CI: yesqa & mdformat (#63)

* add yesqa & mdformat
* fix require py2.7
* fix MD links
* prune code check
* drop pep8speaks
* docker py3.9

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

.github/CODE_OF_CONDUCT.md

@@ -10,19 +10,19 @@ In the interest of fostering an open and welcoming environment, we as contributo
 
 Examples of behavior that contributes to creating a positive environment include:
 
-* Using welcoming and inclusive language
-* Being respectful of differing viewpoints and experiences
-* Gracefully accepting constructive criticism
-* Focusing on what is best for the community
-* Showing empathy towards other community members
+- Using welcoming and inclusive language
+- Being respectful of differing viewpoints and experiences
+- Gracefully accepting constructive criticism
+- Focusing on what is best for the community
+- Showing empathy towards other community members
 
 Examples of unacceptable behavior by participants include:
 
-* The use of sexualized language or imagery and unwelcome sexual attention or advances
-* Trolling, insulting/derogatory comments, and personal or political attacks
-* Public or private harassment
-* Publishing others' private information, such as a physical or electronic address, without explicit permission
-* Other conduct which could reasonably be considered inappropriate in a professional setting
+- The use of sexualized language or imagery and unwelcome sexual attention or advances
+- Trolling, insulting/derogatory comments, and personal or political attacks
+- Public or private harassment
+- Publishing others' private information, such as a physical or electronic address, without explicit permission
+- Other conduct which could reasonably be considered inappropriate in a professional setting
 
 ## Our Responsibilities
 

.github/CONTRIBUTING.md

@@ -7,101 +7,113 @@ Developing Open Source is great fun! =)
 Here's the long and short of it:
 
 1. Develop your contribution:
-   * Pull the latest changes from upstream::
-   ```
+
+   - Pull the latest changes from upstream:
+
+   ```bash
       git checkout master
       git pull upstream master
    ```
-   * Create a branch for the feature you want to work on. Since the branch name will appear in the merge message, use a sensible name such as 'transform-speedups'::
-     ```
+
+   - Create a branch for the feature you want to work on. Since the branch name will appear in the merge message, use a sensible name such as 'transform-speedups':
+     ```bash
       git checkout -b transform-speedups
      ```
-   * Commit locally as you progress (``git add`` and ``git commit``)
+   - Commit locally as you progress (`git add` and `git commit`)
+
 1. To submit your contribution:
 
-   * Push your changes back to your fork on GitHub::
-     ```
+   - Push your changes back to your fork on GitHub:
+     ```bash
       git push origin transform-speedups
      ```
-   * Enter your GitHub username and password (repeat contributors or advanced users can remove this step by connecting to GitHub with SSH. See detailed instructions below if desired).
-   * Go to GitHub. The new branch will show up with a green Pull Request  button - click it.
+   - Enter your GitHub username and password (repeat contributors or advanced users can remove this step by connecting to GitHub with SSH. See detailed instructions below if desired).
+   - Go to GitHub. The new branch will show up with a green Pull Request  button - click it.
+
 1. Review process:
-   * Reviewers (the other developers and interested community members) will write inline and/or general comments on your Pull Request (PR) to help you improve its implementation, documentation and style.  Every single developer working on the project has their code reviewed, and we've come to see it as friendly conversation from which we all learn and the overall code quality benefits.  Therefore, please don't let the review discourage you from contributing: its only aim is to improve the quality of project, not to criticize (we are, after all, very grateful for the time you're donating!).
-   * To update your pull request, make your changes on your local repository and commit. As soon as those changes are pushed up (to the same branch as before) the pull request will update automatically.
-   * `Travis-CI <http://travis-ci.org/>`__, a continuous integration service, is triggered after each Pull Request update to build the code, run unit tests, measure code coverage and check coding style (PEP8) of your branch. The Travis tests must pass before your PR can be merged. If Travis fails, you can find out why by clicking on the "failed" icon (red cross) and inspecting the build and test log.
-   * A pull request must be approved by two core team members before merging.
 
