using enlighten progress-bar

* upgrade pip
* drop opencv sys pkg
* typo OpenSlide #42

.shippable.yml

@@ -25,7 +25,7 @@ before_install:
   - apt-get install freetype*
   - apt-get install python-dev python-tk python3-dev python3-tk
   - apt-get install pkg-config
-  - apt-get install python-opencv openslide-tools
+  - apt-get install openslide-tools
   - pip install --upgrade pip
 
 install:

.travis.yml

@@ -31,15 +31,15 @@ matrix:
 cache: pip
 
 install:
-  - sudo apt-get install python-opencv openslide-tools
+  - sudo apt-get install openslide-tools
   - pip install -r requirements.txt
   - pip install -r ./tests/requirements.txt
   - pip install tox
   - pip --version ; pip list
 
 script:
   # integration
-  - tox --sitepackages
+  - tox -v --sitepackages
   # sample run
   - mkdir results && touch configs/sample_config.yaml
   - python bm_experiments/bm_comp_perform.py -o ./results -n 1

appveyor.yml

@@ -55,10 +55,13 @@ install:
   # The AppVeyor 'rollout builds' option is supposed to serve the same
   # purpose but it is problematic because it tends to cancel builds pushed
   # directly to master instead of just PR builds (or the converse).
-  - choco upgrade chocolatey
-  - choco install -y opencv
-  - SET PATH=%PYTHON%;%PYTHON%\\Scripts;%path%
-  - pip install -U --user pip
+  #- choco upgrade chocolatey
+  #- choco install -y opencv
+  # Prepend newly installed Python to the PATH of this build (this cannot be
+  # done from inside the powershell script as it would require to restart
+  # the parent CMD process).
+  - "SET PATH=%PYTHON%;%PYTHON%\\Scripts;%PATH%"
+  - python -m pip install --upgrade pip
   - pip install -r requirements.txt
   - pip install -r ./tests/requirements.txt
   - pip install tox
@@ -72,7 +75,7 @@ before_test:
 
 # to run your custom scripts instead of automatic tests
 test_script:
-  - tox --sitepackages --parallel auto
+  - tox -v --sitepackages --parallel auto
   - mkdir results && touch configs/sample_config.yaml
   - python bm_experiments/bm_comp_perform.py -o ./results -n 1
   - python birl/bm_template.py -t ./data_images/pairs-imgs-lnds_mix.csv -o ./results --preprocessing matching-rgb gray --unique --visual -cfg configs/sample_config.yaml

birl/utilities/experiments.py

@@ -19,7 +19,7 @@
 import multiprocessing as mproc
 from functools import wraps
 
-import tqdm
+import enlighten
 import numpy as np
 from pathos.multiprocessing import ProcessPool
 
@@ -541,10 +541,12 @@ def iterate_mproc_map(wrap_func, iterate_vals, nb_workers=CPU_COUNT, desc=''):
     nb_workers = 1 if not nb_workers else int(nb_workers)
     nb_workers = CPU_COUNT if nb_workers < 0 else nb_workers
 
-    tqdm_bar = None
     if desc is not None:
-        desc = '%r @%i-threads' % (desc, nb_workers)
-        tqdm_bar = tqdm.tqdm(total=len(iterate_vals), desc=desc)
+        pbar = enlighten.Counter(total=len(iterate_vals),
+                                 desc=str('%r @%i-threads' % (desc, nb_workers)),
+                                 stream=sys.stderr)
+    else:
+        pbar = None
 
     if nb_workers > 1:
         logging.debug('perform parallel in %i threads', nb_workers)
@@ -563,15 +565,15 @@ def iterate_mproc_map(wrap_func, iterate_vals, nb_workers=CPU_COUNT, desc=''):
         mapping = map
 
     for out in mapping(wrap_func, iterate_vals):
-        tqdm_bar.update() if tqdm_bar is not None else None
+        pbar.update() if pbar else None
         yield out
 
     if pool:
         pool.close()
         pool.join()
         pool.clear()
 
-    tqdm_bar.close() if tqdm_bar is not None else None
+    pbar.close() if pbar else None
 
 
 # from pathos.helpers import mp

bm_dataset/convert_tiff2png.py

@@ -34,8 +34,8 @@
 try:
     from openslide import OpenSlide
 except Exception:
-    print('It seems that you do not have installed OpenSlides on your computer.'
-          ' To do so, please follow instructions - https://openslides.org')
+    print('It seems that you do not have installed OpenSlide on your computer.'
+          ' To do so, please follow instructions - https://openslide.org/')
 
 sys.path += [os.path.abspath('.'), os.path.abspath('..')]  # Add path to root
 from birl.utilities.experiments import iterate_mproc_map, nb_workers

circle.yml

@@ -8,7 +8,7 @@ references:
       command: |
         sudo apt-get update
         sudo apt-get install tk-dev pkg-config python-dev python-tk tree
-        sudo apt-get install python-opencv openslide-tools
+        sudo apt-get install openslide-tools
 
   install_pips: &install_pips
     run:

requirements.txt

@@ -13,4 +13,5 @@ nibabel
 SimpleITK
 mock
 psutil
-pathos
+pathos
+enlighten>=1.3.3  # fix for Windows

tox.ini

@@ -11,6 +11,9 @@
 #
 #  and also to help confirm pull requests to this project.
 
+[build-system]
+requires = [ "pip >= 18.0" ]
+
 [tox]
 envlist = py{27,35,36,37}
 
@@ -24,6 +27,9 @@ log_file_format = %(asctime)s [%(levelname)8s] %(message)s (%(filename)s:%(linen
 log_file_date_format=%Y-%m-%d %H:%M:%S
 
 [testenv]
+# https://github.com/tox-dev/tox/issues/791
+download = true
+sitepackages = True
 basepython =
     py27: python2.7
     py35: python3.5
@@ -34,7 +40,8 @@ deps =
     -r ./tests/requirements.txt
 commands =
     check-manifest --ignore tox.ini
-    python setup.py check -m -s
+    python setup.py check --metadata --strict
+    python setup.py install --dry-run --user
     coverage run --source birl -m py.test birl tests bm_dataset bm_experiments bm_ANHIR -v --doctest-modules
     flake8 .