Migrate from cookiecutter to copier

This migrates from cookiecutter template to copier while keeping all
original features.

Closes #348

Co-authored-by: Olga Lyashevska <olga.lyashevska@gmail.com>
Co-authored-by: Sander van Rijn <s.vanrijn@esciencecenter.nl>

.github/ISSUE_TEMPLATE/10_generated_package.md

@@ -7,5 +7,5 @@ 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`.
 -->

.github/ISSUE_TEMPLATE/20_template.md

@@ -7,5 +7,5 @@ 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`.
 -->

.gitignore

@@ -26,3 +26,5 @@ env
 env3
 venv
 venv3
+
+.swp

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

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: yourname@esciencecenter.nl
+copyright_holder:
+  type: str
+  default: Netherlands eScience Center
+code_of_conduct_email:
+  type: str
+  default: "{{ email }}"
+
+_subdirectory: template
+
+repository:
+  default: git@github.com:{{ github_organization }}/{{ directory_name }}
+  when: false
+
+repository_url:
+  default: https://github.com/{{ github_organization }}/{{ directory_name }}
+  when: false
+
+
+# Optional questions

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 {{directory_name}}

template/.editorconfig

@@ -0,0 +1,26 @@
+# EditorConfig is awesome: http://EditorConfig.org
+
+# top-most EditorConfig file
+root = true
+
+# Unix-style newlines with a newline ending every file
+[*]
+end_of_line = lf
+insert_final_newline = true
+trim_trailing_whitespace = true
+charset = utf-8
+
+# 4 space indentation
+[*.{py,java,r,R}]
+indent_style = space
+indent_size = 4
+
+# 2 space indentation
+[*.{js,json,y{a,}ml,html,cwl}]
+indent_style = space
+indent_size = 2
+
+[*.{md,Rmd,rst}]
+trim_trailing_whitespace = false
+indent_style = space
+indent_size = 2

template/.githooks/pre-commit

@@ -0,0 +1,19 @@
+#!/bin/sh
+
+echo "Script $0 triggered ..."
+
+# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
+echo "Starting ruff analysis..."
+
+# quietly run ruff
+ruff . --fix
+
+# use return code to abort commit if necessary
+if [ $? != "0" ]; then
+    echo "Commit aborted. Fix linter issues found by ruff before committing."
+    exit 1
+fi
+
+# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
+echo "Pre-commit checks completed successfully."
+exit 0

template/.github/next_steps/01_sonarcloud_integration.md.jinja

@@ -0,0 +1,16 @@
+---
+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]({{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={{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/{{github_organization}}/{{directory_name}}/settings/secrets/actions)

template/.github/next_steps/02_citation.md.jinja

@@ -0,0 +1,28 @@
+---
+title: 'Next step: Citation data'
+---
+
+It is likely that your `CITATION.cff` currently doesn't pass validation. The error messages you get from the [`cffconvert`]({{repository_url}}/actions/workflows/cffconvert.yml) GitHub Action are unfortunately a bit cryptic, but doing the following helps:
+
+- [ ] Check if the `given-name` and `family-name` keys need updating. If your family name has a name particle like `von` or `van` or `de`, use the `name-particle` key; if your name has a suffix like `Sr` or `IV`, use `name-suffix`. For details, refer to the schema description: https://github.com/citation-file-format/citation-file-format
+- [ ] Update the value of the `orcid` key. If you do not have an orcid yet, you can get one here [https://orcid.org/](https://orcid.org/).
+- [ ] Add more authors if needed
+- [ ] Update `date-released` using the YYYY-MM-DD format.
+- [ ] Update the `doi` key with the conceptDOI for your repository (see [https://help.zenodo.org](https://help.zenodo.org/) for more information on what a conceptDOI is). If your project doesn't have a DOI yet, you can use the string `10.0000/FIXME` to pass validation.
+- [ ] Verify that the `keywords` array accurately describes your project.
+
+Afterwards, the `cffconvert` GitHub Action should be green.
+
+To make sure services like [Zenodo](https://zenodo.org) and the [Research Software Directory](https://research-software-directory.org/) can keep your citation data up to date, the [`cffconvert`]({{repository_url}}/actions/workflows/cffconvert.yml) GitHub Action checks the following:
+
+1. Whether your repository includes a `CITATION.cff` file.
+
+    _By including this file, authors of the software can receive credit for the work they put in._
+
+1. Whether your `CITATION.cff` is valid YAML.
+
+    _Visit http://www.yamllint.com/ to see if the contents of your CITATION.cff are valid YAML._
+
+1. Whether your `CITATION.cff` adheres to the schema (as listed in the `CITATION.cff` file itself under key `cff-version`).
+
+    _The Citation File Format schema can be found [here](https://github.com/citation-file-format/citation-file-format), along with an explanation of all the keys. You're advised to use the latest available schema version._

template/.github/next_steps/03_readthedocs.md

@@ -0,0 +1,20 @@
+---
+title: 'Next step: Read the Docs'
+---
+
+Your Python package should have publicly available documentation, including API documentation for your users.
+[Read the Docs](https://readthedocs.org) can host your user documentation for you.
+
+To host the documentation of this repository please perform the following instructions:
+
+1. go to [Read the Docs](https://readthedocs.org/dashboard/import/?)
+1. log in with your GitHub account
+1. find `{{ github_organization }}/{{ directory_name }}` in list and press `+` button.
+   * If repository is not listed,
+      1. go to [Read the Docs GitHub app](https://github.com/settings/connections/applications/fae83c942bc1d89609e2)
+      2. make sure {{ github_organization }} has been granted access.
+      3. reload repository list on Read the Docs import page
+1. wait for the first build to be completed at <https://readthedocs.org/projects/{{ directory_name }}/builds>
+1. check that the link of the documentation badge in the [README.md]({{ repository_url }}) works
+
+See [README.dev.md#]({{repository_url}}/blob/main/README.dev.md#generating-the-api-docs) how to build documentation site locally.