-## Guidelines
+   - Reviewers (the other developers and interested community members) will write inline and/or general comments on your Pull Request (PR) to help you improve its implementation, documentation and style.  Every single developer working on the project has their code reviewed, and we've come to see it as friendly conversation from which we all learn and the overall code quality benefits.  Therefore, please don't let the review discourage you from contributing: its only aim is to improve the quality of project, not to criticize (we are, after all, very grateful for the time you're donating!).
+   - To update your pull request, make your changes on your local repository and commit. As soon as those changes are pushed up (to the same branch as before) the pull request will update automatically.
+   - [Travis-CI](http://travis-ci.org/), a continuous integration service, is triggered after each Pull Request update to build the code, run unit tests, measure code coverage and check coding style (PEP8) of your branch. The Travis tests must pass before your PR can be merged. If Travis fails, you can find out why by clicking on the "failed" icon (red cross) and inspecting the build and test log.
+   - A pull request must be approved by two core team members before merging.
 
-* All code should have tests (see `test coverage`_ below for more details).
-* All code should be documented, to the same
-  `standard <https://github.com/numpy/numpy/blob/master/doc/HOWTO_DOCUMENT.rst.txt#docstring-standard>`_ as NumPy and SciPy.
-* For new functionality, always add an example to the gallery.
-* No changes are ever committed without review and approval by two core team members. **Never merge your own pull request.**
-* Examples in the gallery should have a maximum figure width of 8 inches.
+## Guidelines
 
+- All code should have tests (see `test coverage`\_ below for more details).
+- All code should be documented, to the same
+  [standard](https://github.com/numpy/numpy/blob/master/doc/HOWTO_DOCUMENT.rst.txt#docstring-standard) as NumPy and SciPy.
+- For new functionality, always add an example to the gallery.
+- No changes are ever committed without review and approval by two core team members. **Never merge your own pull request.**
+- Examples in the gallery should have a maximum figure width of 8 inches.
 
 ## Stylistic Guidelines
 
-* Set up your editor to remove trailing whitespace.  Follow `PEP08 <http://www.python.org/dev/peps/pep-0008/>`__.  Check code with pyflakes / flake8.
-* Use numpy data types instead of strings (``np.uint8`` instead of ``"uint8"``).
-* Use the following import conventions::
-  ```
-   import numpy as np
-   import matplotlib.pyplot as plt
-   from scipy import ndimage as ndi
+- Set up your editor to remove trailing whitespace.  Follow [PEP08](http://www.python.org/dev/peps/pep-0008/).  Check code with pyflakes / flake8.
+- Use numpy data types instead of strings (`np.uint8` instead of `"uint8"`).
+- Use the following import conventions:
+  ```python
+  import numpy as np
+  import matplotlib.pyplot as plt
+  from scipy import ndimage as ndi
 
-   cimport numpy as cnp  # in Cython code
+  cimport numpy as cnp  # in Cython code
   ```
-* When documenting array parameters, use ``image : (M, N) ndarray`` and then refer to ``M`` and ``N`` in the docstring, if necessary.
-* Refer to array dimensions as (plane), row, column, not as x, y, z. See :ref:`Coordinate conventions <numpy-images-coordinate-conventions>` in the user guide for more information.
-* Functions should support all input image dtypes.  Use utility functions such as ``img_as_float`` to help convert to an appropriate type.  The output format can be whatever is most efficient.  This allows us to string together several functions into a pipeline
-* Use ``Py_ssize_t`` as data type for all indexing, shape and size variables in C/C++ and Cython code.
-* Use relative module imports, i.e. ``from .._shared import xyz`` rather than ``from skimage._shared import xyz``.
-* Wrap Cython code in a pure Python function, which defines the API. This improves compatibility with code introspection tools, which are often not aware of Cython code.
-* For Cython functions, release the GIL whenever possible, using
-  ``with nogil:``.
-
+- When documenting array parameters, use `image : (M, N) ndarray` and then refer to `M` and `N` in the docstring, if necessary.
+- Refer to array dimensions as (plane), row, column, not as x, y, z. See :ref:`Coordinate conventions <numpy-images-coordinate-conventions>` in the user guide for more information.
+- Functions should support all input image dtypes.  Use utility functions such as `img_as_float` to help convert to an appropriate type.  The output format can be whatever is most efficient.  This allows us to string together several functions into a pipeline
+- Use `Py_ssize_t` as data type for all indexing, shape and size variables in C/C++ and Cython code.
+- Use relative module imports, i.e. `from .._shared import xyz` rather than `from skimage._shared import xyz`.
+- Wrap Cython code in a pure Python function, which defines the API. This improves compatibility with code introspection tools, which are often not aware of Cython code.
+- For Cython functions, release the GIL whenever possible, using
+  `with nogil:`.
 
 ## Testing
 
 This package has an extensive test suite that ensures correct execution on your system.  The test suite has to pass before a pull request can be merged, and tests should be added to cover any modifications to the code base.
 
-We make use of the `pytest <https://docs.pytest.org/en/latest/>`__ testing framework, with tests located in the various ``tests`` folders.
+We make use of the [pytest](https://docs.pytest.org/en/latest/) testing framework, with tests located in the various `tests` folders.
 
-To use ``pytest``, ensure that Cython extensions are built and that
-the library is installed in development mode::
-```
-    $ pip install -e .
-```
-Now, run all tests using::
-```
-    $ PYTHONPATH=. pytest <package>
+To use `pytest`, ensure that Cython extensions are built and that
+the library is installed in development mode:
+
+```bash
+$ pip install -e .
 ```
-Use ``--doctest-modules`` to run doctests.
-For example, run all tests and all doctests using::
+
+Now, run all tests using:
+
+```bash
+$ PYTHONPATH=. pytest <package>
 ```
-    $ PYTHONPATH=. pytest --doctest-modules --with-xunit --with-coverage <package>
+
+Use `--doctest-modules` to run doctests.
+For example, run all tests and all doctests using:
+
+```bash
+$ PYTHONPATH=. pytest --doctest-modules --with-xunit --with-coverage <package>
 ```
 
