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DeiC-HPC · Sep 3, 2024 · d27d179 · d27d179
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diff --git a/.coveragerc b/.coveragerc
@@ -1,4 +1,4 @@
 [run]
 source = cotainr
 omit = cotainr/tests/*
-branch = True
+branch = True
diff --git a/.gitignore b/.gitignore
@@ -140,4 +140,4 @@ dmypy.json
 # Sphinx
 _build/
 
-systems.json
+systems.json
diff --git a/LICENSE b/LICENSE
@@ -284,4 +284,4 @@ the rights granted in Article 2 of this Licence and protect the covered Source
 Code from exclusive appropriation.
 
 All other changes or additions to this Appendix require the production of a new
-EUPL version.
+EUPL version.
diff --git a/doc/_static/switcher.json b/doc/_static/switcher.json
@@ -24,4 +24,4 @@
     "version": "2022.12.0",
     "url": "https://cotainr.readthedocs.io/en/2022.12.0/"
   }
-]
+]
diff --git a/doc/_templates/cotainr_footer.html b/doc/_templates/cotainr_footer.html
@@ -1,3 +1,3 @@
 <p class="copyright">
     &copy Copyright {{copyright}}. See <a href="https://github.com/DeiC-HPC/cotainr#licensing-information">Licensing Information</a>.
-</p>
+</p>
diff --git a/doc/development/cli_internals.rst b/doc/development/cli_internals.rst
@@ -24,7 +24,7 @@ The command line interface is implemented in the :mod:`cotainr.cli` module. It c
 The :class:`~cotainr.cli.CotainrCLI` class is intended to be used as:
 
 .. code-block:: python
-    
+
     cli = CotainrCLI()
     cli.subcommand.execute()
 

diff --git a/doc/development/documentation.rst b/doc/development/documentation.rst
@@ -28,4 +28,4 @@ In order to build the HTML version of the documentation, you must have the Pytho
 .. include:: ../../docs-requirements.txt
     :literal:
 
-Also, in order to run the above :code:`make` commands, you muse have `make <https://www.gnu.org/software/make/>`_ installed.
+Also, in order to run the above :code:`make` commands, you muse have `make <https://www.gnu.org/software/make/>`_ installed.
diff --git a/doc/development/systems.rst b/doc/development/systems.rst
@@ -28,4 +28,4 @@ The base image path can be one of the support targets for `apptainer/singularity
       "another-system-name": {
         "base-image": "/path/to/file/on/system"
       }
-    }
+    }
diff --git a/doc/development/tracing_logging.rst b/doc/development/tracing_logging.rst
@@ -46,7 +46,7 @@ This setup is primarily implemented by two classes :class:`cotainr.tracing.LogDi
 - Apply any filters to modify and/or remove log messages.
 - Add colored console output based on log level, as implemented in :class:`cotainr.tracing.ColoredOutputFormatter`, if requested.
 
-The :class:`~cotainr.tracing.LogDispatcher` then defines methods :meth:`~cotainr.tracing.LogDispatcher.log_to_stdout` and :meth:`~cotainr.tracing.LogDispatcher.log_to_stderr` which may be used with subprocesses to log to `stdout` / `stderr`, respectively, at a message log level determined by the provided `map_log_level_func` function. 
+The :class:`~cotainr.tracing.LogDispatcher` then defines methods :meth:`~cotainr.tracing.LogDispatcher.log_to_stdout` and :meth:`~cotainr.tracing.LogDispatcher.log_to_stderr` which may be used with subprocesses to log to `stdout` / `stderr`, respectively, at a message log level determined by the provided `map_log_level_func` function.
 
 In order to take advantage of this machinery, CLI subcommands must:
 
@@ -94,4 +94,4 @@ Adding a console spinner
 ~~~~~~~~~~~~~~~~~~~~~~~~
 For a given block of code, a spinner may be added to any console output to `stdout` / `stderr` from that code by running it in a :class:`cotainr.tracing.ConsoleSpinner` context.
 
-The spinner is implemented in the :class:`cotainr.tracing.MessageSpinner` class which manages a separate thread updating the spinner for each individual message. Within the :class:`~cotainr.tracing.ConsoleSpinner` context, the spinning message is updated by monkey patching :py:meth:`sys.stdout.write`/:py:meth:`std.stderr.write` with :class:`cotainr.tracing.StreamWriteProxy` wrappers that make sure to update the spinning message whenever something is written to :py:data:`sys.stdout`/:py:data:`sys.stderr`.
+The spinner is implemented in the :class:`cotainr.tracing.MessageSpinner` class which manages a separate thread updating the spinner for each individual message. Within the :class:`~cotainr.tracing.ConsoleSpinner` context, the spinning message is updated by monkey patching :py:meth:`sys.stdout.write`/:py:meth:`std.stderr.write` with :class:`cotainr.tracing.StreamWriteProxy` wrappers that make sure to update the spinning message whenever something is written to :py:data:`sys.stdout`/:py:data:`sys.stderr`.
diff --git a/doc/index.rst b/doc/index.rst
@@ -13,7 +13,7 @@ cotainr documentation
    :maxdepth: 1
    :hidden:
    :includehidden:
-   
+
    Getting Started <getting_started>
    User Guide <user_guide/index>
    API reference <api_reference/index>
@@ -92,4 +92,4 @@ cotainr documentation
             To the development guide
 
 .. _Apptainer: https://apptainer.org/
-.. _Singularity: https://sylabs.io/singularity/
+.. _Singularity: https://sylabs.io/singularity/
diff --git a/doc/user_guide/conda_env.rst b/doc/user_guide/conda_env.rst
@@ -18,7 +18,7 @@ As an example, consider the following `conda environment file <https://conda.io/
 
 .. code-block:: yaml
     :caption: my_conda_env.yml
-    
+
     channels:
       - conda-forge
     dependencies:
@@ -52,7 +52,7 @@ Pip packages
 
 .. code-block:: yaml
     :caption: my_conda_env.yml
-    
+
     channels:
       - conda-forge
     dependencies:

diff --git a/doc/user_guide/index.rst b/doc/user_guide/index.rst
@@ -123,4 +123,4 @@ Further examples of using `cotainr` are included with the source code, https://g
 .. _Singularity: https://sylabs.io/singularity/
 
 .. rubric:: Footnotes
-.. [#] As of version 3.8.0, Sylabs have changed the name of their version to SingularityCE. However, we only officially support their version from 3.9.2.
+.. [#] As of version 3.8.0, Sylabs have changed the name of their version to SingularityCE. However, we only officially support their version from 3.9.2.
diff --git a/docs-requirements.txt b/docs-requirements.txt
@@ -2,4 +2,4 @@ numpydoc>=1.5.0
 pydata-sphinx-theme>=0.13.3
 sphinx>=7.2.5
 sphinx-design>=0.5.0
-myst-parser>=2.0.0
+myst-parser>=2.0.0
diff --git a/pytest.ini b/pytest.ini
@@ -6,4 +6,4 @@ junit_suite_name = cotainr_test_suite
 markers =
     conda_integration: marks tests of integration with conda/mamba
     endtoend: marks end-to-end test cases
-    singularity_integration: marks tests of integration with singularity
+    singularity_integration: marks tests of integration with singularity
diff --git a/test-requirements.txt b/test-requirements.txt
@@ -1,2 +1,2 @@
 pytest>=6.0
-pytest-cov>=2.10
+pytest-cov>=2.10