Merge 53fd7ee into ad5c098

Author: tobiasraabe

.github/workflows/main.yml

@@ -27,26 +27,17 @@ jobs:
       fail-fast: false
       matrix:
         os: ['ubuntu-latest', 'macos-latest', 'windows-latest']
-        python-version: ['3.8', '3.9', '3.10', '3.11']
+        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
 
     steps:
       - uses: actions/checkout@v4
-      - uses: mamba-org/setup-micromamba@v1
+      - uses: julia-actions/setup-julia@v1
+      - uses: actions/setup-python@v4
         with:
-          environment-name: gha-testing
-          condarc: |
-            channels:
-              - nodefaults
-              - conda-forge
-          create-args: >-
-            python=${{ matrix.python-version }}
-            mamba
-            tox-conda
-          cache-environment: true
-
-      - name: Install core dependencies.
-        shell: bash -l {0}
-        run: mamba install -c conda-forge tox-conda coverage mamba
+          python-version: ${{ matrix.python-version }}
+          cache: pip
+          allow-prereleases: true
+      - run: pip install tox
 
       # Unit, integration, and end-to-end tests.
 
@@ -55,7 +46,7 @@ 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'
+        if: runner.os == 'Linux' && matrix.python-version == '3.10'
         shell: bash -l {0}
         run: bash <(curl -s https://codecov.io/bash) -F unit -c
 
@@ -64,6 +55,6 @@ 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'
+        if: runner.os == 'Linux' && matrix.python-version == '3.10'
         shell: bash -l {0}
         run: bash <(curl -s https://codecov.io/bash) -F end_to_end -c

.pre-commit-config.yaml

@@ -64,13 +64,10 @@ repos:
     rev: 'v1.5.1'
     hooks:
     -   id: mypy
-        args: [
-            --no-strict-optional,
-            --ignore-missing-imports,
-        ]
         additional_dependencies: [
             attrs>=21.3.0,
             click,
+            pytask>=0.4.0,
             types-PyYAML,
             types-setuptools
         ]

CHANGES.md

@@ -5,7 +5,11 @@ chronological order. Releases follow [semantic versioning](https://semver.org/)
 releases are available on [PyPI](https://pypi.org/project/pytask-julia) and
 [Anaconda.org](https://anaconda.org/conda-forge/pytask-julia).
 
-## 0.3.0 - 2023-xx-xx
+## 0.4.0 - 2023-10-08
+
+- {pull}`24` prepares the release of pytask v0.4.0.
+
+## 0.3.0 - 2023-01-24
 
 - {pull}`16` adds mypy, refurb, and ruff.
 - {pull}`18` deprecates INI configurations and aligns the package with pytask v0.3.

README.md

@@ -50,10 +50,12 @@ task module to the Julia script.
 
 ```python
 import pytask
+from pathlib import Path
+from pytask import task
 
 
+@task(kwargs={"path": Path("out.csv")})
 @pytask.mark.julia(script="script.jl")
-@pytask.mark.produces("out.csv")
 def task_run_jl_script():
     pass
 ```
@@ -64,11 +66,12 @@ more information.
 
 ### Dependencies and Products
 
-Dependencies and products can be added as with a normal pytask task using the
-`@pytask.mark.depends_on` and `@pytask.mark.produces` decorators. which is explained in
-this
+Dependencies and products can be added as usual. Read this
 [tutorial](https://pytask-dev.readthedocs.io/en/stable/tutorials/defining_dependencies_products.html).
 
+For example, with the `@pytask.task` decorator as shown before. (The choice of the kwarg
+name, here `path`, is arbitrary.)
+
 ### Accessing dependencies and products in the script
 
 To access the paths of dependencies and products in the script, pytask-julia stores the
@@ -82,21 +85,19 @@ path_to_json = ARGS[1]  # Contains the path to the .json file.
 
 config = JSON.parse(read(path_to_json, String))  # A dictionary.
 
