Skip to content

Commit

Permalink
Apache 2.0 LICENSE (#415)
Browse files Browse the repository at this point in the history 
* Apache 2.0 LICENSE
* modfy READMEs, LICENSE; add EXTERNAL_ATTRIBUTION.md
* wrong url
* pep-ify barlow.py, add attribution as attrs; update stats.py
  • Loading branch information
@jllanfranchi
jllanfranchi authored Nov 26, 2017
1 parent 4ee67f9 commit fc323b4
Show file tree
Hide file tree
Showing 6 changed files with 512 additions and 173 deletions.
87 changes: 87 additions & 0 deletions EXTERNAL_ATTRIBUTION.md
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,87 @@
# External software and data in PISA

PISA is distributed with some software and data obtained from outside the IceCube Collaboration.
The authors and any pertinent copyrights are listed below.
If you identify any mistakes in the below or find any other such components being distributed with PISA that are not listed here, please [email]([email protected]) or [file an issue](http://github.com/icecubeopensource/pisa).

Unless noted below or in the contents of an individual file, all files distributed with PISA are Copyright (c) 2014-2017, The IceCube Collaboration, and are licensed under the Apache 2.0 license.
See the LICENSE file for details.

## Prob3++

Files in the directory `pisa/stages/osc/prob3` were written by members of the Super-Kamiokande collaboration and are offered for public use. The original source code can be found at
> http://webhome.phy.duke.edu/~raw22/public/Prob3++
and that work is based on the paper
> V. D. Barger, K. Whisnant, S. Pakvasa, and R. J. N. Phillips, Phys. Rev. D 22, 2718 (1980)
## prob3GPU

Files in the directory `pisa/pisa/stages/osc/prob3cuda` were adapted from the CUDA re-implementation of Prob3++ called prob3GPU
> https://github.com/rcalland/probGPU
which is cited by the paper
> R. G. Calland, A. C. Kaboth, and D. Payne, Journal of Instrumentation 9, P04016 (2014).
## Honda et al. flux models

Files in the directory `pisa/resources/flux` containing the name *honda* are from
> http://www.icrr.u-tokyo.ac.jp/~mhonda
with associated paper
> M. Honda, M. S. Athar, T. Kajita, K. Kasahara, and S. Midorikawa, Phys. Rev. D 92, 023004 (2015).
## Barr et al. flux models

Files in the directory `pisa/resources/flux` containing the name *bartol* are modified slightly (to have similar format to the work by Honda et al. cited above) from
> http://www-pnp.physics.ox.ac.uk/~barr/fluxfiles
with associated paper
G. D. Barr, T. K. Gaisser, P. Lipari, S. Robbins, and T. Stanev, Phys. Rev. D 70, 023006 (2004).

## PREM

The preliminary reference Earth model data in the `pisa/resources/osc` directory (named `PREM*`) come from the paper
> A. M. Dziewonski and D. L. Anderson, Physics of the Earth and Planetary Interiors 25, 297 (1981)
## KDE

The file `pisa/pisa/utils/vbwkde.py` contains an implementation of (part of) the paper
> Z. I. Botev, J. F. Grotowski, and D. P. Kroese, Ann. Statist. 38, 2916 (2010).
The functions `isj_bandwidth` and `fixed_point` therein are adapted directly from the Matlab implementation by Zdravko Botev at
> https://www.mathworks.com/matlabcentral/fileexchange/14034-kernel-density-estimator
and are therefore subject to the following copyright:
```
Copyright (c) 2007, Zdravko Botev
All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are
met:
* Redistributions of source code must retain the above copyright
notice, this list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright
notice, this list of conditions and the following disclaimer in
the documentation and/or other materials provided with the
distribution
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS
IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED
TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER
OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
```

## Versioneer

Automatic versioning is provided by public-domain sofware The Versioneer, written by Brian Warner (files `versioneer.py` and `pisa/_version.py`).
This project can be found at
> https://github.com/warner/python-versioneer
201 changes: 201 additions & 0 deletions LICENSE
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,201 @@
Apache License
Version 2.0, January 2004
http://www.apache.org/licenses/

TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION

1. Definitions.

"License" shall mean the terms and conditions for use, reproduction,
and distribution as defined by Sections 1 through 9 of this document.

