prisma-flow 0.1.1__tar.gz

prisma_flow-0.1.1/LICENSE

@@ -0,0 +1,28 @@
+BSD 3-Clause License
+
+Copyright (c) 2026, Open Science Labs Incubator
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

prisma_flow-0.1.1/PKG-INFO

@@ -0,0 +1,236 @@
+Metadata-Version: 2.4
+Name: prisma-flow
+Version: 0.1.1
+Summary: Lightweight Python tools for generating PRISMA-style flow diagrams without system dependencies.
+License-Expression: BSD-3-Clause
+License-File: LICENSE
+Keywords: prisma,systematic-review,scoping-review,evidence-synthesis,literature-review,svg,python,open-science
+Author: Open Science Labs Incubator contributors
+Requires-Python: >=3.10,<4
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: Intended Audience :: Healthcare Industry
+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 :: Scientific/Engineering
+Classifier: Topic :: Text Processing :: Markup
+Provides-Extra: dev
+Provides-Extra: docs
+Provides-Extra: png
+Provides-Extra: yaml
+Requires-Dist: douki (>=0.12.1) ; extra == "dev"
+Requires-Dist: makim (==1.29.0) ; extra == "dev"
+Requires-Dist: mypy (>=1.10) ; extra == "dev"
+Requires-Dist: pre-commit (>=3) ; extra == "dev"
+Requires-Dist: pydantic (>=2)
+Requires-Dist: pytest (>=8) ; extra == "dev"
+Requires-Dist: pytest-cov (>=5) ; extra == "dev"
+Requires-Dist: pyyaml (>=6) ; extra == "yaml"
+Requires-Dist: resvg (>=0.1.2) ; extra == "png"
+Requires-Dist: ruff (>=0.6) ; extra == "dev"
+Project-URL: Documentation, https://osl-incubator.github.io/prisma-flow/
+Project-URL: Homepage, https://github.com/osl-incubator/prisma-flow
+Project-URL: Issues, https://github.com/osl-incubator/prisma-flow/issues
+Project-URL: Repository, https://github.com/osl-incubator/prisma-flow
+Description-Content-Type: text/markdown
+
+# prisma-flow
+
+![CI](https://img.shields.io/github/actions/workflow/status/osl-incubator/prisma-flow/ci.yml?logo=github&label=CI)
+[![Python Versions](https://img.shields.io/pypi/pyversions/prisma-flow)](https://pypi.org/project/prisma-flow/)
+[![Package Version](https://img.shields.io/pypi/v/prisma-flow?color=blue)](https://pypi.org/project/prisma-flow/)
+![License](https://img.shields.io/pypi/l/prisma-flow?color=blue)
+
+`prisma-flow` is a lightweight Python package for generating PRISMA-style flow
+diagrams for evidence synthesis workflows.
+
+Unlike Graphviz-based tools, `prisma-flow` does not require system-level graph
+layout binaries. Unlike Mermaid-based tools, it does not require Node or Mermaid
+CLI. The default renderer is a pure-Python, template-based SVG generator.
+
+The project is designed for systematic reviews, scoping reviews, evidence
+syntheses, and literature review workflows.
+
+## Features
+
+- Pure-Python SVG rendering by default
+- Standalone HTML export
+- Mermaid text export without Mermaid CLI
+- JSON input/output in the base install
+- Optional YAML input/output via `prisma-flow[yaml]`
+- Optional PNG method that clearly reports the missing optional dependency
+- Python API and `prisma-flow` command-line interface
+- PRISMA count validation with errors and warnings
+
+## Installation
+
+```bash
+pip install prisma-flow
+```
+
+or:
+
+```bash
+uv add prisma-flow
+```
+
+Optional YAML support:
+
+```bash
+uv add "prisma-flow[yaml]"
+```
+
+Optional PNG support, when a supported backend is added:
+
+```bash
+uv add "prisma-flow[png]"
+```
+
+## Python API
+
+```python
+from prismaflow import PrismaFlow
+
+flow = PrismaFlow.new_review(
+    records_identified_databases=1240,
+    records_identified_registers=50,
+    records_removed_duplicates=210,
+    records_removed_automation=0,
+    records_removed_other=0,
+    records_screened=1080,
+    records_excluded=950,
+    reports_sought=130,
+    reports_not_retrieved=10,
+    reports_assessed=120,
+    reports_excluded={
+        "Wrong population": 30,
+        "Wrong intervention": 20,
+        "Wrong outcome": 15,
+        "Not primary research": 15,
+    },
+    studies_included=40,
+)
+
+report = flow.validate()
+print(report.format_text())
+
+flow.to_svg("prisma.svg")
+flow.to_html("prisma.html")
+flow.to_mermaid("prisma.mmd")
+flow.to_json("review.json")
+```
+
+## CLI usage
+
+Validate input data:
+
+```bash
+prisma-flow validate examples/basic_new_review.json
+```
+
+Render SVG:
+
+```bash
+prisma-flow render examples/basic_new_review.json -o prisma.svg
+```
+
+Render other base-install formats:
+
+```bash
+prisma-flow render examples/basic_new_review.json --format html -o prisma.html
+prisma-flow render examples/basic_new_review.json --format mermaid -o prisma.mmd
+```
+
+If validation fails, the CLI prints a report and exits with a non-zero status:
+
+```text
+Validation failed:
+- records_screened should equal identified records minus removed records. Expected: 1080 Found: 1090
+```
+
+## Data model
+
+The v0.1 implementation supports the PRISMA 2020 new-review databases/registers
+template:
+
+```python
+from prismaflow import (
+    EligibilityStage,
+    IdentificationStage,
+    IncludedStage,
+    PrismaFlow,
+    PrismaTemplate,
+    ScreeningStage,
+)
+
+flow = PrismaFlow(
+    template=PrismaTemplate.PRISMA_2020_NEW_DATABASES_REGISTERS,
+    identification=IdentificationStage(
+        records_identified_databases=1240,
+        records_identified_registers=50,
+    ),
+    screening=ScreeningStage(
+        records_removed_duplicates=210,
+        records_removed_automation=0,
+        records_removed_other=0,
+        records_screened=1080,
+        records_excluded=950,
+    ),
+    eligibility=EligibilityStage(
+        reports_sought=130,
+        reports_not_retrieved=10,
+        reports_assessed=120,
+        reports_excluded={"Wrong population": 30},
+    ),
+    included=IncludedStage(studies_included=40),
+)
+```
+
+## Dependency policy
+
+SVG, HTML, Mermaid, and JSON work with the base install. YAML is optional. PNG
+is intentionally optional and not implemented as a required renderer in v0.1.
+
+The package does **not** require Graphviz, Cairo, CairoSVG, Node, Mermaid CLI,
+Inkscape, Playwright, browser engines, Matplotlib, or Plotly.
+
+## Development
+
+```bash
+conda env create -f conda/dev.yaml
+conda activate prismaflow
+poetry config virtualenvs.create false
+poetry install --extras "dev yaml"
+```
+
+Run the same workflow through Makim:
+
+```bash
+makim tests.linter
+makim tests.unit
+makim package.build
+makim docs.build
+makim all.ci
+```
+
+## Documentation
+
+The documentation site is built with Quarto:
+
+```bash
+quarto render docs
+```
+
+Preview locally:
+
+```bash
+quarto preview docs
+```
+
+## License
+
+BSD-3-Clause.
+