 ## Test coverage
 
 Tests for a module should ideally cover all code in that module, i.e., statement coverage should be at 100%.
 
-To measure the test coverage, install `pytest-cov <http://pytest-cov.readthedocs.io/en/latest/>`__ (using ``easy_install pytest-cov``) and then run::
-```
-  $ coverage report
+To measure the test coverage, install [pytest-cov](http://pytest-cov.readthedocs.io/en/latest/) (using `easy_install pytest-cov`) and then run:
+
+```bash
+$ coverage report
 ```
+
 This will print a report with one line for each file in `skimage`,
-detailing the test coverage::
+detailing the test coverage:
+
 ```
-  Name                             Stmts   Exec  Cover   Missing
-  --------------------------------------------------------------
-  package/module1                     77     77   100%
-  package/__init__                     1      1   100%
-  ...
+Name                             Stmts   Exec  Cover   Missing
+--------------------------------------------------------------
+package/module1                     77     77   100%
+package/__init__                     1      1   100%
+...
 ```
 
 ## Bugs
 
-Please `report bugs on GitHub <https://github.com/Borda/pyImRegBenchmark/issues>`_.
+Please [report bugs on GitHub](https://github.com/Borda/pyImRegBenchmark/issues).

.github/ISSUE_TEMPLATE/Bug_report.md

@@ -4,23 +4,23 @@ about: Create a report to help us improve
 title: ''
 labels: bug
 assignees: ''
-
 ---
 
 ## 🐛 Bug
 
 ### Description
+
 <!-- Please provide a general introduction to the issue/proposal. -->
 
 <!--
 If reporting a bug, attach the entire traceback from Python.
 If proposing an enhancement/new feature, provide links to related articles, reference examples, etc.
 -->
 
-
 ### Way to reproduce
 
 If reporting a bug, please include the following important information:
+
 - [ ] Code example
 - [ ] Relevant images (if any)
 - Operating system and version: ...

.github/ISSUE_TEMPLATE/Feature_request.md

@@ -4,10 +4,10 @@ about: Suggest an idea for this project
 title: ''
 labels: enhancement, help wanted
 assignees: ''
-
 ---
 
 ## 🚀 Feature
+
 <!-- A clear and concise description of the feature proposal -->
 
 ### Motivation

.github/ISSUE_TEMPLATE/Question.md

@@ -4,12 +4,12 @@ about: Asking a questions about...
 title: ''
 labels: question
 assignees: ''
-
 ---
 
 ## ❓ Questions and Help
 
 ### Before asking:
+
 <!--
 1. search the issues.
 2. search the docs.
@@ -27,5 +27,5 @@ assignees: ''
 
 #### What's your environment?
 
- - OS: [e.g. iOS, Linux, Win]
- - Version [e.g. 0.2.1]
+- OS: \[e.g. iOS, Linux, Win\]
+- Version \[e.g. 0.2.1\]

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,12 +1,12 @@
 ## Before submitting
 
-- [ ] Was this discussed/approved via a Github issue? (no need for typos, doc improvements)
-- [ ] My code follows the style guidelines of this project, see the [contributor guideline](https://github.com/Borda/BIRL/blob/master/.github/CONTRIBUTING.md)
-- [ ] I have performed a self-review of my own code
-- [ ] I have commented my code, particularly in hard-to-understand areas
-- [ ] I have made corresponding changes to the documentation
-- [ ] I have added tests that prove my fix is effective or that my feature works
