Mlxtk

Description:
------------

This update adds support for SQR simulations, providing the necessary tasks to
create wave functions and operators as well as the Bose-Hubbard system.
Some minor fixes were also required (e.g. in the propagation task) to work with
these distinguishable DoFs.
The Bose-Hubbard model has also been implemented as a MCTDHB system to be able to
compare the two approaches.

**Breaking Change**: From now on file extensions have to be specified manually.
Tasks do not add extensions like `.mb_opr` or `.wfn` by default anymore.

Furthermore, some bugs were fixed and many dependencies have been updated.

Included Commits:
-----------------
- 8cffd7c: (HEAD -> master, origin/master, origin/HEAD) Fix file extesion for mb operator pickle files.
- ee875a7: Merge pull request 151 from f-koehler/dependabot/pip/memory-profiler-tw-0.58.0
- d11d4c3: Update memory-profiler requirement from ^0.57.0 to ^0.58.0
- ce6d0d1: Do not use exproj for SQR simulation. It seems that this projector does not work for SQR.
- 789fc1c: Fix initial filling for SQR.
- 799b859: Use clearer naming in SQR penalty term.
- 7b46f4b: Clean up DVR module.
- 2ba85f5: Add correlator for Bose-Hubbard model.
- c749121: Merge branch 'master' of github.com:f-koehler/mlxtk into master
- b31011a: Fix hardcoded file extension expectation value task.
- 08c3c6d: Implement terms of type n_i n_j in MCTDHB Bose-Hubbard model.
- 48f910b: Implement occupation operators for MCTDHB BoseHubbard model.
- e42f87a: Fix site occupation squared operator.
- 57d3853: Add site occupation operators for SQR.
- 7f6a2f6: Remove erroneous default file extensions in static expval task.
- 93bb5eb: Remove old print statement.
- f8930e9: Fix a bug in a regex used in the natpop ASCII reader when the node number has two digits. In this situation, a whitespace is not present anymore.
- 1abb456: Merge pull request 150 from f-koehler/dependabot/pip/mypy-tw-0.790
- 5f153ef: Update mypy requirement from ^0.782 to ^0.790
- e4132ac: Add MCTDHB BoseHubbard example and fix some bugs in the corresponding modules.
- cf468d8: Implement interaction term and Hamiltonian in MCTDHB BoseHubbard.
- 574144c: Handle penalty=0 in BoseHubbard by not creating term.
- 929394d: Fix bug in BoseHubbard system.
- e0843db: Do not create hopping/interaction term if not necessary.
- 3e0fc7c: Add hopping constant to BoseHubbard model.
- 75cfd8c: Merge pull request 149 from f-koehler/dependabot/pip/rope-tw-0.18.0
- 99e97c9: Update rope requirement from ^0.17.0 to ^0.18.0
- 8039ae6: Introduce m parameter to SQR example.
- 22feb88: Increase verbosity of SQR Wfn task.
- b2688e1: Add function to map numpy types when serializing parameters to JSON.
- e7b6f1c: Fix two typos.
- 819ad92: Use caret specification of dependencies.
- 606cde9: Fix interaction strength factor in SQR Bose-Hubbard interaction term.
- ba8dcc1: Add SQR example.
- 4f3e375: Remove file extensions from tasks (some might still be to be done).
- 9b0397f: Fix some imports.
- 2925f50: Add option for penalty strength in SQR BoseHubbard Hamiltonian.
- 8d289d0: Rename SQR module to sqr.
- 160bc99: Add task to create SQR wave function.
- d4914e8: Merge pull request 147 from f-koehler/dependabot/pip/flake8-3.8.4
- 17bdab1: Merge pull request 148 from f-koehler/dependabot/pip/pytest-6.1.1
- 2dc3e39: Update pytest requirement from 6.1.0 to 6.1.1
- 1abacbd: Update flake8 requirement from 3.8.3 to 3.8.4
- 99d4e0e: Merge pull request 146 from f-koehler/dependabot/pip/isort-5.5.4
