PoreMS · Ajax23 · Jun 29, 2026 · Jul 4, 2026 · Jul 4, 2026 · Jul 4, 2026
diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
@@ -0,0 +1,18 @@
+name: Lint
+
+on:
+  push:
+  pull_request:
+
+jobs:
+  ruff:
+    name: ruff
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+      - uses: astral-sh/setup-uv@v5
+      - name: Lint
+        run: uvx ruff check poresim/
+      - name: Format check
+        run: uvx ruff format --check poresim/
diff --git a/.github/workflows/security.yml b/.github/workflows/security.yml
@@ -0,0 +1,22 @@
+name: Security
+
+on:
+  push:
+    branches: [main]
+  schedule:
+    - cron: "0 6 * * 1"  # every Monday at 06:00 UTC
+
+jobs:
+  pip-audit:
+    name: pip-audit
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+      - uses: astral-sh/setup-uv@v5
+        with:
+          python-version: "3.12"
+      - name: Install dependencies
+        run: uv pip install --system pip-audit .
+      - name: Audit dependencies
+        run: pip-audit
diff --git a/.github/workflows/workflow.yml b/.github/workflows/workflow.yml
@@ -1,38 +1,69 @@
-name: Build Status
+name: CI
 
 on:
   push:
-    branches:
-      - main
-      - 'feature/*'   
+    branches: [main]
+  pull_request:
+  workflow_dispatch:
 
 jobs:
-  build:
-
+  test-unit:
+    name: Unit tests (Python ${{ matrix.python-version }})
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
       matrix:
-        python-version: [3.11,3.12,3.13]
+        python-version: ["3.12", "3.13"]
+
+    steps:
+      - uses: actions/checkout@v4
+      - uses: astral-sh/setup-uv@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: uv pip install ".[dev]"
+      - name: Run unit tests
+        run: uv run pytest tests/test_unit.py --cov=poresim -q
+      - name: Upload coverage
+        uses: codecov/codecov-action@v5
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          slug: PoreMS/PoreSim
+
+  test-integration:
+    name: Integration tests
+    runs-on: ubuntu-latest
+    if: github.ref == 'refs/heads/main'
 
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        python -m pip install -r requirements.txt
-        python -m pip install pytest-cov pytest
-        python -m pip install .
-    - name: Run tests
-      run: |
-        pytest --cov --cov-branch --cov-report=xml tests/
-    - name: Upload results to Codecov
-      uses: codecov/codecov-action@v5
-      with:
-        token: ${{ secrets.CODECOV_TOKEN }}
-        slug: PoreMS/PoreSim
+      - uses: actions/checkout@v4
+      - uses: astral-sh/setup-uv@v5
+        with:
+          python-version: "3.12"
+      - name: Install dependencies
+        run: uv pip install pytest .
+      - name: Run integration tests
+        run: uv run pytest tests/test_integration.py -q
+
+  docs:
+    name: Build and deploy docs
+    runs-on: ubuntu-latest
 
+    steps:
+      - uses: actions/checkout@v4
+      - uses: astral-sh/setup-uv@v5
+        with:
+          python-version: "3.12"
+      - name: Install dependencies
+        run: uv pip install -r docs/requirements.txt .
+      - name: Build Sphinx docs
+        run: |
+          cd docs
+          uv run make html
+      - name: Deploy to GitHub Pages
+        if: github.ref == 'refs/heads/main'
+        uses: peaceiris/actions-gh-pages@v4
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: docs/_build/html
+          publish_branch: gh-pages
diff --git a/.gitignore b/.gitignore
@@ -1,9 +1,16 @@
 poresim.egg-info
 build
+dist
 __pycache__
 *.pyc
 .DS_Store
 ._.DS_Store
 .ipynb_checkpoints
 .coverage
 .pytest_cache
+.claude
+venv
+docs/_build
+docs/autoapi/
+docs/generated/
+tests/output
diff --git a/MANIFEST.in b/MANIFEST.in
diff --git a/README.md b/README.md
@@ -1,34 +1,36 @@
-<img src="https://github.com/PoreMS/PoreSim/blob/main/docsrc/pics/logo_text_sub.svg" width="60%">
+<img src="https://github.com/PoreMS/PoreSim/blob/main/docs/pics/logo_text_sub.svg" width="60%">
 
 --------------------------------------
 
-[![PyPI Version](https://img.shields.io/badge/PyPI-0.3.0-orange)](https://pypi.org/project/PoreSim/)
-[![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://github.com/PoreMS/PoreSim/blob/master/LICENSE)
+[![PyPI Version](https://img.shields.io/badge/PyPI-1.0.0-orange)](https://pypi.org/project/poresim/)
+[![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://github.com/PoreMS/PoreSim/blob/main/LICENSE)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.17395962.svg)](https://doi.org/10.5281/zenodo.17395962)
 [![Build Status](https://github.com/PoreMS/PoreSim/actions/workflows/workflow.yml/badge.svg)](https://github.com/PoreMS/PoreSim/actions/workflows/workflow.yml)
 [![codecov](https://codecov.io/gh/PoreMS/PoreSim/branch/main/graph/badge.svg)](https://codecov.io/gh/PoreMS/PoreSim)
 
 ## Documentation
 
-Online documentation is available at [PoreMS.github.io/PoreSim](http://PoreMS.github.io/PoreSim).
+Online documentation is available at [porems.github.io/PoreSim](https://porems.github.io/PoreSim/).
 