-config["produces"]  # Is the path to the output file "../out.csv".
+config["path"]  # Is the path to the output file "../out.csv".
 ```
 
 The `.json` file is stored in the same folder as the task in a `.pytask` directory.
 
 To parse the JSON file, you need to install
 [JSON.jl](https://github.com/JuliaIO/JSON.jl).
 
-You can also pass any other information to your script by using the `@pytask.mark.task`
-decorator.
+You can also pass any other information to your script by using the `@task` decorator.
 
 ```python
-@pytask.mark.task(kwargs={"number": 1})
+@task(kwargs={"path": Path("out.csv"), "number": 1})
 @pytask.mark.julia(script="script.jl")
-@pytask.mark.produces("out.csv")
 def task_run_jl_script():
     pass
 ```
@@ -141,8 +142,8 @@ You can also define environments for each task which will overwrite any other de
 with the `project` keyword argument. Pass a path to the task module.
 
 ```python
+@task(kwargs={"path": Path("out.csv")})
 @pytask.mark.julia(script="script.jl", project=".")
-@pytask.mark.produces("out.csv")
 def task_run_jl_script():
     pass
 ```
@@ -152,8 +153,8 @@ def task_run_jl_script():
 Command line options can be pass via the `options` keyword argument.
 
 ```python
+@task(kwargs={"path": Path("out.csv")})
 @pytask.mark.julia(script="script.jl", options=["--threads", "2"])
-@pytask.mark.produces("out.csv")
 def task_run_jl_script():
     pass
 ```
@@ -171,22 +172,20 @@ produce different outputs.
 ```python
 for i in range(2):
 
-    @pytask.mark.task
+    @task(kwargs={"path": Path(f"out_{i}.csv")})
     @pytask.mark.julia(script=f"script_{i}.jl")
-    @pytask.mark.produces(f"out_{i}.csv")
     def task_execute_julia_script():
         pass
 ```
 
 If you want to pass different inputs to the same Julia script, pass these arguments with
-the `kwargs` keyword of the `@pytask.mark.task` decorator.
+the `kwargs` keyword of the `@task` decorator.
 
 ```python
 for i in range(2):
 
-    @pytask.mark.task(kwargs={"i": i})
+    @task(kwargs={"path": Path(f"out_{i}.csv"), "i": i})
     @pytask.mark.julia(script="script.jl")
-    @pytask.mark.produces(f"output_{i}.csv")
     def task_execute_julia_script():
         pass
 ```
@@ -200,7 +199,7 @@ path_to_json = ARGS[1]  # Contains the path to the .json file.
 
 config = JSON.parse(read(path_to_json, String))  # A dictionary.
 
-config["produces"]  # Is the path to the output file "../output_{i}.csv".
+config["path"]  # Is the path to the output file "../output_{i}.csv".
 
 config["i"]  # Is the number.
 ```

environment.yml

@@ -2,6 +2,8 @@ name: pytask-julia
 
 channels:
   - conda-forge
+  - conda-forge/label/pytask_rc
+  - conda-forge/label/pytask_parallel_rc
   - nodefaults
 
 dependencies:
@@ -12,8 +14,8 @@ dependencies:
 
   # Package dependencies
   - julia
-  - pytask >=0.3
-  - pytask-parallel >=0.3
+  - pytask >=0.4.0
+  - pytask-parallel >=0.4.0
 
   # Optional package dependencies
   - pyyaml

pyproject.toml

@@ -62,3 +62,14 @@ extend-ignore = [
 
 [tool.ruff.pydocstyle]
 convention = "numpy"
+
+[tool.pytest.ini_options]
+# Do not add src since it messes with the loading of pytask-parallel as a plugin.
+testpaths = ["tests"]
+markers = [
+    "wip: Tests that are work-in-progress.",
+    "unit: Flag for unit tests which target mainly a single function.",
+    "integration: Flag for integration tests which may comprise of multiple unit tests.",
+    "end_to_end: Flag for tests that cover the whole program.",
+]
+norecursedirs = [".idea", ".tox"]

setup.cfg

@@ -24,8 +24,8 @@ project_urls =
 [options]
 packages = find:
 install_requires =
-    pybaum>=0.1.1
-    pytask>=0.3
+    pluggy>=1.0.0
+    pytask>=0.4.0
 python_requires = >=3.8
 include_package_data = True
 package_dir = =src