Remove dead code and untrack DS_Store

- Remove if 0: debug/tracing blocks from CHRIS.py, ChemID.py, and qrf/qrf_train.py (236 lines of unreachable code)
- Remove commented-out v1 blueprint registrations (color_module, exposure_module) from CHRIS.py
- Untrack static/.DS_Store (already in .gitignore)

Co-Authored-By: Claude Code <noreply@anthropic.com>

CHRIS.py

@@ -11,32 +11,6 @@ app.debug = True
 #    sort_by=("tottime",) # total time spent in function body
 #)
 
-### DEBUGGING
-if 0:
-    from pprint import pformat
-    from flask import g, request
-
-    @app.after_request
-    def dump_chem_trace(response):
-        trace = getattr(g, "chem_trace", None)
-        if trace:
-            bases = sorted(set(getattr(g, "chem_bases", [])))
-            payload = {
-                "path": request.path,
-                "query": request.values.to_dict(flat=False),
-                "base_urls": bases,
-                "remote_trace": [x for x in trace if x.get("kind") == "remote"],
-                "app_trace": [x for x in trace if x.get("kind") == "app"],
-            }
-            app.logger.warning("CHEMTRACE\n%s", pformat(payload, sort_dicts=False, width=120))
-        return response
-
-#from color_module import blueprint
-#app.register_blueprint(blueprint)
-
-#from exposure_module import blueprint
-#app.register_blueprint(blueprint)
-
 from efficiency_module import blueprint
 app.register_blueprint(blueprint)
 

ChemID.py

@@ -74,178 +74,6 @@ def _cirpy_available(force=False):
             _cirpy_last_check = time.monotonic()
         return try_cirpy
 
-if 0:
-    ## DEBUGGING
-    import time
-    import functools
-    import inspect
-    import logging
-    import os
-    import urllib.request
-    import urllib.parse
-
-    try:
-        from flask import has_request_context, g
-    except Exception:
-        def has_request_context():
-            return False
-        g = None
-
-    TRACE_THRESHOLD = float(os.environ.get("CHEM_TRACE_THRESHOLD", "0.0"))
-
-    chemtrace_logger = logging.getLogger("chemtrace")
-    if not chemtrace_logger.handlers:
-        chemtrace_logger.setLevel(logging.INFO)
-
-    def _short(x, n=200):
-        s = repr(x)
-        return s if len(s) <= n else s[:n-3] + "..."
-
-    def _find_app_caller():
-        for frame in inspect.stack()[2:]:
-            fn = frame.filename.replace("\\", "/")
-            if (
-                "site-packages" not in fn
-                and "/lib/python" not in fn
-                and not fn.endswith("/logging/__init__.py")
-            ):
-                return {
-                    "file": os.path.basename(frame.filename),
-                    "func": frame.function,
-                    "line": frame.lineno,
-                }
-        return None
-
-    def _url_info(url):
-        if not url:
-            return None
-        try:
-            parts = urllib.parse.urlsplit(str(url))
-            base = f"{parts.scheme}://{parts.netloc}" if parts.scheme and parts.netloc else None
-            return {
-                "url": str(url),
-                "base": base,
-                "host": parts.netloc or None,
-                "path": parts.path or "",
-            }
-        except Exception:
-            return {"url": _short(url), "base": None, "host": None, "path": None}
-
-    def _append_trace_event(event):
-        if has_request_context():
-            if getattr(g, "chem_trace", None) is None:
-                g.chem_trace = []
-            g.chem_trace.append(event)
-
-            info = event.get("target")
-            base = info.get("base") if isinstance(info, dict) else None
-            if base:
-                if getattr(g, "chem_bases", None) is None:
-                    g.chem_bases = []
-                g.chem_bases.append(base)
-        else:
-            chemtrace_logger.info("%r", event)
-
-    def trace_call(fn):
-        @functools.wraps(fn)
-        def wrapper(*args, **kwargs):
-            t0 = time.perf_counter()
-            ok = False
-            err = None
-            try:
-                result = fn(*args, **kwargs)
-                ok = True
-                return result
-            except Exception as e:
-                err = f"{type(e).__name__}: {e}"
-                raise
-            finally:
-                dt = time.perf_counter() - t0
-                if dt >= TRACE_THRESHOLD:
-                    _append_trace_event({
-                        "kind": "app",
-                        "fn": fn.__name__,
-                        "secs": round(dt, 4),
-                        "arg0": _short(args[0]) if args else None,
-                        "ok": ok,
-                        "err": err,
-                    })
-        return wrapper
-
-    def trace_external(label, fn, formatter=None):
-        @functools.wraps(fn)
-        def wrapper(*args, **kwargs):
-            t0 = time.perf_counter()
-            ok = False
-            err = None
-            caller = _find_app_caller()
-            target = None
-            if formatter is not None:
-                try:
-                    target = formatter(args, kwargs)
-                except Exception:
-                    target = None
-            try:
-                result = fn(*args, **kwargs)
-                ok = True
-                return result
-            except Exception as e:
-                err = f"{type(e).__name__}: {e}"
-                raise
-            finally:
-                dt = time.perf_counter() - t0
-                if dt >= TRACE_THRESHOLD:
-                    _append_trace_event({
-                        "kind": "remote",
-                        "fn": label,
-                        "caller": caller,
-                        "target": target,
-                        "secs": round(dt, 4),
-                        "ok": ok,
-                        "err": err,
-                    })
-        return wrapper
-
-    def _fmt_urlopen(args, kwargs):
-        url = args[0] if len(args) > 0 else kwargs.get("url")
-        info = _url_info(url)
-        if info is not None:
-            info["timeout"] = kwargs.get("timeout")
-        return info
-
-    def _fmt_requests(args, kwargs):
-        method = args[1] if len(args) > 1 else kwargs.get("method")
-        url = args[2] if len(args) > 2 else kwargs.get("url")
-        info = _url_info(url)
-        if info is not None:
-            info["method"] = method
-            info["timeout"] = kwargs.get("timeout")
-        return info
-
-    def _fmt_selenium_get(args, kwargs):
-        url = args[1] if len(args) > 1 else kwargs.get("url")
-        return _url_info(url)
-
-    def _fmt_pcp(args, kwargs):
-        query = args[0] if len(args) > 0 else kwargs.get("identifier")
-        namespace = args[1] if len(args) > 1 else kwargs.get("namespace")
-        info = _url_info(getattr(pcp, "API_BASE", None)) or {}
-        info.update({
-            "query": _short(query),
-            "namespace": namespace,
-        })
-        return info
-
-    def _fmt_cirpy(args, kwargs):
-        query = args[0] if len(args) > 0 else None
-        resolver = args[1] if len(args) > 1 else kwargs.get("resolver")
-        info = _url_info(getattr(cirpy, "API_BASE", None)) or {}
-        info.update({
-            "query": _short(query),
-            "resolver": resolver,
-        })
-        return info
-
 ORGANIC_ATOM_SET = {5, 6, 7, 8, 9, 15, 16, 17, 35, 53}
 METAL_ATOM_SET = set([3,4,11,12,13] + list(range(19,31+1)) + list(range(37,50+1)) + list(range(55,84+1)) + list(range(87,114+1)) + [116])
 with open('data/ceramics_list.txt', 'r') as fp:
@@ -1525,37 +1353,3 @@ def getLogP(cas,mol):
         LogP_origin = 'rdkit/calc'
     return LogP, LogP_origin
 
