Adjusting tests to julia. (#2)

Author: hildebrandecon

.github/workflows/main.yml

@@ -11,15 +11,14 @@ jobs:
 
   run-tests:
 
-    name: Run tests for ${{ matrix.os }} on ${{ matrix.python-version }} and ${{ matrix.julia-version }}
+    name: Run tests for ${{ matrix.os }} on ${{ matrix.python-version }}
     runs-on: ${{ matrix.os }}
 
     strategy:
       fail-fast: false
       matrix:
         os: ['ubuntu-latest', 'macos-latest', 'windows-latest']
         python-version: ['3.7', '3.8', '3.9']
-        julia-version: ['main_version']
 
     steps:
       - uses: actions/checkout@v2
@@ -39,7 +38,7 @@ jobs:
         run: tox -e pytest -- -m "unit or (not integration and not end_to_end)" --cov=./ --cov-report=xml -n auto
 
       - name: Upload coverage report for unit tests and doctests.
-        if: runner.os == 'Linux' && matrix.python-version == '3.8' && matrix.julia-version == 'main_version'
+        if: runner.os == 'Linux' && matrix.python-version == '3.8'
         shell: bash -l {0}
         run: bash <(curl -s https://codecov.io/bash) -F unit -c
 
@@ -48,11 +47,11 @@ jobs:
         run: tox -e pytest -- -m end_to_end --cov=./ --cov-report=xml -n auto
 
       - name: Upload coverage reports of end-to-end tests.
-        if: runner.os == 'Linux' && matrix.python-version == '3.8' && matrix.julia-version == 'main_version'
+        if: runner.os == 'Linux' && matrix.python-version == '3.8'
         shell: bash -l {0}
         run: bash <(curl -s https://codecov.io/bash) -F end_to_end -c
 
       - name: Validate codecov.yml
-        if: runner.os == 'Linux' && matrix.python-version == '3.8' && matrix.julia-version == 'main_version'
+        if: runner.os == 'Linux' && matrix.python-version == '3.8'
         shell: bash -l {0}
         run: cat codecov.yml | curl --data-binary @- https://codecov.io/validate

.pre-commit-config.yaml

@@ -8,7 +8,6 @@ repos:
     -   id: check-merge-conflict
     -   id: check-vcs-permalinks
     -   id: check-yaml
-        exclude: meta.yaml
     -   id: debug-statements
     -   id: end-of-file-fixer
     -   id: fix-byte-order-marker
@@ -33,7 +32,7 @@ repos:
     rev: v2.21.2
     hooks:
     -   id: pyupgrade
-        args: [--py36-plus]
+        args: [--py37-plus]
 -   repo: https://github.com/asottile/reorder_python_imports
     rev: v2.5.0
     hooks:

CHANGES.rst

@@ -8,7 +8,8 @@ them in reverse chronological order. Releases follow `semantic versioning
 <https://anaconda.org/conda-forge/pytask-julia>`_.
 
 
-0.0.1 - 202X-XX-XX
+0.1.0 - 2022-xx-xx
 ------------------
 
-- :gh:`01` fixes ...
+- :gh:`2` polishes the first release of pytask-julia. (Thanks to :ghuser:`hmgaudecker`,
+  :ghuser:`hildebrandecon`)

LICENSE

@@ -1,4 +1,3 @@
-
 MIT License
 
 Copyright (c) 2022, Tobias Raabe et al.
@@ -19,6 +18,3 @@ PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
 LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT
 OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
 OTHER DEALINGS IN THE SOFTWARE.
-
-
-

README.rst

@@ -15,18 +15,18 @@ pytask-julia
     :alt: PyPI - License
     :target: https://pypi.org/project/pytask-julia
 
-.. image:: https://img.shields.io/github/workflow/status/hmgaudecker/pytask-julia/main/main
-    :target: https://github.com/hmgaudecker/pytask-julia/actions?query=branch%3Amain
+.. image:: https://img.shields.io/github/workflow/status/pytask-dev/pytask-julia/main/main
+    :target: https://github.com/pytask-dev/pytask-julia/actions?query=branch%3Amain
 
 .. image:: https://readthedocs.org/projects/pytask-julia/badge/?version=latest
     :target: https://pytask-julia.readthedocs.io/en/latest/?badge=latest
     :alt: Documentation Status
 
-.. image:: https://codecov.io/gh/hmgaudecker/pytask-julia/branch/main/graph/badge.svg
-    :target: https://codecov.io/gh/hmgaudecker/pytask-julia
+.. image:: https://codecov.io/gh/pytask-dev/pytask-julia/branch/main/graph/badge.svg
+    :target: https://codecov.io/gh/pytask-dev/pytask-julia
 
-.. image:: https://results.pre-commit.ci/badge/github/hmgaudecker/pytask-julia/main.svg
-    :target: https://results.pre-commit.ci/latest/github/hmgaudecker/pytask-julia/main
+.. image:: https://results.pre-commit.ci/badge/github/pytask-dev/pytask-julia/main.svg
+    :target: https://results.pre-commit.ci/latest/github/pytask-dev/pytask-julia/main
     :alt: pre-commit.ci status
 
