Merge pull request #171 from LUMC/release_2.0.1

Release 2.0.1

Author: rhpvorderman

.github/workflows/ci.yml

@@ -60,38 +60,45 @@ jobs:
       - name: Upload coverage report
         uses: codecov/codecov-action@v1
 
-  test-functional:
+  test-functional-python-tools:
     runs-on: ubuntu-latest
-    needs: lint
     strategy:
       matrix:
         python-version: ["3.7"]
-        test-program: [cromwell, snakemake, miniwdl]
+        test-program: [snakemake, miniwdl]
     steps:
       - uses: actions/[email protected]
 
-      # Setup python program requirements
       - name: Set up Python ${{ matrix.python-version }}
-        if: ${{ matrix.test-program != 'cromwell' }}
         uses: actions/setup-python@v2
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install tox
-        if: ${{ matrix.test-program != 'cromwell' }}
         run: pip install tox
 
-      # Setup cromwell requirements
+      - name: Test
+        shell: bash -l {0}  # Needed for conda
+        run: tox -e ${{ matrix.test-program }}
+
+  test-functional-other:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        test-program: [ cromwell, nextflow ]
+    steps:
+      - uses: actions/[email protected]
+
       - name: Install conda
-        if: ${{ matrix.test-program == 'cromwell' }}
         uses: conda-incubator/[email protected] # https://github.com/conda-incubator/setup-miniconda.
         with:
-          channels: conda-forge,defaults
-      - name: Install cromwell and tox
+          channels: conda-forge,bioconda,defaults
+          installer-url: https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh
+          channel-priority: true
+
+      - name: Install test program and tox
         shell: bash -l {0}  # Needed for conda
-        if: ${{ matrix.test-program == 'cromwell' }}
-        run: conda install cromwell tox
+        run: mamba install ${{ matrix.test-program }} tox
 
-      # Test
       - name: Test
         shell: bash -l {0}  # Needed for conda
-        run: tox -e ${{ matrix.test-program }}
+        run: tox -e ${{ matrix.test-program }}

HISTORY.rst

@@ -7,6 +7,12 @@ Changelog
 .. This document is user facing. Please word the changes in such a way
 .. that users understand how the changes affect the new version.
 
+version 2.0.1
+---------------------------
++ Fixed a bug where pytest-workflow would crash on logs that used non-ASCII
+  characters where the chunk of size ``--stderr-bytes`` did not properly align
+  with the used encoding.
+
 version 2.0.0
 ---------------------------
 This major release greatly cleans up the output of pytest-workflow in case of

setup.py

@@ -20,7 +20,7 @@
 
 setup(
     name="pytest-workflow",
-    version="2.0.0",
+    version="2.0.1",
     description="A pytest plugin for configuring workflow/pipeline tests "
                 "using YAML files",
     author="Leiden University Medical Center",

src/pytest_workflow/plugin.py

@@ -30,7 +30,8 @@
 from .content_tests import ContentTestCollector
 from .file_tests import FileTestCollector
 from .schema import WorkflowTest, workflow_tests_from_schema
-from .util import duplicate_tree, is_in_dir, replace_whitespace
+from .util import (decode_unaligned, duplicate_tree, is_in_dir,
+                   replace_whitespace)
 from .workflow import Workflow, WorkflowQueue
 
 
@@ -450,7 +451,10 @@ def collect(self):
         tests += [ExitCodeTest.from_parent(
             parent=self,
             workflow=workflow,
-            stderr_bytes=self.config.getoption("stderr_bytes"))]
+            stderr_bytes=self.config.getoption("stderr_bytes"),
+            stdout_encoding=self.workflow_test.stdout.encoding,
+            stderr_encoding=self.workflow_test.stderr.encoding,
+        )]
 
         tests += [
             FileTestCollector.from_parent(
@@ -476,11 +480,16 @@ def collect(self):
 
 class ExitCodeTest(pytest.Item):
     def __init__(self, parent: pytest.Collector,
-                 workflow: Workflow, stderr_bytes: int):
+                 workflow: Workflow,
+                 stderr_bytes: int,
+                 stdout_encoding: Optional[str] = None,
+                 stderr_encoding: Optional[str] = None):
         name = f"exit code should be {workflow.desired_exit_code}"
         super().__init__(name, parent=parent)
         self.stderr_bytes = stderr_bytes
         self.workflow = workflow
+        self.stdout_encoding = stdout_encoding
+        self.stderr_encoding = stderr_encoding
 
