yw-core 0.1.0
Essential elements of YesWorkflow
Requires Python: >=3.7
Keywords: yesworkflow, yw, scientific, provenance, python

# yw_core

Core elements of YesWorkflow in Python.

## Installation

```bash
git clone <url>
cd yw_core
pip install .
```

## An example using a Python notebook with 3 code cells
Here is the example Python notebook that will be used as the running example to explain the CLI and Python API.
```python
# cell 1
x = 1

# cell 2
func(x)

# cell 3
x
```

### CLI

```python
Usage: yw [OPTIONS]

Options:
  -f, --filepath TEXT  Path of a Python notebook to extract YesWorkflow
                       annotations  [required]
  -u, --upper          Extract upper estimate of cell I/O sets for YesWorkflow
                       annotations
  --help               Show this message and exit.
```

#### Lower estimate

```bash
yw -f YOUR_PYTHON_NOTEBOOK_PATH
```

Expected output for lower estimate:
```text
# @BEGIN cell-1
# @OUT x
# @END cell-1

# @BEGIN cell-2
# @IN x
# @END cell-2

# @BEGIN cell-3
# @IN x
# @END cell-3
```

#### Upper estimate

```bash
yw -f YOUR_PYTHON_NOTEBOOK_PATH -u
```

Expected output for upper estimate:
```
# @BEGIN cell-1
# @OUT x
# @END cell-1

# @BEGIN cell-2
# @IN x
# @OUT x @AS x-1
# @END cell-2

# @BEGIN cell-3
# @IN x @AS x-1
# @END cell-3
```

### Python API

#### Lower estimate
```python
from yw_core.yw_core import extract_code_cells, extract_records, records2annotations
code_cells = extract_code_cells("YOUR_PYTHON_NOTEBOOK_PATH")
records = extract_records(code_cells, is_upper_estimate=False)
annotations = records2annotations(records)
```

Expected outputs for lower estimate:
```python
code_cells = ['x = 1', 'func(x)', 'x']
records = [
  {'inputs': set(), 'output_candidates': {'x'}, 'refers_code': set(), 'defines_code': set(), 'alias_stmt': None, 'alias_vars': set(), 'outputs': {'x'}}, 
  {'inputs': {'x'}, 'output_candidates': set(), 'refers_code': set(), 'defines_code': set(), 'alias_stmt': None, 'alias_vars': set(), 'outputs': set()}, 
  {'inputs': {'x'}, 'output_candidates': set(), 'refers_code': set(), 'defines_code': set(), 'alias_stmt': None, 'alias_vars': set(), 'outputs': set()}
]
annotations = '# @BEGIN cell-1\n# @OUT x\n# @END cell-1\n\n# @BEGIN cell-2\n# @IN x\n# @END cell-2\n\n# @BEGIN cell-3\n# @IN x\n# @END cell-3'
```

#### Upper estimate
```python
from yw_core.yw_core import extract_code_cells, extract_records, records2annotations
code_cells = extract_code_cells("YOUR_PYTHON_NOTEBOOK_PATH")
records = extract_records(code_cells, is_upper_estimate=True)
annotations = records2annotations(records)
```

Expected outputs for upper estimate:
```python
code_cells = ['x = 1', 'func(x)', 'x']
records = [
  {'inputs': set(), 'output_candidates': {'x'}, 'refers_code': set(), 'defines_code': set(), 'alias_stmt': None, 'alias_vars': set(), 'outputs': {'x'}}, 
  {'inputs': {'x'}, 'output_candidates': {'x'}, 'refers_code': set(), 'defines_code': set(), 'alias_stmt': None, 'alias_vars': set(), 'outputs': {'x-1'}}, 
  {'inputs': {'x-1'}, 'output_candidates': set(), 'refers_code': set(), 'defines_code': set(), 'alias_stmt': None, 'alias_vars': set(), 'outputs': set()}
]
annotations = '# @BEGIN cell-1\n# @OUT x\n# @END cell-1\n\n# @BEGIN cell-2\n# @IN x\n# @OUT x @AS x-1\n# @END cell-2\n\n# @BEGIN cell-3\n# @IN x @AS x-1\n# @END cell-3'
```

## Tests

We use [`tox`](https://tox.wiki/en/4.11.3/installation.html) to run Python unit test ([`pytest`](https://docs.pytest.org/en/7.4.x/)):
```bash
# If you the tox package is not installed
pip install tox

# Run unit test
tox
```