Deprecate INI configurations and align with pytask v0.3. (#18)

Author: tobiasraabe

.github/workflows/main.yml

@@ -40,7 +40,7 @@ jobs:
 
       - name: Install core dependencies.
         shell: bash -l {0}
-        run: conda install -c conda-forge tox-conda coverage mamba
+        run: mamba install -c conda-forge tox-conda coverage mamba
 
       # Unit, integration, and end-to-end tests.
 

CHANGES.md

@@ -5,6 +5,10 @@ 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
+
+- {pull}`18` deprecates INI configurations and aligns the package with pytask v0.3.
+
 ## 0.2.1 - 2022-04-16
 
 - {pull}`12` includes `pyproject.toml` in the package.

Manifest.toml

@@ -1,10 +1,12 @@
 # This file is machine-generated - editing it directly is not advised
 
-julia_version = "1.7.1"
+julia_version = "1.8.5"
 manifest_format = "2.0"
+project_hash = "df1f4ff6ff5c9fd1541ff7a0d1e10d339e63d6ac"
 
 [[deps.ArgTools]]
 uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f"
+version = "1.1.1"
 
 [[deps.Artifacts]]
 uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33"
@@ -19,6 +21,7 @@ uuid = "ade2ca70-3891-5945-98fb-dc099432e06a"
 [[deps.Downloads]]
 deps = ["ArgTools", "FileWatching", "LibCURL", "NetworkOptions"]
 uuid = "f43a241f-c20a-4ad4-852c-f6b1247861c6"
+version = "1.6.0"
 
 [[deps.FileWatching]]
 uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee"
@@ -42,10 +45,12 @@ version = "0.21.3"
 [[deps.LibCURL]]
 deps = ["LibCURL_jll", "MozillaCACerts_jll"]
 uuid = "b27032c2-a3e7-50c8-80cd-2d36dbcbfd21"
+version = "0.6.3"
 
 [[deps.LibCURL_jll]]
 deps = ["Artifacts", "LibSSH2_jll", "Libdl", "MbedTLS_jll", "Zlib_jll", "nghttp2_jll"]
 uuid = "deac9b47-8bc7-5906-a0fe-35ac56dc84c0"
+version = "7.84.0+0"
 
 [[deps.LibGit2]]
 deps = ["Base64", "NetworkOptions", "Printf", "SHA"]
@@ -54,15 +59,16 @@ uuid = "76f85450-5226-5b5a-8eaa-529ad045b433"
 [[deps.LibSSH2_jll]]
 deps = ["Artifacts", "Libdl", "MbedTLS_jll"]
 uuid = "29816b5a-b9ab-546f-933c-edad1886dfa8"
+version = "1.10.2+0"
 
 [[deps.Libdl]]
 uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb"
 
 [[deps.Libiconv_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
-git-tree-sha1 = "42b62845d70a619f063a7da093d995ec8e15e778"
+git-tree-sha1 = "c7cb1f5d892775ba13767a87c7ada0b980ea0a71"
 uuid = "94ce4f54-9a6c-5748-9c1c-f9c7231a4531"
-version = "1.16.1+1"
+version = "1.16.1+2"
 
 [[deps.Logging]]
 uuid = "56ddb016-857b-54e1-b83d-db4d58db5568"
@@ -74,31 +80,35 @@ uuid = "d6f4376e-aef5-505a-96c1-9c027394607a"
 [[deps.MbedTLS_jll]]
 deps = ["Artifacts", "Libdl"]
 uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1"
+version = "2.28.0+0"
 
 [[deps.Mmap]]
 uuid = "a63ad114-7e13-5084-954f-fe012c677804"
 
 [[deps.MozillaCACerts_jll]]
 uuid = "14a3606d-f60d-562e-9121-12d972cd8159"
+version = "2022.2.1"
 
 [[deps.NetworkOptions]]
 uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908"
+version = "1.2.0"
 