     def runtest(self):
         # workflow.exit_code waits for workflow to finish.
@@ -489,16 +498,21 @@ def runtest(self):
     def repr_failure(self, excinfo, style=None):
         standerr = self.workflow.stderr_file
         standout = self.workflow.stdout_file
-        with open(standout, "rb") as standout_file, \
-             open(standerr, "rb") as standerr_file:
-            if os.path.getsize(standerr) >= self.stderr_bytes:
-                standerr_file.seek(-self.stderr_bytes, os.SEEK_END)
+
+        with open(standout, "rb") as standout_file:
             if os.path.getsize(standout) >= self.stderr_bytes:
                 standout_file.seek(-self.stderr_bytes, os.SEEK_END)
-            message = (f"'{self.workflow.name}' exited with exit code " +
-                       f"'{self.workflow.exit_code}' instead of "
-                       f"'{self.workflow.desired_exit_code}'.\nstderr: "
-                       f"{standerr_file.read().strip().decode('utf-8')}"
-                       f"\nstdout: "
-                       f"{standout_file.read().strip().decode('utf-8')}")
-        return message
+            stdout_text = decode_unaligned(standout_file.read().strip(),
+                                           encoding=self.stdout_encoding)
+        with open(standerr, "rb") as standerr_file:
+            if os.path.getsize(standerr) >= self.stderr_bytes:
+                standerr_file.seek(-self.stderr_bytes, os.SEEK_END)
+            stderr_text = decode_unaligned(standerr_file.read().strip(),
+                                           encoding=self.stderr_encoding)
+
+        return (
+            f"'{self.workflow.name}' exited with exit code " +
+            f"'{self.workflow.exit_code}' instead of "
+            f"'{self.workflow.desired_exit_code}'.\n"
+            f"stderr: {stderr_text}\n"
+            f"stdout: {stdout_text}")

src/pytest_workflow/util.py

@@ -7,7 +7,7 @@
 import sys
 import warnings
 from pathlib import Path
-from typing import Callable, Iterator, List, Set, Tuple, Union
+from typing import Callable, Iterator, List, Optional, Set, Tuple, Union
 
 Filepath = Union[str, os.PathLike]
 
@@ -209,3 +209,17 @@ def file_md5sum(filepath: Path, block_size=64 * 1024) -> str:
         for block in iter(lambda: file_handler.read(block_size), b''):
             hasher.update(block)
     return hasher.hexdigest()
+
+
+def decode_unaligned(data: bytes, encoding: Optional[str] = None):
+    if encoding is None:
+        encoding = sys.getdefaultencoding()
+    for offset in range(4):
+        try:
+            decoded = data[offset:].decode(encoding=encoding, errors="strict")
+            return decoded
+        except UnicodeDecodeError:
+            continue
+    # When no return happens in the loop, decode again. This will throw an
+    # error that is not caught and shown to the user.
+    return data.decode(encoding=encoding)

tests/pipelines/nextflow/nextflow_testpipeline.nf

@@ -1,30 +1,31 @@
 #!/usr/bin/env nextflow
 
-# Copyright (C) 2018 Leiden University Medical Center
-# This file is part of pytest-workflow
-#
-# pytest-workflow is free software: you can redistribute it and/or modify
-# it under the terms of the GNU Affero General Public License as
-# published by the Free Software Foundation, either version 3 of the
-# License, or (at your option) any later version.
-#
-# pytest-workflow is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# GNU Affero General Public License for more details.
-#
-# You should have received a copy of the GNU Affero General Public License
-# along with pytest-workflow.  If not, see <https://www.gnu.org/licenses/
+/* Copyright (C) 2018 Leiden University Medical Center
+   This file is part of pytest-workflow
 
