From 5683a77db67a38db615fba06ad89eeeace229ec2 Mon Sep 17 00:00:00 2001
From: Peter Karalekas <peter@rigetti.com>
Date: Tue, 28 May 2019 15:32:35 -0700
Subject: [PATCH 1/9] Remove .coveragerc file as we're not testing coverage
 anymore

---
 .coveragerc | 2 --
 1 file changed, 2 deletions(-)
 delete mode 100644 .coveragerc

diff --git a/.coveragerc b/.coveragerc
deleted file mode 100644
index d1c6592..0000000
--- a/.coveragerc
+++ /dev/null
@@ -1,2 +0,0 @@
-[run]
-omit = forestopenfermion/*_test.py
\ No newline at end of file

From 023b031bd8e425127829132bd0e0afa0cb63678a Mon Sep 17 00:00:00 2001
From: Peter Karalekas <peter@rigetti.com>
Date: Tue, 28 May 2019 15:33:09 -0700
Subject: [PATCH 2/9] Add GitLab CI YAML file for an additional CI pipeline

---
 .gitlab-ci.yml | 8 ++++++++
 1 file changed, 8 insertions(+)
 create mode 100644 .gitlab-ci.yml

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
new file mode 100644
index 0000000..2d24cbf
--- /dev/null
+++ b/.gitlab-ci.yml
@@ -0,0 +1,8 @@
+image: python:3.6
+
+test:
+  tags:
+    - github
+  script:
+    - pip install -r requirements.txt
+    - pytest

From 8f886a48006166b663309b6939e3958e54fc8144 Mon Sep 17 00:00:00 2001
From: Peter Karalekas <peter@rigetti.com>
Date: Tue, 28 May 2019 15:56:37 -0700
Subject: [PATCH 3/9] Rename PyPI package to forest-openfermion

---
 README.md | 4 ++--
 setup.py  | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/README.md b/README.md
index 25f65f2..066c505 100644
--- a/README.md
+++ b/README.md
@@ -1,7 +1,7 @@
 The Rigetti Forest Plugin for OpenFermion
 =========================================
 
-[![Build Status](https://semaphoreci.com/api/v1/rigetti/forestopenfermion/branches/master/shields_badge.svg)](https://semaphoreci.com/rigetti/forestopenfermion)
+[![Build Status](https://semaphoreci.com/api/v1/rigetti/forest-openfermion/branches/master/shields_badge.svg)](https://semaphoreci.com/rigetti/forest-openfermion)
 
 [OpenFermion](http://openfermion.org>) is an open source package for compiling and analyzing
 quantum algorithms that simulate fermionic systems. This plugin library allows the circuit
@@ -20,7 +20,7 @@ pip install -e .
 Alternatively, one can install the last major release from PyPI via:
 
 ```bash
-pip install forestopenfermion
+pip install forest-openfermion
 ```
 
 Development and Testing
diff --git a/setup.py b/setup.py
index 0af2d04..64bce7c 100755
--- a/setup.py
+++ b/setup.py
@@ -19,7 +19,7 @@
 from setuptools import setup
 
 if sys.version_info < (3, 6):
-    raise ImportError('The forestopenfermion library requires Python 3.6 or above.')
+    raise ImportError('The forest-openfermion library requires Python 3.6 or above.')
 
 with open('README.md', 'r') as f:
     long_description = f.read()
@@ -36,7 +36,7 @@
     f.write(f'__version__ = \'{__version__}\'\n')
 
 setup(
-    name='forestopenfermion',
+    name='forest-openfermion',
     version=__version__,
     author='Rigetti Computing',
     author_email='software@rigetti.com',

From b3a29899f0813b5652b928d74ac475bd6b983713 Mon Sep 17 00:00:00 2001
From: Peter Karalekas <peter@rigetti.com>
Date: Tue, 28 May 2019 16:02:04 -0700
Subject: [PATCH 4/9] Add note about the archiving of the repository

