Migrate from cookiecutter to copier

This migrates from cookiecutter template to copier while keeping all original features. Closes #348 Co-authored-by: Olga Lyashevska <[email protected]> Co-authored-by: Sander van Rijn <[email protected]>
NLeSC · Jul 25, 2024 · c56305a · c56305a
1 parent 780e6a4
commit c56305a
Show file tree

Hide file tree

Showing 65 changed files with 888 additions and 642 deletions.
diff --git a/...rectory_name}}/docs/_templates/.gitignore → .copier-answers.yml b/...rectory_name}}/docs/_templates/.gitignore → .copier-answers.yml
diff --git a/.github/ISSUE_TEMPLATE/10_generated_package.md b/.github/ISSUE_TEMPLATE/10_generated_package.md
@@ -1,3 +1,4 @@
+<<<<<<< HEAD
 ---
 name: Related to the generated package
 about: Related to the generated package, as opposed to the template itself.
@@ -7,5 +8,5 @@ assignees: ''
 
 ---
 <!--
-Whatever you write here must have something to do with the code you get from running `cookiecutter`.
+Whatever you write here must have something to do with the code you get from running `copier`.
 -->
diff --git a/.github/ISSUE_TEMPLATE/20_template.md b/.github/ISSUE_TEMPLATE/20_template.md
@@ -1,3 +1,4 @@
+<<<<<<< HEAD
 ---
 name: Related to the template itself
 about: Related to the template itself, as opposed to the generated package.
@@ -7,5 +8,19 @@ assignees: ''
 
 ---
 <!--
-Whatever you write here must have something to do with the code of the template itself, i.e. before you run `cookiecutter`.
+Whatever you write here must have something to do with the code of the template itself, i.e. before you run `copier`.
 -->
+||||||| empty tree
+=======
+---
+name: Related to the template itself
+about: Related to the template itself, as opposed to the generated package.
+title: ''
+labels: template
+assignees: ''
+
+---
+<!--
+Whatever you write here must have something to do with the code of the template itself, i.e. before you run `copier`.
+-->
+>>>>>>> copier/main
diff --git a/.gitignore b/.gitignore
@@ -26,3 +26,6 @@ env
 env3
 venv
 venv3
+
+.swp
+.orig
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -105,6 +105,172 @@
 * Removed unit tests doing the linting
 
