merged

Author: Julien Roussel

.bumpversion.cfg

@@ -0,0 +1,16 @@
+[bumpversion]
+current_version = 0.0.5
+commit = True
+tag = True
+
+[bumpversion:file:setup.py]
+search = VERSION = "{current_version}"
+replace = VERSION = "{new_version}"
+
+[bumpversion:file:qolmat/_version.py]
+search = __version__ = "{current_version}"
+replace = __version__ = "{new_version}"
+
+[bumpversion:file:docs/conf.py]
+search = version = "{current_version}"
+replace = version = "{new_version}"

.flake8

@@ -0,0 +1,9 @@
+[flake8]
+exclude = .git,__pycache__,.vscode,tests
+max-line-length=99
+ignore=E302,E305,W503,E203,E731,E402,E501,E266,E712,F401,F821
+indent-size = 4
+per-file-ignores=
+    qolmat/imputations/imputers.py:F401
+    */__init__.py:F401
+    examples/test.py:F401

.github/workflows/publish.yml

@@ -0,0 +1,29 @@
+name: Publish Package on PYPI
+
+on:
+  release:
+    types: [published]
+
+
+jobs:
+  deploy:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python
+      uses: actions/setup-python@v3
+      with:
+        python-version: '3.10'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install setuptools wheel twine
+    - name: Build package
+      run: python setup.py sdist bdist_wheel
+    - name: Publish package
+      uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
+      with:
+        user: __token__
+        password: ${{ secrets.PYPI_API_TOKEN }}

.github/workflows/test.yml

@@ -0,0 +1,37 @@
+name: Unit test Qolmat
+
+on: [push, pull_request,workflow_dispatch]
+
+
+jobs:
+  build-linux:
+    runs-on: ${{matrix.os}}
+    strategy:
+      matrix:
+        os: [ubuntu-latest,windows-latest]
+        python-version: [3.8,3.9]
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    steps:
+    - name: Git clone
+      uses: actions/checkout@v3
+    - name: Set up venv for ci
+      uses: conda-incubator/setup-miniconda@v2
+      with:
+        python-version: ${{matrix.python-version}}
+        channels: default, conda-forge
+    - name: Lint with flake8
+      run: |
+        conda install flake8
+        flake8
+    - name: Test with pytest
+      run: |
+        conda install pytest
+        #pytest
+        echo you should uncomment pytest and delete this line
+    - name: typing with mypy
+      run: |
+        #mypy qolmat
+        echo you should uncomment mypy qolmat and delete this line

.gitignore

@@ -1,16 +1,67 @@
-__pycache__/
-.pyc
-.DS_Store
-.ipynb_checkpoints
+#Ignore Data file
 /data
+
+# Figures
 /figures
 qolmat/notebooks/figures
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+.pyc
+.DS_Store
+.mypy*
+
+
+
+# Distribution / packaging
+
+.Python
+env/
+build/
+develop-eggs/
+dist/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+VERSION
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*,cover
+.hypothesis/
+qolmat/.converge
+
+
+# Notebooks
+**.ipynb_checkpoints
 qolmat/notebooks/*.ipynb
 qolmat/examples/*.ipynb
-*.ipynb
-*.egg-info
-/dist
-/build
-*SOURCES.txt
-TimeSynth*
-/scripts
+
+
+# VSCode
+.vscode

.pre-commit-config.yaml

@@ -16,14 +16,7 @@ repos:
         args:
           - "-l 99"
   # Flake8
-  - repo: https://gitlab.com/pycqa/flake8
+  - repo: https://github.com/PyCQA/flake8
     rev: 4.0.1
     hooks:
       - id: flake8
-        exclude: (tests/)
-        args:
-          - --max-line-length=99
-          - --ignore=E302,E305,W503,E203,E203,E731,E402
-          - --per-file-ignores=
-            - */__init__.py:F401
-            - qolmat/imputations/models.py:F401

.readthedocs.yml

@@ -0,0 +1,18 @@
+version: 2
+
+build:
+  image: latest
+
+python:
+  version: 3.8
+  install:
+    - method: pip
+      path: .
+
+conda:
+  environment: environment.doc.yml
+
+sphinx:
+  builder: html
+  configuration: docs/conf.py
+  fail_on_warning: false

.vscode/settings.json

@@ -48,12 +48,13 @@ On each sample, different imputation models are tested and reconstruction errors
 <img src="docs/images/comparator.png" alt="comparator" width="60%"/>
 </p>
 
-### **Installation**
+### **Installation for conda user**
 
 ```
-conda env create -f conda.yml
-conda activate env_qolmat
+cconda env create -f environment.dev.yml
+conda activate env_qolmat_dev
 ```
+
 ### Install pre-commit
 
 Once the environment is installed, pre-commit is installed, but need to be activated using the following command:

README.md

@@ -1,3 +1,4 @@
+
 ##############################################
 RPCA for anomaly detection and data imputation
 ##############################################
@@ -71,7 +72,7 @@ What’s in this repo?
 
 Some classes are implemented:
 
-* :class:`RPCA` class (see p.29 of this `paper <https://arxiv.org/abs/0912.3599>`__). The optimisation problem is the following
+**RPCA** class based on `RPCA <https://arxiv.org/abs/0912.3599>`_ p.29.
 
 .. math::
 
@@ -80,7 +81,7 @@ Some classes are implemented:
    & \text{s.t.} \quad \mathbf{D} = \mathbf{X} + \mathbf{A}
    \end{align*}
 
-* :class:`GraphRPCA` class (based on this `paper <https://arxiv.org/abs/1507.08173>`__). The optimisation problem is the following
+**GraphRPCA** class based on  `GraphRPCA <https://arxiv.org/abs/1507.08173>`_.
 
 .. math::
 
@@ -89,7 +90,7 @@ Some classes are implemented:
    & \text{s.t.} \quad \mathbf{D} = \mathbf{X} + \mathbf{A}
    \end{align*}
 
-* :class:`TemporalRPCA` class (based on this `paper <https://arxiv.org/abs/2001.05484>`__ and this `paper <https://www.hindawi.com/journals/jat/2018/7191549/>`__). The optimisation problem is the following
+**TemporalRPCA** class based on  `Link 1 <https://arxiv.org/abs/2001.05484>`__ and this `Link 2 <https://www.hindawi.com/journals/jat/2018/7191549/>`__). The optimisation problem is the following
 
 .. math::