"Licensor" shall mean the copyright owner or entity authorized by
the copyright owner that is granting the License.

"Legal Entity" shall mean the union of the acting entity and all
other entities that control, are controlled by, or are under common
control with that entity. For the purposes of this definition,
"control" means (i) the power, direct or indirect, to cause the
direction or management of such entity, whether by contract or
otherwise, or (ii) ownership of fifty percent (50%) or more of the
outstanding shares, or (iii) beneficial ownership of such entity.

"You" (or "Your") shall mean an individual or Legal Entity
exercising permissions granted by this License.

"Source" form shall mean the preferred form for making modifications,
including but not limited to software source code, documentation
source, and configuration files.

"Object" form shall mean any form resulting from mechanical
transformation or translation of a Source form, including but
not limited to compiled object code, generated documentation,
and conversions to other media types.

"Work" shall mean the work of authorship, whether in Source or
Object form, made available under the License, as indicated by a
copyright notice that is included in or attached to the work
(an example is provided in the Appendix below).

"Derivative Works" shall mean any work, whether in Source or Object
form, that is based on (or derived from) the Work and for which the
editorial revisions, annotations, elaborations, or other modifications
represent, as a whole, an original work of authorship. For the purposes
of this License, Derivative Works shall not include works that remain
separable from, or merely link (or bind by name) to the interfaces of,
the Work and Derivative Works thereof.

"Contribution" shall mean any work of authorship, including
the original version of the Work and any modifications or additions
to that Work or Derivative Works thereof, that is intentionally
submitted to Licensor for inclusion in the Work by the copyright owner
or by an individual or Legal Entity authorized to submit on behalf of
the copyright owner. For the purposes of this definition, "submitted"
means any form of electronic, verbal, or written communication sent
to the Licensor or its representatives, including but not limited to
communication on electronic mailing lists, source code control systems,
and issue tracking systems that are managed by, or on behalf of, the
Licensor for the purpose of discussing and improving the Work, but
excluding communication that is conspicuously marked or otherwise
designated in writing by the copyright owner as "Not a Contribution."

"Contributor" shall mean Licensor and any individual or Legal Entity
on behalf of whom a Contribution has been received by Licensor and
subsequently incorporated within the Work.

2. Grant of Copyright License. Subject to the terms and conditions of
this License, each Contributor hereby grants to You a perpetual,
worldwide, non-exclusive, no-charge, royalty-free, irrevocable
copyright license to reproduce, prepare Derivative Works of,
publicly display, publicly perform, sublicense, and distribute the
Work and such Derivative Works in Source or Object form.

3. Grant of Patent License. Subject to the terms and conditions of
this License, each Contributor hereby grants to You a perpetual,
worldwide, non-exclusive, no-charge, royalty-free, irrevocable
(except as stated in this section) patent license to make, have made,
use, offer to sell, sell, import, and otherwise transfer the Work,
where such license applies only to those patent claims licensable
by such Contributor that are necessarily infringed by their
Contribution(s) alone or by combination of their Contribution(s)
with the Work to which such Contribution(s) was submitted. If You
institute patent litigation against any entity (including a
cross-claim or counterclaim in a lawsuit) alleging that the Work
or a Contribution incorporated within the Work constitutes direct
or contributory patent infringement, then any patent licenses
granted to You under this License for that Work shall terminate
as of the date such litigation is filed.