 
+## 0.2.0
+
+Released on July 17, 2019
+
+### Added
+
+* Set up logging and provide a logging example (#9)
+* Fix for displaying wide tables in the documentation (#37)
+* Single source version number (+ documentation) (#29)
+* Cookiecutter tests (#15)
+* Linter test for the generated project
+* CITATION.cff
+* Support for pypi deployment using travis (#36)
+
+### Changed
+
+* Replace dashes and spaces in project_slug with underscore (#33)
+* Put project setup documentation in a separate document (#39)
+* Fix numbered lists in .rst files (#40)
+* Added rst, y(a)ml and cwl to .editorconfig (#35)
+* Default documentation theme is `sphinx_rtd_theme` (#34)
+* Improve licensing
+* Fix example tests that failed to run (#28)
+* Remove quotes from project name and project description (#27)
+* Update prospector configuration (#26)
+	- Make prospector less strict
+	- Have prospector ignore the docs directory
+* Add `install_requires` to `setup.py` (#21)
+* Improved .gitignore (#22)
+* More detailed documentation about
+	- Project setup
+	- Setup instructions
+	- NOTICE file
+
+### Removed
+
+* Python 2 support
+
+## 0.1.0
+
+Released on July 12, 2018.
+
+### Added
+
+* First version of the Python project template that follows the Netherlands eScience Center software development guide, containing:
+	- Tests,
+	- Documentation,
+	- Code style checking
+	- Editorconfig
+	- Default Travis configuration
+	- Change log
+	- Code of Conduct
+	- Contributing guidelines
+	- License
+	- Manifest.in
+	- README
+	- Requirements.txt
+	- Setup configuration
+||||||| empty tree
+=======
+# Change Log
+
+## Unreleased
+
+### Added
+
+* Added Python 3.12 support [#356](https://github.com/NLeSC/python-template/issues/356)
+* Template unit tests for documentation generation, linting and version bumping
+* Docstring for function
+* Intersphinx to documentation
+* Coverage and doctest commands for documentation [#97](https://github.com/NLeSC/python-template/issues/97)
+
+### Changed
+
+* Moved to src/ based layout for generated packages
+* Moved from setup.cfg/.py to pyproject.toml [#351](https://github.com/NLeSC/python-template/issues/351)
+* Moved from prospector to ruff [#336](https://github.com/NLeSC/python-template/issues/336)
+* Renamed `project_name` to `directory_name` in cookiecutter questionnaire
+* Initial linting is error free [#227](https://github.com/NLeSC/python-template/issues/227)
+* Consolidated test/lint/build/docs into single matrix workflow [#270](https://github.com/NLeSC/python-template/issues/276)
+* Enforce isort configuration
+* Default for `package_short_description` in cookiecutter questionnaire
+* Link checker ignores GH private pages and test pypi site [#288](https://github.com/NLeSC/python-template/issues/288)
+* In CI build workflow make prospector die if there are errors [#275](https://github.com/NLeSC/python-template/issues/275)
+* All example tests make use of example function
+* Use bumpversion for version in Sphinx config [#44](https://github.com/NLeSC/python-template/issues/44)
+* Regenerated docs/conf.py with sphinx-quickstart v3.5.4 + enabled built-in extensions [#44](https://github.com/NLeSC/python-template/issues/44)
+* Generate api rst files with extension instead of custom function [#95](https://github.com/NLeSC/python-template/issues/95)
+* Change from bump2version (unmaintained) to bump-my-version.
+
+### Removed
+
+* Removed Python 3.7 support [#343](https://github.com/NLeSC/python-template/issues/343)
+* `.pylintrc` file, was too strict, too soon [#267](https://github.com/NLeSC/python-template/issues/267)
+* Unused development dependencies [#167](https://github.com/NLeSC/python-template/issues/167)
+* Statements in project_setup.md already mentioned in README.dev.md
+* .zenodo.json is no longer necessary, CITATION.cff also works with Zenodo.
+
+## 0.4.0
+
+### Added
+
+* Instructions to add your existing code to directory generated by the NLeSC Python template [#202](https://github.com/NLeSC/python-template/issues/202)
+* Keywords to questionnaire [#270](https://github.com/NLeSC/python-template/issues/270)
+* Next step issue generation workflow [#228](https://github.com/NLeSC/python-template/issues/228)
+* Next step issue for SonarCloud integration [#234](https://github.com/NLeSC/python-template/issues/234)
+* Next step issue for Zenodo integration [#235](https://github.com/NLeSC/python-template/issues/235)
+* Next step issue for Read the Docs [#236](https://github.com/NLeSC/python-template/issues/236)
+* Next step issue for citation data [#237](https://github.com/NLeSC/python-template/issues/237)
+* Next step issue for linting [#238](https://github.com/NLeSC/python-template/issues/238)
+* Next steps documentation [#240](https://github.com/NLeSC/python-template/issues/240)
+* Support for sub packages in distro [#160](https://github.com/NLeSC/python-template/issues/160)
+* Tests for api doc generation [#213](https://github.com/NLeSC/python-template/issues/213)
+* CI Tests on Windows [#140](https://github.com/NLeSC/python-template/issues/140) [#223](https://github.com/NLeSC/python-template/issues/223)
+* `.pylintrc` file
+* Valid license name and first author name in `CITATION.cff`
+* SonarCloud integration for code quality and coverage [#89](https://github.com/NLeSC/python-template/issues/89)
+* Read the Docs [#78](https://github.com/NLeSC/python-template/issues/78)
+
+### Changed
+
+* Always generate API docs [#176](https://github.com/NLeSC/python-template/issues/176)
+* Have 100% test coverage in generated code [#88](https://github.com/NLeSC/python-template/issues/88)
+
+### Removed
+
+* Automatic publish to PyPi after GitHub release [#196](https://github.com/NLeSC/python-template/issues/196)
+
+## 0.3.0
+
+### Added
+
+* Added Python 3.9 support
+* Template is being tested for Python 3.6, 3.7, 3.8, 3.9
+* Added extra badges such as fair-software.eu badges and SonarCloud, GitHub Actions [#52](https://github.com/NLeSC/python-template/issues/52) [#57](https://github.com/NLeSC/python-template/issues/57)
+* Added issue templates [#159](https://github.com/NLeSC/python-template/issues/159)
+* Added cffconvert GitHub action [#91](https://github.com/NLeSC/python-template/issues/91)
+* Added Markdown Link Checker GitHub action
+* Added Developer documentation
+* Added cookiecutter post-hook to point to document with more information
+* Migrated to static setup.cfg as per the recommended practice [#84](https://github.com/NLeSC/python-template/issues/84)
+* Added Pre-commit githook to automatically run the linters before committing to GitHub [#82](https://github.com/NLeSC/python-template/issues/82)
+* Added Sonarcloud integration for static analysis and code coverage [#172](https://github.com/NLeSC/python-template/issues/172)
+* Added badges to the generated package
+
+### Changed
+
+* Moved requirements.txt dependencies to setup.cfg and removed requirements.txt [#67](https://github.com/NLeSC/python-template/issues/67)
+* Replaced all ReStructuredText (rst) files by Markdown [#190](https://github.com/NLeSC/python-template/issues/190) [#162](https://github.com/NLeSC/python-template/issues/162)
+* Use matrix build for generated project to support all current Python versions on Windows, Linux, Mac [#160](https://github.com/NLeSC/python-template/issues/160)
+* Updated CITATION.cff, .zenodo.json; removed codemeta.json [#127](https://github.com/NLeSC/python-template/issues/127) [#137](https://github.com/NLeSC/python-template/issues/137)
+* Updated Code of Conduct of the template
+* Simplified templating variables using cookiecutter pre-hook [#82](https://github.com/NLeSC/python-template/issues/82)
+* Consolidated pytest.ini into setup.cfg [#155](https://github.com/NLeSC/python-template/issues/155)
+* Versioning now handled with bump2version [#192](https://github.com/NLeSC/python-template/issues/192)
+* Updated project_setup.md [#165](https://github.com/NLeSC/python-template/issues/165)
+* Updated Code of Conduct for generated package
+* Improved the documentation for the generated package and template itself
+
+## Removed
+* Dropped appveyor [#160](https://github.com/NLeSC/python-template/issues/160)
+* Dropped everything Conda related
+* Drop Python 3.5 support
+* Removed unit tests doing the linting
+
+
 ## 0.2.0
 
