Huge update - Compatibility with Ansys 2022 R2 (#142)

* Update README.md * Update README.md * fix typo * update information on conda forge install * add conda badge to readme * add information on pypi install and name * fix typo * add info on pypi install and note on package name * add pypi badge to readme via fury.io * Merge remote-tracking branch 'upstream/master' into Asaf_branch * Update core_quantum_analysis.py allows to print result and print variation to be used togther where the variation to be printed is give by an integer * Update core_quantum_analysis.py * Update core_quantum_analysis.py * Update README.md * Update README.md * Update README.md * Update README.md * Update README.md * Update README.md * Update README.md * Update README.md * Update README.md * Update about.rst * Update about.rst * Update about.rst * Update installation.rst * Update README.md * Update README.md * Sorted Qs and freqs Instead of having the sorting of the dataframe as string indices (e.g. '0', '1', '10', '2'...) it is now sorted as integers ('0', '1', '2', ... , '10'). Only relevant for >10 variations. * Update README.md * Make package name in setup.py match name on PyPI * Remove old conda recipe See https://github.com/conda-forge/pyepr-quantum-feedstock for conda recipe * Version 0.8.4 * Create greetings.yml * Create manual.yml * Create Q3D setup within HfssDesign * Create publish-to-pypi * Rename publish-to-pypi to publish-to-pypi.yml * Update README.md * Update version from 0.8.4 to 0.8.4.2 * Fixed bug with port impedance in ansys.py * Modify how to connect to Ansys * Update config_user.py * Edit yml file * Update publish-to-pypi.yml * Updated version number * If a project or design is missing in Ansys app, then return None and … (#68) * If a project or design is missing in Ansys app, then return None and give a warning. * Update warnings to be more accurate. * Revert accidental change. * typo and logger add for no active design * Add method to allow user to add a new Q3d to project referenced in ProjectInfo * Updated version number * Fix get_setup method * correction to enable q3d design setup default + removing error in get_objects_in_group() (#70) * correction to enable q3d design setup default * prevent unnecessary error when modeler is not defined in get_objects_in_group * 209 if design exists add it (#71) * Save before switching branches. * Add changes which were part of merge. * Update where the flag needs to be passed. * Need method instead of getting a list of designs. * Remove the previous solution, Decide with different solution. * Change to version 0.8.4.5 . * Remove reference to yapf. * Ansys version update for Z matrices * Update ansys.py for Ansys 2020 * get_setup fixed to use the passed setup name + typos * up-rev * Create pyEPR.bib * Update pyEPR.bib * Update README.md * Update README.md * Update README.md * Added ansys calculator functions Two functions that return vectors tangent and normal to a surface. I used it to calculate surface participation ratios, e.g.: p_metal = t* (E_surface_metal / UE) print(f'Metal-Air/Metal-Substrate participation ratio, p_MA = p_MS = {p_metal:.3}') #SA participation ratio vecE_normal = vecE.normal2surface('chip_holder1').__div__(epsilon_r) #Complex Vector vecE_tangent = vecE.tangent2surface('chip_holder1').__mul__(epsilon_r) #Complex Vector vec_E_total = vecE_normal.__add__(vecE_tangent) E_squared = vec_E_total.dot(vecE).__abs__().real().__pow__(2) E_surface = E_squared.integrate_surf(name='chip_holder1').evaluate() E_surface -= E_surface_metal p_SA = t* (E_surface / UE) print(f'Air-Substrate participation ratio, p_SA = {p_SA:.3}') * Typos mainly Also one change where an error is raised when `pint` is not properly imported. * Update ansys.py * Update ansys.py * Update README.md * Update pyEPR.bib * Update pyEPR.bib * Update pyEPR.bib * Update core_quantum_analysis.py Get numeric frequencies results should retrieve f_ND, not f_1. Some typos. * Updates linguist's calculation for pyEPR * Typos * Mostly typos, some corrections In core_quantum_analysis: Rows 671-674: update to modes that are not the first. Row 917: trying to get pandas to plot with the right label. Unsuccessfully. * clean_up_solutions functions and some typos clean_up_solutions function for an Ansys design (to avoid analysis of all variations). Also removed index name for frequencies and typos * Update core_quantum_analysis.py Fixed #83 * Tutorial2: Correct import of CalcObject to pyEPR.ansys * Indentation after was wrong and variable swp_var was never defined * fixed mode number error in QuantumAnalysis fixed KeyError when '0' is not in variations for QuantumAnalysis. updated type hint for QuantumAnalysis.analyze_variation fix mode number error in QuantumAnalysis * Update back_box_numeric.py * fix log plot bug if q__coupling isnot there * Update core_quantum_analysis.py * Update the init and setup files before creating a tag. * Update back_box_numeric.py Fix typo * Add pylint CI check * Fix old keyword argument name in first tutorial * Check for infinite values in the Quality Factors. * Change