Pin scipy version

.clang-format

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+---
+Language:        Cpp
+# BasedOnStyle:  Google
+AccessModifierOffset: -1
+AlignAfterOpenBracket: Align
+AlignConsecutiveAssignments: false
+AlignConsecutiveDeclarations: false
+AlignEscapedNewlines: Left
+AlignOperands:   true
+AlignTrailingComments: true
+AllowAllParametersOfDeclarationOnNextLine: true
+AllowShortBlocksOnASingleLine: false
+AllowShortCaseLabelsOnASingleLine: false
+AllowShortFunctionsOnASingleLine: All
+AllowShortIfStatementsOnASingleLine: true
+AllowShortLoopsOnASingleLine: true
+AlwaysBreakAfterDefinitionReturnType: None
+AlwaysBreakAfterReturnType: None
+AlwaysBreakBeforeMultilineStrings: true
+AlwaysBreakTemplateDeclarations: Yes
+BinPackArguments: true
+BinPackParameters: true
+BraceWrapping:
+  AfterClass:      false
+  AfterControlStatement: false
+  AfterEnum:       false
+  AfterFunction:   false
+  AfterNamespace:  false
+  AfterObjCDeclaration: false
+  AfterStruct:     false
+  AfterUnion:      false
+  AfterExternBlock: false
+  BeforeCatch:     false
+  BeforeElse:      false
+  IndentBraces:    false
+  SplitEmptyFunction: true
+  SplitEmptyRecord: true
+  SplitEmptyNamespace: true
+BreakBeforeBinaryOperators: None
+BreakBeforeBraces: Attach
+BreakBeforeInheritanceComma: false
+BreakInheritanceList: BeforeColon
+BreakBeforeTernaryOperators: true
+BreakConstructorInitializersBeforeComma: false
+BreakConstructorInitializers: BeforeColon
+BreakAfterJavaFieldAnnotations: false
+BreakStringLiterals: true
+ColumnLimit:     80
+CommentPragmas:  '^ IWYU pragma:'
+CompactNamespaces: false
+ConstructorInitializerAllOnOneLineOrOnePerLine: true
+ConstructorInitializerIndentWidth: 4
+ContinuationIndentWidth: 4
+Cpp11BracedListStyle: true
+DerivePointerAlignment: true
+DisableFormat:   false
+ExperimentalAutoDetectBinPacking: false
+FixNamespaceComments: true
+ForEachMacros:
+  - foreach
+  - Q_FOREACH
+  - BOOST_FOREACH
+IncludeBlocks:   Preserve
+IncludeCategories:
+  - Regex:           '^<ext/.*\.h>'
+    Priority:        2
+  - Regex:           '^<.*\.h>'
+    Priority:        1
+  - Regex:           '^<.*'
+    Priority:        2
+  - Regex:           '.*'
+    Priority:        3
+IncludeIsMainRegex: '([-_](test|unittest))?$'
+IndentCaseLabels: true
+IndentPPDirectives: None
+IndentWidth:     2
+IndentWrappedFunctionNames: false
+JavaScriptQuotes: Leave
+JavaScriptWrapImports: true
+KeepEmptyLinesAtTheStartOfBlocks: false
+MacroBlockBegin: ''
+MacroBlockEnd:   ''
+MaxEmptyLinesToKeep: 1
+NamespaceIndentation: None
+ObjCBinPackProtocolList: Never
+ObjCBlockIndentWidth: 2
+ObjCSpaceAfterProperty: false
+ObjCSpaceBeforeProtocolList: true
+PenaltyBreakAssignment: 2
+PenaltyBreakBeforeFirstCallParameter: 1
+PenaltyBreakComment: 300
+PenaltyBreakFirstLessLess: 120
+PenaltyBreakString: 1000
+PenaltyBreakTemplateDeclaration: 10
+PenaltyExcessCharacter: 1000000
+PenaltyReturnTypeOnItsOwnLine: 200
+PointerAlignment: Left
+RawStringFormats:
+  - Language:        Cpp
+    Delimiters:
+      - cc
+      - CC
+      - cpp
+      - Cpp
+      - CPP
+      - 'c++'
+      - 'C++'
+    CanonicalDelimiter: ''
+    BasedOnStyle:    google
+  - Language:        TextProto
+    Delimiters:
+      - pb
+      - PB
+      - proto
+      - PROTO
+    EnclosingFunctions:
+      - EqualsProto
+      - EquivToProto
+      - PARSE_PARTIAL_TEXT_PROTO
+      - PARSE_TEST_PROTO
+      - PARSE_TEXT_PROTO
+      - ParseTextOrDie
+      - ParseTextProtoOrDie
+    CanonicalDelimiter: ''
+    BasedOnStyle:    google
+ReflowComments:  true
+SortIncludes:    true
+SortUsingDeclarations: true
+SpaceAfterCStyleCast: false
+SpaceAfterTemplateKeyword: true
+SpaceBeforeAssignmentOperators: true
+SpaceBeforeCpp11BracedList: false
+SpaceBeforeCtorInitializerColon: true
+SpaceBeforeInheritanceColon: true
+SpaceBeforeParens: ControlStatements
+SpaceBeforeRangeBasedForLoopColon: true
+SpaceInEmptyParentheses: false
+SpacesBeforeTrailingComments: 2
+SpacesInAngles:  false
+SpacesInContainerLiterals: true
+SpacesInCStyleCastParentheses: false
+SpacesInParentheses: false
+SpacesInSquareBrackets: false
+Standard:        Auto
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+  - QT_REQUIRE_VERSION
+TabWidth:        8
+UseTab:          Never
+...

