Pydra

- fixing `TaskBase.__call__` so `submitter` is not overwritten
- improving `checksum_states` so it doesn't calculate the content hash of big files for multiple times (using `files_hash` that keeps track of all the files)
- removing output after task is run to save memory
- adding `Directory`, `int`, `float`, `bool`, `str`, and `list` to the types allowed by `output_spec` of `ShelloCommandTask`.
- adding python 3.9 to GA
- fixing GA singularity workflow

- removing `checksum` from `submitter` and `workers` to avoid hash calculation before running the tasks (using `uid` instead)
- saving the hash values for files to avoid content hash recalculation (the content is recalculated only if the time of the last modification has changed)
- adding `MultiInputFile` and `MultiOutputFile` to the pydra special types
- fixing environment variable for GithubAction CI
- fixing `input_spec` for `ShellCommandTask` with the `container_info`, spec `bases` has to be changed `DockerSpec` or `SingularitySpec` in order to be used by `Docker/SingularityTask`
- fixing automatic binding detections for `ContainerTask` that have files as input (`is_local_file` is now slightly more robust that work for input that has more complex type in the spec)
- expanding `callable` function used in field `metadata`, it can now use `output_dir`, entire `inputs` object or a specific `field` from the `inputs`

- fixing issues with quadratic memory increase for workflows with big splitters - removing `state_inputs` from `Task` (not used anymore)
- allowing for directory with broken symlinks for an input
- fixing tests so could be run on a cluster (using `tmpdir` as a `cache_dir`, so pytest can be run with `--basetemp`)
- fixing `cache_Dir` setting for worflows used as nodes
- fixing `Submitter._run_workflow` so it doesn't stop when there are still tasks in the graph, will try getting runnable tasks for another 60s (in case the previous tasks finished, but the results are still not available to read)
- fixing template formatting for files from `ShellCommandTask`, so it works for directories that have dots in the name
- fixing tests that were resubmitting tasks to the queue

- disable etelemetry in tests
- removing old pip (10.0.1) from testing (removing testallowfail from GA workflows)
- removing min_requirements
- adding rescheduling to the slurm worker for all jobs that are CANCELLED, TIMEOUT, or PREEMPTED
- adding generate_output_updates, to be able to predict names of the generated outputs before running

- allows README to be displayed on pypi
- limits testing to valid pytests

- fixing issue with `checksum_states` performance (it doesn't run `self.state.prepare_states` if not needed)