---
 README.md | 12 ++++++++----
 1 file changed, 8 insertions(+), 4 deletions(-)

diff --git a/README.md b/README.md
index 066c505..9077553 100644
--- a/README.md
+++ b/README.md
@@ -1,11 +1,16 @@
 The Rigetti Forest Plugin for OpenFermion
 =========================================
 
+> **NOTE**: This repository is not being actively developed at Rigetti, and therefore we have
+decided to archive it. It should work in its current state, but if you find issues or would like
+to suggest that we re-open development on this project (or, even better, if you would like to
+develop it!) please send us an email at [software@rigetti.com](mailto:software@rigetti.com).
+
 [![Build Status](https://semaphoreci.com/api/v1/rigetti/forest-openfermion/branches/master/shields_badge.svg)](https://semaphoreci.com/rigetti/forest-openfermion)
 
-[OpenFermion](http://openfermion.org>) is an open source package for compiling and analyzing
+[OpenFermion](http://openfermion.org) is an open-source package for compiling and analyzing
 quantum algorithms that simulate fermionic systems. This plugin library allows the circuit
-construction and simulation environment [Forest](http://www.rigetti.com/forest>) to
+construction and simulation environment [Forest](http://www.rigetti.com/forest) to
 interface with OpenFermion.
 
 Getting Started
@@ -26,8 +31,7 @@ pip install forest-openfermion
 Development and Testing
 -----------------------
 
