When I build my Python package, I get no warnings or errors:
H:\git\graphab4py>py -m build
* Creating venv isolated environment...
* Installing packages in isolated environment... (setuptools>=61.0, wheel)
* Getting build dependencies for sdist...
running egg_info
writing src\graphab4py.egg-info\PKG-INFO
writing dependency_links to src\graphab4py.egg-info\dependency_links.txt
writing requirements to src\graphab4py.egg-info\requires.txt
writing top-level names to src\graphab4py.egg-info\top_level.txt
reading manifest file 'src\graphab4py.egg-info\SOURCES.txt'
adding license file 'LICENSE'
writing manifest file 'src\graphab4py.egg-info\SOURCES.txt'
* Building sdist...
running sdist
running egg_info
writing src\graphab4py.egg-info\PKG-INFO
writing dependency_links to src\graphab4py.egg-info\dependency_links.txt
writing requirements to src\graphab4py.egg-info\requires.txt
writing top-level names to src\graphab4py.egg-info\top_level.txt
reading manifest file 'src\graphab4py.egg-info\SOURCES.txt'
adding license file 'LICENSE'
writing manifest file 'src\graphab4py.egg-info\SOURCES.txt'
running check
creating graphab4py-1.0.4
creating graphab4py-1.0.4\src
creating graphab4py-1.0.4\src\graphab4py
creating graphab4py-1.0.4\src\graphab4py.egg-info
copying files to graphab4py-1.0.4...
copying LICENSE -> graphab4py-1.0.4
copying README.rst -> graphab4py-1.0.4
copying pyproject.toml -> graphab4py-1.0.4
copying setup.py -> graphab4py-1.0.4
copying src\graphab4py\__init__.py -> graphab4py-1.0.4\src\graphab4py
copying src\graphab4py\functions.py -> graphab4py-1.0.4\src\graphab4py
copying src\graphab4py\project.py -> graphab4py-1.0.4\src\graphab4py
copying src\graphab4py.egg-info\PKG-INFO -> graphab4py-1.0.4\src\graphab4py.egg-info
copying src\graphab4py.egg-info\SOURCES.txt -> graphab4py-1.0.4\src\graphab4py.egg-info
copying src\graphab4py.egg-info\dependency_links.txt -> graphab4py-1.0.4\src\graphab4py.egg-info
copying src\graphab4py.egg-info\requires.txt -> graphab4py-1.0.4\src\graphab4py.egg-info
copying src\graphab4py.egg-info\top_level.txt -> graphab4py-1.0.4\src\graphab4py.egg-info
copying src\graphab4py.egg-info\SOURCES.txt -> graphab4py-1.0.4\src\graphab4py.egg-info
Writing graphab4py-1.0.4\setup.cfg
Creating tar archive
removing 'graphab4py-1.0.4' (and everything under it)
* Building wheel from sdist
* Creating venv isolated environment...
* Installing packages in isolated environment... (setuptools>=61.0, wheel)
* Getting build dependencies for wheel...
running egg_info
writing src\graphab4py.egg-info\PKG-INFO
writing dependency_links to src\graphab4py.egg-info\dependency_links.txt
writing requirements to src\graphab4py.egg-info\requires.txt
writing top-level names to src\graphab4py.egg-info\top_level.txt
reading manifest file 'src\graphab4py.egg-info\SOURCES.txt'
adding license file 'LICENSE'
writing manifest file 'src\graphab4py.egg-info\SOURCES.txt'
* Installing packages in isolated environment... (wheel)
* Building wheel...
running bdist_wheel
running build
running build_py
creating build
creating build\lib
creating build\lib\graphab4py
copying src\graphab4py\functions.py -> build\lib\graphab4py
copying src\graphab4py\project.py -> build\lib\graphab4py
copying src\graphab4py\__init__.py -> build\lib\graphab4py
running egg_info
writing src\graphab4py.egg-info\PKG-INFO
writing dependency_links to src\graphab4py.egg-info\dependency_links.txt
writing requirements to src\graphab4py.egg-info\requires.txt
writing top-level names to src\graphab4py.egg-info\top_level.txt
reading manifest file 'src\graphab4py.egg-info\SOURCES.txt'
adding license file 'LICENSE'
writing manifest file 'src\graphab4py.egg-info\SOURCES.txt'
installing to build\bdist.win-amd64\wheel
running install
running install_lib
creating build\bdist.win-amd64
creating build\bdist.win-amd64\wheel
creating build\bdist.win-amd64\wheel\graphab4py
copying build\lib\graphab4py\functions.py -> build\bdist.win-amd64\wheel\.\graphab4py
copying build\lib\graphab4py\project.py -> build\bdist.win-amd64\wheel\.\graphab4py
copying build\lib\graphab4py\__init__.py -> build\bdist.win-amd64\wheel\.\graphab4py
running install_egg_info
Copying src\graphab4py.egg-info to build\bdist.win-amd64\wheel\.\graphab4py-1.0.4-py3.11.egg-info
running install_scripts
creating build\bdist.win-amd64\wheel\graphab4py-1.0.4.dist-info\WHEEL
creating 'H:\git\graphab4py\dist\.tmp-wmoibnbf\graphab4py-1.0.4-py3-none-any.whl' and adding 'build\bdist.win-amd64\wheel' to it
adding 'graphab4py/__init__.py'
adding 'graphab4py/functions.py'
adding 'graphab4py/project.py'
adding 'graphab4py-1.0.4.dist-info/LICENSE'
adding 'graphab4py-1.0.4.dist-info/METADATA'
adding 'graphab4py-1.0.4.dist-info/WHEEL'
adding 'graphab4py-1.0.4.dist-info/top_level.txt'
adding 'graphab4py-1.0.4.dist-info/RECORD'
removing build\bdist.win-amd64\wheel
Successfully built graphab4py-1.0.4.tar.gz and graphab4py-1.0.4-py3-none-any.whl
However, when I try to upload it to PyPI, it fails with the following output:
H:\git\graphab4py>twine upload dist/*
Uploading distributions to https://upload.pypi.org/legacy/
Uploading graphab4py-1.0.4-py3-none-any.whl
100% ---------------------------------------- 29.3/29.3 kB • 00:00 • 271.1 kB/s
WARNING Error during upload. Retry with the --verbose option for more details.