-The docs include an example for creating [simulation boxes](http://PoreMS.github.io/PoreSim/simulation.html), and an [API reference](http://PoreMS.github.io/PoreSim/api.html).
+The docs include an example for creating [simulation boxes](https://porems.github.io/PoreSim/simulation.html) and an [API reference](https://porems.github.io/PoreSim/autoapi/index.html).
 
 
 ## Dependencies
 
-PoreSim supports Python 3.5+.
+PoreSim requires Python 3.12+.
 
-Installation requires [pyyaml](https://pypi.org/project/PyYAML/) and [jinja2](https://pypi.org/project/Jinja2/).
+Installation requires [pyyaml](https://pypi.org/project/PyYAML/), [numpy](https://numpy.org/), and [jinja2](https://pypi.org/project/Jinja2/).
 
 
 ## Installation
 
-You may instead want to use the development version from GitHub:
+The latest stable release can be installed from PyPI:
 
-    pip install git+https://github.com/PoreMS/PoreSim.git#egg=poresim
+    pip install poresim
+
+Or install the development version directly from GitHub:
 
-    pip install git+https://github.com/PoreMS/PoreSim.git@develop#egg=poresim
+    pip install git+https://github.com/PoreMS/PoreSim.git#egg=poresim
 
 Or download the repository and install in the top directory via:
 
@@ -37,12 +39,19 @@ Or download the repository and install in the top directory via:
 
 ## Testing
 
-To test PoreSim, run the test in the test directory.
+Install in editable mode with test dependencies:
+
+    pip install -e ".[dev]"
+
+Then run the tests:
+
+    pytest tests/test_unit.py          # fast unit tests
+    pytest tests/test_integration.py   # full integration tests (slow)
 
 
 ## Development
 
-PoreSim development takes place on Github: [www.github.com/PoreMS/PoreSim](https://github.com/PoreMS/PoreSim)
+PoreSim development takes place on GitHub: [www.github.com/PoreMS/PoreSim](https://github.com/PoreMS/PoreSim)
 
 Please submit any reproducible bugs you encounter to the [issue tracker](https://github.com/PoreMS/PoreSim/issues).
 
@@ -53,11 +62,11 @@ When citing PoreSim please use the current **Zenodo DOI** corresponding to the u
 
 ## Legacy Code Notice
 
-This repository contains the actively maintained and current codebase.  
-Earlier development stages and archived versions (including those used in publication XYZ) are stored in the following legacy repository:
+This repository contains the actively maintained and current codebase.
+Earlier development stages and archived versions are stored in the following legacy repository:
 
 [https://github.com/Ajax23/PoreSim](https://github.com/Ajax23/PoreSim)
 