syntax to pass pylint. In particular, separate numpy from pandas. * Add int cast to pass pylint. * Change syntax to pass pylint. * Disable the pylint warning. * Use updated tag to include fix for issue #96. * Systematically fix typos in code and documentation (#99) * Test compiling docs in CI (#104) * Add dissipative elements as arguments to `ProjectInfo` (#103) * Fix docstrings formatting (#101) * https://securitylab.github.com/research/github-actions-preventing-pwn-requests/ is the reason to update. This allows first time users that have forked the repository to make a pull request. (#110) * Replace attrdict to addict for python 3.10 compatibility (#108) * Replace Attrdict to addict.Dict for python>=3.10 compatibility * Add one line for filtering addict.Dict from obj's attributes. * replace attrdict to addict * add python 3.10 to classifiers * Add python 3.9 in setup.py * Prepare for new tag for pyepr for pypi. (#112) * Update the README to reflect addict vs attrdict in both files. * Make the type hint more accurate. * Current code expects None values, as opposed to empty list. * Prepare to use next tag for Metal. * Add variation labels to plots in `hfss_report_full_convergence` (#119) * Improve assorted docstrings * Add variation labels to HFSS convergence report * Add other parametric sweep options (#117) * fix keyboard mash? * Implemented all available options for parametric sweep definitions and parametric sweep from file. * Addition of demo tutorial and associated csv file * Add DrivenTerminal support (#121) * Add single surface `DistributedAnalysis.get_Qsurface` (#123) * Fix EPR sign bug that caused EPR to always be positive (#125) * Update README.md * Update version to 0.8.5.6 for EPR sign bug fix (#126) * Fix EPR bug and bump to version 0.8.5.7 * Pass lv=lv to evaluate * Update version to 0.8.5.7 in __init__.py * Variation support to `calc_p_electric_volume` (#132) * Support synchronised variables in `Optimetrics.create_setup` (#130) * Fix code block formattings * Implement synchronised sweep support in Optimetrics * Don't extend `hfss_report_full_convergence` vertically (#135) * Support loss tangents for different surfaces in `do_EPR_analysis` (#144) * Fix #145 .gitignore (#146) * Add dtype to empty Pandas Series (#139) * Refactor `DataFrame.append` to `pd.concat` (#138) * Replace usage of np.float with float (#147) (#150) The epr_numerical_diagonalization function uses np.float which has been deprecated in Numpy. Refer https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations The continued usage of np.float yields the following error in the epr_numerical_diaganolization function when later versions of Numpy is used. "AttributeError: module 'numpy' has no attribute 'float'." This commit replace np.float with float to solve this error. * Correctly select a few modes in analyze_variation (#149) * Fix mode selection in analyze_variation Addressing issue #148: analyze_variation incorrectly chooses Pj, Sj, Om, PHI_zpf when passed a subset of modes * Remove redundant frequency selection The frequencies are already correctly selected outside of this if-statement, so this is not necessary * Update setup.py * Update __init__.py * Update core_distributed_analysis.py (#152) out-commenting a property not supported in latest version. Only visual impact --------- Co-authored-by: Zlatko Minev <[email protected]> Co-authored-by: Nathan Shammah <[email protected]> Co-authored-by: SQClab <[email protected]> Co-authored-by: Barkay Guttel <[email protected]> Co-authored-by: willsALMANJ <[email protected]> Co-authored-by: Will Shanks <[email protected]> Co-authored-by: Dennis Wang <[email protected]> Co-authored-by: Priti Ashvin Shah <[email protected]> Co-authored-by: Marco Facchini <[email protected]> Co-authored-by: Ashish Panigrahi <[email protected]> Co-authored-by: Xinyu <[email protected]> Co-authored-by: CHAO ZHOU <[email protected]> Co-authored-by: Priti A Shah <[email protected]> Co-authored-by: Niko Savola <[email protected]> Co-authored-by: Niko Savola <[email protected]> Co-authored-by: GyeonghunKim <[email protected]> Co-authored-by: Thomas G McConkey <[email protected]> Co-authored-by: Zach Parrott <[email protected]> Co-authored-by: Patrick J. O'Brien <[email protected]> Co-authored-by: Jagatheesan Jack <[email protected]> Co-authored-by: Clara Fontaine <[email protected]> Co-authored-by: Christian Kraglund Andersen <[email protected]>
zlatko-minev · Nov 9, 2023 · 6dd5dc6 · 6dd5dc6
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diff --git a/.gitattributes b/.gitattributes
@@ -0,0 +1 @@
+*.ipynb linguist-vendored
diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
@@ -0,0 +1,70 @@
+name: CI
+
+on:
+  push:
+    branches:
+      - master
+  pull_request: ~
+
+env:
+  # Increment this to invalidate the cache without modifying requirements.txt
+  PIPCACHEVERSION: 0
+  PYTHONVERSION: '3.9.x'  # qutip does not support 3.10 yet
+
+jobs:
+  pylint:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out repo
+        uses: actions/checkout@v2
+      - name: Set up Python
+        id: setup-python
