Bump test coverage to 20%

.devcontainer/devcontainer.json

@@ -6,12 +6,13 @@
     // Sets the run context to one level up instead of the .devcontainer folder.
     "context": "..",
     // Update the 'dockerFile' property if you aren't using the standard 'Dockerfile' filename.
-    "dockerfile": "../Dockerfile"
+    "dockerfile": "../Dockerfile",
+    "target": "base"
   },
   "features": {},
   "customizations": {
     "vscode": {
-      "extensions": ["ms-python.python"]
+      "extensions": ["ms-python.python", "eamodio.gitlens"]
     }
   },
   // Features to add to the dev container. More info: https://containers.dev/features.

.github/workflows/lint-code.yml

@@ -76,7 +76,7 @@ jobs:
         run: pip install -r requirements.txt
 
       - name: Run pipreqs
-        run: pipreqs --savepath pipreqs.txt
+        run: pipreqs --savepath pipreqs.txt taca
 
       - name: Compare requirements
         run: |

Dockerfile

@@ -1,14 +1,13 @@
-FROM python:3.10
+FROM python:3.10 AS base
 
 # Update pip to latest version
 RUN python -m pip install --upgrade pip
 
-
-# Install Nextflow dependencies
+# Install dependencies
 RUN apt-get update \
     && apt-get upgrade -y \
-    && apt-get install -y git \
-    && apt-get install -y curl
+    && apt-get install -y curl \
+    && apt-get install -y rsync
 
 # Needed to install requirements,
 # in devcontainer a local mounted version of flowcell_parser is used
@@ -25,3 +24,9 @@ RUN python -m pip install -r requirements-dev.txt
 
 RUN mkdir /root/.taca/
 COPY tests/data/taca_test_cfg.yaml /root/.taca/taca.yaml
+
+FROM base AS testing
+COPY . /taca
+RUN python -m pip install -e /taca
+WORKDIR /taca/tests
+CMD ["python", "-m", "unittest"]

README.md

@@ -12,6 +12,15 @@
 
 This package contains several tools for projects and data management in the [National Genomics Infrastructure](https://ngisweden.scilifelab.se/) in Stockholm, Sweden.
 
+### Run tests in docker
+
+```shell
+git clone https://github.com/SciLifeLab/TACA.git
+cd TACA
+docker build -t taca_testing --target testing .
+docker run -it taca_testing
+```
+
 ## Installation
 
 Inside the repo, run `pip install .`

VERSIONLOG.md

@@ -1,5 +1,9 @@
 # TACA Version Log
 
+## 20240229.1
+
+Increase test coverage to 20%.
+
 ## 20240209.1
 
 Implement CodeCoverage in CI.

pyproject.toml

@@ -2,6 +2,9 @@ title = "taca"
 
 # === LINTING ================================================================
 
+[tool.ruff]
+exclude = ["tests_old/**"]
+
 [tool.ruff.lint]
 select = [
     #         Ruff default rules
@@ -34,7 +37,7 @@ filterwarnings = [
     'ignore::DeprecationWarning:couchdb.*',
     'ignore::DeprecationWarning:pkg_resources.*',
 ]
-addopts = "--cov=./taca --cov-report term-missing -vv --cache-clear tests/pytest/"
+addopts = "--cov=./taca --cov-report term-missing -vv --cache-clear tests/"
 
 [tool.coverage.run]
 # The comment "# pragma: no cover" can be used to exclude a line from coverage

requirements.txt

@@ -6,4 +6,3 @@ pandas
 python_crontab
 python_dateutil
 setuptools
-sphinx_rtd_theme

taca/analysis/analysis.py

@@ -19,14 +19,11 @@
 logger = logging.getLogger(__name__)
 
 
-def get_runObj(run, software):
+def get_runObj(
+    run: os.PathLike, software: str
+) -> MiSeq_Run | NextSeq_Run | NovaSeq_Run | NovaSeqXPlus_Run | None:
     """Tries to read runParameters.xml to parse the type of sequencer
-        and then return the respective Run object (MiSeq, HiSeq..)
-
-    :param run: run name identifier
-    :type run: string
-    :returns: returns the sequencer type object,
-    None if the sequencer type is unknown of there was an error
+    and then return the respective Run object (MiSeq, HiSeq..)
     """
 
     if os.path.exists(os.path.join(run, "runParameters.xml")):