Merge branch 'main' into 82-githooks

Author: jspaaks

.github/workflows/tests.yml

@@ -15,8 +15,8 @@ jobs:
         python-version: '3.x'
     - name: Install dependencies
       run: |
-        python -m pip install --upgrade pip
-        pip install -r requirements.txt
+        python3 -m pip install --upgrade pip setuptools
+        python3 -m pip install .[dev]
     - name: Run tests
       run: |
         pytest

.gitignore

@@ -20,3 +20,9 @@ docs/apidocs
 
 # Mac
 .DS_Store
+
+# virtual environments
+env
+env3
+venv
+venv3

.mlc-config.json

@@ -6,6 +6,12 @@
         },
         {
             "pattern": "\\{\\{"
+        },
+        {
+          "pattern": "^https://doi.org/<replace-with-created-DOI>"
+        },
+        {
+          "pattern": "^https://bestpractices.coreinfrastructure.org/projects/<replace-with-created-project-identifier>"
         }
     ],
     "replacementPatterns": [

CODE_OF_CONDUCT.md

@@ -55,7 +55,7 @@ further defined and clarified by project maintainers.
 ## Enforcement
 
 Instances of abusive, harassing, or otherwise unacceptable behavior may be
-reported by contacting the project team at j.vanderzwaan@esciencecenter.nl. All
+reported by contacting the project team at XXX@esciencecenter.nl. All
 complaints will be reviewed and investigated and will result in a response that
 is deemed necessary and appropriate to the circumstances. The project team is
 obligated to maintain confidentiality with regard to the reporter of an incident.

CONTRIBUTING.md

@@ -34,7 +34,7 @@ The sections below outline the steps in each case.
 1. make sure the existing tests still work by running ``pytest``. If project tests fails use ``pytest --keep-baked-projects`` to keep generated project in /tmp/pytest-* and investigate;
 1. add your own tests (if necessary);
 1. update or expand the documentation;
-1. [push](http://rogerdudler.github.io/git-guide/) your feature branch to (your fork of) the Python Template repository on GitHub;
+1. push your feature branch to (your fork of) the Python Template repository on GitHub;
 1. create the pull request, e.g. following the instructions [here](https://help.github.com/articles/creating-a-pull-request/).
 
 In case you feel like you've made a valuable contribution, but you don't know how to write or run tests for it, or how to generate the documentation: don't let this discourage you from making the pull request; we can help you! Just go ahead and submit the pull request, but keep in mind that you might be asked to append additional commits to your pull request.

README.dev.md

@@ -10,9 +10,9 @@ path/to/package/
 ├── .gitignore
 ├── pyproject.toml
 ├── .prospector.yml
-├── CHANGELOG.rst
-├── CODE_OF_CONDUCT.rst
-├── CONTRIBUTING.rst
+├── CHANGELOG.md
+├── CODE_OF_CONDUCT.md
+├── CONTRIBUTING.md
 ├── docs
 │   ├── conf.py
 │   ├── index.rst
@@ -24,8 +24,8 @@ path/to/package/
 │   ├── __init__.py
 │   ├── __version__.py
 │   └── package.py
-├── README.rst
-├── project_setup.rst
+├── README.md
+├── project_setup.md
 ├── requirements.txt
 ├── setup.cfg
 ├── setup.py

README.md

@@ -13,8 +13,8 @@ an empty Python package. Features include:
 - [Default Github actions]({{cookiecutter.project_name}}/.github/workflows) for building, testing and deployment
 - Code style checking,
 - [Editorconfig]({{cookiecutter.project_name}}/.editorconfig),
-- Miscellaneous files, such as [Change log]({{cookiecutter.project_name}}/CHANGELOG.rst), [Code of Conduct]({{cookiecutter.project_name}}/CODE_OF_CONDUCT.rst), and [Contributing guidelines]({{cookiecutter.project_name}}/CONTRIBUTING.rst),
-- A [README]({{cookiecutter.project_name}}/README.rst) and [a separate document]({{cookiecutter.project_name}}/project_setup.md) with extensive documentation about project setup.
+- Miscellaneous files, such as [Change log]({{cookiecutter.project_name}}/CHANGELOG.md), [Code of Conduct]({{cookiecutter.project_name}}/CODE_OF_CONDUCT.md), and [Contributing guidelines]({{cookiecutter.project_name}}/CONTRIBUTING.md),
+- A [README]({{cookiecutter.project_name}}/README.md) and [a separate document]({{cookiecutter.project_name}}/project_setup.md) with extensive documentation about project setup.
 - Continuous code quality and code coverage reporting using [Sonarcloud](https://sonarcloud.io/)
 
 ## Badges
@@ -76,10 +76,10 @@ Good job! You have now generated the skeleton for your package:
 
 ```text
 my-python-project/
-├── CHANGELOG.rst
+├── CHANGELOG.md
 ├── CITATION.cff
-├── CODE_OF_CONDUCT.rst
-├── CONTRIBUTING.rst
+├── CODE_OF_CONDUCT.md
+├── CONTRIBUTING.md
 ├── docs
 │   ├── conf.py
 │   ├── index.rst
@@ -96,7 +96,7 @@ my-python-project/
 │   └── __version__.py
 ├── NOTICE
 ├── project_setup.md
-├── README.rst
+├── README.md
 ├── setup.cfg
 ├── setup.py
 └── tests

pytest.ini

@@ -0,0 +1,50 @@
+# see documentation, e.g.
+# - https://packaging.python.org/tutorials/packaging-projects/#configuring-metadata
+# - https://setuptools.readthedocs.io/en/latest/userguide/declarative_config.html
+# - https://www.python.org/dev/peps/pep-0314/
+
+
+[metadata]
+author = Netherlands eScience Center
+classifiers =
+    Development Status :: 2 - Pre-Alpha
+    Intended Audience :: Developers
+    License :: OSI Approved :: Apache Software License
+    Natural Language :: English
+    Programming Language :: Python :: 3
+    Programming Language :: Python :: 3.6
+    Programming Language :: Python :: 3.7
+    Programming Language :: Python :: 3.8
+    Programming Language :: Python :: 3.9
+description = Cookiecutter template to initialize Python projects in accordance with Netherlands eScience Center best practices
+long_description = file: README.md
+long_description_content_type = text/markdown
+name = Netherlands eScience Center Python Template
+project_urls =
+    Bug Tracker = https://github.com/NLeSC/python-template/issues
+url = https://github.com/NLeSC/python-template
+version = 0.2.0
+
+
+[options]
+zip_safe = False
+include_package_data = True
+packages =
+install_requires =
+    cookiecutter==1.7.2
+
+[options.data_files]
+# This section requires setuptools>=40.6.0
+# It remains empty for now
+# Check if MANIFEST.in works for your purposes
+
+
+[options.extras_require]
+dev =
+    pytest<5.0.0,>=3.3.0
+    pytest-cookies
+
+
+[tool:pytest]
+testpaths = tests
+norecursedirs = .git .github hooks {{cookiecutter.project_name}}