- 05edac1: Update isort requirement from 5.5.3 to 5.5.4
- a4a92eb: Start implementing MCTDHB Bose-Hubbard.
- 57b4ebf: Merge branch 'master' of github.com:f-koehler/mlxtk into master
- 4b1507d: Implement SQR DVR and Bose-Hubbard (SQR).
- bf98a69: Add export scripts for ouput and expval.
- 1afdbfa: Merge pull request 145 from f-koehler/dependabot/pip/tqdm-4.50.0
- 2e6d8d9: Merge pull request 144 from f-koehler/dependabot/pip/pytest-6.1.0
- cee225e: Update tqdm requirement from 4.49.0 to 4.50.0
- 73089a8: Update pytest requirement from 6.0.2 to 6.1.0
- a104127: Merge pull request 143 from f-koehler/dependabot/add-v2-config-file
- 2eed4f1: (origin/dependabot/add-v2-config-file) Create Dependabot config file
- 2196c7f: Add pre-commit config.
- f396393: Merge pull request 140 from f-koehler/dependabot/pip/isort-5.5.3
- 062c718: Update isort requirement from 5.5.2 to 5.5.3
- 304ad33: Merge pull request 139 from f-koehler/dependabot/pip/matplotlib-3.3.2
- 461dd39: Update matplotlib requirement from 3.3.1 to 3.3.2
- 57b296e: Revert "Fix normalization of truncated CoM operators."
- 9072b14: Fix normalization of truncated CoM operators.
- 38d221f: Update isort to 5.5.2.
- 482284c: Merge pull request 136 from f-koehler/dependabot/pip/pyside2-5.15.1
- a54c892: Merge pull request 135 from f-koehler/dependabot/pip/numpy-1.19.2
- 807adc0: Merge pull request 137 from f-koehler/dependabot/pip/tqdm-4.49.0
- 4d37442: Update numpy requirement from 1.19.1 to 1.19.2
- 456c0c6: Update pyside2 requirement from 5.15.0 to 5.15.1
- 0779463: Merge pull request 132 from f-koehler/dependabot/pip/doit-0.33.1
- 9728659: Merge pull request 133 from f-koehler/dependabot/pip/pandas-1.1.2
- 04a7176: Merge pull request 138 from f-koehler/dependabot/pip/pytest-6.0.2
- 15270b0: Update pytest requirement from 6.0.1 to 6.0.2
- 228b20d: Update tqdm requirement from 4.48.2 to 4.49.0
- d099b6c: Update pandas requirement from 1.1.1 to 1.1.2
- 9a6660f: Update doit requirement from 0.33 to 0.33.1
- 559324f: Upgrade doit.
- f15b086: Merge pull request 128 from f-koehler/dependabot/pip/prompt-toolkit-3.0.7
- fd080e5: Update prompt-toolkit requirement from 3.0.6 to 3.0.7
- a8dcd49: Reformat code using new black version.
- 88834c2: Merge pull request 127 from f-koehler/dependabot/pip/black-20.8b1
- 3d39ad7: Update black requirement from 19.10b0 to 20.8b1
- 33259d0: Re-enable pylint.
- 649eca7: Merge pull request 126 from f-koehler/dependabot/pip/pandas-1.1.1
- 4cf9c7d: Update pandas requirement from 1.1.0 to 1.1.1
- 61f6b64: Update isort to 5.4.2 and reformat code.
- 496b66c: Disable pylint for now.
- c7ab52c: Merge pull request 125 from f-koehler/dependabot/pip/matplotlib-3.3.1
- 2ced6f7: Update matplotlib requirement from 3.3.0 to 3.3.1
- 56034a4: Merge pull request 124 from f-koehler/dependabot/pip/prompt-toolkit-3.0.6
- d2e0c6b: Update prompt-toolkit requirement from 3.0.5 to 3.0.6
- 0c8835b: Merge branch 'master' of github.com:f-koehler/mlxtk into master
- 52dbba8: Add export script for gpop.
- 91c13f5: Merge pull request 123 from f-koehler/dependabot/pip/sympy-1.6.2
- 4abc996: Update sympy requirement from 1.6.1 to 1.6.2
- 4943c9f: Merge pull request 122 from f-koehler/dependabot/pip/tqdm-4.48.2
- 11dd0c0: Update tqdm requirement from 4.48.1 to 4.48.2
- bb375c9: Merge pull request 121 from f-koehler/dependabot/pip/tqdm-4.48.1
- aeb28c8: Update tqdm requirement from 4.48.0 to 4.48.1
- 57500e8: Merge pull request 120 from f-koehler/dependabot/pip/pytest-6.0.1
- 74876c7: Update pytest requirement from 6.0.0 to 6.0.1

