Bring qchem inside pennylane (#2420)

.github/workflows/docs.yml

@@ -11,5 +11,5 @@ jobs:
       with:
         docs-folder: "doc/"
         repo-token: "${{ secrets.GITHUB_TOKEN }}"
-        pre-build-command: "apt install -y graphviz && pip3 install -r doc/requirements.txt && pip3 install . && pip3 install -r qchem/requirements.txt && pip3 install ./qchem"
+        pre-build-command: "apt install -y graphviz && pip3 install -r doc/requirements.txt && pip3 install . pip3 install openfermionpyscf"
         build-command: "sphinx-build -b html . _build -W --keep-going"

.github/workflows/format.yml

@@ -26,4 +26,3 @@ jobs:
         run: |
           black -l 100 pennylane/ --check
           black -l 100 tests/ --check
-          black -l 100 qchem/ --check

.github/workflows/tests.yml

@@ -25,6 +25,7 @@ jobs:
           - {python-version: 3.9, interfaces: []}
           - {python-version: '3.10', interfaces: []}
 
+
     steps:
       - name: Cancel Previous Runs
         uses: styfle/cancel-workflow-action@0.4.1
@@ -46,6 +47,10 @@ jobs:
           pip install -r requirements-ci.txt
           pip install wheel pytest pytest-cov pytest-mock flaky --upgrade
 
+      - name: Conditionally install openfermionpyscf
+        if: contains(' 3.9', matrix.config.python-version)
+        run: pip3 install openfermionpyscf
+
       - name: Conditionally install PyTorch
         if: contains(matrix.config.interfaces, 'torch')
         run: pip3 install torch==$TORCH_VERSION -f https://download.pytorch.org/whl/torch_stable.html
@@ -148,54 +153,4 @@ jobs:
       - name: Upload coverage to Codecov
         uses: codecov/codecov-action@v3
         with:
-          file: ./coverage.xml
-
-
-  qchem-tests:
-    runs-on: ubuntu-latest
-
-    steps:
-      - name: Cancel Previous Runs
-        uses: styfle/cancel-workflow-action@0.4.1
-        with:
-          access_token: ${{ github.token }}
-
-      - uses: actions/checkout@v2
-        with:
-          fetch-depth: 2
-
-      - name: Setup conda
-        uses: s-weigand/setup-conda@v1
-        with:
-          activate-conda: true
-          python-version: 3.7
-          conda-channels: anaconda, conda-forge
-
-      - name: Install dependencies
-        run: |
-          conda install psi4 psi4-rt python=3.7 -c psi4
-          pip uninstall h5py -y
-          pip install pytest pytest-cov pytest-mock flaky h5py==3.2.1
-
-      - name: Install QChem
-        run: |
-          pip install -r requirements-ci.txt
-          python setup.py bdist_wheel
-          pip install dist/PennyLane*.whl
-          cd qchem && python setup.py bdist_wheel && cd ../
-          pip install qchem/dist/PennyLane_Qchem*.whl
-
-      - name: Run tests
-        run: |
-          python -m pytest tests/hf --cov=pennylane $COVERAGE_FLAGS
-          cd qchem && python -m pytest tests --cov=pennylane_qchem $COVERAGE_FLAGS
-
-      - name: Upload HF coverage to Codecov
-        uses: codecov/codecov-action@v3
-        with:
-          file: ./coverage.xml
-
-      - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v3
-        with:
-          file: ./qchem/coverage.xml
+          file: ./coverage.xml

.gitignore

@@ -18,14 +18,6 @@ doc/code/api/*
 !doc/_static/code.png
 *.DS_Store
 /.vscode/*
-pennylane_qchem/build/*
-pennylane_qchem/dist/*
-pennylane_qchem/.pytest_cache/*
-qchem/tmp/*
-qchem/timer.dat
-qchem/tests/tmp/*
-qchem/tests/qchem_tests/tmp/*
-qchem/tests/tmp/timer.dat
 timer.dat
 tmp/*
 benchmark/revisions/

