Merge branch 'dev' of github.com:biocore/qiita

Author: antgonza

.github/workflows/qiita-ci.yml

@@ -2,7 +2,7 @@
 
 on:
   push:
-    branches: [ dev ]
+    branches: [dev]
   pull_request:
 
 jobs:
@@ -45,7 +45,7 @@ jobs:
         uses: conda-incubator/setup-miniconda@v2
         with:
           auto-update-conda: true
-          python-version: '3.9'
+          python-version: "3.9"
 
       - name: Basic dependencies install
         env:
@@ -169,17 +169,20 @@ jobs:
           conda deactivate
 
           echo "8. Setting up SSH"
-          ssh-keygen -t rsa -b 4096 -N '' -f $PWD/qiita_ware/test/test_data/test_key
+          ssh-keygen -t ed25519 -a 200 -N '' -f $PWD/qiita_ware/test/test_data/test_key
           mkdir ~/.ssh/
           cp $PWD/qiita_ware/test/test_data/test_key* ~/.ssh/
           cat ~/.ssh/test_key.pub > ~/.ssh/authorized_keys
+          cat ~/.ssh/test_key.pub > ~/.ssh/authorized_keys2
           chmod 600 $PWD/qiita_ware/test/test_data/test_key*
           chmod 600 ~/.ssh/*
           chmod 700 ~/.ssh/
           echo "Connecting as $USER@localhost"
           # this line (and the -o StrictHostKeyChecking=no) is so the server
           # is added to the list of known servers
-          scp -O -o StrictHostKeyChecking=no -i $PWD/qiita_ware/test/test_data/test_key $USER@localhost:/home/runner/work/qiita/qiita/qiita_ware/test/test_data/random_key /home/runner/work/qiita/qiita/qiita_ware/test/test_data/random_key_copy_1
+
+          # 05/22/25: commenting this line out as github actions is not allowing this step
+          # scp -O -o StrictHostKeyChecking=no -i $PWD/qiita_ware/test/test_data/test_key $USER@localhost:/home/runner/work/qiita/qiita/qiita_ware/test/test_data/random_key /home/runner/work/qiita/qiita/qiita_ware/test/test_data/random_key_copy_1
 
       - name: Main tests
         shell: bash -l {0}
@@ -239,24 +242,24 @@ jobs:
     needs: main
     runs-on: ubuntu-latest
     steps:
-    - name: Coveralls Finished
-      uses: AndreMiras/coveralls-python-action@develop
-      with:
-        github-token: ${{ secrets.github_token }}
-        parallel-finished: true
+      - name: Coveralls Finished
+        uses: AndreMiras/coveralls-python-action@develop
+        with:
+          github-token: ${{ secrets.github_token }}
+          parallel-finished: true
 
   lint:
     runs-on: ubuntu-latest
     steps:
-    - name: flake8
-      uses: actions/setup-python@v2
-      with:
-        python-version: '3.9'
-    - name: install dependencies
-      run: python -m pip install --upgrade pip
-    - name: Check out repository code
-      uses: actions/checkout@v2
-    - name: lint
-      run: |
-        pip install -q flake8
-        flake8 qiita_* setup.py scripts/qiita* notebooks/*/*.py
+      - name: flake8
+        uses: actions/setup-python@v2
+        with:
+          python-version: "3.9"
+      - name: install dependencies
+        run: python -m pip install --upgrade pip
+      - name: Check out repository code
+        uses: actions/checkout@v2
+      - name: lint
+        run: |
+          pip install -q flake8
+          flake8 qiita_* setup.py scripts/qiita* notebooks/*/*.py

.gitignore

@@ -75,3 +75,6 @@ notebooks/*/*.tsv.gz
 
 # jupyter notebooks input data
 notebooks/resource-allocation/data
+
+# ignore plugin SQL injection file
+qiita_db/support_files/patches/test_db_sql/91.sql

CHANGELOG.md

@@ -1,5 +1,22 @@
 # Qiita changelog
 
+Version 2025.07
+---------------
+
+Deployed on July 15th, 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.
+* SPP: Added a new [subsample method](https://github.com/qiita-spots/qp-knight-lab-processing/pull/138) to randomly select sequences from paired files when they are larger than expected: 720,000,000.
+* SPP: Storing `TellReadJob/QC_Analysis_TellReadJob.html` in the results folder.
+
+
+
 Version 2025.04
 ---------------
 
@@ -10,6 +27,7 @@ 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_core/support_files/config_test.cfg

@@ -25,9 +25,6 @@ REQUIRE_APPROVAL = True
 # Base URL: DO NOT ADD TRAILING SLASH
 BASE_URL = https://localhost:8383
 
-# Download path files
-UPLOAD_DATA_DIR = /home/runner/work/qiita/qiita/qiita_db/support_files/test_data/uploads/
-
 # Working directory path
 WORKING_DIR = /home/runner/work/qiita/qiita/qiita_db/support_files/test_data/working_dir/
 

qiita_core/tests/test_configuration_manager.py

@@ -306,9 +306,6 @@ def test_get_portal_latlong(self):
 # Base URL: DO NOT ADD TRAILING SLASH
 BASE_URL = https://localhost
 
-# Download path files
-UPLOAD_DATA_DIR = /tmp/
-
 # Working directory path
 WORKING_DIR = /tmp/
 

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/metadata_template/test/test_base_metadata_template.py

@@ -125,12 +125,13 @@ def test_restrictions(self):
         obs = MT.prep_template.PrepTemplate(1).restrictions
         exp = {
             'target_gene': ['16S rRNA', '18S rRNA', 'ITS1/2', 'LSU'],
-            'platform': ['FASTA', 'Illumina', 'Ion_Torrent', 'LS454',
+            'platform': ['DNBSEQ', 'FASTA', 'Illumina', 'Ion_Torrent', 'LS454',
                          'Oxford Nanopore'],
             'target_subfragment': ['V3', 'V4', 'V6', 'V9', 'ITS1/2'],
             'instrument_model': [
                 '454 GS', '454 GS 20', '454 GS FLX', '454 GS FLX+',
-                '454 GS FLX Titanium', '454 GS Junior',
+                '454 GS FLX Titanium', '454 GS Junior', 'DNBSEQ-G400',
+                'DNBSEQ-T7', 'DNBSEQ-G800',
                 'Illumina Genome Analyzer', 'Illumina Genome Analyzer II',
                 'Illumina Genome Analyzer IIx', 'Illumina HiScanSQ',
                 'Illumina HiSeq 1000', 'Illumina HiSeq 1500',