scistack 0.1.0__py3-none-any.whl

scistack-0.1.0.dist-info/METADATA

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+Metadata-Version: 2.4
+Name: scistack
+Version: 0.1.0
+Summary: Scientific data pipeline framework — versioning, lineage, and caching for research workflows
+License: MIT
+Keywords: data-management,lineage,pipeline,provenance,reproducibility,scientific-computing
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Database
+Classifier: Topic :: Scientific/Engineering
+Requires-Python: >=3.9
+Requires-Dist: scidb>=0.1.0
+Provides-Extra: all
+Requires-Dist: sci-matlab>=0.1.0; extra == 'all'
+Requires-Dist: scidb-net>=0.1.0; extra == 'all'
+Provides-Extra: dev
+Requires-Dist: pytest-cov>=4.0.0; extra == 'dev'
+Requires-Dist: pytest>=7.0.0; extra == 'dev'
+Provides-Extra: matlab
+Requires-Dist: sci-matlab>=0.1.0; extra == 'matlab'
+Provides-Extra: net
+Requires-Dist: scidb-net>=0.1.0; extra == 'net'
+Description-Content-Type: text/markdown
+
+# SciDB
+
+## Better Research Tools, Better Research Outcomes
+
+SciDB is a database framework purpose-built for scientific data analysis. It gives you a structured, versioned, and queryable home for every piece of data your pipeline produces — from raw signals to final results — with near zero infrastructure code on your part, and **zero changes to your analysis code**.
+
+It works natively in both **Python** and **MATLAB**.
+
+## The Problem
+
+Every scientist who writes analysis code eventually builds the same thing: a tangle of folders, naming conventions, and bookkeeping scripts to track which data came from where, which version of a function produced it, and whether it's already been computed.
+
+That infrastructure code is never the point. But it eats weeks of your time, it's fragile, and it's different in every lab.
+
+**Scientists want to focus on the science, not data management.**
+
+SciDB replaces all of it with three ideas:
+
+- **Named variable types** — instead of files on disk, your data lives in typed database tables you can query by metadata
+- **Automatic lineage** — a simple decorator records exactly what function and inputs produced each result
+- **Computation caching** — if you've already computed something, SciDB knows and skips it
+
+With SciDB, your analysis scripts contain _only_ analysis logic. The infrastructure is handled for you.
+
+## Quick Start
+
+### Installation
+
+```bash
+pip install scidb
+```
+
+This pulls in all core dependencies (`sciduckdb`, `thunk`, `scipathgen`, `canonicalhash`, `scirun`).
+
+For development (editable installs of all packages):
+
+```bash
+git clone https://github.com/mtillman14/general-sqlite-database
+cd general-sqlite-database
+./dev-install.sh
+```
+
+### One-Time Setup
+
+Every project starts by configuring a database. You do this once.
+
+```python
+from scidb import configure_database
+
+db = configure_database(
+    "my_experiment_data.duckdb",                  # DuckDB file for data + lineage
+    dataset_schema_keys=["subject", "session"],   # How your dataset is organized
+)
+```
+
+`dataset_schema_keys` describes the structure of your experiment. If your data is organized by subject and session, say so — SciDB uses this to let you save and query data naturally.
+
+### Define Your Variable Types
+
+Each kind of data in your pipeline gets its own type. This is just a one-liner:
+
+```python
+from scidb import BaseVariable
+
+class RawEMG(BaseVariable):
+    pass
+
+class FilteredEMG(BaseVariable):
+    pass
+
+class MaxActivation(BaseVariable):
+    pass
+```
+
+That's it. No configuration, no serialization code. SciDB handles numpy arrays, scalars, lists, dicts, and DataFrames natively.
+
+### Save and Load Data
+
+```python
+import numpy as np
+
+# Save with metadata that matches your schema
+RawEMG.save(np.random.randn(1000), subject=1, session="baseline")
+
+# Load it back — by the metadata you care about
+raw = RawEMG.load(subject=1, session="baseline")
+print(raw.data)  # your numpy array
+```
+
+### Track Lineage Automatically
+
+Which function created that variable? Were the most recent settings used the last time I ran this?
+
+Wrap your analysis functions with `@thunk` and SciDB records which functions produced what **and the input variable values** — automatically:
+
+```python
+from scidb import thunk
+
+@thunk
+def bandpass_filter(signal, low_hz, high_hz):
+    # your filtering logic
+    return filtered_signal
+
+@thunk
+def compute_max(signal):
+    return float(np.max(np.abs(signal)))
+
+# Run the pipeline — lineage is tracked behind the scenes
+raw = RawEMG.load(subject=1, session="baseline")
+filtered = bandpass_filter(raw, low_hz=20, high_hz=450)