ERROR HTTPError: 400 Bad Request from https://upload.pypi.org/legacy/
The description failed to render for 'text/x-rst'. See https://pypi.org/help/#description-content-type for
more information.
With the --verbose option, I get:
H:\git\graphab4py>twine upload dist/* --verbose
INFO Using configuration from C:\Users\poppman\.pypirc
Uploading distributions to https://upload.pypi.org/legacy/
INFO dist\graphab4py-1.0.4-py3-none-any.whl (18.3 KB)
INFO dist\graphab4py-1.0.4.tar.gz (19.2 KB)
INFO username set from config file
INFO password set from config file
INFO username: __token__
INFO password: <hidden>
Uploading graphab4py-1.0.4-py3-none-any.whl
100% ---------------------------------------- 29.3/29.3 kB • 00:00 • 1.3 MB/s
INFO Response from https://upload.pypi.org/legacy/:
400 The description failed to render for 'text/x-rst'. See https://pypi.org/help/#description-content-type for
more information.
INFO <html>
<head>
<title>400 The description failed to render for 'text/x-rst'. See
https://pypi.org/help/#description-content-type for more information.</title>
</head>
<body>
<h1>400 The description failed to render for 'text/x-rst'. See
https://pypi.org/help/#description-content-type for more information.</h1>
The server could not comply with the request since it is either malformed or otherwise incorrect.<br/><br/>
The description failed to render for 'text/x-rst'. See
https://pypi.org/help/#description-content-type for more information.
</body>
</html>
ERROR HTTPError: 400 Bad Request from https://upload.pypi.org/legacy/
The description failed to render for 'text/x-rst'. See https://pypi.org/help/#description-content-type for
more information.
I was able to upload earlier versions. Since then, I only changed some docstrings and built a documentation using Sphinx. This version of the package is already on GitHub where the README.rst is displayed correctly.
I assumed the issue was related to the Sphinx files and excluded ./docs in setup.py, but I still get the error.
The current README.rst looks like this:
.. role:: bash(code)
:language: bash
.. role:: python(code)
:language: python
.. raw:: html
<p align="center">
<img src="/docs/img/Ga4Py.png" alt="Graphab4py Logo" width="400">
</p>
----
.. image:: https://img.shields.io/pypi/v/graphab4py.svg
:target: https://pypi.org/project/graphab4py/
.. image:: https://img.shields.io/pypi/pyversions/graphab4py.svg
:target: https://pypi.org/project/graphab4py
.. _Supported Python Versions: https://pypi.org/project/graphab4py
.. image:: https://travis-ci.org/username/graphab4py.svg?branch=master
:target: https://travis-ci.org/username/graphab4py
.. _Build Status: https://travis-ci.org/username/graphab4py
.. image:: https://img.shields.io/pypi/dm/graphab4py.svg?label=PyPI%20downloads
:target: https://pypi.org/project/graphab4py
.. _PyPI Downloads: https://pypi.org/project/graphab4py
.. image:: https://img.shields.io/badge/license-UNLICENSE-green.svg
:target: https://unlicense.org/
=====
About
=====
This package provides a Python interface to the program `Graphab <https://sourcesup.renater.fr/www/graphab/en/home.html/>`_.
The author(s) of this Python package are not developing Graphab.
Rather, Graphab is an independent software which provides a graphical user interface, as well as a command line interface.
Further information on Graphab can be found `here <https://sourcesup.renater.fr/www/graphab/en/home.html>`_.
Also view the `documentation <https://htmlpreview.github.io/?https://github.com/ManuelPopp/graphab4py/blob/main/docs/build/html/index.html>`_ of this Python package.
=============
Prerequisites
=============
In order to install and use Graphab4py, `Python <https://www.python.org>`_ >= 3.8 and `Java <https://www.java.com>`_ >= 8 are both required.