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ env.PYTHONVERSION }}
+      - name: Set up cache
+        id: cache
+        uses: actions/cache@v2
+        with:
+          path: ~/.cache/pip
+          key: ${{ runner.os }}-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('requirements.txt') }}-${{ env.PIPCACHEVERSION }}
+          restore-keys: |
+            ${{ runner.os }}-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('requirements.txt') }}-
+            ${{ runner.os }}-${{ steps.setup-python.outputs.python-version }}-
+      - name: Install package and pylint
+        run: python -m pip install . pylint
+      - name: Run pylint
+        run: pylint --errors-only --jobs=0 pyEPR
+
+  test_docs:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out repo
+        uses: actions/checkout@v2
+      - name: Set up Python
+        id: setup-python
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ env.PYTHONVERSION }}
+      - name: Set up cache
+        id: cache
+        uses: actions/cache@v2
+        with:
+          path: ~/.cache/pip
+          key: ${{ runner.os }}-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('requirements.txt') }}-${{ env.PIPCACHEVERSION }}
+          restore-keys: |
+            ${{ runner.os }}-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('requirements.txt') }}-
+            ${{ runner.os }}-${{ steps.setup-python.outputs.python-version }}-
+      - name: Install package and sphinx
+        run: python -m pip install . Sphinx
+      - name: Make docs
+        run: |
+          cd docs
+          make html
+      - name: Upload docs to artifact
+        uses: actions/upload-artifact@v2
+        if: always()
+        with:
+          name: docs
+          path: docs/build/html/
+          retention-days: 5
diff --git a/.github/workflows/greetings.yml b/.github/workflows/greetings.yml
@@ -0,0 +1,13 @@
+name: Greetings
+
+on: [pull_request_target, issues]
+
+jobs:
+  greeting:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/first-interaction@v1
+      with:
+        repo-token: ${{ secrets.GITHUB_TOKEN }}
+        issue-message: '👏👏👏 You are awesome! Thank you for making your first issue to pyEPR '' first issue'
+        pr-message: '👏👏👏 You are awesome! Thank you for making your first pull request to pyEPR! This team work makes the pyEPR dream work! '' first pr'
diff --git a/.github/workflows/manual.yml b/.github/workflows/manual.yml
@@ -0,0 +1,30 @@
+# This is a basic workflow that is manually triggered
+
+name: Manual workflow
+
+# Controls when the action will run. Workflow runs when manually triggered using the UI
+# or API.
+on:
+  workflow_dispatch:
+    # Inputs the workflow accepts.
+    inputs:
+      name:
+        # Friendly description to be shown in the UI instead of 'name'
+        description: 'Person to greet'
+        # Default value if no value is explicitly provided
+        default: 'World'
+        # Input has to be provided for the workflow to run
+        required: true
+
+# A workflow run is made up of one or more jobs that can run sequentially or in parallel
+jobs:
+  # This workflow contains a single job called "greet"
+  greet:
+    # The type of runner that the job will run on
+    runs-on: ubuntu-latest
+
+    # Steps represent a sequence of tasks that will be executed as part of the job
+    steps:
+    # Runs a single command using the runners shell
+    - name: Send greeting
+      run: echo "Hello ${{ github.event.inputs.name }}"
diff --git a/.github/workflows/publish-to-pypi.yml b/.github/workflows/publish-to-pypi.yml
@@ -0,0 +1,51 @@
+# This is a basic workflow to help you get started with Actions
+
+name: Publish Python 🐍 distributions 📦 to PyPI 
+
+# Controls when the action will run. 
+on:
+  release:
+    types: [created]
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+# A workflow run is made up of one or more jobs that can run sequentially or in parallel
+jobs:
+  # This workflow contains a single job called "build"
+  build:
+    name: Build and publish Python 🐍 distributions 📦 to PyPI and TestPyPI
+    # The type of runner that the job will run on
+    runs-on: ubuntu-latest
+
+    # Steps represent a sequence of tasks that will be executed as part of the job
+    steps:
+      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
+      - uses: actions/checkout@master
+      - name: Set up Python 3.7
+        uses: actions/setup-python@v1
+        with:
+          python-version: 3.7
+
+      - name: Install pypa/build
+        run: >-
+          python -m
+          pip install
+          build
+          --user
+
+      - name: Build a binary wheel and a source tarball
+        run: >-
+          python -m
+          build
+          --sdist
+          --wheel
+          --outdir dist/
+          .
+
+      - name: Publish distribution 📦 to PyPI
+        if: startsWith(github.ref, 'refs/tags')
+        uses: pypa/gh-action-pypi-publish@master
+        with:
+          password: ${{ secrets.pypi_password }}
+
diff --git a/.gitignore b/.gitignore
@@ -102,13 +102,13 @@ ENV/
 
