This would be very helpful, if you are still waiting for one last simulation but already want to look into the data.
One could even add this information as meta data to the HDF5 file.

• group type (ParameterScan, Simulation, Gpop, etc.)

It would be nice to list all the tasks of the scan simulations and run parts of them on-demand.

This would prevent running a simulation multiple times at once.

When submitting a parameter scan the script sleeps correctly after every 80th job, but also after the 0th. Easy to fix

When using large grids, the operators take up a lot of disk space. In some scenarios, e.g. when only computing one-body spectra which do not actually require the operator in file form one might save space by keeping the operator in memory only.

A more sophisticated way of locating the correct executables is needed to test new features that should not be used in production.

• Use QDTK_PREFIX environment variable (look for ${QDTK_PREFIX}/bin/qdtk_*.x)
• override executable path

E.g. -q for --queue

The expectation value names are too long!

Hi, as shown in the following full dependency graph of mlxtk, mlxtk requires numpy >=1.18,<1.19, mlxtk requires matplotlib >=3.2,<3.3 (matplotlib 3.2.1 will be installed, i.e., the newest version satisfying the version constraint), and directed dependency matplotlib 3.2.1 transitively introduces numpy >=1.11.

Obviously, there are multiple version constraints set for numpy in this project. However, according to pip's “first found wins” installation strategy, numpy 1.18.4 (i.e., the newest version satisfying constraint >=1.18,<1.19) is the actually installed version.

Although the first found package version numpy 1.18.4 just satisfies the later dependency constraint （numpy >=1.18,<1.19), such installed version is very close to the upper bound of the version constraint of numpy specified by matplotlib 3.2.1.

Once matplotlib upgrades，its newest version will be installed. Therefore, it will easily cause a dependency conflict (build failure), if the upgraded matplotlib version introduces a higher version of numpy, violating its another version constraint >=1.18,<1.19.

According to the release history of matplotlib, it habitually upgrates Numpy in its recent releases. For instance, matplotlib #15645 upgrated Numpy’s constraint from >=1.11 to >=1.12, and matplotlib #15698 upgrated Numpy’s constraint from >=1.12 to >=1.15.

As such, it is a warm warning of a potential dependency conflict issue for mlxtk.

Dependency tree

mlxtk - 0.8.2
| +- colorama(install version:0.4.3 version range:>=0.4,<0.5)
| +- doit(install version:0.32.0 version range:>=0.32,<0.33)
| | +- cloudpickle(install version:1.3.0 version range:*)
| +- future(install version:0.18.2 version range:>=0.18,<0.19)
| +- h5py(install version:2.10.0 version range:>=2.10,<3.0)
| +- jinja2(install version:2.11.2 version range:>=2.10,<3.0)
| | +- MarkupSafe(install version:2.0.0a1 version range:>=0.23)
| +- matplotlib(install version:3.2.1 version range:>=3.2,<3.3)
| | +- cycler(install version:0.10.0 version range:>=0.10)
| | | +- six(install version:1.14.0 version range:*)
| | +- kiwisolver(install version:1.2.0 version range:>=1.0.1)
| | +- numpy(install version:1.18.4 version range:>=1.11)
| | +- pyparsing(install version:3.0.0a1 version range:>=2.0.1)
| | +- python-dateutil(install version:2.8.1 version range:>=2.1)
| +- numpy(install version:1.18.4 version range:>=1.18,<1.19)
| +- numpy-stl(install version:2.11.2 version range:>=2.11,<2.12)
| +- pandas(install version:0.25.3 version range:>=0.25,<0.26)
| +- pathos(install version:0.2.5 version range:>=0.2,<0.3)
| +- prompt-toolkit(install version:3.0.5 version range:>=3.0.0,<4.0.0)
| | +- wcwidth(install version:0.1.9 version range:*)
| +- pyside2(install version:5.14.2.1 version range:>=5.14,<6.0)
| +- pyyaml(install version:5.3.1 version range:>=5.1,<6.0)
| +- scipy(install version:1.4.1 version range:>=1.3,<2.0)
| +- sympy(install version:1.6rc1 version range:>=1.4,<2.0)
| +- tabulate(install version:0.8.7 version range:>=0.8,<0.9)
| +- tqdm(install version:4.46.0 version range:>=4.39,<5.0)```


Thanks for your help.
Best,
Neolith

Implement the computation of a one body spectrum as a task to make use of all the nice mlxtk when dealing with single particle problems.

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• Update dependency doit to ^0.36.0

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I'm very interested in ML-MCTDH-X simulations and I tried to install this toolkit. The problem is: it depends on the QDTK package, but I couldn't find QDTK anywhere on the web. Where can I find and install QDTK?

• full parameter table
• only constants
• only variables
• everything (summary)

Use rsync and sshpass to synchronize running simulations. Normally the data is synced using the AFS only after the job terminated.

• composition of sshpass/rsync command (407d28f)
• tool to accept the server keys of all nodes (4b2e093)
• store job ids when submitting (to look up the correct nodes) (e2d25a4, 3908f5e, 7da13e2)
• actual synchronization

• energy_diff (implemeted in 154a70e)
• norm_diff (implemented in fe967f2)
• overlap_diff (implemented in 40a6883)
• expval_diff (implemented in 662d929)

Due to my recent fails where for some reason some parts of parameter scans where rerun (which cost me a lot of data and forced me to rerun two complete scans) it would be nice to perform a dry run first to see what work will be performed

The --queue should have a default option (e.g. quantix.q)

Given <O> and <O²>, compute the variance <(O-<O>)²>=<O²>-<O>². Just implement a new task type for this purpose.

Dependabot can't resolve your Python dependency files.

As a result, Dependabot couldn't update your dependencies.

The error Dependabot encountered was:

Updating dependencies
Resolving dependencies...
                                                                                
[SolverProblemError]                                             
Because mlxtk depends on doit-graph (^0.4) which doesn't match any versions,  
 version solving failed.                                                      
                                                                                
update [--no-dev] [--dry-run] [--lock] [--] [<packages>]...

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The parameter scan should issue a warning/error when trying to scan over a non-existent parameter.

Handle SIGTERM and pass it to subprocesses, even though the qdtk_*.x executables do not handle it at the moment.

Automatically determine when to do a continuation run

Compute the reduced two body density from a restart file (not the dynamic one from a psi file)

• Task/Simulation support
• I/O routines / HDF5 (3085b08)
• Plotting tool (3085b08)

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• expval I/O
• basic plotting program
• each expval as a tab (commit 7165c19)
• embed into scan_view (commit 7165c19)
• controls to toggle real/imaginary part (commit 8474aa9)
• add the usual matploblib controls to each tab (commit f7131e8)
• only show tabs if more than one expval is available (commit a63226a)

Call the open_plot method if enter or return is pressed

Store log messages in files as well.

Show origin file in the title bar and also maybe simulation parameters as plot title

Use these labels in the plotting programs

Before computing the difference between two wave functions, check if they have the same dimension. If the shape changed the wavefunction is not up to date.

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Use scipy.interpolate.griddata to interpolate if times/grid differ. This will be useful especially when comparing different grids.