define pre-commit (#33)

* adding pre-commit
* apply formatting
* add CI check
* prune CI triggers

.codecov.yml

@@ -39,4 +39,4 @@ comment:
   layout: header, diff
   require_changes: false
   behavior: default  # update if exists else create new
-  # branches: *
+  # branches: *

.github/CONTRIBUTING.md

@@ -79,7 +79,7 @@ Now, run all tests using::
 Use ``--doctest-modules`` to run doctests.
 For example, run all tests and all doctests using::
 ```
-    $ pytest -v --doctest-modules --with-xunit --with-coverage pyImSegm 
+    $ pytest -v --doctest-modules --with-xunit --with-coverage pyImSegm
 ```
 
 ## Test coverage
@@ -102,4 +102,4 @@ detailing the test coverage::
 
 ## Bugs
 
-Please `report bugs on GitHub <https://github.com/Borda/pyImSegm/issues>`_.
+Please `report bugs on GitHub <https://github.com/Borda/pyImSegm/issues>`_.

.github/PULL_REQUEST_TEMPLATE.md

@@ -35,4 +35,4 @@ Please describe the tests that you ran to verify your changes. Provide instructi
 - [ ] My changes generate no new warnings
 - [ ] 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
-- [ ] Any dependent changes have been merged and published in downstream modules
+- [ ] Any dependent changes have been merged and published in downstream modules

.github/workflows/ci-experiment.yml

@@ -6,10 +6,12 @@ on:  # Trigger the workflow on push or pull request, but only for the master bra
     branches: [master]
   pull_request:
     branches: [master]
+    types: [opened, reopened, ready_for_review, synchronize]
 
 jobs:
 
   bash-expt:
+    if: github.event.pull_request.draft == false
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false

.github/workflows/ci-install-pkg.yml

@@ -4,13 +4,13 @@ name: Install pkg
 on:
   # Trigger the workflow on push or pull request,
   # but only for the master branch
-  - push
-  - pull_request
+  push:
+    branches: [ master ]
+  pull_request: { }
 
 jobs:
   pkg-check:
     runs-on: ubuntu-20.04
-
     steps:
       - uses: actions/checkout@master
       - uses: actions/setup-python@v2
@@ -19,7 +19,7 @@ jobs:
 
       - name: Install dependenies
         run: |
-          pip install --upgrade cython setuptools wheel check-manifest twine==3.2 "numpy<1.17"
+          pip install --upgrade cython setuptools wheel check-manifest twine==3.2
 
       - name: Check package
         run: |
@@ -44,7 +44,6 @@ jobs:
       matrix:
         os: [ubuntu-20.04, macOS-10.15]  # , windows-2019
         python-version: [3.7]
-
     steps:
       - uses: actions/checkout@master
       - uses: actions/setup-python@v2

.github/workflows/ci-testing.yml

@@ -2,8 +2,9 @@ name: CI testing
 
 # see: https://help.github.com/en/actions/reference/events-that-trigger-workflows
 on:  # Trigger the workflow on push or pull request, but only for the master branch
-  - push
-  - pull_request
+  push:
+    branches: [ master ]
+  pull_request: {}
 
 jobs:
   pytest:
@@ -12,8 +13,8 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-20.04, macOS-10.15]  # , windows-2019
-        python-version: [3.6, 3.7, 3.8, 3.9]
+        os: [ubuntu-20.04, macOS-10.15] # , windows-2019
+        python-version: [3.6, 3.8, 3.9]
         requires: ['latest']
         include:
           - os: ubuntu-18.04

.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:

.gitignore

@@ -31,4 +31,4 @@ coverage.xml
 .hypothesis/
 
 # Documentation
-docs/build
+docs/build

.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

@@ -22,7 +22,7 @@ recursive-include imsegm *.py *.pyx
 include setup.*
 
 # Exclude build configs
-exclude *.yml
+exclude *.yml *.yaml
 # Exclude testing
 exclude pytest.*
 recursive-exclude tests *

README.md

@@ -80,10 +80,10 @@ Reference: _Borovec J., Kybic J., Sugimoto, A. (2017). **Region growing using su
 
