EnergyFileReader: Check if input is an empty file

BoxReader for .box file. Needed in PQEnalyzer box plotting feature.

Pylint is not set as a dependency. You have to install it manually. Should it be a dependency at all?

BaseReader does not check for empty files. In my opinion, since function such as calculate_number_of_frames fail when files are empty, I would raise an Exception to ensure that the function to work properly.

I did not enter the log file name after the --log-file flag:

$ build_nep_traj zif8-md-03 zif8-md-06 zif8-md-09 --use-forces --use-virial -o zif8_out.traj --log-file --total-ratios 80:10:10 

***header ***

Traceback (most recent call last):
  File "/home/bre/.conda/envs/pq/bin/build_nep_traj", line 8, in <module>
    sys.exit(main())
             ^^^^^^
  File "/home/bre/.conda/envs/pq/lib/python3.12/site-packages/PQAnalysis/cli/build_nep_traj.py", line 82, in main
    writer = NEPWriter(filename=args.output, mode=args.mode)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<@beartype(PQAnalysis.io.nep.NEPWriter.NEPWriter.__init__) at 0x7fa4223cc5e0>", line 59, in __init__
  File "/home/bre/.conda/envs/pq/lib/python3.12/site-packages/PQAnalysis/io/nep/NEPWriter.py", line 55, in __init__
    self.logger = setup_logger(self.logger)
                  ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/bre/.conda/envs/pq/lib/python3.12/site-packages/PQAnalysis/utils/custom_logging.py", line 47, in setup_logger
    print_header(stream=file)
TypeError: print_header() got an unexpected keyword argument 'stream'

Maybe provide a more detailed error description or check if string of log file is given.

for both qmcfc and pq

Build a more efficient version of frame_generator:

• Directly skip the non-indexed frames
• Build benchmark for this method

Describe the bug
pytest does not start in dev, since it could not recognize arguments.

To Reproduce
Steps to reproduce the behavior:

• Clean environment with Python 3.12.3: python -m venv venv
• Activate env: source venv/bin/activate
• Install project: pip install .
• Try testing: pytest (Maybe add as depedency, for easy use)

$ pytest
ERROR: usage: pytest [options] [file_or_dir] [file_or_dir] [...]
pytest: error: unrecognized arguments: --cov=PQAnalysis --cov-report=html
  inifile: /home/jog/projects/PQAnalysis/pytest.ini
  rootdir: /home/jog/projects/PQAnalysis

Expected behavior
Should result in test execution.

Create function to convert timesteps into simulation time in fs or ps

Is your feature request related to a problem? Please describe.
In order to read in multiple file formats it would really make sense to have multiple subclasses from FrameRead to make it much cleaner implementationwise. So depending on the input the TrajectoryReader class can decide which one to call.

Is your feature request related to a problem? Please describe.
The MSD routine would need a possibility to choose the center of mass of a molecule as a target.

Describe the solution you'd like
The grammar could be adapted for molecular selection.

Additional context
If it is possible to select by molecules e.g. H ₂ the center of mass can be used as target. The selection is using AtomicSystem which can call the property center of mass.

Is your feature request related to a problem? Please describe.
The beartype exceptions are quiet difficult to read and in general not applicable for API usage. Therefore, it would be best to catch them on package level and reraise them.

Describe the solution you'd like
sys.excepthook

Since nep needs uppercased atom names build_nep_traj should generate output including the atomnames as their uppercase version.

To Reproduce
Run nep with test.xyz and train.xyz files with unchanged output files from build_nep_traj. Generates an input error when trying to read train.xyz

Combine all the CLIs into a single pq CLI that would allow the different tools to be called from a single tool. This way users can see the different tools that have been built into the project.

Describe the bug
Logger printing stacktrace for type checking.

To Reproduce

from PQAnalysis.analysis import RDF

RDF(1,1,1)

Expected behavior
If environment variable PQANALYSIS_BEARTYPE_LEVEL is not set to DEBUG it shouldn't print any stacktrace

Energy should, in my opinion, contain the base name of the original energy_filename, so that it can be distinguished from other Energy classes

Describe alternatives you've considered
Use either ase as dependency or custom frame reader

Is your feature request related to a problem? Please describe.
In order to work with large trajectories that do not fit into the RAM, as window generator function directly from a trajectory would be really helpful.

Describe the solution you'd like
Add new method to TrajectoryReader, which calls the frame_generator method.

The length of info dictionary has to be equal to the length of data. Is the current error message when the worng MDEngineFormat is provided.

insert logo

Is your feature request related to a problem? Please describe.
There are some unit package out there. Haven't had the time to test them all.
But the units handling is still to much hardcoding at the moment.

Describe the solution you'd like
Either find a nice external package or build one specialized for PQAnalysis

create release.yml

Is your feature request related to a problem? Please describe.
Rewrite RDFLogfile with a logger to make output format consistent

Describe the solution you'd like
Probably the best way would be to implement a new logger for all analysis submodukes to maje output of PQanalysis consistent

Describe alternatives you've considered
maybe inherit from a AnalysisLogFilelogger to customize RDFlogFile writing