4. Redistribution. You may reproduce and distribute copies of the
Work or Derivative Works thereof in any medium, with or without
modifications, and in Source or Object form, provided that You
meet the following conditions:

(a) You must give any other recipients of the Work or
Derivative Works a copy of this License; and

(b) You must cause any modified files to carry prominent notices
stating that You changed the files; and

(c) You must retain, in the Source form of any Derivative Works
that You distribute, all copyright, patent, trademark, and
attribution notices from the Source form of the Work,
excluding those notices that do not pertain to any part of
the Derivative Works; and

(d) If the Work includes a "NOTICE" text file as part of its
distribution, then any Derivative Works that You distribute must
include a readable copy of the attribution notices contained
within such NOTICE file, excluding those notices that do not
pertain to any part of the Derivative Works, in at least one
of the following places: within a NOTICE text file distributed
as part of the Derivative Works; within the Source form or
documentation, if provided along with the Derivative Works; or,
within a display generated by the Derivative Works, if and
wherever such third-party notices normally appear. The contents
of the NOTICE file are for informational purposes only and
do not modify the License. You may add Your own attribution
notices within Derivative Works that You distribute, alongside
or as an addendum to the NOTICE text from the Work, provided
that such additional attribution notices cannot be construed
as modifying the License.

You may add Your own copyright statement to Your modifications and
may provide additional or different license terms and conditions
for use, reproduction, or distribution of Your modifications, or
for any such Derivative Works as a whole, provided Your use,
reproduction, and distribution of the Work otherwise complies with
the conditions stated in this License.

5. Submission of Contributions. Unless You explicitly state otherwise,
any Contribution intentionally submitted for inclusion in the Work
by You to the Licensor shall be under the terms and conditions of
this License, without any additional terms or conditions.
Notwithstanding the above, nothing herein shall supersede or modify
the terms of any separate license agreement you may have executed
with Licensor regarding such Contributions.

6. Trademarks. This License does not grant permission to use the trade
names, trademarks, service marks, or product names of the Licensor,
except as required for reasonable and customary use in describing the
origin of the Work and reproducing the content of the NOTICE file.

7. Disclaimer of Warranty. Unless required by applicable law or
agreed to in writing, Licensor provides the Work (and each
Contributor provides its Contributions) on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
implied, including, without limitation, any warranties or conditions
of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A
PARTICULAR PURPOSE. You are solely responsible for determining the
appropriateness of using or redistributing the Work and assume any
risks associated with Your exercise of permissions under this License.

8. Limitation of Liability. In no event and under no legal theory,
whether in tort (including negligence), contract, or otherwise,
unless required by applicable law (such as deliberate and grossly
negligent acts) or agreed to in writing, shall any Contributor be
liable to You for damages, including any direct, indirect, special,
incidental, or consequential damages of any character arising as a
result of this License or out of the use or inability to use the
Work (including but not limited to damages for loss of goodwill,
work stoppage, computer failure or malfunction, or any and all
other commercial damages or losses), even if such Contributor
has been advised of the possibility of such damages.

9. Accepting Warranty or Additional Liability. While redistributing
the Work or Derivative Works thereof, You may choose to offer,
and charge a fee for, acceptance of support, warranty, indemnity,
or other liability obligations and/or rights consistent with this
License. However, in accepting such obligations, You may act only
on Your own behalf and on Your sole responsibility, not on behalf
of any other Contributor, and only if You agree to indemnify,
defend, and hold each Contributor harmless for any liability
incurred by, or claims asserted against, such Contributor by reason
of your accepting any such warranty or additional liability.

END OF TERMS AND CONDITIONS

APPENDIX: How to apply the Apache License to your work.

To apply the Apache License to your work, attach the following
boilerplate notice, with the fields enclosed by brackets "[]"
replaced with your own identifying information. (Don't include
the brackets!) The text should be enclosed in the appropriate
comment syntax for the file format. We also recommend that a
file or class name and description of purpose be included on the
same "printed page" as the copyright notice for easier
identification within third-party archives.