 Create your own local environment, for more see the [User Guide](https://pip.pypa.io/en/latest/user_guide.html), and install dependencies requirements.txt contains list of packages and can be installed as
 ```bash
-@duda:~$ cd pyImSegm  
+@duda:~$ cd pyImSegm
 @duda:~/pyImSegm$ virtualenv env
-@duda:~/pyImSegm$ source env/bin/activate  
-(env)@duda:~/pyImSegm$ pip install -r requirements.txt  
+@duda:~/pyImSegm$ source env/bin/activate
+(env)@duda:~/pyImSegm$ pip install -r requirements.txt
 (env)@duda:~/pyImSegm$ python ...
 ```
 and in the end terminating...
@@ -111,11 +111,11 @@ If loading of compiled descriptors in `cython` fails, it is automatically swappe
 
 **Installation**
 
-The package can be installed via pip 
+The package can be installed via pip
 ```bash
 pip install git+https://github.com/Borda/pyImSegm.git
 ```
-or using `setuptools` from a local folder 
+or using `setuptools` from a local folder
 ```bash
 python setup.py install
 ```
@@ -147,7 +147,7 @@ We introduce some useful tools for work with image annotation and segmentation.
         -imgs "./data-images/drosophila_ovary_slice/segm/*.png" \
         -out ./data-images/drosophila_ovary_slice/segm_rgb
     ```
-* **Visualisation:** having input image and its segmentation we can use simple visualisation which overlap the segmentation over input image. 
+* **Visualisation:** having input image and its segmentation we can use simple visualisation which overlap the segmentation over input image.
     ```bash
     python handling_annotations/run_overlap_images_segms.py \
         -imgs "./data-images/drosophila_ovary_slice/image/*.jpg" \
@@ -164,7 +164,7 @@ We introduce some useful tools for work with image annotation and segmentation.
     ```bash
     python handling_annotations/run_segm_annot_relabel.py \
         -out ./results/relabel_center_levels \
-        --label_old 2 3 --label_new 1 1 
+        --label_old 2 3 --label_new 1 1
     ```
 
