v2.0.0 (#92)

- Remove Python 3.5 from testing. - Remove deprecated functions. - Use f-strings for printing. * Replace numexpr by numba (#77) * Shorten runtime of examples * Deg/Unwrap/Lag => closes #76 (#78) * f-strings: fix existing and implement forgotten (#80) * Change `htarg`/`ftarg` to dicts internally (#81) * Always assume isotropy for {e;m}perm by default * Rename `transform.get_spline_values` -> `transform.get_dlf_points` * Undo #26 for consistency reasons * Documentation (#82) * Ensure src/rec are not altered (#83) * Renaming (#84) * Renaming all Hankel- and Fourier-routines * `factAng` -> `ang_fact` * `{fht;qwe;quad}arg{s}` -> `htarg` * `{qwe}arg{s}` -> `ftarg` * Closes #13 * Use `kwargs` for settings (#85) * All settings (`xdirect`, `ht`, `htarg`, `ft`, `ftarg`, `loop`, `verb`) are now extracted from `kwargs`. This makes it possible that all model-functions take the same keyword-arguments; warnings are raised if a particular parameter is not used in this function, but it doesn't fail (it fails, however, for unknown parameters). Pure positional calls including those parameters will therefore not work any longer. Closes #14 * Adjust manual and docstrings, intersphinx (#86) * EMArray: .amp and .pha are now methods (#87) * Fix dlf if 'fht' provided (#88) * Replace outer by broadcasting * htarg and ftarg MUST be dicts (#89) * Only one possibility for each method of `ht` and `ft` * Undo #7a9437ca * Reduce top namespace (#91)
emsig · Apr 29, 2020 · eeba70b · eeba70b
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diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -0,0 +1,18 @@
+# Required
+version: 2
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  configuration: docs/conf.py
+
+# Optionally build your docs in additional formats such as PDF and ePub
+formats: all
+
+# Optionally set the version of Python and requirements required to build your
+# docs
+python:
+  version: 3.7
+  install:
+    - requirements: requirements-dev.txt
+    - method: pip
+      path: .
diff --git a/.travis.yml b/.travis.yml
@@ -4,24 +4,20 @@ language: python
 # which follows the `PYTHON=X.Y` var.
 matrix:
   include:
-    - python: 3.5
-      env: PYTHON=3.5 CHAN="defaults" PCKGS="numexpr matplotlib" TEST="--mpl" INST="pytest-mpl scooby"
     - python: 3.6
-      env: PYTHON=3.6 CHAN="defaults" PCKGS="numexpr matplotlib" TEST="--mpl" INST="pytest-mpl scooby"
+      env: PYTHON=3.6 PCKGS="matplotlib" TEST="--mpl" INST="pytest-mpl scooby"
     - python: 3.7
-      env: PYTHON=3.7 CHAN="defaults" DEPLOY_PYPI=true PCKGS="numexpr matplotlib" TEST="--mpl" INST="pytest-mpl scooby"
-    - python: 3.8  # => without matplotlib, numexpr
-      env: PYTHON=3.8 CHAN="defaults" PCKGS="" TEST="" INST=""
-    - python: 3.7  # => with conda-forge
-      env: PYTHON=3.7 CHAN="conda-forge" PCKGS="" TEST="" INST=""
-    - python: 3.7  # => without matplotlib, numexpr
-      env: PYTHON=3.7 CHAN="defaults" PCKGS="" TEST="" INST=""
+      env: PYTHON=3.7 DEPLOY_PYPI=true PCKGS="matplotlib" TEST="--mpl" INST="pytest-mpl scooby"
+    - python: 3.8  # => without matplotlib
+      env: PYTHON=3.8 PCKGS="" TEST="" INST=""
+    - python: 3.7  # => without matplotlib
+      env: PYTHON=3.7 PCKGS="" TEST="" INST=""
     - python: 3.7  # => just linkcheck
-      env: PYTHON=3.7 CHAN="defaults" CHCKLNKS=true PCKGS="" TEST="" INST="sphinx numpydoc sphinx_rtd_theme sphinx_numfig sphinx_gallery memory_profiler"
+      env: PYTHON=3.7 CHCKLNKS=true PCKGS="matplotlib pillow" TEST="" INST="sphinx numpydoc sphinx_rtd_theme sphinx_numfig sphinx_gallery memory_profiler"
 
 jobs:
   allow_failures:  # env must be EXACTLY as env allowed to fail.
-    - env: PYTHON=3.7 CHAN="defaults" CHCKLNKS=true PCKGS="" TEST="" INST="sphinx numpydoc sphinx_rtd_theme sphinx_numfig sphinx_gallery memory_profiler"
+    - env: PYTHON=3.7 CHCKLNKS=true PCKGS="matplotlib pillow" TEST="" INST="sphinx numpydoc sphinx_rtd_theme sphinx_numfig sphinx_gallery memory_profiler"
 
 install:
   - sudo apt-get update
@@ -37,10 +33,14 @@ install:
   - conda info -a
 
