fix: Fix issues with dependencies and default tools (#274)

.makim.yaml

@@ -1,7 +1,7 @@
 version: 1.0
 groups:
   clean:
-    targets:
+    tasks:
       tmp:
         help: Clean unnecessary temporary files
         shell: bash
@@ -20,7 +20,7 @@ groups:
           find . -name '*~' -exec rm -f {} +
 
   docs:
-    targets:
+    tasks:
       build:
         help: Build documentation
         run: |
@@ -45,7 +45,7 @@ groups:
         -p "@google/semantic-release-replace-plugin" \
         semantic-release
 
-    targets:
+    tasks:
       dry:
         help: Run semantic release in dry-run mode
         run: ${{ vars.app }} --dry-run
@@ -54,7 +54,7 @@ groups:
         run: ${{ vars.app }} --ci
 
   tests:
-    targets:
+    tasks:
       lint:
         help: Run linter tools
         run: pre-commit run --all-files --verbose

conda/dev.yaml

@@ -11,5 +11,5 @@ dependencies:
   - compilers
   - pip
   - pip:
-      - makim==1.12.0
+      - makim==1.15.1
       - paginate

pyproject.toml

@@ -38,7 +38,7 @@ mkdocs-material = ">=8.3.9"
 mkdocstrings-python = ">=0.7.1"
 mkdocstrings-python-legacy = ">=0.2.3"
 pymdown-extensions = ">=9.5"
-makim = ">=1.14.0,<1.15"
+makim = "1.15.1"
 
 [build-system]
 requires = ["poetry-core>=1.0.0"]

src/scicookie/cookiecutter.json

@@ -40,9 +40,9 @@
     "pybind11"
   ],
   "use_bandit": "no",
-  "use_black": "yes",
-  "use_conda": "yes",
-  "use_makim": "yes",
+  "use_black": "no",
+  "use_conda": "no",
+  "use_makim": "no",
   "use_make": "no",
   "use_containers": ["None", "Docker", "Podman"],
   "use_coverage": "no",
@@ -51,11 +51,12 @@
   "use_isort": "no",
   "use_mccabe": "no",
   "use_mypy": "no",
-  "use_pre_commit": "yes",
+  "use_pre_commit": "no",
   "use_prettier": "no",
   "use_pydocstyle": "no",
-  "use_pytest": "yes",
-  "use_ruff": "yes",
+  "use_pyenv": "no",
+  "use_pytest": "no",
+  "use_ruff": "no",
   "use_shellcheck": "no",
   "use_vulture": "no",
   "git_username": "zoro_roronoa",

src/scicookie/hooks/post_gen_project.py

@@ -37,6 +37,9 @@
 USE_MAKIM = {{ cookiecutter.use_makim == "yes" }}
 USE_MYPY = {{ cookiecutter.use_mypy == "yes" }}
 USE_PRETTIER = {{ cookiecutter.use_prettier == "yes" }}
+USE_PRE_COMMIT = {{ cookiecutter.use_pre_commit == "yes" }}
+USE_PYTEST = {{ cookiecutter.use_pytest == "yes" }}
+USE_HYPOTHESIS = {{ cookiecutter.use_hypothesis == "yes" }}
 {% if cookiecutter.code_of_conduct == "contributor-covenant" -%}
 COC_PATH = PROJECT_DIRECTORY / 'coc' / 'CONTRIBUTOR_COVENANT.md'
 {%- elif cookiecutter.code_of_conduct == "citizen-code-of-conduct" -%}
@@ -119,6 +122,11 @@ def move_selected_doc_dir():
     shutil.rmtree(DOCS_SPEC_DIR)
 
 
+def clean_up_tests():
+    if not USE_PYTEST and not USE_HYPOTHESIS:
+        remove_project_file("tests/test_main.py")
+
+
 def clean_up_automation():
     if not USE_MAKE:
         remove_project_file("Makefile")
@@ -185,11 +193,6 @@ def clean_up_cli():
         remove_package_file("cli.py")
 
 
-def clean_up_prettier():
-    if not USE_PRETTIER:
-        remove_project_file(".prettierrc.yaml")
-        remove_project_file(".prettierignore")
-
 def clean_up_build_system():
     build_system_dir = PROJECT_DIRECTORY / "build-system"
 
@@ -274,6 +277,28 @@ def http2ssh(url):
     url = url.replace("https://", "git@")
     return url.replace("/", ":", 1)
 
+def clean_up_linter():
+    if not USE_MYPY:
+        remove_package_file("py.typed")
+
+    if not USE_PRE_COMMIT:
+        remove_project_file(".pre-commit-config.yaml")
+
+    if not USE_PRETTIER:
+        remove_project_file(".prettierrc.yaml")
+        remove_project_file(".prettierignore")
+
+    # keep this one at the end
+    if USE_PRETTIER:
+        subprocess.call([
+            "npx",
+            "--yes",
+            "prettier",
+            "--write",
+            "--ignore-unknown",
+            PROJECT_DIRECTORY
+        ])
+
 
 def prepare_git() -> None:
     git_https_origin = http2ssh("{{cookiecutter.git_https_origin}}")
@@ -362,27 +387,23 @@ def add_binding_source_files():
         pass
 
 
-def clean_up_mypy():
-    if not USE_MYPY:
-        remove_package_file("py.typed")
-
-
 def post_gen():
-
     # keep this one first, because it changes the package folder
     clean_up_project_layout()
     add_binding_source_files()
     clean_up_automation()
     clean_up_cli()
-    clean_up_mypy()
     clean_up_code_of_conduct()
     clean_up_conda()
     clean_up_containers()
     clean_up_docs()
     clean_up_governance()
     clean_up_roadmap()
     clean_up_build_system()
-    clean_up_prettier()
+    clean_up_tests()
+
+    # keep it before the prepare_git function call
+    clean_up_linter()
 
