fix: Split build system config by tools, fix typos, and fix the `defa…

…ult` attribute in profile (#323)

- split build system config by tools
- fix the creation of .github folder
- fix the usage of the attribute `default` in the profile yaml file
- fix typo `continuos` to `continuous`
- create an alias for check_schema.py command in the ci.sh
- fix compose.yaml content structure
- improve configuration .editorconfig
- update makim to 1.19.0

.editorconfig

@@ -3,25 +3,27 @@
 root = true
 
 [*]
-indent_style = space
-indent_size = 2
-trim_trailing_whitespace = true
-insert_final_newline = true
 charset = utf-8
 end_of_line = lf
+insert_final_newline = true
+trim_trailing_whitespace = true
 
-[*.py]
+[*.{py,rst,ini}]
 indent_style = space
 indent_size = 4
 
-[*.bat]
-indent_style = tab
-end_of_line = crlf
+[*.{html,css,scss,json,yml,xml}]
+indent_style = space
+indent_size = 2
 
-[LICENSE]
-insert_final_newline = true
+[*.md]
+trim_trailing_whitespace = false
+
+[default.conf]
+indent_style = space
+indent_size = 2
 
-[Makefile]
+["Makefile"]
 indent_style = tab
 
 [*.{diff,patch}]

.github/workflows/main.yaml

@@ -88,7 +88,7 @@ jobs:
 
       - name: Run tests
         if: ${{ matrix.os != 'windows' }}
-        run: makim tests.unittest
+        run: makim tests.unit
 
       - name: Run tests
         if: ${{ matrix.os == 'windows' }}

.makim.yaml

@@ -1,10 +1,9 @@
-version: 1.0
 groups:
   clean:
     tasks:
       tmp:
         help: Clean unnecessary temporary files
-        shell: bash
+        backend: bash
         run: |
           rm -fr build/
           rm -fr dist/
@@ -59,23 +58,26 @@ groups:
         help: Run linter tools
         run: pre-commit run --all-files --verbose
 
-      unittest:
+      unit:
         help: Run tests
         run: pytest -s -vv --template src/scicookie tests
 
       smoke:
         help: Run smoke tests
+        matrix:
+          script:
+            - auto-format-tools.sh
+            - build-systems.sh
+            - ci.sh
+            - cli.sh
+            - containers.sh
+            - docs-jupyter-book.sh
+            - docs-mkdocs.sh
+            - docs-quarto.sh
+            - docs-sphinx.sh
+            - files.sh
+            - linters.sh
+            - tests.sh
+            - virtual-envs.sh
         run: |
-          ./tests/smoke/auto-format-tools.sh
-          ./tests/smoke/build-systems.sh
-          ./tests/smoke/ci.sh
-          ./tests/smoke/cli.sh
-          ./tests/smoke/containers.sh
-          ./tests/smoke/docs-jupyter-book.sh
-          ./tests/smoke/docs-mkdocs.sh
-          ./tests/smoke/docs-quarto.sh
-          ./tests/smoke/docs-sphinx.sh
-          ./tests/smoke/files.sh
-          ./tests/smoke/linters.sh
-          ./tests/smoke/tests.sh
-          ./tests/smoke/virtual-envs.sh
+          ./tests/smoke/${{ matrix.script }}

README.md

@@ -111,7 +111,7 @@ For testing your changes locally, you can run:
 
 ```bash
 makim tests.lint
-makim tests.unittest
+makim tests.unit
 makim tests.smoke
 ```
 

conda/dev-win.yaml

@@ -12,5 +12,5 @@ dependencies:
   - compilers
   - pip
   - pip:
-      - makim==1.18.1
+      - makim==1.19.0
       - paginate

conda/dev.yaml

@@ -12,5 +12,5 @@ dependencies:
   - compilers
   - pip
   - pip:
-      - makim==1.18.1
+      - makim==1.19.0
       - paginate==0.5.6

docs/contributing.md

@@ -194,7 +194,7 @@ environment:
    or
 
    ```bash
-   $ makim tests.unittest
+   $ makim tests.unit
    ```
 
 9. **Commit and Push Changes**: Stage, commit, and push your changes to GitHub.

docs/guide.md

@@ -31,7 +31,7 @@ The structure of the guide is as follows:
     - [Governance document](#governance-document)
     - [Roadmap document](#roadmap-document)
   - [Version control](#version-control)
-  - [Continuos Integration](#continuos-integration)
+  - [Continuous Integration](#continuous-integration)
 
 ## Notes about the text-based user interface (TUI)
 
@@ -973,7 +973,7 @@ GitHub and take advantage of its powerful version control features. These
 functionalities in SciCookie make it easy to manage your project and collaborate
 with others, while ensuring that your code is properly versioned and tracked.
 
