Adding static release

README.md

@@ -1,8 +1,18 @@
 # lsdtopytools
 
-Repository for `lsdtopytools`. So far, it only contains instructions to install and wheels (python installers). Will evolve soon. Source code in the `LSDTT_development` repository. `lsdtt-xtensor-python` is a direct wrapper to the `c++` code and `lsdtopytools` a nicer `python` interface easier to use. 
+Repository for `lsdtopytools`, a python wrapper on LSDTopoTools. It binds the c++ code with `lsdtt-xtensor` and expose it to `python` via `numpy`. It allows us to take advantage of both world: `c++` speed and python flexibility. `lsdtopytools` suite can be done using Docker or Anaconda.
 
-`lsdtopytools` suite can be done using Docker or Anaconda, you have the choice, really.
+This repository host the static version of the code available for installation, it is updated at each release (usually when we are publishing a new manuscript utilising new features). Tutorial and example notebooks can be found in [this dedicated repository](https://github.com/LSDtopotools/lsdtt_notebooks/tree/master/lsdtopytools).
+
+# Features
+
+- Raster i/o and basic operations
+- Preprocessing depressions (carving, filling, nodata, ...)
+- River extraction (drainage area threshold)
+- ksn from segmented profiles (Mudd et al. 2014)
+- concavity index (Mudd et al., 2018, Gailleton et al., 2021 (preprint))
+- polyfit metrics
+- ...
 
 # Installation using docker
 
@@ -12,63 +22,37 @@ See https://github.com/LSDtopotools/lsdtt_pytools_docker for intruction on how t
 
 ## Installation through `conda` and `pip`
 
-Best installation is from `conda`, it has been tested for windows and different linuxes. Other OSes will need to build from source (explanation bellow).
+You need first to have a valid installation of `anaconda` on your computer. I really reccomend `miniforge` [see readme here](https://github.com/conda-forge/miniforge) which guarentee a full open-source and open-license installation.
 
-First create a `conda` environment and activate it:
+Installation from `conda` has been tested for windows10, MacOS and different linuxes (ubuntu, Debian, Redhat, WSL). Other OSes will need to build from source (explanation bellow).
+
+First create a `conda` environment `with python <= 3.8` (3.9 will come shortly) and activate it:
 
 ```
-conda create -n lsdtopytools python=3.7
+conda create -n lsdtopytools python=3.8
 
 conda activate lsdtopytools
 ```
 
-**RECOMENDED STEP** - *basically except if you have a specific reason not to do it*: you need to fix an annoying tendency of gdal to rely on messed up dependencies:
+**RECOMENDED STEP IF YOU HAVE ANOTHER DISTRIBUTION THAN MINIFORGE**: you need to fix an annoying tendency of gdal to rely on messed up dependencies:
 ```
 conda config --prepend channels defaults
 conda config --prepend channels conda-forge
 conda config --set channel_priority strict
 ```
 
-Then install the required dependencies:
-
-```
-conda install -c conda-forge gdal rasterio geopandas matplotlib=3.1 numpy scipy pytables numba feather-format pandas pip pybind11 xtensor xtensor-python
-```
-
-We are now ready to install the wheels, let's clone the github repository on the computer:
-
-```
-git clone https://github.com/LSDtopotools/lsdtopytools
-```
-
-This downloads the ropository in the current folder, then you can navigate to teh wheels and list the files:
+Then, you can install by simply running:
 
 ```
-cd lsdtopytools/wheels/lsdtt-xtensor-python
-ls
+conda install lsdtopytools
 ```
 
-This will display the available wheels. One of them should correspond to your architecture (= computer type).
-
-```
-pip install lsdtt_xtensor_python-YYY-cp37-cp37m-XXX.whl
-```
-where YYY is the latest version of lsdtt-xtensor-python, e.g. `0.0.3`, and XXX your architecture, e.g. `linux_x86_64` for linux 64 bits. Finally:
-
-```
-cd ../lsdtopytools
-pip install lsdtopytools-XXX-py2.py3-none-any.whl
-```
-
-where XXX is the latest version available. And everything is installed!
-
-## No compatible wheels for lsdtt-xtensor-python?
+## Something went wrong
 