 # exclude config
 pyEPR/config.py
+pyEPR/_user_config.py
 __src__not_incl/
 pyEPR/.vscode/
 pyEPR/.pylintrc
 *.lock
 *.aedtresults/*
 *.aedtresults*
 pyEPR/core.py.rej
-pyEPR/core.py.rej
-pyEPR/core.py.rej
 .vscode/
+.idea/
diff --git a/README.md b/README.md
@@ -1,51 +1,64 @@
-Welcome to pyEPR :beers:!
+Welcome to pyEPR :beers:! &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(see [arXiv:2010.00620](https://arxiv.org/abs/2010.00620))
 ===================
 [![Open Source Love](https://badges.frapsoft.com/os/v1/open-source.png?v=103)](https://github.com/zlatko-minev/pyEPR)
 [![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://github.com/zlatko-minev/pyEPR)
 [![star this repo](http://githubbadges.com/star.svg?user=zlatko-minev&repo=pyEPR&style=flat)](https://github.com/zlatko-minev/pyEPR)
 [![fork this repo](http://githubbadges.com/fork.svg?user=zlatko-minev&repo=pyEPR&style=flat)](https://github.com/zlatko-minev/pyEPR/fork)
+[![Anaconda-Server Badge](https://anaconda.org/conda-forge/pyepr-quantum/badges/installer/conda.svg)](https://conda.anaconda.org/conda-forge)
+[![PyPI version](https://badge.fury.io/py/pyEPR-quantum.svg)](https://badge.fury.io/py/pyEPR-quantum)
+[![DOI](https://zenodo.org/badge/101073856.svg)](https://zenodo.org/badge/latestdoi/101073856)
+
+### Automated Python module for the design and quantization of Josephson quantum circuits
 
