PyFilesystem2 AnVIL plugin

A plugin for representing AnVIL resources in Python environments as a file system; particularly, in an AnVIL-launched Galaxy instances.

Galaxy installation requirements:

• file_sources_conf.yml in the Galaxy config directory with an AnVIL entry:

- doc: <whatever you would like to call it>
  id: <root folder name>
  namespace: <your google billing project == Terra namespace >
  type: anvil
  workspace: <name of the Terra workspace you wish to browse>
  api_url: <OPTIONAL - if not specified default production url will be used>
  on_anvil: <OPTIONAL - (true/false) must be true to manage AnVIL workload identity scopes>
  drs_url: <OPTIONAL - if not specified  default production url will be used>
  writable: <OPTIONAL - (true/false) if not specified plugin will be read-only>

NOTES:

• doc and id can be any string you choose but type MUST be anvil
• for off-AnVIL use, Galaxy and Data Fetch tools require the following environment variables:
  • GOOGLE_APPLICATION_CREDENTIALS="<path to credentials json>"
  • TERRA_NOTEBOOK_GOOGLE_ACCESS_TOKEN="$(gcloud auth print-access-token)"

Dependencies:

• FISS -- (Fi)reCloud (S)ervice (S)elector python library
• Google Cloud Python client library
• Google Cloud SDK
  • authenticated / configured with AnVIL project
• terra-notebook-utils
• gs-chunked-io
• getm

Releasing:

• Pushing a version tag such as 0.2.7 builds the sdist and wheel and publishes them to PyPI via the Release GitHub Actions workflow. Nothing else publishes; there is no manual upload step.
• The tag must equal __version__ in anvilfs/__about__.py or the workflow fails before building, so bump the version and merge it first, then tag the merge commit:

  git checkout dev && git pull
  git tag 0.2.7 && git push origin 0.2.7
  

• Only bare N.N.N tags trigger a release.
• Uploads use PyPI trusted publishing, so no API token is stored in the repository.

Known upstream incompatibilities:

anvilfs/__init__.py carries two compatibility shims. Both exist only because an unmaintained dependency fails at import time on a runtime Galaxy actually ships, and without them import anvilfs raises, the anvil file source never registers, and Galaxy will not start at all.

• FISS on Python 3.12+. firecloud.fiss calls configparser.SafeConfigParser() when imported, and Python 3.12 removed that name. terra_notebook_utils.workspace imports fiss at module scope, so anvilfs/drs.py cannot avoid it. Tracked upstream in fiss#194, open since May 2025; firecloud 0.16.39 still makes the call. The shim restores the name, which has been a plain alias of ConfigParser since Python 3.2.
• getm on urllib3 2.x. getm.http builds a module-level Retry(method_whitelist=[...]). urllib3 renamed that argument to allowed_methods in 1.26 and removed it in 2.0. getm 0.0.5, the latest release, still uses the old name, and pinning urllib3<2 is not possible inside Galaxy. The shim translates the keyword.

These are temporary. Each shim is a stopgap for a bug that belongs upstream, not a feature of this package, and each mutates a module that the whole host process shares. Delete the corresponding block as soon as a fixed release of that dependency exists and the floor in setup.py can be raised past it; the guards make each one inert in the meantime, so a stale shim fails quietly rather than loudly.