-We use `pytest` for testing. Tests can be executed from the top-level
-directory by simply running:
+Tests can be executed from the top-level directory by simply running:
 
 ```bash
 pytest

From ce845d30db814ed612ec8b83288cb209915988bd Mon Sep 17 00:00:00 2001
From: Peter Karalekas <peter@rigetti.com>
Date: Tue, 28 May 2019 17:13:59 -0700
Subject: [PATCH 5/9] Change the module structure from forestopenfermion to
 forest.openfermion

---
 forest/openfermion/__init__.py                | 30 +++++++++++++++++
 .../openfermion}/pyquil_circuit_generator.py  |  4 +--
 .../openfermion}/pyquil_connector.py          |  0
 .../openfermion}/rdm_estimation.py            | 15 ++++-----
 .../openfermion}/rdm_utilities.py             |  3 +-
 .../openfermion}/tests/__init__.py            |  0
 .../tests/pyquil_connector_test.py            |  6 ++--
 .../tests/pyquil_generator_test.py            |  5 +--
 .../openfermion}/tests/rdm_estimation_test.py | 16 +++++-----
 .../openfermion}/tests/rdm_utilities_test.py  |  8 ++---
 .../openfermion}/version.py                   |  0
 forestopenfermion/__init__.py                 | 32 -------------------
 setup.py                                      |  8 ++---
 13 files changed, 63 insertions(+), 64 deletions(-)
 create mode 100644 forest/openfermion/__init__.py
 rename {forestopenfermion => forest/openfermion}/pyquil_circuit_generator.py (97%)
 rename {forestopenfermion => forest/openfermion}/pyquil_connector.py (100%)
 rename {forestopenfermion => forest/openfermion}/rdm_estimation.py (98%)
 rename {forestopenfermion => forest/openfermion}/rdm_utilities.py (99%)
 rename {forestopenfermion => forest/openfermion}/tests/__init__.py (100%)
 rename {forestopenfermion => forest/openfermion}/tests/pyquil_connector_test.py (95%)
 rename {forestopenfermion => forest/openfermion}/tests/pyquil_generator_test.py (95%)
 rename {forestopenfermion => forest/openfermion}/tests/rdm_estimation_test.py (97%)
 rename {forestopenfermion => forest/openfermion}/tests/rdm_utilities_test.py (93%)
 rename {forestopenfermion => forest/openfermion}/version.py (100%)
 delete mode 100644 forestopenfermion/__init__.py

diff --git a/forest/openfermion/__init__.py b/forest/openfermion/__init__.py
new file mode 100644
index 0000000..0939c88
--- /dev/null
+++ b/forest/openfermion/__init__.py
@@ -0,0 +1,30 @@
+#   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.
+
+from forest.openfermion.pyquil_circuit_generator import exponentiate, TimeEvolution
+
+from forest.openfermion.pyquil_connector import pyquilpauli_to_qubitop, qubitop_to_pyquilpauli
+
+from forest.openfermion.rdm_estimation import (pauli_terms_for_tpdm,
+                                               pauli_to_tpdm,
+                                               pauli_terms_for_tpdm_aa,
+                                               pauli_terms_for_tpdm_bb,
+                                               pauli_terms_for_tpdm_ab,
+                                               pauli_to_tpdm_aa,
+                                               pauli_to_tpdm_bb,
+                                               pauli_to_tpdm_ab)
+
+from forest.openfermion.rdm_utilities import (get_sz_spin_adapted,
+                                              unspin_adapt,
+                                              pauli_term_from_string,
+                                              pauli_term_relabel,
+                                              pauli_dict_relabel)
diff --git a/forestopenfermion/pyquil_circuit_generator.py b/forest/openfermion/pyquil_circuit_generator.py
similarity index 97%
rename from forestopenfermion/pyquil_circuit_generator.py
rename to forest/openfermion/pyquil_circuit_generator.py
index 779b8f8..90af957 100644
--- a/forestopenfermion/pyquil_circuit_generator.py
+++ b/forest/openfermion/pyquil_circuit_generator.py
@@ -16,12 +16,12 @@
 """
 An interface from OpenFermion QubitObjects to some of the circuit generating functionality in pyquil
 """
-from forestopenfermion.pyquil_connector import qubitop_to_pyquilpauli
 from openfermion.ops import QubitOperator
-
 from pyquil.quil import Program
 from pyquil.paulis import exponentiate as pyquil_exponentiate
 
+from forest.openfermion.pyquil_connector import qubitop_to_pyquilpauli