Description:
------------

This update implements the functionalities to create ML-X simulations of Bose-Bose mixtures.
Therefore a new task has been added to create the initial wave function.
A generic Bose-Bose system as well as a colliding Gaussian well system have been added to the systems module.

Furthermore, some bugs were fixed and many dependencies have been updated.

Included Commits:
-----------------
- 168b097: Fix typo in compute g1 script.
- 2a04f15: Add option to normalize g1/g2 to the maximum of rho1/rho2.
- dd913a2: Disable pyup; it does not resolve the full dependency graph when checking for updates which leads to conflicts.
- 022897f: Merge pull request 117 from f-koehler/dependabot/pip/scipy-1.5.2
- d61a3c8: Merge pull request 116 from f-koehler/pyup-update-scipy-1.5.1-to-1.5.2
- 1bc39f8: Update scipy requirement from 1.5.1 to 1.5.2
- e0904cb: Update scipy from 1.5.1 to 1.5.2
- 2c25e73: Change normalization of truncated CoM operators.
- 5fd93b9: Add function to compute one-body Hamiltonian of two moved Gaussian traps.
- c81b66a: Merge pull request 115 from f-koehler/dependabot/pip/numpy-1.19.1
- 84c2f0f: Merge pull request 114 from f-koehler/pyup-update-numpy-1.19.0-to-1.19.1
- 8f639e1: Update numpy requirement from 1.19.0 to 1.19.1
- 7f8c56a: Update numpy from 1.19.0 to 1.19.1
- 840bd86: Add some checks when trying to delete a simulation directory in wave function DB.
- d427f79: Merge branch 'master' of github.com:f-koehler/mlxtk
- c6e454b: Skip not executed simulations when repickling.
- 7a18b10: Merge pull request 112 from f-koehler/dependabot/pip/jedi-0.17.2
- 17a3445: Merge pull request 109 from f-koehler/pyup-update-jedi-0.17.1-to-0.17.2
- 3beba41: Update jedi requirement from 0.17.1 to 0.17.2
- ff7e207: Update jedi from 0.17.1 to 0.17.2
- 84caea5: Merge pull request 108 from f-koehler/dependabot/pip/matplotlib-3.3.0
- 1b4b84f: Merge pull request 107 from f-koehler/dependabot/pip/tqdm-4.48.0
- 547ae18: Merge pull request 105 from f-koehler/pyup-update-matplotlib-3.2.2-to-3.3.0
- b9cfb26: Merge pull request 106 from f-koehler/pyup-update-tqdm-4.47.0-to-4.48.0
- 7901c4c: Update matplotlib requirement from 3.2.2 to 3.3.0
- a0eb2fe: Update tqdm requirement from 4.47.0 to 4.48.0
- 53ac685: Update tqdm from 4.47.0 to 4.48.0
- 2711f91: Update matplotlib from 3.2.2 to 3.3.0
- ba3f011: Fix bug in lattice system.
- b2a0ae0: Fix parameter order in recoil conversion.
- 8d74a44: Fix parameters of lattice system.
- 3d18f53: Make convert_recoil_energy a staticmethod.
- 5c3d3bb: Rename lattice class.
- eb36922: Add experimental lattice system.
- 3c22d3d: Fix com_B operator.
- f77fae6: Add CoM operator to Bose-Bose systems.
- 6fcaa9c: Merge pull request 96 from f-koehler/dependabot/pip/scipy-1.5.1
- 53019d0: Merge pull request 94 from f-koehler/pyup-update-scipy-1.5.0-to-1.5.1
- 2acab3d: Update scipy requirement from 1.5.0 to 1.5.1
- a244248: Update scipy from 1.5.0 to 1.5.1
- 69873c1: Fix colliding Hamiltonian.
- 9f9336a: Merge branch 'master' of github.com:f-koehler/mlxtk
- 73aab77: Ignore rope files.
- eeb38f8: Cleanup tasks module.
- a77f832: Fix various issues in the Bose-Bose systems.
- 091cfaa: Fix issues in Bose-Bose wfn. module.
- aef470e: Add example for Bose-Bose system.
- ae6f52e: Add missing operators.
- 62e1694: Merge pull request 90 from f-koehler/dependabot/pip/sympy-1.6.1
- 80f7954: Merge pull request 89 from f-koehler/pyup-update-sympy-1.6-to-1.6.1
- b4ba595: Update sympy requirement from 1.6 to 1.6.1
- 2754410: Add memory_profiler dep; update requirements.txt.
- b06072e: Update sympy from 1.6 to 1.6.1
- 2050219: Add a test Bose-Bose system.

Description:
------------

In this update I have added a task to compute momentum distributions using `qdtk_analysis.x` and added a plotting script.
A lot of dependencies have been updated and the code has been reformatted using `black`.


