Release v0.6.0 (#372)

Main changes: - 3921795 Remove string variables (#365) - b23ff22 Splitting `pulser` into `pulser-core` and `pulser-simulation`. (#362) - 4f684f3 Address qubits with indices (#356) - f2ee5e2 Make evaluation times uniform including final time (#330) - c34dffb Changes for compatibility with upcoming export format (#353) - 3ac1f66 Sequence sampler (#345)
pasqal-io · May 13, 2022 · 9d978ab · 9d978ab
2 parents 9304b65 + de2248a
commit 9d978ab
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diff --git a/.coveragerc b/.coveragerc
@@ -7,6 +7,14 @@ exclude_lines =
     # Don't test pass statements
     pass
 
-omit = pulser/tests/*
+omit =
+    tests/*
+    setup.py
+
 
 show_missing = True
+
+[run]
+source =
+    pulser-core/pulser/
+    pulser-simulation/pulser_simulation/
diff --git a/.flake8 b/.flake8
@@ -10,6 +10,6 @@ per-file-ignores =
   # D100 Missing docstring in public module
   # D103 Missing docstring in public function
   # F401 Module imported but unused
-  pulser/tests/*: D100, D103
+  tests/*: D100, D103
   __init__.py: F401
   setup.py: D100
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -23,7 +23,7 @@ jobs:
       - name: Install Python dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install -e .
+          pip install -e ./pulser-core -e ./pulser-simulation
           pip install -r requirements.txt
       - name: Lint with flake8
         run: flake8
@@ -55,7 +55,7 @@ jobs:
       - name: Install Python dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install -e .
+          pip install -e ./pulser-core -e ./pulser-simulation
           pip install -r requirements.txt
       - name: Check import sorting with isort
         run: isort --check-only --diff .
@@ -71,7 +71,7 @@ jobs:
       - name: Install Python dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install -e .
+          pip install -e ./pulser-core -e ./pulser-simulation
           pip install -r requirements.txt
       - name: Type check with mypy
         run: mypy
@@ -91,7 +91,7 @@ jobs:
       - name: Install Python dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install -e .
+          pip install -e ./pulser-core -e ./pulser-simulation
           pip install -r requirements.txt
       - name: Run the unit tests & generate coverage report
-        run: pytest --cov --cov-fail-under=100 pulser
+        run: pytest --cov --cov-fail-under=100
diff --git a/.gitignore b/.gitignore
@@ -15,3 +15,5 @@ docs/build/
 dist/
 env*
 pulser.egg-info/
+pulser_simulation.egg-info/
+pulser_core.egg-info/
diff --git a/.mypy.ini b/.mypy.ini
@@ -1,5 +1,5 @@
 [mypy]
-files = pulser
+files = pulser-core/pulser, pulser-simulation/pulser_simulation, tests
 python_version = 3.8
 warn_return_any = True
 warn_redundant_casts = True
@@ -11,5 +11,5 @@ disallow_untyped_defs = True
 follow_imports = silent
 ignore_missing_imports = true
 
-[mypy-pulser.tests.*]
+[mypy-tests.*]
 disallow_untyped_defs = False
diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -15,5 +15,5 @@ python:
    install:
      - requirements: docs/requirements.txt
      - requirements: requirements.txt
-     - method: setuptools
-       path: .
+     - requirements: pulser-core/rtd_requirements.txt
+     - requirements: pulser-simulation/rtd_requirements.txt
diff --git a/MANIFEST.in b/MANIFEST.in
@@ -1,4 +1,4 @@
 include README.md
 include requirements.txt
 include LICENSE
-include pulser/devices/interaction_coefficients/C6_coeffs.json
+include VERSION.txt
diff --git a/README.md b/README.md
@@ -15,23 +15,35 @@ and also allows the creation of **analog** quantum simulations, outside of the
 scope of traditional quantum circuit approaches. Whatever the type of experiment
 or paradigm, if it can be done on the device, it can be done with Pulser.
 
