Mlxtk

Description:
------------
This update re-enables SGE job arrays for faster job submissions and improves the code to detect HDF5 files.
Also missing units are now handle in a better way by introducing `ArbitraryUnit`.
Add save functionality to plot scripts.
Fix various small bugs.


Included Commits:
-----------------
- 2f522eb: Re-enable SGE job arrays to speed up submission of jobs.
- 0b498a5: Add output option to plot scripts; handle missing units by introducing `ArbitraryUnit`.
- 838ebff: Fix a bug in new HDF5 file detection.
- 85e9752: Reimplement HDF5 file detection.
- 5233be4: Format code.
- 765e48d: Add option to specify a different plot name for gpop plots.
- 3fc7fbf: Merge pull request 48 from f-koehler/dependabot/pip/mypy-tw-0.730
- 2db6647: Update mypy requirement from ^0.720 to ^0.730
- 49c7bdd: Add the option to multiple expval with a coefficient.
- d191a7b: Make plot energy use the UnitSystem.
- 571e026: Fix a bug in the regex for reading eigenenergies.
- 922a01a: Fix Hamiltonian with both wells in double well system.
- 77aebac: Fix a bug when not specifying an email adress when submitting SGE jobs that caused undeliverable emails to be sent.

Description:
------------
This updates adds and refactors many of the analysis scripts.

Included Commits:
-----------------
- 67f0a64: Add gitignore file to `wave_function_db` example.
- 586c584: Add doit analysis to plot energy evolution.
- af27691: Use multiple threads to render individual frames in `dmat2_gridrep_video`.
- b1812de: Fix `dmat2_gridrep_video` script.
- be40944: Read HDF5 files in `dmat2_slider` script.
- 9c94187: Add script to create a video for dmat2 in gridrep; currently there output file is not present, there is some issue with the temporary work dir.
- 942db7d: Make `dmat2_gridrep` output HDF5 files.
- a7acdcb: Add script to compute dmat2 (grid representation).
- 75e937d: Remove old debug print statement from I/O routine.
- 107b289: Add hdf5 I/O support for dmat2.
- 62e99ed: Re-enable units for `dmat2_slider` script.
- 0cecd97: Add doit function to plot gpop in momentum space.
- b4b073a: Reformat some files.
- 2bc7d2a: Add function to plot gpop heatmap in momentum space.
- 97854ff: Fix a bug in `dmat2_slider` script.
- 45bb31c: Refactor `thin_out_psi` script.
- c74744f: Update to h5py>=2.10.0.
- 27e5801: Merge pull request 47 from f-koehler/dependabot/pip/numpy-1.17.2
- 00f2cd9: Update numpy requirement from 1.17.1 to 1.17.2
- 5530862: Fix `gpop_slider` script to use unit system.
- 966fc94: Add doit analysis to extract initial expectation values.
- 2569cb0: Add function to extract final energies and format code.
- fbaa6ca: Handle 0 values properly when computing entropy.
- 890766c: Change default propagation name in `DefaultNatpopAnalysis`.
- dbd8eba: Add function to get all variables values to `parameter_selection`; store variable values in output of the default natpop analysis.
- 5a59a6e: Update example dodo file.
- 0c889f7: Add default analyses for natpop.
- 4c0a2b7: Add table tool to create a table from multiple 1d arrays by aligning the closest elements.
- 9596685: Add delta interaction unit; add function to format UnitSystem as a string; add a script to print the default unit system.
- 0b3acc8: Merge pull request 46 from f-koehler/dependabot/pip/numpy-1.17.1
- 001f17b: Update numpy requirement from 1.17.0 to 1.17.1

Description:
------------
This update adds signal analysis tools to find minima, maxima and roots of 1d signals. Furthermore tools to fetch the final total magnitudes from fixed number state analyses using doit.

Included Commits:
-----------------
- 22d8c87: Disable optimization of plots for now.
- 96c5940: Add tools to find minima, maxima and roots in 1d signals.
- 1f13401: Move `max_depletion` related analyses into the `natpop` module.
- bbdc7bc: Do not import methods directly into `mlxtk.doit_analyses`.
- aa13dd8: Add routines to load total magnitude from fixed number state analysis.

