Merge pull request SHTOOLS#57 from SHTOOLS/develop

Version 3.4

Author: Mark Wieczorek

.gitignore

@@ -6,6 +6,7 @@
 *.so.dSYM/
 NONE/
 build/
+dist/
 pyshtools/doc/
 examples/notebooks/.ipynb_checkpoints/
 pyshtools.egg-info/

.travis.yml

@@ -19,6 +19,7 @@ before_install:
   - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then
        brew install fftw --with-fortran;
     else
+       sudo apt-get update; 
        sudo apt-get install libblas-dev liblapack-dev g++ gfortran libfftw3-dev tcsh;
     fi
 
@@ -45,10 +46,17 @@ install:
         numpy
         scipy
         matplotlib
+        jupyter
+  - conda install nbconvert
   - source activate test-environment
   - pip install --no-deps .  
 
 script:
+  - if [[ "${PYTHON_VERSION:0:1}" == '2' ]]; then
+      make notebooks2;
+    else
+      make notebooks3;
+    fi
   - mkdir empty
   - cd empty
   - python -c "import pyshtools"

MANIFEST.in

@@ -9,11 +9,10 @@ graft examples/ExampleDataFiles
 recursive-include examples/fortran *.f95 input* Makefile
 recursive-include examples/python *.py Makefile
 recursive-include examples/notebooks *.ipynb
-include examples/python/ClassInterface/topo.dat.gz
 
 graft src/pydoc
 graft src/fdoc
-recursive-include src *.py
+recursive-include src *.py *.pyf
 
 graft man
 graft www

Makefile

@@ -97,6 +97,12 @@
 #	make clean-python-tests
 #		Detele all compiled python tests
 #
+#	make notebooks
+#		Detele all compiled python tests
+#
+#	make clean-notebooks
+#		Detele all compiled python tests
+#
 #	make doc
 #		Create the man and html-man pages from input Markdown files.
 #		These are PRE-MADE in the distribution. To remake these
@@ -109,7 +115,7 @@
 #
 #####################################################################################
 
-VERSION = 3.3
+VERSION = 3.4
 LIBNAME = SHTOOLS
 LIBNAMEMP = SHTOOLS-mp
 
@@ -119,6 +125,8 @@ F2PY3 = f2py3
 PYTHON = python
 PYTHON3 = python3
 PYTHON_VERSION = all
+JUPYTER = "jupyter nbconvert --ExecutePreprocessor.kernel_name=python2"
+JUPYTER3 = "jupyter nbconvert --ExecutePreprocessor.kernel_name=python3"
 
 SYSLIBPATH = /usr/local/lib
 
@@ -136,6 +144,7 @@ LIBDIR = lib
 INCDIR = modules
 FEXDIR = examples/fortran
 PEXDIR = examples/python
+NBDIR = examples/notebooks
 
 LIBPATH = $(PWD)/$(LIBDIR)
 MODPATH = $(PWD)/$(INCDIR)
@@ -200,7 +209,7 @@ endif
 	run-python2-tests run-python3-tests install-fortran install-python\
 	install-python2 install-python3 uninstall fortran-mp clean\
 	clean-fortran-tests clean-python-tests clean-python2 clean-python3\
-	clean-libs 
+	clean-libs clean-notebooks notebooks notebooks2 notebooks3
 
 
 all: fortran python
@@ -240,14 +249,17 @@ ifeq ($(PYTHON_VERSION),all)
 python: python2 python3
 install-python: install-python2 install-python3
 python-tests: python2-tests python3-tests
+notebooks: notebooks3 notebooks2
 else ifeq ($(PYTHON_VERSION),2)
 python: python2
 install-python: install-python2
 python-tests: python2-tests
+notebooks: notebooks2
 else ifeq ($(PYTHON_VERSION),3)
 python: python3
 install-python: install-python3
 python-tests: python3-tests
+notebooks: notebooks3
 else
 $(error $(PYTHON_VERSION) is unsupported.)
 endif
@@ -381,6 +393,14 @@ remove-doc:
 	@echo
 	@echo REMOVED MAN AND HTML-MAN FILES
 
+notebooks2:
+	@$(MAKE) -C $(NBDIR) -f Makefile JUPYTER=$(JUPYTER)
+	@echo NOTEBOOK HTML FILES SUCCESSFULLY CREATED
+
+notebooks3:
+	@$(MAKE) -C $(NBDIR) -f Makefile JUPYTER=$(JUPYTER3)
+	@echo NOTEBOOK HTML FILES SUCCESSFULLY CREATED
+
 clean: clean-fortran-tests clean-python-tests clean-python2 clean-python3 clean-libs
 
 clean-fortran-tests:
@@ -425,12 +445,18 @@ clean-libs:
 	-rm -rf build
 	-rm -rf pyshtools.egg-info
 	-rm -f src/_SHTOOLS-f2pywrappers.f src/_SHTOOLSmodule.c
+	-rm -f dist
 	@echo
 	@echo REMOVED LIB, MODULE, OBJECT FILES, COMPILED PYTHON FILES AND TESTS
 	@echo
 	@echo \*\*\* If you installed pyshtools using \"pip install -e .\" you should
 	@echo \*\*\* also execute \"pip uninstall pyshtools\".
 