 In that case you need to check several things:
-- You are on iOS, I do not own a mac and cannot generate the wheel, you need to generate it from source.
 - You are on a previously created conda environment and trying to install lsdtt-xtensor-python in it, check that you DO have `python=3.7.X`
-- You have a `32 bits` OS/processor, You need to install from source (also it's been like 15 years all the computers are 64 bits)
-- You are on an antiquated computer unable to get recent `libc`, `libc++` or `libstdc++`, there is nothing we can do unfortunately although I'd be surprised if it happens.
+- You have a `32 bits` OS/processor, You need to install from source (also it's been like 15 years all the computers are 64 bits, this is the reason we do not guarentee compatibility)
+- You are on an antiquated computer unable to get recent `libc`, `libc++` or `libstdc++`, there is nothing we can do unfortunately although I'd be surprised if it happens. We need `c++14` for `lsdtt-xtensor` and that is a hard-pass unfortunately.
 
 ## Installation from source
 
@@ -91,32 +75,10 @@ pip install .
 ```
 Done.
 
-# Updating the code
-
-So far I will post updated wheel in that repository, in the future I will create a more sofisticated and simpler installing method. To update the `lsdtt-xtensor-python`:
-
-```
-pip uninstall -y lsdtt-xtensor-python
-cd wheels/lsdtt-xtensor-python
-pip install XXX
-```
-
-where XXX is the newest wheel. To update `lsdtopytools`:
-
-```
-cd wheels/lsdtopytools
-pip install --force-reinstall --no-deps XXX
-```
-where XXX is the newest wheel.
-
-# Quick start
-
-I will put tutorial and example scripts and jupyter notebooks in the future.
-
 # Troubleshoots
 
 - **[LINUX] GLIBC error**: I am working on it, but basically your linux is older than the one with which I installed it and does not have as recent glibc. Good news is that there is a solution, bad news is that It will take me a bit of time to implement and you need to install from source. I need to build `manylinux2010` wheels which involve using docker, which is not compatible with any of my hardware without accessing the BIOS and I cannot.
 
-So far in early development stage, all of that code will evolve very rapidly and probably drastically. Contact `b.gailleton@sms.ed.ac.uk` for questions.
+So far in early development stage, all of that code will evolve very rapidly and probably drastically. Contact `boris.gailleton@gfz-potsdam.de` for questions.
 
 

lsdtopytools/AUTHORS.rst

@@ -0,0 +1,17 @@
+=======
+Credits
+=======
+
+Development Lead
+----------------
+
+* Boris Gailleton <[email protected]>
+
+Contributors
+------------
+
+* Python development: Boris Gailleton
+
+* Cpp lsdtopotools: Simon M. Mudd (lead dev.), (unordered) Dave T. Miladowski, Stuart Grieves, Fiona J. Clubb, Declan Valters, Boris Gailleton
+
+* lsdtopytools alpha tester: Emma Graf, Jorien Van Der Hoeven, Rebbeca Harries, Arturo Tamay 

lsdtopytools/CONTRIBUTING.rst

@@ -0,0 +1,128 @@
+.. highlight:: shell
+
+============
+Contributing
+============
+
+Contributions are welcome, and they are greatly appreciated! Every little bit
+helps, and credit will always be given.
+
+You can contribute in many ways:
+
+Types of Contributions
+----------------------
+
+Report Bugs
+~~~~~~~~~~~
+
+Report bugs at https://github.com/bgailleton/lsdtopytools/issues.
+
+If you are reporting a bug, please include:
+
+* Your operating system name and version.
+* Any details about your local setup that might be helpful in troubleshooting.
+* Detailed steps to reproduce the bug.
+
+Fix Bugs
+~~~~~~~~
+
+Look through the GitHub issues for bugs. Anything tagged with "bug" and "help
+wanted" is open to whoever wants to implement it.
+
+Implement Features
+~~~~~~~~~~~~~~~~~~
+
+Look through the GitHub issues for features. Anything tagged with "enhancement"
+and "help wanted" is open to whoever wants to implement it.
+
+Write Documentation
+~~~~~~~~~~~~~~~~~~~
+
+LSDTopyTools could always use more documentation, whether as part of the
+official LSDTopyTools docs, in docstrings, or even on the web in blog posts,
+articles, and such.
+
+Submit Feedback
+~~~~~~~~~~~~~~~
+