template/.github/next_steps/04_zenodo_integration.md.jinja

@@ -0,0 +1,22 @@
+---
+title: 'Next step: Enable Zenodo integration'
+---
+
+By enabling Zenodo integration, your package will automatically get a DOI which can be used to cite your package. After enabling Zenodo integration for your GitHub repository, Zenodo will create a snapshot and archive each release you make on GitHub. Moreover, Zenodo will create a new DOI for each GitHub release of your code.
+
+To enable Zenodo integration:
+
+1. Go to http://zenodo.org and login with your GitHub account. When you are redirected to GitHub, *Authorize application* to give permission to Zenodo to access your account.
+1. Go to <https://zenodo.org/account/settings/github/> and enable Zenodo integration of your repository by clicking on `On` toggle button.
+2. Your package will get a DOI only after you make a release. Create a new release as described in [README.dev.md]({{repository_url}}/blob/main/README.dev.md#33-github)
+3. At this point you should have a DOI. To find out the DOI generated by Zenodo:
+   1. Visit https://zenodo.org/deposit and click on your repository link
+   2. You will find the latest DOI in the right column in Versions box in **Cite all versions?** section
+   3. Copy the text of the link. For example `10.5281/zenodo.1310751`
+4. Update the badge in your repository
+   1. Edit README.md and replace the badge placeholder with the badge link you copied in previous step.
+   The badge placeholder is shown below.
+
+      `[![DOI](https://zenodo.org/badge/DOI/<replace-with-created-DOI>.svg)](https://doi.org/<replace-with-created-DOI>)`
+
+For FAQ about Zenodo please visit <https://help.zenodo.org/>.

template/.github/next_steps/05_linting.md

@@ -0,0 +1,17 @@
+---
+title: 'Next step: Linting'
+---
+
+Your repository has a [workflow]({{ repository_url }}/blob/main/.github/workflows/build.yml) which [lints](https://en.wikipedia.org/wiki/Lint_(software)) your code after every push and when creating a pull request.
+
+Linter workflow may fail if `description` or `keywords` field in [pyproject.toml]({{ repository_url }}/blob/main/pyproject.toml) is empty. Please update these fields. To validate your changes run:
+
+```shell
+ruff .
+```
+
+Enabling [githook](https://git-scm.com/docs/githooks) will automatically lint your code in every commit. You can enable it by running the command below.
+
+```shell
+git config --local core.hooksPath .githooks
+```

template/.github/workflows/build.yml

@@ -0,0 +1,62 @@
+name: Python package
+
+on:
+  push:
+    branches:
+    - main
+  pull_request:
+    branches:
+    - main
+
+jobs:
+
+  build:
+    name: Build for (${{ '{{ ' -}} matrix.python-version }}, ${{ '{{ ' -}} matrix.os }})
+    runs-on: ${{ '{{ ' -}} matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: ['ubuntu-latest', 'macos-latest', 'windows-latest']
+        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python ${{ '{{ ' -}} matrix.python-version }}
+        uses: actions/setup-python@v3
+        with:
+          python-version: ${{ '{{ ' -}} matrix.python-version }}
+      - name: Python info
+        shell: bash -e {0}
+        run: |
+          which python
+          python --version
+      - name: Upgrade pip and install dependencies
+        run: |
+          python -m pip install --upgrade pip setuptools
+          python -m pip install .[dev,publishing]
+      - name: Run unit tests
+        run: python -m pytest -v
+      - name: Verify that we can build the package
+        run: python -m build
+
+  lint:
+    name: Linting build
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python 3.9
+        uses: actions/setup-python@v3
+        with:
+          python-version: 3.9
+      - name: Python info
+        shell: bash -e {0}
+        run: |
+          which python
+          python --version
+      - name: Upgrade pip and install dependencies
+        run: |
+          python -m pip install --upgrade pip setuptools
+          python -m pip install .[dev,publishing]
+      - name: Check style against standards using ruff
+        run: ruff .

template/.github/workflows/cffconvert.yml

@@ -0,0 +1,23 @@
+name: cffconvert
+
+on:
+  push:
+    branches:
+    - main
+  pull_request:
+    branches:
+    - main
+
+jobs:
+
+  verify:
+    name: "cffconvert"
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+        name: Check out a copy of the repository
+
+      - name: Check whether the citation metadata from CITATION.cff is valid
+        uses: citation-file-format/cffconvert-github-action@2.0.0
+        with:
+          args: "--validate"