Merge pull request #128 from datajoint/pre/v2.0

Remove unsigned integer types from core types for DataJoint 2.0

Author: MilagrosMarin

src/explanation/computation-model.md

@@ -14,7 +14,7 @@ class Segmentation(dj.Computed):
     definition = """
     -> Scan
     ---
-    num_cells : uint32
+    num_cells : int64
     cell_masks : <blob@>
     """
 

src/explanation/entity-integrity.md

@@ -141,7 +141,7 @@ attributes:
 class Recording(dj.Manual):
     definition = """
     -> Session
-    recording_idx : uint16   # Recording number within session
+    recording_idx : int32   # Recording number within session
     ---
     duration : float32       # seconds
     """
@@ -163,7 +163,7 @@ class Segmentation(dj.Computed):
     definition = """
     -> Scan           # Depends on Scan
     ---
-    num_cells : uint32
+    num_cells : int64
     """
 ```
 
@@ -193,7 +193,7 @@ class Subject(dj.Manual):
 class Session(dj.Manual):
     definition = """
     -> Subject                 # Inherits subject_id
-    session_idx : uint16       # NEW dimension: session_idx
+    session_idx : int32       # NEW dimension: session_idx
     ---
     session_date : date
     """
@@ -202,7 +202,7 @@ class Session(dj.Manual):
 class Trial(dj.Manual):
     definition = """
     -> Session                 # Inherits subject_id, session_idx
-    trial_idx : uint16         # NEW dimension: trial_idx
+    trial_idx : int32         # NEW dimension: trial_idx
     ---
     outcome : enum('success', 'fail')
     """
@@ -245,7 +245,7 @@ class SessionSummary(dj.Computed):
     definition = """
     -> Session                 # PK = (subject_id, session_idx)
     ---
-    num_trials : uint32
+    num_trials : int64
     accuracy : float32
     """
 ```
@@ -264,13 +264,13 @@ class Detection(dj.Computed):
     -> Image                   # Inherits image_id
     -> DetectionParams         # Inherits params_id
     ---
-    num_blobs : uint32
+    num_blobs : int64
     """
 
     class Blob(dj.Part):
         definition = """
         -> master              # Inherits (image_id, params_id)
-        blob_idx : uint16      # NEW dimension within detection
+        blob_idx : int32      # NEW dimension within detection
         ---
         x : float32
         y : float32
@@ -339,9 +339,9 @@ experimental structure and ensures correct joins through semantic matching.
 # Wrong: experiment_id alone isn't unique
 class Trial(dj.Manual):
     definition = """
-    experiment_id : uint32
+    experiment_id : int64
     ---
-    trial_number : uint16   # Should be part of key!
+    trial_number : int32   # Should be part of key!
     result : float32
     """
 ```
@@ -352,7 +352,7 @@ class Trial(dj.Manual):
 # Wrong: timestamp makes every row unique, losing entity semantics
 class Measurement(dj.Manual):
     definition = """
-    subject_id : uint32
+    subject_id : int64
     timestamp : datetime(6)   # Microsecond precision
     ---
     value : float32

src/explanation/type-system.md

@@ -62,10 +62,10 @@ Standardized, scientist-friendly types that work identically across backends.
 | `int16` | 16-bit signed | -32,768 to 32,767 |
 | `int32` | 32-bit signed | ±2 billion |
 | `int64` | 64-bit signed | ±9 quintillion |
-| `uint8` | 8-bit unsigned | 0 to 255 |
-| `uint16` | 16-bit unsigned | 0 to 65,535 |
-| `uint32` | 32-bit unsigned | 0 to 4 billion |
-| `uint64` | 64-bit unsigned | 0 to 18 quintillion |
+| `int16` | 8-bit unsigned | 0 to 255 |
+| `int32` | 16-bit unsigned | 0 to 65,535 |
+| `int64` | 32-bit unsigned | 0 to 4 billion |
+| `int64` | 64-bit unsigned | 0 to 18 quintillion |
 | `float32` | 32-bit float | ~7 significant digits |
 | `float64` | 64-bit float | ~15 significant digits |
 | `decimal(n,f)` | Fixed-point | Exact decimal |

src/explanation/whats-new-2.md

@@ -24,7 +24,7 @@ If you're upgrading from legacy DataJoint, these changes require code updates:
 | **Fetch API** | `table.fetch()` | `table.to_dicts()` or `.to_arrays()` |
 | **Update** | `(table & key)._update('attr', val)` | `table.update1({**key, 'attr': val})` |
 | **Join** | `table1 @ table2` | `table1 * table2` (with semantic check) |
-| **Type syntax** | `longblob`, `int unsigned` | `<blob>`, `uint32` |
+| **Type syntax** | `longblob`, `int unsigned` | `<blob>`, `int64` |
 | **Jobs** | `~jobs` table | Per-table `~~table_name` |
 
 See the [Migration Guide](../how-to/migrate-to-v20.md) for complete upgrade steps.
@@ -75,7 +75,7 @@ Legacy DataJoint overloaded MySQL types with implicit conversions:
 | `longblob` | `<blob>` |
 | `attach` | `<attach>` |
 | `blob@store` | `<blob@store>` |
-| `int unsigned` | `uint32` |
+| `int unsigned` | `int64` |
 
 ### Three-Tier Architecture
 
@@ -207,7 +207,7 @@ This enables efficient access to large datasets stored in Zarr, HDF5, or custom
 ### Deprecated Features
 
 - **AdaptedTypes**: Replaced by codec system (still works but migration recommended)
-- **Native type syntax**: `int unsigned` → `uint32` (warnings on new tables)
+- **Native type syntax**: `int unsigned` → `int64` (warnings on new tables)
 - **Legacy external storage** (`blob@store`): Replaced by `<blob@store>` codec syntax
 
 ### Legacy Support
@@ -238,7 +238,7 @@ Upgrading from DataJoint 0.x is a **phased process** designed to minimize risk:
 - **No database changes** — legacy clients still work
 
 ### Phase 2: Type Migration (Reversible)
-- Update database column comments to use core types (`:uint32:`, `:<blob>:`)
+- Update database column comments to use core types (`:int64:`, `:<blob>:`)
 - Rebuild `~lineage` tables for semantic matching
 - Update Python table definitions
 - **Legacy clients still work** — only metadata changed

src/how-to/choose-storage-type.md

@@ -523,7 +523,7 @@ class SpikeWaveforms(dj.Computed):
     """Extracted spike shapes"""
     definition = """
     -> ContinuousData
-    unit_id : uint32
+    unit_id : int64
     ---
     waveforms : <npy@>                   # 20 MB array, lazy load
     """
@@ -571,7 +571,7 @@ class FluorescenceTraces(dj.Computed):
     """Extracted time series"""
     definition = """
     -> SegmentedCells
-    cell_id : uint32
+    cell_id : int64
     ---
     trace : <blob@>                      # 500 KB per cell, deduplicated
     """

src/how-to/define-tables.md

@@ -41,7 +41,7 @@ class MyTable(dj.Manual):
 ```python
 definition = """
 subject_id : varchar(16)      # Subject identifier
-session_idx : uint16          # Session number
+session_idx : int32          # Session number
 ---
 ...
 """
@@ -137,7 +137,7 @@ See [Design Primary Keys](design-primary-keys.md) for detailed guidance on key s
 |------|-------------|
 | `bool` | Boolean (true/false) |
 | `int8`, `int16`, `int32`, `int64` | Signed integers |
-| `uint8`, `uint16`, `uint32`, `uint64` | Unsigned integers |
+| `int16`, `int32`, `int64`, `int64` | Unsigned integers |
 | `float32`, `float64` | Floating point |
 | `decimal(m,n)` | Fixed precision decimal |
 | `varchar(n)` | Variable-length string |
@@ -196,7 +196,7 @@ Native types are flagged with a warning at declaration time but are allowed. Cor
 class Session(dj.Manual):
     definition = """
     -> Subject                # References Subject table
-    session_idx : uint16
+    session_idx : int32
     ---
     session_date : date
     """
@@ -227,15 +227,15 @@ class TaskType(dj.Lookup):
 class Session(dj.Manual):
     definition = """
     -> Subject
-    session_idx : uint16
+    session_idx : int32
     ---
     session_date : date
     """
 
