Python Package Management#
RStudio Connect installs the Python package dependencies of Python-based content when that content is deployed. This includes Flask APIs, Jupyter notebooks, and R projects that include Python.
Package dependencies are captured in one of two ways:
requirements.txtfile exists in the directory containing the project being deployed, then the contents of that file specify the dependencies. See the pip documentation for details. If you provide a
requirements.txtfile, you must ensure that the listed dependencies are correct for the content you are deploying.
pip freezecommand is used to produce a full specification of the current Python environment including all installed packages and their version numbers. In a Jupyter notebook,
pip freezewill be run with the version of Python being used by the active Jupyter notebook kernel. In the RStudio IDE, the environment variable
RETICULATE_PYTHONwill be used to determine which Python environment to inspect.
The resulting package list is included in the bundle archive file, which
is uploaded to RStudio Connect. RStudio Connect receives the bundle
archive file, unpacks it, and uses
pip to install the
identified package dependencies. In addition to the specified dependencies,
RStudio Connect will also install packages that it uses to deploy and render
The execution environment created by RStudio Connect contains the same
package versions you are using in your development environment. The use
virtualenv isolates environments from one another to avoid package
RStudio Connect maintains a cache of Python environments to enable faster deployments. New environments are created as needed, based on the list of package dependencies received in the bundle and the python version in use.
Subsequent deployments that have the same list of dependencies will reuse the previously-built environment. If any dependencies are different, a new environment will be created. This enables published content to make use of different versions of dependent packages without conflict.
requirements.txt file which is the same across multiple
projects is one way to facilitate environment reuse and enable faster
deployments. A similar benefit is achieved in the automatic (
freeze) case if the Python environment on the publishing computer
remains the same between deployments.
External Package Installation#
Adding external packages decreases the reproducibility and isolation of content on RStudio Connect, and should only be done as a last resort.
You can indicate that a system-wide installation of a package should be used
instead of one fetched by
configuration setting can be used to enumerate each system-provided package.
For example, to make
scipy external packages:
Install these packages in every Python installation that RStudio Connect will be using, e.g.:
/opt/Python/3.8.1/bin/python -m pip install numpy scipy
Then configure RStudio Connect to treat those packages as external:
; /etc/rstudio-connect/rstudio-connect.gcfg [Python] External = numpy External = scipy
If any configured Python installation is missing one of the external packages,
RStudio Connect will treat this as an error at startup. If this is a required
configuration (for example, because an external package is not compatible with
one of the installed Python versions), you can set
External Package Version Matching#
By default, RStudio Connect attempts to match external packages by name. In
the example above, if an uploaded bundle requests
numpy==1.15 and the
Python installation in RStudio Connect has
numpy 1.18.1 installed, the
external version will be used even though the version number does not
match. This is similar to how external R packages are handled. Effectively,
the version number specified in the incoming
requirements.txt file is
ignored for external packages.
To require strict version matching, honoring exactly what is specified in the
requirements.txt file, you can set
true. In this case, the version requested in the bundle's
requirements.txt file will be installed if needed, and the external version
will only be used if it's the correct version.
Excluding Python Packages#
To exclude a certain Python package from being utilized, set
to the name of the package. Specify this property once for each Python package
that is to be excluded.
This may be used, for example, when deploying Python-enabled content that utilizes OS-specific packages which are unavailable on the OS that RStudio Connect runs on.
RStudio Connect excludes certain Python packages by default. For a list of these packages please see the Python configuration appendix.
Configuration options for
pip may be set in
options will be read by
pip when installing Python packages. This may
be used, for example, to add additional package indexes or to control
Refer to the pip documentation for further information.