+
 
 def exponentiate(qubit_operator):
     """
diff --git a/forestopenfermion/pyquil_connector.py b/forest/openfermion/pyquil_connector.py
similarity index 100%
rename from forestopenfermion/pyquil_connector.py
rename to forest/openfermion/pyquil_connector.py
diff --git a/forestopenfermion/rdm_estimation.py b/forest/openfermion/rdm_estimation.py
similarity index 98%
rename from forestopenfermion/rdm_estimation.py
rename to forest/openfermion/rdm_estimation.py
index 6fa65a6..e6a3c7d 100644
--- a/forestopenfermion/rdm_estimation.py
+++ b/forest/openfermion/rdm_estimation.py
@@ -1,19 +1,18 @@
 """
 A module for generating pauli terms corresponding to the 2-RDMs
 """
-import numpy as np
 from itertools import product
-from grove.measurements.estimation import (remove_imaginary_terms,
-                                           estimate_pauli_sum,
+
+import numpy as np
+from grove.measurements.estimation import (remove_imaginary_terms, estimate_pauli_sum,
                                            remove_identity)
 from grove.measurements.term_grouping import commuting_sets_by_zbasis
-from pyquil.paulis import PauliTerm, PauliSum
-
 from openfermion.transforms import jordan_wigner
 from openfermion.ops import FermionOperator
-from forestopenfermion.rdm_utilities import (pauli_dict_relabel,
-                                             pauli_term_relabel)
-from forestopenfermion.pyquil_connector import qubitop_to_pyquilpauli
+from pyquil.paulis import PauliTerm, PauliSum
+
+from forest.openfermion.rdm_utilities import pauli_dict_relabel, pauli_term_relabel
+from forest.openfermion.pyquil_connector import qubitop_to_pyquilpauli
 
 
 def _measure_list_of_pauli_terms(pauli_terms, variance_bound, program,
diff --git a/forestopenfermion/rdm_utilities.py b/forest/openfermion/rdm_utilities.py
similarity index 99%
rename from forestopenfermion/rdm_utilities.py
rename to forest/openfermion/rdm_utilities.py
index 64e2e6b..b63618b 100644
--- a/forestopenfermion/rdm_utilities.py
+++ b/forest/openfermion/rdm_utilities.py
@@ -1,8 +1,9 @@
 """
 Utilities for RDMs
 """
-import numpy as np
 from itertools import product
+
+import numpy as np
 from pyquil.paulis import PauliTerm, PauliSum
 
 
diff --git a/forestopenfermion/tests/__init__.py b/forest/openfermion/tests/__init__.py
similarity index 100%
rename from forestopenfermion/tests/__init__.py
rename to forest/openfermion/tests/__init__.py
diff --git a/forestopenfermion/tests/pyquil_connector_test.py b/forest/openfermion/tests/pyquil_connector_test.py
similarity index 95%
rename from forestopenfermion/tests/pyquil_connector_test.py
rename to forest/openfermion/tests/pyquil_connector_test.py
index 5855526..49d50f2 100644
--- a/forestopenfermion/tests/pyquil_connector_test.py
+++ b/forest/openfermion/tests/pyquil_connector_test.py
@@ -3,15 +3,15 @@
 """
 import pytest
 import numpy as np
-from openfermion.ops import (FermionOperator, 
+from openfermion.ops import (FermionOperator,
                              QubitOperator, InteractionOperator,
                              InteractionRDM)
 from openfermion.utils import hermitian_conjugated
 from openfermion.transforms import jordan_wigner
-from forestopenfermion.pyquil_connector import (pyquilpauli_to_qubitop,
-                                                qubitop_to_pyquilpauli)
 from pyquil.paulis import PauliTerm, PauliSum
 
+from forest.openfermion.pyquil_connector import pyquilpauli_to_qubitop, qubitop_to_pyquilpauli
+
 
 def test_confirm_interface():
     """
diff --git a/forestopenfermion/tests/pyquil_generator_test.py b/forest/openfermion/tests/pyquil_generator_test.py
similarity index 95%
rename from forestopenfermion/tests/pyquil_generator_test.py
rename to forest/openfermion/tests/pyquil_generator_test.py
index cb0bc19..fb5744b 100644
--- a/forestopenfermion/tests/pyquil_generator_test.py
+++ b/forest/openfermion/tests/pyquil_generator_test.py
@@ -1,11 +1,12 @@
 """Testing interface to pyqui.paulis"""
-import numpy as np
 import pytest
+import numpy as np
 from openfermion.ops import QubitOperator, FermionOperator
-from forestopenfermion.pyquil_circuit_generator import exponentiate, TimeEvolution
 from pyquil.gates import H, RX, CNOT, RZ
