reactorcheck 0.2.2__tar.gz → 0.2.3__tar.gz

reactorcheck-0.2.3/.github/ISSUE_TEMPLATE/bug-report.yml

@@ -0,0 +1,72 @@
+name: Bug report
+description: Report reproducible incorrect software behavior.
+title: "bug: "
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Do not upload unpublished, confidential, proprietary, licensed, identifying, or sensitive research data. Never include credentials, tokens, or internal paths. Prefer a minimal synthetic reproducer.
+  - type: input
+    id: version
+    attributes:
+      label: ReactorCheck version
+      placeholder: "reactorcheck --version"
+    validations:
+      required: true
+  - type: input
+    id: python
+    attributes:
+      label: Python version
+    validations:
+      required: true
+  - type: dropdown
+    id: os
+    attributes:
+      label: Operating system
+      options: [Linux, macOS, Windows, Other]
+    validations:
+      required: true
+  - type: input
+    id: installation
+    attributes:
+      label: Installation method
+      placeholder: "PyPI, editable source install, or other"
+    validations:
+      required: true
+  - type: dropdown
+    id: interface
+    attributes:
+      label: Interface
+      options: [CLI, GUI, Python API]
+    validations:
+      required: true
+  - type: textarea
+    id: expected
+    attributes:
+      label: Expected behavior
+    validations:
+      required: true
+  - type: textarea
+    id: observed
+    attributes:
+      label: Observed behavior
+    validations:
+      required: true
+  - type: textarea
+    id: error
+    attributes:
+      label: Sanitized error message
+  - type: textarea
+    id: reproducer
+    attributes:
+      label: Minimal reproducer
+      description: Use synthetic or clearly redistributable data only.
+    validations:
+      required: true
+  - type: checkboxes
+    id: privacy
+    attributes:
+      label: Public-data safety
+      options:
+        - label: I have not included private research data, credentials, internal paths, or identifying metadata.
+          required: true

reactorcheck-0.2.3/.github/ISSUE_TEMPLATE/config.yml

@@ -0,0 +1,5 @@
+blank_issues_enabled: false
+contact_links:
+  - name: Security vulnerability
+    url: https://github.com/hdkim99/ReactorCheck/security/advisories/new
+    about: Report security issues privately; never attach sensitive research data.

reactorcheck-0.2.3/.github/ISSUE_TEMPLATE/feature-request.yml

@@ -0,0 +1,42 @@
+name: Feature request
+description: Propose a change backed by a concrete research workflow.
+title: "feature: "
+body:
+  - type: textarea
+    id: workflow
+    attributes:
+      label: Research workflow requiring this feature
+    validations:
+      required: true
+  - type: input
+    id: instrument
+    attributes:
+      label: Instrument or data format involved
+  - type: input
+    id: public_data
+    attributes:
+      label: Public example dataset DOI / URL
+  - type: textarea
+    id: workaround
+    attributes:
+      label: Current manual workaround
+    validations:
+      required: true
+  - type: textarea
+    id: interpretation
+    attributes:
+      label: Scientific interpretation impact
+      description: Explain whether this could change definitions, units, assumptions, or numerical results.
+    validations:
+      required: true
+  - type: textarea
+    id: proposal
+    attributes:
+      label: Proposed behavior
+  - type: checkboxes
+    id: privacy
+    attributes:
+      label: Public-data safety
+      options:
+        - label: I have not included confidential research data, personal information, credentials, or proprietary files.
+          required: true

