diff --git a/.all-contributorsrc b/.all-contributorsrc new file mode 100644 index 0000000..8a69bfb --- /dev/null +++ b/.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" +} diff --git a/README.md b/README.md index 5136546..4ab7536 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,7 @@ # MIP Dataset Mapper (`mip_dmp`) + +[![All Contributors](https://img.shields.io/badge/all_contributors-2-orange.svg?style=flat-square)](#contributors-) + ![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)): + + + + + + + + + + + +
Sébastien Tourbier
Sébastien Tourbier
🐛 💻 🎨 📖 💡 🤔 🚇 🚧 🧑‍🏫 👀 ⚠️		BSchaffhauser
BSchaffhauser
💵 🔍
+ + + + + + +This project follows the [all-contributors](https://github.com/all-contributors/all-contributors) specification. Contributions of any kind welcome! \ No newline at end of file diff --git a/mip_dmp/cli/mip_dataset_mapper_cli.py b/mip_dmp/cli/mip_dataset_mapper_cli.py index 715d699..8930867 100644 --- a/mip_dmp/cli/mip_dataset_mapper_cli.py +++ b/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(): diff --git a/mip_dmp/process/embedding.py b/mip_dmp/process/embedding.py index 490573e..43f2333 100644 --- a/mip_dmp/process/embedding.py +++ b/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): diff --git a/mip_dmp/qt5/components/dataset_mapper_window.py b/mip_dmp/qt5/components/dataset_mapper_window.py index a0334d2..b10b0a1 100644 --- a/mip_dmp/qt5/components/dataset_mapper_window.py +++ b/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, diff --git a/mip_dmp/utils/__init__.py b/mip_dmp/utils/__init__.py new file mode 100644 index 0000000..2865c7a --- /dev/null +++ b/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.""" diff --git a/mip_dmp/io.py b/mip_dmp/utils/io.py similarity index 100% rename from mip_dmp/io.py rename to mip_dmp/utils/io.py diff --git a/mip_dmp/logger.py b/mip_dmp/utils/logger.py similarity index 100% rename from mip_dmp/logger.py rename to mip_dmp/utils/logger.py diff --git a/mip_dmp/parser.py b/mip_dmp/utils/parser.py similarity index 100% rename from mip_dmp/parser.py rename to mip_dmp/utils/parser.py