Typos after v1.10.0, setuptools_scm (#50)

.gitignore

@@ -2,10 +2,19 @@
 __pycache__/
 
 # Sphinx
-_build/
+docs/_build/
 
 # Pytest and coverage related
 htmlcov
 .coverage
 .coverage.*
 .pytest_cache/
+
+# setuptools_scm
+empymod/version.py
+
+# Build related
+.eggs/
+build/
+dist/
+empymod.egg-info/

.travis.yml

@@ -30,7 +30,7 @@ install:
   # Install and activate environment, install packages
   - conda create -q -n test-environment -c $CHAN python=$PYTHON numpy scipy pytest pytest-cov $PCKGS
   - source activate test-environment
-  - pip install coveralls pytest-flake8 $INST
+  - pip install setuptools_scm coveralls pytest-flake8 $INST
   - python setup.py install
   - cp tests/matplotlibrc .
 

CHANGELOG.rst

@@ -2,6 +2,16 @@ Changelog
 #########
 
 
+v1.10.1: setuptools_scm
+-----------------------
+
+**2019-10-22**
+
+- Typos from v1.10.0; update example in ``model.loop``.
+- Implement ``setuptools_scm`` for versioning (adds git hashes for
+  dev-versions).
+
+
 v1.10.0: Loop source and receiver
 ---------------------------------
 

MAINTENANCE.rst

@@ -1,8 +1,7 @@
 Maintainers Guide
 =================
 
-A release is currently done completely manually, no automatic deployment is
-set up.
+Releases of ``empymod`` are currently done manually. This is the 'recipe'.
 
 
 Making a release
@@ -11,85 +10,81 @@ Making a release
 1. Update:
 
    - ``CHANGELOG``
-   - ``setup.py``: Version number, download url; DO NOT CHANGE THAT
-   - ``empymod/__init__.py``: Check version number, remove '.dev?'.
-   - ``README.md``: Remove all badges
+   - ``empymod/__init__.py``: Update version number.
 
-2. Check syntax of README::
+2. Remove any old stuff (just in case)::
 
-       python setup.py --long-description | rst2html.py --no-raw > index.html
+       rm -rf build/ dist/ empymod.egg-info/
 
-3. Remove any old stuff (just in case)::
+3. Push it to GitHub, create a release tagging it
 
-       rm -rf build/ dist/ empymod.egg-info/
+4. Get the Zenodo-DOI and add it to release notes
 
-4. Push it to GitHub, create a release tagging it
+5. Create tar and wheel::
 
-5. Get the Zenodo-DOI and add it to release notes
+       python setup.py sdist
+       python setup.py bdist_wheel
 
-6. Ensure ``python3-setuptools`` is installed::
+6. Push it to PyPi (requires ~/.pypircs)::
 
-       sudo apt install python3-setuptools
+       ~/anaconda3/bin/twine upload dist/*
 
-7. Create tar and wheel::
+7. conda build
 
-       python setup.py sdist
-       python setup.py bdist_wheel
+   Has to be done outside of ~/, because conda skeleton cannot handle, at the
+   moment, the encrypted home
+   (https://conda.io/docs/build_tutorials/pkgs.html).
 
-8. Test it on testpypi (requires ~/.pypirc)::
 
-       ~/anaconda3/bin/twine upload dist/* -r testpypi
+   1. Install miniconda in /opt::
 
-   Optionally test it already in conda if skeleton builds::
+          wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
+          bash miniconda.sh -b -p /opt/miniconda/miniconda
+          export PATH="/opt/miniconda/miniconda/bin:$PATH"
+          conda update conda
+          conda install -y conda-build anaconda-client
+          conda config --set anaconda_upload yes
+          anaconda login
 
-       conda skeleton pypi --pypi-url https://test.pypi.io/pypi/ empymod
+   2. Now to the conda-build part::
 
-9. Push it to PyPi (requires ~/.pypircs)::
+          conda skeleton pypi empymod
+          conda build --python 3.5 empymod
+          conda build --python 3.6 empymod
+          conda build --python 3.7 empymod
 
-       ~/anaconda3/bin/twine upload dist/*
+   3. Convert for all platforms::
 
-10. conda build
+          conda convert --platform all /opt/miniconda/miniconda/conda-bld/linux-64/empymod-[version]-py35_0.tar.bz2
+          conda convert --platform all /opt/miniconda/miniconda/conda-bld/linux-64/empymod-[version]-py36_0.tar.bz2
+          conda convert --platform all /opt/miniconda/miniconda/conda-bld/linux-64/empymod-[version]-py37_0.tar.bz2
 
-    Has to be done outside of ~/, because conda skeleton cannot handle, at the
-    moment, the encrypted home
-    (https://conda.io/docs/build_tutorials/pkgs.html).
+   4. Upload them::
 
+          anaconda upload osx-64/*
+          anaconda upload win-*/*
+          anaconda upload linux-32/*
 
-    1. Install miniconda in /opt::
+   5. Logout::
 
-           wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
-           bash miniconda.sh -b -p /opt/miniconda/miniconda
-           export PATH="/opt/miniconda/miniconda/bin:$PATH"
-           conda update conda
-           conda install -y conda-build anaconda-client
-           conda config --set anaconda_upload yes
-           anaconda login
+          anaconda logout
 
-    2. Now to the conda-build part::
 
-           conda skeleton pypi empymod
-           conda build --python 3.5 empymod
-           conda build --python 3.6 empymod
-           conda build --python 3.7 empymod
+Useful things
+-------------
 
-    3. Convert for all platforms::
+- If unsure, test it first on testpypi (requires ~/.pypirc)::
 
-           conda convert --platform all /opt/miniconda/miniconda/conda-bld/linux-64/empymod-[version]-py35_0.tar.bz2
-           conda convert --platform all /opt/miniconda/miniconda/conda-bld/linux-64/empymod-[version]-py36_0.tar.bz2
-           conda convert --platform all /opt/miniconda/miniconda/conda-bld/linux-64/empymod-[version]-py37_0.tar.bz2
+       ~/anaconda3/bin/twine upload dist/* -r testpypi
 
-    4. Upload them::
+- If unsure, test the test-pypi for conda if the skeleton builds::
 
-           anaconda upload osx-64/*
-           anaconda upload win-*/*
-           anaconda upload linux-32/*
+       conda skeleton pypi --pypi-url https://test.pypi.io/pypi/ empymod
 
-    5. Logout::
+- If there were changes to README, check it with::
 
-           anaconda logout
+       python setup.py --long-description | rst2html.py --no-raw > index.html
 
-10. Post-commit changes
+- If it fails, you might have to install ``python3-setuptools``::
 
-    - ``setup.py``: Bump number, add '.dev0' to version number
-    - ``empymod/__init__.py``: Bump number, add '.dev0' to version number
-    - ``README.md``: Add the current badges (|docs| |tests| |coverage|)
+       sudo apt install python3-setuptools

docs/manual.rst

@@ -211,8 +211,7 @@ If you prefer to contact me outside of GitHub use the contact form on my
 personal website, https://werthmuller.org.
 
 To install empymod from source, you can download the latest version from GitHub
-and either add the path to ``empymod`` to your python-path variable, or install
-it in your python distribution via:
+and install it in your python distribution via:
 
 .. code-block:: console
 

empymod/__init__.py

@@ -48,4 +48,16 @@
            'DigitalFilter']
 