-- [ ] New and existing unit tests pass locally with my changes
+- [ ] Was this **discussed/approved** via a Github issue? (no need for typos, doc improvements)
+- [ ] My code follows the **style guidelines** of this project, see the [contributor guideline](https://github.com/Borda/BIRL/blob/master/.github/CONTRIBUTING.md)
+- [ ] I have performed a **self-review** of my own code
+- [ ] I have **commented my code**, particularly in hard-to-understand areas
+- [ ] I have made corresponding changes to the **documentation**
+- [ ] I have **added tests** that prove my fix is effective or that my feature works
+- [ ] New and existing **unit tests pass** locally with my changes
 
 ## What does this PR do?
 
@@ -24,8 +24,10 @@ Fixes # (issue).
 - This change requires a documentation update
 
 ## PR review
+
 Anyone in the community is free to review the PR once the tests have passed.
 If we didn't discuss your PR in Github issues there's a high chance it will not be merged.
 
 ## Did you have fun?
+
 Make sure you had fun coding 🙃

.github/workflows/ci_testing.yml

@@ -76,7 +76,7 @@ jobs:
         pip install $(grep "numpy" requirements.txt)
         # v46 crashes openslide-python install
         pip install "setuptools<46" -U
-        pip install --requirement requirements.txt --quiet --upgrade
+        pip install --requirement requirements.txt --upgrade
         pip install --requirement tests/requirements.txt --quiet --upgrade
         python --version
         pip --version

.github/workflows/code-format.yml

@@ -22,36 +22,6 @@ jobs:
       - name: PEP8
         run: flake8 .
 
-  format-check-yapf:
-    runs-on: ubuntu-20.04
-    steps:
-      - uses: actions/checkout@master
-      - uses: actions/setup-python@v2
-        with:
-          python-version: 3.8
-      - name: Install dependencies
-        run: |
-          pip install --upgrade pip
-          pip install yapf
-          pip list
-        shell: bash
-      - name: yapf
-        run: yapf --diff --parallel --recursive .
-
-  imports-check-isort:
-    runs-on: ubuntu-20.04
-    steps:
-      - uses: actions/checkout@master
-      - uses: actions/setup-python@v2
-        with:
-          python-version: 3.8
-      - name: Install isort
-        run: |
-          pip install isort
-          pip list
-      - name: isort
-        run: isort --check-only .
-
   pre-commit:
     runs-on: ubuntu-latest
     steps:

.github/workflows/docker-builds.yml

@@ -15,7 +15,7 @@ jobs:
     runs-on: ubuntu-20.04
     strategy:
       matrix:
-        python_version: [3.6, 3.7, 3.8]
+        python_version: [3.7, 3.8, 3.9]
     steps:
       - name: Checkout
         uses: actions/checkout@v2

.pre-commit-config.yaml

@@ -37,6 +37,20 @@ repos:
         language: python
         require_serial: false
 
+  - repo: https://github.com/executablebooks/mdformat
+    rev: 0.7.7
+    hooks:
+      - id: mdformat
+        additional_dependencies:
+          - mdformat-gfm
+          - mdformat-black
+          - mdformat_frontmatter
+
+  - repo: https://github.com/asottile/yesqa
+    rev: v1.2.3
+    hooks:
+      - id: yesqa
+
   - repo: https://github.com/PyCQA/flake8
     rev: 3.9.2
     hooks: