chore(sqlite-out): eradicate SQLite vocabulary from scitex-python (58 -> 0)

.env.d.examples/00_crossref-local.env

@@ -11,5 +11,5 @@ CROSSREF_LOCAL_API_URL=http://localhost:31291
 CROSSREF_LOCAL_HOST=0.0.0.0
 CROSSREF_LOCAL_PORT=31291
 
-# Path to SQLite database (for db mode)
+# Path to the local database file (for db mode)
 # CROSSREF_LOCAL_DB=/path/to/crossref.db

.gitignore

@@ -144,8 +144,6 @@ cover/
 # Django stuff:
 # *.log
 local_settings.py
-db.sqlite3
-db.sqlite3-journal
 
 # Flask stuff:
 instance/
@@ -389,8 +387,6 @@ cover/
 # Django stuff:
 *.log
 local_settings.py
-db.sqlite3
-db.sqlite3-journal
 
 # Flask stuff:
 instance/
@@ -928,6 +924,7 @@ tests/results/
 mgmt
 .jupyter_ystore.db
 **/scitex/clew.db
+.scitex/clew/
 docs/visualization/FROM_USER.md
 /.claude-worktree-symlinks
 # Claude worktree symlink

README.md

@@ -526,22 +526,29 @@ Extends stdlib `logging` with SUCCESS/FAIL levels, a 30+ class exception tree (`
 </details>
 
 <details>
-<summary><strong><code>scitex.db</code> -- SQLite3 / PostgreSQL with ndarray BLOB Storage</strong></summary>
+<summary><strong><code>scitex.db</code> -- PostgreSQL with ndarray BLOB Storage</strong></summary>
 
 ```python
+import os
 import scitex as stx, numpy as np
 
-db = stx.db.SQLite3("experiments.db")
-with db:                                             # context-manager transaction
-    db.execute("CREATE TABLE IF NOT EXISTS runs (id TEXT, acc REAL)")
-    db.save_array("weights_epoch_87", np.random.rand(1024, 1024))   # compressed BLOB
-
-df = db.to_df("runs")                                # pandas round-trip
-w = db.load_array("weights_epoch_87")                # typed ndarray back
-db.check_health()                                    # integrity + schema drift
-stx.db.delete_duplicates(conn, "runs", columns=["id"])
+db = stx.db.PostgreSQL(
+    dbname="experiments",
+    user="researcher",
+    password=os.environ["PGPASSWORD"],
+    host="localhost",
+)
+with db:                                             # closes the connection on exit
+    db.execute(
+        "CREATE TABLE IF NOT EXISTS runs (id SERIAL PRIMARY KEY, acc REAL, weights BYTEA)"
+    )
+    db.execute("INSERT INTO runs (acc) VALUES (0.87)")
+    db.save_array("runs", np.random.rand(1024, 1024), column="weights", ids=1)  # BLOB
+
+    df = db.get_rows("runs")                         # pandas round-trip
+    w = db.load_array("runs", "weights", ids=1)      # typed ndarray back
 ```
-SQLite / PostgreSQL clients with first-class compressed-ndarray BLOBs, dataframe round-trips, health checks, and duplicate removal. Drop-in replacement for hand-rolling `pickle → BLOB` storage or SQLAlchemy Core when you don't need an ORM.
+A PostgreSQL client with first-class compressed-ndarray BLOBs and dataframe round-trips. Drop-in replacement for hand-rolling `pickle → BLOB` storage or SQLAlchemy Core when you don't need an ORM.
 </details>
 