+max_val = compute_max(filtered)
+
+# Save results
+FilteredEMG.save(filtered, subject=1, session="baseline")
+MaxActivation.save(max_val, subject=1, session="baseline")
+
+# Later: "What function produced this, and with what settings?"
+provenance = db.get_provenance(FilteredEMG, subject=1, session="baseline")
+print(provenance["function_name"])  # "bandpass_filter"
+print(provenance["constants"])      # {"low_hz": 20, "high_hz": 450}
+```
+
+Your functions stay clean, no boilerplate required. They receive normal numpy arrays and return normal values. The `@thunk` decorator handles all the bookkeeping at the boundary.
+
+If the `@thunk` decorator is still too close to your code for your test, wrap it in a `Thunk()` call later on:
+
+```python
+
+from scidb.thunk import Thunk
+
+compute_max = Thunk(compute_max)
+```
+
+**Run the same pipeline again and every step is skipped** — SciDB recognizes the same function + same inputs and returns the cached result instantly.
+
+## Scaling Up with `for_each()`
+
+Real experiments can have dozens of subjects and conditions, or thousands. SciDB can handle it all, using `for_each()` runs your pipeline over every combination automatically:
+
+```python
+from scidb import for_each
+
+# 5 subjects
+for_each(
+    bandpass_filter,
+    inputs={"signal": RawEMG},
+    outputs=[FilteredEMG],
+    subject=[1, 2, 3, 4, 5],
+    session=["baseline", "post"],
+)
+
+# 10,000 subjects
+for_each(
+    bandpass_filter,
+    inputs={"signal": RawEMG},
+    outputs=[FilteredEMG],
+    subject=range(1,10000),
+    session=["baseline", "post"],
+)
+
+# Specify subject list of any size
+subject_list = config["subjects"] # Load from some configuration file
+for_each(
+    bandpass_filter,
+    inputs={"signal": RawEMG},
+    outputs=[FilteredEMG],
+    subject=subject_list,
+    session=["baseline", "post"],
+)
+```
+
+This loads `RawEMG` for each subject/session combination, runs `bandpass_filter`, and saves the result as `FilteredEMG` — multiple iterations, zero boilerplate. If a subject is missing data, that iteration is skipped gracefully. In the future, logging support is planned to document what ran successfully and what failed, and why.
+
+Need one input to stay fixed while others iterate? Use `Fixed`:
+
+```python
+from scidb import Fixed
+
+for_each(
+    compare_to_baseline,
+    inputs={
+        "baseline": Fixed(RawEMG, session="baseline"),  # always load baseline
+        "current": RawEMG,                               # iterates normally
+    },
+    outputs=[Delta],
+    subject=[1, 2, 3, 4, 5],
+    session=["post_1", "post_2", "post_3"],
+)
+```
+
+## Powerful Querying
+
+Because your data lives in a real database (not scattered files), querying is simple and powerful:
+
+```python
+# Load one specific record
+emg = FilteredEMG.load(subject=3, session="post")
+
+# Load all sessions for a subject — returns a list
+all_sessions = FilteredEMG.load(subject=3)
+for var in all_sessions:
+    print(var.metadata["session"], var.data.shape)
+
+# Load everything as a DataFrame for analysis
+import pandas as pd
+df = MaxActivation.load_all(as_df=True)
+#   subject  session    data
+#   1        baseline   0.82
+#   1        post       1.47
+#   2        baseline   0.91
+#   ...
+```
+
+No folder traversal. No filename parsing. No `results_v2_final_FINAL.csv`. Just ask for what you want by the metadata that matters.
+
+### Your Data Is Not Locked Away
+
+Worried that putting data in a database means you can't see or inspect it? Don't be. SciDB uses [DuckDB](https://duckdb.org/) under the hood, and every variable type gets a human-readable **view** that you can query directly with SQL — in DBeaver, the DuckDB CLI, or any tool that speaks SQL.
+
+For example, the `MaxActivation` view looks like this:
+
+| subject | session  | value |
+| ------- | -------- | ----- |
+| 1       | baseline | 0.82  |
+| 1       | post     | 1.47  |
+| 2       | baseline | 0.91  |
+| 2       | post     | 1.38  |
+| 3       | baseline | 0.76  |
+| 3       | post     | 1.22  |
+
+You can query it directly:
+
+```sql
+SELECT subject, session, value
+FROM MaxActivation;
+```
+
+Or use database viewer tools like [DBeaver](https://dbeaver.com) to view the database directly.
+
+Your data is always one SQL query or visualization away — no Python or MATLAB required.
+
+## Works in MATLAB Too
+
+SciDB isn't Python-only. The entire framework works in MATLAB with a nearly identical API:
+
+```matlab
+% One-time setup
+scidb.configure_database("my_experiment.duckdb", ["subject", "session"], "pipeline.db");
+
+% Save and load
+RawEMG().save(randn(1000, 1), subject=1, session="baseline");
+raw = RawEMG().load(subject=1, session="baseline");