-Additionally, Pulser features built-in tools for classical simulation (using [QuTiP][qutip] libraries) to aid in the development and testing of new pulse sequences.
+Additionally, the ``pulser_simulation`` extension provides tools for classical simulation (using [QuTiP][qutip] libraries) to aid in the development and testing of new pulse sequences.
 
-For a comprehensive overview of Pulser, check out [Pulser's arXiv preprint](https://arxiv.org/abs/2104.15044).
+For a comprehensive overview of Pulser, check out [Pulser's white paper](https://quantum-journal.org/papers/q-2022-01-24-629/).
 
 ## Installation
 
+**Note**: *Pulser v0.6 introduced a split of the ``pulser`` package that prevents it from being correctly upgraded. If you have an older version of ``pulser`` installed and wish to upgrade, make sure to uninstall it first by running ``pip uninstall pulser``.*
+
 To install the latest release of ``pulser``, have Python 3.7.0 or higher installed, then use ``pip``:
 
 ```bash
 pip install pulser
 ```
 
+The standard ``pulser`` distribution will install the core ``pulser`` package
+and the ``pulser_simulation`` extension package, which is required if you want
+to access the emulation features.
+
+If you wish to install only the core ``pulser`` features, you can instead run:
+
+```bash
+pip install pulser-core
+```
+
 If you wish to **install the development version of Pulser from source** instead, do the following from within this repository after cloning it:
 
 ```bash
 git checkout develop
-pip install -e .
+pip install -e ./pulser-core -e ./pulser-simulation
 ```
 
 Bear in mind that this installation will track the contents of your local
@@ -49,7 +61,7 @@ pip install -r requirements.txt
 Then, you can do the following to run the test suite and report test coverage:
 
 ```bash
-pytest --cov pulser
+pytest --cov
 ```
 
 ## Contributing

diff --git a/VERSION.txt b/VERSION.txt
@@ -0,0 +1 @@
+0.6.0
diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -1,6 +1,6 @@
 # For generating documentation.
 Sphinx
-sphinx_rtd_theme
+sphinx-rtd-theme # documentation theme
 nbsphinx
 nbsphinx-link
 

diff --git a/docs/source/_static/css/max_width.css b/docs/source/_static/css/max_width.css
@@ -0,0 +1,4 @@
+.wy-nav-content {
+    width: 80% !important;
+    max-width: 1600px !important;
+}
diff --git a/docs/source/apidoc/creation.rst b/docs/source/apidoc/creation.rst
@@ -11,10 +11,47 @@ Sequence
 Register
 ----------------------
 
-.. automodule:: pulser.register
+Register classes
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+The register classes allow for the creation of arbitrary registers.
+
+.. autoclass:: pulser.register.base_register.BaseRegister
+  :members:
+
+.. autoclass:: pulser.register.register.Register
   :members:
   :show-inheritance:
 
+.. autoclass:: pulser.register.register3d.Register3D
+  :members:
+  :show-inheritance:
+
+
+Register layout
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+A ``RegisterLayout`` is used to define a register from a set of traps. It is
+intended to be given to the user by the hardware provided as a way of showing
+which layouts are already available on a given device. In turn, the user
+can create a ``Register`` by selecting the traps on which to place atoms, or
+even a ``MappableRegister``, which allows for the creation of sequences whose
+register can be defined at build time.
+
+.. autoclass:: pulser.register.register_layout.RegisterLayout
+  :members:
+
+.. autoclass:: pulser.register.mappable_reg.MappableRegister
+  :members:
+
+
+
+Special cases
+""""""""""""""""""
+
+.. automodule:: pulser.register.special_layouts
+  :members:
+  :show-inheritance:
+
+
 Pulse
 -------------------
 
@@ -46,6 +83,8 @@ which when associated with a :class:`pulser.Sequence` condition its development.
 
