Make a proper package out of pyfftlog (#1)

- Converted to package
- Test and CI with Travis
- PEP8 with flake8

Author: prisae

.gitattributes

@@ -0,0 +1,19 @@
+# Directories
+__pycache__/
+
+# Cython
+*.so
+fftlog/_fftlogmodule.c
+
+# Pytest
+.pytest_cache/
+
+# setuptools_scm
+fftlog/version.py
+
+# Build related
+.eggs/
+build/
+dist/
+fftlog.egg-info/
+MANIFEST

.gitignore

@@ -0,0 +1,49 @@
+language: python
+
+addons:
+  apt:
+    - gfortran
+
+# Note: the `python: X.Y` is not actually used, as internally conda is used,
+# which follows the `PYTHON=X.Y` var.
+matrix:
+  include:
+    - python: 3.6
+      env: PYTHON=3.6
+    - python: 3.7
+      env: PYTHON=3.7 DEPLOY_PYPI=true
+    - python: 3.8
+      env: PYTHON=3.8
+
+install:
+  - sudo apt-get update
+  # We do this conditionally because it saves us some downloading if the
+  # version is the same.
+  - wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
+  - bash miniconda.sh -b -p $HOME/miniconda
+  - export PATH="$HOME/miniconda/bin:$PATH"
+  - hash -r
+  - conda config --set always_yes yes --set changeps1 no
+  - conda update --all
+  # Useful for debugging any issues with conda
+  - conda info -a
+
+  # Install and activate environment, install packages
+  - conda create -q -n test-environment python=$PYTHON $PCKGS scipy pytest pytest-cov
+  - source activate test-environment
+  - pip install setuptools_scm pytest-flake8 $INST
+  - pip install -e .
+
+script:
+  - pytest --cov=fftlog --flake8 $TEST
+
+deploy:
+  provider: pypi
+  user: "__token__"
+  password:
+    secure: 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
+  on:
+    branch: master
+    tags: true
+    condition: '$DEPLOY_PYPI = "true"'
+  distributions: "sdist"

.travis.yml

@@ -0,0 +1,26 @@
+Changelog
+#########
+
+
+v0.2.0 : First packaged release
+-------------------------------
+
+**2020-05-16**
+
+First packaged release on PyPi and conda-forge. This includes:
+
+- Re-structuring the repo.
+- Link to proper documentation, https://pyfftlog.readthedocs.io
+  (which is for pyfftlog), which contains as well the example.
+- Add tests and CI on Travis, https://travis-ci.org/github/prisae/pyfftlog.
+- Link to Zenodo, https://zenodo.org/record/3830366.
+- PEP8 checking.
+- Add the relevant badges to README.
+
+
+v0.1.0 : Initial upload to GitHub
+---------------------------------
+
+**2016-12-05**
+
+- Initially working version uploaded to GitHub.

CHANGELOG.rst

@@ -0,0 +1,5 @@
+prune tests
+exclude requirements.txt
+exclude requirements-dev.txt
+exclude .gitignore
+exclude .travis.yml

MANIFEST.in

@@ -1,25 +1,37 @@
-`fftlog` - python wrapper FFTLog
-================================
+.. image:: https://travis-ci.org/prisae/fftlog.svg?branch=master
+   :target: https://travis-ci.org/prisae/fftlog
+   :alt: Travis-CI
+.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.3830534.svg
+   :target: https://doi.org/10.5281/zenodo.3830534
+   :alt: Zenodo DOI
+
+
+`fftlog` - A python wrapper for FFTLog
+======================================
 
 This is a simple `f2py`-wrapper for the logarithmic FFT code *FFTLog* as
-presented in Appendix B of [Hamilton_2000]_ and published at
+presented in Appendix B of [Hami00]_ and published at
 `casa.colorado.edu/~ajsh/FFTLog <http://casa.colorado.edu/~ajsh/FFTLog>`_.
 
-A pure python version (`pyfftlog`) can be found on
-`github.com/prisae/pyfftlog <https://github.com/prisae/pyfftlog>`_.
-Tests have shown that `fftlog` is a bit faster than `pyfftlog`, but `pyfftlog`
-is easier to implement, as you only need `NumPy` and `SciPy`, without the
-need to compile anything.
+A pure python version (`pyfftlog`) can be found on `github.com/prisae/pyfftlog
+<https://github.com/prisae/pyfftlog>`_. Tests have shown that `fftlog` is a bit
+faster than `pyfftlog`, but `pyfftlog` is easier to implement, as you only need
+`NumPy` and `SciPy`, without the need to compile anything.
 