.readthedocs.yml

@@ -22,11 +22,8 @@ python:
   version: 3.8
   install:
     - requirements: doc/requirements.txt
-    - requirements: qchem/requirements.txt
     - method: pip
       path: .
-    - method: pip
-      path: qchem
 
 build:
   image: latest

Makefile

@@ -46,7 +46,6 @@ clean:
 	rm -rf .coverage coverage_html_report/
 	rm -rf tmp
 	rm -rf *.dat
-	make -C qchem clean
 
 docs:
 	make -C doc html

codecov.yml

@@ -1,12 +1,9 @@
-fixes:
-  - "pennylane_qchem/::qchem/pennylane_qchem/"
-
 ignore:
   - "pennylane/devices/tests/*"
 
 codecov:
   notify:
-    after_n_builds: 10
+    after_n_builds: 9
 
 comment:
-  after_n_builds: 10
+  after_n_builds: 9

doc/code/qml_qchem.rst

@@ -3,18 +3,9 @@ qml.qchem
 
 The PennyLane quantum chemistry library.
 
-.. note::
-
-    To access the ``qml.qchem`` package, ``pennylane-qchem`` must be installed
-    via pip:
-
-    .. code-block:: bash
-
-        pip install pennylane-qchem
-
 .. currentmodule:: pennylane.qchem
 
-.. automodapi:: pennylane_qchem.qchem
+.. automodapi:: pennylane.qchem
     :no-heading:
     :include-all-objects:
     :no-inheritance-diagram:

doc/conf.py

@@ -91,31 +91,6 @@
 
 import pennylane
 
-try:
-    import pennylane_qchem
-except ImportError:
-    from unittest.mock import MagicMock
-
-    class Mock(MagicMock):
-        __name__ = 'foo'
-        __repr__ = lambda self: __name__
-
-        @classmethod
-        def __getattr__(cls, name):
-            return MagicMock()
-
-    MOCK_MODULES = [
-        'pennylane_qchem',
-        'pennylane_qchem.qchem',
-        ]
-
-    mock_fn = Mock(__name__='foo')
-    mock_fns = {"__all__": list(), "__dir__": list(), "__dict__": dict()}
-
-    mock = Mock(**mock_fns)
-    for mod_name in MOCK_MODULES:
-        sys.modules[mod_name] = mock
-
 # The full version, including alpha/beta/rc tags.
 release = pennylane.__version__
 

doc/development/guide/documentation.rst

@@ -509,8 +509,7 @@ the following additional packages are required:
 In addition, some pages in the documentation have additional dependencies:
 
 * The latest version of PyTorch and TensorFlow are required to build the interface documentation,
-* The latest version of TensorNetwork is required to build the ``default.tensor`` documentation, and
-* PennyLane-QChem must be installed to build the quantum chemistry documentation.
+* The latest version of TensorNetwork is required to build the ``default.tensor`` documentation.
 
 These can all be installed via ``pip``:
 

doc/development/guide/installation.rst

@@ -87,12 +87,6 @@ using development mode:
     cd pennylane
     pip install -e .
 
-If also developing for the QChem package, this will need to installed as well:
-
-.. code-block:: bash
-
-    pip install -e qchem
-
 The ``-e`` flag ensures that edits to the source code will be reflected when
 importing PennyLane in Python.
 
@@ -155,25 +149,3 @@ Build a PennyLane image with a plugin
   .. code-block:: bash
 
     make -f docker/Makefile build-plugin plugin-name=qiskit
-
-Build a PennyLane-Qchem image
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-- You can also build an image with the PennyLane Qchem package and its
-  dependencies. Use the following commands:
-
-  .. code-block:: bash
-
-    make -f docker/Makefile build-qchem
-
-- To check all available interfaces, run the following:
-
-  .. code-block:: bash
-
-    make -f docker/Makefile available-interfaces
-
-- To check all available plugins, run the following:
-
-  .. code-block:: bash
-
-    make -f docker/Makefile available-plugins

doc/introduction/chemistry.rst

@@ -1,23 +1,15 @@
 Quantum Chemistry
 =================
 
-PennyLane provides a differentiable Hartree-Fock solver module :mod:`~.hf` and a quantum chemistry
-module :mod:`~.qchem` to perform quantum simulations of the electronic structure of molecules. These
-modules contain tools to construct the electronic Hamiltonian of molecules that can be used to
-implement the Variational Quantum Eigensolver (VQE) algorithm.
+PennyLane provides a differentiable Hartree-Fock solver module :mod:`~.qchem` to perform quantum
+simulations of the electronic structure of molecules. This module contain tools to construct the
+electronic Hamiltonian of molecules that can be used to implement the Variational Quantum
+Eigensolver (VQE) algorithm.
 
