Merge pull request #11 from gmrukwa/develop

Release 2.1.8

.github/actions/build-python-dist/Dockerfile

@@ -0,0 +1,10 @@
+FROM spectreteam/python_msi:v5.0.0
+
+RUN pip install --no-cache-dir --upgrade \
+    setuptools \
+    wheel \
+    twine
+
+COPY entrypoint.sh /entrypoint.sh
+
+ENTRYPOINT ["/entrypoint.sh"]

.github/actions/build-python-dist/action.yml

@@ -0,0 +1,5 @@
+name: 'Build Python distribution'
+description: 'Builds Python package distribution for upload'
+runs:
+  using: 'docker'
+  image: 'Dockerfile'

.github/actions/build-python-dist/entrypoint.sh

@@ -0,0 +1,7 @@
+#!/usr/bin/env bash
+
+pip install --no-cache-dir -r requirements.txt
+
+python setup.py sdist bdist_wheel
+
+ls dist

.github/actions/patch-version/Dockerfile

@@ -0,0 +1,5 @@
+FROM alpine:3
+
+COPY entrypoint.sh /entrypoint.sh
+
+ENTRYPOINT ["/entrypoint.sh"]

.github/actions/patch-version/action.yml

@@ -0,0 +1,25 @@
+name: 'Patch version number'
+description: 'Patches version number of the Python package'
+inputs:
+  packageInitFile:
+    description: '__init__.py file that should be patched'
+    required: true
+  isAlpha:
+    description: 'if true, package will be annotated with alpha'
+    required: true
+    default: false
+  isBeta:
+    description: 'if true, package will be annotated with beta'
+    required: true
+    default: false
+  version:
+    description: 'version of the Python package'
+    required: true
+runs:
+  using: 'docker'
+  image: 'Dockerfile'
+  args:
+    - ${{ inputs.packageInitFile }}
+    - ${{ inputs.isAlpha }}
+    - ${{ inputs.isBeta }}
+    - ${{ inputs.version }}

.github/actions/patch-version/entrypoint.sh

@@ -0,0 +1,16 @@
+#!/bin/sh -l
+
+TARGET=$1
+IS_ALPHA=$2
+IS_BETA=$3
+VERSION=$4
+
+if $IS_ALPHA; then
+  SUFIX=a
+elif $IS_BETA; then
+  SUFIX=b
+fi
+
+VERSION=${VERSION}${SUFIX:+$SUFIX}
+sed -i "1s/.*/__version__ = \"${VERSION}\"/" ${TARGET}
+cat ${TARGET}