 I hope that `FFTLog` will make it into `SciPy` in the future, which will make
-this project redundant.
+this project redundant. (If you have the bandwidth and are willing to chip in
+have a look at `SciPy PR #7310 <https://github.com/scipy/scipy/pull/7310>`_.)
+
+Be aware that `pyfftlog` has not been tested extensively. It works fine for the
+test from the original code, and my use case, which is `pyfftlog.fftl` with
+`mu=0.5` (sine-transform), `q=0` (unbiased), `k=1`, `kropt=1`, and `tdir=1`
+(forward). Please let me know if you encounter any issues.
 
-Be aware that `pyfftlog` has not been tested extensively. It works fine
-for the attached test, which is the test from the original code, and my use
-case, which is `pyfftlog.fftl` with `mu=0.5` (sine-transform), `q=0`
-(unbiased), `k=1`, `kropt=1`, and `tdir=` (forward). Please let me know if you
-encounter any issues.
+- **Documentation**: https://pyfftlog.readthedocs.io
+- **Source Code**: https://github.com/prisae/fftlog
 
+**Note** that the documentation is for the pure python version `pyfftlog`, but
+equally applies to `fftlog`.
 
 Description of FFTLog from the FFTLog-Website
 ---------------------------------------------
@@ -39,32 +51,26 @@ steps) and aliasing (periodic folding of frequencies), but under appropriate
 circumstances FFTLog may approximate the results of a continuous Fourier or
 Hankel transform.
 
-The FFTLog algorithm was originally proposed by [Talman_1978]_.
+The FFTLog algorithm was originally proposed by [Talm78]_.
 
-*For the full documentation, see*
-`casa.colorado.edu/~ajsh/FFTLog <http://casa.colorado.edu/~ajsh/FFTLog>`_.
+*For the full documentation, see* `casa.colorado.edu/~ajsh/FFTLog
+<http://casa.colorado.edu/~ajsh/FFTLog>`_.
 
 
 Installation
 ------------
 
-To install it in your python distribution:
+You can install fftlog either via **conda**:
 
-.. code:: bash
+.. code-block:: console
 
-   python setup.py install
+   conda install -c conda-forge fftlog
 
+or via **pip**:
 
-To just create the module that you can import locally:
+.. code-block:: console
 
-.. code:: bash
-
-   f2py -c fftlog.pyf src/*
-
-You need a fortran compiler for this to work.
-
-Check out the Jupyter Notebook `fftlogtest.ipynb` in the root directory. It is
-a translation of the test-function `fftlogtest.f`, and should get you started.
+   pip install fftlog
 
 
 Creation
@@ -89,39 +95,42 @@ command, generating only hooks for the functions `fhti`, `fttl`, `fht`, and
 
    f2py src/* -m fftlog -h fftlog.pyf only: fhti fftl fht fhtq :
 
-Lastly I amended the `pyf`-instructions, mainly with some :code:`intent` and
-:code:`optional` statements as well as the corresponding default values.
+Lastly I amended the `pyf`-instructions, mainly with some `intent` and
+`optional` statements as well as the corresponding default values.
 
 
 Notes
------
-1. :code:`kropt = 3` (interactive adjusting) is not possible with `fftlog`
-2. :code:`wsave`-dimension is set to :code:`2*n+3*(n/2)+19`, the biggest of the
-   four minimum sizes described in `fftlog.f`.
+'''''
+1. `kropt=3` (interactive adjusting) is not possible with `fftlog`
+2. `wsave`-dimension is set to `2*n+3*(n/2)+19`, the biggest of the four
+   minimum sizes described in `fftlog.f`.
 
 
 References
 ----------
 
-.. [Hamilton_2000] Hamilton, A. J. S., 2000, Uncorrelated modes of the
-    non-linear power spectrum: Monthly Notices of the Royal Astronomical
-    Society, 312, pages 257-284; DOI: `10.1046/j.1365-8711.2000.03071.x
+.. [Hami00] Hamilton, A. J. S., 2000, Uncorrelated modes of the non-linear
+    power spectrum: Monthly Notices of the Royal Astronomical Society, 312,
+    pages 257-284; DOI: `10.1046/j.1365-8711.2000.03071.x
     <http://dx.doi.org/10.1046/j.1365-8711.2000.03071.x>`_; Website of FFTLog:
     `casa.colorado.edu/~ajsh/FFTLog <http://casa.colorado.edu/~ajsh/FFTLog>`_.
 
