiita-philosophy/index.rst b/qiita_pet/support_files/doc/source/qiita-philosophy/index.rst
@@ -15,13 +15,6 @@ system, from raw sequence to contingency tables or even data visualizations,
 permits the system to store any kind of data but also define within each
 pipelines which commands and parameters can applied to them.
 
-The current plugins available are:
-
-* Target gene processing via `QIIME <http://qiime.org>`__: sequence
-  demultiplexing, and QC of SFF, fasta/qual, fastq and per sample fastq.
-  Closed reference OTU picking.
-* BIOM table analysis via `QIIME2 <http://qiime2.org>`__: rarefaction, filtering, alpha diversity, beta diversity, alpha correlation, beta correlation, and principal coordinate analysis
-
 A Study
 -------
 
diff --git a/qiita_ware/__init__.py b/qiita_ware/__init__.py
@@ -6,4 +6,4 @@
 # The full license is in the file LICENSE, distributed with this software.
 # -----------------------------------------------------------------------------
 
-__version__ = "2021.01"
+__version__ = "2021.03"
diff --git a/setup.py b/setup.py
@@ -10,7 +10,7 @@
 from setuptools import setup
 from glob import glob
 
-__version__ = "2021.01"
+__version__ = "2021.03"
 
 
 classes = """
