Merge remote-tracking branch 'origin/main' into 237-issue-template-for-citation-data

Author: jspaaks

.mlc-config.json

@@ -12,6 +12,9 @@
         },
         {
           "pattern": "^https://bestpractices.coreinfrastructure.org/projects/<replace-with-created-project-identifier>"
+        },
+        {
+          "pattern": "^.github/workflows/sonarcloud.yml$"
         }
     ],
     "replacementPatterns": [

tests/test_project.py

@@ -1,6 +1,9 @@
 import os
 import subprocess
-import shlex
+from sys import platform
+from typing import Sequence
+
+import pytest
 
 
 def test_project_folder(cookies):
@@ -12,25 +15,47 @@ def test_project_folder(cookies):
     assert project.project.isdir()
 
 
-def run(command: str, dirpath: os.PathLike) -> subprocess.CompletedProcess:
-    return subprocess.run(shlex.split(command),
+def run(args: Sequence[str], dirpath: os.PathLike) -> subprocess.CompletedProcess:
+    return subprocess.run(args=args,
                           stdout=subprocess.PIPE,
                           stderr=subprocess.PIPE,
                           cwd=dirpath,
                           encoding="utf-8")
 
 
-def test_pytest(cookies):
+@pytest.fixture
+def baked_with_development_dependencies(cookies):
     result = cookies.bake()
-    env_output = run('python3 -m venv env', result.project)
+    env_output = run(['python3', '-m', 'venv', 'env'], result.project)
     assert env_output.returncode == 0
-    latest_pip_output = run('env/bin/pip3 install --upgrade pip setuptools', result.project)
+    env_bin = 'env/Scripts/' if platform.startswith("win") else 'env/bin/'
+    latest_pip_output = run([f'{env_bin}pip3', 'install', '--upgrade', 'pip', 'setuptools'], result.project)
     assert latest_pip_output.returncode == 0
-    pip_output = run('env/bin/pip3 install --editable .[dev]', result.project)
+    pip_output = run([f'{env_bin}pip3', 'install', '--editable', '.[dev]'], result.project)
     assert pip_output.returncode == 0
+    return result.project, env_bin
+
 
-    pytest_output = run('env/bin/pytest', result.project)
+def test_pytest(baked_with_development_dependencies):
+    project_dir, env_bin = baked_with_development_dependencies
+    pytest_output = run([f'{env_bin}pytest'], project_dir)
     assert pytest_output.returncode == 0
-    assert '== 3 passed in' in  pytest_output.stdout
-    assert (result.project / 'coverage.xml').exists()
-    assert (result.project / 'htmlcov/index.html').exists()
+    assert '== 3 passed in' in pytest_output.stdout
+    assert (project_dir / 'coverage.xml').exists()
+    assert (project_dir / 'htmlcov/index.html').exists()
+
+
+def test_subpackage(baked_with_development_dependencies):
+    project_dir, env_bin = baked_with_development_dependencies
+    subpackage = (project_dir / 'my_python_package' / 'mysub')
+    subpackage.mkdir()
+    (subpackage / '__init__.py').write_text('FOO = "bar"', encoding="utf-8")
+
+    subsubpackage = (project_dir / 'my_python_package' / 'mysub' / 'mysub2')
+    subsubpackage.mkdir()
+    (subsubpackage / '__init__.py').write_text('FOO = "bar"', encoding="utf-8")
+
+    build_output = run([f'{env_bin}python3', 'setup.py', 'build'], project_dir)
+    assert build_output.returncode == 0
+    assert (project_dir / 'build' / 'lib' / 'my_python_package' / 'mysub' / '__init__.py').exists()
+    assert (project_dir / 'build' / 'lib' / 'my_python_package' / 'mysub' / 'mysub2' / '__init__.py').exists()

{{cookiecutter.project_name}}/.github/next_steps/01_sonarcloud_integration.md

@@ -1,7 +1,5 @@
 ---
 title: 'Next step: Sonarcloud integration'
-labels: 
-  - 'action required'
 ---
 
 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.
@@ -12,7 +10,7 @@ In order to configure Sonarcloud analysis [GitHub Action workflow](.github/workf
 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.project_name }}) and select `Number of days` option
+1. go to [new code definition administration page](https://sonarcloud.io/project/new_code?id={{cookiecutter.github_organization}}_{{cookiecutter.project_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.project_name }}/settings/secrets/actions)
+   1. the created token must be added as `SONAR_TOKEN` to [secrets on GitHub](https://github.com/{{cookiecutter.github_organization}}/{{cookiecutter.project_name}}/settings/secrets/actions)

{{cookiecutter.project_name}}/.github/next_steps/02_zenodo_integration.md

@@ -1,7 +1,5 @@
 ---
 title: 'Next step: Zenodo integration'
-labels:
-  - 'action required'
 ---
 
 Zenodo integration instructions.

{{cookiecutter.project_name}}/.github/next_steps/03_readthedocs.md

@@ -1,7 +1,20 @@
 ---
-title: 'Next step: readthedocs'
-labels:
-  - 'action required'
+title: 'Next step: Read the Docs'
 ---
 
-Readthedocs instructions.
+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 `{{ cookiecutter.github_organization }}/{{ cookiecutter.project_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 {{ cookiecutter.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/{{ cookiecutter.project_name }}/builds>
+1. check that the link of the documentation badge in the [README.md]({{ cookiecutter.repository }}) works
+
+See [README.dev.md#]({{cookiecutter.repository}}/blob/main/README.dev.md#generating-the-api-docs) how to build documentation site locally.

{{cookiecutter.project_name}}/.github/next_steps/04_citation.md

@@ -1,7 +1,5 @@
 ---
 title: 'Next step: Citation data'
-labels:
-  - 'action required'
 ---
 
 The repository has been set up with a [GitHub action](https://github.com/marketplace/actions/cffconvert) that monitors your citation data. It checks the following 6 aspects:

{{cookiecutter.project_name}}/.github/next_steps/05_linting.md

@@ -1,7 +1,5 @@
 ---
 title: 'Next step: Linting'
-labels:
-  - 'action required'
 ---
 
 Linting instructions

{{cookiecutter.project_name}}/.github/next_steps/labels.yml

@@ -5,12 +5,6 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v2
-      - name: Create labels
-        uses: crazy-max/ghaction-github-labeler@v3
-        with:
-          github-token: ${{ secrets.GITHUB_TOKEN }}
-          yaml-file: .github/next_steps/labels.yml
-          skip-delete: true
       - name: Create Sonarcloud integration issue
         uses: JasonEtco/create-an-issue@v2
         env:
@@ -51,7 +45,7 @@ jobs:
           echo 'Created issues that must be completed to have fully working Python package:
           * Sonarcloud integration ${{ steps.sonarcloud.outputs.url }}
           * Zenodo integration ${{ steps.zenodo.outputs.url }}
-          * Readthedocs instructions ${{ steps.readthedocs.outputs.url }}
+          * Read the Docs instructions ${{ steps.readthedocs.outputs.url }}
           * Citation data ${{ steps.citation.outputs.url }}
           * Linting fixes ${{ steps.linting.outputs.url }}'
       - name: Cleanup files needed to create next steps issues