Updating main to version 0.2 (#75)

* Backendbuddy (#60)

- agnostic_simulator source code now moved under qsdk submodule "backendbuddy"
- qsdk installation changed to reflect better these changes (simulators are now optional dependencies)
- Simulator class uses now a default simulator: qulacs if found, Cirq otherwise (Cirq always installed as a dependency with openfermion). This enables Mac users to be able to run tests properly, despite qulacs not installing for them.

* Backendbuddy qsdk examples moved (#62)
* agnostic simulator removed, top level of repo cleared (#65)
* qsdk reorg (helpers and "algorithms" folders), updated install (#69)
* Simplified the readme, added placeholder for citations and other upcoming things (#71)
* License: adding blob to all python files (#73)
* Forcing DMET energy to be real.
* Fixing verbose output for DMET and ONIOM get_resources method.
* minor-test-improvements (#70)


Co-authored-by: Valentin Senicourt <valentinsenicourt@Valentins-MacBook-Pro.local>
Co-authored-by: AlexandreF-1qbit <76115575+AlexandreF-1qbit@users.noreply.github.com>
Co-authored-by: JamesB-1qbit <84878946+JamesB-1qbit@users.noreply.github.com>

.github/workflows/github_actions_automated_testing.yml

@@ -24,15 +24,15 @@ jobs:
         pip install pytest-cov 
         pip install jupyter
 
-    - name: Install backends except qsharp (see next section)
+    - name: Install backends except qsharp/qdk
       run: |
         pip install qiskit
         pip install qulacs
         pip install amazon-braket-sdk
         pip install cirq
         pip install projectq
 
-    - name: Microsoft qsharp
+    - name: Install Microsoft qsharp/qdk
       run: |
         wget https://packages.microsoft.com/config/ubuntu/20.04/packages-microsoft-prod.deb -O packages-microsoft-prod.deb
         sudo dpkg -i packages-microsoft-prod.deb
@@ -42,26 +42,20 @@ jobs:
         dotnet tool install -g Microsoft.Quantum.IQSharp
         $(which dotnet-iqsharp) install --user
         pip install qsharp
-      
-    - name: agnostic_simulator install
-      run: |
-        cd agnostic_simulator
-        python setup.py install
-    
-    - name: agnostic_simulator tests
-      run: |
-        cd agnostic_simulator
-        pytest tests --doctest-modules --junitxml=junit/test-results.xml --cov=com --cov-report=xml --cov-report=html
 
     - name: qsdk install
       run: |
-        pip install pyscf
-        cd qsdk
         python setup.py install
       if: always()
-        
+
     - name: qsdk tests
       run: |
-        cd qsdk/qsdk
+        cd qsdk
         pytest --doctest-modules --junitxml=junit/test-results.xml --cov=com --cov-report=xml --cov-report=html
       if: always()
+
+    - name: qsdk notebooks as tests
+      run: |
+        cd examples
+        pytest --doctest-modules --junitxml=junit/test-results.xml --cov=com --cov-report=xml --cov-report=html test_notebooks.py
+      if: always()

Dockerfile

@@ -0,0 +1,42 @@
+FROM fedora:30
+
+RUN dnf -y update
+RUN dnf -y install wget libgomp openblas-devel pandoc
+RUN dnf clean all
+
+# Python, C/C++ compilers, git
+RUN dnf -y install gcc redhat-rpm-config gcc-c++ python3-devel make cmake git
+
+# Set up a virtual environment, set all calls to pip3 and python3 to use it
+RUN pip3 install virtualenv
+ENV VIRTUAL_ENV=/root/env
+RUN virtualenv -p python3 $VIRTUAL_ENV
+ENV PATH="$VIRTUAL_ENV/bin:$PATH"
+RUN ls -al /root/.bashrc
+RUN more /root/.bashrc
+RUN echo "export PATH=$PATH" >> /root/.bashrc
+
+# Python packages for documentation, Jupyter notebook support and visualization
+RUN pip3 install --upgrade pip
+RUN pip3 install h5py==2.9.0 ipython jupyter setuptools wheel sphinx py3Dmol sphinx_rtd_theme nbsphinx scikit-build
+
+# Copy and set root directory,
+ENV PYTHONPATH=/root/qsdk:$PYTHONPATH
+WORKDIR /root/
+COPY . /root
+
+# Install qSDK and its immediate dependencies (pyscf, openfermion, ...)
+RUN python3 /root/setup.py install
+
+# Install Microsoft QDK qsharp package
+WORKDIR /tmp/
+RUN dnf clean all
+RUN rpm --import https://packages.microsoft.com/keys/microsoft.asc
+RUN wget -q -O /etc/yum.repos.d/microsoft-prod.repo https://packages.microsoft.com/config/fedora/30/prod.repo
+RUN dnf install -y dotnet-sdk-3.1
+RUN dotnet tool install -g Microsoft.Quantum.IQSharp
+RUN /root/.dotnet/tools/dotnet-iqsharp install --user
+RUN pip3 install qsharp
+
+# Install other simulators
+RUN pip install amazon-braket-sdk qiskit qulacs projectq