 from pyquil.quil import Program
 
+from forest.openfermion.pyquil_circuit_generator import exponentiate, TimeEvolution
+
 
 def test_exponentiate():
     one_pauli_term = QubitOperator('X0 Y2 Z3')
diff --git a/forestopenfermion/tests/rdm_estimation_test.py b/forest/openfermion/tests/rdm_estimation_test.py
similarity index 97%
rename from forestopenfermion/tests/rdm_estimation_test.py
rename to forest/openfermion/tests/rdm_estimation_test.py
index 9466181..d43600d 100644
--- a/forestopenfermion/tests/rdm_estimation_test.py
+++ b/forest/openfermion/tests/rdm_estimation_test.py
@@ -2,8 +2,14 @@
 Test RDM acquisition for accuracy
 """
 import os
+
 import numpy as np
-from forestopenfermion.rdm_estimation import (pauli_terms_for_tpdm,
+from openfermion.config import DATA_DIRECTORY
+from openfermion.hamiltonians import MolecularData
+from pyquil.paulis import term_with_coeff
+
+from forest.openfermion.pyquil_connector import pyquilpauli_to_qubitop
+from forest.openfermion.rdm_estimation import (pauli_terms_for_tpdm,
                                               pauli_to_tpdm,
                                               pauli_terms_for_tpdm_aa,
                                               pauli_terms_for_tpdm_bb,
@@ -11,13 +17,7 @@
                                               pauli_to_tpdm_aa,
                                               pauli_to_tpdm_bb,
                                               pauli_to_tpdm_ab)
-
-from forestopenfermion.rdm_utilities import get_sz_spin_adapted
-
-from forestopenfermion.pyquil_connector import pyquilpauli_to_qubitop
-from openfermion.config import DATA_DIRECTORY
-from openfermion.hamiltonians import MolecularData
-from pyquil.paulis import term_with_coeff
+from forest.openfermion.rdm_utilities import get_sz_spin_adapted
 
 
 def test_h2_tpdm_build():
diff --git a/forestopenfermion/tests/rdm_utilities_test.py b/forest/openfermion/tests/rdm_utilities_test.py
similarity index 93%
rename from forestopenfermion/tests/rdm_utilities_test.py
rename to forest/openfermion/tests/rdm_utilities_test.py
index ac41cfd..4ddebfa 100644
--- a/forestopenfermion/tests/rdm_utilities_test.py
+++ b/forest/openfermion/tests/rdm_utilities_test.py
@@ -3,14 +3,14 @@
 """
 import os
 import numpy as np
-from forestopenfermion.rdm_utilities import (get_sz_spin_adapted, unspin_adapt,
-                                             pauli_term_from_string,
-                                             pauli_dict_relabel,
-                                             pauli_term_relabel)
 from openfermion.config import DATA_DIRECTORY
 from openfermion.hamiltonians import MolecularData
 from pyquil.paulis import PauliTerm
 
+from forest.openfermion.rdm_utilities import (get_sz_spin_adapted, pauli_dict_relabel,
+                                              pauli_term_from_string, pauli_term_relabel,
+                                              unspin_adapt)
+
 
 def test_spin_adapt_h2():
     """
diff --git a/forestopenfermion/version.py b/forest/openfermion/version.py
similarity index 100%
rename from forestopenfermion/version.py
rename to forest/openfermion/version.py
diff --git a/forestopenfermion/__init__.py b/forestopenfermion/__init__.py
deleted file mode 100644
index 5b69c7a..0000000
--- a/forestopenfermion/__init__.py
+++ /dev/null
@@ -1,32 +0,0 @@
-#   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.
-
-from forestopenfermion.pyquil_circuit_generator import (exponentiate,
-                                                        TimeEvolution)
-
-from forestopenfermion.pyquil_connector import (pyquilpauli_to_qubitop,
-                                                qubitop_to_pyquilpauli)
-
-from forestopenfermion.rdm_estimation import (pauli_terms_for_tpdm,
-                                              pauli_to_tpdm,
-                                              pauli_terms_for_tpdm_aa,
-                                              pauli_terms_for_tpdm_bb,
-                                              pauli_terms_for_tpdm_ab,
-                                              pauli_to_tpdm_aa,
-                                              pauli_to_tpdm_bb,
-                                              pauli_to_tpdm_ab)
-
-from forestopenfermion.rdm_utilities import (get_sz_spin_adapted,
