Merge pull request #18 from QTC-UMD/release_1.2.0

v1.1.0 to v1.2.0 commits

CITATION.cff

@@ -0,0 +1,95 @@
+cff-version: 1.2.0
+message: If you use this software, please cite it using the preferred article citation.
+title: RydIQule
+abstract: >-
+  The Rydberg Interactive Quantum module is a modeling library designed to simulate the response of Rydberg atoms to arbitrary input RF waveforms.
+  It functions as a general master equation solver for quantum systems based on the semi-classical density matrix method.
+authors:
+  - family-names: Miller
+    given-names: Benjamin N
+    orcid: 'https://orcid.org/0000-0003-0017-1355'
+  - family-names: Meyer
+    given-names: David H
+    orcid: 'https://orcid.org/0000-0003-2452-2017'
+  - family-names: Virtanen
+    given-names: Teemu
+  - family-names: O'Brien
+    given-names: Christopher M
+    orcid: 'https://orcid.org/0000-0003-2974-0531'
+  - family-names: Cox
+    given-names: Kevin C
+    orcid: 'https://orcid.org/0000-0001-5049-3999'
+
+version: 1.1.0
+date-released: "2023-10-11"
+license: Apache-2.0
+repository-code: "https://github.com/QTC-UMD/rydiqule"
+url: "https://doi.org/10.1016/j.cpc.2023.108952"
+
+identifiers:
+  - description: Journal article describing the software
+    doi: 10.1016/j.cpc.2023.108952
+
+preferred-citation:
+  type: article
+  title: "RydIQule: A Graph-based paradigm for modeling Rydberg and atomic sensors"
+  authors:
+    - family-names: Miller
+      given-names: Benjamin N
+    - family-names: Meyer
+      given-names: David H
+      orcid: 'https://orcid.org/0000-0003-2452-2017'
+    - family-names: Virtanen
+      given-names: Teemu
+    - family-names: O'Brien
+      given-names: Christopher M
+    - family-names: Cox
+      given-names: Kevin C
+  doi: "10.1016/j.cpc.2023.108952"
+  journal: "Computer Physics Communications"
+  month: 1
+  year: 2024
+  start: 108952 # page number
+  issue: 294
+
+references:
+  - type: software
+    title: ARC (Alkali.ne Rydberg Calculator)
+    authors:
+      - family-names: Šibalić
+        given-names: Nikola
+    repository-code: "https://github.com/nikolasibalic"
+    url: "http://arc-alkali-rydberg-calculator.readthedocs.io/"
+  - type: software
+    title: NetworkX
+    repository-code: "https://github.com/networkx/networkx"
+    url: "https://networkx.org"
+  - type: software
+    title: NumPy
+    repository-code: "https://github.com/numpy/numpy"
+    url: "https://numpy.org"
+  - type: software
+    title: SciPy
+    repository-code: "https://github.com/scipy/scipy"
+    url: "https://scipy.org"
+  - type: software
+    title: numbakit-ode
+    authors:
+      - family-names: Grecco
+        given-names: Hernan E
+    repository-code: "https://github.com/hgrecco/numbakit-ode"
+    url: "https://numbakit-ode.readthedocs.io/en/latest/index.html"
+  - type: software
+    title: CyRK
+    authors:
+      - family-names: Renaud
+        given-names: Joe P
+    repository-code: "https://github.com/jrenaud90/CyRK"
+  - type: software
+    title: leveldiagram
+    authors:
+      - family-names: Meyer
+        given-names: David H
+    repository-code: "https://github.com/dihm/leveldiagram"
+    url: "https://leveldiagram.readthedocs.io/en/latest"
+

README.md

@@ -1,14 +1,21 @@
 <img src="https://raw.githubusercontent.com/QTC-UMD/rydiqule/main/docs/source/img/Rydiqule_Logo_Transparent_300.png" alt="rydiqule" style="max-width: 100%;">
 
-The Rydberg Interactive Quantum module is a modelling library designed to simulate
-the response of a Rydberg atoms to arbitrary input RF waveforms.
+The Rydberg Interactive Quantum module is a modeling library designed to simulate
+the response of Rydberg atoms to arbitrary input RF waveforms.
 It also functions as a general master equation solver based on the semi-classical density matrix method.
 
