diff --git a/README.md b/README.md index 79fe722..b2ebe39 100644 --- a/README.md +++ b/README.md @@ -19,12 +19,15 @@ + +

- **Documentation:** https://ibm.github.io/AutoPeptideML - **Source Code:** https://github.com/IBM/AutoPeptideML - **Webserver:** http://peptide.ucd.ie/AutoPeptideML +- **Paper Pre-print:** https://www.biorxiv.org/content/10.1101/2023.11.13.566825v1 AutoPeptideML allows researchers without prior knowledge of machine learning to build models that are: @@ -213,7 +216,7 @@ There is an example available in the [default configuration file](https://github
4. API -Example notebooks and documentation in how to use the API can be found in the `examples` directory. +Please check the [Code reference documentation](https://ibm.github.io/AutoPeptideML/autopeptideml/)
diff --git a/docs/imgs/APML_dark.png b/docs/imgs/APML_dark.png index 51458a0..1b9d01d 100644 Binary files a/docs/imgs/APML_dark.png and b/docs/imgs/APML_dark.png differ diff --git a/mkdocs.yml b/mkdocs.yml index ff0bda6..3984494 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -23,16 +23,16 @@ theme: scheme: default primary: black accent: purple - toggle: - icon: material/weather-sunny - name: Switch to light mode + # toggle: + # icon: material/weather-sunny + # name: Switch to light mode - media: "(prefers-color-scheme: dark)" scheme: slate primary: black accent: lime - toggle: - icon: material/weather-night - name: Switch to dark mode + # toggle: + # icon: material/weather-night + # name: Switch to dark mode features: - search.suggest - search.highlight @@ -84,4 +84,4 @@ markdown_extensions: extra: social: - icon: fontawesome/brands/github-alt - link: https://github.com/IBM/AutoPeptideML \ No newline at end of file + link: https://github.com/IBM/AutoPeptideML diff --git a/requirements.txt b/requirements.txt deleted file mode 100644 index dd99242..0000000 --- a/requirements.txt +++ /dev/null @@ -1,54 +0,0 @@ -alembic==1.11.1 -beautifulsoup4==4.12.2 -certifi==2023.5.7 -charset-normalizer==3.2.0 -cmaes==0.10.0 -colorlog==6.7.0 -contourpy==1.1.0 -cycler==0.11.0 -dill==0.3.6 -filelock==3.12.2 -fonttools==4.41.0 -fsspec==2023.6.0 -gdown==4.7.1 -graph-part==1.0.2 -huggingface-hub==0.16.4 -idna==3.4 -Jinja2==3.1.2 -joblib==1.3.1 -kiwisolver==1.4.4 -Mako==1.2.4 -MarkupSafe==2.1.3 -matplotlib==3.7.2 -mpmath==1.3.0 -networkx==3.1 -numpy==1.25.1 -optuna==3.2.0 -packaging==23.1 -pandarallel==1.6.5 -pandas==2.0.3 -Pillow==10.0.0 -psutil==5.9.5 -pyparsing==3.0.9 -PySocks==1.7.1 -python-dateutil==2.8.2 -pytz==2023.3 -PyYAML==6.0.1 -regex==2023.6.3 -requests==2.31.0 -safetensors==0.3.1 -scikit-learn==1.3.0 -scikit-plot==0.3.7 -scipy==1.11.1 -six==1.16.0 -soupsieve==2.4.1 -SQLAlchemy==2.0.19 -sympy==1.12 -threadpoolctl==3.2.0 -tokenizers==0.13.3 -torch==2.0.1 -tqdm==4.65.0 -transformers==4.31.0 -typing_extensions==4.7.1 -tzdata==2023.3 -urllib3==2.0.3 diff --git a/setup.py b/setup.py index e601cfc..0067981 100644 --- a/setup.py +++ b/setup.py @@ -51,6 +51,6 @@ name='autopeptideml', packages=find_packages(exclude=['examples']), url='https://github.ibm.com/raulfd/autopeptideml', - version='0.1.0', + version='0.1.1', zip_safe=False, )