.github/workflows/deploy.yml

@@ -0,0 +1,90 @@
+name: Build and push deployment images
+
+on:
+  push:
+    branches:
+      - master
+      - develop
+  schedule:
+    - cron: '0 17 * * *'
+
+
+env:
+  MAJOR: ${{ 2 }}
+  MINOR: ${{ 1 }}
+  FIXUP: ${{ 8 }}
+  PACKAGE_INIT_FILE: ${{ 'divik/__init__.py' }}
+  DOCKER_REPO: ${{ 'gmrukwa/divik' }}
+  IS_ALPHA: ${{ github.event_name == 'pull_request' }}
+  IS_BETA: ${{ github.event_name == 'push' && endsWith(github.event.ref, 'heads/develop') }}
+
+
+jobs:
+  push_images:
+
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v1
+      - name: Embed version to package
+        uses: ./.github/actions/patch-version
+        with:
+          packageInitFile: ${{ env.PACKAGE_INIT_FILE }}
+          isAlpha: ${{ env.IS_ALPHA }}
+          isBeta: ${{ env.IS_BETA }}
+          version: ${{ env.MAJOR }}.${{ env.MINOR }}.${{ env.FIXUP }}
+      - name: Authenticate to Docker Hub
+        run: echo $DOCKER_PASSWORD | docker login -u $DOCKER_USER --password-stdin
+        env:
+          DOCKER_PASSWORD: ${{ secrets.DOCKER_PASSWORD }}
+          DOCKER_USER: ${{ secrets.DOCKER_USER }}
+      - name: Build image
+        run: |
+          docker build \
+            --file docker/deploy.dockerfile \
+            --tag deployment \
+            .
+      - name: Push annotated images
+        run: |
+          if $IS_ALPHA; then
+            STAGE=alpha
+          elif $IS_BETA; then
+            STAGE=beta
+          fi
+          echo "STAGE=$STAGE"
+          docker tag deployment $DOCKER_REPO:$MAJOR.$MINOR.$FIXUP${STAGE:+-$STAGE}
+          docker tag deployment $DOCKER_REPO:$MAJOR.$MINOR${STAGE:+-$STAGE}
+          docker tag deployment $DOCKER_REPO:$MAJOR${STAGE:+-$STAGE}
+          docker push $DOCKER_REPO:$MAJOR.$MINOR.$FIXUP${STAGE:+-$STAGE}
+          docker push $DOCKER_REPO:$MAJOR.$MINOR${STAGE:+-$STAGE}
+          docker push $DOCKER_REPO:$MAJOR${STAGE:+-$STAGE}
+      - name: Push latest image for master branch
+        if: github.event_name == 'push' && endsWith(github.event.ref, 'heads/master')
+        run: |
+          docker tag deployment $DOCKER_REPO:latest
+          docker push $DOCKER_REPO:latest
+
+  push_pypi_package:
+
+    if: github.event_name != 'schedule'
+
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v1
+      - name: Embed version to package
+        uses: ./.github/actions/patch-version
+        with:
+          packageInitFile: ${{ env.PACKAGE_INIT_FILE }}
+          isAlpha: ${{ env.IS_ALPHA }}
+          isBeta: ${{ env.IS_BETA }}
+          version: ${{ env.MAJOR }}.${{ env.MINOR }}.${{ env.FIXUP }}
+      - name: Build Python package
+        uses: ./.github/actions/build-python-dist
+      - name: Publish Python package
+        uses: pypa/gh-action-pypi-publish@master
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_TOKEN }}

.github/workflows/unittest.yml

@@ -0,0 +1,14 @@
+name: Run unit tests in MCR environment
+
+on: push
+
+jobs:
+  tests:
+
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v1
+      - name: Run unit tests in MCR environment
+        run: docker build . --file docker/unittest.dockerfile --tag unittest

.gitignore

@@ -1,6 +1,3 @@
-# Quilt
-quilt-config/
-
 # PyCharm
 .idea/
 
@@ -105,3 +102,8 @@ ENV/
 
 # mypy
 .mypy_cache/
+
+# local tests
+data.csv
+xy.csv
+result

.readthedocs.yml

@@ -0,0 +1,24 @@
+# .readthedocs.yml
+# 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/conf.py
+
+# Build documentation with MkDocs
+#mkdocs:
+#  configuration: mkdocs.yml
+
+# Optionally build your docs in additional formats such as PDF and ePub
+formats: all
+
+# Optionally set the version of Python and requirements required to build your docs
+python:
+  version: 3.5
+  install:
+    - requirements: requirements.txt
+    - requirements: docs/requirements.txt

README.md

@@ -1,25 +1,25 @@
-[![CodeFactor](https://www.codefactor.io/repository/github/spectre-team/spectre-divik/badge)](https://www.codefactor.io/repository/github/spectre-team/spectre-divik)
-[![BCH compliance](https://bettercodehub.com/edge/badge/spectre-team/spectre-divik?branch=master)](https://bettercodehub.com/)
-[![Maintainability](https://api.codeclimate.com/v1/badges/12bf3a9343ab563e2b89/maintainability)](https://codeclimate.com/github/spectre-team/spectre-divik/maintainability)
-[![Windows build status](https://ci.appveyor.com/api/projects/status/962q796vgnve968u/branch/master?svg=true)](https://ci.appveyor.com/project/gmrukwa/spectre-divik/branch/master)
-[![Linux build Status](https://travis-ci.org/spectre-team/spectre-divik.svg?branch=master)](https://travis-ci.org/spectre-team/spectre-divik)
+[![CodeFactor](https://www.codefactor.io/repository/github/gmrukwa/divik/badge)](https://www.codefactor.io/repository/github/gmrukwa/divik)
+[![BCH compliance](https://bettercodehub.com/edge/badge/gmrukwa/divik?branch=master)](https://bettercodehub.com/)
+[![Maintainability](https://api.codeclimate.com/v1/badges/4cf5d42d0a0076c38445/maintainability)](https://codeclimate.com/github/gmrukwa/divik/maintainability)
+![](https://github.com/gmrukwa/divik/workflows/.github/workflows/push_images.yml/badge.svg)
+![](https://github.com/gmrukwa/divik/workflows/.github/workflows/unittest.yml/badge.svg)
+[![Documentation Status](https://readthedocs.org/projects/divik/badge/?version=latest)](https://divik.readthedocs.io/en/latest/?badge=latest)
 
