Mlxtk

Description:
------------
This update adds a lot of functions to manually compute tensor elements in order to debug ml-x.
Furthermore, the `WaveFunctionDB` class now has a command to remove wave functions and a nice terminal UI for this purpose.
When using a gauge, the constraint error is added to `propagate.h5`.
Various small fixes are also included and I got rid of all relative imports in order to increase readability.

Included Commits:
-----------------
- 76ce10f: Get rid of relative imports.
- abbfe85: Add function to remove wave functions from wavefunction databases and a corresponding terminal based UI.
- ac0d5ea: Add constraint error to `propagate.h5`.
- d70fb3d: Streamline poetry and direnv workflow.
- 2a158e4: Fix workind-dir issue in `WaveFunctionDB`.
- bd082fe: Add `set_to` method to `Parameters` class.
- bdfaea8: Add minimum spacing option for peak detection; add .envrc file.
- 9533a5d: Work on one-body tensors in SPF representation.
- dae77d2: Implement arithmetic operations for arbitrary units.
- fe77985: Add function to compute kinetic/potential term in SPF representation.
- 78b0c57: Add naive implementation for dmat/dmat2 spf tensors.
- 1d37a70: Make normalization of density matrix tensors optional.
- c390175: Change code for dmat1 spf tensor.
- 88346c9: Add function to compute dmat2 in SPF representation.
- d8e00dc: Rename function to compute dmat.
- 36e8297: Add function to compute dmat in SPF representation; move number state related code to extra module.
- 772969b: Reformat code.
- 629d5c4: Add example to compute delta interaction in spf representation.
- 2dbece9: Add unittest for delta interaction (DVR representation).
- e664bd4: Add pytest dependency.
- 2fe5d5c: Add functions to directly get matrix/eigenvectors+eigenvalues from OperatorSpecification.
- 2787bb1: Move operator specification classes to extra module.
- 04d62e0: Add module to compute delta interaction tensors.
- c5110e8: Correctly copy indices when fixing a parameter in a parameter selection.
- c3e68ee: Add function to create directory.
- 395fdc5: Add script to extract MCTDHB spfs.
- 8bdf92f: Append to HDF5 files when computing dmat/dmat2.
- ca65854: Update vscode settings.
- 5da8838: Add function to list directories and to create relative symlinks.
- ef292de: Fix bug in momentum operator.
- 8c465f6: Add script to anmiate dmat.
- 8768649: Add missing string conversion for arbitrary units; add `remove_file` function.
- b025235: Add a script for 1b projector in the harmonic trap example.
- f388222: Add script to extract a single eigenfunction from a one-body operator.
- 8bdda5b: Set default simulation name.
- 9e9bebc: Add new task to compute overlap between MCTDHB wavefunctions.
- 388d1ce: Add function and task type to grab a frame from a psi file; store total magnitude in `fixed_ns` task.
- e02d654: Allow python==3.6.
- 2ef36ca: Update minimal required pyside2 version and allow Python 3.8.
- e206f16: Import single species systems.

Description:
------------
This update adds a lot of functionality most related to density matrix and correlation function analysis (plot scripts, I/O routines).
Furthermore, some more signal analysis routines are provided and expectation values can be plotted in frequency space.
Some specialized scripts have been added to create video animations.

Included Commits:
-----------------
- ff8e226: Update dependency `doit` to 0.32.0.
- d81e81c: Add momentum operator to single-species system.
- 32f493e: Reformat `signal.py`.
- 1562c59: Add routine to detect sign changes in a numpy array.
- 0edc105: Make fft available via a standard signal processing routine.
- 45ab892: Add option to plot expectation value in frequency space.
- 2f69500: Fix usage of plotting args in animate scripts.
- eb861eb: Add scripts to animate two-body density and g1/g2 correlation functions.
- ce9ba75: Merge branch 'master' of github.com:f-koehler/mlxtk
- 441cc76: Add diff option for `compute_g1` script.
- c1415e2: Add diff option for `compute_g1` script.
- b0fddc2: Add a script to animate one-body density; create symlinks instead of copying files when creating a slideshow.
- c653afc: Use temporary directory for `recreate_output.py` script.
- f892f98: Format code with `yapf=0.29.0`.
- 41552d7: Add a script to recreate output from a psi and an operator file.
- e65e7e9: Add another way to calculate two-body correlation functions.
- 784f010: Merge branch 'master' of github.com:f-koehler/mlxtk
- c2f19b1: Add support to read ASCII files to `slider_dmat` and `slider_dmat2`.
- 9fb824b: Merge pull request 54 from f-koehler/dependabot/pip/yapf-tw-0.29
- 66a1e10: Update yapf requirement from ^0.28 to ^0.29
- 6bef7e3: Add function to filter parameter scan combinations.
- af11c89: Add momentum option to `slider_gpop`.
- e3da941: Work on slider scripts for dmat1 and dmat2.
- 0e55b74: Update sliders for dmat/dmat2 (grid representation).
- 9b427df: Update gpop slider script.
- fe789ae: Remove old `.ui` files.
- bcb065e: Fix some linter issues.
- cbd8e8f: Add a slider script for g2.
- 439810e: Add g slider script.
- 47e8f13: Add I/O routines for g1/g2.
- ca39658: Add a script to compute g1.
- 605ed3b: Add script to compute g1.
- 91bdbe1: Add a script to compute g2 (have to change I/O though, also the dmat2_slider script needs fixing).
- 22a6582: Add a script to compute dmat2.
- 57df2e7: Change `compute_dmat.py` script to use a real temporary directory.
- 11f5d9a: Add script to for dmat analysis and improve dmat I/O routines.
- f3504cd: Remove some old tooling configs and cleanup script module.
- 9276244: Pin pickle protocol to v3.
- 2e28599: Merge pull request 53 from f-koehler/dependabot/pip/numpy-1.17.4
- d9a1c33: (origin/dependabot/pip/numpy-1.17.4) Update numpy requirement from 1.17.3 to 1.17.4
- f097af3: Save g1 and g2 as HDF5.
- e7bd29c: Add missing return value to `compute_g2` function.
- 67286b1: Add code to compute g1 and g2; add function load and save dmat to ASCII file in gridrep; add slider script to plot dmat.
- b2fc422: Add a script to create a slideshow from individual frames.
- 4db080a: Ignore missing image files in `create_slideshow`.