 # Version
-__version__ = '1.10.1dev0'
+try:
+    # - Released versions just tags: v1.10.0;
+    # - GitHub commits add 'dev#'+hash: 1.10.1.dev3+g973038c;
+    # - Uncommited changes add timestamp: 1.10.1.dev3+g973038c.d20191022.
+    from .version import version as __version__
+except ImportError:
+    # If used without using setup.py or without the .git-directory, or using
+    # the Git or Zenodo zip-files or other unthought of ways of using it, we
+    # provide here the last stable released version number, with a '-hc' for
+    # hard-coded.
+    # So v1.10.0-hc is most likely v1.10.0, but it can be anything between
+    # v1.10.0 and v1.10.1.
+    __version__ = '1.10.1-hc'

empymod/model.py

@@ -350,7 +350,7 @@ def bipole(src, rec, depth, res, freqtime, signal=None, aniso=None,
     >>> from empymod import bipole
     >>> # x-directed bipole source: x0, x1, y0, y1, z0, z1
     >>> src = [-50, 50, 0, 0, 100, 100]
-    >>> # x-directed dipole source-array: x, y, z, azimuth, dip
+    >>> # x-directed dipole receiver-array: x, y, z, azimuth, dip
     >>> rec = [np.arange(1, 11)*500, np.zeros(10), 200, 0, 0]
     >>> # layer boundaries
     >>> depth = [0, 300, 1000, 1050]
@@ -1246,60 +1246,59 @@ def loop(src, rec, depth, res, freqtime, signal=None, aniso=None, epermH=None,
     --------
     >>> import numpy as np
     >>> from empymod import loop
-    >>> # x-directed bipole source: x0, x1, y0, y1, z0, z1
-    >>> src = [-50, 50, 0, 0, 100, 100]
-    >>> # x-directed dipole source-array: x, y, z, azimuth, dip
-    >>> rec = [np.arange(1, 11)*500, np.zeros(10), 200, 0, 0]
+    >>> # z-directed loop source: x, y, z, azimuth, dip
+    >>> src = [0, 0, 0, 0, 90]
+    >>> # z-directed magnetic dipole receiver-array: x, y, z, azimuth, dip
+    >>> rec = [np.arange(1, 11)*500, np.zeros(10), 200, 0, 90]
     >>> # layer boundaries
-    >>> depth = [0, 300, 1000, 1050]
+    >>> depth = [0, 300, 500]
     >>> # layer resistivities
-    >>> res = [1e20, .3, 1, 50, 1]
+    >>> res = [2e14, 10, 500, 10]
     >>> # Frequency
     >>> freq = 1
-    >>> # Calculate electric field due to an electric source at 1 Hz.
+    >>> # Calculate magnetic field due to a loop source at 1 Hz.
     >>> # [mrec = True (default)]
-    >>> EMfield = bipole(src, rec, depth, res, freq, verb=4)
+    >>> EMfield = loop(src, rec, depth, res, freq, verb=4)
     :: empymod START  ::
     ~
-       depth       [m] :  0 300 1000 1050
-       res     [Ohm.m] :  1E+20 0.3 1 50 1
-       aniso       [-] :  1 1 1 1 1
-       epermH      [-] :  1 1 1 1 1
-       epermV      [-] :  1 1 1 1 1
-       mpermH      [-] :  1 1 1 1 1
-       mpermV      [-] :  1 1 1 1 1
+       depth       [m] :  0 300 500
+       res     [Ohm.m] :  2E+14 10 500 10
+       aniso       [-] :  1 1 1 1
+       epermH      [-] :  1 1 1 1
+       epermV      [-] :  1 1 1 1
+       mpermH      [-] :  1 1 1 1
+       mpermV      [-] :  1 1 1 1
+       direct field    :  Calc. in wavenumber domain
        frequency  [Hz] :  1
        Hankel          :  DLF (Fast Hankel Transform)
          > Filter      :  Key 201 (2009)
          > DLF type    :  Standard
        Kernel Opt.     :  None
        Loop over       :  None (all vectorized)
-       Source(s)       :  1 bipole(s)
-         > intpts      :  1 (as dipole)
-         > length  [m] :  100
-         > x_c     [m] :  0
-         > y_c     [m] :  0
-         > z_c     [m] :  100
+       Source(s)       :  1 dipole(s)
+         > x       [m] :  0
+         > y       [m] :  0
+         > z       [m] :  0
          > azimuth [°] :  0
-         > dip     [°] :  0
+         > dip     [°] :  90
        Receiver(s)     :  10 dipole(s)
          > x       [m] :  500 - 5000 : 10  [min-max; #]
                        :  500 1000 1500 2000 2500 3000 3500 4000 4500 5000
          > y       [m] :  0 - 0 : 10  [min-max; #]
                        :  0 0 0 0 0 0 0 0 0 0
          > z       [m] :  200
          > azimuth [°] :  0
-         > dip     [°] :  0
-       Required ab's   :  11
-    ~
-    :: empymod END; runtime = 0:00:00.005536 :: 1 kernel call(s)
+         > dip     [°] :  90
+       Required ab's   :  33
     ~
+    :: empymod END; runtime = 0:00:00.005025 :: 1 kernel call(s)
+
     >>> print(EMfield)
-    [  1.68809346e-10 -3.08303130e-10j  -8.77189179e-12 -3.76920235e-11j
-      -3.46654704e-12 -4.87133683e-12j  -3.60159726e-13 -1.12434417e-12j
-       1.87807271e-13 -6.21669759e-13j   1.97200208e-13 -4.38210489e-13j
-       1.44134842e-13 -3.17505260e-13j   9.92770406e-14 -2.33950871e-13j
-       6.75287598e-14 -1.74922886e-13j   4.62724887e-14 -1.32266600e-13j]
+    [ -3.05449848e-10 -2.00374185e-11j  -7.12528991e-11 -5.37083268e-12j
+      -2.52076501e-11 -1.62732412e-12j  -1.18412295e-11 -8.99570998e-14j
+      -6.44054097e-12 +5.61150066e-13j  -3.77109625e-12 +7.89022722e-13j
+      -2.28484774e-12 +8.08897623e-13j  -1.40021365e-12 +7.32151174e-13j
+      -8.55487532e-13 +6.18402706e-13j  -5.15642408e-13 +4.99091919e-13j]
 
