New release v0.3.4 into main (#277)

* Update develop to catch up with main version 0.3.3 (#249) * Fix link of fig in qchem & excited states notebook (#250) * allow single flip index dis for qcc (#247) * allow single flip index dis for jkmn * Richardson extrapolation: bug fix + error estimation (#252) * Bugfix: DMET with QCC (#253) * iQCC using only Clifford circuits notebook (#254) * pUCCD ansatz (#251) * UHF reference (#240) * uhf implementation with VQESolver functionality * support for all types of orbital freezing * add active_spin and uhf attributes to SecondQuantizedDMETFragment * add spin to adapt_ansatz arguments * added multi-product, grid_circuits and discrete_clock (#257) * added multi-product, grid_circuits and discrete_clock * translation to pennylane (#260) * tangelo to pennylane format translation Co-authored-by: Valentin Senicourt <41597680+ValentinS4t1qbit@users.noreply.github.com> * bump testing version to 3.8 (#262) Updating python version to 3.8 in automated tests, as 3.7 is no longer maintained by the Python dev team * Auto threshold cutoff for small coefficients in LCU (#261) * check for small value lcu * changed to keep same vector length but apply no operations * Openshell DMET (#208) * Open-shell DMET. * Fix for get_rdm CCSD. * Added NAO localization. * Added LiO2 spin=1 DMET test. * Added UHF MF for DMET. New get_rdm for VQESolver. * Save mid-circuit measurement (#256) * A flag now allows users to save mid-circuit measurements for each shot run. Co-authored-by: Valentin Senicourt <valentin.senicourt@1qbit.com> * Fix for IBMQConnection (#264) * Updated copyright year to 2023 (#267) * added draw method to circuit (#266) * added draw method to circuit (warning about font comes up in linux env) * Cirq, qulacs, pennylane and projectq operator translation functions (#268) * Support to bidirectional translation of operators for cirq, qulacs, PennyLane, projectq. * Fixed a bug in QulacsSimulator.expectation_value_from_prepared_state. * Important bug in qiskit -> tangelo op translation fixed * Fixed identity operator evaluation and extended the accepted input types in compute_rdms (#269) * Compute RDMs function can now hangle both term formats (string and openfermion tuple). * Unhashable list for of -> conversion to tuples. * Handling all the inputs in compute_rdms. * Temporarily disabling OS-DMET (#271) * Temporarily disabling for code verification purpose, as the implementation seems to return very odd and incorrect results for simple systems. * Link to new example repo * Update README.rst * Revert changes that broke tests (#275) * reverted changes that broke tests * DMET + frozen orbitals for each fragment (#276) * DMET + frozen orbitals, added DMET/frozen tests. * Example folder relocated to new repo Tangelo-Examples (#274) * removed examples folder, removed notebooks from automated tests, added link higher in README.rst * Docs update (#272) * Updated conf.py, tested building docs and fixed comments/docs. * Removed tutorials.rst with the notebooks. * Desired measurement result (#263) * New feature: return frequencies matching desired mid-circuit measurement values. --------- Co-authored-by: James Brown <james.brown@1qbit.com> * Bumping Tangelo version number in _version.py * Update Changelog (v0.3.4) --------- Co-authored-by: Valentin Senicourt <41597680+ValentinS4t1qbit@users.noreply.github.com> Co-authored-by: AlexandreF-1qbit <76115575+AlexandreF-1qbit@users.noreply.github.com> Co-authored-by: James Brown <84878946+JamesB-1qbit@users.noreply.github.com> Co-authored-by: KrzysztofB-1qbit <86750444+KrzysztofB-1qbit@users.noreply.github.com> Co-authored-by: Valentin Senicourt <valentin.senicourt@1qbit.com> Co-authored-by: James Brown <james.brown@1qbit.com> Co-authored-by: GitHub Actions <noreply@github.com>
sandbox-quantum · Feb 16, 2023 · 85d406a · 85d406a
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diff --git a/.github/workflows/continuous_integration.yml b/.github/workflows/continuous_integration.yml
@@ -69,12 +69,6 @@ jobs:
         pytest --doctest-modules --junitxml=junit/tangelo-test-results.xml --cov=. --cov-report=xml --cov-report=html
       if: always()
 
-    - name: tangelo notebooks as tests
-      run: |
-        cd examples
-        pytest --doctest-modules --junitxml=junit/notebook-test-results.xml test_notebooks.py
-      if: always()
-
     - name: Upload pytest test results
       uses: actions/upload-artifact@v3
       with:

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,6 +3,36 @@
 This file documents the main changes between versions of the code.
 
