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,
)