-<br>
-
-## :bangbang: :bangbang: pyEPR Working group meeting -- Planning for the future of pyEPR 
 
-* Please sign-up here: https://github.com/zlatko-minev/pyEPR/issues/45 :bangbang: :beers:
+### Documentation
 
+[Read the docs here.](https://pyepr-docs.readthedocs.io)
 <br>
 
-### Automated Python module for the design and quantization of Josephson quantum circuits
+## Scientific work:
+* Minev, Z. K., Leghtas, Z., Mudhada, S. O., Reinhold, P., Diringer, A., & Devoret, M. H. (2018). [pyEPR: The energy-participation-ratio (EPR) open-source framework for quantum device design.](https://github.com/zlatko-minev/pyEPR/blob/master/pyEPR.bib)  [![DOI](https://zenodo.org/badge/101073856.svg)](https://zenodo.org/badge/latestdoi/101073856)
+* Minev, Z. K., Leghtas, Z., Mundhada, S. O., Christakis, L., Pop, I. M., & Devoret, M. H. (2020). Energy-participation quantization of Josephson circuits. ArXiv. Retrieved from http://arxiv.org/abs/2010.00620 (2020)
+* Z.K. Minev, Ph.D. Dissertation, Yale University (2018), Chapter 4. ([arXiv:1902.10355](https://arxiv.org/abs/1902.10355))  (2018) 
 
-**Abstract:** Superconducting circuits incorporating non-linear devices, such as Josephson junctions and nanowires, are among the leading platforms for emerging quantum technologies. Promising applications require designing and optimizing circuits with ever-increasing complexity and controlling their dissipative and Hamiltonian parameters to several significant digits. Therefore, there is a growing need for a systematic, simple, and robust approach for precise circuit design, extensible to increased complexity. The energy-participation ratio (EPR) approach presents such an approach to unify the design of dissipation and Hamiltonians around a single concept — the energy participation, a number between zero and one — in a single-step electromagnetic simulation. This markedly reduces the required number of simulations and allows for robust extension to complex systems. The approach is general purpose, derived ab initio, and valid for arbitrary non-linear devices and circuit architectures. Experimental results on a variety of circuit quantum electrodynamics (cQED) devices and architectures, 3D and flip-chip (2.5D), have been demonstrated to exhibit ten percent to percent-level agreement for non-linear coupling and modal Hamiltonian parameters over five-orders of magnitude and across a dozen samples. Here, in this package, all routines of the EPR approach are fully automated.
+## pyEPR Working group meeting -- Planning for the future of pyEPR
 
-## Documentation
+* Please sign-up here: https://github.com/zlatko-minev/pyEPR/issues/45 or [directly here](https://docs.google.com/forms/d/e/1FAIpQLScd3WyfzDS47D0WB9skkSPQAXCnKLf7JMxsZ7BnMwK0LjE3Sw/viewform?usp=sf_link) :bangbang: :beers:
+- See [pyEPR wiki](https://github.com/zlatko-minev/pyEPR/wiki) for notes from first meeting.
+- We will schedule a follow-up meeting in 1-2 mo.
 