Description:
------------
This update introduces several new features:

- Analyses with doit:
- plotting for each simulation in a scan
- collecting data from each simulation in a scan
- some rudimentary routine to plot aggregated data (TODO: this might need some refactoring or maybe it is just easier to always write a custom task)
- Units:
- unit class: units are now objects and provide formatting routines as well as arithmetic operations
- units are loaded using the UnitSystem class which also allows to calculate missing units from known ones
- Make the code more robust agains flukes of network file systems (like NFS and AFS) by not using the sqlite backend for doit wherever possible
- Plotting of one body densities in momentum space by means of FFT.

Furthermore this release contains many minor additions, fixes and some updated dependencies.

Included Commits:
-----------------
- 2a956e4: Add an integrity check for `WaveFunctionDB`.
- 7787dd0: Add `__pow__` methods to `Unit`.
- e768230: Add function to plot expectation value for a parameter scan.
- ac02fde: Add multiply/divide functions to `Unit`.
- 2be441d: Port `plot_natpop` to use `UnitSystem`.
- fcf6cb4: Port `plot_gpop` to use `UnitSystem`.
- 181ce71: Add UnitSystem functionality to clean up the unit management code.
- 6d806a7: Change automatic name when collecting final expectation value.
- bfb293c: Add function to collect final expectation values.
- dc50336: Add functions to get/compute unit for speed/acceleration.
- b5a1139: Refactor `doit_analyses`; add function to create individual plots.
- f5e6791: Split `doit_analyses` into multiple files.
- af6dae8: Update doit-graph dependency.
- acd9471: Add function to collect data from parameter scans.
- 5de3083: Add function to determine the variables in a parameter selection.
- 7c8a0ae: Add option to execute `ParameterSelection.foreach` in serial, useful when employing parallel doit tasks.
- b226e27: Fix more pylint issues.
- 0814674: Fix a missing import related to `Wavefunction` vs `WaveFunction`.
- 45914b8: Add a function to generate subpaths from parameter selections.
- fb53c2b: Fix bugs related to plotting natpop with doit.
- 207389a: Fix a bug in doit individual plot.
- f676472: Pad number in doit plot file names.
- 133e292: Add missing typed-ast dependency for mypy.
- ef70a89: Implement some suggestions by pylint and mypy.
- 1000424: Add doit plotting for natpop.
- d87a069: Add doit-graph and mypy to dependencies.
- 6535187: Add decorator functions when plotting with doit.
- 7044c86: Move args.pickle to the right place.
- 38d133f: Properly close plots with doit and handle equal signs in file names.
- 6b1f77b: Introduce a general function to create plots for individual parameter entries of a parameter scan using doit.
- 14c39a9: Add PlotArgs2D class to handle plotting arguments.
- 3d343da: Add functionality to partition parameter selection according to a single parameter.
- e7e880c: Add a new module for doing analyses using doit.
- 4b80d7e: Add an exemplary dodo file to parameter scan example.
- 8503938: Add momentum unit to `gpop_slider.py`.
- 0673a83: Start to introduce wave vector units.
- a8de362: Merge pull request 43 from f-koehler/dependabot/pip/numpy-1.17.0
- 8fd5c58: Update numpy requirement from 1.16.4 to 1.17.0
- 79359ee: Add option to plot gpop heatmap in momentum space.
- 4940cf7: Actually respect `--momentum` option in `gpop_slider.py`.
- 55a1a71: Add function to transform gpop data to momentum space.
- 97fe9f2: Add option to transform to momemntum space when using `gpop_slider.py`.
- ad77175: Fix `gpop_slider.py` to default to HDF5 paths.
- cc544d8: Merge branch 'master' of github.com:f-koehler/mlxtk
- e02cfd0: Fix a bug when reading gpop from HDF5 without specifying the DOF.
- 2e440df: Move pylint to dev dependencies.
- 5897a35: Use json backend for simulation states.
- a35546a: Remove sphinx dependency for now.
- 1d172d8: Fix a bug in sge submit.
- d2ebf02: Use in memory sqlite databases where a persistent doit state file is not required.
- 7e249d8: Merge pull request 42 from f-koehler/dependabot/pip/numba-gte-0.43.1-and-lt-0.46.0
- 0129f43: Update numba requirement from >=0.43.1,<0.45.0 to >=0.43.1,<0.46.0
- 3222f8b: Proper modfunc handling to modify `scan_plot_gpop` and `scan_plot_natpop` plots.
- 7264d0a: Make `scan_plot_natpop` read HDF5 file by default.