reactorcheck-0.2.3/.github/ISSUE_TEMPLATE/real-dataset-compatibility.yml

@@ -0,0 +1,74 @@
+name: Real dataset compatibility
+description: Report a laboratory export or public dataset that ReactorCheck cannot process as documented.
+title: "compatibility: "
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Do not upload confidential, unpublished, proprietary, sensitive, or licensed raw files to this public issue. A sanitized header/schema or minimal synthetic reproducer is usually enough.
+  - type: input
+    id: version
+    attributes:
+      label: Project version
+    validations:
+      required: true
+  - type: input
+    id: python
+    attributes:
+      label: Python version
+    validations:
+      required: true
+  - type: input
+    id: os_install
+    attributes:
+      label: Operating system and installation method
+    validations:
+      required: true
+  - type: input
+    id: instrument
+    attributes:
+      label: Instrument / vendor
+      description: Omit serial numbers and institutional identifiers.
+    validations:
+      required: true
+  - type: input
+    id: file_type
+    attributes:
+      label: Input file type
+      placeholder: "CSV or XLSX; include worksheet layout when relevant"
+    validations:
+      required: true
+  - type: textarea
+    id: expected
+    attributes:
+      label: Expected behavior
+    validations:
+      required: true
+  - type: textarea
+    id: observed
+    attributes:
+      label: Observed behavior and sanitized error message
+    validations:
+      required: true
+  - type: dropdown
+    id: shareable
+    attributes:
+      label: Can the data be shared publicly under clear redistribution terms?
+      options: [Yes, No, Unsure]
+    validations:
+      required: true
+  - type: input
+    id: public_source
+    attributes:
+      label: Public dataset DOI / URL, if applicable
+  - type: textarea
+    id: reproducer
+    attributes:
+      label: Minimal reproducer or sanitized header/schema
+  - type: checkboxes
+    id: privacy
+    attributes:
+      label: Public-data safety
+      options:
+        - label: I have not uploaded confidential data, personal information, credentials, proprietary files, or internal paths.
+          required: true

reactorcheck-0.2.3/.github/ISSUE_TEMPLATE/scientific-result-question.yml

@@ -0,0 +1,56 @@
+name: Scientific definition or result question
+description: Ask about a metric, basis, unit, equation, or numerical result.
+title: "science: "
+body:
+  - type: markdown
+    attributes:
+      value: Do not attach confidential or unpublished measurements. Use a hand-checkable minimal example.
+  - type: input
+    id: metric
+    attributes:
+      label: Metric / analysis
+      placeholder: "conversion, selectivity, balance, rate, flow reconstruction, ..."
+    validations:
+      required: true
+  - type: textarea
+    id: expected_definition
+    attributes:
+      label: Expected definition
+    validations:
+      required: true
+  - type: textarea
+    id: observed
+    attributes:
+      label: Observed result
+    validations:
+      required: true
+  - type: input
+    id: basis
+    attributes:
+      label: Input basis
+      placeholder: "wet/dry, raw/normalized, molar/carbon, internal standard, ..."
+    validations:
+      required: true
+  - type: input
+    id: units
+    attributes:
+      label: Units
+    validations:
+      required: true
+  - type: textarea
+    id: reference
+    attributes:
+      label: Reference, DOI, and relevant equation
+  - type: textarea
+    id: example
+    attributes:
+      label: Hand-checkable minimal example
+    validations:
+      required: true
+  - type: checkboxes
+    id: privacy
+    attributes:
+      label: Public-data safety
+      options:
+        - label: This report contains no confidential data or identifying research metadata.
+          required: true

reactorcheck-0.2.3/.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,16 @@
+## What and why
+
+<!-- Describe the focused change and the researcher workflow it addresses. -->
+
+## Scientific behavior
+
+<!-- State definitions, equations, units, basis, assumptions, references/DOIs, and whether existing results change. Write "No scientific behavior change" when applicable. -->
+
+## Verification
+
+- [ ] Formatting, Ruff, mypy, pytest, and package build pass.
+- [ ] New behavior has normal, boundary, invalid, and regression coverage where applicable.
+- [ ] CLI, GUI/service wiring, and exports remain consistent.
+- [ ] Documentation and support claims match verified behavior.
+- [ ] No confidential data, credentials, identifying metadata, or unlicensed fixtures are included.
+- [ ] Dependency/license changes and public-data provenance are documented.

reactorcheck-0.2.3/.github/dependabot.yml

@@ -0,0 +1,22 @@
+version: 2
+updates:
+  - package-ecosystem: github-actions
+    directory: "/"
+    schedule:
+      interval: weekly
+      day: monday
+      timezone: Asia/Seoul
+    open-pull-requests-limit: 5
+    groups:
+      github-actions:
+        patterns: ["*"]
+  - package-ecosystem: pip
+    directory: "/"
+    schedule:
+      interval: weekly
+      day: monday
+      timezone: Asia/Seoul
+    open-pull-requests-limit: 5
+    groups:
+      development-tools:
+        patterns: ["build", "mypy", "pandas-stubs", "pytest", "pytest-cov", "ruff", "twine", "types-*"]

