Updating PlantCV¶
The general procedure for updating PlantCV if you are using the master branch
cloned from the danforthcenter/plantcv repository is to update your local
repository and reinstall the package.
If you are not sure that you have cloned the danforthcenter/plantcv repository
and are on the master branch, here is how you can tell:
cd plantcv
git remote -v
# You should see something like:
# origin https://github.com/danforthcenter/plantcv.git (fetch)
git status
# You should see:
# On branch master
# nothing to commit, working directory clean
If the above is true, updating can be done simply by:
git pull
python setup.py install
# Or with sudo if needed
If you have put the cloned plantcv repository folder in your PYTHONPATH then
pulling alone is enough to update.
Updating from v1 to v2¶
The setuptools installation method was not available in PlantCV v1, so users
put the plantcv/lib directory in their custom PYTHONPATH. In PlantCV v2, the
plantcv library directory is no longer in the lib directory, now it is in the
main repository folder (plantcv/plantcv). If you want to continue to have
plantcv in your PYTHONPATH you will need to update by simply removing lib
from the path. You can also remove the lib folder after pulling the new version.
Git will automatically remove the *.py files but because we do not track the
*.pyc files they will remain behind and can technically be imported, which can
cause confusion.
For Linux/Unix, PYTHONPATH can be edited in ~/.bash_profile, ~/.bashrc,
~/.profile, ~/.cshrc, ~/.zshrc, etc. For Windows, right-click on My
Computer/This PC and select Properties > Advanced system settings >
Environmental Variables... and edit the User variables entry for PYTHONPATH.
Also note that the method for parallelizing PlantCV has changed, please see the new parallel processing documentation for more details.
Updating to v3¶
In order to support the installation of optional add-on subpackages, we converted PlantCV to a namespace package. To achieve this new functionality, existing functions had to be moved into a subpackage to maintain easy importing. To maintain previous behavior, PlantCV analysis scripts simply need to have updated PlantCV import syntax. So if you were previously doing something like:
import plantcv as pcv
You would now do this instead:
from plantcv import plantcv as pcv
Another feature we will be rolling out for PlantCV v3 an update to the existing
package API. The goal is to make each PlantCV function easier to use. This will
be apparent in two ways at first. 1) all existing functions/functionality will
remain intact but we will be adding deprecation warnings to outdated functions
that are being replaced. 2) New functions will utilize a global parameters class
to inherit values for standard inputs like debug and device so that these
values will not need to be explicitly input to each function. An instance of the
class Params as params is created automatically when PlantCV is imported and
it can be imported to set global defaults. For example, to change debug from
None to 'plot' or 'print':
from plantcv import plantcv as pcv
pcv.params.debug = "plot"
For more information, see the Params documentation.