Merge pull request #65 from LUMC/release_1.1.1

Release 1.1.1

.github/release_checklist.md

@@ -5,13 +5,17 @@ Release checklist
 - [ ] Create a release branch 
   - [ ] Set version to a stable number.
   - [ ] Change current development version in `HISTORY.rst` to stable version.
-- [ ] Create a test pypi package from the release branch. ([Instructions.](
+- [ ] Merge the release branch into `master`
+- [ ] Create a test pypi package from the master branch. ([Instructions.](
 https://packaging.python.org/tutorials/packaging-projects/#generating-distribution-archives
 ))
-- [ ] Merge the release branch into `master`
+- [ ] Install the packages from the test pypi repository to see if they work.
 - [ ] Created an annotated tag with the stable version number. Include changes 
 from history.rst.
 - [ ] Push tag to remote.
-- [ ] Create packages and push to pypi
+- [ ] Push tested packages to pypi
 - [ ] merge `master` branch back into `develop`.
-- [ ] Add updated version number to develop
+- [ ] Add updated version number to develop
+- [ ] Update the package on bioconda
+- [ ] Build the new tag on readthedocs. Only build the last patch version of
+each minor version. So `1.1.1` and `1.2.0` but not `1.1.0`, `1.1.1` and `1.2.0`.

HISTORY.rst

@@ -7,6 +7,13 @@ Changelog
 .. NOTE: This document is user facing. Please word the changes in such a way
 .. that users understand how the changes affect the new version.
 
+version 1.1.1
+---------------------------
++ Added ``--kwd`` as alias for ``--keep-workflow-wd``. Notify the user of
+  deletion of temporary directories and logs.
++ Released pytest-workflow as a `conda package on bioconda
+  <https://bioconda.github.io/recipes/pytest-workflow/README.html>`_.
+
 version 1.1.0
 ---------------------------
 + Enabled custom tests on workflow files.

README.rst

@@ -8,10 +8,18 @@ pytest-workflow
   :target: https://pypi.org/project/pytest-workflow/
   :alt:
 
+.. image:: https://img.shields.io/conda/v/bioconda/pytest-workflow.svg
+  :target: https://https://bioconda.github.io/recipes/pytest-workflow/README.html
+  :alt:
+
 .. image:: https://img.shields.io/pypi/pyversions/pytest-workflow.svg
   :target: https://pypi.org/project/pytest-workflow/
   :alt:
 
+.. image:: https://img.shields.io/pypi/l/pytest-workflow.svg
+  :target: https://github.com/LUMC/pytest-workflow/blob/master/LICENSE
+  :alt:
+
 .. image:: https://api.codacy.com/project/badge/Grade/f8bc14b0a507429eac7c06194fafcd59
   :target: https://www.codacy.com/app/LUMC/pytest-workflow?utm_source=github.com&utm_medium=referral&utm_content=LUMC/pytest-workflow&utm_campaign=Badge_Grade
   :alt:
@@ -41,6 +49,12 @@ and 3.7. Python 2 is not supported.
 - Create a ``tests`` directory in the root of your repository.
 - Create your test yaml files in the ``tests`` directory.
 
+Pytest-workflow is also available as a `conda package on bioconda
+<https://bioconda.github.io/recipes/pytest-workflow/README.html>`_. Follow
+`these instructions <https://bioconda.github.io/index.html#set-up-channels>`_
+to set up channels properly in order to use bioconda. After that ``conda
+install pytest-workflow`` can be used to install pytest-workflow.
+
 Quickstart
 ==========
 
@@ -52,7 +66,7 @@ To check the progress of a workflow while it is running you can use ``tail -f``
 on the ``stdout`` or ``stderr`` file of the workflow. The locations of these
 files are reported in the log as soon as a workflow is started.
 
-For debugging pipelines using the ``--keep-workflow-wd`` flag  is
+For debugging pipelines using the ``--kwd`` or ``--keep-workflow-wd`` flag  is
 recommended. This will keep the workflow directory and logs after the test run
 so it is possible to check where the pipeline crashed. The ``-v`` flag can come
 in handy as well as it gives a complete overview of succeeded and failed tests.

docs/installation.rst

@@ -26,3 +26,11 @@ On Ubuntu or Debian:
     environment will not work with ``pytest-workflow`` because this will start
     the python2 version of ``pytest``. This is because python2 is the default
     python on any distribution released before January 1st 2020.
+
+Pytest-workflow is also available as a `conda package on bioconda
+<https://bioconda.github.io/recipes/pytest-workflow/README.html>`_.
+To install with conda:
+
+- `Set up conda to use the bioconda channel
+  <https://bioconda.github.io/index.html#set-up-channels>`_
+- ``conda install pytest-workflow``

docs/running_pytest_workflow.rst

@@ -10,8 +10,8 @@ The workflows are run automatically. Each workflow gets its own temporary
 directory to run. The ``stdout`` and ``stderr`` of the workflow command are
 also saved to this directory. The temporary directories are cleaned up after
 the tests are completed. If you wish to inspect the output of a failing
-workflow you can use the ``--keep-workflow-wd`` flag to disable cleanup. This
-will also make sure the logs of the pipeline are not deleted. The
+workflow you can use the ``--kwd`` or ``--keep-workflow-wd`` flag to disable
+cleanup. This will also make sure the logs of the pipeline are not deleted. The
 ``--keep-workflow-wd`` flag is highly recommended when debugging pipelines.
 
 If you wish to change the temporary directory in which the workflows are run

setup.py

@@ -21,7 +21,7 @@
 
 setup(
     name="pytest-workflow",
-    version="1.1.0",
+    version="1.1.1",
     description="A pytest plugin for configuring workflow/pipeline tests "
                 "using YAML files",
     author="Leiden University Medical Center",
@@ -43,6 +43,7 @@
         "Programming Language :: Python :: 3.5",
         "Programming Language :: Python :: 3.6",
         "Programming Language :: Python :: 3.7",
+        "Development Status :: 5 - Production/Stable",
         "License :: OSI Approved :: "
         "GNU Affero General Public License v3 or later (AGPLv3+)",
         "Framework :: Pytest",

src/pytest_workflow/plugin.py

@@ -39,7 +39,7 @@
 
 def pytest_addoption(parser: PytestParser):
     parser.addoption(
-        "--keep-workflow-wd",
+        "--kwd", "--keep-workflow-wd",
         action="store_true",
         help="Keep temporary directories where workflows are run for "
              "debugging purposes. This also triggers saving of stdout and "
@@ -191,6 +191,9 @@ def pytest_runtestloop(session: pytest.Session):
 
 def pytest_sessionfinish(session: pytest.Session):
     if not session.config.getoption("keep_workflow_wd"):
+        # The newline is needed otherwise everything looks ugly.
+        print("\nRemoving temporary directories and logs. Use '--kwd' or "
+              "'--keep-workflow-wd' to disable this behaviour.")
         for tempdir in session.config.workflow_cleanup_dirs:
             shutil.rmtree(str(tempdir))
 

tests/test_temp_directory.py

@@ -38,6 +38,9 @@ def test_directory_not_kept(testdir):
     working_dir = re.search(r"with command 'echo moo' in '([\w\/_-]*)'",
                             result.stdout.str()).group(1)
     assert not Path(working_dir).exists()
+    assert ("Removing temporary directories and logs. Use '--kwd' or "
+            "'--keep-workflow-wd' to disable this behaviour."
+            ) in result.stdout.str()
 
 
 def test_basetemp_correct(testdir):