   # Install and activate environment, install packages
-  - conda create -q -n test-environment -c $CHAN python=$PYTHON numpy scipy pytest pytest-cov $PCKGS
+  - conda create -q -n test-environment python=$PYTHON numpy scipy numba pytest pytest-cov $PCKGS
   - source activate test-environment
   - pip install setuptools_scm coveralls pytest-flake8 $INST
-  - python setup.py install
+  - if [ "$CHCKLNKS" = true ]; then
+        pip install .;
+    else
+        python setup.py install;
+    fi
   - cp tests/matplotlibrc .
 
 script:  # No pytest for linkcheck-run.
@@ -50,8 +50,8 @@ script:  # No pytest for linkcheck-run.
         pytest --cov=empymod --flake8 $TEST;
     fi
 
-after_success:  # No coveralls for linkcheck-run.
-  - if [ "$CHCKLNKS" = "" ]; then coveralls; fi
+after_success:
+  - if [ "$CHCKLNKS" == "" ]; then coveralls; fi
 
 deploy:
   provider: pypi

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -2,12 +2,98 @@ Changelog
 #########
 
 
-Minor v1.10.x
-"""""""""""""
+Version 2
+~~~~~~~~~
+
+
+v2.0.x
+""""""
+
+
+v2.0.0: Numba
+-------------
+
+**2020-04-29**
+
+This version is backwards incompatible and requires Python 3.6+.
+
+- Numba:
+
+  - Using ``numexpr`` is no longer a possibility. Instead, ``numba`` is a new
+    dependency. All four kernel routines (``wavenumber``, ``greenfct``,
+    ``reflections``, and ``fields``) are now numba-jitted functions.
+
+- Removed:
+
+  - Removed all deprecated functions.
+  - Dropped support for Python 3.5; moved to f-strings.
+  - Dropped testing for channel conda-forge. The problems encountered at the
+    early development cycle of empymod with conda-forge do not exist any
+    longer.
+
+- New defaults:
+
+  - ``EMArray``: ``.amp`` and ``.pha`` are now methods, not properties. Phase
+    takes three optional boolean parameters ``deg=False``, ``unwrap=True``, and
+    ``lag=True``, to get radians or degrees; unwrapped or not; and lag or lead
+    defined phases.
+  - The parameters ``epermV`` and ``mpermV`` are set to the values of
+    ``epermH`` and ``mpermH``, respectively, if not provided (hence assuming
+    isotropic behaviour). Before they were set to ones if not provided.
+
+- Renaming:
+
+  - ``transform.fht`` -> ``transform.hankel_dlf``
+  - ``transform.hqwe`` -> ``transform.hankel_qwe``
+  - ``transform.hquad`` -> ``transform.hankel_quad``
+  - ``transform.ffht`` -> ``transform.fourier_dlf``
+  - ``transform.fqwe`` -> ``transform.fourier_qwe``
+  - ``transform.fftlog`` -> ``transform.fourier_fftlog``
+  - ``transform.fft`` -> ``transform.fourier_fft``
+  - ``transform.fhti`` -> ``transform.get_fftlog_input``
+  - ``transform.get_spline_values`` -> ``transform.get_dlf_points``.
+  - ``factAng`` -> ``ang_fact``
+  - In ``htarg``-dict: ``fftfilt``-> ``dlf`` (filter name for Hankel-DLF)
+  - In ``ftarg``-dict: ``fhtfilt``-> ``dlf`` (filter name for Fourier-DLF)
+  - In ``ftarg``-dict: ``ft``-> ``kind`` (method in Fourier-DLF [sine/cosine])
+  - Only dictionaries allowed for ``htarg`` and ``ftarg``; strings, lists, or
+    tuples are not allowed any longer. They are also dictionaries internally
+    now.
+  - ``ht``: There is only one unique name for each method:  'dlf', 'qwe',
+    'quad'.
+  - ``ft``: There is only one unique name for each method:  'dlf', 'qwe',
+    'fftlog', 'fft'.
+  - Within ``transform``, change ``fhtarg``, ``qweargs``, and ``quadargs`` to
+    ``htarg``; ``qweargs`` to ``ftarg``.
+
+- Other changes:
+
+  - All settings (``xdirect``, ``ht``, ``htarg``, ``ft``, ``ftarg``, ``loop``,
+    ``verb``) are now extracted from ``kwargs``. This makes it possible that
+    all ``model``-functions take the same keyword-arguments; warnings are
+    raised if a particular parameter is not used in this function, but it
+    doesn't fail (it fails, however, for unknown parameters). Pure positional
+    calls including those parameters will therefore not work any longer.
+  - Undo a change introduced in v1.8.0: ``get_dlf_points`` is calculated
+    directly within ``transform.fht`` [`empymod#26
+    <https://github.com/empymod/empymod/issues/26>`_].
+  - Ensured that source and receiver inputs are not altered.
+  - Significantly reduced top namespace; only functions from ``model`` are
+    loaded into the top namespace now.
+
+
+Version 1
+~~~~~~~~~
+
+
+v1.10.x
+"""""""
 
 v1.10.6: Various azimuths and dips at same depth
 ------------------------------------------------
 
+**2020-03-04**
+
 - ``empymod.bipole``
 
   - In the source and receiver format ``[x, y, z, azimuth, dip]``, azimuth and
@@ -22,6 +108,8 @@ v1.10.6: Various azimuths and dips at same depth
 v1.10.5: Continuously in- or decreasing
 ---------------------------------------
 
+**2020-02-21**
+
 This is a small appendix to v1.10.4: Depths can now be defined in increasing or
 decreasing order, as long as they are consistent. Model parameters have to be
 defined in the same order. Hence all these are possible:
@@ -104,8 +192,8 @@ v1.10.0: Loop source and receiver
   more inclusive and open the project for new contributors.
 
