fix expt. path sep (Win)

* CI: test push * lazy logging
Borda · Jul 23, 2021 · 6603ca6 · 6603ca6
1 parent 01fddd7
commit 6603ca6
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Showing 8 changed files with 9 additions and 27 deletions.
diff --git a/.github/workflows/ci-experiment.yml b/.github/workflows/ci-experiment.yml
@@ -29,16 +29,6 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
 
-    # Note: This uses an internal pip API and may not always work
-    # https://github.com/actions/cache/blob/master/examples.md#multiple-oss-in-a-workflow
-    - name: Cache pip
-      uses: actions/cache@v2
-      with:
-        path: ~/.cache/pip
-        key: ${{ runner.os }}-pip-py${{ matrix.python-version }}-${{ hashFiles('requirements.txt') }}
-        restore-keys: |
-          ${{ runner.os }}-pip-py${{ matrix.python-version }}-
-
     - name: install ImSegm
       run: |
         python --version
@@ -75,10 +65,3 @@ jobs:
         DISPLAY: ""
       run: |
         bash experiments_ovary_detect/test_ovary_detect.sh
-
-    - name: remove ImSegm
-      env:
-        DISPLAY: ""
-      run: |
-        # just to not being cached
-        pip uninstall -y imsegm
diff --git a/.github/workflows/ci-install-pkg.yml b/.github/workflows/ci-install-pkg.yml
@@ -19,7 +19,7 @@ jobs:
 
       - name: Install dependenies
         run: |
-          pip install --upgrade cython setuptools wheel check-manifest twine==3.2
+          pip install --upgrade cython setuptools wheel check-manifest "twine==3.2"
 
       - name: Check package
         run: |

diff --git a/.github/workflows/ci-testing.yml b/.github/workflows/ci-testing.yml
@@ -2,8 +2,7 @@ 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:
-    branches: [ master ]
+  push: {}
   pull_request: {}
 
 jobs:
@@ -13,7 +12,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-20.04, macOS-10.15, windows-2019]
-        python-version: [3.6, 3.8, 3.9]
+        python-version: [3.7, 3.9]
         requires: ['latest']
         include:
           - os: ubuntu-18.04

diff --git a/experiments_ovary_detect/run_egg_swap_orientation.py b/experiments_ovary_detect/run_egg_swap_orientation.py
@@ -106,7 +106,7 @@ def main(params):
     logging.info(tl_expt.string_dict(params, desc='PARAMETERS'))
 
     list_img_paths = sorted([p for p in glob.glob(params['path_images']) if os.path.isfile(p)])
-    logging.info('found images: %i' % len(list_img_paths))
+    logging.info('found images: %i', len(list_img_paths))
 
     if not os.path.isdir(params['path_output']):
         os.mkdir(params['path_output'])

diff --git a/experiments_ovary_detect/run_ellipse_annot_match.py b/experiments_ovary_detect/run_ellipse_annot_match.py
@@ -147,7 +147,7 @@ def filter_table(df_info, path_pattern):
     :return DF: filterd dataframe
     """
     list_name = [os.path.splitext(os.path.basename(p))[0] for p in glob.glob(path_pattern) if os.path.isfile(p)]
-    logging.info('loaded item in table %i and found %i in dir' % (len(df_info), len(list_name)))
+    logging.info('loaded item in table %i and found %i in dir', len(df_info), len(list_name))
 
     df_info['image_name'] = [os.path.splitext(p)[0] for p in df_info['image_path']]
     df_info = df_info[df_info['image_name'].isin(list_name)]
@@ -164,7 +164,7 @@ def main(params):
 
     df_info = pd.read_csv(params['path_infofile'], sep='\t', index_col=0)
     df_info = filter_table(df_info, params['path_ellipses'])
-    logging.info('filtered %i item in table' % len(df_info))
+    logging.info('filtered %i item in table', len(df_info))
     path_csv = os.path.join(params['path_output'], NAME_CSV_RESULTS)
 
     list_evals = []

diff --git a/experiments_ovary_detect/run_ellipse_cut_scale.py b/experiments_ovary_detect/run_ellipse_cut_scale.py
@@ -81,7 +81,7 @@ def perform_stage(df_group, stage, path_images, path_out, nb_workers=1):
     :param str path_images: path to the image folder
     :param str path_out: path to the output folder
     """
-    logging.info('stage %i listing %i items' % (stage, len(df_group)))
+    logging.info('stage %i listing %i items', stage, len(df_group))
     stat_a = NORM_FUNC(df_group['ellipse_a'])
     stat_b = NORM_FUNC(df_group['ellipse_b'])
     norm_size = (int(stat_b), int(stat_a))

diff --git a/imsegm/utilities/data_io.py b/imsegm/utilities/data_io.py
@@ -236,7 +236,7 @@ def save_landmarks_csv(path_file, landmarks, dtype=float):
     if not os.path.isdir(os.path.dirname(path_file)):
         raise FileNotFoundError('missing "%s"' % os.path.dirname(path_file))
     path_file = os.path.splitext(path_file)[0] + '.csv'
-    logging.debug(' save_landmarks_csv: -> creating CSV file: %s' % path_file)
+    logging.debug(' save_landmarks_csv: -> creating CSV file: %s', path_file)
     # create the results file in CSV
     landmarks = np.array(landmarks, dtype=dtype)
     if not landmarks.size:

diff --git a/imsegm/utilities/experiments.py b/imsegm/utilities/experiments.py
@@ -172,7 +172,7 @@ def create_experiment_folder(params, dir_name, stamp_unique=True, skip_load=True
         path_expt += '_' + time.strftime(FORMAT_DT, date)
         if os.path.isdir(path_expt):
             logging.warning('particular out folder already exists')
-            path_expt += ':' + str(uuid.uuid4().hex)
+            path_expt += '+' + str(uuid.uuid4().hex)
 
     logging.info('creating experiment folder "{}"'.format(path_expt))
     if not os.path.exists(path_expt):