Description:
------------
Add some functions to create slideshow videos (currently for gpop and natpop).


Included Commits:
-----------------
- 9de2728: Fix output file names for slideshows.
- f8e6e24: Fix the output path in natpop slideshow.
- ce566cc: Add function to create a natpop slideshow.
- 0dd8b61: Add methods to create slideshows using `ffmpeg`.
- 8968ad2: Add some badges to highlight some information about the project.
- e2a4d23: Add tuna as a dependency.
- e0fd375: Merge pull request 52 from f-koehler/dependabot/pip/numpy-1.17.3
- d53b879: Merge pull request 51 from f-koehler/dependabot/pip/mypy-tw-0.740
- 8a74f86: Update numpy requirement from 1.17.2 to 1.17.3
- 6c82f20: Update mypy requirement from ^0.730 to ^0.740
- b8ca92b: Weight com operators with the particle number.
- 2b379f1: Remove `.pdf` from the list of default output formats and add doit task to plot variance.
- 74efa9b: Change file extension for variance files.
- 4d323c3: Set default output formats for doit plots to only `.png`.
- eb8d932: Fix propagation status check.

Description:
------------
This update changes only internals. The code for simulations and simulation sets has been refactored.


Included Commits:
-----------------
- af4bc9a: Fix `ParameterSelection` and `WaveFunctionDB` to work with the latest version of `SimulationSet`.
- edb65dd: Move cli argument handling to daughter classes.
- f1832c8: Refactor argument parsing in `Simulation` and `SimulationSet`.
- ed2f5c8: Add some type info for the splitted classes.
- fa134c9: Fix `parameter_scan.py` to reflect latest changes in the `SimulationSet` class.
- 50159d4: Add a subparsers variable to SimulationSet.
- c18deeb: Move construction of CLI interface for SimulaztionSet to extra file.
- c968f3a: Split simulation set into multiple files.
- 84998ac: Split simulation class into multiple files.

Description:
------------
This is a bugfix release to fix the propagation status check.


Included Commits:
-----------------
- 75ea20b: Fix another bug in propagation status check.
- e3ef666: Fix a typo in the output file path in the propagation status check.
- 9d2ce91: Merge pull request 50 from f-koehler/dependabot/pip/numba-gte-0.43.1-and-lt-0.47.0
- e79c6c6: Update numba requirement from >=0.43.1,<0.46.0 to >=0.43.1,<0.47.0

Description:
------------
Add subcommands to check the status of propagations.
Add a subcommand to list all lockfiles.
Fix some minor bugs including an issue with the logfiles created by SGE job arrays.

Included Commits:
-----------------
- 2d9978e: Another approach for the job array fix.
- 1d3121e: Try to fix a bug in job array.
- 6bebe84: Add propagation progress check to simulation set (and consequently to parameter scan and wave function db).
- b3e70b4: Add vscode task to format all python code.
- aeca624: Add command to check propagation status to `Simulation`-class.
- bd2de65: Merge pull request 49 from f-koehler/dependabot/pip/future-gte-0.17.1-and-lt-0.19.0
- b5f27dc: Add subcommand to check for lock files.
- e779025: (origin/dependabot/pip/future-gte-0.17.1-and-lt-0.19.0) Update future requirement from ^0.17.1 to >=0.17.1,<0.19.0
- a727a03: Add option to specify propagation name for `collect_final_energy` analysis.
- 251ffce: Remove unused variable.
- d8f5b74: Fix some minor bugs in natpop analysis with doit.
- adcd4fd: Fix a bug in `direct_plot` routine.