-#### DEBUGGING
-if 0:
-    ResolveChemical = trace_call(ResolveChemical)
-    smiles2name = trace_call(smiles2name)
-    cas2smiles = trace_call(cas2smiles)
-    cas2name = trace_call(cas2name)
-    name2iupac = trace_call(name2iupac)
-    name2cas = trace_call(name2cas)
-    name2smiles = trace_call(name2smiles)
-    string2density = trace_call(string2density)
-    string2mp = trace_call(string2mp)
-    mol2mp = trace_call(mol2mp)
-    if hasattr(pcp, "urlopen"):
-        pcp.urlopen = trace_external("pubchempy.urlopen", pcp.urlopen, _fmt_urlopen)
-
-    if hasattr(cirpy, "urlopen"):
-        cirpy.urlopen = trace_external("cirpy.urlopen", cirpy.urlopen, _fmt_urlopen)
-
-    pcp.get_compounds = trace_external("pcp.get_compounds", pcp.get_compounds, _fmt_pcp)
-    pcp.get_substances = trace_external("pcp.get_substances", pcp.get_substances, _fmt_pcp)
-    cirpy.resolve = trace_external("cirpy.resolve", cirpy.resolve, _fmt_cirpy)
-    urllib.request.urlopen = trace_external("urllib.request.urlopen", urllib.request.urlopen, _fmt_urlopen)
-    requests.sessions.Session.request = trace_external(
-        "requests.Session.request",
-        requests.sessions.Session.request,
-        _fmt_requests,
-    )
-
-    if try_dsstox:
-        selenium.webdriver.Chrome.get = trace_external(
-            "selenium.webdriver.Chrome.get",
-            selenium.webdriver.Chrome.get,
-            _fmt_selenium_get,
-            )

qrf/qrf_train.py

@@ -37,10 +37,6 @@ for T_target in QRF_T_list:
             sub_desc_list = df_params.loc[mask_T, 'sub_desc_list'].iloc[0].split('|')
             params = df_params.loc[mask_T, ['bootstrap', 'max_depth', 'max_features', 'max_samples', 'min_samples_leaf', 'min_samples_split', 'n_estimators']].iloc[0].to_dict()
             params['max_samples'] = float(params['max_samples'])
-    if 0:
-        sub_desc_list = ['MW', 'Polymer_Tg', 'Polymer_Density', 'VR2_A', 'ATS0Z', 'AATS5d', 'BCUTv-1h', 'BCUTse-1l', 'Xch-7dv', 'Mp', 'Mi', 'SaasC', 'ETA_epsilon_5', 'fragCpx', 'JGI5', 'JGI8']
-        params = {'bootstrap': True, 'max_depth': 7, 'max_features': 0.4, 'max_samples': 1.0, 'min_samples_leaf': 2, 'min_samples_split': 2, 'n_estimators': 1000} # best from -18-2.py w fout<0.040 (and 0.045)
-
     ## read data
     #df_X = pd.read_excel('qrf_x.xlsx')
     #df_y = pd.read_excel('qrf_y.xlsx')