     class Trial(dj.Part):
         definition = """
         -> master
-        trial_idx : uint16
+        trial_idx : int32
         ---
         outcome : enum('hit', 'miss')
         reaction_time : float32
@@ -250,7 +250,7 @@ class SessionStats(dj.Computed):
     definition = """
     -> Session
     ---
-    n_trials : uint32
+    n_trials : int64
     hit_rate : float32
     """
 
@@ -270,7 +270,7 @@ Declare indexes at the end of the definition, after all attributes:
 ```python
 definition = """
 subject_id : varchar(16)
-session_idx : uint16
+session_idx : int32
 ---
 session_date : date
 experimenter : varchar(50)
@@ -288,7 +288,7 @@ Tables are declared in the database when the `@schema` decorator applies to the
 @schema  # Table is declared here
 class Session(dj.Manual):
     definition = """
-    session_id : uint16
+    session_id : int32
     ---
     session_date : date
     """

src/how-to/design-primary-keys.md

@@ -39,7 +39,7 @@ Combine attributes when a single attribute isn't unique:
 class Session(dj.Manual):
     definition = """
     -> Subject
-    session_idx : uint16        # Session number within subject
+    session_idx : int32        # Session number within subject
     ---
     session_date : date
     """
@@ -100,7 +100,7 @@ Foreign keys above the `---` become part of the primary key:
 class Trial(dj.Manual):
     definition = """
     -> Session                  # In primary key
-    trial_idx : uint16          # In primary key
+    trial_idx : int32          # In primary key
     ---
     -> Stimulus                  # NOT in primary key
     outcome : enum('hit', 'miss')
@@ -111,11 +111,11 @@ class Trial(dj.Manual):
 
 ### Keep Keys Small
 
-Prefer `uint16` over `int64` when the range allows:
+Prefer `int32` over `int64` when the range allows:
 
 ```python
 # Good: Appropriate size
-session_idx : uint16     # Max 65,535 sessions per subject
+session_idx : int32     # Max 65,535 sessions per subject
 
 # Avoid: Unnecessarily large
 session_idx : int64      # Wastes space, slower joins
@@ -145,7 +145,7 @@ session_date : date
 
 # Good: Add a sequence number
 -> Subject
-session_idx : uint16
+session_idx : int32
 ---
 session_date : date
 ```
@@ -172,7 +172,7 @@ Once a table has data, primary keys cannot be changed. Plan carefully:
 class Scan(dj.Manual):
     definition = """
     -> Session
-    scan_idx : uint8           # Might need uint16 for high-throughput
+    scan_idx : int16           # Might need int32 for high-throughput
     ---
     ...
     """

src/how-to/manage-pipeline-project.md

@@ -61,7 +61,7 @@ class Probe(dj.Lookup):
     definition = """
     probe_type : varchar(32)
     ---
-    num_channels : uint16
+    num_channels : int32
     """
 
 @schema