 
+## [0.3.4] - 2023-02-15
+
+### Added
+
+- Richardson extrapolation: support for variance and std dev (+ bugfix)
+- Allow single flip index dis for QCC
+- Notebook: iQCC using only Clifford circuits
+- UHF reference mean-field
+- Multi-product, grid circuits and discrete clock
+- translate_circuit now supports Pennylane format and full bidirectional translation for all formats
+- translate_op now supports all formats, both ways
+- Saving mid-circuit measurements
+- Selecting a desired mid-circuit measurement for simulation
+- compute_rdms from a classical shadow, experimental data or using a backend on the fly
+- support for frozen orbitals for each fragment in DMET
+- Notebook for Tangelo + IBM Quantum demo (IBMQConnection)
+- draw method for circuits
+
+### Changed
+
+- Bumped Python version number to 3.8 as 3.7 is no longer supported
+- Bugfix: DMET + QCC
+- Auto-threshold cutoff for small coefficients in LCU
+- examples folder no longer in main repo, moved to Tangelo-Examples repo
+- Bugfix: IBMQConnection (API update)
+
+### Deprecated
+
+
+
 ## [0.3.3] - 2022-11-09
 
 ### Added

diff --git a/CONTRIBUTIONS.rst b/CONTRIBUTIONS.rst
@@ -1,7 +1,7 @@
 Contributions guidelines
 ========================
 
-Thank you very much for considering contributing to this project ! 
+Thank you very much for considering contributing to this project !
 
 Do not feel intimidated by the guidelines and processes we describe in this document: we are here to assist you and help you take things to the finish line. We do not expect you to be an expert in software development or to get everything right on the first attempt: don’t hesitate to open an issue or a pull request, or simply contact us.
 
@@ -42,7 +42,7 @@ In your terminal, clone the repo on your local machine, and move into the newly
   git clone https://github.com/USERNAME/Tangelo.git
   cd Tangelo
 
-From the perspective of your local clone, your fork is called the ``origin`` remote. 
+From the perspective of your local clone, your fork is called the ``origin`` remote.
 Let's synchronize your fork with the main Tangelo repo by adding the latter as the upstream remote, and then update your local ``main`` branch:
 
 .. code-block:: shell
@@ -85,7 +85,7 @@ Every time you open a PR or push more code into an open one, several automated p
 
 
 Continuous integration
-======================
+----------------------
 
 When a pull request is created or updated, several automated processes are launched. You will find most of them in the "checks" tab of your pull request, and can look into the details. These processes check for a few things:
 
@@ -112,7 +112,7 @@ When a pull request is created or updated, several automated processes are launc
   We rely on a tool called pycodestyle. If you want to know exactly what this linting enforces and ignores, you can refer to this `file <./dev_tools/pycodestyle>`_ and `pycodestyle's documentation <https://pycodestyle.pycqa.org/en/latest/intro.html>`_.
 
 
-Developing notebooks 
-====================
+Developing notebooks
+--------------------
 
 Jupyter notebooks are great ! If you feel like making a notebook to show how to do something cool with Tangelo and educate others, don't hesitate to reach out. It counts as code, so it will go through the standard PR process and will need to meet a few requirements. The developer team has made several notebooks you can look at, for inspiration.
diff --git a/README.rst b/README.rst
@@ -47,8 +47,9 @@ published in scientific journals, co-authored by professionals from the chemical
 
 We hope to grow a healthy community around Tangelo, collaborate, and together leverage the best of what the field has to offer.
 