 .. autodata:: pulser.devices.Chadoq2
 
+.. autodata:: pulser.devices.IroiseMVP
+
 The MockDevice
 ^^^^^^^^^^^^^^^^
 A very permissive device that supports sequences which are currently unfeasible

diff --git a/docs/source/apidoc/emulation.rst b/docs/source/apidoc/emulation.rst
@@ -2,16 +2,19 @@
 Classical Simulation
 *********************
 
+Since version 0.6.0, all simulation classes (previously under the ``pulser.simulation`` module)
+are in the ``pulser-simulation`` extension and should be imported from ``pulser_simulation``.
+
 Simulation
 ----------------------
 
-.. automodule:: pulser.simulation.simulation
+.. automodule:: pulser_simulation.simulation
    :members:
 
 SimConfig
 ----------------------
 
-.. automodule:: pulser.simulation.simconfig
+.. automodule:: pulser_simulation.simconfig
    :members:
 
 Simulation Results
@@ -29,14 +32,14 @@ within them.
 CoherentResults
 ^^^^^^^^^^^^^^^^
 
-.. autoclass:: pulser.simulation.simresults.CoherentResults
+.. autoclass:: pulser_simulation.simresults.CoherentResults
    :members:
    :inherited-members:
 
 
 NoisyResults
 ^^^^^^^^^^^^^^^^
 
-.. autoclass:: pulser.simulation.simresults.NoisyResults
+.. autoclass:: pulser_simulation.simresults.NoisyResults
   :members:
   :inherited-members:
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -13,15 +13,15 @@
 import os
 import sys
 
-sys.path.insert(0, os.path.abspath("../../pulser"))
+sys.path.insert(0, os.path.abspath("../../"))
 
-__version__ = ""
-exec(open("../../pulser/_version.py").read())
+with open("../../VERSION.txt", "r") as f:
+    __version__ = f.read().strip()
 
 # -- Project information -----------------------------------------------------
 
 project = "Pulser"
-copyright = "2020, Pulser Development Team"
+copyright = "2022, Pulser Development Team"
 author = "Pulser Development Team"
 
 # The full version, including alpha/beta/rc tags
@@ -69,3 +69,7 @@
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
 html_static_path = ["_static"]
+
+html_css_files = [
+    "css/max_width.css",
+]
diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -8,6 +8,8 @@ and simulation.
 
 **Online documentation**: `<https://pulser.readthedocs.io>`_
 
+**White paper**: `Quantum 6, 629 (2022) <https://quantum-journal.org/papers/q-2022-01-24-629/>`_
+
 **Source code repository** (go `here <https://pulser.readthedocs.io/en/latest/>`_
 for the latest docs): `<https://github.com/pasqal-io/Pulser>`_
 

diff --git a/docs/source/installation.rst b/docs/source/installation.rst
@@ -1,13 +1,26 @@
 Installation
 ==============
 
+**Note**: Pulser v0.6 introduced a split of the ``pulser`` package that prevents
+it from being correctly upgraded. If you have an older version of ``pulser`` installed
+and wish to upgrade, make sure to uninstall it first by running ``pip uninstall pulser``
+before proceeding to any of the steps below.
+
 Stable version
 -----------------
 To install the latest release of ``pulser``, have Python 3.7.0 or higher
 installed, then use ``pip``: ::
 
   pip install pulser
 
+The standard ``pulser`` distribution will install the core ``pulser`` package
+and the ``pulser_simulation`` extension package, which is required if you want
+to access the :doc:`apidoc/emulation` features.
+
+If you wish to install only the core ``pulser`` features, you can instead run: ::
+
+  pip install pulser-core
+
 
 Latest version
 ---------------
@@ -18,7 +31,7 @@ the ``develop`` branch - which holds the latest (unstable) version of Pulser -
 and install from source by running: ::
 
   git checkout develop
-  pip install -e .
+  pip install -e ./pulser-core -e ./pulser-simulation
 
 Bear in mind that your installation will track the contents of your local
 Pulser repository folder, so if you checkout a different branch (e.g. ``master``),

diff --git a/docs/source/intro_rydberg_blockade.ipynb b/docs/source/intro_rydberg_blockade.ipynb
@@ -196,7 +196,7 @@
    ],
    "source": [
     "import matplotlib.pyplot as plt\n",
-    "from pulser.simulation import Simulation\n",
+    "from pulser_simulation import Simulation\n",
     "\n",
     "data = []\n",
     "distances = np.linspace(6.5, 14, 7)\n",