Merge branch 'dev' of github.com:biocore/qiita into fix-3471

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

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_ware/test/test_commands.py

@@ -6,7 +6,7 @@
 # The full license is in the file LICENSE, distributed with this software.
 # -----------------------------------------------------------------------------
 from unittest import TestCase, main, skipIf
-from os.path import join, basename, exists
+from os.path import join, basename
 from tempfile import mkdtemp
 import pandas as pd
 from datetime import datetime
@@ -56,26 +56,31 @@ def test_list_scp_wrong_key(self):
             list_remote('scp://runner@localhost:'+self.remote_dir_path,
                         self.test_wrong_key)
 
-    def test_list_scp_nonexist_key(self):
-        with self.assertRaises(IOError):
-            list_remote('scp://runner@localhost:'+self.remote_dir_path,
-                        join(self.self_dir_path, 'nokey'))
-
     def test_list_scp(self):
         kpath = join(self.temp_local_dir, 'tmp-key')
         copyfile(self.test_ssh_key, kpath)
-        read_file_list = list_remote(
-            'scp://runner@localhost:'+self.remote_dir_path, kpath)
-        self.assertCountEqual(read_file_list, self.exp_files)
+        # 05/22/25: this test requires a scp/ssh connection and github
+        # actions is broken; thus commenting out
+        # read_file_list = list_remote(
+        #     'scp://runner@localhost:'+self.remote_dir_path, kpath)
+        # self.assertCountEqual(read_file_list, self.exp_files)
+
+    def test_download_remote_nonexist_key(self):
+        with self.assertRaises(IOError):
+            download_remote('scp://runner@localhost:'+self.remote_dir_path,
+                            join(self.self_dir_path, 'nokey'),
+                            self.temp_local_dir)
 
     def test_download_scp(self):
         kpath = join(self.temp_local_dir, 'tmp-key')
         copyfile(self.test_ssh_key, kpath)
-        download_remote('scp://runner@localhost:'+self.remote_dir_path,
-                        kpath, self.temp_local_dir)
-        local_files = self._get_valid_files(self.temp_local_dir)
-        self.assertCountEqual(local_files, self.exp_files)
-        self.assertFalse(exists(kpath))
+        # 05/22/25: this test requires a scp/ssh connection and github
+        # actions is broken; thus commenting out
+        # download_remote('scp://runner@localhost:'+self.remote_dir_path,
+        #                 kpath, self.temp_local_dir)
+        # local_files = self._get_valid_files(self.temp_local_dir)
+        # self.assertCountEqual(local_files, self.exp_files)
+        # self.assertFalse(exists(kpath))
 
 
 class CommandsTests(TestCase):