Add a check for exit codes to be equal to zero and release v0.0.3. (#3)

Author: tobiasraabe

.conda/meta.yaml

@@ -20,7 +20,7 @@ requirements:
 
   run:
     - python >=3.6
-    - pytask >=0.0.5
+    - pytask >=0.0.7
 
 test:
   requires:
@@ -32,11 +32,13 @@ test:
   commands:
     - pytask --version
     - pytask --help
+    - pytask markers
+    - pytask clean
 
     - pytest tests
 
 about:
   home: https://github.com/pytask-dev/pytask-r
   license: none
-  summary: Compile LaTeX documents.
+  summary: Run R scripts with pytask.
   dev_url: https://github.com/pytask-dev/pytask-r/

CHANGES.rst

@@ -6,10 +6,12 @@ chronological order. Releases follow `semantic versioning <https://semver.org/>`
 all releases are available on `Anaconda.org <https://anaconda.org/pytask/pytask-r>`_.
 
 
-0.0.3 - 2020-xx-xx
+0.0.3 - 2020-10-04
 ------------------
 
-:gh:`2` fixes marker description and adds some changes to the readme.
+- :gh:`2` fixes marker description and adds some changes to the readme.
+- :gh:`3` check for exit code equal to 0, preparation for pytask v0.0.7, and releases
+  v0.0.3.
 
 
 0.0.2 - 2020-08-14

README.rst

@@ -5,7 +5,7 @@
     :target: https://anaconda.org/pytask/pytask-r
 
 .. image:: https://github.com/pytask-dev/pytask-r/workflows/Continuous%20Integration%20Workflow/badge.svg?branch=main
-    :target: https://github.com/pytask-dev/pytask/actions?query=branch%3Amain
+    :target: https://github.com/pytask-dev/pytask-r/actions?query=branch%3Amain
 
 .. image:: https://codecov.io/gh/pytask-dev/pytask-r/branch/main/graph/badge.svg
     :target: https://codecov.io/gh/pytask-dev/pytask-r
@@ -18,7 +18,7 @@
 pytask-r
 ========
 
-pytask-r allows you to run R scripts with pytask.
+Run R scripts with pytask.
 
 
 Installation
@@ -31,17 +31,17 @@ Install the plugin with
     $ conda config --add channels conda-forge --add channels pytask
     $ conda install pytask-r
 
-You also need to have R installed and ``Rscript`` on your command line. To test
-whether it is installed, type the following on the command line
+You also need to have R installed and ``Rscript`` on your command line. Test it by
+typing the following on the command line
 
 .. code-block:: console
 
     $ Rscript --help
 
 If an error is shown instead of a help page, you can install R with ``conda`` by
-choosing either the normal R or Microsoft R Open (MRO). The command is one of the two
-following commands. (See `here <https://docs.anaconda.com/anaconda/user-guide/tasks/
-using-r-language>`_  for further explanation on Anaconda, R, and MRO.)
+choosing either R or Microsoft R Open (MRO). Choose one of the two following commands.
+(See `here <https://docs.anaconda.com/anaconda/user-guide/tasks/ using-r-language>`_
+for further explanation on Anaconda, R, and MRO.)
 
 .. code-block:: console
 
@@ -54,9 +54,9 @@ Or install install R from the official `R Project <https://www.r-project.org/>`_
 Usage
 -----
 
-Similarly to normal task functions which execute Python code, you also define tasks to
+Similarly to normal task functions which execute Python code, you define tasks to
 execute scripts written in R with Python functions. The difference is that the function
-body does not contain any logic, but the decorators tell pytask how to handle the task.
+body does not contain any logic, but the decorator tells pytask how to handle the task.
 
 Here is an example where you want to run ``script.r``.
 
@@ -72,27 +72,27 @@ Here is an example where you want to run ``script.r``.
         pass
 
 Note that, you need to apply the ``@pytask.mark.r`` marker so that pytask-r handles the
-task. The first dependency is always treated as the executable script. With multiple
-dependencies it may look like this
+task. The executable script must be the first dependency. Other dependencies can be
+added after that.
 
 .. code-block:: python
 
     @pytask.mark.r
-    @pytask.mark.depends_on("script.r", "input.rds")
+    @pytask.mark.depends_on(["script.r", "input.rds"])
     @pytask.mark.produces("out.rds")
     def task_run_r_script():
         pass
 
 If you are wondering why the function body is empty, know that pytask-r replaces the
-body with an predefined internal function. See the section on implementation details for
+body with a predefined internal function. See the section on implementation details for
 more information.
 
 
 Command Line Arguments
 ~~~~~~~~~~~~~~~~~~~~~~
 
-The decorator can be used to pass command line arguments to ``Rscript`` which is by
-default the only the ``--vanilla`` flag. If you want to pass arguments to the script via
+The decorator can be used to pass command line arguments to ``Rscript`` which is, by
+default, only the ``--vanilla`` flag. If you want to pass arguments to the script via
 the command line, use
 
 .. code-block:: python
@@ -115,7 +115,7 @@ Parametrization
 ~~~~~~~~~~~~~~~
 
 You can also parametrize the execution of scripts, meaning executing multiple R scripts
-as well as passing different command line arguments to an R script.
+as well as passing different command line arguments to the same R script.
 
 The following task executes two R scripts which produce different outputs.
 
@@ -130,29 +130,30 @@ The following task executes two R scripts which produce different outputs.
 
