Skip to content
Merged
Show file tree
Hide file tree
Changes from all commits
Commits
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 2 additions & 0 deletions src/about/publications.md
Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,8 @@ If your work uses DataJoint or DataJoint Elements, please cite the respective

## 2025

+ Campagner, D., Bhagat, J., Lopes, G., Calcaterra, L., Pouget, A. G., Almeida, A., ... & SWC GCNU Experimental Neuroethology Group. (2025). [Aeon: an open-source platform to study the neural basis of ethological behaviours over naturalistic timescales](https://doi.org/10.1101/2025.07.31.664513). *bioRxiv*.

+ Bae, J. A., Baptiste, M., Bodor, A. L., Brittain, D., Buchanan, J., Bumbarger, D. J., Castro, M. A., Celii, B., Cobos, E., Collman, F., ... (2025). [Functional connectomics spanning multiple areas of mouse visual cortex](https://doi.org/10.1038/s41586-025-08790-w). *Nature*, 640(8058), 435-447.

+ Celii, B., Papadopoulos, S., Ding, Z., Fahey, P. G., Wang, E., Papadopoulos, C., ... & Reimer, J. (2025). [NEURD offers automated proofreading and feature extraction for connectomics](https://doi.org/10.1038/s41586-025-08660-5). *Nature*, 640(8058), 487-496.
Expand Down
16 changes: 13 additions & 3 deletions src/how-to/migrate-to-v20.md
Original file line number Diff line number Diff line change
Expand Up @@ -245,6 +245,8 @@ DataJoint 2.0 replaces `external.*` with unified `stores.*` configuration:
| `dj.ERD(schema)` | `dj.Diagram(schema)` | I |
| `table.insert([(1, 'a'), (2, 'b')])` | Must use dicts/DataFrames (no positional tuples) | I |

> **Note:** The `fetch()` method remains available in DataJoint 2.0 with a deprecation warning. Your existing code will work immediately—`fetch()` automatically delegates to the appropriate 2.0 method (`to_arrays()`, `to_dicts()`, or `to_pandas()`). You can migrate incrementally as time permits.
**Learn more:** [Fetch API Reference](../reference/specs/fetch-api.md) · [Query Operators Reference](../reference/operators.md) · [Semantic Matching](../reference/specs/semantic-matching.md)

---
Expand Down Expand Up @@ -1437,6 +1439,9 @@ Update all DataJoint API calls to 2.0 patterns.
**Fetch API:**
> **Note:** `fetch()` remains available with a deprecation warning and works immediately.
> Convert to new methods when convenient for cleaner, more explicit code.
- `fetch()``to_arrays()` (recarray-like) or `to_dicts()` (list of dicts)
- `fetch(..., format="frame")``to_pandas()` (pandas DataFrame)
- `fetch('attr1', 'attr2')``to_arrays('attr1', 'attr2')` (returns tuple)
Expand Down Expand Up @@ -1486,9 +1491,14 @@ CONTEXT:

API CONVERSIONS:

1. Fetch API (always convert):
1. Fetch API (recommended conversion - fetch() still works with deprecation warning):

NOTE: fetch() remains available in 2.0 and automatically delegates to the
new methods. Existing code works immediately. Convert when convenient.

OLD: data = table.fetch()
NEW: data = table.to_arrays() # recarray-like
# OR: keep as fetch() - works with deprecation warning

OLD: data = table.fetch(as_dict=True)
NEW: data = table.to_dicts() # list of dicts
Expand Down Expand Up @@ -1588,7 +1598,7 @@ PROCESS:

VERIFICATION:

- No .fetch() calls remaining (except fetch1)
- .fetch() calls either converted OR intentionally kept (works with deprecation warning)
- No .fetch1('KEY') calls remaining (replaced with .keys())
- No ._update() calls remaining
- No @ operator between tables
Expand Down Expand Up @@ -1732,7 +1742,7 @@ API conversions: X fetch, Y update, Z join"
- [ ] All table definitions use 2.0 type syntax
- [ ] All in-table codecs converted (`<blob>`, `<attach>`)
- [ ] All in-store codecs converted (`<blob@>`, `<attach@>`, `<filepath@>`)
- [ ] All `fetch()` calls converted (except `fetch1()`)
- [ ] All `fetch()` calls converted OR intentionally kept (works with deprecation warning)
- [ ] All `fetch(..., format="frame")` converted to `to_pandas()`
- [ ] All `fetch1('KEY')` converted to `keys()`
- [ ] All `._update()` calls converted
Expand Down
16 changes: 9 additions & 7 deletions src/reference/configuration.md
Original file line number Diff line number Diff line change
Expand Up @@ -15,12 +15,13 @@ Configuration is loaded in priority order:

| Setting | Environment | Default | Description |
|---------|-------------|---------|-------------|
| `database.backend` | `DJ_BACKEND` | `mysql` | Database backend: `mysql` or `postgresql` *(new in 2.1)* |
| `database.host` | `DJ_HOST` | `localhost` | Database server hostname |
| `database.port` | `DJ_PORT` | `3306` | Database server port |
| `database.port` | `DJ_PORT` | `3306`/`5432` | Database server port (auto-detects from backend) |
| `database.user` | `DJ_USER` || Database username (required) |
| `database.password` | `DJ_PASS` || Database password (required) |
| `database.reconnect` || `True` | Auto-reconnect on connection loss |
| `database.use_tls` | | `None` | Enable TLS encryption |
| `database.use_tls` | `DJ_USE_TLS` | `None` | Enable TLS encryption *(env var new in 2.1)* |
| `database.database_prefix` | `DJ_DATABASE_PREFIX` | `""` | Prefix for database/schema names |
| `database.create_tables` | `DJ_CREATE_TABLES` | `True` | Default for `Schema(create_tables=)`. Set `False` for production mode |

Expand Down Expand Up @@ -157,11 +158,12 @@ If table lacks partition attributes, it follows normal path structure.

## Display Settings

| Setting | Default | Description |
|---------|---------|-------------|
| `display.limit` | `12` | Max rows to display |
| `display.width` | `14` | Column width |
| `display.show_tuple_count` | `True` | Show row count in output |
| Setting | Environment | Default | Description |
|---------|-------------|---------|-------------|
| `display.limit` || `12` | Max rows to display |
| `display.width` || `14` | Column width |
| `display.show_tuple_count` || `True` | Show row count in output |
| `display.diagram_direction` | `DJ_DIAGRAM_DIRECTION` | `LR` | Diagram layout: `LR` (left-right) or `TB` (top-bottom) *(new in 2.1)* |

## Top-Level Settings

Expand Down