-![Spectre](https://user-images.githubusercontent.com/1897842/31115297-0fe2c3aa-a822-11e7-90e6-92ceccf76137.jpg)
-
-# spectre-divik
+# divik
 
 Python implementation of Divisive iK-means (DiviK) algorithm.
 
 # Tools within this package
 
 > This section will be further developed soon.
 
-1) [`divik`](./spdivik/README.md) - runs DiviK in one of many scenarios
-2) [`kmeans`](./spdivik/kmeans/README.md) - runs K-means
+1) [`divik`](divik/_cli/divik.md) - runs DiviK in one of many scenarios
+2) [`kmeans`](divik/_cli/auto_kmeans.md) - runs K-means
 3) `linkage` - runs agglomerative clustering
-4) [`inspect`](./spdivik/inspect/README.md) - visualizes DiviK result
-5) `visualize` - generates `.png` file with visualization of clusters
-6) [`spectral`](./spdivik/spectral.md) - generates spectral embedding of a
+4) [`inspect`](divik/_cli/inspect.md) - visualizes DiviK result
+5) `visualize` - generates `.png` file with visualization of clusters for 2D
+maps
+6) [`spectral`](divik/_cli/spectral.md) - generates spectral embedding of a
 dataset
 
 # Installation
@@ -40,17 +40,16 @@ docker pull gmrukwa/divik
 To install specific version, you can specify it in the command, e.g.:
 
 ```bash
-docker pull gmrukwa/divik:1.12.0
+docker pull gmrukwa/divik:2.1.8
 ```
 
 ## Python package
 
 Prerequisites for installation of base package:
 
 - Python 3.5
-- [functional helpers](https://github.com/gmrukwa/functional-helpers)
 
-These are required for using `divik` application:
+These are required for using `divik` application and GMM-based filtering:
 
 - [MATLAB Compiler Runtime](https://www.mathworks.com/products/compiler/matlab-runtime.html),
 version 2016b or newer, installed to default path
@@ -66,38 +65,17 @@ compiled legacy code onto MCR image
 - [`divik` image](https://github.com/spectre-team/spectre-divik/blob/master/dockerfile) -
 installs DiviK software onto legacy code image
 
-Functional helpers should be installed with:
-
-```bash
-pip install git+https://github.com/gmrukwa/functional-helpers.git@2e68a8801f894a14601d70db76086ada723bac35#egg=functional_helpers
-```
-
 Having prerequisites installed, one can install latest base version of the
 package:
 
 ```bash
-pip install git+https://github.com/spectre-team/spectre-divik.git@master#egg=spectre-divik
+pip install divik
 ```
 
 or any stable tagged version, e.g.:
 
 ```bash
-pip install git+https://github.com/spectre-team/spectre-divik.git@v1.12.0#egg=spectre-divik
-```
-
-Installation of `divik` program dependencies can be validated via:
-
-```bash
-pip install git+https://github.com/spectre-team/spectre-divik.git@master#egg=spectre-divik[divik]
-```
-
-**Note:** *Using zsh you may need to escape square brackets with `\ `*
-
-If you want to take advantage of using [Quilt](https://quiltdata.com) for data
-management, you can install also this extra:
-
-```bash
-pip install git+https://github.com/spectre-team/spectre-divik.git@master#egg=spectre-divik[quilt_packages]
+pip install divik==2.1.8
 ```
 
 # References