v0.7.0 Redo Release

.github/ISSUE_TEMPLATE/lineage-validation.md

@@ -10,7 +10,7 @@
 ## Immunity
 
 **RBD Level**:
-**RBD Substitutions**
+**RBD Substitutions**:
 **Immune Escape**:
 **ACE2 Binding**:
 

.github/workflows/install.yaml

@@ -45,7 +45,8 @@ jobs:
         uses: conda-incubator/setup-miniconda@v2
         with:
           auto-update-conda: true
-          mamba-version: "*"
+          #mamba-version: "*"
+          miniforge-variant: Mambaforge
           channels: conda-forge
 
       # install conda environment

.github/workflows/pipeline.yaml

@@ -47,7 +47,8 @@ jobs:
         uses: conda-incubator/setup-miniconda@v2
         with:
           auto-update-conda: true
-          mamba-version: "*"
+          #mamba-version: "*"
+          miniforge-variant: Mambaforge
           channels: conda-forge
 
       # install conda environment
@@ -107,7 +108,8 @@ jobs:
         uses: conda-incubator/setup-miniconda@v2
         with:
           auto-update-conda: true
-          mamba-version: "*"
+          #mamba-version: "*"
+          miniforge-variant: Mambaforge
           channels: conda-forge
 
       # install conda environment
@@ -167,7 +169,8 @@ jobs:
         uses: conda-incubator/setup-miniconda@v2
         with:
           auto-update-conda: true
-          mamba-version: "*"
+          #mamba-version: "*"
+          miniforge-variant: Mambaforge
           channels: conda-forge
 
       # install conda environment
@@ -227,7 +230,8 @@ jobs:
         uses: conda-incubator/setup-miniconda@v2
         with:
           auto-update-conda: true
-          mamba-version: "*"
+          #mamba-version: "*"
+          miniforge-variant: Mambaforge
           channels: conda-forge
 
       # install conda environment

.github/workflows/profile_creation.yaml

@@ -51,7 +51,8 @@ jobs:
         uses: conda-incubator/setup-miniconda@v2
         with:
           auto-update-conda: true
-          mamba-version: "*"
+          #mamba-version: "*"
+          miniforge-variant: Mambaforge
           channels: conda-forge
 
       # install conda environment
@@ -111,7 +112,8 @@ jobs:
         uses: conda-incubator/setup-miniconda@v2
         with:
           auto-update-conda: true
-          mamba-version: "*"
+          #mamba-version: "*"
+          miniforge-variant: Mambaforge
           channels: conda-forge
 
       # install conda environment
@@ -171,7 +173,8 @@ jobs:
         uses: conda-incubator/setup-miniconda@v2
         with:
           auto-update-conda: true
-          mamba-version: "*"
+          #mamba-version: "*"
+          miniforge-variant: Mambaforge
           channels: conda-forge
 
       # install conda environment
@@ -231,7 +234,8 @@ jobs:
         uses: conda-incubator/setup-miniconda@v2
         with:
           auto-update-conda: true
-          mamba-version: "*"
+          #mamba-version: "*"
+          miniforge-variant: Mambaforge
           channels: conda-forge
 
       # install conda environment

.gitignore

@@ -27,9 +27,13 @@ data/custom*
 data/X*
 data/proposed*
 data/*gisaid*
+data/tutorial-*
 data/v*
 data/full
 data/misc
 
 # all-contributors and yarn
 yarn.lock
+
+# sphinx readthedocs
+docs/sphinx/build

.pre-commit-config.yaml

@@ -10,7 +10,7 @@ repos:
       - id: black
 
   # flake8: Python PEP8 Compliance
-  - repo: https://gitlab.com/pycqa/flake8
+  - repo: https://github.com/pycqa/flake8
     rev: 3.9.2
     hooks:
     - id: flake8

.readthedocs.yaml

@@ -0,0 +1,22 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+   configuration: docs/sphinx/source/conf.py
+
+build:
+   image: latest
+
+# Optionally declare the Python requirements required to build your docs
+python:
+   install:
+   - requirements: docs/sphinx/requirements.txt
+
+# If using Sphinx, optionally build your docs in additional formats such as PDF
+# formats:
+#    - pdf