-[Read the docs here.](https://pyepr-docs.readthedocs.io)
-
-#### Legacy users
-Warning: pyEPR organization was significnatly improved in v0.8-dev (starting 2020; current branch: master \[to be made stable soon\]). If you used a previous version, you will find that all key classes have been renamed. Please, see the tutorials and docs.  In the meantime, if you cannot switch yet, revert to use the stable v0.7.
+<br>
 
 ## Who uses pyEPR?
 * Yale University, Michel Devoret lab [QLab](https://qulab.eng.yale.edu/), CT, USA
 * Yale University, Rob Schoelkopf lab [RSL](https://rsl.yale.edu/), CT, USA
-* [IBM Quantum](https://www.ibm.com/quantum-computing/)
+* [IBM Quantum](https://www.ibm.com/quantum-computing/) and IBM's Qiskit Metal
 * [QUANTIC](https://team.inria.fr/quantic/people.html#) (QUANTUM INFORMATION CIRCUITS), PARISINRIA, ENS, MINES PARISTECH, UPMC, CNRS. Groups of Zaki Leghtas and team. France
-* [Quantum Circuit Group](http://www.physinfo.fr/) Emanuel Flurin, Benjamin Huard, Ecole Normale Supérieure de Lyon, France
+* [Quantum Circuit Group](http://www.physinfo.fr/) Benjamin Huard, Ecole Normale Supérieure de Lyon, France
+* Emanuel Flurin, CEA Saclay, France
+* Ioan Pop group, KIT Physikalisches Institut, Germany 
 * UC Berkeley, [Quantum Nanoelectronics Laboratory](https://physics.berkeley.edu/quantum-nanoelectronics-laboratory), Irfan Siddiqi, CA, USA
 * [Quantum Circuits, Inc.](https://quantumcircuits.com/), CT, USA
 * [Seeqc](https://seeqc.com/) (spin-out of Hypres) Digital Quantum Computing, USA
-* Serge [Rosenblum Lab](https://www.weizmann.ac.il/condmat/rosenblum/) in the Weizmann Instatue, Israel
-* Peter [Leek Lab](https://leeklab.org/), UK
+* Serge [Rosenblum Lab] quantum circuits group (https://www.weizmann.ac.il/condmat/rosenblum/) in the Weizmann Instatue, Israel
+* University of Oxford - LeekLab - Peter [Leek Lab](https://leeklab.org/), UK
 * Britton [Plourde Lab](https://bplourde.expressions.syr.edu/), Syracuse University, USA
 * Javad [Shabani Lab](https://wp.nyu.edu/shabanilab/) Quantum Materials & Devices, NYU, NY, USA
+* UChicago Dave Schuster Lab, USA
+* SQC lab - Shay Hacohen Gourgy, Israel
+* Lawrence Berkeley National Lab
+* Colorado School of Mines, USA
+* Syracuse University, USA
+* IPQC, SJTU, Shanghai, China
+* Bhabha Atomic Research Centre, India
+* Quantum Computing UK
+* Alice&Bob, France
+* Centre for Quantum Technologies / Qcrew
+* Quantum Device Lab ETHZ; Andreas Wallraff
+* Bleximo
 * ... and many more! (Please e-mail `[email protected]` with updates.)
 
