fix requirements for plan2sobp

[grzanka]

To properly install plan2sobp you need to install pymchelper via pipx install pymchelper[dicom] instead of pipx install pymchelper. The last command will install only basic features of the converter, namely conversion to plain text files.

This pull request includes several changes to improve the handling of optional dependencies and enhance the readability of the code. The most important changes include adding error handling for missing dependencies, updating the installation instructions, and improving code formatting.

Error handling for missing dependencies:

• pymchelper/utils/radiotherapy/plan.py: Added error handling for missing scipy and pydicom dependencies in the __init__ and load_DICOM_VARIAN methods, respectively. [1] [2]

Installation instructions:

• docs/install.rst: Updated the installation instructions to include the plan2sobp program by specifying the pymchelper[dicom] option.

Code formatting improvements:

• pymchelper/utils/radiotherapy/plan.py: Reformatted argument definitions in the main function for better readability. [1] [2] [3]
• setup.py: Consolidated numpy version specifications for different Python versions into a more compact format.

Dependency updates:

• setup.py: Updated the dicom extra to include both pydicom and scipy packages.

[grzanka]

Should work now, you can test with this branch state.

root@bc82196b495f:/# pipx install git+https://github.com/DataMedSci/pymchelper@605-missing-pydicom-dependency#egg=pymchelper[dicom]
  installed package pymchelper 2.7.5+rev2, installed using Python 3.11.2
  These apps are now globally available
    - convertmc
    - mcscripter
    - plan2sobp
    - runmc
done! ✨ 🌟 ✨
root@bc82196b495f:/# plan2sobp -h
usage: plan2sobp [-h] [-b beam_model.csv] [-i] [-x] [-y] [-f FIELD_NR] [-d] [-n] [-s SCALE] [-c COLS] [-v] [-V] input_file [output_file]

positional arguments:
  input_file            path to input file in IBA '.pld'-format or Varian DICOM-RN.
  output_file           path to the SHIELD-HIT12A/FLUKA output_file. Default: 'sobp.dat'

options:
  -h, --help            show this help message and exit
  -b beam_model.csv     optional input beam model in commasparated CSV format
  -i, --flip            flip XY axis of input (x -> y and y -> x)
  -x, --xflip           flip x axis of input (x -> -x)
  -y, --yflip           flip y axis of input (y -> -y)
  -f FIELD_NR, --field FIELD_NR
                        select which field to export, for dicom files holding several fields. '0' will produce multiple output files with a running number.
  -d, --diag            print diagnostics of input dicom file, but do not export data
  -n, --nominal         save nominal energies instead of beam model energies
  -s SCALE, --scale SCALE
                        number of particles*dE/dx per MU
  -c COLS, --columns COLS
                        number of columns in output file. 5, 6, 7 col format supported, default is 7.
  -v, --verbosity       increase output verbosity
  -V, --version         show program's version number and exit
root@bc82196b495f:/#