seeq-correlation code, initial transfer

LICENSE

@@ -0,0 +1,144 @@
+                                 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 [yyyy] [name of copyright owner]
+
+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.

MANIFEST.in

@@ -0,0 +1,5 @@
+include LICENSE
+global-exclude *.pyc
+global-exclude .ipynb_checkpoints
+graft seeq/addons/correlation/deployment_notebook
+prune tests

NOTICE

@@ -0,0 +1,10 @@
+Copyright [2021] [Seeq Corporation]
+
+Licensed under the Apache License, Version 2.0 (the "License"); you may not use this work except in compliance with the
+License. You may obtain a copy of the License at
+
+    https://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.

README.md

@@ -0,0 +1,162 @@
+[![N|Solid](https://www.seeq.com/sites/default/files/seeq-logo-navbar-small.png)](https://www.seeq.com)
+
+[![N|Scheme](LargeMatrixExample.png)](https://www.seeq.com)
+
+----
+
+**seeq-correlation** is a Python module to calculate and monitor cross-correlations among time-series signals. It also
+calculates the time shifts (lead or lag) that maximize the cross-correlations of each signal pair. The module includes a
+user interface (UI) designed to interact with the Seeq server. Specifically, the UI can be installed as an Add-on Tool
+in Seeq Workbench.
+
+----
+
+# User Guide
+
+[**seeq-correlation User Guide**](https://seeq12.github.io/seeq-correlation/user_guide.html)
+provides a more in-depth explanation of correlation analysis and how seeq-correlation works. Examples of typical types
+of analyses using **seeq-correlation** can be found in the
+section [Use Cases](https://seeq12.github.io/seeq-correlation/examples.html).
+
+----
+
+# Documentation
+
+[Documentation for **seeq-correlation**](https://seeq12.github.io/seeq-correlation/documentation.html).
+
+-----
+
+# Installation
+
+The backend of **seeq-correlation** requires **Python 3.7** or later.
+
+## Dependencies
+
+See [`requirements.txt`](https://github.com/seeq12/seeq-correlation/tree/master/requirements.txt) file for a list of
+dependencies and versions. Additionally, you will need to install the `seeq` module with the appropriate version that
+matches your Seeq server. For more information on the `seeq` module see [seeq at pypi](https://pypi.org/project/seeq/)
+
+## User Installation Requirements (Seeq Data Lab)
+
+If you want to install **seeq-correlation** as a Seeq Add-on Tool, you will need:
+
+- Seeq Data Lab (>= R50.5.0, >=R51.1.0, or >=R52.1.0)
+- `seeq` module whose version matches the Seeq server version
+- Seeq administrator access
+- Enable Add-on Tools in the Seeq server
+
+## User Installation (Seeq Data Lab)
+
+The latest build of the project can be found [here](https://pypi.seeq.com/) as a wheel file. The file is published as a
+courtesy to the user, and it does not imply any obligation for support from the publisher. Contact
+[Seeq](mailto:[email protected]?subject=[seeq-correlation]%20General%20Question) if you required credentials to
+access the site.
+
+1. Create a **new** Seeq Data Lab project and open the **Terminal** window
+2. Run `pip install seeq-correlation --extra-index-url https://pypi.seeq.com --trusted-host pypi.seeq.com`
+3. Run `python -m seeq.addons.correlation [--users <users_list> --groups <groups_list>]`
+
+----
+
+# Development
+
+We welcome new contributors of all experience levels. The **Development Guide** has detailed information about
+contributing code, documentation, tests, etc.
+
+## Important links
+
+* Official source code repo: https://github.com/seeq12/seeq-correlation
+* Issue tracker: https://github.com/seeq12/seeq-correlation/issues
+
+## Source code
+
+You can get started by cloning the repository with the command:
+
+```shell
+git clone [email protected]:seeq12/seeq-correlation.git
+```
+
+## Installation from source
+
+For development work, it is highly recommended creating a python virtual environment and install the package in that
+working environment. If you are not familiar with python virtual environments, you can take a
+look [here](https://docs.python.org/3.8/tutorial/venv.html)
+
+Once your virtual environment is activated, you can install **seeq-correlation** from source with:
+
+```shell
+python setup.py install
+```
+
+## Testing
+
+There are several types of testing available for **seeq-correlation**
+
+### Automatic Testing
+
+After installation, you can launch the test suite from the root directory of the project (i.e. `seeq-correlation`
+directory). You will need to have pytest >= 5.0.1 installed
+
+To run all tests:
+
+```shell
+pytest
+```
+
+There are several pytest markers set up in the project. You can find the description of the marks in the `pytest.ini`
+file. You can use the `-m` flag to run only a subset of tests. For example, to run only the `backend` tests, you can
+use:
+
+```shell
+pytest -m backend
+```
+
+The integration tests requires a connection to a Seeq server. The tests are configured to try to access a local Seeq
+server with the data directory set up in `ProgramData/Seeq/data` of the local drive. However, you can set the
+`seeq_url`, `credentials_file` configuration options in the `test_config.ini` file to run the integration tests on a
+remote Seeq server, or change the local seeq data directory with `data_dir`.
+
+*Note:* Remember that the `seeq` module version in your local environment should match the Seeq server version
+
+### User Interface Testing
+
+To test the UI, use the `developer_notebook.ipynb` in the `development` folder of the project. This notebook can also be
+used while debugging from your IDE. You can also create a whl first, install it on your virtual environment, and then
+run `developer_notebook.ipynb` notebook there.
+
+----
+
+# Changelog
+
+The change log can be found [**here**](https://seeq12.github.io/seeq-correlation/changelog.html)
+
+
+----
+
+# Support
+
+Code related issues (e.g. bugs, feature requests) can be created in the
+[issue tracker](https://github.com/seeq12/seeq-correlation/issues)
+Any other general comments or questions (non-code related) can be emailed to
+[Seeq](mailto:[email protected]?subject=[seeq-correlation]%20General%20Question)
+
+Maintainer: Alberto Rivas
+
+
+----
+
+# Citation
+
+Please cite this work as:
+
+```shell
+seeq-correlation v0.0.20
+Seeq Corporation, 2021
+https://github.com/seeq12/seeq-correlation
+```
+
+
+
+
+
+