Merge pull request #24 from HBPMedical/main

Merge main into dev branch

.all-contributorsrc

@@ -0,0 +1,46 @@
+{
+  "files": [
+    "README.md"
+  ],
+  "imageSize": 100,
+  "commit": false,
+  "commitType": "docs",
+  "commitConvention": "angular",
+  "contributors": [
+    {
+      "login": "sebastientourbier",
+      "name": "Sébastien Tourbier",
+      "avatar_url": "https://avatars.githubusercontent.com/u/22279770?v=4",
+      "profile": "https://github.com/sebastientourbier",
+      "contributions": [
+        "bug",
+        "code",
+        "design",
+        "doc",
+        "example",
+        "ideas",
+        "infra",
+        "maintenance",
+        "mentoring",
+        "review",
+        "test"
+      ]
+    },
+    {
+      "login": "BSchaffhauser",
+      "name": "BSchaffhauser",
+      "avatar_url": "https://avatars.githubusercontent.com/u/91893580?v=4",
+      "profile": "https://github.com/BSchaffhauser",
+      "contributions": [
+        "financial",
+        "fundingFinding"
+      ]
+    }
+  ],
+  "contributorsPerLine": 7,
+  "skipCi": true,
+  "repoType": "github",
+  "repoHost": "https://github.com",
+  "projectName": "mip-dmp",
+  "projectOwner": "HBPMedical"
+}

README.md

@@ -1,4 +1,7 @@
 # MIP Dataset Mapper (`mip_dmp`)
+<!-- ALL-CONTRIBUTORS-BADGE:START - Do not remove or modify this section -->
+[![All Contributors](https://img.shields.io/badge/all_contributors-2-orange.svg?style=flat-square)](#contributors-)
+<!-- ALL-CONTRIBUTORS-BADGE:END -->
 
 ![Latest GitHub Release](https://img.shields.io/github/v/release/HBPMedical/mip-dmp) ![Latest GitHub Release Date](https://img.shields.io/github/release-date/HBPMedical/mip-dmp) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.8056371.svg)](https://doi.org/10.5281/zenodo.8056371)
 
@@ -106,3 +109,26 @@ If you are using the MIP Dataset Mapper (`mip_dmp`) in your work, please acknowl
 ## Funding
 
 This project received funding from the European Union's H2020 Framework Programme for Research and Innovation under the Specific Grant Agreement No. 945539 (Human Brain Project SGA3, as part the Medical Informatics Platform (MIP)).
+
+## Contributors ✨
+
+Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/docs/en/emoji-key)):
+
+<!-- ALL-CONTRIBUTORS-LIST:START - Do not remove or modify this section -->
+<!-- prettier-ignore-start -->
+<!-- markdownlint-disable -->
+<table>
+  <tbody>
+    <tr>
+      <td align="center" valign="top" width="14.28%"><a href="https://github.com/sebastientourbier"><img src="https://avatars.githubusercontent.com/u/22279770?v=4?s=100" width="100px;" alt="Sébastien Tourbier"/><br /><sub><b>Sébastien Tourbier</b></sub></a><br /><a href="https://github.com/HBPMedical/mip-dmp/issues?q=author%3Asebastientourbier" title="Bug reports">🐛</a> <a href="https://github.com/HBPMedical/mip-dmp/commits?author=sebastientourbier" title="Code">💻</a> <a href="#design-sebastientourbier" title="Design">🎨</a> <a href="https://github.com/HBPMedical/mip-dmp/commits?author=sebastientourbier" title="Documentation">📖</a> <a href="#example-sebastientourbier" title="Examples">💡</a> <a href="#ideas-sebastientourbier" title="Ideas, Planning, & Feedback">🤔</a> <a href="#infra-sebastientourbier" title="Infrastructure (Hosting, Build-Tools, etc)">🚇</a> <a href="#maintenance-sebastientourbier" title="Maintenance">🚧</a> <a href="#mentoring-sebastientourbier" title="Mentoring">🧑‍🏫</a> <a href="https://github.com/HBPMedical/mip-dmp/pulls?q=is%3Apr+reviewed-by%3Asebastientourbier" title="Reviewed Pull Requests">👀</a> <a href="https://github.com/HBPMedical/mip-dmp/commits?author=sebastientourbier" title="Tests">⚠️</a></td>
+      <td align="center" valign="top" width="14.28%"><a href="https://github.com/BSchaffhauser"><img src="https://avatars.githubusercontent.com/u/91893580?v=4?s=100" width="100px;" alt="BSchaffhauser"/><br /><sub><b>BSchaffhauser</b></sub></a><br /><a href="#financial-BSchaffhauser" title="Financial">💵</a> <a href="#fundingFinding-BSchaffhauser" title="Funding Finding">🔍</a></td>
+    </tr>
+  </tbody>
+</table>
+
+<!-- markdownlint-restore -->
+<!-- prettier-ignore-end -->
+
+<!-- ALL-CONTRIBUTORS-LIST:END -->
+
+This project follows the [all-contributors](https://github.com/all-contributors/all-contributors) specification. Contributions of any kind welcome!

mip_dmp/cli/mip_dataset_mapper_cli.py

@@ -12,7 +12,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-
 """Standalone script which runs the MIP Dataset Mapper from the terminal."""
 
 import sys
@@ -21,15 +20,15 @@
 # import logging
 from mip_dmp.process.mapping import map_dataset
 
-from mip_dmp.io import (
+from mip_dmp.utils.io import (
     load_csv,
     load_excel,
     # load_excel,
     load_json,
 )
-from mip_dmp.parser import create_parser
+from mip_dmp.utils.parser import create_parser
 
-# from mip_dmp.logger import setup_logging
+# from mip_dmp.utils.logger import setup_logging
 
 
 def main():

mip_dmp/process/embedding.py

@@ -21,7 +21,7 @@
 from sklearn.decomposition import PCA
 
 # Internal imports
-from mip_dmp.io import load_glove_model, load_c2v_model
+from mip_dmp.utils.io import load_glove_model, load_c2v_model
 
 
 def glove_embedding(text, glove_model):

mip_dmp/qt5/components/dataset_mapper_window.py

@@ -48,7 +48,7 @@
 import pkg_resources
 
 # Internal imports
-from mip_dmp.io import load_mapping_json
+from mip_dmp.utils.io import load_mapping_json
 from mip_dmp.process.mapping import (
     map_dataset,
     MAPPING_TABLE_COLUMNS,

mip_dmp/utils/__init__.py

@@ -0,0 +1,15 @@
+# Copyright 2023 The HIP team, University Hospital of Lausanne (CHUV), Switzerland & Contributors
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+"""Sub-package that contains modules with utility functions for i/o, logging, and script argument parsing."""