 [![PyPI](https://img.shields.io/pypi/v/rydiqule.svg)](https://pypi.org/project/rydiqule)
 [![Python Version](https://img.shields.io/pypi/pyversions/rydiqule.svg)](https://python.org)
 [![License](https://img.shields.io/pypi/l/rydiqule.svg)](https://github.com/QTC-UMD/rydiqule/raw/main/LICENSE)
 [![Docs](https://readthedocs.org/projects/rydiqule/badge/?version=latest)](https://rydiqule.readthedocs.io/en/latest)
 
+### Please cite as
+
+B. N Miller, D. H. Meyer, T. Virtanen, C. M O'Brien, and K. C. Cox,
+RydIQule: A Graph-based paradigm for modeling Rydberg and atomic sensors,
+*Computer Physics Communications*, **294**, 108952 (2024)
+[https://doi.org/10.1016/j.cpc.2023.108952](https://doi.org/10.1016/j.cpc.2023.108952)
+
 ## Installation
 
 Presently, installation is done via pip.
@@ -43,8 +50,8 @@ Now use pip to install rydiqule and remaining dependencies.
 ```shell
 # for normal installation
 (rydiqule) ~/> pip install rydiqule
-# for editable installation, so source can be modified locally
-(rydiqule) ~/> pip install -e rydiqule
+# for editable installation of cloned repo, so source can be modified locally
+(rydiqule) ~/> pip install -e .
 ```
 
