Merge pull request #34 from SciLifeLab/master

Version sync

.devcontainer/devcontainer.json

@@ -7,12 +7,13 @@
     "context": "..",
     // Update the 'dockerFile' property if you aren't using the standard 'Dockerfile' filename.
     "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.
   // "features": {},
@@ -24,6 +25,6 @@
   // Uncomment to connect as an existing user other than the container default. More info: https://aka.ms/dev-containers-non-root.
   // "remoteUser": "devcontainer"
   "mounts": [
-    "source=${localEnv:HOME}/repos/flowcell_parser,target=/workspaces/flowcell_parser,type=bind,consistency=cached",
-  ],
+    "source=${localEnv:HOME}/repos/flowcell_parser,target=/workspaces/flowcell_parser,type=bind,consistency=cached"
+  ]
 }

.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: |

.github/workflows/test-code.yml

@@ -0,0 +1,32 @@
+name: Test code
+on: [push, pull_request]
+
+jobs:
+  pytest:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r requirements.txt
+          pip install -r requirements-dev.txt
+      - name: Install TACA
+        run: pip install -e .
+      - name: pytest
+        # Options are configured in pyproject.toml
+        run: pytest
+      - name: CodeCov
+        run: |
+          # Replace `linux` below with the appropriate OS
+          # Options are `alpine`, `linux`, `macos`, `windows`
+          curl -Os https://uploader.codecov.io/latest/linux/codecov
+          chmod +x codecov
+          ./codecov -t ${{ secrets.CODECOV_TOKEN }}

.gitignore

@@ -13,3 +13,4 @@ __pycache__
 .vscode
 .ruff_cache
 .mypy_cache
+node_modules

.pre-commit-config.yaml

@@ -9,6 +9,7 @@ repos:
     rev: "v1.7.1"
     hooks:
       - id: mypy
+        additional_dependencies: [types-PyYAML]
   - repo: https://github.com/pre-commit/mirrors-prettier
     rev: "v4.0.0-alpha.8"
     hooks:

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 +1,25 @@
 # TACA Version Log
 
+## 20240304.1
+
+- Make sure TACA can handle runs that generate NO sequencing data at all
+- Refactor logic of control function to reduce complexity
+- Introduce custom Exception for quiet skipping (waiting on) runs
+- Improve documentation
+- Minor polishing of test to pass
+
+## 20240229.1
+
+Increase test coverage to 20%.
+
+## 20240209.1
+
+Implement CodeCoverage in CI.
+
+## 20240208.2
+
+Implement CI testing and increase testing coverage.
+
 ## 20240208.1
 
 Fix bug with isinstance clause

pyproject.toml

@@ -1,27 +1,45 @@
 title = "taca"
 
+# === LINTING ================================================================
+
+[tool.ruff]
+exclude = ["tests_old/**"]
 
 [tool.ruff.lint]
-select =[
+select = [
     #         Ruff default rules
     # ------------------------------
-    "E4",   # pycodestyle Imports
-    "E7",   # pycodestyle Statements
-    "E9",   # pycodestyle Runtime
-    "F",    # Pyflakes
+    "E4", # pycodestyle Imports
+    "E7", # pycodestyle Statements
+    "E9", # pycodestyle Runtime
+    "F",  # Pyflakes
 
     #         Additional    Comment
     # ------------------------------------------------------
-    "I",    # isort         Best-practice sorting of imports
-    "UP",   # pyupgrade     Make sure syntax is up-to-date
+    "I",  # isort         Best-practice sorting of imports
+    "UP", # pyupgrade     Make sure syntax is up-to-date
 ]
 ignore = [
     "E402", # Module level import not at top of file
     "E722", # Do not use bare 'except'
     "E741", # Ambiguous variable name
 ]
 
-
 [tool.mypy]
 ignore_missing_imports = true
 follow_imports = 'skip'
+
+# === Testing ================================================================
+
+[tool.pytest.ini_options]
+# Omit deprecation warnings from 3rd party packages
+filterwarnings = [
+    'ignore::DeprecationWarning:couchdb.*',
+    'ignore::DeprecationWarning:pkg_resources.*',
+]
+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
+source = ["taca"]
+omit = ["**/__init__.py"]

requirements-dev.txt

@@ -5,6 +5,7 @@ mock
 sphinx
 sphinx-rtd-theme
 pytest
+pytest-cov
 ipython
 ipdb
 ruff

requirements.txt

@@ -3,8 +3,6 @@ PyYAML
 click
 flowcell_parser @ git+https://github.com/SciLifeLab/flowcell_parser
 pandas
-pytest
 python_crontab
 python_dateutil
 setuptools
-sphinx_rtd_theme

taca/__init__.py

@@ -1,4 +1,3 @@
-""" Main TACA module
-"""
+"""Main TACA module"""
 
 __version__ = "1.0.0"

taca/analysis/analysis.py

@@ -1,4 +1,5 @@
 """Analysis methods for TACA."""
+
 import glob
 import logging
 import os
@@ -19,14 +20,11 @@
 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")):
@@ -37,7 +35,7 @@ def get_runObj(run, software):
         logger.error(
             f"Cannot find RunParameters.xml or runParameters.xml in the run folder for run {run}"
         )
-        return
+        return None
 
     run_parameters_path = os.path.join(run, run_parameters_file)
     try: