Update to py3.10 (#108)

* Use match keyword in run_type_organizer

* Upgrade to python 3.10

* Remove travis and use github actions instead

* Bump myst-parser requirement

Author: matrulda

.github/workflows/unit_tests.yml

@@ -0,0 +1,26 @@
+name: Run Unit Tests
+
+on: [push]
+
+jobs:
+  build:
+    runs-on: ubuntu-22.04
+    steps:
+    - uses: actions/checkout@v4
+    
+    - name: Set up Python 3.10
+      uses: actions/setup-python@v4
+      with:
+        python-version: '3.10'
+    
+    - name: Install dependencies
+      run: |
+        python3 -m pip install --upgrade pip
+        pip install -r requirements/dev .
+    
+    - name: Launch tests
+      run: |
+        pytest --cov=checkQC --cov-report=xml tests/
+    
+    - name: Update data on codecov
+      uses: codecov/codecov-action@v3

.travis.yml

@@ -1,5 +1,5 @@
 # Use an official Python runtime as a parent image
-FROM python:3.6-slim
+FROM python:3.10-slim
 
 # Set the working directory to /app
 WORKDIR /app

Dockerfile

@@ -28,7 +28,7 @@ Instrument types supported in checkQC are the following:
 
 Install instructions
 --------------------
-CheckQC **requires Python 3.6** (or higher to run). CheckQC can be installed with pip.
+CheckQC requires **Python 3.10**. CheckQC can be installed with pip.
 
 ```
 pip install checkqc

README.md

@@ -112,14 +112,15 @@ def _reagent_kit_version(runtype_recognizer):
         def _flowcell_type(runtype_recognizer):
             try:
                 tiles_per_swath = int(runtype_recognizer.run_parameters["RunParameters"]["Setup"]["NumTilesPerSwath"])
-                if tiles_per_swath == 2:
-                    return "nano"
-                elif tiles_per_swath == 4:
-                    return "micro"
-                elif tiles_per_swath >= 14:
-                    return "standard"
-                else:
-                    raise ReagentVersionUnknown()
+                match tiles_per_swath:
+                    case 2:
+                        return "nano"
+                    case 4:
+                        return "micro"
+                    case x if x >= 14:
+                        return "standard"
+                    case _:
+                        raise ReagentVersionUnknown()
             except (KeyError, ReagentVersionUnknown):
                 raise ReagentVersionUnknown("Unable to identify flowcell type through number of tiles per swath")
 

checkQC/run_type_recognizer.py

@@ -118,39 +118,6 @@ An example of what a full `QCHandler` class might look like can be found below,
                 else:
                     continue
 
-Upload to PyPI
---------------
-Releases to PyPI should happen automatically when a release is created in GitHub. However, if for one reason or another, 
-you need to manually upload a new release to PyPi, you need to carry out the following steps:
-
-- make sure you have a `~/.pyirc` file which has the following content (substitute your own credentials here)
-
-.. code-block:: console
-
-    [distutils]
-    index-servers =
-      pypi
-      pypitest
-
-    [pypi]
-    username:<your user name>
-    password:<your password>
-
-    [pypitest]
-    repository: https://test.pypi.org/legacy/
-    username:<your user name>
-    password:<your password>
-
-- Make sure that you have updated the version in `checkQC/__init__.py` so that it matches the tag you are releasing
-- Then to create the distributable files and upload them to the correct index (you might want to start by trying to upload them to pypitest before uploading them to the real pypi):
-
-.. code-block :: console
-
-    python setup.py sdist bdist_wheel
-    twine upload -r <pypitest or pypi> dist/*
-
-Once these steps are finished, the current checkQC release should be up on PyPI.
-
 
 Creating docs
 =============

docs/development.rst

@@ -22,12 +22,10 @@ Instrument types supported in checkQC are the following:
 
 Install instructions
 --------------------
-CheckQC **requires Python 3.5** (or higher to run). Furthermore, right now the Illumina Interop
-library needs to be installed separately before moving on to installing checkqc.
+CheckQC requires **Python 3.10**. CheckQC can be installed with pip.
 
 .. code-block :: console
 
-  pip install -f https://github.com/Illumina/interop/releases/tag/v1.1.1 interop
   pip install checkqc
 
 Running CheckQC

docs/index.rst

@@ -3,6 +3,6 @@ pytest~=7.4.0
 pytest-cov~=4.1.0
 codecov~=2.1.13
 sphinx-autobuild~=2021.3.14
-myst-parser~=1.0.0
+myst-parser~=2.0.0
 sphinx~=7.0.1
 mock~=5.0.2

requirements/dev

@@ -11,10 +11,11 @@
     author_email='johan.dahlberg@medsci.uu.se',
     url="https://www.github.com/Molmed/checkQC",
     download_url='https://github.com/Molmed/checkQC/archive/{}.tar.gz'.format(__version__),
+    python_requires='>3.10, <3.11',
     install_requires=[
         "click",
         "PyYAML>=6.0",
-        "interop>=1.2.3",
+        "interop>=1.2.4",
         "xmltodict",
         "tornado",
         "sample_sheet"],