diff --git a/.env.d.examples/00_crossref-local.env b/.env.d.examples/00_crossref-local.env index 00eaaeeaa..b381c40ba 100644 --- a/.env.d.examples/00_crossref-local.env +++ b/.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 CrossRef database file (for db mode) # CROSSREF_LOCAL_DB=/path/to/crossref.db diff --git a/.gitignore b/.gitignore index 20d3a496a..8e3334abf 100755 --- a/.gitignore +++ b/.gitignore @@ -147,6 +147,15 @@ local_settings.py db.sqlite3 db.sqlite3-journal +# Embedded database files. These are binary, so `git grep` skips them and a +# committed one stays invisible until something opens it. Two were already +# tracked here (a clew runtime store and a legacy example's) before these +# rules existed; the rules are what stop the next one. +**/*.sqlite +**/*.sqlite3 +**/clew.db +.scitex/clew/runtime/ + # Flask stuff: instance/ .webassets-cache diff --git a/.scitex/clew/runtime/db.sqlite b/.scitex/clew/runtime/db.sqlite deleted file mode 100644 index e51371676..000000000 Binary files a/.scitex/clew/runtime/db.sqlite and /dev/null differ diff --git a/docs/sphinx/core_concepts.rst b/docs/sphinx/core_concepts.rst index 4484557c4..aa77bbd09 100644 --- a/docs/sphinx/core_concepts.rst +++ b/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 +124,8 @@ 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 Clew provenance store. This +enables: - **Verification**: Check if output files have been modified since creation - **DAG reconstruction**: Trace which inputs produced which outputs diff --git a/docs/sphinx/modules/io.rst b/docs/sphinx/modules/io.rst index 222150bb8..d52fd27ac 100644 --- a/docs/sphinx/modules/io.rst +++ b/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 Clew provenance store for reproducibility verification. .. code-block:: python diff --git a/examples/_legacy/scitex/clew/multi_parent/scitex/clew.db b/examples/_legacy/scitex/clew/multi_parent/scitex/clew.db deleted file mode 100644 index 01dc4efe0..000000000 Binary files a/examples/_legacy/scitex/clew/multi_parent/scitex/clew.db and /dev/null differ diff --git a/pyproject.toml b/pyproject.toml index 93d9f2ea1..1c405ca78 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -792,7 +792,7 @@ web = [ # Clew Module - Hash-based verification for reproducible science (Ariadne's thread) # Use: pip install scitex[clew] -# Note: No extra dependencies - uses only stdlib (sqlite3, hashlib) +# Note: clew owns its own store; nothing extra is pulled in here. clew = ["scitex-clew==0.17.0"] # Writer Module - Academic paper writing diff --git a/tests/integration/test_cross_package_imports.py b/tests/integration/test_cross_package_imports.py index d56e80540..88f7b327f 100755 --- a/tests/integration/test_cross_package_imports.py +++ b/tests/integration/test_cross_package_imports.py @@ -165,7 +165,6 @@ "scitex_io._load_modules._pandas", "scitex_io._load_modules._pdf", "scitex_io._load_modules._pickle", - "scitex_io._load_modules._sqlite3", "scitex_io._load_modules._torch", "scitex_io._load_modules._txt", "scitex_io._load_modules._xml",