Merge branch 'dev'

.gitignore

@@ -3,7 +3,7 @@
 *.egg
 build/
 dist/
-opmd_viewer.egg-info/
+openpmd_viewer.egg-info/
 .cache/
 .eggs/
 .vs/

.travis.yml

@@ -43,7 +43,7 @@ install:
 before_script :
   # static code analysis
   #   pyflakes: mainly warnings, unused code, etc.
-  - python -m pyflakes opmd_viewer
+  - python -m pyflakes openpmd_viewer
 
 script:
   - "python setup.py test"

CHANGELOG.md

@@ -1,5 +1,39 @@
 # Change Log / Release Log for openPMD-viewer
 
+## 1.0.0
+
+This version introduces major changes and breaks backward compatibility.
+
+Here is a list of the changes:
+- The import statement now uses `openpmd_viewer` instead of `opmd_viewer`, e.g.
+```
+from openpmd_viewer import OpenPMDTimeSeries
+```
+- For consistency, `ts.get_particle` now return particle positions in meters,
+instead of microns. For instance, in the code below, `x`, `y`, `z` will be in
+meters
+```
+x, y, z = ts.get_particle(['x', 'y', 'z'], iteration=1000)
+```
+- In `ts.get_field`, slicing can now be done in several directions, and for
+1d, 2d, 3d, and circ geometries. As a consequence, this breaks backward
+compatibility for 3d field:
+```get_field(field=field, coord=coord, iteration=iteration)```
+used to return the central slice along `y` while it now returns the full 3d field.
+In addition, the name of the argument of `get_field` that triggers slicing
+has been changed from `slicing_dir` to `slice_across` (and `slicing` has been
+changed to `slice_relative_position`).
+- `openPMD-viewer` does not rely on Cython anymore. Instead, it uses `numba`
+for functions that perform a substantial amount of computation.
+- A new function (`ts.iterate`) was introduced in order to quickly apply a
+given function to all iterations of a time series. See the docstring of
+`ts.iterate` for more information.
+- The function `get_laser_envelope` does not support the argument `index` anymore
+(which was effectively used in order to perform slicing). Instead, users should use
+the argument `slicing_dir`. In addition, `get_laser_envelope` now supports the
+argument `plot_range`.
+- The function `get_laser_waist` does not support the agument `slicing_dir` anymore.
+
 ## 0.9.0
 
 This release adds two features:
@@ -106,7 +140,7 @@ This new version includes:
 - an additional option `use_field_mesh` when plotting the particle. When set
 to `True`, this option uses information from the field mesh to choose the parameters of the particle histograms (esp. the bins). This is useful in order to avoid plotting/binning artifacts (aliasing) when the particles are evenly spaced.
 
-In addition, the package `opmd_viewer` now has an attribute `__version__`.
+In addition, the module `openpmd_viewer` now has an attribute `__version__`.
 