{reactorcheck-0.2.2 → reactorcheck-0.2.3}/.github/workflows/ci.yml

@@ -17,10 +17,11 @@ concurrency:
 jobs:
   required:
     name: CI / required
-    # Public fork code must never execute on persistent self-hosted research hardware.
+    # Only owner-authored same-repository PRs may execute on persistent research hardware.
     if: >-
       github.event_name != 'pull_request' ||
-      github.event.pull_request.head.repo.full_name == github.repository
+      (github.actor == github.repository_owner &&
+       github.event.pull_request.head.repo.full_name == github.repository)
     runs-on: [self-hosted, dgx-spark]
     timeout-minutes: 60
     env:

{reactorcheck-0.2.2 → reactorcheck-0.2.3}/.github/workflows/release.yml

@@ -12,6 +12,8 @@ jobs:
       contents: read
     steps:
       - uses: actions/checkout@d23441a48e516b6c34aea4fa41551a30e30af803 # v6
+        with:
+          persist-credentials: false
       - uses: actions/setup-python@ece7cb06caefa5fff74198d8649806c4678c61a1 # v6
         with:
           python-version: "3.12"
@@ -61,4 +63,4 @@ jobs:
         with:
           name: python-package-distributions
           path: dist/
-      - uses: pypa/gh-action-pypi-publish@dc37677b2e1c63e2034f94d8a5b11f265b73ba33 # release/v1
+      - uses: pypa/gh-action-pypi-publish@7245906fb61fa33a13554f9d5fb856fe61758086 # v1.14.3

{reactorcheck-0.2.2 → reactorcheck-0.2.3}/CHANGELOG.md

@@ -3,6 +3,13 @@
 All notable changes follow [Keep a Changelog](https://keepachangelog.com/) and
 versions follow semantic versioning.
 
+## [0.2.3] - 2026-11-16
+
+### Security
+
+- Update the PyPI publishing action to v1.14.3 (GHSA-5xjx-3w67-w9x9).
+  Scientific calculations and public APIs are unchanged.
+
 ## [0.2.2] - 2026-08-23
 
 ### Added

{reactorcheck-0.2.2 → reactorcheck-0.2.3}/CITATION.cff

@@ -2,7 +2,7 @@ cff-version: 1.2.0
 message: "If you use ReactorCheck, please cite this software."
 title: "ReactorCheck"
 type: software
-version: 0.2.2
+version: 0.2.3
 date-released: 2026-08-23
 license: MIT
 repository-code: "https://github.com/hdkim99/ReactorCheck"

reactorcheck-0.2.3/CONTRIBUTING.md

@@ -0,0 +1,60 @@
+# Contributing
+
+Thank you for helping make catalytic-reactor calculations more transparent and
+reproducible.
+
+## Before opening an issue
+
+- Search existing issues and choose the dataset-compatibility or scientific-result
+  form when applicable.
+- Never upload unpublished, confidential, proprietary, licensed, or identifying
+  research data to a public issue. Share a minimal synthetic reproducer or sanitized
+  headers/schema instead.
+- Do not include credentials, internal paths, instrument serial numbers, or private
+  sample names.
+
+## Development checks
+
+Install `.[dev]`, create a focused branch, and run:
+
+```bash
+ruff format --check .
+ruff check .
+mypy src
+pytest
+python -m build
+```
+
+## Scientific changes
+
+Keep equations in the core, never in GUI callbacks. A change to conversion,
+selectivity, yield, rate, STY, GHSV/WHSV, unit conversion, flow reconstruction, or
+mass/element balance must state:
+
+- the scientific definition and equation;
+- input/output units, basis, assumptions, and physical bounds;
+- a primary reference or DOI when relevant;
+- whether existing numerical results change and why; and
+- a hand-calculated, synthetic, or legally usable regression case covering invalid
+  as well as normal inputs.
+
+`pytest` passing alone does not establish scientific correctness. Do not weaken an
+assertion to conceal a disagreement; classify the cause as implementation, test,
+definition, unit, data model, or environment.
+
+Use small Conventional Commit-style changes such as `feat:`, `fix:`, `test:`, and
+`docs:`. Synthetic data must be redistributable, and public-data-derived fixtures must
+identify their source, license, and reduction method.
+
+After changing the public composition example, run
+`python scripts/generate_example_assets.py` and inspect both PNG files before
+committing the regenerated XLSX/visual assets.
+
+## Self-hosted CI safety
+
+The required CI job runs on the persistent `dgx-spark` self-hosted runner.
+Pushes and manual dispatches may use that runner. Pull requests run there only when
+the current repository owner opens them from a same-repository branch. Fork and
+bot-authored pull-request jobs are deliberately skipped so unreviewed code or dependency
+updates cannot execute on research hardware. Maintainers must review those changes before
+reproducing them in an owner-authored same-repository branch.