 Released on July 17, 2019

diff --git a/CITATION.cff b/CITATION.cff
@@ -72,7 +72,7 @@ cff-version: "1.2.0"
 date-released: 2018-07-17
 doi: 10.5281/zenodo.1310751
 keywords:
-  - cookiecutter
+  - copier
   - template
   - Python
 license: Apache-2.0

diff --git a/LICENSE b/LICENSE
@@ -178,7 +178,7 @@
    APPENDIX: How to apply the Apache License to your work.
 
       To apply the Apache License to your work, attach the following
-      boilerplate notice, with the fields enclosed by brackets "{}"
+      boilerplate notice, with the fields enclosed by brackets "[]"
       replaced with your own identifying information. (Don't include
       the brackets!)  The text should be enclosed in the appropriate
       comment syntax for the file format. We also recommend that a

diff --git a/README.md b/README.md
@@ -1,5 +1,7 @@
 # Netherlands eScience Center Python Template
 
+|[![Copier](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/copier-org/copier/master/img/badge/badge-grayscale-inverted-border-purple.json)](https://github.com/copier-org/copier)
+
 Spend less time setting up and configuring your new Python packages and comply with the
 [Netherlands eScience Center Software Development Guide](https://guide.esciencecenter.nl/)
 from the start.
@@ -162,3 +164,12 @@ list below:
 ## How to contribute
 
