Fixes #4 issue with tapis filenames have spaces

[kks32]

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[Copilot]

Pull Request Overview

This PR addresses issue #4 by fixing the handling of filenames with spaces, ensuring that Tapis URIs are no longer URL‐encoded when constructed. Key changes include:

• Replacing URL encoding (via urllib.parse.quote) with direct construction of Tapis URIs in dapi/jobs.py and dapi/files.py.
• Updating tests and examples to expect unencoded space characters in filenames.
• Adjusting import paths and patch targets in tests and authentication modules.

Reviewed Changes

Copilot reviewed 10 out of 12 changed files in this pull request and generated no comments.

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File	Description
tests/jobs/test_job_gen_jobinfo.py	Updated import and function calls to use generate_job_request.
tests/jobs/test_dir_uri.py	Modified expected URI output to ensure spaces are preserved.
tests/files/test_uri_translation.py	Added tests for handling paths with spaces.
tests/auth/test_auth.py	Updated patch decorators and import paths for auth functions.
examples/mpm/uniaxial_stress/test_benchmark.py	Entire file removal; verify that functionality is covered elsewhere.
docs/installation.md & docs/examples/openfoam.md	Documentation updates for new installation branch and clarity.
dapi/jobs.py	Removed URL encoding in archive URI and list_outputs, download_output.
dapi/files.py	Removed URL encoding when generating file URIs in get_ds_path_uri.
README.md	Removed deprecated API docs instructions.

Comments suppressed due to low confidence (3)

dapi/jobs.py:1010

• Removing URL encoding for the archive URI may lead to issues if downstream consumers or Tapis APIs expect encoded paths for filenames with spaces. Please confirm that all parts of the system properly handle unencoded spaces.

            return f"tapis://{details.archiveSystemId}/{archive_path}"

dapi/files.py:317

• There is an inconsistency in encoding strategy: the Tapis URI is constructed without URL encoding, but verification uses an encoded version for the API call. Ensure that this approach does not lead to double encoding or unexpected mismatches in behavior.

            encoded_remote_path = urllib.parse.quote(remote_path)