 [[deps.Parsers]]
-deps = ["Dates"]
-git-tree-sha1 = "13468f237353112a01b2d6b32f3d0f80219944aa"
+deps = ["Dates", "SnoopPrecompile"]
+git-tree-sha1 = "6466e524967496866901a78fca3f2e9ea445a559"
 uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0"
-version = "2.2.2"
+version = "2.5.2"
 
 [[deps.Pkg]]
 deps = ["Artifacts", "Dates", "Downloads", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"]
 uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
+version = "1.8.0"
 
 [[deps.Preferences]]
 deps = ["TOML"]
-git-tree-sha1 = "2cf929d64681236a2e074ffafb8d568733d2e6af"
+git-tree-sha1 = "47e5f437cc0e7ef2ce8406ce1e7e24d44915f88d"
 uuid = "21216c6a-2e73-6563-6e65-726566657250"
-version = "1.2.3"
+version = "1.3.0"
 
 [[deps.Printf]]
 deps = ["Unicode"]
@@ -114,10 +124,16 @@ uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 
 [[deps.SHA]]
 uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce"
+version = "0.7.0"
 
 [[deps.Serialization]]
 uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b"
 
+[[deps.SnoopPrecompile]]
+git-tree-sha1 = "f604441450a3c0569830946e5b33b78c928e1a85"
+uuid = "66db9d55-30c0-4569-8b51-7e840670fc0c"
+version = "1.0.1"
+
 [[deps.Sockets]]
 uuid = "6462fe0b-24de-5631-8697-dd941f90decc"
 
@@ -130,10 +146,12 @@ version = "0.3.5"
 [[deps.TOML]]
 deps = ["Dates"]
 uuid = "fa267f1f-6049-4f14-aa54-33bafae1ed76"
+version = "1.0.0"
 
 [[deps.Tar]]
 deps = ["ArgTools", "SHA"]
 uuid = "a4e569a6-e804-4fa4-b0f3-eef7a1d5b13e"
+version = "1.10.1"
 
 [[deps.UUIDs]]
 deps = ["Random", "SHA"]
@@ -144,18 +162,21 @@ uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5"
 
 [[deps.YAML]]
 deps = ["Base64", "Dates", "Printf", "StringEncodings"]
-git-tree-sha1 = "3c6e8b9f5cdaaa21340f841653942e1a6b6561e5"
+git-tree-sha1 = "dbc7f1c0012a69486af79c8bcdb31be820670ba2"
 uuid = "ddb6d928-2868-570f-bddf-ab3f9cf99eb6"
-version = "0.4.7"
+version = "0.4.8"
 
 [[deps.Zlib_jll]]
 deps = ["Libdl"]
 uuid = "83775a58-1f1d-513f-b197-d71354ab007a"
+version = "1.2.12+3"
 
 [[deps.nghttp2_jll]]
 deps = ["Artifacts", "Libdl"]
 uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d"
+version = "1.48.0+0"
 
 [[deps.p7zip_jll]]
 deps = ["Artifacts", "Libdl"]
 uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0"
+version = "17.4.0+0"

README.md

@@ -5,7 +5,7 @@
 [![image](https://img.shields.io/conda/vn/conda-forge/pytask-julia.svg)](https://anaconda.org/conda-forge/pytask-julia)
 [![image](https://img.shields.io/conda/pn/conda-forge/pytask-julia.svg)](https://anaconda.org/conda-forge/pytask-julia)
 [![PyPI - License](https://img.shields.io/pypi/l/pytask-julia)](https://pypi.org/project/pytask-julia)
-[![image](https://img.shields.io/github/workflow/status/pytask-dev/pytask-julia/main/main)](https://github.com/pytask-dev/pytask-julia/actions?query=branch%3Amain)
+[![image](https://img.shields.io/github/actions/workflow/status/pytask-dev/pytask-julia/main.yml?branch=main)](https://github.com/pytask-dev/pytask-julia/actions?query=branch%3Amain)
 [![image](https://codecov.io/gh/pytask-dev/pytask-julia/branch/main/graph/badge.svg)](https://codecov.io/gh/pytask-dev/pytask-julia)
 [![pre-commit.ci status](https://results.pre-commit.ci/badge/github/pytask-dev/pytask-julia/main.svg)](https://results.pre-commit.ci/latest/github/pytask-dev/pytask-julia/main)
 [![image](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/ambv/black)
@@ -296,3 +296,16 @@ julia_project = "environment"
 ## Changes
 