-- Our `release document on arXiv <https://arxiv.org/pdf/2206.12424.pdf>`_.
+- Our `release document on arXiv <https://arxiv.org/abs/2206.12424>`_.
 - Our `Sphinx documentation <http://tangelo-docs.goodchemistry.com>`_.
+- Our `examples repository <https://github.com/goodchemistryco/Tangelo-Examples>`_.
 
 What will you do with Tangelo ?
 
@@ -70,7 +71,7 @@ The easiest way to install Tangelo in your local environment. We recommend upgra
 
 .. code-block::
 
-   python -m pip install -–upgrade pip.
+   python -m pip install --upgrade pip.
    pip install tangelo-gc
 
 If you'd like to install via pip the code in a specific branch of this Github repository (let's say ``develop``)
@@ -155,7 +156,7 @@ them in whatever way your OS supports it, or even inside your python script usin
 Tutorials and examples
 ----------------------
 
-We have a `dedicated repository <https://github.com/goodchemistryco/Tangelo-Examples>`_ for examples and tutorials ! 
+We have a `dedicated repository <https://github.com/goodchemistryco/Tangelo-Examples>`_ for examples and tutorials !
 
 We wrote a number of them, and tried to provide material that doesn't just explain how to use the software, but provides insights into the complex topics of chemistry, quantum computing, and digs into the challenges we encountered in our previous hardware experiments.
 Nothing prevents users from contributing and showcasing what they have been doing with Tangelo.
@@ -191,7 +192,7 @@ find and run all tests (assuming you are in the ``tangelo`` subfolder that conta
 Contributions
 -------------
 
-Thank you very much for considering contributing to this project; we’d love to have you on board !
+Thank you very much for considering contributing to this project; we'd love to have you on board !
 You do not need to be a seasoned software developer or expert in your field to make contributions to this project: it will take various kinds of people and backgrounds to tackle the challenges that await us.
 
 However we need some guidelines and processes to ensure that we build something of quality for the community. We describe them in the `contributions <./CONTRIBUTIONS.rst>`_ file.

diff --git a/docs/source/CONTRIBUTIONS.rst b/docs/source/CONTRIBUTIONS.rst
@@ -0,0 +1 @@
+../../CONTRIBUTIONS.rst
diff --git a/docs/source/TUTORIALS.rst b/docs/source/TUTORIALS.rst
@@ -0,0 +1 @@
+../../TUTORIALS.rst
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -4,6 +4,9 @@
 # list see the documentation:
 # https://www.sphinx-doc.org/en/master/usage/configuration.html
 
+from tangelo._version import __version__
+
+
 # -- Path setup --------------------------------------------------------------
 
 # If extensions (or modules to document with autodoc) are in another directory,
@@ -18,11 +21,11 @@
 # -- Project information -----------------------------------------------------
 
 project = 'tangelo'
-copyright = '2022 Good Chemistry Company'
+copyright = '2023 Good Chemistry Company'
 author = 'Valentin senicourt, Alexandre Fleury, Ryan Day, James Brown'
 
 # The full version, including alpha/beta/rc tags
-release = '0.3.1'
+release = __version__
 
 
 # -- General configuration ---------------------------------------------------

diff --git a/docs/source/dmet.ipynb b/docs/source/dmet.ipynb
diff --git a/docs/source/img b/docs/source/img
diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -11,6 +11,8 @@ Welcome to Tangelo's documentation!
    :caption: Contents:
 
    overview
+   TUTORIALS
+   CONTRIBUTIONS
    tangelo
 
 Indices and tables

diff --git a/docs/source/linq_basics.ipynb b/docs/source/linq_basics.ipynb
diff --git a/docs/source/mifno.ipynb b/docs/source/mifno.ipynb
diff --git a/docs/source/overview_endtoend.ipynb b/docs/source/overview_endtoend.ipynb
diff --git a/docs/source/qemist_cloud_hardware_experiments_braket.ipynb b/docs/source/qemist_cloud_hardware_experiments_braket.ipynb
diff --git a/docs/source/tutorials.rst b/docs/source/tutorials.rst
diff --git a/docs/source/vqe.ipynb b/docs/source/vqe.ipynb
diff --git a/examples/adapt.ipynb b/examples/adapt.ipynb