perf(template): Update deps used by the template (#126)

* Revisit and update deps in the template.
* Mypy threw a hint in the pre-commit for the __init__.py file. Change # type: ignore[attr-defined] to # mypy: disable-error-code="attr-defined".
* Fix the issue where the .bandit file was deleted incorrectly

src/scicookie/hooks/post_gen_project.py

@@ -93,7 +93,7 @@ def clean_up_project_layout():
 
 
 def clean_up_bandit():
-    if USE_BANDIT:
+    if not USE_BANDIT:
         remove_project_file(PROJECT_DIRECTORY / '.bandit')
 
 

src/scicookie/{{cookiecutter.project_slug}}/pyproject.toml

@@ -41,31 +41,31 @@ python = "^3.8.1"
 urllib3 = "<2"  # fix poetry issues
 {# keep this line here #}
 {%- if cookiecutter.use_pytest == "yes" -%}
-pytest = "^7"
+pytest = "^7.3.2"
 {% if cookiecutter.use_coverage == "yes" -%}
-pytest-cov = "^4"
+pytest-cov = "^4.1.0"
 {% endif %}
 {%- endif -%}{#- end of use_pytest -#}
 {%- if cookiecutter.use_coverage == "yes" -%}
-coverage = "^7"
+coverage = "^7.2.7"
 {% endif %}
 {%- if cookiecutter.use_blue == "yes" -%}
 blue = "^0.9.1"
 {% endif %}
 {%- if cookiecutter.use_black == "yes" -%}
-black = "^22.3"
+black = "^23.3.0"
 {% endif %}
 {%- if cookiecutter.use_isort == "yes" -%}
-isort = "^5"
+isort = "^5.12.0"
 {% endif %}
 {%- if cookiecutter.use_pre_commit -%}
-pre-commit = "^2"
+pre-commit = "^3.3.2"
 {% endif %}
 {%- if cookiecutter.use_flake8 == "yes" -%}
-flake8 = "^4"
+flake8 = ">=4.0.1, <7"
 {% endif %}
 {%- if cookiecutter.use_mypy == "yes" -%}
-mypy = "^0.931"
+mypy = "^1.3.0"
 {% endif %}
 {%- if cookiecutter.use_bandit == "yes" -%}
 bandit = "^1.7.5"
@@ -81,26 +81,26 @@ mccabe = "^0.6.1"
 {% endif %}
 {%- if cookiecutter.use_containers in ['Docker', 'Podman'] -%}
 # if you want to use docker-compose from your system, remove compose-go here
-compose-go = "^2.18.0"
+compose-go = "^2.18.1"
 {% endif %}
 {%- if cookiecutter.documentation_engine == 'mkdocs' -%}
-Jinja2 = "<3.1.0"
-mkdocs = ">=1.2.3,<2"
-mkdocs-exclude = ">=1.0.2,<2"
-mkdocs-jupyter = ">=0.20.0,<1"
-mkdocs-literate-nav = ">=0.4.1,<1"
-mkdocs-macros-plugin = ">=0.6.3,<1"
-mkdocs-material = ">=8.2.1,<9"
-mkdocstrings = ">=0.17.0,<0.18.0"
-mkdocstrings-python = "^0.4.0"
+Jinja2 = "^3.1.2"
+mkdocs = "^1.4.3"
+mkdocs-exclude = "^1.0.2"
+mkdocs-jupyter = "^0.24.1"
+mkdocs-literate-nav = "^0.6.0"
+mkdocs-macros-plugin = ">=0.7.0,<1"
+mkdocs-material = "^9.1.15"
+mkdocstrings = "^0.21.2"
+mkdocstrings-python = "^1.1.2"
 {% elif cookiecutter.documentation_engine == 'sphinx' -%}
-Sphinx = "^5.0.0"
-sphinx-rtd-theme = "^1.1.1"
-importlib-metadata = "^5.0.0"
-myst-parser = "^0.18.1"
+Sphinx = "^6.2.1"
+sphinx-rtd-theme = "^1.2.2"
+importlib-metadata = "^6.5.1"
+myst-parser = "^0.19.2"
 {% elif cookiecutter.documentation_engine == 'jupyter-book' -%}
-jupyter-book = "^0.12.3"
-myst-parser = "^0.15.0"
+jupyter-book = "^0.15.1"
+myst-parser = "^0.18.1"
 {% endif %}
 {%- if cookiecutter.use_pytest == "yes" %}
 [tool.pytest.ini_options]

src/scicookie/{{cookiecutter.project_slug}}/{{cookiecutter.package_slug}}/__init__.py

@@ -1,4 +1,4 @@
-# type: ignore[attr-defined]
+# mypy: disable-error-code="attr-defined"
 """{{ cookiecutter.project_name }}."""
 {%- if cookiecutter.use_blue == "yes" %}
   {%- set QUOTE = "'" -%}