 ### Pure pip installation
@@ -55,9 +62,10 @@ pip install rydiqule
 ```
 This command will use pip to install all necessary dependencies.
 
-To install in an editable way (which allows edits of the source code), run:
+To install in an editable way (which allows edits of the source code),
+run the following from the root directory of the cloned repository:
 ```shell
-pip install -e rydiqule
+pip install -e .
 ```
 
 ### Confirm installation
@@ -70,8 +78,8 @@ Proper installation can be confirmed by executing the following commands in a py
         Rydiqule
     ================
 
-Rydiqule Version:     1.0.0
-Installation Path:    C:\Users\naqsL\Miniconda3\envs\rydiqule\lib\site-packages\rydiqule
+Rydiqule Version:     1.1.0
+Installation Path:    ~\Miniconda3\envs\rydiqule\lib\site-packages\rydiqule
 
       Dependencies
     ================
@@ -81,7 +89,7 @@ SciPy Version:        1.10.1
 Matplotlib Version:   3.7.1
 ARC Version:          3.3.0
 Python Version:       3.9.16
-Python Install Path:  C:\Users\naqsL\Miniconda3\envs\rydiqule
+Python Install Path:  ~\Miniconda3\envs\rydiqule
 Platform Info:        Windows (AMD64)
 CPU Count:            12
 Total System Memory:  128 GB
@@ -90,16 +98,17 @@ Total System Memory:  128 GB
 ### Updating an existing installation
 
 Upgrading an existing installation is simple.
-Simply run the pip installation commands described above with the update flag.
+Simply run the pip installation commands described above.
+Optionally, include the update flag to greedily update dependencies as well.
 ```shell
 pip install -U rydiqule
 ```
 This command will also install any new dependencies that are required.
 
 If using an editable install, simply replacing the files in the same directory is sufficient.
-Though it is recommended to also run the appropriate pip update command as well.
+Though it is recommended to also run the appropriate pip update command as well to capture updated dependencies.
 ```shell
-pip install -U -e rydiqule
+pip install -U -e .
 ```
 
 ### Dependencies

docs/source/changelog.rst

@@ -1,6 +1,30 @@
 Changelog
 =========
 
+v1.2.0
+------
+
+Improvements
+++++++++++++
+
+- Level diagrams now use `Sensor.get_rotating_frames` to provide better plotting of energy ordering of levels.
+- Level diagrams now allow for optional control of plotting parameters by manually specifying `ld_kw` options on nodes and edges.
+- Added the ability to specify energy level shifts (additional Hamiltonian digonal terms) not accounted for by the coupling infrastructure.
+
+
+Bug Fixes
++++++++++
+
+- `Sensor.make_real` now returns correct sized `const` array when ground is not removed.
+- Many updates to type hints to improve their accuracy.
+
+Deprecations
+++++++++++++
+
+- Remove `Solution._variable_parameters` in favor of property checking the observable parameters.
+- Renamed `Sensor.basis()` and `Solution.basis` to `Sensor.dm_basis()` and `Solution.dm_basis`
+  to disambiguate physical basis from computational basis.
+
 v1.1.0
 ------
 

docs/source/index.rst

@@ -25,6 +25,31 @@ For more details, see the :doc:`overview`.
 
 For detailed usage examples, see the :doc:`_intro_nbs/Introduction_To_Rydiqule/Introduction_To_Rydiqule` Jupyter notebook.
 
+If you use rydiqule in your work, please cite as
+
+.. raw:: html
+
+   <details>
+     <summary>B. N. Miller, <em>et. al.</em>, <u><a href="https://doi.org/10.1016/j.cpc.2023.108952">RydIQule: A Graph-based paradigm for modeling Rydberg and atomic sensors</a>,</u> <em>Computer Physics Communications</em> <b>294</b>, 108952 (2024). arXiv:<a href="http://arxiv.org/abs/2307.15673">2307.15673</a>.</summary>
+
+.. code-block:: bibtex
+
+   @article{rydiqule_2024,
+      author = {Miller, B. N. and Meyer, D. H. and Virtanen, T. and O'Brien, C. M. and Cox, K. C.},
+      title = {RydIQule: A Graph-based paradigm for modeling Rydberg and atomic sensors},
+      journal = {Computer Physics Communications},
+      volume = {294},
+      pages = {108952},
+      year = {2024},
+      doi = {10.1016/j.cpc.2023.108952},
+      url = {https://doi.org/10.1016/j.cpc.2023.108952},
+      eprint = {https://doi.org/10.1016/j.cpc.2023.108952}
+   }
+
+.. raw:: html
+
+   </details>
+
 .. toctree::
    :maxdepth: 2
    :hidden:

docs/source/installation.rst

@@ -40,8 +40,8 @@ Now use pip to install rydiqule and remaining dependencies.
 
   # for normal installation
   (rydiqule) ~/Rydiqule> pip install rydiqule
-  # for editable installation, so source can be modified locally
-  (rydiqule) ~/Rydiqule> pip install -e rydiqule
+  # for editable installation of cloned repo, so source can be modified locally
+  (rydiqule) ~/Rydiqule> pip install -e .
 
 Pure pip installation
 ---------------------
@@ -54,11 +54,12 @@ To install normally, run:
 
 This command will use pip to install all necessary dependencies.
 
-To install in an editable way (which allows edits of the source code), run:
+To install in an editable way (which allows edits of the source code), 
+run the following from the root directory of the cloned repository:
 
 .. code-block:: shell
 
-  pip install -e rydiqule
+  pip install -e .
 
 Confirm installation
 --------------------
@@ -73,8 +74,8 @@ Proper installation can be confirmed by executing the following commands in a py
           Rydiqule
       ================
 
-  Rydiqule Version:     1.0.0
-  Installation Path:    C:\Users\naqsL\Miniconda3\envs\rydiqule\lib\site-packages\rydiqule
+  Rydiqule Version:     1.1.0
+  Installation Path:    ~\Miniconda3\envs\rydiqule\lib\site-packages\rydiqule
 
         Dependencies
       ================
@@ -84,7 +85,7 @@ Proper installation can be confirmed by executing the following commands in a py
   Matplotlib Version:   3.7.1
   ARC Version:          3.3.0
   Python Version:       3.9.16
-  Python Install Path:  C:\Users\naqsL\Miniconda3\envs\rydiqule
+  Python Install Path:  ~\Miniconda3\envs\rydiqule
   Platform Info:        Windows (AMD64)
   CPU Count:            12
   Total System Memory:  128 GB
@@ -93,7 +94,8 @@ Updating an existing installation
 ---------------------------------
 
 Upgrading an existing installation is simple.
-Simply run the pip installation commands described above with the update flag.
+Simply run the pip installation commands described above.
+Optionally, include the update flag to greedily update dependencies as well.
 
 .. code-block:: shell
 
@@ -102,11 +104,11 @@ Simply run the pip installation commands described above with the update flag.
 This command will also install any new dependencies that are required.
 
 If using an editable install, simply replacing the files in the same directory is sufficient.
-Though it is recommended to also run the appropriate pip update command as well.
+Though it is recommended to also run the appropriate pip update command as well to capture updated depedencies.
 
 .. code-block:: shell
 
-  pip install -U -e rydiqule
+  pip install -U -e .
 
 
 Dependencies

mypy.ini

@@ -7,6 +7,7 @@ warn_redundant_casts = True
 warn_unused_ignores = True
 warn_unreachable = True
 show_error_codes = True
+allow_redefinition = True
 files = src/**/*.py
 plugins = numpy.typing.mypy_plugin
 
@@ -32,7 +33,13 @@ ignore_missing_imports = True
 [mypy-psutil.*]
 ignore_missing_imports = True
 
-# Module options
+[mypy-CyRK.*]
+ignore_missing_imports = True
+
+[mypy-networkx.*]
+ignore_missing_imports = True
 
-[mypy-rydiqule.energy_diagram]
-ignore_errors = False
+[mypy-leveldiagram.*]
+ignore_missing_imports = True
+
+# Module options

readthedocs.yaml

@@ -8,7 +8,7 @@ version: 2
 build:
   os: ubuntu-22.04
   tools:
-    python: "3.8"
+    python: "3.11"
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:

src/rydiqule/__init__.py

@@ -15,4 +15,4 @@
 
 from .slicing.slicing import compute_grid, matrix_slice, memory_size, get_slice_num, get_slice_num_t
 
-__version__ = '1.1.0'
+__version__ = '1.2.0'