fix: Fix issues with docs, makim/make, release, and CI (#182)

- Implement properly the makim targets, including tests and documentation tasks
- Fix main CI workflow and the Release workflow
- Fix the semantic-release configuration
- Fix the some URLs in the GitHub ISSUES templates that was pointing to the repository
- Fix some configurations in the pyprojet.toml
- Add tests for the automation tools to CI
- Update cookiecutter.json and the base profile respect to makim and make
- Update some python pinning from 3.8 to 3.8.1

.github/workflows/main.yaml

@@ -58,6 +58,7 @@ jobs:
     strategy:
       matrix:
         smoke_file:
+          - automation.sh
           - auto-format-tools.sh
           - build-systems.sh
           - containers.sh

LICENSE

@@ -1,27 +1,29 @@
-Copyright (c) Open Science Labs and individual contributors.
+BSD License
 
+Copyright (c) 2023, Open Science Labs
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without modification,
 are permitted provided that the following conditions are met:
 
-    * Redistributions of source code must retain the above copyright notice,
-      this list of conditions and the following disclaimer.
-    * Redistributions in binary form must reproduce the above copyright notice,
-      this list of conditions and the following disclaimer in the documentation
-      and/or other materials provided with the distribution.
-    * Neither the name of Audrey Roy Greenfeld nor the names of its contributors
-      may be used to endorse or promote products derived from this software
-      without specific prior written permission.
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
 
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
-"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
-LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
-A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
-CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
-EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
-PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
-PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
-LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
-NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
-SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+* Redistributions in binary form must reproduce the above copyright notice, this
+  list of conditions and the following disclaimer in the documentation and/or
+  other materials provided with the distribution.
+
+* Neither the name of the copyright holder nor the names of its
+  contributors may be used to endorse or promote products derived from this
+  software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
+IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
+INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
+BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY
+OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
+OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED
+OF THE POSSIBILITY OF SUCH DAMAGE.

docs/guide.md

@@ -24,6 +24,7 @@ The structure of the guide is as follows:
     - [Static analysis of shell scripts](#static-analysis-of-shell-scripts)
     - [Pre-commit verification](#pre-commit-verification)
   - [Integration with DevOps tools](#integration-with-devops-tools)
+  - [Automation tools](#automation-tools)
   - [Project team](#project-team)
     - [Code of conduct](#code-of-conduct)
     - [Governance document](#governance-document)
@@ -189,7 +190,7 @@ two alternatives: *src* and *flat*.
   subdirectories that represent different modules or packages. Each module or
   package within the "src" directory focuses on a specific aspect of the
   project's functionality.
-  
+
   For example, a project following the src structure might have the following
   layout:
 
@@ -215,7 +216,7 @@ two alternatives: *src* and *flat*.
   code files directly in the project's root directory without any
   subdirectories. This means that all modules and packages are at the same level
   and there is no explicit separation between different aspects of the project.
-  
+
   Here's an example of a flat structure:
 