+clean-notebooks:
+	$(MAKE) -C $(NBDIR) -f Makefile clean
+	@echo
+	@echo REMOVED NOTEBOOK HTML FILES
+
 fortran-tests: fortran
 	$(MAKE) -C $(FEXDIR) -f Makefile all F95=$(F95) F95FLAGS="$(F95FLAGS)" LIBNAME="$(LIBNAME)" FFTW="$(FFTW)" LAPACK="$(LAPACK)" BLAS="$(BLAS)"
 	@echo

README.md

@@ -1,4 +1,4 @@
-![LOGO](logo.png)
+![LOGO](misc/logo.png)
 
 [![Join the chat at https://gitter.im/SHTOOLS/SHTOOLS](https://badges.gitter.im/SHTOOLS/SHTOOLS.svg)](https://gitter.im/SHTOOLS/SHTOOLS?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
 [![DOI](https://zenodo.org/badge/doi/10.5281/zenodo.60010.svg)](http://dx.doi.org/10.5281/zenodo.60010)
@@ -40,29 +40,28 @@ brew install fftw --with-fortran
 ```
 
 #### Python Library ####
-[Download](https://github.com/SHTOOLS/SHTOOLS/zipball/master) or clone the SHTOOLS repository. Enter the SHTOOLS folder that contains the file ```setup.py```, and then execute one of the following commands:
+```bash
+pip install pyshtools
+```
+Or, to install a developer version, [download](https://github.com/SHTOOLS/SHTOOLS/zipball/master) or clone the SHTOOLS repository, enter the SHTOOLS folder and then execute one of the following commands:
 ```bash
 pip install .  # installs into the active python environment lib folder
 pip install -v -e .  # installs into the SHTOOLS/pyshtools folder and links to the active python environment
 ```
 
-#### Fortran Library and Manual Installation ####
-To install the Fortran 95 library or compile the Python 2 and Python 3 components manually
-enter one of the following
-```
+#### Fortran Library ####
+To install the Fortran 95 library, enter one of the following
+```bash
 make fortran
-make python2
-make python3
 make fortran-mp  # Open-MP Fortran routines
 ```
 
-#### Brew package manager (OSX) ####
-
-To install the Fortran 95, Python 2, and Python 3 components using the [brew](http://brew.sh/) package manager, enter
-```
+Or, with OSX, use the [brew](http://brew.sh/) package manager:
+```bash
 brew tap shtools/shtools
 brew install shtools
 ```
+To also install the OpenMP components, add ```--with-openmp``` to the last command.
 
 More installation instructions and options can be found in the [web documentation](https://shtools.ipgp.fr) and GitHub 
 [wiki](https://github.com/SHTOOLS/SHTOOLS/wiki).
@@ -77,14 +76,14 @@ well as simple interfaces.
 
 To get started, check out the following Python tutorial notebooks:
 
-* [Introduction 1: A simple introduction to pyshtools: Grids and Coeffs](examples/notebooks/Introduction-1.ipynb)
-* [Introduction 2: A simple introduction to pyshtools: Localization windows and spectral analysis](examples/notebooks/Introduction-2.ipynb)
-* [tutorial 1: Simple Spherical Harmonic Expansions](examples/notebooks/tutorial_1.ipynb)
-* [tutorial 2: Localized Spectral Analysis on the Sphere](examples/notebooks/tutorial_2.ipynb)
-* [tutorial 3: The SHTOOLS Class Interface](examples/notebooks/tutorial_3.ipynb)
-* [tutorial 4: Spherical Harmonic Normalizations and Parseval's theorem](examples/notebooks/tutorial_4.ipynb)
-* [tutorial 5: Multitaper Spectral Estimation - SHWindows Class Interface](examples/notebooks/tutorial_5.ipynb)
-* [tutorial 6: 3D Spherical Harmonic Plots](examples/notebooks/tutorial_6.ipynb)
+* Introduction 1: Grids and Spherical Harmonic Coefficients [\[ipynb\]](examples/notebooks/Introduction-1.ipynb)
+* Introduction 2: Localization Windows and Spectral Analysis [\[ipynb\]](examples/notebooks/Introduction-2.ipynb)
+* Tutorial 1: Simple Spherical Harmonic Expansions [\[ipynb\]](examples/notebooks/tutorial_1.ipynb)
+* Tutorial 2: Localized Spectral Analysis on the Sphere [\[ipynb\]](examples/notebooks/tutorial_2.ipynb)
+* Tutorial 3: The SHTOOLS Class Interface [\[ipynb\]](examples/notebooks/tutorial_3.ipynb)
+* Tutorial 4: Spherical Harmonic Normalizations and Parseval's theorem [\[ipynb\]](examples/notebooks/tutorial_4.ipynb)
+* Tutorial 5: Multitaper Spectral Estimation - SHWindows Class Interface [\[ipynb\]](examples/notebooks/tutorial_5.ipynb)
+* Tutorial 6: 3D Spherical Harmonic Plots [\[ipynb\]](examples/notebooks/tutorial_6.ipynb)
 
 You can keep up to date by following SHTOOLS on [Twitter](https://twitter.com/SH_tools).
 

VERSION

@@ -1,2 +1,2 @@
-SHTOOLS Version: 3.3
-Released August 11, 2016
+SHTOOLS Version: 3.4
+Released August 30, 2016