Maintenance on test infrastructure (#659)

* make tests a module
This is needed because we want to have a common.py file at the root of the Test folder and the only way to get relative imports working is to make everything a module

* skip tests with mpi
Skip all existing tests under mpi
* mark legacy tests
Skip them by default
* change github actions
* Add SR MPI tests

* fix mpi tests

* simplify sr tests

* fixup!

* fixup!

* document a bit more

* switch to myst_parser instead of recommonmark

recommonmark is now deprecated in favour of myst parser

* Add documentation for contributors

* update README badges

- change the anaconda badge to display last version - - uploaded rather than nothing
- remove travis badge, as we dont use it anymore
- add codecov badge ( i never find the right link)
- remove github issue badget (it's just above there)
[ci skip]

.github/workflows/CI.yml

@@ -1,4 +1,4 @@
-name: Coverage
+name: CI
 
 on:
   pull_request:
@@ -14,9 +14,19 @@ jobs:
       fail-fast: false
       matrix:
         include:
+          - os: ubuntu-latest
+            python-version: 3.8
+            mpi: ""
+            legacy: true
+
           - os: ubuntu-latest
             python-version: 3.8
             mpi: "mpich"
+
+          - os: macos-latest
+            python-version: 3.8
+            mpi: "mpich"
+
           - os: macos-latest
             python-version: 3.8
             mpi: ""
@@ -37,36 +47,41 @@ jobs:
           python-version: ${{ matrix.python-version }}
 
       - name: Install MPI
+        if: matrix.mpi != ''
         run: |
-          sh ./conf/travis-install-mpi.sh mpich
+          sh ./conf/travis-install-mpi.sh ${{ matrix.mpi }}
 
       - name: Get pip cache dir
         id: pip-cache
         run: |
           python -m pip install --upgrade pip
           echo "::set-output name=dir::$(pip cache dir)"
 
-      #- name: pip cache
-      #  uses: actions/cache@v2
-      #  with:
-      #    path: ${{ steps.pip-cache.outputs.dir }}
-      #    key: ${{ runner.os }}-pip-${{ hashFiles('**/setup.py', '**/pyproject.toml') }}
-      #    restore-keys: |
-      #      ${{ runner.os }}-pip-
-
-      - name: Pip install python dependencies
+      - name: Pip install packages
         run: |
           pip install jaxlib
-          pip install -e ".[dev,mpi]"
+          if [ -z "${{ matrix.mpi }}" ]; then
+            pip install -e ".[dev]"
+          else
+            pip install -e ".[dev, mpi]"
+          fi
 
       - name: MPI tests
+        if: matrix.mpi != '' 
         run: |
-          mpirun -host localhost:2 -np 2 coverage run -m pytest -n 0 Test/MPI
+          mpirun -host localhost:2 -np 2 coverage run -m pytest -n 0 Test
 
       - name: Netket tests
+        if: ${{ !matrix.legacy }}
+        run : |
+          export NETKET_EXPERIMENTAL=1
+          pytest --cov=netket --cov-append Test
+
+      - name: Netket Legacy tests
+        if: ${{ matrix.legacy }}
         run : |
           export NETKET_EXPERIMENTAL=1
-          pytest --cov=netket --cov-append
+          pytest --cov=netket --cov-append --legacy-only Test
 
       - name: Upload coverage
         uses: codecov/codecov-action@v1

CONTRIBUTING.md

@@ -1,96 +1,5 @@
 # Contributing guidelines
 
-Thank you for getting involved in NetKet. It is only thanks to the involvement of
-a large community of developers that open-source software like NetKet can thrive.
-Please take the time to read the following guidelines, to ensure that your contributions
-are in line with the general goals of this project and its requirements.  
+Those have been moved to our website. Please visit
 