{reactorcheck-0.2.2 → reactorcheck-0.2.3}/PKG-INFO

@@ -1,11 +1,12 @@
 Metadata-Version: 2.5
 Name: reactorcheck
-Version: 0.2.2
+Version: 0.2.3
 Summary: Unit-aware catalytic reactor analysis from compositions or measured species flows.
 Project-URL: Homepage, https://github.com/hdkim99/ReactorCheck
 Project-URL: Repository, https://github.com/hdkim99/ReactorCheck
 Project-URL: Issues, https://github.com/hdkim99/ReactorCheck/issues
 Project-URL: Documentation, https://github.com/hdkim99/ReactorCheck#readme
+Project-URL: Releases, https://github.com/hdkim99/ReactorCheck/releases
 Author: Hyun Dong Kim
 License: MIT License
         
@@ -62,6 +63,7 @@ Description-Content-Type: text/markdown
 **Turn reactor compositions or measured species flows into auditable catalytic metrics and QC.**
 
 [![CI](https://github.com/hdkim99/ReactorCheck/actions/workflows/ci.yml/badge.svg)](https://github.com/hdkim99/ReactorCheck/actions/workflows/ci.yml)
+[![PyPI](https://img.shields.io/pypi/v/reactorcheck)](https://pypi.org/project/reactorcheck/)
 [![Python 3.10+](https://img.shields.io/badge/python-3.10%2B-blue.svg)](https://www.python.org/)
 [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://github.com/hdkim99/ReactorCheck/blob/main/LICENSE)
 
@@ -88,22 +90,24 @@ Python 3.10 or newer is required. Tk is needed only for the desktop GUI.
 python -m pip install reactorcheck
 ```
 
-For the bundled example datasets, unreleased development code, or contributions,
-clone the public source and use an editable install instead:
+## 30-second example
 
-## 30-second bundled example (source install)
+Download the two public-safe example inputs and run them with the PyPI installation:
 
 ```bash
-git clone https://github.com/hdkim99/ReactorCheck.git
-cd ReactorCheck
-python -m pip install -e .
-reactorcheck analyze examples/synthetic_composition.csv \
-  --config examples/synthetic_composition_config.json \
+mkdir reactorcheck-demo && cd reactorcheck-demo
+curl -LO https://raw.githubusercontent.com/hdkim99/ReactorCheck/main/examples/synthetic_composition.csv
+curl -LO https://raw.githubusercontent.com/hdkim99/ReactorCheck/main/examples/synthetic_composition_config.json
+reactorcheck analyze synthetic_composition.csv \
+  --config synthetic_composition_config.json \
   --output reactorcheck-composition.xlsx \
   --plot reactorcheck-composition.png
 reactorcheck-gui
 ```
 
+If you are already in a source checkout, use the paths under `examples/` shown in
+the repository instead. Clone the repository and install `-e .` only for development.
+
 The synthetic CO hydrogenation example is available as both
 [`CSV`](https://github.com/hdkim99/ReactorCheck/blob/main/examples/synthetic_composition.csv) and
 [`XLSX`](https://github.com/hdkim99/ReactorCheck/blob/main/examples/synthetic_composition.xlsx). Its hand calculation reconstructs
@@ -191,6 +195,7 @@ tabular/JSON schemas rather than shared private code.
 ## Development
 
 ```bash
+python -m pip install -e .
 python -m pip install -e ".[dev]"
 ruff format --check .
 ruff check .