+
+% Lineage-tracked functions
+filter_fn = scidb.Thunk(@bandpass_filter);
+filtered = filter_fn(raw, 20, 450);
+FilteredEMG().save(filtered, subject=1, session="baseline");
+
+% Batch processing
+scidb.for_each(@bandpass_filter, ...
+    struct('signal', RawEMG()), ...
+    {FilteredEMG()}, ...
+    subject=[1 2 3 4 5], ...
+    session=["baseline" "post"]);
+```
+
+Data saved from MATLAB can be loaded in Python and vice versa. Lineage chains are continuous across languages. Use whichever language fits the task.
+
+## What a Full Pipeline Looks Like
+
+Here's a complete, realistic pipeline from setup to results:
+
+```python
+from scidb import BaseVariable, configure_database, thunk, for_each
+
+# --- Setup (once per project) ---
+db = configure_database("gait_study.duckdb",                # Where your data is stored
+                        ["subject", "session", "trial"],    # How your dataset is organized
+                         "pipeline.db"                      # Where lineage is tracked
+                    )
+
+# --- Define variable types ---
+class RawKinematicData(BaseVariable):
+    pass
+
+class StepLength(BaseVariable):
+    pass
+
+class MeanStepLength(BaseVariable):
+    pass
+
+class RawForce(BaseVariable):
+    pass
+
+class FilteredForce(BaseVariable):
+    pass
+
+# --- Define processing functions ---
+@thunk
+def extract_step_length(kinematic_data):
+    # your biomechanics logic here
+    return step_lengths
+
+@thunk
+def compute_mean(values):
+    return float(np.mean(values))
+
+# --- Run the pipeline ---
+for_each(
+    extract_step_length,
+    inputs={"kinematic_data": RawKinematicData},
+    outputs=[StepLength],
+    subject=[1, 2, 3],
+    session=["pre", "post"],
+    trial=[1, 2, 3, 4, 5],
+)
+
+for_each(
+    compute_mean,
+    inputs={"values": StepLength},
+    outputs=[MeanStepLength],
+    subject=[1, 2, 3],
+    session=["pre", "post"],
+    trial=[1, 2, 3, 4, 5],
+)
+
+for_each(
+    filter_data,
+    inputs={"values": RawForce, "smoothing": 0.2},
+    outputs=[FilteredForce],
+    subject=[1, 2, 3],
+    session=["pre", "post"],
+    trial=[1, 2, 3, 4, 5],
+)
+
+# --- Analyze results ---
+df = MeanStepLength.load_all(as_df=True)
+print(df.groupby("session")["data"].mean())
+```
+
+That's the entire pipeline. No file I/O code. No path management. No version tracking logic. Just the science.
+
+Want to change the function logic? SciDB will automatically detect the change, and will re-run that processing step on the next run of the script. Want to change a setting to the function? SciDB will detect that too, and re-run the processing step. Data will be saved to the database, **and the previous data will be preserved**. Understanding the effect of analysis decisions on our results has never been easier.
+
+```python
+for_each(
+    filter_data,
+    inputs={"values": RawForce, "smoothing": 0.3}, # Changed from smoothing=0.2
+    outputs=[FilteredForce],
+    subject=[1, 2, 3],
+    session=["pre", "post"],
+    trial=[1, 2, 3, 4, 5],
+)
+
+# Get the FilteredForce created with smoothing=0.2
+filtered_force0_2 = FilteredForce.load(smoothing=0.2) # Returns all subjects, sessions, and trials.
+
+# Get the FilteredForce created with smoothing=0.3
+filtered_force0_3 = FilteredForce.load(smoothing=0.3) # Returns all subjects, sessions, and trials.
+```
+
+## The Bigger Picture: Shareable Pipelines
+
+By abstracting away all infrastructure — file paths, storage formats, naming conventions — SciDB decouples your analysis logic from your local environment. Your pipeline code contains _only_ the scientific computation.
+
+This opens the door to **truly portable, shareable data processing pipelines.** When a pipeline is just a sequence of typed functions with declared inputs and outputs, it can be shared, reproduced, and built upon by anyone — regardless of how their data is organized on disk.
+
+Today, sharing a pipeline means sharing a pile of scripts with hardcoded paths and implicit assumptions. With SciDB, the pipeline _is_ the science, and the infrastructure adapts to wherever it runs.
+
+## Learn More
+
+- [Quickstart Guide](docs/quickstart.md) — Get running in 5 minutes
+- [VO2 Max Walkthrough](docs/guide/walkthrough.md) — Full example pipeline with design explanations
+- [Variables Guide](docs/guide/variables.md) — Deep dive into variable types
+- [Lineage Guide](docs/guide/lineage.md) — How provenance tracking works
+- [API Reference](docs/api.md) — Complete API documentation

scistack-0.1.0.dist-info/RECORD

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scistack-0.1.0.dist-info/WHEEL

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