adding pre-commit (#57)

* define pre-commit
* apply to format
* CI check

.codecov.yml

@@ -42,4 +42,4 @@ comment:
   layout: header, diff
   require_changes: false
   behavior: default  # update if exists else create new
-  # branches: *
+  # branches: *

.github/CONTRIBUTING.md

@@ -81,7 +81,7 @@ Now, run all tests using::
 Use ``--doctest-modules`` to run doctests.
 For example, run all tests and all doctests using::
 ```
-    $ PYTHONPATH=. pytest --doctest-modules --with-xunit --with-coverage <package> 
+    $ PYTHONPATH=. pytest --doctest-modules --with-xunit --with-coverage <package>
 ```
 
 ## Test coverage
@@ -104,4 +104,4 @@ detailing the test coverage::
 
 ## 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

@@ -12,7 +12,7 @@ assignees: ''
 ### 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.
 -->

.github/ISSUE_TEMPLATE/Question.md

@@ -9,10 +9,10 @@ assignees: ''
 
 ## ❓ Questions and Help
 
-### Before asking:   
+### Before asking:
 <!--
-1. search the issues.   
-2. search the docs.    
+1. search the issues.
+2. search the docs.
 -->
 
 <!-- If you still can't find what you need: -->
@@ -21,7 +21,7 @@ assignees: ''
 
 #### Code
 
-<!-- Please paste a code snippet if your question requires it! -->   
+<!-- Please paste a code snippet if your question requires it! -->
 
 #### What have you tried?
 

.github/PULL_REQUEST_TEMPLATE.md

@@ -23,8 +23,8 @@ Fixes # (issue).
 - Breaking change (fix or feature that would cause existing functionality to not work as expected)
 - This change requires a documentation update
 
-## PR review    
-Anyone in the community is free to review the PR once the tests have passed.     
+## 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?

.github/workflows/ci_testing.yml

@@ -117,4 +117,4 @@ jobs:
         rm ./data-images/*_/*/*_HE.csv
         python birl/bm_template.py -n anhir -t ./data-images/pairs-imgs-lnds_histol.csv -d ./data-images -o ./results --preprocessing matching-rgb gray -cfg configs/sample_config.yaml
         python bm_experiments/evaluate_experiment.py -d ./data-images -e ./results/BmTemplate_anhir --visual
-      shell: bash
+      shell: bash

.github/workflows/code-format.yml

@@ -52,6 +52,25 @@ jobs:
       - name: isort
         run: isort --check-only .
 
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v2
+
+      - name: set PY
+        run: echo "PY=$(python -VV | sha256sum | cut -d' ' -f1)" >> $GITHUB_ENV
+      - uses: actions/cache@v2
+        with:
+          path: ~/.cache/pre-commit
+          key: pre-commit|${{ env.PY }}|${{ hashFiles('.pre-commit-config.yaml') }}
+
+      - uses: pre-commit/[email protected]
+        # this action also provides an additional behaviour when used in private repositories
+        # when configured with a github token, the action will push back fixes to the pull request branch
+        # with:
+        #   token: ${{ secrets.GITHUB_TOKEN }}
+
   #typing-check-mypy:
   #  runs-on: ubuntu-20.04
   #  steps:

.github/workflows/docker-builds.yml

@@ -40,4 +40,4 @@ jobs:
           file: bm_experiments/Dockerfile
           push: ${{ github.ref == 'refs/heads/master' }}
           tags: borda/birl:SOTA-py${{ matrix.python_version }}
-        timeout-minutes: 240
+        timeout-minutes: 240

