Merge branch 'main' into 615_pyproject_python_version

Author: sjvrijn

.github/ISSUE_TEMPLATE/01_bug_report.md

@@ -2,7 +2,7 @@
 name: Bug report
 about: Create a report to help us improve
 title: ''
-labels: 'bug'
+labels: bug
 assignees: ''
 
 ---
@@ -44,9 +44,7 @@ If applicable, add screenshots to help explain your problem.
   - [ ] minimum
   - [ ] let me choose 
 - OS:
-<!-- run this command: uname -a -->
 - version:
-<!-- run this command: python -c "import kunefe; print(kunefe.__version__)" -->
 
 **Additional context**
 

.github/workflows/build.yml

@@ -18,9 +18,9 @@ jobs:
         os: ['ubuntu-latest', 'macos-latest', 'windows-latest']
         python-version: ['3.10', '3.11', '3.12']
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v6
       with:
         python-version: ${{ matrix.python-version }}
     - name: Python info

.github/workflows/cffconvert.yml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out a copy of the repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
 
       - name: Check whether the citation metadata from CITATION.cff is valid
         uses: citation-file-format/[email protected]

.github/workflows/link-check.yml

@@ -2,12 +2,6 @@ name: link-check
 
 on:
   workflow_dispatch:
-  push:
-    branches:
-    - main
-  pull_request:
-    branches:
-    - main
   schedule:
     - cron: '0 0 1 * *' # first day of every month at midnight
 
@@ -19,11 +13,11 @@ jobs:
   linkChecker:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
 
       - name: Link Checker
         id: lychee
-        uses: lycheeverse/lychee-action@v1
+        uses: lycheeverse/lychee-action@v2
 
       - name: Set Issue Title
         id: set_title

.github/workflows/tests.yml

@@ -18,9 +18,9 @@ jobs:
         os: ['ubuntu-latest', 'macos-latest', 'windows-latest']
         python-version: ['3.10', '3.11', '3.12']
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v6
       with:
         python-version: ${{ matrix.python-version }}
     - name: Python info

.gitignore

@@ -26,5 +26,7 @@ env
 env3
 venv
 venv3
+.venv
+.venv3
 
 .swp

CHANGELOG.md

@@ -3,6 +3,32 @@
 ## [Unreleased]
 
 ### Added
+
+### Changed
+
+### Removed
+
+## 0.6.1
+
+### Added
+
+* Add .gitignore and .editorconfig to the list of files that are not updated if they exist [#655](https://github.com/NLeSC/python-template/pull/655)
+
+### Changed
+
+* copyright owner is asked in all profiles [#629](https://github.com/NLeSC/python-template/pull/629)
+* license files includes year and copyright owner information [#629](https://github.com/NLeSC/python-template/pull/629)
+* combine all the next step jobs in a single workflow [#657](https://github.com/NLeSC/python-template/pull/657)
+* fix CITATION.cff validation issues which also helps cffconvert workflow to pass [#657](https://github.com/NLeSC/python-template/pull/657)
+
+### Removed
+
+* Remove pyproject.toml and CITATION.cff from the list of files that are not updated if they exist [#655](https://github.com/NLeSC/python-template/pull/655)
+
+## [0.6.0]
+
+### Added
+
 * Keep project_setup.md for all the profiles and remove from the menu [#576](https://github.com/NLeSC/python-template/pull/576)
 * Make contributing guidelines optional [#465](https://github.com/NLeSC/python-template/pull/465)
 * Make linting optional [#568](https://github.com/NLeSC/python-template/pull/568)
@@ -15,8 +41,12 @@
 * Make SonarCloud optional [#515](https://github.com/NLeSC/python-template/pull/515)
 * Make citation optional [#471](https://github.com/NLeSC/python-template/pull/471)
 * Make online documentation optional [#476](https://github.com/NLeSC/python-template/pull/476)
+* Make local documentation optional [#593](https://github.com/NLeSC/python-template/pull/593)
+* Make local test optional [#594](https://github.com/NLeSC/python-template/pull/594)
 
 ### Changed
+
+* Update the user documentation (README.md) of the template [#575](https://github.com/NLeSC/python-template/pull/623)
 * Updated .gitignore [#622](https://github.com/NLeSC/python-template/pull/622)
 * add extra info for sub-menus [#628](https://github.com/NLeSC/python-template/pull/628)
 * skip merging CHANGELOG.md and CODE_OF_CONDUCT.md if they exist [#628](https://github.com/NLeSC/python-template/pull/628)
@@ -29,8 +59,10 @@
 * Fix broken link checker [#546](https://github.com/NLeSC/python-template/pull/546)
 * pre-commit script is optional ([#457](https://github.com/NLeSC/python-template/issues/457))
 * CHANGELOG.md is now optional ([#462](https://github.com/NLeSC/python-template/issues/462))
+* Restored default line-length of 79 characters, as recommended by [PEP-8](https://peps.python.org/pep-0008/#maximum-line-length) [#389](https://github.com/NLeSC/python-template/pull/389)
 
 ### Removed
+
 * Remove the configuration of isort ([#591](https://github.com/NLeSC/python-template/pull/591)), which is no longer used since [#347](https://github.com/NLeSC/python-template/issues/347).
 