 
-Minor v1.9.x
-"""""""""""""
+v1.9.x
+"""""""
 
 v1.9.0 : Laplace
 ----------------
@@ -128,8 +216,8 @@ v1.9.0 : Laplace
 - Other tiny improvements and bug fixes.
 
 
-Minor v1.8.x
-""""""""""""
+v1.8.x
+""""""
 
 
 v1.8.3 : Scooby
@@ -196,7 +284,7 @@ v1.8.0 : Hook for Cole-Cole IP and similar
 
 - ``model.wavenumber`` renamed to ``model.dipole_k`` to avoid name clash with
   ``kernel.wavenumber``. For now ``model.wavenumber`` continues to exist, but
-  raises a depreciation warning.
+  raises a deprecation warning.
 
 - ``xdirect`` default value changed from ``True`` to ``False``.
 
@@ -217,8 +305,8 @@ for the user-facing routines in ``model``:
   Move there in version 2.0.
 
 
-Minor v1.7.x
-""""""""""""
+v1.7.x
+""""""
 
 
 v1.7.3 : Speed improvements following benchmarks
@@ -320,8 +408,8 @@ Merge ``empyscripts`` into ``empymod`` under ``empymod.scripts``.
   ``empymod`` directly.
 
 
-Minor v1.6.x
-""""""""""""
+v1.6.x
+""""""
 
 
 v1.6.2 : Speed improvements for QUAD/QWE
@@ -431,8 +519,8 @@ are affected.
 - Bugfix in ``model.wavenumber`` for ``ab=[36, 63]`` (zeroes).
 
 
-Minor v1.5.x
-""""""""""""
+v1.5.x
+""""""
 
 
 v1.5.2 : Improved DLF
@@ -498,8 +586,8 @@ v1.5.0 : Hankel filter wer_201_2018
 - Version of manuscript submission to geophysics for the DLF article.
 
 
-Minor v1.4.x
-""""""""""""
+v1.4.x
+""""""
 
 
 v1.4.4 : TE/TM split
@@ -570,8 +658,8 @@ push it to 1.4.1; so there isn't really a version 1.4.0.]
     only fullspace solution (all for the diffusive approximation).
 
 
-Minor v1.3.x
-"""""""""""""
+v1.3.x
+"""""""
 
 
 v1.3.0 : New transforms QUAD (Hankel) and FFT (Fourier)
@@ -607,8 +695,8 @@ v1.3.0 : New transforms QUAD (Hankel) and FFT (Fourier)
 - Bug fixes and documentation improvements
 
 
-Minor v1.2.x
-""""""""""""
+v1.2.x
+""""""
 
 
 v1.2.1 : Installable via pip and conda
@@ -661,8 +749,8 @@ v1.2.0 : Bipole
 - Bug fixes
 
 
-Minor v1.1.x
-""""""""""""
+v1.1.x
+""""""
 
 
 v1.1.0 : Include source bipole
@@ -692,8 +780,8 @@ v1.1.0 : Include source bipole
 - Bug fixes
 
 
-Minor v1.0.x
-""""""""""""
+v1.0.x
+""""""
 
 
 v1.0.0 : Initial release

diff --git a/CREDITS.rst b/CREDITS.rst
@@ -4,9 +4,15 @@ Credits
 This project was initiated and is still mainly maintained by **Dieter
 Werthmüller**. However, it is a community effort as many people helped to
 improve it over time. The copyright is therefore attributed to «The empymod
-Developers», which includes everyone involved in the project. In the following
-some particular credits.
+Developers», which includes everyone involved in the project.
 
+Code contributors:
+
+- `Dieter Werthmüller <https://github.com/prisae>`_
+
+
+There are various other ways how people have contributed. In the following some
+particular credits.
 
 Special thanks to
 
@@ -27,14 +33,18 @@ Special thanks to
   `github.com/empymod/article-fdesign
   <https://github.com/empymod/article-fdesign>`_).
 
+- **The electromagnetic group** of Aleksander Mousatov at the Mexican Petroleum
+  Institute, Mexico City (see note below).
+
 
 Many more helped through their feedback, feature request, bug reports etc. A
 certainly incomplete list (get in touch if you think you should appear here):
 
-- Seogi Kang
+- `Seogi Kang <https://github.com/sgkang>`_
 - Svein-Erik Hamran
 - Peter van der Sman
-- Ralph-Uwe Börner
+- `Ralph-Uwe Börner <https://github.com/ruboerner>`_
+- `Leon Foks <https://github.com/leonfoks>`_
 
 
 .. note::