Started on AminoAcid class (#28)

* Started on AminoAcid class * Added comments in core, still bugs to sort out * Fixed more bugs in the core when adding AminoAcid class * Moved part of bind * Integrated AminoAcid class and fixed Protein tests * Mid way testing for new depth-first approach * Added local check script and depth_first works for HPPH * Fixed depth_first search new version * Fixed depth_first_bnb algorithm using new system * Fixed small core bugs, working on new logo * Mid-way of changing bond_value structure * Cleaned up bugs from intermediate version. Bumped versions of requirements. Introduced max_weights string for keeping track of possible future scores. Merged bond_semetry model setup with the else model setup. Fixed bug with cur_len of protein always being 1. Fixed getting the weight of a amino bond * Bumbed python version in github workflow for matplotlib version dependency * Bumped workflow python version to 3.9 as numpy 1.23 requires so * Removed h_idxs from prune function. Nothing has been tested * Fixed Protein signature for pybind build * Setup for debugging current protein issues * Introduced core testing code * Finished test script for amino acids * Started on Protein core tests * Fixed protein test compilation * Fixed first couple protein generation checks * Added more debug statements for core tests * Fixed bugs with bond checks * Fixed generation of weighted amino maps * Finished all protein generation test * Added debug options in script to run core tests with gdb * Added removal of amino tests * Updated some pytest asserts. Added pytest and core_test asserts for score updates * Updated reference for black in pre-commit * Try adding core build in github actions pipeline * Fixed local algorithm core tests * Fixed dfs_bnb * Fixed pybind11 change to providing protein pointers * Added special compilation case for MacOS * Changed minimum Python version to 3.9 as 3.11 will release soon * Changed always build to only build python 3.9 versions * Changed CIwheel builds to be specific instead of exlcuding based * Leaving documentation as is and adding issue for the future * Added more licensing references * Added config file for rtfd to set python version to 3.9
okkevaneck · okkevaneck · Feb 6, 2023 · Mar 19, 2021 · Mar 22, 2021 · Mar 22, 2021
commit 39be57a8e787803bf49ca33e781b2bfee62c3134
diff --git a/.github/workflows/build_deploy.yml b/.github/workflows/build_deploy.yml
@@ -9,7 +9,7 @@ jobs:
     outputs:
       matrix: ${{ steps.set-matrix.outputs.matrix }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - uses: nelonoel/branch-name@v1.0.1
 
@@ -23,7 +23,7 @@ jobs:
     name: Check for syntax errors
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - name: Flake8 - Error on syntax errors or undefined names
         uses: py-actions/flake8@v1.1.0
@@ -43,11 +43,11 @@ jobs:
     needs: syntax_check
     strategy:
       matrix:
-        python-version: [3.6]
+        python-version: [3.9]
         os: [ubuntu-latest, windows-latest, macos-latest]
     runs-on: ${{ matrix.os }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v2
@@ -58,6 +58,7 @@ jobs:
         run: |
           python -m pip install --upgrade pip
           python -m pip install -r requirements.txt
+          ./manage.sh build
           python -m pip install -e .
 
       - name: Test with pytest
@@ -70,19 +71,19 @@ jobs:
       matrix: ${{ fromJson(needs.matrix_prep.outputs.matrix) }}
     runs-on: ${{ matrix.os }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - name: Set up Python
         uses: actions/setup-python@v2
 
       - name: Build wheels
-        uses: joerick/cibuildwheel@v1.10.0
+        uses: pypa/cibuildwheel@v2.10.1
         env:
           CIBW_BUILD: ${{ matrix.cibw_build }}
           CIBW_SKIP: ${{ matrix.cibw_skip }}
-          CIBW_PROJECT_REQUIRES_PYTHON: ">=3.6"
+          CIBW_PROJECT_REQUIRES_PYTHON: ">=3.9"
 
-      - uses: actions/upload-artifact@v2
+      - uses: actions/upload-artifact@v3
         with:
           path: ./wheelhouse/*.whl
 
@@ -91,7 +92,7 @@ jobs:
     needs: pytest
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - name: Setup Python
         uses: actions/setup-python@v2
@@ -105,7 +106,7 @@ jobs:
       - name: Check metadata
         run: twine check dist/*
 