 .. image:: https://img.shields.io/badge/code%20style-black-000000.svg
@@ -36,7 +36,8 @@ pytask-julia
 Installation
 ------------
 
-pytask-julia is available on `PyPI <https://pypi.org/project/pytask-julia>`_ and `Anaconda.org <https://anaconda.org/conda-forge/pytask-julia>`_. Install it with
+pytask-julia is available on `PyPI <https://pypi.org/project/pytask-julia>`_ and
+`Anaconda.org <https://anaconda.org/conda-forge/pytask-julia>`_. Install it with
 
 .. code-block:: console
 
@@ -53,7 +54,13 @@ typing the following on the command line
 
     $ julia -h
 
-If an error is shown instead of a help page, you can install Julia ....
+If an error is shown instead of a help page, you can install Julia on Unix systems with
+
+.. code-block:: console
+
+    $ conda install -c conda-forge julia
+
+or choose one of the installers on this `page <https://julialang.org/downloads/>`_.
 
 
 Usage
@@ -77,8 +84,8 @@ Here is an example where you want to run ``script.julia``.
     def task_run_jl_script():
         pass
 
-Note that, you need to apply the ``@pytask.mark.julia`` marker so that pytask-julia handles the
-task.
+Note that, you need to apply the ``@pytask.mark.julia`` marker so that pytask-julia
+handles the task.
 
 If you are wondering why the function body is empty, know that pytask-julia replaces the
 body with a predefined internal function. See the section on implementation details for
@@ -88,8 +95,8 @@ more information.
 Multiple dependencies and products
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-What happens if a task has more dependencies? Using a list, the Julia script which should be
-executed must be found in the first position of the list.
+What happens if a task has more dependencies? Using a list, the Julia script which
+should be executed must be found in the first position of the list.
 
 .. code-block:: python
 
@@ -132,31 +139,65 @@ for a ``"source"`` key in the dictionary and, secondly, under the key ``0``.
 Command Line Arguments
 ~~~~~~~~~~~~~~~~~~~~~~
 
-The decorator can be used to pass command line arguments to ``julia``. See the
-following example.
+The decorator can be used to pass command line arguments to ``julia``. An important
+detail is that you need to differentiate between options passed to the Julia executable
+and arguments passed to the script.
+
+First, pass options to the executable, then, use ``"--"`` as a separator, and after that
+arguments to the script. Provide all arguments in a tuple or a list as below.
+
+The following shows how to pass both with the decorator.
 
 .. code-block:: python
 
-    @pytask.mark.julia("value")
+    @pytask.mark.julia(("--threads", "2", "--", "value"))
     @pytask.mark.depends_on("script.jl")
     @pytask.mark.produces("out.csv")
     def task_run_jl_script():
         pass
 
+which executes the something similar to the following on the command line.
+
+.. code-block:: console
+
+    $ julia --threads 2 -- value
+
 And in your ``script.jl``, you can intercept the value with
 
 .. code-block:: Julia
 
-    FIXME FOR YOUR LANGUAGE
-    args <- commandArgs(trailingOnly=TRUE)
-    arg <- args[1]  # holds ``"value"``
+    arg = ARGS[1]  # holds ``"value"``
+
+If you pass only of of them, either options for the executable or arguments to the
+script, you still need to include the separator.
+
+.. code-block:: python
+
+    @pytask.mark.julia(("--verbose", "--"))  # for options for the executable.
+    @pytask.mark.depends_on("script.jl")
+    def task_func():
+        ...
+
+
+    @pytask.mark.julia(("--", "value"))  # for arguments for the script.
+    @pytask.mark.depends_on("script.jl")
+    def task_func():
+        ...
+
+The corresponding commands on the command line are
+
+.. code-block:: console
+
+    $ julia --verbose -- script.jl
+
+    $ julia -- script.jl value
 
 
 Parametrization
 ~~~~~~~~~~~~~~~
 
-You can also parametrize the execution of scripts, meaning executing multiple Julia scripts
-as well as passing different command line arguments to the same Julia script.
+You can also parametrize the execution of scripts, meaning executing multiple Julia
+scripts as well as passing different command line arguments to the same Julia script.
 
 The following task executes two Julia scripts which produce different outputs.
 
@@ -173,23 +214,25 @@ The following task executes two Julia scripts which produce different outputs.
     def task_execute_julia_script():
         pass
 
-And the R script includes something like
+And the Julia script includes something like
 
-.. code-block:: r
+.. code-block:: julia
 
-    args <- commandArgs(trailingOnly=TRUE)
-    produces <- args[1]  # holds the path
+    produces = ARGS[1]  # holds the path
 
-If you want to pass different command line arguments to the same Julia script, you have to
-include the ``@pytask.mark.julia`` decorator in the parametrization just like with
-``@pytask.mark.depends_on`` and ``@pytask.mark.produces``.
+If you want to pass different command line arguments to the same Julia script, you
+have to include the ``@pytask.mark.julia`` decorator in the parametrization just like
+with ``@pytask.mark.depends_on`` and ``@pytask.mark.produces``.
 