 
 If you want to pass different command line arguments to the same R script, you have to
-include the R decorator in the parametrization just like with
+include the ``@pytask.mark.r`` decorator in the parametrization just like with
 ``@pytask.mark.depends_on`` and ``@pytask.mark.produces``.
 
 .. code-block:: python
 
     @pytask.mark.depends_on("script.r")
-    @pytask.mark.parametrize("produces, r", [("out_1.rds", 1), ("out_2.rds", 2)])
+    @pytask.mark.parametrize(
+        "produces, r",
+        [("output_1.rds", ["--vanilla", 1]), ("output_2.rds", ["--vanilla", 2])],
+    )
     def task_execute_r_script():
         pass
 
 
-.. _implementation_details:
-
 Implementation Details
 ----------------------
 
-The plugin is only a convenient wrapper around
+The plugin is a convenient wrapper around
 
 .. code-block:: python
 
     import subprocess
 
-    subprocess.run(["Rscript", "--vanilla", "script.r"])
+    subprocess.run(["Rscript", "--vanilla", "script.r"], check=True)
 
 to which you can always resort to when the plugin does not deliver functionality you
 need.

environment.yml

@@ -13,7 +13,7 @@ dependencies:
   - conda-verify
 
   # Package dependencies
-  - pytask >= 0.0.5
+  - pytask >= 0.0.7
   - r-base
 
   # Misc

setup.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.0.2
+current_version = 0.0.3
 parse = (?P<major>\d+)\.(?P<minor>\d+)(\.(?P<patch>\d+))(\-?((dev)?(?P<dev>\d+))?)
 serialize = 
 	{major}.{minor}.{patch}dev{dev}

setup.py

@@ -3,7 +3,7 @@
 
 setup(
     name="pytask-r",
-    version="0.0.2",
+    version="0.0.3",
     packages=find_packages(where="src"),
     package_dir={"": "src"},
     entry_points={"pytask": ["pytask_r = pytask_r.plugin"]},

src/pytask_r/__init__.py

@@ -1 +1 @@
-__version__ = "0.0.2"
+__version__ = "0.0.3"

src/pytask_r/collect.py

@@ -1,3 +1,4 @@
+"""Collect tasks."""
 import copy
 import functools
 import subprocess
@@ -8,6 +9,7 @@
 from _pytask.config import hookimpl
 from _pytask.mark import get_specific_markers_from_task
 from _pytask.mark import has_marker
+from _pytask.nodes import FilePathNode
 from _pytask.nodes import PythonFunctionTask
 from _pytask.parametrize import _copy_func
 from _pytask.shared import to_list
@@ -30,8 +32,9 @@ def r(options: Optional[Union[str, Iterable[str]]] = None):
 
 
 def run_r_script(depends_on, r):
+    """Run an R script."""
     script = to_list(depends_on)[0]
-    subprocess.run(["Rscript", script.as_posix(), *r])
+    subprocess.run(["Rscript", script.as_posix(), *r], check=True)
 
 
 @hookimpl
@@ -50,26 +53,30 @@ def pytask_collect_task(session, path, name, obj):
         r_function = _copy_func(run_r_script)
         r_function.pytaskmark = copy.deepcopy(task.function.pytaskmark)
 
-        args = _create_command_line_arguments(task)
+        merged_marks = _merge_all_markers(task)
+        args = r(*merged_marks.args, **merged_marks.kwargs)
         r_function = functools.partial(r_function, r=args)
 
         task.function = r_function
 
-        if task.depends_on[0].value.suffix not in [".r", ".R"]:
+        return task
+
+
+@hookimpl
+def pytask_collect_task_teardown(task):
+    if task is not None:
+        if isinstance(task.depends_on[0], FilePathNode) and task.depends_on[
+            0
+        ].value.suffix not in [".r", ".R"]:
             raise ValueError(
-                "The first dependency of an R task must be the script which will be "
-                "executed."
+                "The first dependency of an R task must be the executable script."
             )
 
-        return task
 
-
-def _create_command_line_arguments(task):
+def _merge_all_markers(task):
+    """Combine all information from markers for the compile r function."""
     r_marks = get_specific_markers_from_task(task, "r")
     mark = r_marks[0]
     for mark_ in r_marks[1:]:
-        mark = mark.combine_with(mark_)
-
-    options = r(*mark.args, **mark.kwargs)
-
-    return options
+        mark = mark.combined_with(mark_)
+    return mark

src/pytask_r/config.py

@@ -1,6 +1,8 @@
+"""Configure pytask."""
 from _pytask.config import hookimpl
 
 
 @hookimpl
 def pytask_parse_config(config):
+    """Register the r marker."""
     config["markers"]["r"] = "Tasks which are executed with Rscript."

src/pytask_r/execute.py

@@ -1,20 +1,15 @@
+"""Execute tasks."""
 import shutil
 
 from _pytask.config import hookimpl
 from _pytask.mark import get_specific_markers_from_task
-from _pytask.nodes import FilePathNode
 
 
 @hookimpl
 def pytask_execute_task_setup(task):
+    """Perform some checks when a task marked with the r marker is executed."""
     if get_specific_markers_from_task(task, "r"):
         if shutil.which("Rscript") is None:
             raise RuntimeError(
                 "Rscript is needed to run R scripts, but it is not found on your PATH."
             )
-
-        if not (
-            isinstance(task.depends_on[0], FilePathNode)
-            and task.depends_on[0].value.suffix in [".r", ".R"]
-        ):
-            raise ValueError("'depends_on' must be a path to a single .r script.")