   ```python
@@ -305,7 +306,7 @@ packages. SciCookie support the following:
   PEP 517 compilation backend, PEP 621 project metadata, a flexible and
   powerful plugin system. It also offers, among other things, versatile
   user scripting, PyPI integration and version management.
-  
+
 - [**Hatch**](https://hatch.pypa.io): It's a PEP 517/PEP 660 compatible
   build backend used by Hatch, a modern, extensible Python project manager.
   It provides a standardized build system with reproducible builds by default,
@@ -333,7 +334,7 @@ packages. SciCookie support the following:
   cross-compilation, and efficient dependency locating with their associated
   build requirements. With its capabilities, it facilitates cross-platform
   builds using CMake and effortless integration with C/C++ libraries, making
-  it a valuable asset for research software engineers. 
+  it a valuable asset for research software engineers.
 
 - [**setuptools + pybind11**](https://pybind11.readthedocs.io/en/stable/): It's build system designed
    for C++ library that simplifies the creation of Python bindings for C++ code,
@@ -346,8 +347,8 @@ packages. SciCookie support the following:
   support have made it a popular choice for projects requiring seamless interoperability
    between C++ and Python, ranging from scientific computing to game development and
   automation. Staying up-to-date with the latest pybind11 documentation ensures the
-  best practices are followed. 
-   
+  best practices are followed.
+
 The idea behind the options in SciCookie is that you can choose from some of the
 most popular system compilers to suit your needs and preferences for developing
 Python packages. If you think we should add more options, you can submit your
@@ -770,18 +771,18 @@ by selecting the option `None` (this is the default option).
 
 ## Automation Tools
 
-An automation tool is software or a platform designed to automate repetitive 
+An automation tool is software or a platform designed to automate repetitive
 tasks, processes, or workflows that are traditionally performed manually.
-These tools are used to streamline and optimize various operations, reduce 
+These tools are used to streamline and optimize various operations, reduce
 human intervention, increase efficiency, and minimize errors.
-Currently SciCookie is using `make` and `Makim`
+Currently, SciCookie allows you to use `Make` and/or `Makim`.
 
-- [Makim](https://osl-incubator.github.io/makim): MakIm is an innovative tool
-inspired by Make, designed to simplify target and dependency definition
+- [Makim](https://osl-incubator.github.io/makim): Makim is an innovative tool
+inspired by make, designed to simplify target and dependency definition
 through YAML format. It introduces advanced features such as conditionals,
 arguments, and dependencies with targeted parameters. It also facilitates
 organized grouping of targets and supports user-defined variables and environment
-variables. MakIm empowers users to streamline documentation and parameterize
+variables. Makim empowers users to streamline documentation and parameterize
 targets effectively. This free and open-source tool offers improved target
 management while maintaining compatibility with familiar YAML syntax.
 

pyproject.toml

@@ -14,7 +14,7 @@ include = [
 "scicookie" = "scicookie.__main__:app"
 
 [tool.poetry.dependencies]
-python = "^3.8.1"
+python = ">=3.8.1,<4"
 cookieninja = "1.0.0"
 sh = "^2.0.4"
 colorama = "^0.4.6"

src/scicookie/cookiecutter.json

@@ -29,10 +29,6 @@
     "sphinx",
     "jupyter-book"
   ],
-  "automation_tools": [
-    "Makim",
-    "Make"
-  ],
   "documentation_url": "{{ cookiecutter.project_url }}",
   "code_of_conduct": [
     "None",
@@ -63,6 +59,8 @@
   "use_black": "yes",
   "use_blue": "no",
   "use_conda": "yes",
+  "use_makim": "yes",
+  "use_make": "no",
   "use_containers": [
     "None",
     "Docker",

src/scicookie/hooks/post_gen_project.py

@@ -33,6 +33,8 @@
 USE_CONTAINERS = {{ cookiecutter.use_containers in ['Docker', 'Podman'] }}
 USE_CLI = {{ cookiecutter.command_line_interface != "No command-line interface" }}
 USE_CONDA = {{ cookiecutter.use_conda == "yes" }}
+USE_MAKE = {{ cookiecutter.use_make == "yes" }}
+USE_MAKIM = {{ cookiecutter.use_makim == "yes" }}
 USE_MYPY = {{ cookiecutter.use_mypy == "yes" }}
 {% if cookiecutter.code_of_conduct == "contributor-covenant" -%}
 COC_PATH = PROJECT_DIRECTORY / 'coc' / 'CONTRIBUTOR_COVENANT.md'
@@ -106,6 +108,13 @@ def move_selected_doc_dir():
     shutil.rmtree(DOCS_SPEC_DIR)
 
 
+def clean_up_automation():
+    if not USE_MAKE:
+        remove_project_file("Makefile")
+
+    if not USE_MAKIM:
+        remove_project_file(".makim.yaml")
+
 def clean_up_docs():
     remove_dirs(UNUSED_DOCS_DIRS)
     move_selected_doc_dir()
@@ -231,7 +240,7 @@ def clean_up_build_system():
         shutil.move(
             build_system_dir / "setup.py",
             PROJECT_DIRECTORY / 'setup.py'
-        )                          
+        )
     else:
         shutil.move(
             build_system_dir / "base-pyproject.toml",
@@ -329,6 +338,7 @@ 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()

src/scicookie/profiles/base.yaml

@@ -132,6 +132,8 @@ use_tools:
     - flake8
     - ruff
     - isort
+    - make
+    - makim
     - mccabe
     - mypy
     - pre-commit

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

@@ -4,18 +4,22 @@ root = true
 