{reactorcheck-0.2.2 → reactorcheck-0.2.3}/README.md

@@ -3,6 +3,7 @@
 **Turn reactor compositions or measured species flows into auditable catalytic metrics and QC.**
 
 [![CI](https://github.com/hdkim99/ReactorCheck/actions/workflows/ci.yml/badge.svg)](https://github.com/hdkim99/ReactorCheck/actions/workflows/ci.yml)
+[![PyPI](https://img.shields.io/pypi/v/reactorcheck)](https://pypi.org/project/reactorcheck/)
 [![Python 3.10+](https://img.shields.io/badge/python-3.10%2B-blue.svg)](https://www.python.org/)
 [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://github.com/hdkim99/ReactorCheck/blob/main/LICENSE)
 
@@ -29,22 +30,24 @@ Python 3.10 or newer is required. Tk is needed only for the desktop GUI.
 python -m pip install reactorcheck
 ```
 
-For the bundled example datasets, unreleased development code, or contributions,
-clone the public source and use an editable install instead:
+## 30-second example
 
-## 30-second bundled example (source install)
+Download the two public-safe example inputs and run them with the PyPI installation:
 
 ```bash
-git clone https://github.com/hdkim99/ReactorCheck.git
-cd ReactorCheck
-python -m pip install -e .
-reactorcheck analyze examples/synthetic_composition.csv \
-  --config examples/synthetic_composition_config.json \
+mkdir reactorcheck-demo && cd reactorcheck-demo
+curl -LO https://raw.githubusercontent.com/hdkim99/ReactorCheck/main/examples/synthetic_composition.csv
+curl -LO https://raw.githubusercontent.com/hdkim99/ReactorCheck/main/examples/synthetic_composition_config.json
+reactorcheck analyze synthetic_composition.csv \
+  --config synthetic_composition_config.json \
   --output reactorcheck-composition.xlsx \
   --plot reactorcheck-composition.png
 reactorcheck-gui
 ```
 
+If you are already in a source checkout, use the paths under `examples/` shown in
+the repository instead. Clone the repository and install `-e .` only for development.
+
 The synthetic CO hydrogenation example is available as both
 [`CSV`](https://github.com/hdkim99/ReactorCheck/blob/main/examples/synthetic_composition.csv) and
 [`XLSX`](https://github.com/hdkim99/ReactorCheck/blob/main/examples/synthetic_composition.xlsx). Its hand calculation reconstructs
@@ -132,6 +135,7 @@ tabular/JSON schemas rather than shared private code.
 ## Development
 
 ```bash
+python -m pip install -e .
 python -m pip install -e ".[dev]"
 ruff format --check .
 ruff check .

{reactorcheck-0.2.2 → reactorcheck-0.2.3}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "reactorcheck"
-version = "0.2.2"
+version = "0.2.3"
 description = "Unit-aware catalytic reactor analysis from compositions or measured species flows."
 readme = "README.md"
 requires-python = ">=3.10"
@@ -59,6 +59,7 @@ Homepage = "https://github.com/hdkim99/ReactorCheck"
 Repository = "https://github.com/hdkim99/ReactorCheck"
 Issues = "https://github.com/hdkim99/ReactorCheck/issues"
 Documentation = "https://github.com/hdkim99/ReactorCheck#readme"
+Releases = "https://github.com/hdkim99/ReactorCheck/releases"
 
 [tool.hatch.build.targets.wheel]
 packages = ["src/reactorcheck"]

{reactorcheck-0.2.2 → reactorcheck-0.2.3}/src/reactorcheck/__init__.py

@@ -18,4 +18,4 @@ __all__ = [
     "analyze_file",
     "analyze_frame",
 ]
-__version__ = "0.2.2"
+__version__ = "0.2.3"

{reactorcheck-0.2.2 → reactorcheck-0.2.3}/src/reactorcheck/units.py

@@ -17,7 +17,7 @@ ureg.define("sccm = centimeter ** 3 / minute")
 