 
-## How do I cite `pyEPR` when I publish?
-Cite the following and/or e-mail [`[email protected]`](https://www.zlatko-minev.com/) or [`zaki leghtas`](http://cas.ensmp.fr/~leghtas/)
-* [arXiv:1902.10355](https://arxiv.org/abs/1902.10355) Z.K. Minev, Ph.D. Dissertation, Yale University (2018), Chapter 4. 
-* Z.K. Minev, Z. Leghtas, _et al._ (to appear soon on arXiv) (2020)
-
-
 <br>
 
 # Contents:
@@ -65,7 +78,9 @@ Cite the following and/or e-mail [`[email protected]`](https://www.zlatk
 2. **Clone** :point_down: your forked repository locally. ([How to clone a GitHub repo?](https://help.github.com/en/articles/cloning-a-repository)). Setup the `pyEPR` python code by following [Installation and Python Setup](#installation-of-pyepr).
 3. **Tutorials**  Learn how to use using the [jupyter notebook tutorials](https://github.com/zlatko-minev/pyEPR/tree/master/_tutorial_notebooks)
 4. **Stay up to date** Enjoy and make sure to git add the master remote branch  `git remote add MASTER_MINEV git://github.com/zlatko-minev/pyEPR.git` [(help?)](https://stackoverflow.com/questions/11266478/git-add-remote-branch).
-5. **Cite `pyEPR`** [arXiv:1902.10355](https://arxiv.org/abs/1902.10355)  and enjoy! :birthday:
+5. **Cite `pyEPR`**  [arXiv:2010.00620](https://arxiv.org/abs/2010.00620) / [arXiv:1902.10355](https://arxiv.org/abs/1902.10355)  and enjoy! :birthday:  [![DOI](https://zenodo.org/badge/101073856.svg)](https://zenodo.org/badge/latestdoi/101073856)
+
+
 
 #### Start-up example
 
@@ -90,14 +105,16 @@ pinfo.junctions['jBob']   = {'Lj_variable':'Lj_bob',   'rect':'rect_bob',   'lin
 pinfo.validate_junction_info() # Check that valid names of variables and objects have been supplied.
 
 # 2b. Dissipative elements: specify
-pinfo.dissipative['dielectrics_bulk']    = ['si_substrate', 'dielectic_object2'] # supply names of hfss objects
+pinfo.dissipative['dielectrics_bulk']    = ['si_substrate', 'dielectric_object2'] # supply names of hfss objects
 pinfo.dissipative['dielectric_surfaces'] = ['interface1', 'interface2']
+# Alternatively, these could be specified in ProjectInfo with
+# pinfo = epr.ProjectInfo(..., dielectrics_bulk = ['si_substrate', 'dielectric_object2'])
 
 # 3.  Perform microwave analysis on eigenmode solutions
 eprd = epr.DistributedAnalysis(pinfo)
 if 1: # automatic reports
   eprd.quick_plot_frequencies(swp_var) # plot the solved frequencies before the analysis
-  eprd.hfss_report_full_convergence() # report convergen
+  eprd.hfss_report_full_convergence() # report convergence
 eprd.do_EPR_analysis()
 
 # 4a.  Perform Hamiltonian spectrum post-analysis, building on mw solutions using EPR
@@ -150,7 +167,7 @@ Use `pyEPR` directly from the source, and pull updates from the master git repo,
 Please keep up to date with `pyEPR` by using git. We like to make it simple using a git-gui manager, [SourceTree](sourcetree.com) or [GitHub Desktop](https://desktop.github.com/).
 
 **Quick setup**
-We recommend the approach in the following section, which will be most up to date, but for quick use you can use the [conda forge chanel](https://anaconda.org/conda-forge/pyepr-quantum) to install
+We recommend the approach in the following section, which will be most up to date, but for quick use you can use the [conda forge channel](https://anaconda.org/conda-forge/pyepr-quantum) to install
 ```
 conda install -c conda-forge pyepr-quantum
 ```
@@ -168,11 +185,11 @@ pip install pyEPR-quantum
       $ echo %PATH%
       `
 
