updated and added ci

.github/workflows/ci.yaml

@@ -0,0 +1,24 @@
+name: Continuous Integration on Push
+
+on:
+  push:
+    branches:
+      - main
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+    - name: Checkout code
+      uses: actions/checkout@v2
+
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: '3.9'
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install -r requirements.txt
+        pytest 

.gitignore

@@ -11,4 +11,5 @@ assets/.env_dev
 .bio-check.json
 bucket.sh
 .env_dev
-NOTES
+NOTES
+cd.yaml

assets/shared.py

@@ -20,6 +20,18 @@
 # BUCKET_URL = "gs://bio-check-requests-1/"
 
 
+def increment_version(version: str, increment_position: int):
+    """Args:
+        version (str): version to increment by
+        increment_position (int): position to increment by: 0 for major 1 for minor and 2 for patch
+    """
+    parts = [int(n) for n in version.split(".")]
+    new_part = parts[increment_position] + 1
+    parts.remove(parts[increment_position])
+    parts.insert(increment_position, new_part)
+    return ".".join([str(n) for n in parts])
+
+
 def refresh_jobs(conn):
     def refresh_collection(conn, coll):
         for job in conn.db[coll].find():

bio_check/demo.ipynb

@@ -150,16 +150,61 @@
    ],
    "execution_count": 7
   },
+  {
+   "metadata": {
+    "ExecuteTime": {
+     "end_time": "2024-07-31T15:39:26.558140Z",
+     "start_time": "2024-07-31T15:39:26.554661Z"
+    }
+   },
+   "cell_type": "code",
+   "source": [
+    "def increment_version(version: str, increment_position: int):\n",
+    "    \"\"\"Args:\n",
+    "        version (str): version to increment by\n",
+    "        increment_position (int): position to increment by: 0 for major 1 for minor and 2 for patch\n",
+    "    \"\"\"\n",
+    "    parts = [int(n) for n in version.split(\".\")]\n",
+    "    new_part = parts[increment_position] + 1\n",
+    "    parts.remove(parts[increment_position])\n",
+    "    parts.insert(increment_position, new_part)\n",
+    "    return \".\".join([str(n) for n in parts])"
+   ],
+   "id": "6351bd4f5ab6e866",
+   "outputs": [],
+   "execution_count": 10
+  },
+  {
+   "metadata": {
+    "ExecuteTime": {
+     "end_time": "2024-07-31T15:39:35.235735Z",
+     "start_time": "2024-07-31T15:39:35.231888Z"
+    }
+   },
+   "cell_type": "code",
+   "source": "increment_version('1.1.0', 1)",
+   "id": "3689a8ffa9d4c123",
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "'1.2.0'"
+      ]
+     },
+     "execution_count": 12,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "execution_count": 12
+  },
   {
    "metadata": {},
    "cell_type": "code",
    "outputs": [],
    "execution_count": null,
-   "source": [
-    "from main import db_connector as conn \n",
-    "conn.pending_jobs()"
-   ],
-   "id": "6351bd4f5ab6e866"
+   "source": "",
+   "id": "c9fc32addb37cd52"
   }
  ],
  "metadata": {

bio_check/verifier.py

@@ -121,6 +121,7 @@ def verify_sbml(
             'rTol': str(rTol),
             'aTol': str(aTol)
         }
+
         if selection_list:
             encoder_fields['selection_list'] = ','.join(selection_list)
         multidata = MultipartEncoder(fields=encoder_fields)

requirements.txt

@@ -0,0 +1,5 @@
+requests-toolbelt~=1.0.0
+seaborn~=0.13.2
+pydantic~=2.8.2
+numpy
+pandas