-# Nextflow using the Snakemake test file as example.
-# Just a simple dummy pipeline that reads some data from /dev/urandom,
-# and does some transformations on it.
+   pytest-workflow is free software: you can redistribute it and/or modify
+   it under the terms of the GNU Affero General Public License as
+   published by the Free Software Foundation, either version 3 of the
+   License, or (at your option) any later version.
+
+   pytest-workflow is distributed in the hope that it will be useful,
+   but WITHOUT ANY WARRANTY; without even the implied warranty of
+   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+   GNU Affero General Public License for more details.
+
+   You should have received a copy of the GNU Affero General Public License
+   along with pytest-workflow.  If not, see <https://www.gnu.org/licenses/
+*/
+
+/* Nextflow using the Snakemake test file as example.
+   Just a simple dummy pipeline that reads some data from /dev/urandom,
+  and does some transformations on it. */
 
 params.N_LINES_TO_READ = 5
 
 process read_random {
 	publishDir = [
-                path: { "${params.outdir}/rand'}
+                path: { "${params.outdir}/rand" }
         ]
 
 	input:
@@ -40,7 +41,7 @@ process read_random {
 
 process base64_random {
 	publishDir = [
-                path: { "${params.outdir}/b64'}
+                path: { "${params.outdir}/b64" }
         ]
 
 	input:
@@ -57,7 +58,7 @@ process base64_random {
 
 process gzip_b64 {
 	publishDir = [
-                path: { "${params.outdir}/randgz'}
+                path: { "${params.outdir}/randgz" }
         ]
 
 	input:
@@ -73,7 +74,7 @@ process gzip_b64 {
 
 process concat_gzip {
 	publishDir = [
-                path: { "${params.outdir}'}
+                path: { "${params.outdir}" }
         ]
 
 	input:

tests/test_miscellaneous_crashes.py

@@ -14,6 +14,10 @@
 # You should have received a copy of the GNU Affero General Public License
 # along with pytest-workflow.  If not, see <https://www.gnu.org/licenses/
 
+import textwrap
+
+from pytest import ExitCode
+
 from .test_success_messages import SIMPLE_ECHO
 
 
@@ -27,3 +31,13 @@ def test_same_name_different_files(pytester):
     conflicting_message = (
         "Conflicting tests: test_b.yml::simple echo, test_a.yml::simple echo.")
     assert conflicting_message in result.stdout.str()
+
+
+def test_non_ascii_logs_stderr_bytes(pytester):
+    test = textwrap.dedent("""
+    - name: print non-ascii
+      command: bash -c 'printf èèèèèèèèè && exit 1'
+    """)
+    pytester.makefile(".yml", test_non_ascii=test)
+    result = pytester.runpytest("--stderr-bytes", "7")
+    assert result.ret == ExitCode.TESTS_FAILED

tests/test_utils.py

@@ -14,16 +14,18 @@
 # You should have received a copy of the GNU Affero General Public License
 # along with pytest-workflow.  If not, see <https://www.gnu.org/licenses/
 import hashlib
+import itertools
 import os
 import shutil
 import subprocess
+import sys
 import tempfile
 from pathlib import Path
 
 import pytest
 
-from pytest_workflow.util import duplicate_tree, file_md5sum, \
-    git_check_submodules_cloned, git_root, \
+from pytest_workflow.util import decode_unaligned, duplicate_tree, \
+    file_md5sum, git_check_submodules_cloned, git_root, \
     is_in_dir, link_tree, replace_whitespace
 
 WHITESPACE_TESTS = [
@@ -227,3 +229,20 @@ def test_duplicate_git_tree_submodule_symlinks(git_repo_with_submodules):
     assert link.exists()
     assert link.is_symlink()
     assert link.resolve() == dest / "bird" / "sub"
+
+
+@pytest.mark.parametrize(["offset", "encoding"],
+                         list(itertools.product(
+                             range(4), (None, "utf-8", "utf-16", "utf-32"))
+                         ))
+def test_decode_unaligned(offset, encoding):
+    string = "èèèèèèèèèèè"
+    data = string.encode(encoding or sys.getdefaultencoding())
+    decoded = decode_unaligned(data[offset:], encoding)
+    assert string.endswith(decoded)
+
+
+def test_decode_unaligned_wrong_encoding_throws_error():
+    data = "hello".encode("utf-8")
+    with pytest.raises(UnicodeDecodeError):
+        decode_unaligned(data, "utf-32-le")