-## Continuos integration
+## Continuous integration
 
 Continuous Integration (CI) is a development practice where code changes are
 frequently merged into a shared repository. Each change is automatically built

docs/index.md

@@ -105,7 +105,7 @@ For testing your changes locally, you can run:
 
 ```bash
 makim tests.lint
-makim tests.unittest
+makim tests.unit
 makim tests.smoke
 ```
 

docs/install.md

@@ -76,7 +76,7 @@ environment:
   or
 
   ```bash
-  $ makim tests.unittest
+  $ makim tests.unit
   ```
 
 - **Commit and Push Changes**: Stage, commit, and push your changes to GitHub.

pyproject.toml

@@ -40,7 +40,7 @@ mkdocs-material = ">=8.3.9"
 mkdocstrings-python = ">=0.7.1"
 mkdocstrings-python-legacy = ">=0.2.3"
 pymdown-extensions = ">=9.5"
-makim = "1.15.1"
+makim = "1.19.0"
 pexpect = ">=4.9.0"
 ensureconda = ">=1.4"
 

src/scicookie/cli.py

@@ -98,7 +98,11 @@ def call_cookiecutter(profile: Profile, answers: dict) -> None:
             answers_profile[question_id] = answer
             continue
 
-        for choice in answer:
+        answer_clean: list[str] = (
+            answer if isinstance(answer, list) else [answer]
+        )
+
+        for choice in answer_clean:
             choice_id = f"use_{choice.replace('-', '_')}"
             answers_profile[choice_id] = "yes"
 
@@ -107,6 +111,9 @@ def call_cookiecutter(profile: Profile, answers: dict) -> None:
     new_path: list[str] = [*pipx_path, os.getenv("PATH", "")]
     os.environ["PATH"] = env_path_sep.join(new_path)
 
+    # TODO: print answers with --verbose
+    # print(answers_profile)
+
     cookiecutter(
         str(PACKAGE_PATH), no_input=True, extra_context=answers_profile
     )

src/scicookie/profiles/base.yaml

@@ -291,7 +291,7 @@ git_main_branch:
   default: main
   visible: true
 
-continuos_integration:
+continuous_integration:
   message: Select one option for Continuous Integration
   help: "For more information, check:\n  https://osl-incubator.github.io/scicookie/guide/#continuous-integration"
   type: multiple-choices

src/scicookie/profiles/osl.yaml

@@ -105,7 +105,8 @@ git_https_upstream:
 git_main_branch:
   visible: true
 
-continuos_integration:
+continuous_integration:
+  default: github_actions
   choices:
     - github_actions
   visible: false

src/scicookie/{{cookiecutter.project_slug}}/.editorconfig

@@ -3,23 +3,32 @@
 root = true
 
 [*]
-indent_style = space
-indent_size = 2
-trim_trailing_whitespace = true
-insert_final_newline = true
 charset = utf-8
 end_of_line = lf
+insert_final_newline = true
+trim_trailing_whitespace = true
 
-[*.py]
+[*.{py,rst,ini}]
 indent_style = space
 indent_size = 4
 
-[*.bat]
+[*.{html,css,scss,json,yml,xml}]
+indent_style = space
+indent_size = 2
+
+[*.md]
+trim_trailing_whitespace = false
+
+[default.conf]
+indent_style = space
+indent_size = 2
+
+["Makefile"]
 indent_style = tab
-end_of_line = crlf
 
-[LICENSE]
-insert_final_newline = true
+[*.{diff,patch}]
+trim_trailing_whitespace = false
 