-                                             unspin_adapt,
-                                             pauli_term_from_string,
-                                             pauli_term_relabel,
-                                             pauli_dict_relabel)
diff --git a/setup.py b/setup.py
index 64bce7c..192a32c 100755
--- a/setup.py
+++ b/setup.py
@@ -28,11 +28,11 @@
     __version__ = f.read().strip()
 
 # save the source code in version.py
-with open('forestopenfermion/version.py', 'r') as f:
+with open('forest/openfermion/version.py', 'r') as f:
     version_file_source = f.read()
 
 # overwrite version.py in the source distribution
-with open('forestopenfermion/version.py', 'w') as f:
+with open('forest/openfermion/version.py', 'w') as f:
     f.write(f'__version__ = \'{__version__}\'\n')
 
 setup(
@@ -51,10 +51,10 @@
         'pyquil < 3.0.0',
         'quantum-grove < 2.0.0'
     ],
-    packages=['forestopenfermion'],
+    packages=['forest.openfermion'],
     python_requires='>=3.6'
 )
 
 # restore version.py to its previous state
-with open('forestopenfermion/version.py', 'w') as f:
+with open('forest/openfermion/version.py', 'w') as f:
     f.write(version_file_source)

From efb40a144533bbbe0e7beffabe31ed1cefaa6994 Mon Sep 17 00:00:00 2001
From: Peter Karalekas <peter@rigetti.com>
Date: Tue, 28 May 2019 17:14:29 -0700
Subject: [PATCH 6/9] Add pkgutil-style namespace package __init__.py to forest
 dir

---
 forest/__init__.py | 1 +
 1 file changed, 1 insertion(+)
 create mode 100644 forest/__init__.py

diff --git a/forest/__init__.py b/forest/__init__.py
new file mode 100644
index 0000000..69e3be5
--- /dev/null
+++ b/forest/__init__.py
@@ -0,0 +1 @@
+__path__ = __import__('pkgutil').extend_path(__path__, __name__)

From e463acad45820cf53e303e078acf41541cb478db Mon Sep 17 00:00:00 2001
From: Peter Karalekas <peter@rigetti.com>
Date: Tue, 28 May 2019 17:18:21 -0700
Subject: [PATCH 7/9] Suggestively pin all reqs in requirements.txt because
 we're archiving

---
 requirements.txt | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/requirements.txt b/requirements.txt
index a1799d0..2361e71 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,8 +1,8 @@
-scipy < 1.0.0
-numpy < 2.0.0
-openfermion < 1.0.0
-pyquil < 3.0.0
-quantum-grove < 2.0.0
+scipy == 0.19.1
+numpy == 1.16.4
+openfermion == 0.9.0
+pyquil == 2.8.0
+quantum-grove == 1.7.0
 
 # for testing
 pytest

From 5711fe66f0e9bab2ce97ea8bdab7f9b901c3c6da Mon Sep 17 00:00:00 2001
From: Peter Karalekas <peter@rigetti.com>
Date: Tue, 28 May 2019 17:19:24 -0700
Subject: [PATCH 8/9] Include NOTICE in MANIFEST.in

---
 MANIFEST.in      | 1 +
 requirements.txt | 1 -
 2 files changed, 1 insertion(+), 1 deletion(-)

diff --git a/MANIFEST.in b/MANIFEST.in
index 01f84eb..add1c9e 100644
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -1,4 +1,5 @@
 include LICENSE
+include NOTICE
 include README.md
 include requirements.txt
 include VERSION.txt
diff --git a/requirements.txt b/requirements.txt
index 2361e71..ca36df4 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -6,4 +6,3 @@ quantum-grove == 1.7.0
 
 # for testing
 pytest
-

From 63954f97003393c2cf1963beaf7e1af36b488963 Mon Sep 17 00:00:00 2001
From: Peter Karalekas <peter@rigetti.com>
Date: Tue, 28 May 2019 17:21:19 -0700
Subject: [PATCH 9/9] Add GitLab CI badge to the README

---
 README.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/README.md b/README.md
index 9077553..4392cb6 100644
--- a/README.md
+++ b/README.md
@@ -6,6 +6,7 @@ decided to archive it. It should work in its current state, but if you find issu
 to suggest that we re-open development on this project (or, even better, if you would like to
 develop it!) please send us an email at [software@rigetti.com](mailto:software@rigetti.com).
 
+[![pipeline status](https://gitlab.com/rigetti/forest/forest-openfermion/badges/master/pipeline.svg)](https://gitlab.com/rigetti/forest/forest-openfermion/commits/master)
 [![Build Status](https://semaphoreci.com/api/v1/rigetti/forest-openfermion/branches/master/shields_badge.svg)](https://semaphoreci.com/rigetti/forest-openfermion)
 
 [OpenFermion](http://openfermion.org) is an open-source package for compiling and analyzing