Merge branch 'main' into 413-add-msi-measure

.gitattributes

@@ -2,3 +2,4 @@
 *.fastq.gz filter=lfs diff=lfs merge=lfs -text
 *.fasta filter=lfs diff=lfs merge=lfs -text
 *.fasta.* filter=lfs diff=lfs merge=lfs -text
+snappy_pipeline/_version.py export-subst

.github/workflows/ci.yml

@@ -26,7 +26,7 @@ jobs:
       - name: Install Python
         uses: actions/setup-python@v2
         with:
-          python-version: "3.8"
+          python-version: "3.10"
 
       - name: Install dependencies
         run: |
@@ -58,7 +58,7 @@ jobs:
       - name: Install Python
         uses: actions/setup-python@v2
         with:
-          python-version: "3.8"
+          python-version: "3.10"
 
       - name: Install dependencies
         run: |
@@ -75,10 +75,9 @@ jobs:
     strategy:
       matrix:
         python-version:
-          - "3.8"
-          - "3.9"
           - "3.10"
           # - "3.11"  # no compatible pysam yet
+          # - "3.12"  # no compatible pysam yet
     needs: linting
     steps:
       - name: Install Python via conda

.gitignore

@@ -1,3 +1,6 @@
+# Pipfiles created by VC Code
+/Pipfile*
+
 # Mac
 .*DS_Store
 

CONTRIBUTING.rst

@@ -103,7 +103,7 @@ Before you submit a pull request, check that it meets these guidelines:
 2. If the pull request adds functionality, the docs should be updated. Put
    your new functionality into a function with a docstring, and add the
    feature to the list in README.rst.
-3. The pull request should work for Python 3.7, 3.8 and 3.9, and for PyPy. Check
+3. The pull request should work for the Python versions from ``setup.py``. Check
    https://travis-ci.org/holtgrewe/cubi_piepline/pull_requests
    and make sure that the tests pass for all supported Python versions.
 

docs/dev_intro.rst

@@ -99,6 +99,9 @@ Usually, you define a :class:`BaseStep <snappy_pipeline.workflows.abstract.BaseS
 The current configuration is passed into the constructor of this class and it then "takes over" and applies default setting, generating cluster resource settings, etc.
 Then, you pass the result of method calls to your :class:`BaseStep <snappy_pipeline.workflows.abstract.BaseStep>` instance as the values for the ``input:``, ``output:``, etc. sections of your ``Snakefile``.
 
+.. warning::
+   By convention your new Workflow step should be instantiated as ``wf = StepClass(...)`` in the ``Snakefile`` during object setup. Otherwise tools including cubi-tk might not be able to detect and parse your step. See existing workflow ``Snakefile`` for reference.
+
 The :class:`BaseStep <snappy_pipeline.workflows.abstract.BaseStep>` sub class itself uses :class:`BaseStepPart <snappy_pipeline.workflows.abstract.BaseStepPart>` sub classes for the implementation of the individual parts.
 One part might be linking in FASTQ files from the raw input directory or linking from the ``work/`` to the ``output/`` directory.
 Another part might be the somatic variant calling using mutect or WGS SV calling using Delly2.

requirements/test.txt

@@ -5,6 +5,7 @@ pytest
 coverage
 pytest-cov
 pytest-mock
+pytest-subprocess
 
 # Fake file system for testing
 pyfakefs

setup.cfg

@@ -30,6 +30,7 @@ line_length = 100
 exclude =
     docs
     tests
+    venv
     .*.py
     .snakemake.*.wrapper.py
     splitMNPsAndComplex.py

setup.py

@@ -124,9 +124,11 @@ def bash_scripts(names):
         "License :: OSI Approved :: MIT License",
         "Natural Language :: English",
         "Programming Language :: Python :: 3",
-        "Programming Language :: Python :: 3.7",
-        "Programming Language :: Python :: 3.8",
-        "Programming Language :: Python :: 3.9",
+        "Programming Language :: Python :: 3.10",
+        # We are missing bioconda pysam packages for 3.11 and 3.12, cf.
+        # https://github.com/bioconda/bioconda-recipes/issues/37805
+        # "Programming Language :: Python :: 3.11",
+        # "Programming Language :: Python :: 3.12",
     ],
     test_suite="tests",
     tests_require=test_requirements,

snappy_pipeline/__init__.py

@@ -8,3 +8,7 @@
 __email__ = "[email protected]"
 __version__ = "master"
 # del get_versions
+
+from . import _version
+
+__version__ = _version.get_versions()["version"]