 ## [0.5.0]
@@ -148,7 +180,6 @@ Released on Apr 22, 2021
 * Drop Python 3.5 support
 * Removed unit tests doing the linting
 
-
 ## [0.2.0]
 
 Released on July 17, 2019
@@ -174,14 +205,14 @@ Released on July 17, 2019
 * 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
+ 	* 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
+ 	* Project setup
+ 	* Setup instructions
+ 	* NOTICE file
 
 ### Removed
 
@@ -194,20 +225,19 @@ 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
-
+ 	* Tests,
+ 	* Documentation,
+ 	* Code style checking
+ 	* Editorconfig
+ 	* Default Travis configuration
+ 	* Change log
+ 	* Code of Conduct
+ 	* Contributing guidelines
+ 	* License
+ 	* Manifest.in
+ 	* README
+ 	* Requirements.txt
+ 	* Setup configuration
 
 [Unreleased]: https://github.com/NLeSC/python-template//compare/0.5.0...HEAD
 [0.5.0]:      https://github.com/NLeSC/python-template/releases/tag/0.5.0

CITATION.cff

@@ -68,6 +68,22 @@ authors:
     family-names: Tjong Kim Sang
     given-names: Erik
     orcid: "https://orcid.org/0000-0002-8431-081X"
+  - given-names: Abel
+    family-names: Soares Siqueira
+    email: [email protected]
+    affiliation: Netherlands eScience Center
+    orcid: "https://orcid.org/0000-0003-4451-281X"
+  - given-names: Olga
+    family-names: Lyashevska
+    email: [email protected]
+    affiliation: Netherlands eScience Center
+    orcid: 'https://orcid.org/0000-0002-8686-8550'
+  - given-names: Sander
+    name-particle: van
+    family-names: Rijn
+    email: [email protected]
+    affiliation: Netherlands eScience Center
+    orcid: 'https://orcid.org/0000-0001-6159-041X'
 cff-version: "1.2.0"
 date-released: 2018-07-17
 doi: 10.5281/zenodo.1310751
@@ -79,4 +95,4 @@ license: Apache-2.0
 message: "If you use this software, please cite it using these metadata."
 repository-code: "https://github.com/NLeSC/python-template"
 title: "Netherlands eScience Center Python Template"
-version: "0.4.0"
+version: "0.6.1"

CONTRIBUTING.md

@@ -27,7 +27,7 @@ The sections below outline the steps in each case.
 
 ## You want to make some kind of change to the code base
 
-1. (**important**) this repository implements the best practices we recommend in the Python chapter of the [Guide](https://guide.esciencecenter.nl/#/best_practices/language_guides/python). Check that your planned contribution is
+1. (**important**) this repository implements the best practices we recommend in the Python chapter of the [Guide](https://guide.esciencecenter.nl/#/language_guides/python). Check that your planned contribution is
 in line with what is recommended there. If not, please [contribute to the guide](https://github.com/NLeSC/guide/blob/main/CONTRIBUTING.md) instead / as well, or at least create an issue there.
 1. (**important**) announce your plan to the rest of the community _before you start working_. This announcement should be in the form of a (new) issue;
 1. (**important**) wait until some kind of consensus is reached about your idea being a good idea;
@@ -54,4 +54,4 @@ To create a release you need write permission on the repository.
 1. Fill version, title and description field
 1. Press the Publish Release button
 
-Also a Zenodo entry will be made for the release with its own DOI.
+Also a Zenodo entry will be made for the release with its own DOI.

README.md

@@ -1,8 +1,28 @@
 # Netherlands eScience Center Python Template
 
-Spend less time setting up and configuring your new Python packages which includes research software good practices from the start.
+<img align="right" width="160" src="logo.png" alt='Python Template logo, created using ChatGPT 4o on 10 September 2024 using prompt "generate a logo of a copier that looks like a snake-scientist"'>
 
-Use this [Copier](https://copier.readthedocs.io) template to generate an empty Python package. Features include:
+Spend less time setting up and configuring your new Python packages by using this template. This [Copier](https://copier.readthedocs.io) template includes best practices for research software so your new package will include these practices from the start. 
+
+You can choose from various user profiles, each offering a range of features to suit your needs.
+
+## User profiles
+
+The template profiles for a Python package offer varying levels of customization to cater to different user needs. Below are the profiles the template offers.
+
+### Minimum
+
+This profile offers the essential features to begin developing a Python package, making it ideal for first-time research software developers. Additional features can be added as needed.
+
+### Recommended
+
+This option provides a pre-selected set of features for research software, which users can fully customize.
+
+### Let me choose
+
+This fully customizable profile enables you to selectively include or exclude features in your Python package.
+
+## Features
 
 - Boilerplate unit tests and documentation,
 - [Python static setup configuration](template/pyproject.toml.jinja),
@@ -14,7 +34,7 @@ Use this [Copier](https://copier.readthedocs.io) template to generate an empty P
   - [README.md](template/README.md.jinja) for package users,
   - [README.dev.md](template/README.dev.md.jinja) for package developer,
   - [project_setup.md](template/project_setup.md.jinja) with extensive documentation about project setup,
-  - [Change log](template/%7B%25%20if%20AddChangeLog%20%25%7DCHANGELOG.md%7B%25%20endif%20%25%7D),
+  - [Changelog](template/%7B%25%20if%20AddChangeLog%20%25%7DCHANGELOG.md%7B%25%20endif%20%25%7D),
   - [Code of Conduct](template/CODE_OF_CONDUCT.md.jinja),
   - [Contributing guidelines](template/CONTRIBUTING.md.jinja),
 - Continuous code quality and code coverage reporting using [Sonarcloud](https://sonarcloud.io/),