prisma_flow-0.1.1/README.md

@@ -0,0 +1,196 @@
+# prisma-flow
+
+![CI](https://img.shields.io/github/actions/workflow/status/osl-incubator/prisma-flow/ci.yml?logo=github&label=CI)
+[![Python Versions](https://img.shields.io/pypi/pyversions/prisma-flow)](https://pypi.org/project/prisma-flow/)
+[![Package Version](https://img.shields.io/pypi/v/prisma-flow?color=blue)](https://pypi.org/project/prisma-flow/)
+![License](https://img.shields.io/pypi/l/prisma-flow?color=blue)
+
+`prisma-flow` is a lightweight Python package for generating PRISMA-style flow
+diagrams for evidence synthesis workflows.
+
+Unlike Graphviz-based tools, `prisma-flow` does not require system-level graph
+layout binaries. Unlike Mermaid-based tools, it does not require Node or Mermaid
+CLI. The default renderer is a pure-Python, template-based SVG generator.
+
+The project is designed for systematic reviews, scoping reviews, evidence
+syntheses, and literature review workflows.
+
+## Features
+
+- Pure-Python SVG rendering by default
+- Standalone HTML export
+- Mermaid text export without Mermaid CLI
+- JSON input/output in the base install
+- Optional YAML input/output via `prisma-flow[yaml]`
+- Optional PNG method that clearly reports the missing optional dependency
+- Python API and `prisma-flow` command-line interface
+- PRISMA count validation with errors and warnings
+
+## Installation
+
+```bash
+pip install prisma-flow
+```
+
+or:
+
+```bash
+uv add prisma-flow
+```
+
+Optional YAML support:
+
+```bash
+uv add "prisma-flow[yaml]"
+```
+
+Optional PNG support, when a supported backend is added:
+
+```bash
+uv add "prisma-flow[png]"
+```
+
+## Python API
+
+```python
+from prismaflow import PrismaFlow
+
+flow = PrismaFlow.new_review(
+    records_identified_databases=1240,
+    records_identified_registers=50,
+    records_removed_duplicates=210,
+    records_removed_automation=0,
+    records_removed_other=0,
+    records_screened=1080,
+    records_excluded=950,
+    reports_sought=130,
+    reports_not_retrieved=10,
+    reports_assessed=120,
+    reports_excluded={
+        "Wrong population": 30,
+        "Wrong intervention": 20,
+        "Wrong outcome": 15,
+        "Not primary research": 15,
+    },
+    studies_included=40,
+)
+
+report = flow.validate()
+print(report.format_text())
+
+flow.to_svg("prisma.svg")
+flow.to_html("prisma.html")
+flow.to_mermaid("prisma.mmd")
+flow.to_json("review.json")
+```
+
+## CLI usage
+
+Validate input data:
+
+```bash
+prisma-flow validate examples/basic_new_review.json
+```
+
+Render SVG:
+
+```bash
+prisma-flow render examples/basic_new_review.json -o prisma.svg
+```
+
+Render other base-install formats:
+
+```bash
+prisma-flow render examples/basic_new_review.json --format html -o prisma.html
+prisma-flow render examples/basic_new_review.json --format mermaid -o prisma.mmd
+```
+
+If validation fails, the CLI prints a report and exits with a non-zero status:
+
+```text
+Validation failed:
+- records_screened should equal identified records minus removed records. Expected: 1080 Found: 1090
+```
+
+## Data model
+
+The v0.1 implementation supports the PRISMA 2020 new-review databases/registers
+template:
+
+```python
+from prismaflow import (
+    EligibilityStage,
+    IdentificationStage,
+    IncludedStage,
+    PrismaFlow,
+    PrismaTemplate,
+    ScreeningStage,
+)
+
+flow = PrismaFlow(
+    template=PrismaTemplate.PRISMA_2020_NEW_DATABASES_REGISTERS,
+    identification=IdentificationStage(
+        records_identified_databases=1240,
+        records_identified_registers=50,
+    ),
+    screening=ScreeningStage(
+        records_removed_duplicates=210,
+        records_removed_automation=0,
+        records_removed_other=0,
+        records_screened=1080,
+        records_excluded=950,
+    ),
+    eligibility=EligibilityStage(
+        reports_sought=130,
+        reports_not_retrieved=10,
+        reports_assessed=120,
+        reports_excluded={"Wrong population": 30},
+    ),
+    included=IncludedStage(studies_included=40),
+)
+```
+
+## Dependency policy
+
+SVG, HTML, Mermaid, and JSON work with the base install. YAML is optional. PNG
+is intentionally optional and not implemented as a required renderer in v0.1.
+
+The package does **not** require Graphviz, Cairo, CairoSVG, Node, Mermaid CLI,
+Inkscape, Playwright, browser engines, Matplotlib, or Plotly.
+
+## Development
+
+```bash
+conda env create -f conda/dev.yaml
+conda activate prismaflow
+poetry config virtualenvs.create false
+poetry install --extras "dev yaml"
+```
+
+Run the same workflow through Makim:
+
+```bash
+makim tests.linter
+makim tests.unit
+makim package.build
+makim docs.build
+makim all.ci
+```
+
+## Documentation
+
+The documentation site is built with Quarto:
+
+```bash
+quarto render docs
+```
+
+Preview locally:
+
+```bash
+quarto preview docs
+```
+
+## License
+
+BSD-3-Clause.