LICENSE

@@ -0,0 +1,14 @@
+# Copyright 2021 1QB Information Technologies Inc.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#   http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+

README.md

@@ -1,19 +1,92 @@
-# QEMIST_qSDK contents
-
-This repository contains two separate packages, called `qSDK` and `agnostic_simulator`.
-Despite living in the same repository, these two packages are different entities. Their respective code, documentation,
-tutorials, and installation instructions are contained in their own dedicated folder. Please refer to them.
-
-- `qSDK` provides access to the tools developed for quantum chemistry simulation on quantum computers and emulators. 
-The package provides access to some problem decomposition techniques, electronic structure solvers, as well as the
-various toolboxes containing the functionalities necessary to build these workflows, or your own.
-It was developed to be compatible with QEMIST Cloud, to seamlessly enable the use of large scale problem decomposition
-combined with both classical and quantum electronic structure solvers in the cloud. The package also provides local
-problem decomposition techniques, and is designed to support the output of a problem decomposition method performed
-through QEMIST Cloud as well.
-
-- `agnostic_simulator` can be thought to be a quantum circuit simulation engine, allowing users to target a variety
-of compute backends (QPUs and simulators) available on their local machine or through cloud services. In itself,
-  it has nothing to do with quantum chemistry, and thus has a wide range of applicability. `qSDK` relies on `agnostic_simulator`
-  for quantum circuit simulation, and requires that this package is installed.
-
+# QEMIST_qSDK
+
+Welcome !
+This open-source quantum SDK provides tools developed for exploring quantum chemistry simulation end-to-end workflows on 
+both gate-model quantum computers and quantum circuit emulators.
+
+It was designed to support the development of quantum algorithms and workflows running by providing building-blocks from various toolboxes.
+It attempts to cover all steps of the process, such as quantum execution, pre- and post-processing techniques, including problem decomposition.
+It provides users with features such as resource estimation, access to various compute backends (noiseless and noisy simulators, 
+quantum devices) and some classical solvers in order to keep track of both accuracy and resource requirements of our workflows,
+and facilitate the design of successful hardware experiments.
+
+## Install
+
+This package requires a Python 3 environment.
+
+We recommend:
+- using [Python virtual environments](https://docs.python.org/3/tutorial/venv.html) in order to set up your environment safely and cleanly
+- installing the "dev" version of Python3 if you encounter missing header errors such as `python.h file not found`.
+- having good C/C++ compilers and BLAS library to ensure the quantum circuit simulators you choose to install have good performance.
+
+### Using pip
+
+TODO: once this package is available on pypi, give the command.
+
+### From source, using setuptools
+
+This package can be installed by first cloning this repository with `git clone`, and typing the following command in the
+root directory:
+```
+python setup.py install
+```
+
+If the installation of a dependency fails and the reason is not obvious, we suggest installing that dependency
+separately with `pip`, before trying again.
+
+If you would like to modify or develop code in `qSDK`, you can add the path to this folder to your `PYTHONPATH` 
+environment variable instead of installing it with pip: 
+```
+export PYTHONPATH=<path_to_this_folder>:$PYTHONPATH
+```
+
+### Optional dependencies
+
+qSDK enables users to target various backends. In particular, it integrates quantum circuit  simulators such as 
+`qulacs`, `qiskit`, `cirq` or `qdk`. We leave it to you to install the packages of your choice.
+Backends such as `qulacs` and `cirq` show good overall performance. Most packages can be installed through pip in a straightforward way:
+```
+pip install qulacs
+pip install qiskit
+pip install cirq
+...
+```
+
+Depending on your OS and environment, some of these packages may be more challenging to install. For installing Microsoft's QDK 
+or any issue regarding the above packages, please check their respective documentation.
+
+### Optional: environment variables
+
+Some environment variables can impact performance (ex: using GPU for quantum circuit simulation, or changing
+the number of CPU threads used) or are used to connect to web services providing access to some compute backends.
+
+See the list of relevant environment variables and their use in `env_var.sh`. In order for these variables to be set to
+the desired values in your environment, you can run this shell script in Linux with the following command line:
+`source env_var.sh` (you may need to set execution permissions with `chmod +x set_env_var.sh` first), or you can set
+them in whatever way your OS supports it, or even inside your python script using the `os` package.
+
+## Docs 
+
+TODO: insert sentence and link to sphinx documentation when its online.
+
+## Tutorials
+
+Please check the `examples` folder jupyter notebook tutorials and other examples.
+TODO: recommend here the one we are doing about the DMET paper once its ready and merged
+
+## Tests
+
+Unit tests can be found in the `tests` folders, located in the various toolboxes they are related to. To automatically
+find and run all tests (assuming you are in the `qsdk` subfolder that contains the code of the package):
+
+```
+python -m unittest
+```
+
+## Citations
+
+If you use qSDK in your research, please cite
+
+[TODO: this is a placeholder for our qSDK paper, to be written and put on arxiv in October]
+
+Copyright 1QBit 2021. This software is released under the Apache Software License version 2.0.

_config.yml

@@ -1 +1 @@
-theme: jekyll-theme-cayman
+theme: jekyll-theme-cayman