 Consult the [release notes](CHANGES.md) to find out about what is new.
+
+## Development
+
+After setting up the environment, enter
+
+```console
+$ julia
+$ ]
+$ pkg> activate .
+$ pkg> instantiate
+```
+
+to set up the Julia environment.

environment.yml

@@ -12,8 +12,8 @@ dependencies:
 
   # Package dependencies
   - julia
-  - pytask >=0.2
-  - pytask-parallel >=0.1
+  - pytask >=0.3
+  - pytask-parallel >=0.3
 
   # Optional package dependencies
   - pyyaml

setup.cfg

@@ -25,7 +25,7 @@ project_urls =
 packages = find:
 install_requires =
     pybaum>=0.1.1
-    pytask>=0.2
+    pytask>=0.3
 python_requires = >=3.7
 include_package_data = True
 package_dir = =src

src/pytask_julia/collect.py

@@ -14,7 +14,7 @@
 from pytask import produces
 from pytask import remove_marks
 from pytask import Task
-from pytask_julia.serialization import SERIALIZER
+from pytask_julia.serialization import SERIALIZERS
 from pytask_julia.shared import julia
 from pytask_julia.shared import parse_relative_path
 
@@ -122,9 +122,9 @@ def _parse_julia_mark(
 
     if (
         isinstance(parsed_kwargs["serializer"], str)
-        and parsed_kwargs["serializer"] in SERIALIZER
+        and parsed_kwargs["serializer"] in SERIALIZERS
     ):
-        proposed_suffix = SERIALIZER[parsed_kwargs["serializer"]]["suffix"]
+        proposed_suffix = SERIALIZERS[parsed_kwargs["serializer"]]["suffix"]
     else:
         proposed_suffix = default_suffix
     parsed_kwargs["suffix"] = suffix if suffix else proposed_suffix

src/pytask_julia/config.py

@@ -1,33 +1,39 @@
 """Configure pytask."""
 from __future__ import annotations
 
+from typing import Any
+
 from pytask import hookimpl
+from pytask_julia.serialization import SERIALIZERS
 from pytask_julia.shared import parse_relative_path
 
 
 @hookimpl
-def pytask_parse_config(config, config_from_file):
+def pytask_parse_config(config):
     """Register the julia marker."""
     config["markers"]["julia"] = "Tasks which are executed with Julia."
-    config["julia_serializer"] = config_from_file.get("julia_serializer", "json")
-    config["julia_suffix"] = config_from_file.get("julia_suffix", "")
+    config["julia_serializer"] = config.get("julia_serializer", "json")
+    if config["julia_serializer"] not in SERIALIZERS:
+        raise ValueError(
+            f"'julia_serializer' is {config['julia_serializer']} and not one of "
+            f"{list(SERIALIZERS)}."
+        )
+    config["julia_suffix"] = config.get("julia_suffix", "")
     config["julia_options"] = _parse_value_or_whitespace_option(
-        config_from_file.get("julia_options")
+        config.get("julia_options")
     )
-    project = config_from_file.get("julia_project")
+    project = config.get("julia_project")
     if project is None:
         config["julia_project"] = project
     else:
         config["julia_project"] = parse_relative_path(project, config["root"])
 
 
-def _parse_value_or_whitespace_option(value: str | None) -> None | str | list[str]:
+def _parse_value_or_whitespace_option(value: Any) -> None | list[str]:
     """Parse option which can hold a single value or values separated by new lines."""
-    if value in ["none", "None", None, ""]:
+    if value is None:
         return None
-    elif isinstance(value, list):
+    if isinstance(value, list):
         return list(map(str, value))
-    elif isinstance(value, str):
-        return [v.strip() for v in value.split(" ") if v.strip()]
     else:
-        raise ValueError(f"Input {value!r} is neither a 'str' nor 'None'.")
+        raise ValueError(f"'julia_options' is {value} and not a list.")