.gitignore

@@ -36,4 +36,4 @@ coverage.xml
 .hypothesis/
 
 # Raw illustrations
-figures/*.png
+figures/*.png

.pre-commit-config.yaml

@@ -0,0 +1,43 @@
+default_language_version:
+  python: python3.8
+
+ci:
+  autofix_prs: true
+  autoupdate_commit_msg: '[pre-commit.ci] pre-commit suggestions'
+  # submodules: true
+
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.0.1
+    hooks:
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+      - id: check-yaml
+      - id: pretty-format-json
+
+  #- repo: https://github.com/pre-commit/mirrors-autopep8
+  #  rev: v1.5.7
+  #  hooks:
+  #    - id: autopep8
+  #      name: fixing PEP8
+
+  - repo: https://github.com/PyCQA/isort
+    rev: 5.8.0
+    hooks:
+      - id: isort
+        name: imports
+        require_serial: false
+
+  - repo: https://github.com/pre-commit/mirrors-yapf
+    rev: v0.31.0
+    hooks:
+      - id: yapf
+        name: formatting
+        language: python
+        require_serial: false
+
+  - repo: https://github.com/PyCQA/flake8
+    rev: 3.9.2
+    hooks:
+      - id: flake8
+        name: PEP8

LICENSE

@@ -24,4 +24,4 @@ DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS
 OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
 CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
 OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

MANIFEST.in

@@ -45,7 +45,7 @@ recursive-include scripts *.r *.ijm *.bsh *.py
 include *.txt
 
 # Exclude build configs
-exclude *.yml
+exclude *.yml *.yaml
 
 prune .git
 prune .github

README.md

@@ -20,7 +20,7 @@
 [![Code Health](https://landscape.io/github/Borda/BIRL/master/landscape.svg?style=flat)](https://landscape.io/github/Borda/BIRL/master)
 [![Run Status](https://api.shippable.com/projects/585bfa66e18a291000c15f24/badge?branch=master)](https://app.shippable.com/github/Borda/BIRL)
 [![Coverage Badge](https://api.shippable.com/projects/585bfa66e18a291000c15f24/coverageBadge?branch=master)](https://app.shippable.com/github/Borda/BIRL)
-[![Image.sc 
+[![Image.sc
 forum](https://img.shields.io/badge/dynamic/json.svg?label=forum&url=https%3A%2F%2Fforum.image.sc%2Ftags%2Fanhir.json&query=%24.topic_list.tags.0.topic_count&colorB=brightgreen&suffix=%20topics&logo=data:image/png;base64,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)](https://forum.image.sc/tags/anhir)
 -->
 
@@ -33,9 +33,9 @@ _This project/framework is the key component of **[Automatic Non-rigid Histologi
 The project contains a set of sample images with related landmark annotations and experimental evaluation of state-of-the-art image registration methods.
 
 The initial [dataset of stained histological tissues](http://cmp.felk.cvut.cz/~borovji3/?page=dataset) is composed by image pairs of related sections (mainly, consecutive cuts).
-Each image in the pair is coloured with a different stain. 
-The registration of those images is a challenging task due to both artefacts and deformations acquired during sample preparation and appearance differences due to staining. 
-For evaluation, we have manually placed landmarks in each image pair. There are at least 40 uniformly spread over the tissue. 
+Each image in the pair is coloured with a different stain.
+The registration of those images is a challenging task due to both artefacts and deformations acquired during sample preparation and appearance differences due to staining.
+For evaluation, we have manually placed landmarks in each image pair. There are at least 40 uniformly spread over the tissue.
 We do not put any landmarks in the background.
 For more information about annotation creation and landmarks handling, we refer to the special repository - [Dataset: histology landmarks](http://borda.github.com/dataset-histology-landmarks).
 
@@ -91,20 +91,20 @@ python setup.py install
 For installing some particular version/releases use following links
 _https://github.com/Borda/BIRL/archive/v0.2.3.zip_
 where the numbers match desired version
-(see package [releases](https://github.com/Borda/BIRL/releases)). 
+(see package [releases](https://github.com/Borda/BIRL/releases)).
 
 ---
 
-## Before benchmarks (pre-processing) 
+## Before benchmarks (pre-processing)
 
-In the `data-images` folder we provide some sample images with landmarks for registration. 
-These sample registration pairs are saved in `data-images/pairs-imgs-lnds_mix.csv`. 
+In the `data-images` folder we provide some sample images with landmarks for registration.
+These sample registration pairs are saved in `data-images/pairs-imgs-lnds_mix.csv`.
 You can create your own costume cover table for a given dataset (folder with images and landmarks) by hand or use script `bm_dataset/create_registration_pairs.py` assuming the same folder structure `<dataset>/<image-set>/<scale>/<images-and-landmarks>` as for the [CIMA dataset](http://cmp.felk.cvut.cz/~borovji3/?page=dataset).
 