-.. [Talman_1978] Talman, J. D., 1978, Numerical Fourier and Bessel transforms
-    in logarithmic variables: Journal of Computational Physics, 29, pages
-    35-48; DOI: `10.1016/0021-9991(78)90107-9
+.. [Talm78] Talman, J. D., 1978, Numerical Fourier and Bessel transforms in
+    logarithmic variables: Journal of Computational Physics, 29, pages 35-48;
+    DOI: `10.1016/0021-9991(78)90107-9
     <http://dx.doi.org/10.1016/0021-9991(78)90107-9>`_.
 
 
-License and Credits
--------------------
+License, Citation, and Credits
+------------------------------
 
 These additions to the original FFTLog-code are released to the public domain
 under the `CC0 1.0 License
 <http://creativecommons.org/publicdomain/zero/1.0>`_.
 
+All releases have a Zenodo-DOI, which can be found on `10.5281/zenodo.3830364
+<https://doi.org/10.5281/zenodo.3830534>`_.
+
 Permission to distribute the original Fortran `FFTLog` code with this Python
 `fftlog` package has been granted (email from Andrew Hamilton to Dieter
 Werthmüller dated 28 September 2016).
@@ -141,3 +150,5 @@ The original gamerf copyright statement states::
 Permission to distribute the modified gamma function code with the FFTLog
 package has been granted (email from Takuya Ooura to Andrew Hamilton dated 16
 March 1999).
+
+Be kind and give credits by citing Hamilton (2000).

README.rst

@@ -0,0 +1,16 @@
+from datetime import datetime
+from fftlog._fftlog import fhti, fftl, fht, fhtq
+
+__all__ = ['fhti', 'fftl', 'fht', 'fhtq']
+
+# Version
+try:
+    # - Released versions just tags:       1.10.0
+    # - GitHub commits add .dev#+hash:     1.10.1.dev3+g973038c
+    # - Uncommitted changes add timestamp: 1.10.1.dev3+g973038c.d20191022
+    from .version import version as __version__
+except ImportError:
+    # If it was not installed, then we don't know the version. We could throw a
+    # warning here, but this case *should* be rare. fftlog should be installed
+    # properly!
+    __version__ = 'unknown-'+datetime.today().strftime('%Y%m%d')

fftlog/__init__.py

@@ -10,9 +10,9 @@
 !
 ! For f2py see http://cens.ioc.ee/projects/f2py2e/
 
-python module fftlog ! in 
+python module _fftlog ! in
     interface  ! in :fftlog
-        subroutine fhti(n,mu,q,dlnr,kr,kropt,wsave,ok) ! in :fftlog:fftlog.f
+        subroutine fhti(n,mu,q,dlnr,kr,kropt,wsave,ok) ! in :fftlog:src/fftlog.f
             integer intent(int) :: n
             real*8 intent(in) :: mu
             real*8 optional, intent(in) :: q=0
@@ -22,24 +22,24 @@ python module fftlog ! in
             real*8 dimension(2*n+3*(n/2)+19), intent(out) :: wsave
             logical intent(out) :: ok
         end subroutine fhti
-        subroutine fftl(n,a,rk,dir,wsave) ! in :fftlog:fftlog.f
+        subroutine fftl(n,a,rk,dir,wsave) ! in :fftlog:src/fftlog.f
             integer, optional, intent(hide), depend(a) :: n=len(a)
             real*8 dimension(n), intent(in, out) :: a
             real*8 optional, intent(in) :: rk=1
             integer optional, intent(in) :: dir=1
             real*8 dimension(2*n+3*(n/2)+19), intent(in) :: wsave
         end subroutine fftl
-        subroutine fht(n,a,dir,wsave) ! in :fftlog:fftlog.f
+        subroutine fht(n,a,dir,wsave) ! in :fftlog:src/fftlog.f
             integer, optional, intent(hide), depend(a) :: n=len(a)
             real*8 dimension(n), intent(in, out) :: a
             integer optional, intent(in) :: dir=1
             real*8 dimension(2*n+3*(n/2)+19), intent(in) :: wsave
         end subroutine fht
-        subroutine fhtq(n,a,dir,wsave) ! in :fftlog:fftlog.f
+        subroutine fhtq(n,a,dir,wsave) ! in :fftlog:src/fftlog.f
             integer, optional, intent(hide), depend(a) :: n=len(a)
             real*8 dimension(n), intent(in, out) :: a
             integer optional, intent(in) :: dir=1
             real*8 dimension(2*n+3*(n/2)+19), intent(in) :: wsave
         end subroutine fhtq
-    end interface 
-end python module fftlog
+    end interface
+end python module _fftlog