[demianw]

What was wrong

Items of #118 addressed here:

• Existing outputs (tract_math): process_output asks Overwrite file ... (y/N)? with input(); in a batch run (stdin not a terminal) this fails with EOFError. Reproduced: tract_math tract.trk count existing.csv < /dev/null ends in EOFError: EOF when reading a line.
• Output format (tract_querier): -o out/subj.01 takes .01 as the output format; reproduced: the files are loaded and the queries computed, then the first save fails with OSError: File format not supported.
• Unclosed files (tract_math): the CSV output is opened without newline='' and never closed; the tractography files opened by argparse.FileType('r') are never closed.
• Shell: TractQuerierCmd.default echoes every input line (print(line)).
• Exception messages: TractQuerierSyntaxError.__str__ and TractQuerierLabelNotFound.__str__ return repr(self.value), so str(e) is quoted and a multi-line message shows a literal \n.
• Help texts: tract_remove_short_tracts says it "subsamples"; tract_affine_transform omits ref_image; tract_point_distance_min_max claims to report distances between consecutive points but prints the shortest and longest tract lengths (tract_length returns the total length of each tract).

The change

• tract_math: new --force optional flag (handled in the decorator, alongside the existing -- flags) overwrites an existing output without asking. Without --force, if stdin is not a terminal, the command fails with Output file <name> exists, use --force to overwrite it instead of prompting. With a terminal, the prompt is unchanged. --force is documented in the usage text.
• tract_querier: the output format is worked out right after the options are parsed (the same logic, moved up; the earlier dead assignment of tractography_extension is removed) and must be .trk, .vtk or .vtp (the formats tractography_to_file writes). Otherwise: error: output format '.01' not supported, it must be .trk, .vtk or .vtp; add it to the output prefix, e.g. -o out/subj.01.trk.
• CSV output is written inside with, opened with newline=''; the FileType handles are closed right after parsing (.name is all that is used afterwards).
• print(line) removed from shell.default.
• Both __str__ return str(self.value). Callers in shell.py and cli_tract_querier.py print e.value, so their output does not change; no test matched on the quoted form.
• Help texts: tract_remove_short_tracts "keeps only the tracts longer than the given length"; tract_affine_transform lists <ref_image> and says it gives the output's affine and dimensions; tract_point_distance_min_max "minimum and maximum tract length".

Behaviour changes: a non-interactive tract_math run with an existing output now exits with an error (exit code 2) instead of an EOFError traceback; tract_querier with an unsupported output extension now errors before loading any file; str() of the two exceptions no longer has quotes.

Not addressed here

• cli_tract_querier.py still uses optparse with version=0.1 (handled separately).
• tract_math's parser reads sys.argv while it is built.
• tract_querier has no overwrite prompt (it overwrites silently), so no --force was added to it.
• In cli_tract_math.py, TractMathWrongArgumentsError is caught with traceback.print_exc() before parser.error, so the new --force message is preceded by a traceback on stdout.
• For the maintainer: tract_affine_transform's [invert] is effectively required (the decorator rejects three positional arguments) and bool(invert) is true for any non-empty string, including False; tract_point_distance_min_max's name suggests it was meant to report point-to-point distances. The help now describes what the code does; the code is unchanged.

Testing

• pytest -q -p no:cacheprovider tract_querier: 45 passed, 1 skipped (master: 42 passed, 1 skipped).
• New tests:
  • test_tract_math.py::test_tract_math_existing_output: with an existing output and a non-terminal stdin, tract_math ... count out.csv fails, mentions --force and leaves the file untouched; with --force it overwrites it and the CSV reads back as 2 rows with 6783 tracts.
  • test_tract_querier.py::test_tract_querier_unsupported_output_format: -o <tmp>/subj.01 fails with the format error and before Loading files.
  • test_tract_querier.py::test_syntax_error_message_is_not_quoted.
• Manually: tract_math tract.trk count existing.csv < /dev/null gives the --force message and keeps the file. I did not test the interactive prompt in a terminal (that code path is unchanged).

Merge order

Touches scripts/cli_tract_querier.py in different hunks from #126 (#99); git merge-tree shows no conflict between the two. Small edits (help strings, a usage line, a few lines in main) in tract_querier/tract_math/operations.py, scripts/cli_tract_math.py, tract_querier/shell.py and tract_querier/query_processor.py, which other open PRs on #102, #105, #106, #112, #38, #103, #104 and #115 may also edit: a rebase may be needed depending on which lands first.

Part of #118

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