 Please note:
-- Legacy versions are no longer actively maintained  
-- APIs, file formats, and dependencies may differ  
+- Legacy versions are no longer actively maintained
+- APIs, file formats, and dependencies may differ
diff --git a/changelog.md b/changelog.md
@@ -1,3 +1,36 @@
+# v1.0.0
+
+### Code quality
+* `construct.py` — extracted `_write_positions(path, positions)` helper: writes an (N, 3) NumPy position array to a GROMACS position file, replacing repeated inline loops; used for all molecule-insertion position files
+* `construct.py` — extracted `_gmx_insert_cmd(folder_gro, file_box, mol, nmol, dr, pos_file)` helper: centralises GROMACS `insert-molecules` command construction with optional `-dr` and `-ip` flags, eliminating duplicated string-building across pore/box/slit code paths
+* `actuate.py` — shared folder/file path constants (`_gro/`, `_top/`, `_mdp/`, `box.gro`, `topol.top`, `index.ndx`) extracted from local variables in each method to instance attributes on `Actuate.__init__`; both `_equilibration` and `_simulation` methods now reference `self._folder_*` / `self._file_*`
+* `actuate.py` — removed unused `from re import A` import
+* `simulate.py` — Jinja2 template rendering for analysis scripts (`auto_dens.py` / `auto_dens_box.py`) refactored: molecule metadata collected into a single `jinja2_dict` loop; `has_fill` flag derived once instead of re-evaluated; template selection unified in a single branch
+* Template scripts `auto_dens.py` and `auto_dens_box.py` trimmed; `sort.py` template removed (dead code)
+* `tests/data/forhlr.sh` — GROMACS module updated from 2016.5 to 2024.3; `#SBATCH --gres` line added for GPU node support
+
+### Tests
+* Converted `tests/test_simple.py` from unittest to pytest
+* Split into `test_unit.py` (fast, no file I/O) and `test_integration.py` (full output generation)
+* `test_unit.py` — new unit tests: `Box` getter/setter round-trips, `add_mol` validation, `add_topol` all types, `Construct._write_positions` byte-level output, `Construct._gmx_insert_cmd` all flag combinations
+
+### Documentation
+* RST source files migrated to MyST Markdown; Sphinx theme updated to furo; API docs via sphinx-autoapi
+* Docs source moved from `docsrc/` to `docs/`; previous built HTML preserved at `docs/v_old/`
+* Copyright year updated to 2026; DESIGN.md added documenting the yellow/amber color palette
+
+### CI / tooling
+* GitHub Actions: added ruff linting workflow (`lint.yml`)
+* GitHub Actions: added pip-audit security scan workflow (`security.yml`)
+* CI matrix updated: Python 3.12–3.13; `python_requires` bumped to `>=3.12`
+* Migrated from `setup.py` + `MANIFEST.in` to a single `pyproject.toml` (PEP 517/621); `[tool.ruff]` config added
+* CI migrated from `pip` to `uv` (`astral-sh/setup-uv@v5`); `requirements.txt` removed (deps resolved via `pyproject.toml`)
+
+### Administrative
+* `pyproject.toml`: version 1.0.0, `requires-python = ">=3.12"`, author email updated, jinja2 unpinned; `[project.optional-dependencies]` dev group added (`pytest`, `pytest-cov`)
+* README: updated image paths, Python version, PyPI badge, testing and installation instructions
+
+
 # v0.3.0
 * New version due to a change of GitHub organisation.
 

diff --git a/docs/.buildinfo b/docs/.buildinfo
diff --git a/docsrc/.gitignore → docs/.gitignore b/docsrc/.gitignore → docs/.gitignore
diff --git a/docs/.nojekyll b/docs/.nojekyll
diff --git a/docs/DESIGN.md b/docs/DESIGN.md
@@ -0,0 +1,40 @@
+# PoreSim Visual Design
+
+## Color Palette
+
+The logo and all visual assets use a strict 3-color amber palette mirroring the
+[Material Design Amber scale](https://m2.material.io/design/color/the-color-system.html),
+following the same structural logic as PoreMS (blue) and PoreAna (red).
+
+| Role | Hex | RGB | Material token |
+|---|---|---|---|
+| Bond lines | `#ECD078` | `rgb(236, 208, 120)` | Amber 200 |
+| Small/medium nodes, accent text ("SIM") | `#CA8B32` | `rgb(202, 139, 50)` | Amber 700 |
+| Large anchor nodes, body text ("PORE") | `#92400E` | `rgb(146, 64, 14)` | Amber 900 |
+
+### Rationale
+
+- **3 colors maximum** keeps the graphic legible at small sizes (favicon, sidebar logo).
+- **Perceptual hierarchy** matches PoreMS exactly: bonds are the lightest element (connectors),
+  large anchor nodes are the darkest (structural weight).
+- **Material Amber scale** provides perceptually uniform steps and is visually distinct from
+  PoreMS (blue) and PoreAna (red) while sharing the same design grammar.
+
+## Logo Files
+
+| File | Usage |
+|---|---|
+| `docs/pics/logo.svg` | Square icon (favicon source, app icon) |
+| `docs/pics/logo_text.svg` | Horizontal logo with "PoreSim" wordmark |
+| `docs/pics/logo_text_sub.svg` | Logo with wordmark + subtitle line |
+
+## Typography
+
+Wordmark uses **Arial / Arial MT** (system sans-serif fallback).
+- "**PORE**": Amber 900 (`#92400E`) — darkest, matches large anchor nodes
+- "**SIM**": Amber 700 (`#CA8B32`) — medium, matches small/medium nodes
+
+## Favicon
+
+The favicon is derived from `logo.svg`. At 32 × 32 px the three-level amber scheme remains
+distinguishable because the large anchor nodes (Amber 900) contrast against the bond lines (Amber 200).
diff --git a/docs/Makefile b/docs/Makefile
@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+SPHINXOPTS    =
+ifdef OS
+   SPHINXBUILD   = python -msphinx
+else
+   SPHINXBUILD   = python3 -msphinx
+endif
+SPHINXPROJ    = PoreSim
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
diff --git a/docs/_images/2phase_il.pdf b/docs/_images/2phase_il.pdf
diff --git a/docs/_images/pore_il.pdf b/docs/_images/pore_il.pdf
diff --git a/docs/_sources/api.rst.txt b/docs/_sources/api.rst.txt