- 2. Install the required packages, including [pint](http://pint.readthedocs.io/en/latest/), [qutip](http://qutip.org/), and [attrdict](https://github.com/bcj/AttrDict). In a terminal window
+ 2. Install the required packages, including [pint](http://pint.readthedocs.io/en/latest/), [qutip](http://qutip.org/), and [addict](https://github.com/mewwts/addict). In a terminal window
  ```sh
  conda install -c conda-forge pint
  conda install -c conda-forge qutip
- pip install attrdict
+ pip install addict
  ```
  3. Fork this pyEPR repository on GitHub with your GitHub account. You may clone the fork to your PC and manage it using the [SourceTree](https://www.sourcetreeapp.com/) git-gui manager.
  4. Add the pyEPR repository folder to your python search path. Make sure to add the git remote to the master is set up,  `git remote add MASTER_MINEV git://github.com/zlatko-minev/pyEPR.git`!  [(Help?)](https://stackoverflow.com/questions/11266478/git-add-remote-branch)
@@ -193,6 +210,10 @@ Follow the same instructions above. You shouldn't have to install mingw or modif
 
 
 
+#### Legacy users
+Warning: pyEPR organization was significantly improved in v0.8-dev (starting 2020; current branch: master \[to be made stable soon\]). If you used a previous version, you will find that all key classes have been renamed. Please, see the tutorials and docs.  In the meantime, if you cannot switch yet, revert to use the stable v0.7.
+
+
 # HFSS Project Setup for `pyEPR`
 -------------
 #### Eigenmode Design --- How to set up junctions
@@ -258,7 +279,7 @@ compiler = mingw32
 [build_ext]
 compiler = mingw32
 ```
-Next, let's install qutip. You can choose to use conda intall or pip install, or pull from the git directly  as done here:
+Next, let's install qutip. You can choose to use conda install or pip install, or pull from the git directly  as done here:
 ```sh
 conda install git
 pip install git+https://github.com/qutip/qutip.git
@@ -285,12 +306,17 @@ This problem is due to pandas 0.20.1, update to 0.20.3 or better solves this iss
 This error happens when trying to read in an hdf file with numpy version 1.16, see [git issue here](https://github.com/numpy/numpy/issues/12791). A solution is to downgrade numpy to 1.15.4 or upgrade to newer versions of hdf and numpy.
 
 # Authors and Contributors
-* _Authors:_ [Zlatko Minev](https://www.zlatko-minev.com/) & [Zaki Leghtas](http://cas.ensmp.fr/~leghtas/), with contributions from many friends and colleagues.
+* _Authors:_ [Zlatko Minev](https://www.zlatko-minev.com/) & [Zaki Leghtas](http://cas.ensmp.fr/~leghtas/), with contributions from many friends and colleagues. ([arXiv:2010.00620](https://arxiv.org/abs/2010.00620))
 * 2015 - present.
 * Contributors: [Phil Rheinhold](https://github.com/PhilReinhold), Lysander Christakis, [Devin Cody](https://github.com/devincody), ...
 Original versions of pyHFSS.py and pyNumericalDiagonalization.py contributed by [Phil Rheinhold](https://github.com/PhilReinhold), excellent original [repo](https://github.com/PhilReinhold/pyHFSS).
 * Terms of use: Use freely and kindly cite the paper (arXiv link to be posted here) and/or this package.
-* How can I contribute? Contact [Z. Minev](https://www.zlatko-minev.com/) or [Z. Leghtas](http://cas.ensmp.fr/~leghtas/).
+* How can I contribute? Contact [Z. Minev](https://www.zlatko-minev.com/) or [Z. Leghtas](http://cas.ensmp.fr/~leghtas/).  [![DOI](https://zenodo.org/badge/101073856.svg)](https://zenodo.org/badge/latestdoi/101073856)
+
+## How do I cite `pyEPR`?
+ [![DOI](https://zenodo.org/badge/101073856.svg)](https://zenodo.org/badge/latestdoi/101073856)
+Use this [bibtex](https://github.com/zlatko-minev/pyEPR/blob/master/pyEPR.bib) for `pyEPR` and for the method use the energy-participation-ratio paper [arXiv:2010.00620](https://arxiv.org/abs/2010.00620). 
+
 
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