 .. figure:: ../_static/sketch_pennylane_qchem.png
     :width: 80%
     :align: center
 
-.. note::
-
-    To access the ``qchem`` module, the ``PennyLane-QChem`` plugin must be installed separately:
-
-    .. code-block::
-
-        pip install pennylane-qchem
-
 Building the electronic Hamiltonian
 -----------------------------------
 
@@ -49,7 +41,7 @@ where:
 Internally, :func:`~.molecular_hamiltonian` calls the following functions in order
 to generate the qubit Hamiltonian:
 
-.. currentmodule:: pennylane_qchem.qchem
+.. currentmodule:: pennylane.qchem
 
 .. autosummary::
 
@@ -88,7 +80,8 @@ using the electronic structure packages `PySCF <https://github.com/sunqm/pyscf>`
 <http://psicode.org/>`_, respectively.
 
 For this, it is required to specify a string to label the molecule. Furthermore, the net charge,
-the `spin multiplicity <https://en.wikipedia.org/wiki/Multiplicity_(chemistry)>`_ and the  `atomic basis functions <https://www.basissetexchange.org/>`_ can also be specified.
+the `spin multiplicity <https://en.wikipedia.org/wiki/Multiplicity_(chemistry)>`_ and the
+`atomic basis functions <https://www.basissetexchange.org/>`_ can also be specified.
 
 .. code-block:: python
 
@@ -111,7 +104,8 @@ Mapping the Hamiltonian to the Pauli basis
 
 The function :func:`~.active_space` is used to create an `active space <https://en.wikipedia
 .org/wiki/Complete_active_space>`__  by classifying the Hartree-Fock molecular orbitals as
-core, active, and external orbitals. Within this approximation, a certain number of *active electrons* can populate the *active orbitals*.
+core, active, and external orbitals. Within this approximation, a certain number of
+*active electrons* can populate the *active orbitals*.
 
 .. code-block:: python
 
@@ -140,7 +134,8 @@ and map it to a linear combination of Pauli operators via the `Jordan-Wigner
         active=active
     )
 
-Here, ``qubit_hamiltonian`` is an instance of the QubitOperator class of `OpenFermion <https://github.com/quantumlib/OpenFermion>`_.
+Here, ``qubit_hamiltonian`` is an instance of the QubitOperator class of
+`OpenFermion <https://github.com/quantumlib/OpenFermion>`_.
 
 .. _pl_qchem_vqe:
 

doc/requirements.txt

@@ -22,3 +22,5 @@ toml
 torch==1.9.0+cpu
 torchvision==0.10.0+cpu
 jinja2==3.0.3
+retworkx==0.10.2
+networkx==2.6

docker/Makefile

@@ -4,7 +4,6 @@
 help:
 	@echo "Makefile commands:"
 	@echo "build-base"
-	@echo "build-qchem"
 	@echo "build-interface"
 	@echo "build-interface-gpu"
 
@@ -20,10 +19,6 @@ available-plugins:
 build-base:
 	@docker build -t pennylane/base -f docker/pennylane.dockerfile .
 
-build-qchem:
-	@docker build -t pennylane/base -f docker/pennylane.dockerfile . \
-	&& docker build -t pennylane/qchem -f docker/qchem.dockerfile .
-
 build-interface:
 	@docker build -t pennylane/base -f docker/pennylane.dockerfile . \
 	&& docker build -t pennylane/$(interface-name) -f docker/interfaces/build_interface.dockerfile \

docker/pennylane.dockerfile

@@ -44,6 +44,7 @@ RUN git submodule update --init --recursive \
     && python3 setup.py install \
     && pip install pytest pytest-cov pytest-mock flaky \
     && pip install -i https://test.pypi.org/simple/ pennylane-lightning --pre --upgrade \
+    && pip install openfermionpyscf \
     && make test && make coverage
 
 # create Second small build.