 ### Prepare synthetic data
 
-There is a script to generate synthetic data. 
-Just set an initial image and their corresponding landmarks. 
+There is a script to generate synthetic data.
+Just set an initial image and their corresponding landmarks.
 The script will generate a set of geometrically deformed images mimicking different stains and compute the new related landmarks.
 
 ```bash
@@ -117,8 +117,8 @@ python bm_dataset/create_real_synth_dataset.py \
 
 ### Creating an image-pairs table
 
-When the synthetic datasets have been created, the cover csv file which contains the registration pairs (Reference and Moving image (landmarks)) is generated. 
-Two modes are created: _"first2all"_ for registering the first image to all others and _"each2all"_ for registering each image to all other. 
+When the synthetic datasets have been created, the cover csv file which contains the registration pairs (Reference and Moving image (landmarks)) is generated.
+Two modes are created: _"first2all"_ for registering the first image to all others and _"each2all"_ for registering each image to all other.
 _(note A-B is the same as B-A)_
 
 ```bash
@@ -144,7 +144,7 @@ We introduce an option how to randomly take only a subset (use `nb_selected`) of
 python bm_dataset/rescale_tissue_landmarks.py \
     -a ./data-images -d ./output \
     --nb_selected 0.5 --nb_total 200
-``` 
+```
 
 Moreover we developed two additional script for converting large images, handling multiple tissue samples in single image and crop to wide background.
  * `bm_dataset/convert_tiff2png.py` converts TIFF or SVS image to PNG in a particular level
@@ -161,7 +161,7 @@ Even though this framework is completely customizable we include several image r
 
 ### Install methods and run benchmarks
 
-For each registration method, different experiments can be performed independently using different values of the parameters or image pairs sets. 
+For each registration method, different experiments can be performed independently using different values of the parameters or image pairs sets.
 
 Sample execution of the "empty" benchmark template:
 ```bash
@@ -197,13 +197,13 @@ The general Image Registration benchmarks contain couple required and optional p
 ![preprocessing-hist-matching](assets/Rat-Kidney_histogram-matching.jpg)
 
 Measure your computer performance using average execution time on several simple image registrations.
-The registration consists of loading images, denoising, feature detection, transform estimation and image warping. 
+The registration consists of loading images, denoising, feature detection, transform estimation and image warping.
 ```bash
 python bm_experiments/bm_comp_perform.py -o ./results
 ```
 This script generate simple report exported in JSON file on given output path.
 
-### Prepared experimental docker image 
+### Prepared experimental docker image
 
 Used prepared docker image from [Docker Hub](https://hub.docker.com/r/borda/birl)
 
@@ -334,14 +334,14 @@ The new image registration methods should be added to `bm_experiments` folder.
 
 ### Re-evaluate experiment
 
-In case you need to re-compute evaluation or add visualisation to existing experiment you can use the following script. 
-The script require complete experiment folder with standard `registration-results.scv` (similar to registration pairs extended by experiment results). 
+In case you need to re-compute evaluation or add visualisation to existing experiment you can use the following script.
+The script require complete experiment folder with standard `registration-results.scv` (similar to registration pairs extended by experiment results).
 
 ```bash
 python bm_experiments/evaluate_experiment.py \
     -e ./results/BmUnwarpJ \
     --visual
-``` 
+```
 
 ---
 
@@ -363,10 +363,10 @@ For complete references see [bibtex](docs/references.bib).
 
 Create your own local environment, for more information see the [User Guide](https://pip.pypa.io/en/latest/user_guide.html), and install dependencies requirements.txt contains a list of packages and can be installed as
 ```bash
-@duda:~$ cd BIRL 
+@duda:~$ cd BIRL
 @duda:~/BIRL$ virtualenv env
-@duda:~/BIRL$ source env/bin/activate  
-(env)@duda:~/BIRL$ pip install -r requirements.txt  
+@duda:~/BIRL$ source env/bin/activate
+(env)@duda:~/BIRL$ pip install -r requirements.txt
 (env)@duda:~/BIRL$ python ...
 ```
 and in the end, terminating...
@@ -376,7 +376,7 @@ and in the end, terminating...
 