-## Pull Request Checklist
-
-Before sending your pull requests, make sure you followed this list.
-
-- Read [contributing guidelines](CONTRIBUTING.md).
-- Read [Code of Conduct](CODE_OF_CONDUCT.md).
-- Check if your changes are consistent with the [guidelines](CONTRIBUTING.md#general-guidelines-and-philosophy-for-contribution).
-- Check if your changes are consistent with the [Python](CONTRIBUTING.md#python-coding-style) code style and run the Black code formatter as needed.
-- Run [Unit Tests](CONTRIBUTING.md#running-unit-tests).
-
-## How to become a contributor and submit your own code
-
-### Contributing code
-
-If you have improvements to NetKet, or want to get involved in one of our [Open Issues](https://github.com/netket/netket/issues) send us your pull requests! For those just getting started, Github has a [howto](https://help.github.com/articles/using-pull-requests/).
-
-NetKet team members will be assigned to review your pull requests. Once the pull requests are approved and pass continuous integration checks, we will merge the pull requests.
-
-If you want to contribute but you're not sure where to start, take a look at the
-[issues with the "help wanted" label](https://github.com/netket/netket/labels/help%20wanted).
-These are issues that we believe are particularly well suited for outside
-contributions. If you decide to start on an issue, leave a comment so that other people know that
-you're working on it. If you want to help out, but not alone, use the issue comment thread to coordinate.
-
-### Contribution guidelines and standards
-
-Before sending your pull request for
-[review](https://github.com/netket/netket/pulls),
-make sure your changes are consistent with the guidelines and follow the
-NetKet coding style.
-
-#### General guidelines and philosophy for contribution
-
-* Include unit tests when you contribute new features, as they help to
-  a) prove that your code works correctly, and b) guard against future breaking
-  changes to lower the maintenance cost.
-* Bug fixes also generally require unit tests, because the presence of bugs
-  usually indicates insufficient test coverage.
-* When you contribute a new feature to NetKet, the maintenance burden is (by
-  default) transferred to the NetKet team. This means that benefit of the
-  contribution must be compared against the cost of maintaining the feature.
-
-#### License
-
-Include a license at the top of new files.
-
-#### Python coding style
-
-Python code should follow [PEP 8](https://www.python.org/dev/peps/pep-0008/).
-For consistency, we use the [Black](https://github.com/python/black) code formatter, which you can install in your Python environment using `pip install black`.
-If you edit Python code, you should run Black on the affected files.
-On the command line, this can be done via
-```bash
-# to reformat a specific file
-black Path/To/The/file.py
-# to reformat all files below the specified directories
-black Test/ Examples/
-```
-before creating a pull request.
-There are other options of running Black: For example, an [Atom package](https://atom.io/packages/python-black) is available and Black is integrated into the [VS Code Python extension](https://code.visualstudio.com/docs/python/editing#_formatting).
-
-
-#### Including new unit tests
-
-Contributions implementing new features **must** include associated unit tests.
-Unit tests in NetKet are based on [pytest](https://docs.pytest.org/en/latest/) and are located in the directory `Test`.
-
-#### Running unit tests
-Unit tests can be run locally doing
-
-```bash
-pytest Test --verbose
-```
-
-this will highlight cases where tests are failing. These must be addressed before any pull request can be merged on stable branches.
-
-#### Test MPI code
-
-For code that relies on MPI operations, there are units tests in the `Test_MPI` subfolder.
-If you add MPI-related code, please also add corresponding unit tests to that directory.
-
-The MPI tests can be run with
-```bash
-mpirun -np 2 pytest Test_MPI --verbose
-```
-Note that this will print the test output twice, as `pytest` itself is not aware of being run with MPI.
-Running these tests also provides a quick way to check if your MPI setup is working.
-If `test_is_running_with_multiple_procs` or `test_mpi_setup` is failing, you should check your MPI configuration,
-for example whether `mpi4py` is compiled against the correct MPI libraries for your machine.
+https://www.netket.org/docs/contributing.html

README.md

@@ -5,13 +5,12 @@
 # __NetKet__
 
 [![Release](https://img.shields.io/github/release/netket/netket.svg)](https://github.com/netket/netket/releases)
-[![Anaconda-Server Badge](https://anaconda.org/conda-forge/netket/badges/installer/conda.svg)](https://conda.anaconda.org/conda-forge)
-[![Build Status](https://travis-ci.org/netket/netket.svg?branch=master)](https://travis-ci.org/netket/netket)
-[![GitHub Issues](https://img.shields.io/github/issues/netket/netket.svg)](http://github.com/netket/netket/issues)
+[![Anaconda-Server Badge](https://anaconda.org/conda-forge/netket/badges/version.svg)](https://anaconda.org/conda-forge/netket)
 [![Paper](https://img.shields.io/badge/paper-SoftwareX%2010%2C%20100311%20(2019)-B31B1B)](https://doi.org/10.1016/j.softx.2019.100311)
 [![License](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](https://opensource.org/licenses/Apache-2.0)
 [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/netket/netket/v.2.0)
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
+[![codecov](https://codecov.io/gh/netket/netket/branch/master/graph/badge.svg?token=gzcOlpO5lB)](https://codecov.io/gh/netket/netket)
 
 NetKet is an open-source project delivering cutting-edge methods for the study
 of many-body quantum systems with artificial neural networks and machine learning techniques.

Test/Graph/test_graph.py

@@ -1,3 +1,5 @@
+import pytest
+
 import netket as nk
 import networkx as nx
 import math
@@ -6,7 +8,9 @@
 
 from netket.graph import *
 
-import pytest
+from .. import common
+
+pytestmark = common.skipif_mpi
 
 nxg = nx.star_graph(10)
 graphs = [

Test/GroundState/test_vmc.py

@@ -13,6 +13,10 @@
 import tempfile
 import re
 
+from .. import common
+
+pytestmark = common.skipif_mpi
+
 SEED = 214748364
 
 

Test/Hilbert/test_hilbert.py

@@ -22,6 +22,10 @@
 import jax
 from jax import numpy as jnp
 
+from .. import common
+
+pytestmark = common.skipif_mpi
+
 hilberts = {}
 
 # Spin 1/2
@@ -83,7 +87,6 @@
 
 # hilberts["Tensor: Spin x Fock"] = Spin(s=0.5, N=4) * Fock(4, N=2)
 
-
 #
 # Tests
 #

Test/Legacy/Callbacks/test_callbacks.py

@@ -1,6 +1,10 @@
 import netket.legacy as nk
 import time
 
+import pytest
+
+pytestmark = pytest.mark.legacy
+
 SEED = 3141592
 L = 8
 

Test/Legacy/Dynamics/test_dynamics.py

@@ -6,6 +6,9 @@
 import netket.legacy as nk
 from netket.exact import PyExactTimePropagation
 
+import pytest
+
+pytestmark = pytest.mark.legacy
 
 ATOL = 1e-9
 RTOL = 1e-9

Test/Legacy/GroundState/test_legacy_groundstate.py

@@ -5,6 +5,10 @@
 import shutil
 import tempfile
 
+import pytest
+
+pytestmark = pytest.mark.legacy
+
 
 SEED = 3141592
 

Test/Legacy/GroundState/test_legacy_vmc.py

@@ -9,6 +9,10 @@
 import tempfile
 import re
 
+import pytest
+
+pytestmark = pytest.mark.legacy
+
 SEED = 214748364
 nk.random.seed(SEED)