 [*]
 indent_style = space
-indent_size = 4
+indent_size = 2
 trim_trailing_whitespace = true
 insert_final_newline = true
 charset = utf-8
 end_of_line = lf
 
+[*.py]
+indent_style = space
+indent_size = 4
+
 [*.bat]
 indent_style = tab
 end_of_line = crlf
 
 [LICENSE]
-insert_final_newline = false
+insert_final_newline = true
 
 [Makefile]
 indent_style = tab

src/scicookie/{{cookiecutter.project_slug}}/.github/ISSUE_TEMPLATE/bug-report.yml

@@ -1,3 +1,10 @@
+{%- if not cookiecutter.git_https_upstream -%}
+{% set github_url = cookiecutter.git_https_upstream -%}
+{%- elif not cookiecutter.git_https_origin -%}
+{% set github_url = cookiecutter.git_https_origin -%}
+{%- else -%}
+{% set github_url = "https://github.com/" + cookiecutter.project_name + "/" + cookiecutter.project_name -%}
+{%- endif -%}
 ---
 name: 🐛  Bug Report
 description: Create a report to help us improve
@@ -15,7 +22,7 @@ body:
       GitHub][issue search].
 
 
-      [issue search]: https://github.com/{{ cookiecutter.project_name }}/issues?q=is%3Aopen+is%3Aissue+label%3Abug
+      [issue search]: {{ github_url }}/issues?q=is%3Aopen+is%3Aissue+label%3Abug
 
 - type: textarea
   attributes:
@@ -141,7 +148,7 @@ body:
     description: |
       Read the [`{{ cookiecutter.project_name }}` Code of Conduct][CoC] first.
 
-      [CoC]: https://github.com/{{cookiecutter.project_slug}}/coc/CODE_OF_CONDUCT.md
+      [CoC]: {{ github_url }}/coc/CODE_OF_CONDUCT.md
     options:
     - label: I agree to follow the Code of Conduct
       required: true

src/scicookie/{{cookiecutter.project_slug}}/.github/ISSUE_TEMPLATE/config.yml

@@ -1,15 +1,22 @@
+{%- if not cookiecutter.git_https_upstream -%}
+{% set github_url = cookiecutter.git_https_upstream -%}
+{%- elif not cookiecutter.git_https_origin -%}
+{% set github_url = cookiecutter.git_https_origin -%}
+{%- else -%}
+{% set github_url = "https://github.com/" + cookiecutter.project_name + "/" + cookiecutter.project_name -%}
+{%- endif -%}
 # Ref: https://help.github.com/en/github/building-a-strong-community/configuring-issue-templates-for-your-repository#configuring-the-template-chooser
 blank_issues_enabled: true
 contact_links:
 - name: 🙋  Usage Questions
-  url: https://github.com/{{cookiecutter.project_slug}}/discussions
+  url: {{ github_url }}/discussions
   about: |
     Use {{ cookiecutter.project_name }}'s GitHub Discussions to ask "How do I do X with Cookiecutter?".
 - name: 📖  Tutorial
-  url: https://github.com/{{cookiecutter.project_slug}}
+  url: {{ github_url }}
   about: |
     The {{ cookiecutter.project_name }} tutorial is continually updated and provides an in depth walkthrough
     of how to use the latest release of Cookiecutter.
 - name: 📝  {{ cookiecutter.project_name }} Code of Conduct
-  url: https://github.com/{{cookiecutter.project_slug}}/coc/CODE_OF_CONDUCT.md
+  url: {{ github_url }}/coc/CODE_OF_CONDUCT.md
   about: Expectations for how people will interact with each other on Cookiecutter's GitHub.

src/scicookie/{{cookiecutter.project_slug}}/.github/ISSUE_TEMPLATE/documentation-report.yml

@@ -1,3 +1,10 @@
+{%- if not cookiecutter.git_https_upstream -%}
+{% set github_url = cookiecutter.git_https_upstream -%}
+{%- elif not cookiecutter.git_https_origin -%}
+{% set github_url = cookiecutter.git_https_origin -%}
+{%- else -%}
+{% set github_url = "https://github.com/" + cookiecutter.project_name + "/" + cookiecutter.project_name -%}
+{%- endif -%}
 ---
 name: 📝  Documentation Report
 description: Create a report for problems with the docs
@@ -15,7 +22,7 @@ body:
       GitHub][issue search].
 
 
-      [issue search]: https://github.com/{{ cookiecutter.project_name }}/issues?q=is%3Aopen+is%3Aissue+label%3Adocs
+      [issue search]: {{ github_url }}/issues?q=is%3Aopen+is%3Aissue+label%3Adocs
 
 - type: textarea
   attributes:
@@ -45,7 +52,7 @@ body:
     description: |
       Read the [`{{ cookiecutter.project_name }}` Code of Conduct][CoC] first.
 
-      [CoC]: https://github.com/{{ cookiecutter.project_name }}/blob/main/CODE_OF_CONDUCT.md
+      [CoC]: {{ github_url }}/blob/main/CODE_OF_CONDUCT.md
     options:
     - label: I agree to follow the Code of Conduct
       required: true

src/scicookie/{{cookiecutter.project_slug}}/.github/ISSUE_TEMPLATE/feature-request.yml

@@ -1,3 +1,10 @@
+{%- if not cookiecutter.git_https_upstream -%}
+{% set github_url = cookiecutter.git_https_upstream -%}
+{%- elif not cookiecutter.git_https_origin -%}
+{% set github_url = cookiecutter.git_https_origin -%}
+{%- else -%}
+{% set github_url = "https://github.com/" + cookiecutter.project_name + "/" + cookiecutter.project_name -%}
+{%- endif -%}
 ---
 name: ✨  Feature Request
 description: Suggest an idea for this project
@@ -17,7 +24,7 @@ body:
       already be implemented in a development release.
 
 
-      [issue search]: https://github.com/{{ cookiecutter.project_name }}/issues?q=is%3Aopen+is%3Aissue+label%3Afeat%2Fenhancement
+      [issue search]: {{ github_url }}/issues?q=is%3Aopen+is%3Aissue+label%3Afeat%2Fenhancement
 
 
 - type: textarea
@@ -73,7 +80,7 @@ body:
     description: |
       Read the [`{{ cookiecutter.project_name }}` Code of Conduct][CoC] first.
 
-      [CoC]: https://github.com/{{cookiecutter.project_slug}}/coc/CODE_OF_CONDUCT.md
+      [CoC]: {{ github_url }}/coc/CODE_OF_CONDUCT.md
     options:
     - label: I agree to follow the Code of Conduct
       required: true