     """
 
@@ -1372,7 +1371,7 @@ def loop(src, rec, depth, res, freqtime, signal=None, aniso=None, epermH=None,
         # Get this source
         srcazmdip = get_azm_dip(src, isz, nsrcz, 1, srcdipole, strength,
                                 'src', verb)
-        tsrc, srcazm, srcdip, srcg_w, _, src_w = srcazmdip
+        tsrc, srcazm, srcdip, _, _, src_w = srcazmdip
 
         for irz in range(nrecz):  # Loop over receiver depths
 

requirements-dev.txt

@@ -0,0 +1,6 @@
+numpy
+scipy >= 1.0.0
+sphinx
+sphinxcontrib-napoleon
+numpydoc >= 0.9
+setuptools_scm

requirements.txt

@@ -1,5 +1,2 @@
 numpy
 scipy >= 1.0.0
-sphinx
-sphinxcontrib-napoleon
-numpydoc >= 0.9

setup.py

@@ -1,19 +1,21 @@
 # -*- coding: utf-8 -*-
+import os
+import re
 from setuptools import setup
 
+# Get README and remove badges.
 readme = open('README.rst').read()
+readme = re.sub('----.*marker', '----', readme, flags=re.DOTALL)
 
 description = 'Open-source full 3D electromagnetic modeller for 1D VTI media'
 
 setup(
     name='empymod',
-    version='1.10.1.dev0',
     description=description,
     long_description=readme,
     author='The empymod Developers',
     author_email='dieter@werthmuller.org',
     url='https://empymod.github.io',
-    download_url='https://github.com/empymod/empymod/tarball/v1.10.0',
     license='Apache License V2.0',
     packages=['empymod', 'empymod.scripts'],
     classifiers=[
@@ -27,4 +29,10 @@
         'numpy',
         'scipy>=1.0.0',
     ],
+    use_scm_version={
+        'root': '.',
+        'relative_to': __file__,
+        'write_to': os.path.join('empymod', 'version.py'),
+    },
+    setup_requires=['setuptools_scm'],
 )