.github/workflows/actionet_python_release.yml

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+name: ACTIONet-py-release
+on:
+  push:
+    branches:
+      - 'python-release'
+jobs:
+  main:
+    runs-on: ubuntu-latest
+    timeout-minutes: 3000
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v1
+      - name: Check file existence
+        id: check_buildx_existence
+        uses: andstor/file-existence-action@v1
+        with:
+          files: "/home/ubuntu/.docker/cli-plugins/docker-buildx"
+      - name: Set up Docker Buildx
+        if: steps.check_buildx_existence.outputs.file_exists == 'false'
+        id: buildx
+        uses: docker/setup-buildx-action@v1
+        with:
+          version: latest
+          driver-opts: network=host
+      - name: Login to DockerHub Registry
+        run: echo ${{ secrets.DOCKERHUB_TOKEN }} | docker login -u ${{ secrets.DOCKERHUB_USERNAME }} --password-stdin
+      - name: Build and push latest docker
+        uses: docker/build-push-action@v2
+        with:
+          context: .
+          file: ./Dockerfile
+          push: true
+          build-args: GITHUB_PAT=${{ secrets.GITHUB_TOKEN }}
+          tags: actionet/python_release:latest

.gitignore

@@ -7,4 +7,17 @@
 ~*
 *.so
 *.a
-
+test/
+dist/
+ACTIONet.egg-info/
+build/
+data/
+!ACTIONet/data
+.vscode
+__pycache__
+.ipynb_checkpoints
+.idea/
+**/.DS_Store
+docker_insitro.txt
+tests/tmp
+tests/data

.gitmodules

@@ -0,0 +1,8 @@
+[submodule "lib/pybind11"]
+	path = lib/pybind11
+	url = https://github.com/pybind/pybind11
+	branch = v2.10
+[submodule "lib/ACTIONet"]
+	path = lib/ACTIONet
+	url = https://github.com/shmohammadi86/ACTIONet.git
+	branch = core

.pre-commit-config.yaml

@@ -0,0 +1,39 @@
+repos:
+# YAML linting and general cleanups
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v2.3.0
+    hooks:
+      - id: check-yaml
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+  # Flake8: Python linter
+  - repo: https://github.com/pycqa/flake8
+    rev: "3.9.2"
+    hooks:
+      - id: flake8
+        exclude: (ACTIONet/plotting/__init__.py|ACTIONet/__init__.py|ACTIONet/decomposition/__init__.py|ACTIONet/preprocessing/__init__.py|ACTIONet/tools/__init__.py|ACTIONet/network/__init__.py|ACTIONet/postprocessing/__init__.py)
+        args:
+          - "--max-line-length=500"
+          - "--ignore=E203"
+
+  # Isort: Python import linter/formatter
+  - repo: https://github.com/pycqa/isort
+    rev: 5.8.0
+    hooks:
+      - id: isort
+        name: isort (python)
+        types: [ python ]
+        args: ["--profile", "black"]
+  # Black: Python code formatter
+  - repo: https://github.com/psf/black
+    rev: 22.3.0
+    hooks:
+      - id: black
+        args:
+          -  --line-length=500
+  # Mypy: Python type-checking
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v0.910
+    hooks:
+      - id: mypy
+        additional_dependencies: [ types-toml==0.1.5 ]

ACTIONet/__init__.py

@@ -0,0 +1,11 @@
+__version__ = "0.4.1"
+__author__ = ", ".join(["Shahin Mohammadi"])
+__email__ = ", ".join(["[email protected]"])
+
+from . import decomposition as dc
+from . import network as nt
+from . import plotting as pl
+from . import postprocessing as po
+from . import preprocessing as pp
+from . import tools as tl
+from .main import *

ACTIONet/decomposition/__init__.py

@@ -0,0 +1,4 @@
+from .aa import *
+from .action import *
+from .actionmr import *
+from .spa import *