Developer’s Guide#
Deepends on Python 3.5+
Getting started#
Quickstart by forking the main repository
Clone your copy of the repository.
Using ssh
git clone git@github.com:[your user name]/DeepForest.git
Using https
git clone https://github.com/[your user name]/DeepForest.git
Link or point your cloned copy to the main repository. (I always name it upstream)
git remote add upstream https://github.com/weecology/DeepForest.git
Check or confirm your settings using
git remote -v
origin git@github.com:[your user name]/DeepForest.git (fetch)
origin git@github.com:[your user name]/DeepForest.git (push)
upstream https://github.com/weecology/DeepForest.git (fetch)
upstream https://github.com/weecology/DeepForest.git (push)
Install the package from the main directory.
Deepforest can be installed using either pip or conda.
Install using Pip
Installing with Pip uses dev_requirements.txt.
$ pip install -r dev_requirements.txt
$ pip install . -U
Install using Conda
Installing with Conda uses environment yaml.
Conda-based installs can be slow. We recommend using mamba to speed them up.
$ conda create -n deepforest python=3
$ conda activate deepforest
$ pip install . -U
Check if the package was installed; please test using the sample code.
Testing#
Running tests locally#
$ pip install . --upgrade # or python setup.py install
$ pytest -v
Testing the Conda Deepforest Build#
We use the conda_recipe/meta.yaml to make sure that the conda build can build the package
$ cd conda_recipe
$ conda build conda_recipe/meta.yaml -c conda-forge -c defaults
Conda staged recipe update#
Update the Conda recipe after every release.
Clone the Weecology staged recipes.
Checkout deepforest branch, update the deepforeset/meta.yaml
with
the new version and the sha256 values. Sha256 values are obtained from
the source on PYPI download files
using the deepforest-{version-number}.tar.gz
{% set version = "fill new" %}
{% set sha256 = "fill new" %}
Documentation#
We are using Sphinx and Read the Docs for the documentation.
Update Documentation
The documentation is automatically updated for changes in functions. However, the documentation should be updated after the addition of new functions or modules.
Change to the docs directory and use sphinx-apidoc to update the doc’s
source
. Exclude the tests and setup.py documentation.
Run
sphinx-apidoc -f -o ./source ../ ../tests/* ../setup.py
The source
is the destination folder for the source rst files. ../
is the path to where the deepforest source code is located relative to
the doc directory.
Test documentation locally
cd docs # Go to the docs directory and install the current changes.
pip install ../ -U
make clean # Run
make html # Run
Note:
Do not commit the build directory after making html.