Rename analyze outputs to search

Author: Kenji Fukushima

README.md

@@ -62,7 +62,7 @@ csubst search --alignment_file alignment.fa.gz --rooted_tree_file tree.nwk --for
 CSUBST provides five main subcommands:
 
 - `csubst dataset`: generate bundled example datasets (e.g., `PGK`, `PEPC`).
-- `csubst search` (legacy alias: `csubst analyze`): run convergence analysis and output metrics such as `omegaC`, `dNC`, and `dSC`.
+- `csubst search` (legacy alias: `csubst analyze`): run convergence analysis and output metrics such as `omegaC`, `dNC`, and `dSC`. Outputs are written to `csubst_search/` by default.
 - `csubst inspect`: summarize branch mappings and inspect ancestral states.
 - `csubst sites` (legacy alias: `csubst site`): compute site-wise combinatorial substitutions for selected branch combinations, generate tree + site summary plots, and optionally map sites to protein structures.
 - `csubst simulate`: simulate codon sequence evolution under user-defined convergent scenarios.

csubst/__init__.py

@@ -1 +1 @@
-__version__ = '1.11.1'
+__version__ = '1.11.2'

csubst/csubst

@@ -42,11 +42,11 @@ _OUTPUT_NAMESPACE_DEFAULTS = {
         'output_prefix': 'csubst',
     },
     'search': {
-        'outdir': 'csubst_analyze',
+        'outdir': 'csubst_search',
         'output_prefix': 'csubst',
     },
     'analyze': {
-        'outdir': 'csubst_analyze',
+        'outdir': 'csubst_search',
         'output_prefix': 'csubst',
     },
     'inspect': {
@@ -279,7 +279,7 @@ def _build_parser():
     psr_co.add_argument('--write_instantaneous_rate_matrix', metavar='yes|no', default='no', type=strtobool,
                         help='default=%(default)s: Write csubst instantaneous codon rate matrix TSV.')
 
-    psr_out_analyze = _make_output_parent_parser(default_outdir='csubst_analyze', default_prefix='csubst')
+    psr_out_analyze = _make_output_parent_parser(default_outdir='csubst_search', default_prefix='csubst')
     psr_out_inspect = _make_output_parent_parser(default_outdir='csubst_inspect', default_prefix='csubst')
     psr_out_simulate = _make_output_parent_parser(default_outdir='csubst_simulate', default_prefix='csubst')
 
@@ -361,7 +361,7 @@ def _build_parser():
                              '"auto" uses --sa_state_cache_file when a compatible cache exists, otherwise computes and writes it. '
                              '"yes" requires a compatible cache file. "no" disables cache read/write.')
     psr_rc.add_argument('--sa_state_cache_file', metavar='PATH', default=_default_sa_state_cache_file(), type=str,
-                        help='default=%(default)s: Shared 3Di-state cache file path used by analyze and inspect.')
+                        help='default=%(default)s: Shared 3Di-state cache file path used by search and inspect.')
     psr_rc.add_argument('--sa_iqtree_model', metavar='STR', default='GTR', type=str,
                         help='default=%(default)s: IQ-TREE model for --sa_asr_mode direct with --nonsyn_recode 3di20 '
                              '(used with --seqtype MORPH).')

tests/test_cli_logging.py

@@ -31,17 +31,17 @@ def test_cli_writes_help_output_to_csubst_log(tmp_path):
 def test_cli_writes_stderr_output_to_csubst_log(tmp_path):
     result = _run_csubst(["search", "--does_not_exist"], cwd=tmp_path)
     assert result.returncode != 0
-    log_file = tmp_path / "csubst_analyze" / "csubst.log"
+    log_file = tmp_path / "csubst_search" / "csubst.log"
     assert log_file.exists()
     log_text = log_file.read_text(encoding="utf-8")
     assert "error:" in log_text.lower()
     assert "--does_not_exist" in log_text
 
 
-def test_legacy_analyze_alias_still_writes_to_csubst_analyze_log(tmp_path):
+def test_legacy_analyze_alias_still_writes_to_csubst_search_log(tmp_path):
     result = _run_csubst(["analyze", "--does_not_exist"], cwd=tmp_path)
     assert result.returncode != 0
-    log_file = tmp_path / "csubst_analyze" / "csubst.log"
+    log_file = tmp_path / "csubst_search" / "csubst.log"
     assert log_file.exists()
     log_text = log_file.read_text(encoding="utf-8")
     assert "error:" in log_text.lower()
@@ -95,11 +95,11 @@ def test_subcommand_output_namespace_defaults_are_command_specific():
     parser = ns["_build_parser"]()
 
     search = parser.parse_args(["search"])
-    assert search.outdir == "csubst_analyze"
+    assert search.outdir == "csubst_search"
     assert search.output_prefix == "csubst"
 
     analyze = parser.parse_args(["analyze"])
-    assert analyze.outdir == "csubst_analyze"
+    assert analyze.outdir == "csubst_search"
     assert analyze.output_prefix == "csubst"
 
     inspect = parser.parse_args(["inspect"])

tests/test_cli_validation.py

@@ -16,9 +16,9 @@ def _resolve_log_path(repo_root, args):
         if args[0] == "simulate":
             return repo_root / "csubst_simulate" / "csubst.log"
         if args[0] == "search":
-            return repo_root / "csubst_analyze" / "csubst.log"
+            return repo_root / "csubst_search" / "csubst.log"
         if args[0] == "analyze":
-            return repo_root / "csubst_analyze" / "csubst.log"
+            return repo_root / "csubst_search" / "csubst.log"
         if args[0] == "inspect":
             return repo_root / "csubst_inspect" / "csubst.log"
         if args[0] == "sites":