Description:
------------
This update adds some HDF5 related I/O routines and a cursor class for matplotlib.
Furthermore, a new task type (`MCTDHBCreateWaveFunctionEnergyThreshold`) allows to create a single particle basis from bound or unbound eigenstates of a one-body operator.
Add some minor fixes/improvements and remove the deprecated sqlite databases for parameter scans.

Included Commits:
-----------------
- 838819f: Merge pull request 41 from f-koehler/dependabot/pip/pandas-gte-0.24.2-and-lt-0.26.0
- ab7f750: Merge branch 'master' of github.com:f-koehler/mlxtk
- fa2a44f: Show index range when using MCTDHBCreateWaveFunctionEnergyThreshold.
- 7b3a1a3: Update pandas requirement from ^0.24.2 to >=0.24.2,<0.26.0
- 27712d6: Remove dprecated sqlite databases from parameter scans.
- f04bcee: Add task to create a basis from (un-)bound single particle eigenstates.
- b64e6e4: Reformat code.
- 9885954: Add cursors for matplotlib.
- 4e9e8be: Merge pull request 40 from f-koehler/dependabot/pip/yapf-tw-0.28.0
- 2b495dd: Update yapf requirement from ^0.27.0 to ^0.28.0
- 67142d8: Add routine to read `fixed_ns` results from HDF5.
- 88b8a6e: Disable numba for the moment, there is a bug leading to a compilation failure. This no priority at the moment.
- 072297b: Fix a bug when removing working directory in an exdiag task.
- 8c9d822: Fix load/save wave function routines.
- 54ef040: Fix some import issues in the `inout` module.
- b149f02: Disable interaction term when N=1 in included systems.
- 6fdcd32: Add option to save extra files from `qdtk_propagate.x`.
- b50999c: Use HDF5 file for `scan_plot_gpop` by default.
- cb5da69: Allow list types as number states when creating a MCTDHB wave function.
- d1fa587: Reset default log level to `DEBUG`.

Description:
------------
Starting with this release with store all data that is not input into `QDTK` again in HDF5 format.
This format offers much better performance when working with the data and also stores everything in a portable binary way.
Additionally contiunation runs are now possible when propagating/relaxing.

Included Commits:
-----------------
- 88d834c: Implement continuation runs.
- 57092d5: Add logging functionality to `TemporaryDir` class.
- 08f5a79: Run `qdtk_propagate.x` in a directory that is only removed upon successful completion.
- 664bfe0: Port the three most essential `plot_tools` to use the HDF5 file.
- f5eefda: Try to save as much data as possible from `qdtk_propagate.x` into a single HDF5 file.
- 56862b9: Add exact diagonalization to `harmonic_trap` example.
- 44755dc: Store expectation values and variances as HDF5 files.
- a5bd919: Use hdf5 for fixed number state analysis.
- 89fd51d: Simplify name of SGE log for job arrays.
- aa13f7b: Simplify name of SGE log.
- b39838f: Merge branch 'master' of github.com:f-koehler/mlxtk
- d70d1f4: Simplify name of SGE log.
- 95efd3b: Merge branch 'master' of github.com:f-koehler/mlxtk
- 51204a6: Perform propagation in temporary directory.
- affe6a3: Perform propagation in temporary directory.
- 9f86210: Add option to archive simulation sets.
- f30ce1a: Add two plot tools.
- baf005d: Remove old environment file.
- a4143fa: Add a configuration for an Anaconda environment.