Allow outputs to STDOUT

[linsalrob]

This pull request enhances the output handling in the agtools CLI and commands by introducing a standardized way to support writing output to either a file or stdout (using -). It refactors all relevant command modules to use a new context manager, improves logging behavior when writing to stdout, and updates dependencies for development and testing.

Output handling improvements:

• Added a new open_output_file context manager in src/agtools/commands/_output.py to unify and simplify writing output to either a file or stdout, and updated all command modules to use this function instead of manual file handling. (src/agtools/commands/_output.py, src/agtools/commands/asqg2gfa.py, src/agtools/commands/concat.py, src/agtools/commands/fastg2gfa.py, src/agtools/commands/gfa2adj.py, src/agtools/commands/gfa2asqg.py, src/agtools/commands/gfa2dot.py, src/agtools/commands/gfa2fasta.py, src/agtools/commands/gfa2fastg.py, src/agtools/commands/rename.py, src/agtools/commands/stats.py, src/agtools/core/gfa_filter.py) [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] [24] [25] [26] [27]

• The CLI --output option now explicitly allows - to write to stdout, and the help text is updated accordingly. (src/agtools/cli.py)

Logging improvements:

• The logger configuration is updated to emit logs to stderr when output is routed to stdout, preventing log messages from mixing with command output. (src/agtools/cli.py, src/agtools/log_config.py) [1] [2]

Development and testing:

• While testing the changes, the development install was failing because the dev extra depended on agtools[test], which caused pip/flit to install the released PyPI package before symlinking the local checkout. This left an existing site-packages/agtools directory and caused flit install --symlink to fail with FileExistsError. The fix removes the self-referential dependency and lists the test dependencies directly in the dev extra, so local development installs use the checked-out branch correctly.
• Updated the development dependencies in pyproject.toml to include pytest, pytest-cov, and pytest-xdist for improved testing. (pyproject.toml)

Other changes:

• Bumped the version number in src/agtools/__init__.py from 1.1.0 to 1.1.1.

[codacy-production]

Not up to standards ⛔

🔴 Issues 12 high

Alerts:
⚠ 12 issues (≤ 0 issues of at least minor severity)

Results:
12 new issues

Category	Results
ErrorProne	1 high
Security	11 high

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🟢 Metrics 4 complexity · 3 duplication

Metric	Results
Complexity	4
Duplication	3

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