 STANDARD_TEMPERATURE = 273.15 * ureg.kelvin
 STANDARD_PRESSURE = 1.0 * ureg.atmosphere
-GAS_CONSTANT = 8.31446261815324 * ureg.joule / ureg.mole / ureg.kelvin
+GAS_CONSTANT: pint.Quantity[Any] = 8.31446261815324 * ureg.joule / ureg.mole / ureg.kelvin
 
 
 class UnitError(ValueError):

{reactorcheck-0.2.2 → reactorcheck-0.2.3}/tests/test_project_metadata.py

@@ -16,12 +16,13 @@ def test_readme_leads_with_pypi_install_and_has_current_status() -> None:
     assert "publication is prepared but has not been performed" not in readme
 
 
-def test_general_ci_targets_dgx_and_blocks_fork_pull_requests() -> None:
+def test_general_ci_targets_dgx_and_blocks_external_or_bot_pull_requests() -> None:
     workflow = (ROOT / ".github" / "workflows" / "ci.yml").read_text()
     assert "runs-on: [self-hosted, dgx-spark]" in workflow
     assert "ubuntu-latest" not in workflow
     assert "workflow_dispatch:" in workflow
-    assert "github.event.pull_request.head.repo.full_name == github.repository" in workflow
+    assert workflow.count("github.actor == github.repository_owner") == 1
+    assert workflow.count("github.event.pull_request.head.repo.full_name == github.repository") == 1
     assert "PIP_NO_CACHE_DIR" in workflow
     assert "actions/checkout@fbc6f3992d24b796d5a048ff273f7fcc4a7b6c09" in workflow
     assert "actions/setup-python@ece7cb06caefa5fff74198d8649806c4678c61a1" in workflow
@@ -53,7 +54,7 @@ def test_release_workflow_is_trusted_publishing_only() -> None:
     assert "/tmp/reactorcheck-release-venv/bin/python -m pip check" in workflow
     assert "id-token: write" in workflow
     assert "name: pypi" in workflow
-    assert "pypa/gh-action-pypi-publish@dc37677b2e1c63e2034f94d8a5b11f265b73ba33" in workflow
+    assert "pypa/gh-action-pypi-publish@7245906fb61fa33a13554f9d5fb856fe61758086" in workflow
     assert "PYPI_API_TOKEN" not in workflow
     assert "secrets." not in workflow
     publish = workflow.split("  publish:\n", maxsplit=1)[1]

{reactorcheck-0.2.2 → reactorcheck-0.2.3}/tests/test_version.py

@@ -18,4 +18,4 @@ def _match(path: Path, pattern: str) -> str:
 def test_version_surfaces_are_consistent() -> None:
     pyproject = _match(ROOT / "pyproject.toml", r'^version = "([^"]+)"$')
     citation = _match(ROOT / "CITATION.cff", r"^version: ([^\s]+)$")
-    assert __version__ == pyproject == citation == "0.2.2"
+    assert __version__ == pyproject == citation == "0.2.3"

reactorcheck-0.2.2/CONTRIBUTING.md

@@ -1,24 +0,0 @@
-# Contributing
-
-Install `.[dev]`, create a focused branch, and run `ruff check .`, `mypy src`,
-`pytest`, and `python -m build` before opening a pull request. Keep scientific
-equations in the core, never in GUI callbacks. New equations require a definition,
-units, assumptions, a hand-calculated or synthetic regression case, and physical
-edge cases. Do not weaken assertions to conceal a scientific disagreement; record
-whether the cause is implementation, test, definition, unit, model, or environment.
-
-Use small Conventional Commit-style changes such as `feat:`, `fix:`, `test:`, and
-`docs:`. Synthetic data must be redistributable. Never commit private experimental
-data, credentials, or personally identifying metadata.
-
-After changing the public composition example, run
-`python scripts/generate_example_assets.py` and inspect both PNG files before
-committing the regenerated XLSX/visual assets.
-
-## Self-hosted CI safety
-
-The required CI job runs on the persistent `dgx-spark` self-hosted runner.
-Pushes, manual dispatches, and pull requests from this repository may use that
-runner. Pull requests from forks are deliberately skipped so unreviewed fork
-code cannot execute on research hardware. Maintainers must not weaken this gate;
-review fork changes before reproducing them in a same-repository branch.