-      - uses: actions/upload-artifact@v2
+      - uses: actions/upload-artifact@v3
         with:
           path: dist/*.tar.gz
 

diff --git a/.github/workflows/matrix_includes.json b/.github/workflows/matrix_includes.json
@@ -2,55 +2,55 @@
     {
         "runOn": "master",
         "os": "ubuntu-latest",
-        "cibw_skip": "cp27-* cp35-* *-win32 pp27-*",
-        "cibw_build": ""
+        "cibw_skip": "",
+        "cibw_build": "cp39-* cp310-* cp311-* pp37-* pp38-* pp39-*"
     },
     {
         "runOn": "master",
         "os": "windows-latest",
-        "cibw_skip": "cp27-* cp35-* *-win32 pp27-*",
-        "cibw_build": ""
+        "cibw_skip": "",
+        "cibw_build": "cp39-* cp310-* cp311-* pp37-* pp38-* pp39-*"
     },
     {
         "runOn": "master",
         "os": "macos-latest",
-        "cibw_skip": "cp27-* cp35-* *-win32 pp27-*",
-        "cibw_build": ""
+        "cibw_skip": "",
+        "cibw_build": "cp39-* cp310-* cp311-* pp37-* pp38-* pp39-*"
     },
     {
         "runOn": "release-",
         "os": "ubuntu-latest",
-        "cibw_skip": "cp27-* cp35-* *-win32 pp27-*",
-        "cibw_build": ""
+        "cibw_skip": "",
+        "cibw_build": "cp39-* cp310-* cp311-* pp37-* pp38-* pp39-*"
     },
     {
         "runOn": "release-",
         "os": "windows-latest",
-        "cibw_skip": "cp27-* cp35-* *-win32 pp27-*",
-        "cibw_build": ""
+        "cibw_skip": "",
+        "cibw_build": "cp39-* cp310-* cp311-* pp37-* pp38-* pp39-*"
     },
     {
         "runOn": "release-",
         "os": "macos-latest",
-        "cibw_skip": "cp27-* cp35-* *-win32 pp27-*",
-        "cibw_build": ""
+        "cibw_skip": "",
+        "cibw_build": "cp39-* cp310-* cp311-* pp37-* pp38-* pp39-*"
     },
     {
         "runOn": "always",
         "os": "ubuntu-latest",
         "cibw_skip": "",
-        "cibw_build": "cp36-manylinux_x86_64"
+        "cibw_build": "cp39-manylinux_x86_64"
     },
     {
         "runOn": "always",
         "os": "windows-latest",
         "cibw_skip": "",
-        "cibw_build": "cp36-win_amd64"
+        "cibw_build": "cp39-win_amd64"
     },
     {
         "runOn": "always",
         "os": "macos-latest",
         "cibw_skip": "",
-        "cibw_build": "cp36-macosx_x86_64"
+        "cibw_build": "cp39-macosx_x86_64"
     }
 ]
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -25,10 +25,10 @@ repos:
         - id: mypy
           exclude: ^docs/
   - repo: https://github.com/psf/black
-    rev: 20.8b1
+    rev: 22.8.0
     hooks:
       - id: black
-        language_version: python3.8
+        language_version: python3.10
   - repo: local
     hooks:
       - id: compress-files

diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -0,0 +1,10 @@
+version: 2
+
+build:
+  os: "ubuntu-20.04"
+  tools:
+    python: "3.9"
+
+# Build from the docs/ directory with Sphinx
+sphinx:
+  configuration: docs/source/conf.py
diff --git a/COPYING.LESSER b/COPYING.LESSER
@@ -0,0 +1,165 @@
+                   GNU LESSER GENERAL PUBLIC LICENSE
+                       Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+
+  This version of the GNU Lesser General Public License incorporates
+the terms and conditions of version 3 of the GNU General Public
+License, supplemented by the additional permissions listed below.
+
+  0. Additional Definitions.
+
+  As used herein, "this License" refers to version 3 of the GNU Lesser
+General Public License, and the "GNU GPL" refers to version 3 of the GNU
+General Public License.
+
+  "The Library" refers to a covered work governed by this License,
+other than an Application or a Combined Work as defined below.
+
+  An "Application" is any work that makes use of an interface provided
+by the Library, but which is not otherwise based on the Library.
+Defining a subclass of a class defined by the Library is deemed a mode
+of using an interface provided by the Library.
+
+  A "Combined Work" is a work produced by combining or linking an
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diff --git a/archives/prospr_core.tar.gz b/archives/prospr_core.tar.gz
diff --git a/archives/prospr_core.zip b/archives/prospr_core.zip
diff --git a/archives/prospr_data.tar.gz b/archives/prospr_data.tar.gz
diff --git a/archives/prospr_data.zip b/archives/prospr_data.zip