libdlf and scooby

The digital linear filters are outsourced to libdlf, reducing the lines of code of empymod by over 50%. In addition to the new requirement libdlf, scooby is added as a requirement. Most user questions can be adressed much better if they provide the output of empymod.Report() - however, most users do not have scooby installed. Having it as a requirement will make support smoother. Both new requirements are very lightweight modules, having at most numpy as a dependency.

• Filters:

  • The digital linear filters are outsourced to libdlf (https://github.com/emsig/libdlf). Note: How to access filters changed! The old way still works, with a deprecation note stating how to change your code. The old way will be removed in v3.0.

• Examples:

  • @efinden expanded the "Cole-Cole IP" example.

• Maintenance:

  • Bumped the minimum requirements to:

    • Python 3.9
    • SciPy 1.9
    • Numba 0.53
    • libdlf (NEW requirement)
    • scooby (NEW requirement)

  • Testing: added Python 3.12, dropped Python 3.8.

  • Fix remaining outdated python setup.py commands.

  • Many small things to keep the package updated.

Flexible dipole coordinates

• Modelling routines: The definition of the coordinates for dipole, dipole_k, and analytical is now more flexible (x and y coordinate can now have different dimension, as long as one is a scalar).

• Bumped the minimum requirements to:

  • Python 3.8
  • NumPy 1.19
  • SciPy 1.5
  • Numba 0.50

• Bug fixes, small improvements and maintenance:

  • Cleaned-up the namespace by setting dir() explicitly.
  • Testing: added Python 3.11, dropped Python 3.7.
  • Adjust copyright notice to only include original year, so it has not to be adjusted each year.

Minimum offset

• Minimum offset:

  Change regarding the enforced minimum horizontal offset, which can be set
  through empymod.set_minimum(min_off=1e-3), where 1e-3, hence 1 mm, is the
  default. Until now, responses for smaller offsets were set to NaN. New, they
  return the response for the minimum offset. The raised warning stays the
  same.

• Maintenance

  • Exclude scipy!=v1.9.0 from MacOS/Windows test.
  • Replace pytest-flake8 by plain flake8.
  • Change the way spacing and shift are calculated in
    fdesign.print_result to avoid numerical precision issues.
  • Replace deprecated sphinx-panels with sphinx-design.

I/O & CLI

• I/O & CLI:

  • New Command-Line Interface (CLI) for the top-level modelling functions
    bipole, dipole, loop, and analytical. Consult the manual
    for its description, or type in your terminal empymod --help. Note that
    the CLI is a simple wrapper and currently lacks proper logging.
  • New module io to save and load inputs and data.

• Maintenance:

  • Improved load time by lazy-loading matplotlib and some scipy submodules.
  • Removed the file runtests.sh; uses make instead.

Squeeze

• The main modelling routines bipole, dipole, loop, and
  analytical take a new keyword argument squeeze, which is set to
  True by default. If true, the output is squeezed (status quo); if false,
  the output is always a three-dimensional array (nfreqtime, nrec, nsrc).

• One can define new +np.infty as interface. Only use-case is to enforce a
  coordinate system in a two-layer case with an interface at z (see example
  coordinate system in the educational section of the gallery).

• Documentation:

  • Expanded note on FFTLog.
  • Expanded note on coordinate system.
  • Changed the description from optional to default: xyz in the main
    modelling routines.

• Maintenance:

  • Use scipy through conda in CI.
  • Fix do_3d_projection for matplotlib>3.5.0.

Random noise example

• New example: Random noise for f-domain CSEM data.

• Maintenance:

  • Change in the njit-settings of kernel.wavenumber to work with numba>=0.54.
  • Cannot use matplotlib==3.5.0 to build the gallery (matplotlib#21688).
  • Move up the minimum matplotlib in the tests.
  • Added a Cron-job to run the tests monthly; every 20th at 14:14.

Bugfix np.seterr(all='ignore')

• Bumped the minimum requirements to:

  • Python 3.7
  • NumPy 1.17
  • SciPy 1.4
  • Numba 0.47

• Legacy clean-up: The kernel of empymod used to switch off all NumPy errors
  via np.seterr(all='ignore'). That means that any script or library that
  used empymod switched off all warnings from NumPy, which is not good. Since
  empymod v2 this does make even less sense, as the entire kernel is jitted
  with numba. This setting is therefore removed.

Bugfix azm/dip broadcasting

• Bugfix in empymod.bipole and empymod.loop when using various azimuths
  and dips (some cases used to cause a shape-mismatch error).

Theme change & streamline

• Streamline some things with emsig and emg3d:

  • Change theme from rtd to pydata.
  • New primary links https://emsig.xyz and https://empymod.emsig.xyz.
  • Move copyright from «The empymod Developers» to «The emsig community».
  • Slight rework of some parts of the docs.

Bugfix Windows int32/64

• Bugfix Windows int32/64.
• New example "Magnetotelluric".