Merge pull request #112 from haniffalab/dev

Create release 0.4.0

Author: dannda

.github/workflows/sphinx-build.yml

@@ -14,14 +14,14 @@ jobs:
     steps:
       - name: Checkout
         uses: actions/checkout@v2
-      - name: Set up Python 3.8
+      - name: Set up Python 3.10
         uses: actions/setup-python@v2
         with:
-          python-version: 3.8
+          python-version: '3.10'
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install -r ./docker/requirements.txt          
+          pip install -r ./envs/requirements.txt          
           pip install sphinx sphinx-rtd-theme
       - name: Sphinx Build
         working-directory: ./sphinx

.github/workflows/tests-python.yml

@@ -17,10 +17,10 @@ jobs:
           sudo apt-get install -y --no-install-recommends libvips
       - name: Checkout
         uses: actions/checkout@v2
-      - name: Set up Python 3.8
+      - name: Set up Python 3.10
         uses: actions/setup-python@v2
         with:
-          python-version: 3.8
+          python-version: '3.10'
       - name: Clone ome-zarr-metadata
         uses: actions/checkout@v2
         with:
@@ -30,7 +30,7 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install -r ./docker/requirements.txt
+          pip install -r ./envs/requirements.txt
           cd ./ome-zarr-metadata && pre-commit install && pip install -e . && cd ../
       - name: Run tests
         run: python -m pytest --cov=bin tests/test_class.py

bin/build_config.py

@@ -21,7 +21,7 @@
     CoordinationType as ct,
     Component as cm,
 )
-from constants import (
+from constants.constants import (
     DATA_TYPES,
     DEFAULT_OPTIONS,
     DEFAULT_LAYOUTS,
@@ -231,7 +231,6 @@ def write_json(
 
     for data_type in DATA_TYPES:
         for file_name, file_type in DATA_TYPES[data_type]:
-
             # first file type found will be used in the config file
             file_exists = False
             if file_name in file_paths_names:
@@ -326,7 +325,7 @@ def write_json(
         views_indx.append((m.start(), m.end(), "views[{}]".format(len(views) - 1)))
 
     # Replace components names in layout string with the corresponding view object
-    for (start, end, view) in sorted(views_indx, key=lambda x: x[0], reverse=True):
+    for start, end, view in sorted(views_indx, key=lambda x: x[0], reverse=True):
         config_layout = config_layout[:start] + view + config_layout[end:]
 
     # Remove remaining | and / operators and empty parenthesis