     # keep it at the end, because it will create a new git commit
     prepare_git()

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

@@ -6,7 +6,7 @@
 version: 1.0
 groups:
   clean:
-    targets:
+    tasks:
       all:
         help: Clean unnecessary temporary files
         run: |
@@ -26,7 +26,7 @@ groups:
           find . -name '*~' -exec rm -f {} +
 
   docs:
-    targets:
+    tasks:
       build:
         help: Build documentation
         run: |
@@ -47,7 +47,7 @@ groups:
       preview:
         help: Preview documentation page locally
         dependencies:
-          - target: docs.build
+          - task: docs.build
         run: |
           {%- if cookiecutter.documentation_engine == "jupyter-book" %}
           cd docs/_build/html/ && python -m http.server
@@ -60,7 +60,7 @@ groups:
           {%- endif %}
 
   tests:
-    targets:
+    tasks:
       linter:
         help: Run linter tools
         run: |
@@ -79,16 +79,22 @@ groups:
             type: string
             default: "-vv"
         run: |
+          {%- if cookiecutter.use_pytest == "yes" %}
           pytest {{ "${{ args.path }} ${{ args.params }}" }}
+          {%- elif cookiecutter.use_hypothesis == "yes" %}
+          python -m unittest discover
+          {%- else %}
+          echo "No test library installed."
+          {%- endif %}
 
       ci:
         help: run the sames tests executed on CI
         dependencies:
-          - target: tests.unit
-          - target: tests.linter
+          - task: tests.unit
+          - task: tests.linter
 
   package:
-    targets:
+    tasks:
       build:
         help: "Build the package"
         run: |
@@ -124,7 +130,7 @@ groups:
         -p "@google/semantic-release-replace-plugin" \
         semantic-release
 
-    targets:
+    tasks:
       ci:
         help: run semantic release on CI
         run: {{ "${{ vars.app }} --ci" }}

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

@@ -70,7 +70,7 @@ test: ## run tests quickly with the default Python
 	{%- elif cookiecutter.use_hypothesis == "yes" %}
 	python -m unittest discover
 	{%- else %}
-	@echo "No test library selected."
+	@echo "No test library installed."
 	{%- endif %}
 
 {% if cookiecutter.documentation_engine == 'mkdocs' -%}

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

@@ -86,4 +86,5 @@ warn_unused_ignores = true
 warn_redundant_casts = true
 warn_unused_configs = true
 {% endif -%}
-{#- keep this line at the end of the file -#}
+{# keep this line at the end of the file #}
+# Add more configuration here!

src/scicookie/{{cookiecutter.project_slug}}/build-system/deps-pyproject.toml

@@ -50,6 +50,16 @@ dynamic = ["version"]
 {% endif -%}
 requires-python = ">=3.8.1,<4"
 dependencies = [
+  # note: add your dependencies here
+]
+{# keep this line here #}
+{%- if cookiecutter.build_system == "pdm" %}
+[tool.pdm.dev-dependencies]
+{%- else %}
+# NOTE: it is not actually optional, instead it is development dependencies
+[project.optional-dependencies]
+{%- endif %}
+dev = [
 {#- keep this line here -#}
 {%- if cookiecutter.build_system in ["setuptools", "pybind11"] %}
   "build>=0.10.0",
@@ -91,7 +101,7 @@ dependencies = [
   "pydocstyle >= 6.3.0",
 {%- endif -%}
 {%- if cookiecutter.use_makim == "yes" %}
-  "makim>=1.14.0,<1.15",
+  "makim == 1.15.1",
 {%- endif -%}
 {%- if cookiecutter.use_vulture == "yes" %}
   "vulture >= 2.7",
@@ -115,23 +125,20 @@ dependencies = [
   "mkdocs-material >= 9.1.15",
   "mkdocstrings >= 0.21.2",
   "mkdocstrings-python >= 1.1.2",
-{# keep this line here #}
 {%- elif cookiecutter.documentation_engine == 'sphinx' %}
   "Sphinx >= 6.2.1",
   "sphinx-rtd-theme >= 1.2.2",
   "importlib-metadata >= 6.5.1",
   "myst-parser >= 0.19.2",
   "nbsphinx >= 0.9.2",
   "pandoc >= 2.3",
-{# keep this line here #}
 {%- elif cookiecutter.documentation_engine == 'jupyter-book' %}
   "jupyter-book >= 0.15.1",
   "myst-parser >= 0.18.1",
-{# keep this line here #}
 {%- elif cookiecutter.documentation_engine == 'quarto' %}
   "quarto-cli >= 1.4.550",
   "quartodoc >= 0.7.2",
-{% endif -%}
+{%- endif %}
   # 'PosixPath' object has no attribute 'endswith'
   "virtualenv<=20.25.1",
 ]
@@ -141,3 +148,4 @@ Homepage = "{{ cookiecutter.project_url }}"
 "Bug Tracker" = "{{ cookiecutter.project_url }}/issues"
 Discussions = "{{ cookiecutter.project_url }}/discussions"
 Changelog = "{{ cookiecutter.project_url }}/releases"
+{#- keep this line at the end of the file -#}

src/scicookie/{{cookiecutter.project_slug}}/build-system/poetry-pyproject.toml

@@ -115,7 +115,7 @@ quarto-cli = ">=1.4.550"
 quartodoc = ">=0.7.2"
 {% endif -%}
 {%- if cookiecutter.use_makim == "yes" -%}
-makim = ">=1.14.0,<1.15"
+makim = "1.15.1"
 {% endif -%}
 # 'PosixPath' object has no attribute 'endswith'
 virtualenv = "<=20.25.1"