 
@@ -220,7 +220,7 @@ The previous two (un)segmentation accept [configuration file](experiments_segmen
 ```yaml
 slic_size: 35
 slic_regul: 0.2
-features: 
+features:
   color_hsv: ['mean', 'std', 'eng']
 classif: 'SVM'
 nb_classif_search: 150

_config.yml

@@ -1,2 +1,2 @@
 show_downloads: true
-theme: jekyll-theme-leap-day
+theme: jekyll-theme-leap-day

docs/Makefile

@@ -16,4 +16,4 @@ help:
 # Catch-all target: route all unknown targets to Sphinx using the new
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
 %: Makefile
-	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/references.bib

@@ -43,4 +43,4 @@ @article{RegionGrowing2017
     year = {2017},
     doi = {10.1117/1.JEI.26.6.061611},
     URL = {http://dx.doi.org/10.1117/1.JEI.26.6.061611}
-}
+}

docs/requirements.txt

@@ -4,4 +4,4 @@ myst-parser
 nbsphinx>=0.8.5
 pandoc
 docutils
-ipython
+ipython

experiments_ovary_centres/test_ovary_centers.sh

@@ -5,4 +5,4 @@ python experiments_ovary_centres/run_create_annotation.py
 python experiments_ovary_centres/run_center_candidate_training.py
 python experiments_ovary_centres/run_center_prediction.py
 python experiments_ovary_centres/run_center_clustering.py
-python experiments_ovary_centres/run_center_evaluation.py
+python experiments_ovary_centres/run_center_evaluation.py

experiments_ovary_detect/test_ovary_detect.sh

@@ -10,4 +10,4 @@ python experiments_ovary_detect/run_export_user-annot-segm.py
 python experiments_ovary_detect/run_cut_segmented_objects.py
 python experiments_ovary_detect/run_ellipse_annot_match.py
 python experiments_ovary_detect/run_ellipse_cut_scale.py
-python experiments_ovary_detect/run_egg_swap_orientation.py
+python experiments_ovary_detect/run_egg_swap_orientation.py

experiments_segmentation/test_segmentations.sh

@@ -13,4 +13,4 @@ python experiments_segmentation/run_segm_slic_classif_graphcut.py \
     -l data-images/drosophila_ovary_slice/list_imgs-annot-struct_short.csv \
     -i "data-images/drosophila_ovary_slice/image/insitu41*.jpg" \
     -cfg ./experiments_segmentation/sample_config.yml \
-    --visual
+    --visual

handling_annotations/test_annotations.sh

@@ -20,4 +20,4 @@ python handling_annotations/run_segm_annot_inpaint.py \
     --label 0
 python handling_annotations/run_segm_annot_relabel.py \
     -imgs "./data-images/drosophila_ovary_slice/center_levels/*.png" \
-    -out ./results/relabel_center_levels
+    -out ./results/relabel_center_levels

ij_macros/convert-image_tif2png.ijm

@@ -22,13 +22,13 @@ print("found: " + toString(list.length));
 for (i=0; i<list.length; i++){
 	name = list[i];
 	nameNew = replace(name, ".tif", ".png");
-	
-	print(toString(i+1) + "#" + toString(list.length) + " -> " + name);	
+
+	print(toString(i+1) + "#" + toString(list.length) + " -> " + name);
 	open(dirIn + name);
-	
+
 	//run("Brightness/Contrast...");
 	run("Enhance Contrast", "saturated=0.35");
-	
-	saveAs("PNG", dirOut + nameNew);	
+
+	saveAs("PNG", dirOut + nameNew);
 	close();
 }

ij_macros/multiPointSet_export.ijm

@@ -4,8 +4,8 @@
  * @author Jiri Borovec
  * @date 13/06/2014
  * @mail [email protected]
- * 
- * @brief: This macro does export set of points from Multi-point tool 
+ *
+ * @brief: This macro does export set of points from Multi-point tool
  * into .csv and .txt files (the name is specified during exporting)
  */
 
@@ -40,4 +40,4 @@ for(i=0; i<lengthOf(xCoordinates); i++) {
     setResult("Y", i, yCoordinates[i]);
 }
 updateResults();
-saveAs("Results", fileName+".csv"); 
+saveAs("Results", fileName+".csv");

ij_macros/multiPointSet_import.ijm

@@ -4,8 +4,8 @@
  * @author Jiri Borovec
  * @date 13/06/2014
  * @mail [email protected]
- * 
- * @brief: This macro does importing set of points from Multi-point tool 
+ *
+ * @brief: This macro does importing set of points from Multi-point tool
  * from .csv and .txt files (the name is specified during exporting)
  */
 
@@ -20,7 +20,7 @@ text = split(allText, "\n");
 
 // define array for points
 var xpoints = newArray;
-var ypoints = newArray; 
+var ypoints = newArray;
 
 // in case input is in TXT format
 if (ext=="txt") {
@@ -32,11 +32,11 @@ if (ext=="txt") {
 	// loading and parsing each line
 	for (i = 2; i < (text.length); i++){
 	   line = split(text[i]," ");
-	   setOption("ExpandableArrays", true);   
+	   setOption("ExpandableArrays", true);
 	   xpoints[i-2] = parseInt(line[iX]);
-	   ypoints[i-2] = parseInt(line[iY]); 
-	   print("p("+i-1+") ["+xpoints[i-2]+"; "+ypoints[i-2]+"]"); 
-	} 
+	   ypoints[i-2] = parseInt(line[iY]);
+	   print("p("+i-1+") ["+xpoints[i-2]+"; "+ypoints[i-2]+"]");
+	}
 // in case input is in CSV format
 } else if (ext=="csv") {
 	print("importing CSV point set...");
@@ -50,15 +50,15 @@ if (ext=="txt") {
 	// loading and parsing each line
 	for (i = 1; i < (text.length); i++){
 	   line = split(text[i],",");
-	   setOption("ExpandableArrays", true);   
+	   setOption("ExpandableArrays", true);
 	   xpoints[i-1] = parseInt(line[iX]);
 	   ypoints[i-1] = parseInt(line[iY]);
-	   print("p("+i+") ["+xpoints[i-1]+"; "+ypoints[i-1]+"]"); 
-	} 
+	   print("p("+i+") ["+xpoints[i-1]+"; "+ypoints[i-1]+"]");
+	}
 // in case of any other format
 } else {
-	print("not supported format...");	
+	print("not supported format...");
 }
- 
+
 // show the points in the image
-makeSelection("point", xpoints, ypoints); 
+makeSelection("point", xpoints, ypoints);