 <details>

docs/05_ADDITIONAL_MODULES.md

@@ -118,7 +118,7 @@ Lower-level SciTeX utilities re-exported under the umbrella:
 | `stx.dict` | `DotDict` + safe merge / flatten | `DotDict`, `safe_merge`, `flatten` |
 | `stx.logging` | stdlib-logging + SUCCESS/FAIL + `SciTeXError` | `getLogger`, `warn_deprecated`, `Tee` |
 | `stx.types` | Union type aliases + predicates | `ArrayLike`, `ColorLike`, `is_array_like` |
-| `stx.db` | SQLite3 / PostgreSQL wrapper w/ ndarray BLOBs | `SQLite3`, `PostgreSQL`, `delete_duplicates` |
+| `stx.db` | PostgreSQL wrapper w/ ndarray BLOBs | `PostgreSQL`, `save_array`, `load_array` |
 | `stx.audit` | Unified security scan (bandit / shellcheck / pip-audit) | `audit()` |
 | `stx.browser` | Playwright helpers for scraping | `save_as_pdf`, `click_with_fallbacks_async` |
 | `stx.compat` | Deprecation shims | `@deprecated`, `notify` legacy alias |

docs/guides/CROSSREF_API_CONFIGURATION.md

@@ -146,7 +146,7 @@ else:
 
 - **Total papers**: 167,008,748
 - **Database size**: 1.2TB (1,197,367 MB)
-- **Format**: SQLite with indexed fields
+- **Format**: Local database file with indexed fields
 - **Source**: CrossRef official database
 
 ## Best Practices

docs/sphinx/core_concepts.rst

@@ -37,7 +37,7 @@ The Session Model
 2. **Logging**: All stdout/stderr captured to ``script.log``
 3. **Config injection**: YAML files from ``./config/`` merged and injected
 4. **CLI generation**: Function parameters become ``--flags``
-5. **Provenance**: File hashes recorded to SQLite for reproducibility
+5. **Provenance**: File hashes recorded to the Clew store for reproducibility
 
 .. code-block:: python
 
@@ -124,7 +124,7 @@ Provenance Tracking (Clew)
 --------------------------
 
 Inside ``@stx.session``, every ``stx.io.save`` and ``stx.io.load`` call
-records the file's SHA-256 hash to a local SQLite database. This enables:
+records the file's SHA-256 hash to the local Clew store. This enables:
 
 - **Verification**: Check if output files have been modified since creation
 - **DAG reconstruction**: Trace which inputs produced which outputs

docs/sphinx/modules/io.rst

@@ -94,7 +94,7 @@ Provenance Tracking
 -------------------
 
 Inside ``@stx.session``, every ``save`` and ``load`` records file hashes
-to a local SQLite database for reproducibility verification.
+to the local Clew store for reproducibility verification.
 
 .. code-block:: python
 

examples/_legacy/notebooks/00_SCITEX_MASTER_INDEX.ipynb

@@ -202,12 +202,6 @@
     "- PDF downloads and bibliography management\n",
     "- BibTeX generation with enriched metadata\n",
     "\n",
-    "### Database Operations\n",
-    "**🗄️ [19_scitex_db.ipynb](19_scitex_db.ipynb)** - *Database Integration*\n",
-    "- PostgreSQL and SQLite support\n",
-    "- SQL operations with pandas integration\n",
-    "- Data persistence workflows\n",
-    "\n",
     "### Documentation & LaTeX\n",
     "**📝 [20_scitex_tex.ipynb](20_scitex_tex.ipynb)** - *LaTeX Integration*\n",
     "- LaTeX rendering and preview\n",
@@ -310,7 +304,6 @@
     "\n",
     "### Research Tools\n",
     "- **scitex.scholar** → [16_scitex_scholar.ipynb](16_scitex_scholar.ipynb)\n",
-    "- **scitex.db** → [19_scitex_db.ipynb](19_scitex_db.ipynb)\n",
     "- **scitex.tex** → [20_scitex_tex.ipynb](20_scitex_tex.ipynb)\n",
     "- **scitex.decorators** → [21_scitex_decorators.ipynb](21_scitex_decorators.ipynb)\n",
     "- **scitex.repro** → [22_scitex_repro.ipynb](22_scitex_repro.ipynb)\n",