+The best way to send feedback is to file an issue at https://github.com/bgailleton/lsdtopytools/issues.
+
+If you are proposing a feature:
+
+* Explain in detail how it would work.
+* Keep the scope as narrow as possible, to make it easier to implement.
+* Remember that this is a volunteer-driven project, and that contributions
+  are welcome :)
+
+Get Started!
+------------
+
+Ready to contribute? Here's how to set up `lsdtopytools` for local development.
+
+1. Fork the `lsdtopytools` repo on GitHub.
+2. Clone your fork locally::
+
+    $ git clone [email protected]:your_name_here/lsdtopytools.git
+
+3. Install your local copy into a virtualenv. Assuming you have virtualenvwrapper installed, this is how you set up your fork for local development::
+
+    $ mkvirtualenv lsdtopytools
+    $ cd lsdtopytools/
+    $ python setup.py develop
+
+4. Create a branch for local development::
+
+    $ git checkout -b name-of-your-bugfix-or-feature
+
+   Now you can make your changes locally.
+
+5. When you're done making changes, check that your changes pass flake8 and the
+   tests, including testing other Python versions with tox::
+
+    $ flake8 lsdtopytools tests
+    $ python setup.py test or py.test
+    $ tox
+
+   To get flake8 and tox, just pip install them into your virtualenv.
+
+6. Commit your changes and push your branch to GitHub::
+
+    $ git add .
+    $ git commit -m "Your detailed description of your changes."
+    $ git push origin name-of-your-bugfix-or-feature
+
+7. Submit a pull request through the GitHub website.
+
+Pull Request Guidelines
+-----------------------
+
+Before you submit a pull request, check that it meets these guidelines:
+
+1. The pull request should include tests.
+2. If the pull request adds functionality, the docs should be updated. Put
+   your new functionality into a function with a docstring, and add the
+   feature to the list in README.rst.
+3. The pull request should work for Python 2.7, 3.4, 3.5 and 3.6, and for PyPy. Check
+   https://travis-ci.org/bgailleton/lsdtopytools/pull_requests
+   and make sure that the tests pass for all supported Python versions.
+
+Tips
+----
+
+To run a subset of tests::
+
+
+    $ python -m unittest tests.test_lsdtopytools
+
+Deploying
+---------
+
+A reminder for the maintainers on how to deploy.
+Make sure all your changes are committed (including an entry in HISTORY.rst).
+Then run::
+
+$ bumpversion patch # possible: major / minor / patch
+$ git push
+$ git push --tags
+
+Travis will then deploy to PyPI if tests pass.

lsdtopytools/HISTORY.rst

@@ -0,0 +1,8 @@
+=======
+History
+=======
+
+0.0.1 (2018-11-07)
+------------------
+
+* First release on PyPI.

lsdtopytools/LICENSE

@@ -0,0 +1,33 @@
+GNU GENERAL PUBLIC LICENSE
+                      Version 3, 29 June 2007
+
+    High-level interface to LSDTopoTools in pyhton. Include as much tools as we can port in python, for the rest see our docker solutions
+    Copyright (C) 2018  Boris Gailleton
+
+    This program is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    This program is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+Also add information on how to contact you by electronic and paper mail.
+
+  You should also get your employer (if you work as a programmer) or school,
+if any, to sign a "copyright disclaimer" for the program, if necessary.
+For more information on this, and how to apply and follow the GNU GPL, see
+<http://www.gnu.org/licenses/>.
+
+  The GNU General Public License does not permit incorporating your program
+into proprietary programs.  If your program is a subroutine library, you
+may consider it more useful to permit linking proprietary applications with
+the library.  If this is what you want to do, use the GNU Lesser General
+Public License instead of this License.  But first, please read
+<http://www.gnu.org/philosophy/why-not-lgpl.html>.
+

lsdtopytools/MANIFEST.in

@@ -0,0 +1,11 @@
+include AUTHORS.rst
+include CONTRIBUTING.rst
+include HISTORY.rst
+include LICENSE
+include README.rst
+
+recursive-include tests *
+recursive-exclude * __pycache__
+recursive-exclude * *.py[co]
+
+recursive-include docs *.rst conf.py Makefile make.bat *.jpg *.png *.gif