More permissive hooks and mamba (#166)

* Remove heavy R pre-commit hook

* Replace conda by mamba where appropriate.

* Make ruff list more lenient / useful.

* [pre-commit.ci] pre-commit autoupdate (#165)

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

.pre-commit-config.yaml

@@ -10,7 +10,7 @@ repos:
     hooks:
       - id: yamlfix
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v5.0.0
     hooks:
       - id: check-added-large-files
         args: [--maxkb=25]
@@ -37,7 +37,7 @@ repos:
     hooks:
       - id: yamllint
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.6.8
+    rev: v0.6.9
     hooks:
       # Run the linter.
       - id: ruff
@@ -72,47 +72,6 @@ repos:
     rev: v2.3.0
     hooks:
       - id: codespell
-
-  # R specific hooks: https://github.com/lorenzwalthert/precommit
-  - repo: https://github.com/lorenzwalthert/precommit
-    rev: v0.4.3.9001
-    hooks:
-      - id: style-files
-        args: [--style_pkg=styler, --style_fun=tidyverse_style]
-      - id: spell-check
-        exclude: >
-          (?x)^(
-          .*\.[rR]|
-          .*\.feather|
-          .*\.jpeg|
-          .*\.pdf|
-          .*\.png|
-          .*\.py|
-          .*\.RData|
-          .*\.rds|
-          .*\.Rds|
-          .*\.Rproj|
-          .*\.sh|
-          (.*/|)\.gitignore|
-          (.*/|)\.gitlab-ci\.yml|
-          (.*/|)\.lintr|
-          (.*/|)\.pre-commit-.*|
-          (.*/|)\.Rbuildignore|
-          (.*/|)\.Renviron|
-          (.*/|)\.Rprofile|
-          (.*/|)\.travis\.yml|
-          (.*/|)appveyor\.yml|
-          (.*/|)NAMESPACE|
-          (.*/|)renv/settings\.dcf|
-          (.*/|)renv\.lock|
-          (.*/|)WORDLIST|
-          \.github/workflows/.*|
-          data/.*|
-          )$
-      - id: readme-rmd-rendered
-      - id: parsable-R
-      - id: no-browser-statement
-      - id: no-debug-statement
   - repo: local
     hooks:
       - id: forbid-to-commit

docs_template/scripts/task_create_visualization_for_docs.py

@@ -14,7 +14,7 @@
 for case in ("model_steps_full", "model_steps_select", "steps_only_full"):
 
     @pytask.task(id=case)
-    def task_visualize_organisational_steps(  # noqa: D103
+    def task_visualize_organisational_steps(
         case=case,
         produces=FIGURES / f"{case}.png",
     ):
@@ -25,7 +25,7 @@ def task_visualize_organisational_steps(  # noqa: D103
 for tex_file in ("root_bld_src", "src"):
 
     @pytask.task(id=tex_file)
-    def task_compile_latex(  # noqa: D103
+    def task_compile_latex(
         depends_on=DOCS_SCRIPTS / "latex" / f"{tex_file}.tex",
         produces=DOCS_SCRIPTS / "latex" / f"{tex_file}.png",
     ):
@@ -43,7 +43,7 @@ def task_compile_latex(  # noqa: D103
         time.sleep(1)
 
     @pytask.task(id=tex_file)
-    def task_copy_png_to_figures(  # noqa: D103
+    def task_copy_png_to_figures(
         depends_on=DOCS_SCRIPTS / "latex" / f"{tex_file}.png",
         produces=FIGURES / f"{tex_file}.png",
     ):

docs_template/source/development/how-to-contribute.md

@@ -22,15 +22,15 @@ for some immediate and clearly defined tasks.
    repo):
 
    ```console
-   $ conda env create -f environment.yml
+   $ mamba env create -f environment.yml
    $ conda activate template_project
    ```
 
 1. In case you work on the documentation, you also have to install and activate the
    documentation environment:
 
 ```console
-$ conda env create -f docs_template/rtd_environment.yml
+$ mamba env create -f docs_template/rtd_environment.yml
 $ conda activate ept-docs
 ```
 

docs_template/source/getting_started/customising_the_template.md

@@ -25,7 +25,7 @@ attributed to changes you make rather than the original template.
 
    ```console
    $ cd /to/root/of/template_project
-   $ conda env create
+   $ mamba env create
    ```
 
 1. Activate the installed environment

docs_template/source/getting_started/second_machine.md

@@ -8,7 +8,7 @@ Powershell on Windows. Then type
 ```console
 $ git clone <url_of_your_repository>
 $ cd <name_of_your_project>
-$ conda env create -f environment.yml
+$ mamba env create -f environment.yml
 $ conda activate <conda_environment_name>
 $ pre-commit install
 ```

docs_template/source/getting_started/template_setup.md

@@ -25,7 +25,7 @@ changes you make rather than the original template.
 
    ```console
    $ cd /to/root/of/template
-   $ conda env create -f environment.yml
+   $ mamba env create -f environment.yml
    ```
 
 1. Activate the installed environment

docs_template/source/guides_explanations/environments.md

@@ -79,7 +79,7 @@ If you want to add a package to your environment, add it to the environment.yml
 Once you have edited the environment.yml file, run
 
 ```console
-$ conda env update -f environment.yml
+$ mamba env update -f environment.yml
 ```
 
 **Choosing between conda and pip**

pyproject.toml

@@ -84,15 +84,15 @@ fix = true
 [tool.ruff.lint]
 select = ["ALL"]
 extend-ignore = [
-    "S101",  # Use of `assert` detected.
     "ANN",  # Missing type annotations
-    "D100",  # Missing docstring in public module
-    "D104",  # Missing docstring in public package (__init__.py files)
-    "S301",  # pickle module is unsafe
+    "COM812", # Conflict with ruff-format
+    "D10",  # Missing docstrings
+    "ISC001", # Conflict with ruff-format
+    "PD901", # df is a great name with functional data management
     "PLR0913",  # Too many arguments in function definition
-    # ignore because conflict with ruff-format
-    "COM812",
-    "ISC001",
+    "RET504", # Don't force to calculate upon return
+    "S101",  # Use of `assert` detected.
+    "S301",  # pickle module is unsafe
 ]
 
 [tool.ruff.lint.per-file-ignores]