Fix pipit docs and add tests

.github/workflows/ci.yml

@@ -1,4 +1,4 @@
 name: UIPS-CI
 
 on:
    push:
@@ -7,20 +7,48 @@
         - '*.md'
         - 'README*'
         - 'LICENSE'
+        - 'documentation/readmeImages/*'
    pull_request:
      branches: [main]
      paths-ignore:
         - '*.md'
         - 'README*'
         - 'LICENSE'
+        - 'documentation/readmeImages/*'
 
 jobs:
-  UIPS:
+  Lint:
+    name: Lint (${{ matrix.python-version }}, ${{ matrix.os }})
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
       matrix:
         python-version: ['3.10']
+        os: ['ubuntu-latest']
+    defaults:
+      run:
+        working-directory: ${{github.workspace}}
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with:
+          python-version: ${{matrix.python-version}}
+      - name: Install dependencies
+        run: |
+          pip install black
+          pip install isort
+          pip install codespell
+      - name: Formatting and sorting import
+        run: |
+          source .github/linters/formatting.sh
+          format . true
+  Test:
+    name: Test (${{ matrix.python-version }}, ${{ matrix.os }})
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ['3.10', '3.11', '3.12']
         mpi: ['openmpi']
     defaults:
       run:
@@ -40,15 +68,7 @@
         run: |
           python -m pip install --upgrade pip
           python -m pip install .
-          pip install black
-          pip install isort
-          pip install codespell
           pip install pytest 
-      - name: Formatting
-        run: |
-          source .github/linters/formatting.sh
-          format . true
-          codespell
       - name: Pytests
         run: |
           python -m pytest tests -v --disable-warnings

README.md

@@ -1,4 +1,4 @@
-# Phase-space sampling of large datasets [![UIPS-CI](https://github.com/NREL/Phase-space-sampling/actions/workflows/ci.yml/badge.svg)](https://github.com/NREL/Phase-space-sampling/actions/workflows/ci.yml) [![UIPS-pypi](https://badge.fury.io/py/uips.svg)](https://badge.fury.io/py/uips) 
+# Phase-space sampling of large datasets [![UIPS-CI](https://github.com/NREL/Phase-space-sampling/actions/workflows/ci.yml/badge.svg)](https://github.com/NREL/Phase-space-sampling/actions/workflows/ci.yml) [![UIPS-pyversion](https://img.shields.io/pypi/pyversions/uips.svg)](https://pypi.org/project/uips/) [![UIPS-pypi](https://badge.fury.io/py/uips.svg)](https://badge.fury.io/py/uips) 
 
 ## Installation for NREL HPC users
 1. `module load openmpi/4.1.0/gcc-8.4.0`
@@ -123,22 +123,22 @@ A script is provided to visualize the losses. Execute `python plotLoss.py -i inp
 Suppose one wants to downsample an dataset where $N=10^7$ and $d=2$. First, the code estimates the probability map of the data in order to identify where are located redundant data points. An example dataset (left) and associated probability map (right) are shown below
 
 <p float="left">
-  <img src="documentation/readmeImages/fulldataset.png" width="350"/>
-  <img src="documentation/readmeImages/probabilityMap.png" width="350"/>
+  <img src="https://raw.githubusercontent.com/NREL/Phase-space-sampling/main/documentation/readmeImages/fulldataset.png" width="350"/>
+  <img src="https://raw.githubusercontent.com/NREL/Phase-space-sampling/main/documentation/readmeImages/probabilityMap.png" width="350"/>
 </p>
 
 Next, the code uses the probability map to define a sampling probability which downselect samples that uniformly span the feature space. The probability map is obtained by training a Neural Spline Flow which implementation was obtained from [Neural Spline Flow repository](https://github.com/bayesiains/nsf). The number of samples in the final dataset can be controlled via the input file.
 
 <p float="left">
-  <img src="documentation/readmeImages/103_uips.png" width="350"/> 
-  <img src="documentation/readmeImages/104_uips.png" width="350"/>
+  <img src="https://raw.githubusercontent.com/NREL/Phase-space-sampling/main/documentation/readmeImages/103_uips.png" width="350"/> 
+  <img src="https://raw.githubusercontent.com/NREL/Phase-space-sampling/main/documentation/readmeImages/104_uips.png" width="350"/>
 </p>
 
 For comparison, a random sampling gives the following result
 
 <p float="left">
-  <img src="documentation/readmeImages/103_randomSampling.png" width="350"/> 
-  <img src="documentation/readmeImages/104_randomSampling.png" width="350"/>
+  <img src="https://raw.githubusercontent.com/NREL/Phase-space-sampling/main/documentation/readmeImages/103_randomSampling.png" width="350"/> 
+  <img src="https://raw.githubusercontent.com/NREL/Phase-space-sampling/main/documentation/readmeImages/104_randomSampling.png" width="350"/>
 </p>
 
 ## Example 11D

requirements.txt

@@ -1,6 +1,5 @@
-openmpi
 torch
 numpy
 mpi4py
 scikit-learn
-prettyPlot>=0.0.25
+prettyPlot>=0.0.27

setup.py

@@ -1,9 +1,26 @@
+import os
+
 from setuptools import setup
 
+here = os.path.abspath(os.path.dirname(__file__))
+
+with open(os.path.join(here, "requirements.txt")) as f:
+    install_requires = f.readlines()
+
+with open(os.path.join(here, "README.md"), encoding="utf-8") as f:
+    readme = f.read()
+
+with open(os.path.join(here, "uips", "version.py"), encoding="utf-8") as f:
+    version = f.read()
+version = version.split("=")[-1].strip().strip('"').strip("'")
+
+
 setup(
     name="uips",
-    version="0.1.0",
+    version=version,
     description="Reduce a large and high-dimensional dataset by downselecting data uniformly in phase space",
+    long_description=readme,
+    long_description_content_type="text/markdown",
     url="https://github.com/NREL/Phase-space-sampling",
     author="Malik Hassanaly",
     license="BSD 3-Clause",
@@ -13,15 +30,11 @@
         "License :: OSI Approved :: BSD License",
         "Natural Language :: English",
         "Programming Language :: Python :: 3.10",
+        "Programming Language :: Python :: 3.11",
+        "Programming Language :: Python :: 3.12",
     ],
     package_data={"": ["input2D", "input2D_bins"]},
     include_package_data=True,
     python_requires=">=3.10",
-    install_requires=[
-        "torch",
-        "numpy",
-        "mpi4py",
-        "scikit-learn",
-        "prettyPlot>=0.0.25",
-    ],
+    install_requires=install_requires,
 )

uips/version.py

@@ -1,3 +1,3 @@
 """UIPS version"""
 
-__version__ = "0.1.0"
+__version__ = "0.1.1"