prisma_flow-0.1.1/pyproject.toml

@@ -0,0 +1,121 @@
+[project]
+name = "prisma-flow"
+version = "0.1.1"  # semantic-release
+description = "Lightweight Python tools for generating PRISMA-style flow diagrams without system dependencies."
+readme = "README.md"
+requires-python = ">=3.10,<4"
+license = "BSD-3-Clause"
+authors = [
+  { name = "Open Science Labs Incubator contributors" }
+]
+keywords = [
+  "prisma",
+  "systematic-review",
+  "scoping-review",
+  "evidence-synthesis",
+  "literature-review",
+  "svg",
+  "python",
+  "open-science",
+]
+classifiers = [
+  "Development Status :: 3 - Alpha",
+  "Intended Audience :: Science/Research",
+  "Intended Audience :: Healthcare Industry",
+  "Programming Language :: Python :: 3",
+  "Programming Language :: Python :: 3.10",
+  "Programming Language :: Python :: 3.11",
+  "Programming Language :: Python :: 3.12",
+  "Programming Language :: Python :: 3.13",
+  "Topic :: Scientific/Engineering",
+  "Topic :: Text Processing :: Markup",
+]
+dependencies = [
+  "pydantic>=2",
+]
+
+[project.urls]
+Homepage = "https://github.com/osl-incubator/prisma-flow"
+Repository = "https://github.com/osl-incubator/prisma-flow"
+Issues = "https://github.com/osl-incubator/prisma-flow/issues"
+Documentation = "https://osl-incubator.github.io/prisma-flow/"
+
+[project.optional-dependencies]
+yaml = ["pyyaml>=6"]
+png = ["resvg>=0.1.2"]
+dev = [
+  "douki>=0.12.1",
+  "pytest>=8",
+  "pytest-cov>=5",
+  "ruff>=0.6",
+  "mypy>=1.10",
+  "pre-commit>=3",
+  "makim==1.29.0",
+]
+docs = []
+
+
+[tool.poetry.group.dev.dependencies]
+quarto-cli = ">=1.9.0"
+pyyaml  = ">=6"
+resvg = ">=0.1.2"
+douki = ">=0.12.1"
+pytest  = ">=8"
+pytest-cov  = ">=5"
+ruff  = ">=0.6"
+mypy  = ">=1.10"
+pre-commit = ">=3"
+makim = "==1.29.0"
+
+[project.scripts]
+prisma-flow = "prismaflow.cli:main"
+
+[build-system]
+requires = ["poetry-core>=2"]
+build-backend = "poetry.core.masonry.api"
+
+[tool.poetry]
+packages = [
+  { include = "prismaflow", from = "src" },
+]
+include = [
+  "src/prismaflow/py.typed",
+]
+
+[tool.ruff]
+line-length = 88
+target-version = "py310"
+src = ["src", "tests"]
+
+[tool.ruff.lint]
+select = [
+  "E",
+  "F",
+  "I",
+  "UP",
+  "B",
+  "RUF",
+]
+ignore = [
+  "D203",
+  "D213",
+]
+
+[tool.ruff.lint.per-file-ignores]
+"tests/**" = ["D"]
+"src/prismaflow/cli.py" = ["B008"]
+
+[tool.ruff.format]
+quote-style = "double"
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+addopts = "-ra"
+
+[tool.mypy]
+python_version = "3.10"
+strict = true
+warn_unused_ignores = true
+warn_redundant_casts = true
+warn_unused_configs = true
+show_error_codes = true

prisma_flow-0.1.1/src/prismaflow/__init__.py

@@ -0,0 +1,40 @@
+"""
+title: Lightweight PRISMA-style flow diagram generation.
+"""
+
+from prismaflow.enums import PrismaTemplate
+from prismaflow.exceptions import (
+    OptionalDependencyError,
+    PrismaFlowError,
+    PrismaValidationError,
+    TemplateNotSupportedError,
+)
+from prismaflow.models import (
+    EligibilityStage,
+    FlowMetadata,
+    IdentificationStage,
+    IncludedStage,
+    PrismaFlow,
+    ScreeningStage,
+)
+from prismaflow.validation import ValidationMessage, ValidationReport, validate_flow
+
+__version__ = "0.1.1"  # semantic-release
+
+__all__ = [
+    "EligibilityStage",
+    "FlowMetadata",
+    "IdentificationStage",
+    "IncludedStage",
+    "OptionalDependencyError",
+    "PrismaFlow",
+    "PrismaFlowError",
+    "PrismaTemplate",
+    "PrismaValidationError",
+    "ScreeningStage",
+    "TemplateNotSupportedError",
+    "ValidationMessage",
+    "ValidationReport",
+    "__version__",
+    "validate_flow",
+]