changes for 2025.07 (#3479)

* changes for 2025.07

* self.assertEqual -> self.assertCountEqual

Author: antgonza

CHANGELOG.md

@@ -1,5 +1,20 @@
 # Qiita changelog
 
+Version 2025.07
+---------------
+
+Deployed on July 14th, 2025
+
+* During EBI-ENA submissions now we automatically renmae `country` to `geographic location (country and/or sea)` and `collection_date` to `collection date`; as the ENA requirements changed.
+* Added platform `DNBSEQ1` and instruments: `DNBSEQ-G400`, `DNBSEQ-T7`, `DNBSEQ-G800` for EBI-ENA submissions.
+* Other general fixes [#3474](https://github.com/qiita-spots/qiita/pull/3474), [#3475](https://github.com/qiita-spots/qiita/pull/3475).
+* SPP: merged and deprecated [mg-scripts](https://github.com/qiita-spots/mg-scripts) to [qp-knight-lab-processing](https://github.com/qiita-spots/qp-knight-lab-processing).
+* SPP: Added integration tests via a couple of PRs: [#129](https://github.com/qiita-spots/qp-knight-lab-processing/pull/129) & [#131](https://github.com/qiita-spots/qp-knight-lab-processing/pull/131).
+* SPP: Added new command `Human Filter & QC existing Prep` to facilitate human-filtering existing preparations.
+* SPP: Cleaned and centralized sequencers information to [kl-metapool](https://github.com/biocore/kl-metapool) & added `MiSeq i100`, thank you @AmandaBirmingham.
+
+
+
 Version 2025.04
 ---------------
 
@@ -10,6 +25,7 @@ Deployed on April 11th, 2025
 * SPP: General updates and clean up: [#169](https://github.com/biocore/mg-scripts/pull/169), [#101](https://github.com/qiita-spots/qp-knight-lab-processing/pull/101).
 * `Remove SynDNA plasmid, insert, & CP026085 reads` superseded `Remove SynDNA inserts & plasmid reads`; which now removes SynDNA plasmids, inserts, and CP026085 reads, in this order.
 
+
 Version 2025.02
 ---------------
 

qiita_core/__init__.py

@@ -6,4 +6,4 @@
 # The full license is in the file LICENSE, distributed with this software.
 # -----------------------------------------------------------------------------
 
-__version__ = "2025.04"
+__version__ = "2025.07"

qiita_db/__init__.py

@@ -27,7 +27,7 @@
 from . import user
 from . import processing_job
 
-__version__ = "2025.04"
+__version__ = "2025.07"
 
 __all__ = ["analysis", "artifact",  "archive", "base", "commands",
            "environment_manager", "exceptions", "investigation", "logger",

qiita_db/test/test_user.py

@@ -482,12 +482,12 @@ def test_mark_messages(self):
         user.mark_messages([1, 2])
         obs = user.messages()
         exp = [True, True, False]
-        self.assertEqual([x[3] for x in obs], exp)
+        self.assertCountEqual([x[3] for x in obs], exp)
 
         user.mark_messages([1], read=False)
         obs = user.messages()
         exp = [False, True, False]
-        self.assertEqual([x[3] for x in obs], exp)
+        self.assertCountEqual([x[3] for x in obs], exp)
 
     def test_delete_messages(self):
         user = qdb.user.User.create('[email protected]', 'password')

qiita_pet/__init__.py

@@ -6,4 +6,4 @@
 # The full license is in the file LICENSE, distributed with this software.
 # -----------------------------------------------------------------------------
 
-__version__ = "2025.04"
+__version__ = "2025.07"

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__ = "2025.04"
+__version__ = "2025.07"
 
 __all__ = ['prep_template_summary_get_req', 'data_types_get_req',
            'study_get_req', 'sample_template_filepaths_get_req',

qiita_pet/templates/study_ajax/prep_summary.html

@@ -433,11 +433,12 @@ <h4>
       {% end %}
 
       <span id="prep-name-span">{{name}}</span> - ID {{prep_id}} ({{data_type}})
-      {% if user_level in ('admin', 'wet-lab admin') and creation_job is not None %}
-          <a class="btn btn-default" download="{{creation_job_filename}}" href="data:text/plain;charset=utf-8,{{creation_job_filename_body}}"><span class="glyphicon glyphicon-download-alt"></span> SampleSheet</a>
-          {% if creation_job_artifact_summary is not None %}
-            <a class="btn btn-default" target="_blank" href="{% raw qiita_config.portal_dir %}/artifact/html_summary/{{creation_job_artifact_summary}}"><span class="glyphicon glyphicon-download-alt"></span> Creation Job Output</a>
+
+      {% if editable and creation_job is not None and creation_job_artifact_summary is not None %}
+          {% if creation_job_filename != 'None' %}
+             <a class="btn btn-default" download="{{creation_job_filename}}" href="data:text/plain;charset=utf-8,{{creation_job_filename_body}}"><span class="glyphicon glyphicon-download-alt"></span> SampleSheet</a>
           {% end %}
+          <a class="btn btn-default" target="_blank" href="{% raw qiita_config.portal_dir %}/artifact/html_summary/{{creation_job_artifact_summary}}"><span class="glyphicon glyphicon-download-alt"></span> Creation Job Output</a>
       {% end %}
       <a class="btn btn-default" data-toggle="modal" data-target="#update-prep-name"><span class="glyphicon glyphicon-pencil"></span> Edit name</a>
       <a class="btn btn-default" href="{% raw qiita_config.portal_dir %}/download/{{download_prep_id}}"><span class="glyphicon glyphicon-download-alt"></span> Prep info</a>

qiita_ware/__init__.py

@@ -6,4 +6,4 @@
 # The full license is in the file LICENSE, distributed with this software.
 # -----------------------------------------------------------------------------
 
-__version__ = "2025.04"
+__version__ = "2025.07"

setup.py

@@ -10,7 +10,7 @@
 from setuptools import setup
 from glob import glob
 
-__version__ = "2025.04"
+__version__ = "2025.07"
 
 
 classes = """