src/pytask_julia/serialization.py

@@ -12,7 +12,7 @@
 _HIDDEN_FOLDER = ".pytask"
 
 
-SERIALIZER = {
+SERIALIZERS = {
     "json": {"serializer": json.dumps, "suffix": ".json"},
 }
 
@@ -21,8 +21,8 @@
 except ImportError:  # pragma: no cover
     pass
 else:
-    SERIALIZER["yaml"] = {"serializer": yaml.dump, "suffix": ".yaml"}
-    SERIALIZER["yml"] = {"serializer": yaml.dump, "suffix": ".yml"}
+    SERIALIZERS["yaml"] = {"serializer": yaml.dump, "suffix": ".yaml"}
+    SERIALIZERS["yml"] = {"serializer": yaml.dump, "suffix": ".yml"}
 
 
 def create_path_to_serialized(task: Task, suffix: str) -> Path:
@@ -57,8 +57,8 @@ def serialize_keyword_arguments(
 ) -> None:
     if callable(serializer):
         serializer_func = serializer
-    elif isinstance(serializer, str) and serializer in SERIALIZER:
-        serializer_func = SERIALIZER[serializer]["serializer"]
+    elif isinstance(serializer, str) and serializer in SERIALIZERS:
+        serializer_func = SERIALIZERS[serializer]["serializer"]
     else:  # pragma: no cover
         raise ValueError(f"Serializer {serializer!r} is not known.")
 

src/pytask_julia/shared.py

@@ -6,45 +6,8 @@
 from typing import Sequence
 
 
-_ERROR_MSG = """The old syntax for @pytask.mark.julia was suddenly deprecated starting \
-with pytask-julia v0.2 to provide a better user experience. Thank you for your \
-understanding!
-
-It is recommended to upgrade to the new syntax, so you enjoy all the benefits of v0.2 of
-pytask and pytask-julia which are
-
-- Access to 'depends_on' and 'produces', and other kwargs inside the Julia script.
-- Support for Julia environments for running scripts with certain packages.
-
-You can find a manual here: \
-https://github.com/pytask-dev/pytask-julia/blob/v0.2.0/README.md
-
-Upgrading can be as easy as rewriting your current task from
-
-    @pytask.mark.julia(["--threads", 2, "--", "path_to_dependency.txt"])
-    @pytask.mark.depends_on("script.jl")
-    @pytask.mark.produces("out.csv")
-    def task_julia():
-        ...
-
-to
-
-    @pytask.mark.julia(script="script.jl", options=("--threads", 2))
-    @pytask.mark.depends_on("path_to_dependency.txt")
-    @pytask.mark.produces("out.csv")
-    def task_julia():
-        ...
-
-You can also fix the version of pytask and pytask-julia to <0.2, so you do not have to \
-to upgrade. At the same time, you will not enjoy the improvements released with \
-version v0.2 of pytask and pytask-julia.
-
-"""
-
-
 def julia(
-    *args,
-    script: str | Path | None = None,
+    script: str | Path,
     options: str | Iterable[str] | None = None,
     serializer: str | Callable[..., str] | str | None = None,
     suffix: str | None = None,
@@ -60,7 +23,7 @@ def julia(
 
     Parameters
     ----------
-    script : str | Path | None
+    script : str | Path
         The path to the Julia script which is executed.
     options : str | Iterable[str] | None
         One or multiple command line options passed to the interpreter for Julia.
@@ -76,9 +39,6 @@ def julia(
         A path to an Julia environment used to execute this task.
 
     """
-    if args or script is None:
-        raise RuntimeError(_ERROR_MSG)
-
     options = [] if options is None else list(map(str, _to_list(options)))
     return script, options, serializer, suffix, project