 ## 0.3.3
 

CONTRIBUTING.md

@@ -49,7 +49,7 @@ git pull [email protected]:openPMD/openPMD-viewer.git dev
   - Use [pyflakes](https://pypi.python.org/pypi/pyflakes) to detect any potential bug.
   ```
   cd openPMD-viewer/
-  pyflakes opmd_viewer
+  pyflakes openpmd_viewer
   ```
   - Make sure that the tests pass (please install `wget` and `jupyter` before running the tests: `pip install wget jupyter`)
   ```
@@ -76,10 +76,10 @@ git push -u origin <NewBranchName>
 
 - Features that **modify** or **improve** the `OpenPMDTimeSeries` object
 should be implemented in the
-`opmd_viewer/opempmd_timeseries` folder. Features that **build upon** the
+`openpmd_viewer/opempmd_timeseries` folder. Features that **build upon** the
 `OpenPMDTimeSeries` object to create domain-specific analysis tools
 (e.g. laser diagnostics for PIC simulations) should be implemented in
-the `opmd_viewer/addons` folder.
+the `openpmd_viewer/addons` folder.
 
 - Document the functions and classes that you write, by using a
   [docstring](https://www.python.org/dev/peps/pep-0257/). List the

MANIFEST.in

@@ -1,5 +1,4 @@
 include README.md
 include requirements.txt
-include opmd_viewer/openpmd_timeseries/cython_function.pyx
-include opmd_viewer/notebook_starter/openPMD_notebook
-include opmd_viewer/notebook_starter/Template_notebook.ipynb
+include openpmd_viewer/notebook_starter/openPMD_notebook
+include openpmd_viewer/notebook_starter/Template_notebook.ipynb

README.md

@@ -52,27 +52,22 @@ browser**. To use this executable, simply type in a regular terminal:
 
 ### Installation on a local computer
 
-#### Installation with conda (recommended)
+#### Installation with conda
 
 In order to install `openPMD-viewer` with `conda`, please install the [Anaconda
 distribution](https://docs.anaconda.com/anaconda/install/), and then type
 ```
-conda install -c rlehe openpmd_viewer
+conda install -c conda-forge openpmd-viewer
 ```
 If you are using JupyterLab, please also install the `jupyter-matplotlib`
 extension (See installation instructions
 [here](https://github.com/matplotlib/jupyter-matplotlib)).
 
 #### Installation with pip
 
-If you cannot install `openPMD-viewer` with `conda`, the alternative
-is to use `pip`. However, you need to first make sure that `h5py` is
-installed on your local computer. This can be done for instance by
-typing `pip install h5py`, though this may require you to install `hdf5` separately.
-
-Once `h5py` is installed, simply type
+You can also install `openPMD-viewer` using `pip`
 ```
-pip install openPMD-viewer
+pip install openpmd-viewer
 ```
 In addition, if you wish to use the interactive GUI, please type
 ```

RELEASING.md

@@ -32,7 +32,7 @@ username = <yourPypiUsername>
 
 ## Creating a release on Github
 
-- Make sure that the version number in `opmd_viewer/__version__.py` **and**
+- Make sure that the version number in `openpmd_viewer/__version__.py` **and**
   in `conda_recipe/meta.yaml` correspond to the new release, and that
   the corresponding changes have been documented in `CHANGELOG.md`.
 
@@ -57,22 +57,3 @@ twine upload dist/* -r pypi
 (NB: You can also first test this by uploading the package to
 [test PyPI](https://testpypi.python.org/pypi) ; to do so, simply
 replace `pypi` by `pypitest` in the above set of commands)
-
-## Uploading the package to Anaconda.org
-
-- `cd` into the folder `conda_recipe`.
-
-- Still in the folder `conda_recipe`, run
-```
-docker build -t openpmd_build .
-docker run -it -v $PWD:/home/ openpmd_build
-```
-This builds the conda packages for Python 2.7, 3.4, 3.5 and 3.6, using a
-reproduceable environment.
-
-- After the build, the Docker container will **not** exit. From the container, type the following commands:
-```
-anaconda login
-anaconda upload osx-64/*
-anaconda upload /opt/conda/conda-bld/linux-64/openpmd_viewer*
-```

openpmd_viewer/__init__.py

@@ -0,0 +1,15 @@
+"""
+openPMD-viewer
+
+Usage
+-----
+See the class OpenPMDTimeSeries to open a set of openPMD files
+"""
+# Make the OpenPMDTimeSeries object accessible from outside the package
+from .openpmd_timeseries import OpenPMDTimeSeries, FieldMetaInformation, \
+    ParticleTracker
+
+# Define the version number
+from .__version__ import __version__
+__all__ = ['OpenPMDTimeSeries', 'FieldMetaInformation',
+           'ParticleTracker', '__version__']

openpmd_viewer/__version__.py

@@ -0,0 +1 @@
+__version__ = "1.0.0"