Copyright (c) 2014-2017 The IceCube Collaboration

Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
51 changes: 29 additions & 22 deletions README.md
View file
Original file line number Diff line number Diff line change
@@ -1,28 +1,35 @@
# PISA
[Introduction](pisa/README.md) |
[Installation](INSTALL.md) |
[Documentation](http://icecube.wisc.edu/%7Epeller/pisa_docs/index.html) |
[Terminology](pisa/glossary.md) |
[License](LICENSE) |
[Contributors](CONTRIBUTORS.md) |
[Others' work](EXTERNAL_ATTRIBUTION.md)

PINGU Simulation and Analysis (PISA) is software written for performing analyses based upon Monte Carlo simulations of the [IceCube neutrino observatory](https://icecube.wisc.edu/), including the [DeepCore](https://arxiv.org/abs/1109.6096) and proposed [PINGU](https://arxiv.org/abs/1401.2046) low-energy in-fill arrays (as well as other similar neutrino detectors).
PISA (PINGU Simulation and Analysis) is software written to analyze the results (or expected results) of an experiment based on Monte Carlo simulation.

PISA was originally developed to cope with low-statistics Monte Carlo (MC) for PINGU using parameterizations of the MC, but its methods should apply equally as well to high-MC situations, and the PISA architecture is general enough to easily accomoodate traditional reweighted-MC-style analyses.
In particular, PISA was written for the [IceCube Neutrino Observatory](https://icecube.wisc.edu/), including the [DeepCore](https://arxiv.org/abs/1109.6096) and the proposed [PINGU](https://arxiv.org/abs/1401.2046) low-energy in-fill arrays.
However, any such experiment—or any experiment at all—can make use of PISA for analyzing expected and actual results.

Visit the project Wiki for the latest documentation (not yet folded into the codebase):
* [PISA Cake wiki](https://github.com/jllanfranchi/pisa/wiki)
PISA was originally developed to cope with low-statistics Monte Carlo (MC) for PINGU when iterating on multiple proposed geometries by using parameterizations of the MC and operate on histograms of the data rather than directly reweighting the MC (as is traditionally done in high-energy Physics experiments).
However, PISA's methods apply equally well to high-MC situations, and PISA also performs traditional reweighted-MC analysis as well.

A compilation of the README files in to a set of documentation using Sphinx can be found at: http://icecube.wisc.edu/~peller/pisa_docs/index.html
## Directory listing


## Directory Listing

* `docs/` - Directory containing the output of Sphinx auto-generating the documentation.
* `images/` - Directory containing the git fork button.
* `pisa/` - Directory containing all of the PISA code.
* `tests/` - Contains all the python scripts for tests on the performance of PISA.
* `.gitattributes`
* `.gitignore` - Ignore files within the directories matching these specifications
* `INSTALL.md` - How to install PISA
* `MANIFEST.in`
* `README.md` - Brief overview of PISA
* `pylintrc` - PISA coding conventions for use with pylint
* `requirements.txt` - Hard dependencies, use with ``pip install -r requirements.txt``
* `setup.cfg` - Setup file for `versioneer`
* `setup.py` - Python setup file, for use with `pip`
* `versioneer.py` - Automatic versioning
| File/directory | Description
| ------------------ | -----------
| `docs/` | Sphinx auto-generated documentation
| `images/` | Images to include in documentation
| `pisa/` | Source code
| `tests/` | Scripts for running physics and unit tests
| `.gitattributes` |
| `.gitignore` | GIT ignores files matching these specifications
| `INSTALL.md` | How to install PISA
| `MANIFEST.in` |
| `README.md` | Brief overview of PISA
| `pylintrc` | PISA coding conventions for use with pylint
| `requirements.txt` | Hard dependencies, use with `pip install -r requirements.txt`
| `setup.cfg` | Setup file for `versioneer`
| `setup.py` | Python setup file, allowing e.g. `pip` installation
| `versioneer.py` | Automatic versioning
Loading

0 comments on commit fc323b4

Please sign in to comment.