 **Running docString tests** - documentation and samples of doc string on [pymotw](https://pymotw.com/2/doctest/) and [python/docs](https://docs.python.org/2/library/doctest.html)
 
-**Listing dataset in command line**  
+**Listing dataset in command line**
 ```bash
 find . | sed -e "s/[^-][^\/]*\// |/g" -e "s/|\([^ ]\)/|-\1/" >> dataset.txt
 ```

_config.yml

@@ -1,2 +1,2 @@
 show_downloads: true
-theme: jekyll-theme-cayman
+theme: jekyll-theme-cayman

bm_ANHIR/automatic-evaluation.md

@@ -47,7 +47,7 @@ Run one of following sample registration experiments:
         ~/Medical-temp/experiments_anhir/BmUnwarpJ/*/*.png
     ```
 
-Running the docker image with mapped folders 
+Running the docker image with mapped folders
 ```bash
 mkdir submission output
 ```
@@ -61,7 +61,7 @@ docker run --rm -it \
 ```
 
 
-### Export 
+### Export
 
 Export the created image to be uploaded to the evaluation system.
 ```bash

bm_ANHIR/emails/text_dataset.txt

@@ -8,4 +8,4 @@ Let us remind you that we will have a challenge workshop at the ISBI conference
 
 Do not hesitate to ask if you have any questions or comments.
 Good luck and we are looking forward to meeting you in Venice.
-Jiri Borovec & Arrate Munoz-Barrutia & Jan Kybic & Ignacio Arganda
+Jiri Borovec & Arrate Munoz-Barrutia & Jan Kybic & Ignacio Arganda

bm_ANHIR/emails/text_invitation.txt

@@ -7,4 +7,4 @@ For more detail visit our webpage:
 https://anhir.grand-challenge.org
 
 Looking forward to your possible participation,
-Jiri Borovec & Arrate Munoz-Barrutia & Jan Kybic & Ignacio Arganda
+Jiri Borovec & Arrate Munoz-Barrutia & Jan Kybic & Ignacio Arganda

bm_ANHIR/emails/text_pre-release.txt

@@ -17,4 +17,4 @@ Do not hesitate to ask if you have any questions or comments.
 
 Good luck!
 We are looking forward to meeting you in Venice.
-Jiri Borovec & Arrate Munoz-Barrutia & Jan Kybic & Ignacio Arganda-Carreras
+Jiri Borovec & Arrate Munoz-Barrutia & Jan Kybic & Ignacio Arganda-Carreras

bm_CIMA/README.md

@@ -29,4 +29,4 @@ Then you can parse just the new results with [evaluation script](../bm_ANHIR/eva
 ## References
 
 For complete references see [bibtex](../docs/references.bib).
-1. Borovec, J. (2019). **BIRL: Benchmark on Image Registration methods with Landmark validation**. arXiv preprint [arXiv:1912.13452.](https://arxiv.org/abs/1912.13452)
+1. Borovec, J. (2019). **BIRL: Benchmark on Image Registration methods with Landmark validation**. arXiv preprint [arXiv:1912.13452.](https://arxiv.org/abs/1912.13452)

bm_experiments/run-all-experiments.sh

@@ -98,4 +98,4 @@ do
          $pproc \
          --visual --unique --nb_workers $jobs
 
-done
+done

configs/ANTs_SyN.txt

@@ -23,4 +23,4 @@
 --use-histogram-matching 1
 --collapse-output-transforms 1
 --float
---verbose
+--verbose

configs/ANTs_spline.txt

@@ -24,4 +24,4 @@
 --use-histogram-matching 1
 --collapse-output-transforms 1
 --float
---verbose
+--verbose

configs/DROP.txt

@@ -20,4 +20,4 @@ increg			= 1
 update			= 0
 sampling		= 0
 bins			= 8
-margin			= 0
+margin			= 0

configs/DROP2.txt

@@ -8,4 +8,4 @@
 --nsim 1
 --nlevels 16 16 16 8 8 8
 --nlambda 0.5
---npin
+--npin