It is also recommended to have `pip <https://pip.pypa.io/en/stable/installation/>`_ available to install the `latest version <https://pypi.org/project/graphab4py/#history>`_ of Graphab4py.
Graphab is not required for installation. It can be installed through Graphab4py if missing. Alternatively, Graphab4py can be set up to use an existing Graphab Java executable.
============
Installation
============
Graphab4Py is available on `PyPI <https://pypi.org/project/graphab4py>`_. To install Graphab4Py, simply run the following line:
.. code-block:: console
pip install graphab4py
========
Examples
========
With Graphab4py installed, we will now look at a few examples.
Creating a project
++++++++++++++++++
In the following, we will create a new Graphab project from scratch.
.. code-block:: python
import graphab4py
graphab4py.set_graphab("/home/rca/opt/")
prj = graphab4py.Project()
prj.create_project(
name = "MyProject", patches = "/home/rca/dat/pat/Patches.tif",
habitat = 1, directory = "/home/rca/prj"
)
prj.create_linkset(
disttype = "cost",
linkname = "L1",
threshold = 100000,
cost_raster = "/home/rca/dat/res/resistance_surface.tif"
)
prj.create_graph(graphname = "G1")
prj.save()
In this example, Graphab has already been downloaded and saved to a folder named :bash:`/home/rca/opt/`.
In a first step, Graphab4py is pointed to this folder. ALternatively, the :python:`get_graphab()` function can be used to download Graphab to a specific location.
Subsequently, the project is initialized. Here, the project is given a name and a project folder is created. Moreover, a file containing habitat patches must be provided.
This file is a raster (e.g., a GeoTIFF \*.tif file) with values encoded as INT2S. (Graphab does not accept another format.) The value or values for habitat patches must also be provided.
Now, we create a linkset. The values allowed for :python:`disttype` are :python:`"euclid"` and :python:`"cost"`, which refer to euclidean distance and cumulated cost.
For a linkset based on euclidean distances, the :python:`cost_raster` argument is not used. When, instead, a resistance surface is used, it needs to be provided as a raster file, as indicated in the example.
Moreover, a threshold can be set, to limit the distance for which links are calculated. This may be necessary when dealing with large sets of habitat patches in order to limit computing time.
Finally, we create a graph and save the project.
Loading an existing project
+++++++++++++++++++++++++++
Graphab4py can load existing Graphab projects (\*.xml). However, it also has its own format (\*.g4p) to save and load projects.
.. code-block:: python
import graphab4py
prj = graphab4py.Project()
prj.load_project_xml("/home/rca/prj/MyProject/MyProject.g4p")
prj.enable_distance_conversion(
save_plot = "/home/rca/out/Distance_conversion.png", max_euc = 2200
)
prj.convert_distance(500, regression = "log")
out = prj.calculate_metric(metric = "EC", d = 1500, p = 0.05)
ec = out["metric_value"]
In this example, we load a project from a Graphab4py project file. Subsequently, we use the linkset that we have created in the previous step to establish a relationship between euclidean and cost distance.
We can set limits to the euclidean distance considered for fitting the model, in order to fit the model to a relevant interval of our data.
When :python:`save_plot` is set to a valid path, a figure is created, so we can inspect the relationship and decide whether we want to use the respective regression mode.
By default, a linear regression is forced through zero. We decided that in our case, a log-log regression might give better results.
We can use the :python:`convert_distance` function directly to establish a relationship and return an estimation for a distance translation.
If no relationship for the given distance interval and regression model has established so far, the method will internally call :python:`enable_distance_conversion` and pass the required arguments.
Note that changing the distance interval will overwrite any previously fit model for the same linkset and model type.
In the last line, we calculate the metric "equivalent connectivity" (EC) for the entire graph. This metric requires additional parameters :python:`d` and :python:`p`.
Other metrics might not require additional parameters. A list of all the available metrics and their parameters and properties can be viewed in the original `Graphab manual <https://sourcesup.renater.fr/www/graphab/en/documentation.html>`_.
=======
License
=======
This is free and unencumbered software released into the public domain, as declared in the `LICENSE <https://github.com/ManuelPopp/graphab4py/blob/main/LICENSE>`_ file.
and it was used in setup.py for the argument long_description with open(). I replaced this with an empty string, but then twine check dist/* returned:
Checking dist\graphab4py-1.0.4-py3-none-any.whl: FAILED
ERROR `long_description` has syntax errors in markup and would not be rendered on PyPI.
line 7: Warning: "raw" directive disabled.
Checking dist\graphab4py-1.0.4.tar.gz: FAILED
ERROR `long_description` has syntax errors in markup and would not be rendered on PyPI.
line 7: Warning: "raw" directive disabled.
The problem was using html in the README.rst file, which is apparently not compatible. Specifically, the following line caused the problem:
.. raw:: html
When replacing this with .. image::, everything works as expected. Except that the image is not centered anymore on the GitHub page when using
.. image:: ./docs/img/Ga4Py.png
:align: center
:alt: Logo
:width: 400px
instead of the html. Unfortunately, the alignment setting is being ignored. At least, it does upload without any warnings or errors.