Merge pull request #16 from nkongenelly/DATAOPS-832_olink_cluster_info

Dataops 832 olink cluster info

Author: nkongenelly

.github/workflows/unit_tests.yaml

@@ -0,0 +1,24 @@
+name: Run Unit Tests
+
+on: [push, pull_request]
+
+jobs:
+  build:
+    runs-on: ubuntu-22.04
+    steps:
+    - uses: actions/checkout@v4
+    
+    - name: Set up Python 3.13.1
+      uses: actions/setup-python@v4
+      with:
+        python-version: '3.13.1'
+    
+    - name: Install dependencies
+      run: |
+        python3 -m pip install --upgrade pip
+        pip install -e . -r requirements_dev.txt
+    
+    - name: Launch tests
+      run: |
+        pytest tests/
+    

.travis.yml

@@ -39,15 +39,15 @@ Install instructions
 
 Installing projman_filler can be done in the following way.
 
-Please note that projman_filler uses python 3.6, ensure this is first installed.
+Please note that projman_filler uses python 3.13.1, ensure this is first installed.
 
  * Download the projman_filler delivery
  * Install projman_filler with pip as normal, i.e. `pip install <path to source>`
 
 
 Development and testing
 -----------------------
-Set up a Python environment using the latest version of Python 3.6 (3.6.12 as of this writing).
+Set up a Python environment using the latest version of Python 3.13.1
 
 Then run:
 ```

README.md

@@ -2,4 +2,4 @@
 
 """Top-level package for ProjMan Filler."""
 
-__version__ = '1.6.3'
+__version__ = '1.7.0'

projman_filler/__init__.py

@@ -120,6 +120,7 @@ def _get_conversion_results(self) -> list:
         lanes = []
         for l in range(1, n_lanes+1):
             rows = df.loc[df['Lane'] == l][['ReadNumber','Reads', 'Reads Pf', 'IsIndex']]
+            rows = rows.reset_index()
             # Each 'Reads Pf' value represents the entire lane,
             # while 'Reads' (total clusters raw) must be summed over the non-index reads
             # See: https://github.com/Illumina/interop/issues/271

projman_filler/interop_run_stats_parser.py

@@ -1,8 +1,7 @@
-pip>=19.2
+pip~=25.0.1
 bumpversion~=0.6.0
-wheel~=0.37.1
-coverage~=6.2
-Sphinx~=5.3.0
-
-pytest~=7.0.1
-pytest-runner~=5.3.2
+wheel~=0.45.1
+coverage~=7.8.0
+Sphinx~=8.2.3
+pytest~=8.3.5
+pytest-runner~=6.0.1

requirements_dev.txt

@@ -11,12 +11,12 @@
     readme = readme_file.read()
 
 requirements = [
-    'Click~=8.0.4',
-    'xmltodict~=0.13.0',
-    'interop~=1.2.3',
-    'SQLAlchemy~=1.4.48',
-    'pymssql~=2.2.7',
-    'pandas~=1.1.5'
+    'Click~=8.1.8',
+    'interop~=1.4.0',
+    'SQLAlchemy~=2.0.40',
+    'pymssql~=2.3.4',
+    'pandas~=2.2.3',
+    'numpy~=2.2.4'
 ]
 
 setup_requirements = [
@@ -51,7 +51,7 @@
         'Intended Audience :: Developers',
         'License :: OSI Approved :: GNU General Public License v3 (GPLv3)',
         'Natural Language :: English',
-        'Programming Language :: Python :: 3.6',
+        'Programming Language :: Python :: 3.13.1',
     ],
     test_suite='tests',
     tests_require=test_requirements,