Release 0.0.2 and transition to pytask 0.0.5. (#1)

Author: tobiasraabe

.conda/meta.yaml

@@ -20,7 +20,7 @@ requirements:
 
   run:
     - python >=3.6
-    - pytask >=0.0.4
+    - pytask >=0.0.5
 
 test:
   requires:

CHANGES.rst

@@ -6,7 +6,13 @@ chronological order. Releases follow `semantic versioning <https://semver.org/>`
 all releases are available on `Anaconda.org <https://anaconda.org/pytask/pytask-r>`_.
 
 
+0.0.2 - 2020-xx-xx
+------------------
+
+- :gh:`1` includes some minor changes like fixing the missing version variable.
+
+
 0.0.1 - 2020-07-22
 ------------------
 
-- :gh:`1` combined the whole effort which went into releasing v0.0.1.
+- Release v0.0.1.

README.rst

@@ -54,6 +54,10 @@ 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
+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.
+
 Here is an example where you want to run ``script.r``.
 
 .. code-block:: python
@@ -79,6 +83,10 @@ dependencies it may look like this
     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
+more information.
+
 
 Command Line Arguments
 ~~~~~~~~~~~~~~~~~~~~~~
@@ -133,6 +141,8 @@ include the R decorator in the parametrization just like with
         pass
 
 
+.. _implementation_details:
+
 Implementation Details
 ----------------------
 
@@ -147,6 +157,10 @@ The plugin is only a convenient wrapper around
 to which you can always resort to when the plugin does not deliver functionality you
 need.
 
+It is not possible to enter a post-mortem debugger when an error happens in the R script
+or enter the debugger when starting the script. If there exists a solution for that,
+hints as well as contributions are highly appreciated.
+
 
 Changes
 -------

environment.yml

@@ -4,7 +4,7 @@ channels:
   - r
   - pytask
 dependencies:
-  - python=3.7
+  - python
   - pip
 
   # Conda
@@ -13,10 +13,11 @@ dependencies:
   - conda-verify
 
   # Package dependencies
-  - pytask >= 0.0.4
+  - pytask >= 0.0.5
   - r-base
 
   # Misc
+  - bumpversion
   - jupyterlab
   - pdbpp
   - pre-commit

setup.cfg

@@ -1,12 +1,10 @@
 [bumpversion]
-current_version = 0.0.1
+current_version = 0.0.2
 parse = (?P<major>\d+)\.(?P<minor>\d+)(\.(?P<patch>\d+))(\-?((dev)?(?P<dev>\d+))?)
-serialize =
-    {major}.{minor}.{patch}dev{dev}
-    {major}.{minor}.{patch}
+serialize = 
+	{major}.{minor}.{patch}dev{dev}
+	{major}.{minor}.{patch}
 
 [bumpversion:file:setup.py]
 
-[bumpversion:file:docs/conf.py]
-
 [bumpversion:file:src/pytask_r/__init__.py]

setup.py

@@ -3,7 +3,7 @@
 
 setup(
     name="pytask-r",
-    version="0.0.1",
+    version="0.0.2",
     packages=find_packages(where="src"),
     package_dir={"": "src"},
     entry_points={"pytask": ["pytask_r = pytask_r.plugin"]},

src/pytask_r/__init__.py

@@ -0,0 +1 @@
+__version__ = "0.0.2"

src/pytask_r/collect.py

@@ -1,21 +1,40 @@
 import copy
 import functools
 import subprocess
+from typing import Iterable
+from typing import Optional
+from typing import Union
 
-import pytask
-from pytask.mark import get_markers_from_task
-from pytask.mark import has_marker
-from pytask.nodes import PythonFunctionTask
-from pytask.parametrize import _copy_func
-from pytask.shared import to_list
+from _pytask.config import hookimpl
+from _pytask.mark import get_specific_markers_from_task
+from _pytask.mark import has_marker
+from _pytask.nodes import PythonFunctionTask
+from _pytask.parametrize import _copy_func
+from _pytask.shared import to_list
+
+
+def r(options: Optional[Union[str, Iterable[str]]] = None):
+    """Specify command line options for Rscript.
+
+    Parameters
+    ----------
+    options : Optional[Union[str, Iterable[str]]]
+        One or multiple command line options passed to Rscript.
+
+    """
+    if options is None:
+        options = ["--vanilla"]
+    elif isinstance(options, str):
+        options = [options]
+    return options
 
 
 def run_r_script(depends_on, r):
     script = to_list(depends_on)[0]
     subprocess.run(["Rscript", script.as_posix(), *r])
 
 
-@pytask.hookimpl
+@hookimpl
 def pytask_collect_task(session, path, name, obj):
     """Collect a task which is a function.
 
@@ -29,7 +48,7 @@ def pytask_collect_task(session, path, name, obj):
             path, name, obj, session
         )
         r_function = _copy_func(run_r_script)
-        r_function.pytestmark = copy.deepcopy(task.function.pytestmark)
+        r_function.pytaskmark = copy.deepcopy(task.function.pytaskmark)
 
         args = _create_command_line_arguments(task)
         r_function = functools.partial(r_function, r=args)
@@ -46,10 +65,11 @@ def pytask_collect_task(session, path, name, obj):
 
 
 def _create_command_line_arguments(task):
-    args = get_markers_from_task(task, "r")[0].args
-    if args:
-        out = list(args)
-    else:
-        out = ["--vanilla"]
+    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 out
+    return options

src/pytask_r/config.py

@@ -0,0 +1,6 @@
+from _pytask.config import hookimpl
+
+
+@hookimpl
+def pytask_parse_config(config):
+    config["markers"]["r"] = "r: Tasks which are executed with Rscript."

src/pytask_r/execute.py

@@ -1,13 +1,13 @@
 import shutil
 
-import pytask
-from pytask.mark import get_markers_from_task
-from pytask.nodes import FilePathNode
+from _pytask.config import hookimpl
+from _pytask.mark import get_specific_markers_from_task
+from _pytask.nodes import FilePathNode
 
 
-@pytask.hookimpl
+@hookimpl
 def pytask_execute_task_setup(task):
-    if get_markers_from_task(task, "r"):
+    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."