-[Makefile]
+[*.bat]
 indent_style = tab
+end_of_line = crlf

src/scicookie/{{cookiecutter.project_slug}}/.github/workflows/main.yaml

@@ -39,7 +39,7 @@ jobs:
         shell: bash -l {0}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 {%- endraw %}
 {% if cookiecutter.use_conda == "yes" %}
       - name: Cache Conda Packages
@@ -61,7 +61,7 @@ jobs:
           auto-update-conda: true
           conda-solver: libmamba
 {% else %}
-      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
         with:
           python-version: "pypy3.9"
 

src/scicookie/{{cookiecutter.project_slug}}/.github/workflows/release.yaml

@@ -23,7 +23,7 @@ jobs:
         shell: bash -l {0}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 {% if cookiecutter.use_conda == "yes" %}
       - uses: conda-incubator/setup-miniconda@v3
         with:

src/scicookie/{{cookiecutter.project_slug}}/.makim.yaml

@@ -3,12 +3,12 @@
 {%- else -%}
 {%- set package_path = cookiecutter.package_slug -%}
 {%- endif -%}
-version: 1.0
 groups:
   clean:
     tasks:
       all:
         help: Clean unnecessary temporary files
+        backend: bash
         run: |
           rm -fr build/
           rm -fr dist/
@@ -46,8 +46,9 @@ groups:
 
       preview:
         help: Preview documentation page locally
-        dependencies:
-          - task: docs.build
+        hooks:
+          pre-run:
+            - task: docs.build
         run: |
           {%- if cookiecutter.documentation_engine == "jupyter-book" %}
           cd docs/_build/html/ && python -m http.server
@@ -90,9 +91,10 @@ groups:
 
       ci:
         help: run the sames tests executed on CI
-        dependencies:
-          - task: tests.unit
-          - task: tests.linter
+        hooks:
+          pre-run:
+            - task: tests.unit
+            - task: tests.linter
 
   package:
     tasks:

src/scicookie/{{cookiecutter.project_slug}}/.pre-commit-config.yaml

@@ -4,7 +4,7 @@
 {%- set package_path = cookiecutter.package_slug -%}
 {%- endif -%}
 default_stages:
-  - commit
+  - pre-commit
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.1.0

src/scicookie/{{cookiecutter.project_slug}}/build-system/base/config-bandit.toml

@@ -0,0 +1,5 @@
+{%- if cookiecutter.use_bandit == "yes" %}
+[tool.bandit]
+exclude_dirs = ["tests"]
+targets = "./"
+{% endif -%}

src/scicookie/{{cookiecutter.project_slug}}/build-system/base/config-black.toml

@@ -0,0 +1,9 @@
+{%- if cookiecutter.use_black == "yes" %}
+[tool.black]
+line-length = 79
+target-version = ["py39"]
+force-exclude = '''(?x)(
+    docs/*
+  | .*\\.egg-info
+)'''  # TOML's single-quoted strings do not require escaping backslashes
+{% endif -%}

src/scicookie/{{cookiecutter.project_slug}}/build-system/base/config-isort.toml

@@ -0,0 +1,8 @@
+{%- if cookiecutter.use_isort == "yes" %}
+[tool.isort]
+ensure_newline_before_comments = true
+line_length = 79
+multi_line_output = 3
+include_trailing_comma = true
+skip_glob = ["docs/*", "*.egg-info"]
+{% endif -%}

src/scicookie/{{cookiecutter.project_slug}}/build-system/base/config-mypy.toml

@@ -0,0 +1,11 @@
+{%- if cookiecutter.use_mypy == "yes" %}
+[tool.mypy]
+python_version = "3.9"
+check_untyped_defs = true
+strict = true
+ignore_missing_imports = true
+warn_unused_ignores = true
+warn_redundant_casts = true
+warn_unused_configs = true
+exclude = ["scripts/"]
+{% endif -%}

src/scicookie/{{cookiecutter.project_slug}}/build-system/base/config-pytest.toml

@@ -0,0 +1,6 @@
+{%- if cookiecutter.use_pytest == "yes" %}
+[tool.pytest.ini_options]
+testpaths = [
+    "tests",
+]
+{% endif -%}