 .. code-block:: python
 
     @pytask.mark.depends_on("script.jl")
     @pytask.mark.parametrize(
         "produces, julia",
-        [(BLD / "output_1.csv", "1"), (BLD / "output_2.csv", "2")],
+        [
+            (BLD / "output_1.csv", ("--", "1")),
+            (BLD / "output_2.csv", ("--", "2")),
+        ],
     )
     def task_execute_julia_script():
         pass
@@ -220,9 +263,9 @@ The plugin is 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 Julia script
-or enter the debugger when starting the script. If there exists a solution for that,
-hints as well as contributions are highly appreciated.
+It is not possible to enter a post-mortem debugger when an error happens in the Julia
+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

@@ -5,13 +5,13 @@ channels:
   - nodefaults
 
 dependencies:
-  - julia
   - python
   - pip
   - setuptools_scm
   - toml
 
   # Package dependencies
+  - julia
   - pytask >=0.1
   - pytask-parallel >=0.1
 
@@ -24,3 +24,6 @@ dependencies:
   - pytest-cov
   - pytest-xdist
   - tox-conda
+
+  - pip:
+    - -e .

setup.cfg

@@ -1,5 +1,5 @@
 [metadata]
-name = pytask-julia
+name = pytask_julia
 description = A Pytask plugin for Julia
 long_description = file: README.rst
 long_description_content_type = text/x-rst
@@ -18,7 +18,6 @@ classifiers =
     Programming Language :: Python :: 3.7
     Programming Language :: Python :: 3.8
     Programming Language :: Python :: 3.9
-    Programming Language :: Python :: 3.10
 project_urls =
     Changelog = https://github.com/pytask-dev/pytask-julia/blob/main/CHANGES.rst
     Documentation = https://github.com/pytask-dev/pytask-julia

src/pytask_julia/collect.py

@@ -15,6 +15,10 @@
 from _pytask.parametrize import _copy_func
 
 
+_SEPARATOR = "--"
+"""str: Separates options for the Julia executable and arguments to the file."""
+
+
 def julia(options: Optional[Union[str, Iterable[str]]] = None):
     """Specify command line options for Julia.
 
@@ -24,8 +28,9 @@ def julia(options: Optional[Union[str, Iterable[str]]] = None):
         One or multiple command line options passed to Julia.
 
     """
-    options = [] if options is None else _to_list(options)
+    options = [_SEPARATOR] if options is None else _to_list(options)
     options = [str(i) for i in options]
+
     return options
 
 
@@ -57,11 +62,10 @@ def pytask_collect_task_teardown(session, task):
     """Perform some checks."""
     if get_specific_markers_from_task(task, "julia"):
         source = _get_node_from_dictionary(task.depends_on, "source")
-        if isinstance(source, FilePathNode) and source.value.suffix not in [
-            ".jl"
-        ]:
+        if isinstance(source, FilePathNode) and source.value.suffix not in [".jl"]:
             raise ValueError(
-                "The first dependency of a Julia task must be the script to be executed."
+                "The first dependency of a Julia task must be the script to be "
+                "executed."
             )
 
         julia_function = _copy_func(run_jl_script)
@@ -91,6 +95,24 @@ def _merge_all_markers(task):
     return mark
 
 
+_ERROR_MSG_MISSING_SEPARATOR = f"""The inputs of the @pytask.mark.julia decorator do not
+contain the separator to differentiate between options for the julia executable and
+arguments to the script. This was passed to the decorator:
+
+{{}}
+
+Construct the inputs to the decorator should contain, first, options to the executable,
+secondly, the separator - "{_SEPARATOR}" -, thirdly, arguments to the script.
+
+Here is an example:
+
+@pytask.mark.julia(("--threads", "1", "{_SEPARATOR}", "input.file"))
+
+Even if you do not need the left or the right side of the decorator, you must put the
+separator at the correct position.
+"""
+
+
 def _prepare_cmd_options(session, task, args):
     """Prepare the command line arguments to execute the do-file.
 
@@ -101,7 +123,21 @@ def _prepare_cmd_options(session, task, args):
     source = _get_node_from_dictionary(
         task.depends_on, session.config["julia_source_key"]
     )
-    return ["julia", source.path.as_posix(), *args]
+
+    if _SEPARATOR not in args:
+        raise ValueError(_ERROR_MSG_MISSING_SEPARATOR.format(args))
+    else:
+        idx_sep = args.index(_SEPARATOR)
+        executable_options = args[:idx_sep]
+        script_arguments = args[idx_sep + 1 :]
+
+    return [
+        "julia",
+        *executable_options,
+        _SEPARATOR,
+        source.path.as_posix(),
+        *script_arguments,
+    ]
 
 
 def _to_list(scalar_or_iter):