 Suggestions/improvements/edits are most welcome. Please read the [contribution guidelines](CONTRIBUTING.md) before creating an issue or a pull request.
+
+
+
+
+<!-- To generate a project from the template:
+```
+pip install copier
+copier copy path/to/project/template path/to/destination
+``` -->
diff --git a/cookiecutter.json b/cookiecutter.json
diff --git a/copier.yml b/copier.yml
@@ -0,0 +1,70 @@
+# Essential questions
+
+package_name:
+  type: str
+  default: my_python_package
+  help: Enter the name of the Python package.
+  validator: >-
+        {% if not (package_name | regex_search('^[a-z][a-z0-9\_]+$')) %}
+        package_name must start with a letter, followed one or more letters, digits or underscores all lowercase.
+        {% endif %}
+package_short_description:
+  type: str
+  default: Short description of package
+  # validator: >-
+  #       {% if '"' in package_short_description %}
+  #       package_short_description must not contain unescaped double quotes. Use \\" for double quotes.
+  #       {% endif %}
+keyword1:
+  type: str
+  default: keyword1
+keyword2:
+  type: str
+  default: keyword2
+version:
+  type: str
+  default: 0.1.0
+github_organization:
+  type: str
+  default: "<my-github-organization>"
+license:
+  type: str
+  choices:
+  - "Apache Software License 2.0"
+  - "MIT license"
+  - "BSD license"
+  - "ISC license"
+  - "GNU General Public License v3 or later"
+  - "GNU Lesser General Public License v3 or later"
+  - "Not open source"
+  default: "MIT license"
+full_name:
+  type: str
+  default: Jane Smith
+  help: Enter your full name.
+  # validator: >-
+  #       {% if '"' in full_name %}
+  #       full_name must not contain unescaped double quotes. Use \\" for double quotes.
+  #       {% endif %}
+email:
+  type: str
+  default: [email protected]
+copyright_holder:
+  type: str
+  default: Netherlands eScience Center
+code_of_conduct_email:
+  type: str
+  default: "{{ email }}"
+
+_subdirectory: template
+
+repository:
+  default: [email protected]:{{ github_organization }}/{{ directory_name }}
+  when: false
+
+repository_url:
+  default: https://github.com/{{ github_organization }}/{{ directory_name }}
+  when: false
+
+
+# Optional questions
diff --git a/hooks/post_gen_project.py b/hooks/post_gen_project.py
diff --git a/hooks/pre_gen_project.py b/hooks/pre_gen_project.py
diff --git a/setup.cfg b/setup.cfg
@@ -33,7 +33,7 @@ include_package_data = True
 python_requires = >=3.8
 packages =
 install_requires =
-    cookiecutter==1.7.2
+    copier==9.2.0
 
 [options.data_files]
 # This section requires setuptools>=40.6.0
@@ -45,9 +45,10 @@ install_requires =
 dev =
     coverage [toml]
     pytest
-    pytest-cookies
+    pytest-copie
+    pyprojroot
 
 
 [tool:pytest]
 testpaths = tests
-norecursedirs = .git .github hooks {{cookiecutter.directory_name}}
+norecursedirs = .git .github hooks template 
diff --git a/...okiecutter.directory_name}}/.editorconfig → template/.editorconfig b/...okiecutter.directory_name}}/.editorconfig → template/.editorconfig
diff --git a/...ter.directory_name}}/.githooks/pre-commit → template/.githooks/pre-commit b/...ter.directory_name}}/.githooks/pre-commit → template/.githooks/pre-commit
diff --git a/...b/next_steps/01_sonarcloud_integration.md → ..._steps/01_sonarcloud_integration.md.jinja b/...b/next_steps/01_sonarcloud_integration.md → ..._steps/01_sonarcloud_integration.md.jinja
@@ -4,13 +4,13 @@ title: 'Next step: Sonarcloud integration'
 
 Continuous code quality can be handled by [Sonarcloud](https://sonarcloud.io/). This repository is configured to use Sonarcloud to perform quality analysis and code coverage report on each push.
 
-In order to configure Sonarcloud analysis [GitHub Action workflow]({{cookiecutter.repository_url}}/blob/main/.github/workflows/sonarcloud.yml) you must follow the steps below:
+In order to configure Sonarcloud analysis [GitHub Action workflow]({{repository_url}}/blob/main/.github/workflows/sonarcloud.yml) you must follow the steps below:
 
 1. go to [Sonarcloud](https://sonarcloud.io/projects/create) to create a new Sonarcloud project
 1. login with your GitHub account
 1. add Sonarcloud organization or reuse existing one
 1. set up a repository
-1. go to [new code definition administration page](https://sonarcloud.io/project/new_code?id={{cookiecutter.github_organization}}_{{cookiecutter.directory_name}}) and select `Number of days` option
+1. go to [new code definition administration page](https://sonarcloud.io/project/new_code?id={{github_organization}}_{{directory_name}}) and select `Number of days` option
 1. To be able to run the analysis:
    1. a token must be created at [Sonarcloud account](https://sonarcloud.io/account/security/)
-   1. the created token must be added as `SONAR_TOKEN` to [secrets on GitHub](https://github.com/{{cookiecutter.github_organization}}/{{cookiecutter.directory_name}}/settings/secrets/actions)
+   1. the created token must be added as `SONAR_TOKEN` to [secrets on GitHub](https://github.com/{{github_organization}}/{{directory_name}}/settings/secrets/actions)
-Original file line number
+Diff line change
@@ Expand Up / @@ -26,3 +26,6 @@ env @@
     env3
     venv
     venv3
+    .swp
+    .orig