Review Python 3 migration

While porting a worker from the API to the ClimateDT VM, to use the testing suite with @rahme1, we found what looks like a left-over issue from the Python 2 → 3 migration - context: https://earth.bsc.es/gitlab/es/testing_suite/-/issues/37#note_224060

There could be other calls besides os.open3. We do not have enough tests covering the code, so the only ways to pick up issues like this are by running the code, or with static analysis.

PyCharm default inspection finds 684 errors, 1191 warnings, 6630 weak warnings, and nearly 6k typos.

There are many false positives in this report, but the popen3 is found.

The are probably many legit bugs found in this inspection, so this could be an easy way to fix issues left after the Python 3 migration, and also any other low-hanging fruit issue that can be fixed in development, rather than wait until someone uses the API and reports it.