Included Commits:
-----------------

- 59751bc: Reformat codebase with black.
- 802631d: Update dev dependencies.
- 5a71fb2: Update tqdm.
- 2408950: Merge pull request 88 from f-koehler/dependabot/pip/tqdm-4.47.0
- e8d5864: Plot average in momentum distribution script.
- 7b4ce63: Update tqdm requirement from 4.46.1 to 4.47.0
- 9d05320: Add two scripts to recalculate pickle files in simulations/scans and update the doit state database. This can be necessary if the pickle protocol is changed in the library or if the pickle output for something (e.g. numpy arrays) changes (maybe due to a change in the underlying library).
- ee90676: Use a shift of the trap as a quench in HO example.
- a575cc5: Initial implementation of momentum distribution tools.
- ecdef15: Update mypy.
- 2b3b271: Merge pull request 86 from f-koehler/pyup-update-mypy-0.781-to-0.782
- 5c1f09d: Update mypy from 0.781 to 0.782
- c536a99: Add log plot options to gpop plot script; add some type hints.
- 304b4ae: Merge pull request 80 from f-koehler/pyup-update-mypy-0.780-to-0.781
- 9ace44e: Merge branch 'master' into pyup-update-mypy-0.780-to-0.781
- 96c92f3: Merge pull request 83 from f-koehler/dependabot/pip/mypy-0.781
- ca72a2f: Update mypy requirement from 0.780 to 0.781
- b61456f: Update numpy requirement from 1.18.5 to 1.19.0
- b732567: Update numpy from 1.18.5 to 1.19.0
- 8e027f5: Update scipy requirement from 1.4.1 to 1.5.0
- 02fb4ae: Update scipy from 1.4.1 to 1.5.0
- 1a76358: Update mypy from 0.780 to 0.781
- e565494: Update pandas to 1.0.5.
- a8efd87: Update pandas from 1.0.4 to 1.0.5

Description:
------------

Update various dependencies and add tools to study parity properties of single particle functions.


Included Commits:
-----------------

- 92a9055: Update matplotlib dep.
- 713f69e: Update matplotlib requirement from 3.2.1 to 3.2.2
- 2f60ecd: Add tools to study one-body state parity.
- 041c705: Update pathos requirement from 0.2.5 to 0.2.6
- b47a576: Update pathos from 0.2.5 to 0.2.6
- d53a1f7: Add doit analysis for entropy.
- 0398964: Fix bug related to grabbing framse from PSI files.
- 3c3dc65: Update pylint to version 2.5.3.
- 4a96e25: Update pylint from 2.5.2 to 2.5.3
- 6781cca: Update tqdm requirement from 4.46.0 to 4.46.1
- eefe263: Update tqdm from 4.46.0 to 4.46.1
- 3336290: Update mypy requirement from 0.770 to 0.780
- accb3c8: Merge branch 'pyup-update-mypy-0.770-to-0.780'
- 8e70c25: Merge branch 'master' into pyup-update-mypy-0.770-to-0.780
- 8d2c09a: Update numpy requirement from 1.18.4 to 1.18.5
- 9fcbbcc: Update numpy from 1.18.4 to 1.18.5
- 0f45c51: Update mypy from 0.770 to 0.780
- db23bef: Update pytest requirement from 5.4.2 to 5.4.3
- 46b378c: Update pytest from 5.4.2 to 5.4.3
- 88385f2: Update pandas requirement from 1.0.3 to 1.0.4
- 55a782d: Update pandas from 1.0.3 to 1.0.4
- 096ba44: Update requiremenets.txt.
- 2022670: Merge pull request 64 from f-koehler/dependabot/pip/pyside2-5.15.0
- 1b55093: Update pyside2 requirement from 5.14.2.1 to 5.15.0

Description:
------------
This update changes some of the projects supporting infrastructure.
We pinned the versions of dependencies and use [requires.io](requires.io) to get informed about updates.

Included Commits:
-----------------
- b79dfb0: Add `sympy==1.6` to `requirements.txt`.
- 8997b64: Merge pull request 63 from f-koehler/dependabot/pip/sympy-1.6
- fb760a5: Update sympy requirement from 1.5.1 to 1.6
- b204c98: Merge branch 'master' of github.com:f-koehler/mlxtk
- abb91a4: Change titles in g1 and g2 animations to indicate that the absolute value is shown.
- bf26267: Update tuna version in `pyproject.toml`.
- df99ae2: Merge pull request 61 from f-koehler/pyup-update-tuna-0.4.4-to-0.4.5
- 737a1be: Update tuna from 0.4.4 to 0.4.5
- 42bde68: Add pyup.io and requires.io badges.
- 0e6a337: Remove some old tools.
- b388a26: Generate `requirements.txt` for pyup/requires.io.
- 374c652: Pin dependency versions.
- c40c81d: Allow the `read_psi_ascii` function to read wave function files in addition to psi files.
- 5860b98: Add `.editorconfig`.
- 263674d: Add `dephell` as dev dependency.

Description:
------------
This is a small update release which updates some dependencies and adds some gauge related flags to the propagation task.
Furthermore, `SingleSpecies`-simulations now have a method to get only the postition operator as a one-body operator.

Included Commits:
-----------------
- 9a74fc7: Reformat code using `yapf==0.30.0`.
- 6927cc9: Merge pull request 58 from f-koehler/dependabot/pip/yapf-tw-0.30
- 5ebac82: Update yapf requirement from ^0.29 to ^0.30
- 51780e3: Enforce new versions of some dependencies.
- a4a5faa: Add gauge related flags to propagation task.
- 1b81108: Add function to obtain the position operator to `single_species` systems.
- c541e66: Update pandas dependency.